Merge pull request #164 from Exabyte-io/fix/standata-for-all

update: add standata to common config
Exabyte-io · Nov 14, 2024 · 15150d2 · 15150d2
2 parents 4a2739a + 0844748
commit 15150d2
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Showing 5 changed files with 30 additions and 22 deletions.
diff --git a/config.yml b/config.yml
@@ -64,3 +64,6 @@ notebooks:
     packages_pyodide:
       - mat3ra-esse
       - mat3ra-made
+  - name: specific_examples
+    packages_common:
+      - mat3ra-standata
diff --git a/other/materials_designer/specific_examples/defect_surface_adatom_graphene.ipynb b/other/materials_designer/specific_examples/defect_surface_adatom_graphene.ipynb
@@ -49,10 +49,10 @@
     "DEFECT_TYPE = \"adatom\"\n",
     "PLACEMENT_METHOD = \"coordinate\"\n",
     "# Using crystal coordinates for the defect placement\n",
-    "USE_CARTESIAN_COORDINATES = False \n",
-    "HOLLOW_SITE_COORDINATE = [1/2, 1/2] # in crystal coordinates\n",
-    "BRIDGE_SITE_COORDINATE = [3/8, 1/2] # in crystal coordinates\n",
-    "TOP_SITE_COORDINATE = [7/12, 5/12] # in crystal coordinates\n",
+    "USE_CARTESIAN_COORDINATES = False\n",
+    "HOLLOW_SITE_COORDINATE = [1 / 2, 1 / 2]  # in crystal coordinates\n",
+    "BRIDGE_SITE_COORDINATE = [3 / 8, 1 / 2]  # in crystal coordinates\n",
+    "TOP_SITE_COORDINATE = [7 / 12, 5 / 12]  # in crystal coordinates\n",
     "\n",
     "# Setting data according to Table 1 in the manuscript, distance_z is the `h` from the table.\n",
     "# Uncomment the lines to create the defect for the desired adatom.\n",
@@ -100,7 +100,8 @@
     "    await micropip.install('mat3ra-api-examples', deps=False)\n",
     "    from utils.jupyterlite import install_packages\n",
     "\n",
-    "    await install_packages(\"create_point_defect.ipynb\", \"../../../config.yml\")"
+    "    await install_packages(\"create_point_defect.ipynb\", \"../../../config.yml\")\n",
+    "    await install_packages(\"specific_examples\", \"../../../config.yml\")"
    ],
    "metadata": {
     "collapsed": false
@@ -174,7 +175,7 @@
    "cell_type": "code",
    "outputs": [],
    "source": [
-    "from mat3ra.made.tools.build.defect import  AdatomSlabPointDefectConfiguration\n",
+    "from mat3ra.made.tools.build.defect import AdatomSlabPointDefectConfiguration\n",
     "from mat3ra.made.tools.build.defect.builders import PointDefectBuilderParameters\n",
     "\n",
     "configurations = [AdatomSlabPointDefectConfiguration(crystal=supercell,\n",
@@ -236,7 +237,8 @@
     "\n",
     "for material_with_defect in materials_with_adatom:\n",
     "    title = f\"{material_with_defect.metadata['build']['configuration']['chemical_element']} adatom\"\n",
-    "    visualize([{\"material\": material_with_defect, \"title\": title}, {\"material\": material_with_defect, \"title\":title, \"rotation\": \"-90x\"}])"
+    "    visualize([{\"material\": material_with_defect, \"title\": title},\n",
+    "               {\"material\": material_with_defect, \"title\": title, \"rotation\": \"-90x\"}])"
    ],
    "metadata": {
     "collapsed": false
@@ -261,7 +263,8 @@
     "from utils.jupyterlite import download_content_to_file\n",
     "\n",
     "for material_with_defect in materials_with_adatom:\n",
-    "    download_content_to_file(material_with_defect.to_json(), f\"{material_with_defect.metadata['build']['configuration']['chemical_element']}_adatom.json\")"
+    "    download_content_to_file(material_with_defect.to_json(),\n",
+    "                             f\"{material_with_defect.metadata['build']['configuration']['chemical_element']}_adatom.json\")"
    ],
    "metadata": {
     "collapsed": false

diff --git a/other/materials_designer/specific_examples/defect_surface_island_titanium_nitride.ipynb b/other/materials_designer/specific_examples/defect_surface_island_titanium_nitride.ipynb
@@ -50,7 +50,7 @@
     "\n",
     "# Create slab with default parameters if imported material is not a slab\n",
     "DEFAULT_SLAB_PARAMETERS = {\n",
-    "    \"miller_indices\": (0,0,1),\n",
+    "    \"miller_indices\": (0, 0, 1),\n",
     "    \"thickness\": 3,\n",
     "    \"vacuum\": 0.0,\n",
     "    \"use_orthogonal_z\": True,\n",
@@ -82,10 +82,12 @@
     "\n",
     "if sys.platform == \"emscripten\":\n",
     "    import micropip\n",
+    "\n",
     "    await micropip.install('mat3ra-api-examples', deps=False)\n",
-    "    await micropip.install('mat3ra-standata')\n",
     "    from utils.jupyterlite import install_packages\n",
-    "    await install_packages(\"\", \"../../../config.yml\")"
+    "\n",
+    "    await install_packages(\"\", \"../../../config.yml\")\n",
+    "    await install_packages(\"specific_examples\", \"../../../config.yml\")"
    ],
    "metadata": {
     "collapsed": false
@@ -110,6 +112,7 @@
    "source": [
     "from mat3ra.made.material import Material\n",
     "from mat3ra.standata.materials import Materials\n",
+    "\n",
     "material = Material(Materials.get_by_name_first_match(\"TiN\"))"
    ],
    "metadata": {
@@ -142,7 +145,7 @@
     "        bulk=material,\n",
     "        miller_indices=DEFAULT_SLAB_PARAMETERS[\"miller_indices\"],\n",
     "        thickness=DEFAULT_SLAB_PARAMETERS[\"thickness\"],\n",
-    "        vacuum= DEFAULT_SLAB_PARAMETERS[\"vacuum\"],\n",
+    "        vacuum=DEFAULT_SLAB_PARAMETERS[\"vacuum\"],\n",
     "        use_orthogonal_z=DEFAULT_SLAB_PARAMETERS[\"use_orthogonal_z\"],\n",
     "        xy_supercell_matrix=DEFAULT_SLAB_PARAMETERS[\"xy_supercell_matrix\"]\n",
     "    )\n",
@@ -179,12 +182,11 @@
     ")\n",
     "from mat3ra.made.tools.build.defect import IslandSlabDefectConfiguration\n",
     "\n",
-    "coordinate_condition= BoxCoordinateCondition(\n",
+    "coordinate_condition = BoxCoordinateCondition(\n",
     "    min_coordinate=SHAPE_PARAMETERS['min_coordinate'],\n",
     "    max_coordinate=SHAPE_PARAMETERS['max_coordinate']\n",
     ")\n",
     "\n",
-    "\n",
     "island_config = IslandSlabDefectConfiguration(\n",
     "    crystal=slab,\n",
     "    condition=coordinate_condition,\n",
@@ -193,6 +195,7 @@
     ")\n",
     "\n",
     "from mat3ra.made.tools.build.defect import IslandSlabDefectBuilder, SlabDefectBuilderParameters\n",
+    "\n",
     "params = SlabDefectBuilderParameters(\n",
     "    auto_add_vacuum=AUTO_ADD_VACUUM,\n",
     "    vacuum_thickness=VACUUM_THICKNESS,\n",
@@ -243,7 +246,7 @@
    "source": [
     "visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
     "           {\"material\": slab_with_island, \"title\": f\"Material with Island Defect ({SHAPE_PARAMETERS['shape']})\"}],\n",
-    "rotation=\"-90x\")\n",
+    "          rotation=\"-90x\")\n",
     "\n",
     "visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
     "           {\"material\": slab_with_island, \"title\": f\"Material with Island Defect ({SHAPE_PARAMETERS['shape']})\"}])"

diff --git a/...cific_examples/interface_bilayer_twisted_commensurate_lattices_molybdenum_disulfide.ipynb b/...cific_examples/interface_bilayer_twisted_commensurate_lattices_molybdenum_disulfide.ipynb
@@ -86,9 +86,9 @@
     "    import micropip\n",
     "\n",
     "    await micropip.install('mat3ra-api-examples', deps=False)\n",
-    "    await micropip.install('mat3ra-standata')\n",
     "    from utils.jupyterlite import install_packages\n",
-    "    await install_packages(\"\", \"../../../config.yml\")"
+    "\n",
+    "    await install_packages(\"specific_examples\", \"../../../config.yml\")"
    ],
    "metadata": {
     "collapsed": false
@@ -150,7 +150,7 @@
     "    CommensurateLatticeTwistedInterfaceBuilder\n",
     "from mat3ra.made.tools.build.interface.configuration import TwistedInterfaceConfiguration\n",
     "\n",
-    "configs = [ TwistedInterfaceConfiguration(\n",
+    "configs = [TwistedInterfaceConfiguration(\n",
     "    film=material,\n",
     "    substrate=material,\n",
     "    twist_angle=parameters[\"angle\"],\n",
@@ -186,7 +186,7 @@
    "cell_type": "code",
    "outputs": [],
    "source": [
-    "interfaces= [ builder.get_material(config) for config in configs]"
+    "interfaces = [builder.get_material(config) for config in configs]"
    ],
    "metadata": {
     "collapsed": false

diff --git a/...ials_designer/specific_examples/interface_bilayer_twisted_nanoribbons_boron_nitride.ipynb b/...ials_designer/specific_examples/interface_bilayer_twisted_nanoribbons_boron_nitride.ipynb
@@ -57,7 +57,6 @@
     "INTERFACE_DISTANCE = 3.23  # Distance between layers in Angstroms\n",
     "INTERFACE_VACUUM = 20.0  # Vacuum layer thickness in Angstroms\n",
     "\n",
-    "\n",
     "# Visualization settings\n",
     "SHOW_INTERMEDIATE_STEPS = True\n",
     "VISUALIZE_REPETITIONS = [1, 1, 1]"
@@ -88,9 +87,9 @@
     "    import micropip\n",
     "\n",
     "    await micropip.install('mat3ra-api-examples', deps=False)\n",
-    "    await micropip.install('mat3ra-standata')\n",
     "    from utils.jupyterlite import install_packages\n",
-    "    await install_packages(\"\", \"../../../config.yml\")\n"
+    "\n",
+    "    await install_packages(\"specific_examples\", \"../../../config.yml\")"
    ],
    "metadata": {
     "collapsed": false