Add some required potcars.

materialsvirtuallab · Jun 28, 2024 · 7130128 · 7130128
1 parent 4add434
commit 7130128
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -27,6 +27,7 @@ jobs:
 
     env:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
+      PMG_VASP_PSP_DIR: /home/runner/matgenb/matgenb/notebooks/psp
 
     steps:
       - name: Check out repo

diff --git a/...Design of Alkali Superionic Conductors Part 2 - Phase and Electrochemical Stability.ipynb b/...Design of Alkali Superionic Conductors Part 2 - Phase and Electrochemical Stability.ipynb
@@ -4484,9 +4484,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/...01-ChemEnv - How to automatically identify coordination environments in a structure.ipynb b/...01-ChemEnv - How to automatically identify coordination environments in a structure.ipynb
@@ -69,7 +69,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -80,7 +80,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -109,9 +109,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "7f07db73c99049268221acd2062338e3",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Retrieving MaterialsDoc documents:   0%|          | 0/1 [00:00<?, ?it/s]"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "# Get a structure from the materials project (alpha-quartz)\n",
     "mpr = MPRester()\n",
@@ -138,7 +153,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -163,25 +178,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "If you use the ChemEnv tool for your research, please consider citing the following reference(s) :\n",
-      "==================================================================================================\n",
-      "David Waroquiers, Xavier Gonze, Gian-Marco Rignanese, Cathrin Welker-Nieuwoudt, Frank Rosowski,\n",
-      "Michael Goebel, Stephan Schenk, Peter Degelmann, Rute Andre, Robert Glaum, and Geoffroy Hautier,\n",
-      "\"Statistical analysis of coordination environments in oxides\",\n",
-      "Chem. Mater., 2017, 29 (19), pp 8346-8360,\n",
-      "DOI: 10.1021/acs.chemmater.7b02766\n",
-      "\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Setup the local geometry finder\n",
     "lgf = LocalGeometryFinder()\n",
@@ -217,67 +216,76 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "INFO:coordination_geometry_finder:compute_structure_environments:Getting DetailedVoronoiContainer\n",
-      "INFO:voronoi:__init__:Setting Voronoi list\n",
-      "INFO:voronoi:setup_voronoi_list:Getting all neighbors in structure\n",
-      "INFO:voronoi:setup_voronoi_list:Setting up Voronoi list :\n",
-      "INFO:voronoi:setup_voronoi_list:  - Voronoi analysis for site #0 (1/9)\n",
-      "INFO:voronoi:setup_voronoi_list:  - Voronoi analysis for site #1 (2/9)\n",
-      "INFO:voronoi:setup_voronoi_list:  - Voronoi analysis for site #2 (3/9)\n",
-      "INFO:voronoi:setup_voronoi_list:  - Voronoi analysis for site #3 (4/9)\n",
-      "INFO:voronoi:setup_voronoi_list:  - Voronoi analysis for site #4 (5/9)\n",
-      "INFO:voronoi:setup_voronoi_list:  - Voronoi analysis for site #5 (6/9)\n",
-      "INFO:voronoi:setup_voronoi_list:  - Voronoi analysis for site #6 (7/9)\n",
-      "INFO:voronoi:setup_voronoi_list:  - Voronoi analysis for site #7 (8/9)\n",
-      "INFO:voronoi:setup_voronoi_list:  - Voronoi analysis for site #8 (9/9)\n",
-      "INFO:voronoi:setup_voronoi_list:Voronoi list set up in 0.28 seconds\n",
-      "INFO:voronoi:__init__:Setting neighbors distances and angles\n",
-      "INFO:voronoi:__init__:Neighbors distances and angles set up in 0.00 seconds\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments:DetailedVoronoiContainer has been set up\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments: ... in site #0/9 (Si)\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments:Getting DetailedVoronoiContainer\n",
+      "DEBUG:voronoi:__init__:Setting Voronoi list\n",
+      "DEBUG:voronoi:setup_voronoi_list:Getting all neighbors in structure\n",
+      "DEBUG:voronoi:setup_voronoi_list:Setting up Voronoi list :\n",
+      "DEBUG:voronoi:setup_voronoi_list:  - Voronoi analysis for site #0 (1/9)\n",
+      "DEBUG:voronoi:setup_voronoi_list:  - Voronoi analysis for site #1 (2/9)\n",
+      "DEBUG:voronoi:setup_voronoi_list:  - Voronoi analysis for site #2 (3/9)\n",
+      "DEBUG:voronoi:setup_voronoi_list:  - Voronoi analysis for site #3 (4/9)\n",
+      "DEBUG:voronoi:setup_voronoi_list:  - Voronoi analysis for site #4 (5/9)\n",
+      "DEBUG:voronoi:setup_voronoi_list:  - Voronoi analysis for site #5 (6/9)\n",
+      "DEBUG:voronoi:setup_voronoi_list:  - Voronoi analysis for site #6 (7/9)\n",
+      "DEBUG:voronoi:setup_voronoi_list:  - Voronoi analysis for site #7 (8/9)\n",
+      "DEBUG:voronoi:setup_voronoi_list:  - Voronoi analysis for site #8 (9/9)\n",
+      "DEBUG:voronoi:setup_voronoi_list:Voronoi list set up in 0.13 seconds\n",
+      "DEBUG:voronoi:__init__:Setting neighbors distances and angles\n",
+      "DEBUG:voronoi:__init__:Neighbors distances and angles set up in 0.00 seconds\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments:DetailedVoronoiContainer has been set up\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments: ... in site #0/9 (Si)\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_set (4, 0)\n",
+      "DEBUG:coordination_geometry_finder:update_nb_set_environments:Getting StructureEnvironments with optimized algorithm\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_sets added from hints\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.02 seconds\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments: ... in site #1/9 (Si)\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.06 seconds\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments: ... in site #1/9 (Si)\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_set (4, 0)\n",
+      "DEBUG:coordination_geometry_finder:update_nb_set_environments:Getting StructureEnvironments with optimized algorithm\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_sets added from hints\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.02 seconds\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments: ... in site #2/9 (Si)\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.16 seconds\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments: ... in site #2/9 (Si)\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_set (4, 0)\n",
+      "DEBUG:coordination_geometry_finder:update_nb_set_environments:Getting StructureEnvironments with optimized algorithm\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_sets added from hints\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.02 seconds\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments: ... in site #3/9 (O)\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.13 seconds\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments: ... in site #3/9 (O)\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_set (2, 0)\n",
+      "DEBUG:coordination_geometry_finder:update_nb_set_environments:Getting StructureEnvironments with optimized algorithm\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_sets added from hints\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.02 seconds\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments: ... in site #4/9 (O)\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.08 seconds\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments: ... in site #4/9 (O)\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_set (2, 0)\n",
+      "DEBUG:coordination_geometry_finder:update_nb_set_environments:Getting StructureEnvironments with optimized algorithm\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_sets added from hints\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.00 seconds\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments: ... in site #5/9 (O)\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.05 seconds\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments: ... in site #5/9 (O)\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_set (2, 0)\n",
+      "DEBUG:coordination_geometry_finder:update_nb_set_environments:Getting StructureEnvironments with optimized algorithm\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_sets added from hints\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.05 seconds\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments: ... in site #6/9 (O)\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.07 seconds\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments: ... in site #6/9 (O)\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_set (2, 0)\n",
+      "DEBUG:coordination_geometry_finder:update_nb_set_environments:Getting StructureEnvironments with optimized algorithm\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_sets added from hints\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.00 seconds\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments: ... in site #7/9 (O)\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.07 seconds\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments: ... in site #7/9 (O)\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_set (2, 0)\n",
+      "DEBUG:coordination_geometry_finder:update_nb_set_environments:Getting StructureEnvironments with optimized algorithm\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_sets added from hints\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.02 seconds\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments: ... in site #8/9 (O)\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.06 seconds\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments: ... in site #8/9 (O)\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_set (2, 0)\n",
+      "DEBUG:coordination_geometry_finder:update_nb_set_environments:Getting StructureEnvironments with optimized algorithm\n",
       "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... getting environments for nb_sets added from hints\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.02 seconds\n",
-      "INFO:coordination_geometry_finder:compute_structure_environments:    ... compute_structure_environments ended in 0.52 seconds\n"
+      "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... computed in 0.07 seconds\n",
+      "DEBUG:coordination_geometry_finder:compute_structure_environments:    ... compute_structure_environments ended in 1.11 seconds\n"
      ]
     }
    ],
@@ -313,7 +321,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -332,14 +340,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[{'ce_symbol': 'A:2', 'ce_fraction': 1.0, 'csm': 2.260276235693848, 'permutation': [0, 1]}]\n"
+      "[{'ce_symbol': 'A:2', 'ce_fraction': 1, 'csm': 1.7441903855731844, 'permutation': [0, 1]}]\n"
      ]
     }
    ],
@@ -366,7 +374,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -389,14 +397,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[{'ce_symbol': 'A:2', 'ce_fraction': 0.6735454833571951, 'csm': 2.260276235693848, 'permutation': [0, 1]}, {'ce_symbol': 'L:2', 'ce_fraction': 0.32645451664280495, 'csm': 2.890279300472483, 'permutation': [0, 1]}]\n"
+      "[{'ce_symbol': 'A:2', 'ce_fraction': 0.8902438549087347, 'csm': 1.7441903855731844, 'permutation': [0, 1]}, {'ce_symbol': 'L:2', 'ce_fraction': 0.10975614509126526, 'csm': 3.5408272192671313, 'permutation': [0, 1]}]\n"
      ]
     }
    ],
@@ -425,14 +433,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[{'ce_symbol': 'T:4', 'ce_fraction': 1.0, 'csm': 0.009888229677272006, 'permutation': [0, 1, 2, 3]}]\n"
+      "[{'ce_symbol': 'T:4', 'ce_fraction': 1.0, 'csm': 0.012762033506339468, 'permutation': [0, 1, 2, 3]}]\n"
      ]
     }
    ],
@@ -452,7 +460,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.10.5 64-bit",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -466,7 +474,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.5"
+   "version": "3.11.8"
   },
   "vscode": {
    "interpreter": {
@@ -475,5 +483,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/notebooks/psp/POTCAR.Cl.gz b/notebooks/psp/POTCAR.Cl.gz
diff --git a/notebooks/psp/POTCAR.Cs_sv.gz b/notebooks/psp/POTCAR.Cs_sv.gz
diff --git a/notebooks/psp/POTCAR.Li_sv.gz b/notebooks/psp/POTCAR.Li_sv.gz
diff --git a/notebooks/psp/POTCAR.P.gz b/notebooks/psp/POTCAR.P.gz
diff --git a/notebooks/psp/POTCAR.S.gz b/notebooks/psp/POTCAR.S.gz
-Original file line number
+Diff line change
@@ Expand Up / @@ -27,6 +27,7 @@ jobs: @@
         env:
           PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
+          PMG_VASP_PSP_DIR: /home/runner/matgenb/matgenb/notebooks/psp
         steps:
           - name: Check out repo
@@ Expand Down @@