Merge branch 'dev' into feature/SOF-7489

Author: VsevolodX

other/materials_designer/specific_examples/defect_surface_adatom_graphene.ipynb

@@ -48,9 +48,11 @@
     "# Defect parameters\n",
     "DEFECT_TYPE = \"adatom\"\n",
     "PLACEMENT_METHOD = \"coordinate\"\n",
-    "HOLLOW_SITE_COORDINATE = [1/2, 1/2]\n",
-    "BRIDGE_SITE_COORDINATE = [3/8, 1/2]\n",
-    "TOP_SITE_COORDINATE = [7/12, 5/12]\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",
     "\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",
@@ -180,7 +182,8 @@
     "                                                     placement_method=PLACEMENT_METHOD,\n",
     "                                                     chemical_element=adatom_parameters[\"chemical_element\"],\n",
     "                                                     distance_z=adatom_parameters[\"distance_z\"],\n",
-    "                                                     position_on_surface=adatom_parameters[\"position_on_surface\"]\n",
+    "                                                     position_on_surface=adatom_parameters[\"position_on_surface\"],\n",
+    "                                                     use_cartesian_coordinates=USE_CARTESIAN_COORDINATES\n",
     "                                                     ) for adatom_parameters in ADATOM_PARAMETERS]\n",
     "\n",
     "defect_builder_parameters = PointDefectBuilderParameters()"

other/materials_designer/specific_examples/defect_surface_island_titanium_nitride.ipynb

@@ -83,6 +83,7 @@
     "if sys.platform == \"emscripten\":\n",
     "    import micropip\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\")"
    ],

…rate_lattices_molybdenum_disulfide.ipynb …rate_lattices_molybdenum_disulfide.ipynbother/materials_designer/specific_examples/twisted_interface_with_commensurate_lattices_molybdenum_disulfide.ipynb renamed to other/materials_designer/specific_examples/interface_bilayer_twisted_commensurate_lattices_molybdenum_disulfide.ipynb other/materials_designer/specific_examples/twisted_interface_with_commensurate_lattices_molybdenum_disulfide.ipynb renamed to other/materials_designer/specific_examples/interface_bilayer_twisted_commensurate_lattices_molybdenum_disulfide.ipynb

@@ -3,7 +3,7 @@
   {
    "cell_type": "markdown",
    "source": [
-    "# interface_bilayer_twisted_commensurate_lattices_molybdenum_disulfide\n",
+    "# Twisted Molybdenum Disulfide bilayers at various angles.\n",
     "\n",
     "## 0. Introduction.\n",
     "\n",
@@ -86,8 +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\")"
+    "    await install_packages(\"\", \"../../../config.yml\")"
    ],
    "metadata": {
     "collapsed": false

other/materials_designer/specific_examples/interface_bilayer_twisted_nanoribbons_boron_nitride.ipynb

@@ -88,8 +88,9 @@
     "    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(\"\", \"../../../config.yml\")\n"
    ],
    "metadata": {
     "collapsed": false