Fix lattice velocities formatting (#3433)

* fix lattice velocities formatting * add test for lattice velocities formatting * link PR in new test --------- Co-authored-by: Janosh Riebesell <[email protected]>
materialsproject · Oct 31, 2023 · eee88ab · eee88ab
1 parent 0e12f81
commit eee88ab
Show file tree

Hide file tree

Showing 2 changed files with 20 additions and 7 deletions.
diff --git a/pymatgen/io/vasp/inputs.py b/pymatgen/io/vasp/inputs.py
@@ -73,9 +73,11 @@ class Poscar(MSONable):
         velocities: Velocities for each site (typically read in from a CONTCAR).
             A Nx3 array of floats.
         predictor_corrector: Predictor corrector coordinates and derivatives for each site;
-            i.e. a list of three 1x3 arrays for each site (typically read in from a MD CONTCAR).
+            i.e. a list of three 1x3 arrays for each site (typically read in from an MD CONTCAR).
         predictor_corrector_preamble: Predictor corrector preamble contains the predictor-corrector key,
             POTIM, and thermostat parameters that precede the site-specific predictor corrector data in MD CONTCAR.
+        lattice_velocities: Lattice velocities and current lattice (typically read
+            in from an MD CONTCAR). A 6x3 array of floats.
         temperature: Temperature of velocity Maxwell-Boltzmann initialization.
             Initialized to -1 (MB hasn't been performed).
     """
@@ -520,8 +522,8 @@ def get_str(self, direct: bool = True, vasp4_compatible: bool = False, significa
 
         format_str = f"{{:{significant_figures + 5}.{significant_figures}f}}"
         lines = [self.comment, "1.0"]
-        for v in latt.matrix:
-            lines.append(" ".join(format_str.format(c) for c in v))
+        for vec in latt.matrix:
+            lines.append(" ".join(format_str.format(c) for c in vec))
 
         if self.true_names and not vasp4_compatible:
             lines.append(" ".join(self.site_symbols))
@@ -544,16 +546,17 @@ def get_str(self, direct: bool = True, vasp4_compatible: bool = False, significa
             try:
                 lines.append("Lattice velocities and vectors")
                 lines.append("  1")
-                for v in self.lattice_velocities:
-                    lines.append(" ".join(format_str.format(i) for i in v))
+                for velo in self.lattice_velocities:
+                    # VASP is strict about the format when reading this quantity
+                    lines.append(" ".join(f" {val: .7E}" for val in velo))
             except Exception:
                 warnings.warn("Lattice velocities are missing or corrupted.")
 
         if self.velocities:
             try:
                 lines.append("")
-                for v in self.velocities:
-                    lines.append(" ".join(format_str.format(i) for i in v))
+                for velo in self.velocities:
+                    lines.append(" ".join(format_str.format(val) for val in velo))
             except Exception:
                 warnings.warn("Velocities are missing or corrupted.")
 

diff --git a/tests/io/vasp/test_inputs.py b/tests/io/vasp/test_inputs.py
@@ -3,6 +3,7 @@
 import copy
 import os
 import pickle
+import re
 import unittest
 from typing import TYPE_CHECKING
 
@@ -297,6 +298,15 @@ def test_write_md_poscar(self):
         poscar = Poscar.from_file(f"{TEST_FILES_DIR}/CONTCAR.MD.npt", check_for_potcar=False)
 
         poscar.write_file(path)
+
+        # check output produced for lattice velocities has required format and spaces
+        # added in https://github.com/materialsproject/pymatgen/pull/3433
+        with open(path) as file:
+            lines = file.readlines()
+        pattern = (r"  [-| ]?\d\.\d{7}E[+-]\d{2}" * 3)[1:]
+        for line in lines[18:24]:
+            assert re.match(pattern, line.rstrip())
+
         p3 = Poscar.from_file(path)
 
         assert_allclose(poscar.structure.lattice.abc, p3.structure.lattice.abc, 5)