Version and doc update

usnistgov · Apr 29, 2024 · 20cf99f · 20cf99f
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diff --git a/UPDATES.rst b/UPDATES.rst
@@ -1,8 +1,30 @@
 Updates
 =======
 
+Version 1.4.11
+--------------
+
+- The structure generation methods of **atomman.defect.Dislocation** now all
+  have a center parameter that allows for the dislocation's position to be
+  shifted.  This is useful for setting up NEB runs.
+
+- **atomman.lammps.run** now supports lammps_command paths that contain spaces.
+
+- **atomman.defect.Boundary** has been further improved and some supporting
+  tools developed.  Not fully finalized yet.
+
+- **neb_replica** dump style added that creates the atomic configurations used
+  by LAMMPS for defining the final (and intermediate) replicas.
+
+- More tools and operations related to Miller crystal vectors and planes have
+  been added.  These should make it possible for future revisions of the
+  defect generators to be simplified and made more uniform.
+
+- Record classes have been updated to support a URL field for assigning
+  persistent identification (PID) values once uploaded to a CDCS database.
+
 Version 1.4.10
--------------
+--------------
 
 - **atomman.lammps.Log** now has more options during flatten allowing for only
   a subset of simulation runs to be merged together.  Bug fix related to type

diff --git a/atomman/VERSION b/atomman/VERSION
@@ -1 +1 @@
-1.4.10
+1.4.11
diff --git a/doc/source/tutorial/index.rst b/doc/source/tutorial/index.rst
@@ -25,6 +25,7 @@ Tutorials
    1.4.13. primitive cell dumping <1.4.13._primitive_cell_dumping>
    1.4.14. Conventional and primitive cell conversion dumping <1.4.14._Conventional_and_primitive_cell_conversion_dumping>
    1.4.15. pdb dumping <1.4.15._pdb_dumping>
+   1.4.16. LAMMPS NEB replica dumping<1.4.16._LAMMPS_NEB_replica_dumping>
    1.5. Settings and databases <1.5._Settings_and_databases>
    2. LAMMPS functionality <2._LAMMPS_functionality>
    2.1. Potential class <2.1._Potential_class>
@@ -44,4 +45,5 @@ Tutorials
    4.6. Dislocation analysis tools <4.6._Dislocation_analysis_tools>
    4.7. Semidiscrete variational Peierls-Nabarro model <4.7._Semidiscrete_variational_Peierls-Nabarro_model>
    4.8. Strain class <4.8._Strain_class>
-   4.9. Dislocation configurations generator <4.9._Dislocation_configurations_generator>
+   4.9. Dislocation configurations generator <4.9._Dislocation_configurations_generator>
+   4.10 Differential Displacement Maps <4.10_Differential_Displacement_Maps>
diff --git a/doc/tutorial/0. Unit conversions.ipynb b/doc/tutorial/0. Unit conversions.ipynb
@@ -44,24 +44,12 @@
     "tags": []
    },
    "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "6654e02fe97f47dfa2fc4db31d3ea538",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": []
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "atomman version = 1.4.10\n",
-      "Notebook executed on 2023-07-28\n"
+      "atomman version = 1.4.11\n",
+      "Notebook executed on 2024-04-29\n"
      ]
     }
    ],
@@ -231,15 +219,15 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "angstrom = 1.4191243424094714e-12\n",
-      "amu =      2.8577039616406894e-27\n",
-      "eV =       5.328594872559533e-26\n",
-      "e =        1.6325720115916934e-18\n",
-      "K =        0.17176160943193114\n",
-      "nm =       1.4191243424094715e-11\n",
-      "g =        0.0017209495513357104\n",
-      "J =        3.325847325120542e-07\n",
-      "ps =       3.2281474606461375e-11\n"
+      "angstrom = 5.600878467584771e-10\n",
+      "amu =      9.610217188572792e-28\n",
+      "eV =       3.2016069566128865e-22\n",
+      "e =        8.43287354913381e-18\n",
+      "K =        14.973876783292686\n",
+      "nm =       5.600878467584771e-09\n",
+      "g =        0.0005787408066375686\n",
+      "J =        0.001998285887255604\n",
+      "ps =       9.531678627120866e-11\n"
      ]
     }
    ],
@@ -749,18 +737,18 @@
      "text": [
       "{\n",
       "  \"value\": [\n",
-      "    0.01004403654185057,\n",
-      "    0.020656878915057856,\n",
-      "    0.029214965887450112,\n",
-      "    0.040306012922664336,\n",
-      "    0.04954549658639971\n",
+      "    0.010573998704568247,\n",
+      "    0.020550301777721776,\n",
+      "    0.029963592945213675,\n",
+      "    0.04079673469155252,\n",
+      "    0.049618650315530734\n",
       "  ],\n",
       "  \"error\": [\n",
-      "    0.0019546543962901085,\n",
-      "    0.0019815859329668237,\n",
-      "    0.0019447626366320926,\n",
-      "    0.0019429728156574704,\n",
-      "    0.002085436036518905\n",
+      "    0.0020089189147024338,\n",
+      "    0.0020843988956897527,\n",
+      "    0.002030431578028036,\n",
+      "    0.001993658438717888,\n",
+      "    0.001915696809118872\n",
       "  ],\n",
       "  \"unit\": \"m\"\n",
       "}\n"
@@ -797,8 +785,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "value = [10.04403654 20.65687892 29.21496589 40.30601292 49.54549659] mm\n",
-      "error = [1.9546544  1.98158593 1.94476264 1.94297282 2.08543604] mm\n"
+      "value = [10.5739987  20.55030178 29.96359295 40.79673469 49.61865032] mm\n",
+      "error = [2.00891891 2.0843989  2.03043158 1.99365844 1.91569681] mm\n"
      ]
     }
    ],
@@ -855,8 +843,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "57 s = 3.111008195072701e-09 GPa\n",
-      "57 s = 0.0033804807501133854 GPa\n"
+      "57 s = 0.028954887018440553 GPa\n",
+      "57 s = 2.385524541195933 GPa\n"
      ]
     }
    ],
@@ -885,9 +873,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 311",
    "language": "python",
-   "name": "python3"
+   "name": "py11"
   },
   "language_info": {
    "codemirror_mode": {
@@ -899,7 +887,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.3"
+   "version": "3.11.5"
   }
  },
  "nbformat": 4,

diff --git a/doc/tutorial/1. Defining atomic systems.ipynb b/doc/tutorial/1. Defining atomic systems.ipynb
diff --git a/doc/tutorial/1.1. Box class.ipynb b/doc/tutorial/1.1. Box class.ipynb
@@ -40,24 +40,12 @@
    "execution_count": 1,
    "metadata": {},
    "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "bffe9c18f2d447de96f6524a781fbc0e",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": []
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "atomman version = 1.4.10\n",
-      "Notebook executed on 2023-07-28\n"
+      "atomman version = 1.4.11\n",
+      "Notebook executed on 2024-04-29\n"
      ]
     }
    ],
@@ -250,10 +238,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "avect =  [ 0.758,  0.421,  3.528]\n",
-      "bvect =  [ 1.131,  2.927,  0.314]\n",
-      "cvect =  [ 0.966,  2.736,  3.084]\n",
-      "origin = [ 0.540,  0.499,  0.814]\n"
+      "avect =  [ 0.493,  3.072,  2.180]\n",
+      "bvect =  [ 3.052,  2.434,  1.904]\n",
+      "cvect =  [ 1.149,  2.004,  1.151]\n",
+      "origin = [ 0.614,  0.488,  0.655]\n"
      ]
     }
    ],
@@ -763,26 +751,26 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[[0.55155781 2.49380003 9.3967093 ]\n",
-      " [3.3184798  1.20799191 7.13164885]\n",
-      " [9.01978498 6.83706011 4.93770814]\n",
-      " [2.28427281 8.89576691 1.36390599]\n",
-      " [9.13244568 8.95582225 0.6753787 ]\n",
-      " [8.82825304 5.60954094 4.37509114]\n",
-      " [8.72884521 6.66389441 0.27514523]\n",
-      " [7.71076227 9.11630048 7.75768688]\n",
-      " [9.48224726 2.40686471 8.43615747]\n",
-      " [3.19980874 3.80016388 2.24761004]\n",
-      " [4.48075767 6.73926091 1.42195919]\n",
-      " [1.61078464 5.56715807 7.12491481]\n",
-      " [7.72580749 7.54518157 4.28075216]\n",
-      " [1.18750119 3.26711573 4.83214076]\n",
-      " [7.90676427 8.19921855 8.48659655]\n",
-      " [7.98902068 0.54456826 0.9633501 ]\n",
-      " [4.12189515 2.0876842  8.70759034]\n",
-      " [5.96837357 2.66878026 8.14396448]\n",
-      " [9.64936991 5.17531275 8.63342089]\n",
-      " [6.50309524 6.88621626 1.06736169]]\n"
+      "[[8.81160358 2.71676184 0.7609669 ]\n",
+      " [8.6408608  8.6335422  6.02160501]\n",
+      " [3.54481945 4.94851122 6.298283  ]\n",
+      " [6.11139741 5.39773988 1.71761718]\n",
+      " [6.79366189 9.12403451 7.12534089]\n",
+      " [5.67935699 3.23007552 6.85816846]\n",
+      " [3.49818923 4.17660433 7.88890672]\n",
+      " [4.19945368 3.97830942 5.78892956]\n",
+      " [8.77414931 3.52906642 3.64925096]\n",
+      " [6.10294056 1.37401047 4.95237431]\n",
+      " [8.70654588 0.744317   1.00229273]\n",
+      " [9.03563524 4.50157033 2.72091936]\n",
+      " [2.37109145 2.79009903 6.90235942]\n",
+      " [6.89840668 8.30112834 6.43754968]\n",
+      " [7.04394381 8.29712298 6.61960962]\n",
+      " [5.53806036 7.02869808 1.7991656 ]\n",
+      " [6.5269522  5.45457678 3.54307   ]\n",
+      " [0.37042938 5.08119027 9.03772685]\n",
+      " [8.57988186 4.99288325 9.47766059]\n",
+      " [8.22989533 8.63759985 3.35406841]]\n"
      ]
     }
    ],
@@ -973,9 +961,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 311",
    "language": "python",
-   "name": "python3"
+   "name": "py11"
   },
   "language_info": {
    "codemirror_mode": {
@@ -987,7 +975,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.3"
+   "version": "3.11.5"
   }
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  "nbformat": 4,