Merge pull request #196 from Exabyte-io/feature/SOF-7513

Feature/sof 7513

Author: timurbazhirov

other/materials_designer/create_interface_with_min_strain_zsl.ipynb

@@ -317,7 +317,7 @@
     "    substrate_configuration=substrate_slab_configuration,\n",
     "    film_termination=film_termination,\n",
     "    substrate_termination=substrate_termination,\n",
-    "    distance=INTERFACE_DISTANCE,\n",
+    "    distance_z=INTERFACE_DISTANCE,\n",
     "    vacuum= INTERFACE_VACUUM\n",
     ")"
    ],

other/materials_designer/specific_examples/interface_2d_2d_boron_nitride_graphene.ipynb

@@ -39,9 +39,9 @@
    "outputs": [],
    "source": [
     "# Enable interactive selection of terminations via UI prompt\n",
-    "IS_TERMINATIONS_SELECTION_INTERACTIVE = False \n",
+    "IS_TERMINATIONS_SELECTION_INTERACTIVE = False\n",
     "\n",
-    "FILM_INDEX = 1 # Index in the list of materials, to access as materials[FILM_INDEX]\n",
+    "FILM_INDEX = 1  # Index in the list of materials, to access as materials[FILM_INDEX]\n",
     "FILM_MILLER_INDICES = (0, 0, 1)\n",
     "FILM_THICKNESS = 1  # in atomic layers\n",
     "FILM_VACUUM = 0.0  # in angstroms\n",
@@ -56,9 +56,9 @@
     "SUBSTRATE_USE_ORTHOGONAL_Z = True\n",
     "\n",
     "# Maximum area for the superlattice search algorithm\n",
-    "MAX_AREA = 50 # in Angstrom^2\n",
+    "MAX_AREA = 50  # in Angstrom^2\n",
     "# Set the termination pair indices\n",
-    "TERMINATION_PAIR_INDEX = 0 # Will be overridden in interactive selection is used\n",
+    "TERMINATION_PAIR_INDEX = 0  # Will be overridden in interactive selection is used\n",
     "INTERFACE_DISTANCE = 3.4  # in Angstrom\n",
     "INTERFACE_VACUUM = 20.0  # in Angstrom"
    ],
@@ -85,9 +85,10 @@
     "\n",
     "if sys.platform == \"emscripten\":\n",
     "    import micropip\n",
-    "  \n",
+    "\n",
     "    await micropip.install('mat3ra-api-examples', deps=False)\n",
     "    from utils.jupyterlite import install_packages\n",
+    "\n",
     "    await install_packages(\"specific_examples|create_interface_with_min_strain_zsl.ipynb\")"
    ],
    "metadata": {
@@ -109,6 +110,7 @@
    "source": [
     "from mat3ra.standata.materials import Materials\n",
     "from mat3ra.made.material import Material\n",
+    "\n",
     "film = Material(Materials.get_by_name_first_match(\"Graphene\"))\n",
     "substrate = Material(Materials.get_by_name_and_categories(\"BN\", \"2D\"))"
    ],
@@ -131,6 +133,7 @@
    "outputs": [],
    "source": [
     "from utils.visualize import visualize_materials as visualize\n",
+    "\n",
     "visualize([substrate, film], repetitions=[3, 3, 1], rotation=\"0x\")"
    ],
    "metadata": {
@@ -158,17 +161,17 @@
     "film_slab_configuration = SlabConfiguration(\n",
     "    bulk=film,\n",
     "    miller_indices=FILM_MILLER_INDICES,\n",
-    "    thickness=FILM_THICKNESS, # in atomic layers\n",
-    "    vacuum=FILM_VACUUM, # in angstroms\n",
+    "    thickness=FILM_THICKNESS,  # in atomic layers\n",
+    "    vacuum=FILM_VACUUM,  # in angstroms\n",
     "    xy_supercell_matrix=FILM_XY_SUPERCELL_MATRIX,\n",
     "    use_orthogonal_z=FILM_USE_ORTHOGONAL_Z\n",
     ")\n",
     "\n",
     "substrate_slab_configuration = SlabConfiguration(\n",
     "    bulk=substrate,\n",
     "    miller_indices=SUBSTRATE_MILLER_INDICES,\n",
-    "    thickness=SUBSTRATE_THICKNESS, # in atomic layers\n",
-    "    vacuum=SUBSTRATE_VACUUM, # in angstroms\n",
+    "    thickness=SUBSTRATE_THICKNESS,  # in atomic layers\n",
+    "    vacuum=SUBSTRATE_VACUUM,  # in angstroms\n",
     "    xy_supercell_matrix=SUBSTRATE_XY_SUPERCELL_MATRIX,\n",
     "    use_orthogonal_z=SUBSTRATE_USE_ORTHOGONAL_Z\n",
     ")"
@@ -211,10 +214,13 @@
    "outputs": [],
    "source": [
     "film_slabs = [create_slab(film_slab_configuration, termination) for termination in film_slab_terminations]\n",
-    "substrate_slabs = [create_slab(substrate_slab_configuration, termination) for termination in substrate_slab_terminations]\n",
+    "substrate_slabs = [create_slab(substrate_slab_configuration, termination) for termination in\n",
+    "                   substrate_slab_terminations]\n",
     "\n",
-    "visualize([{\"material\":slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in film_slabs ], repetitions=[3, 3, 1], rotation=\"-90x\")\n",
-    "visualize([{\"material\":slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in substrate_slabs ], repetitions=[3, 3, 1], rotation=\"-90x\")  "
+    "visualize([{\"material\": slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in film_slabs],\n",
+    "          repetitions=[3, 3, 1], rotation=\"-90x\")\n",
+    "visualize([{\"material\": slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in substrate_slabs],\n",
+    "          repetitions=[3, 3, 1], rotation=\"-90x\")"
    ],
    "metadata": {
     "collapsed": false
@@ -236,7 +242,7 @@
    "source": [
     "from itertools import product\n",
     "\n",
-    "termination_pairs = list(product(film_slab_terminations, substrate_slab_terminations))    \n",
+    "termination_pairs = list(product(film_slab_terminations, substrate_slab_terminations))\n",
     "print(\"Termination Pairs (Film, Substrate)\")\n",
     "for idx, termination_pair in enumerate(termination_pairs):\n",
     "    print(f\"    {idx}: {termination_pair}\")"
@@ -266,9 +272,11 @@
     "termination_pair = termination_pairs[termination_pair_index]\n",
     "if IS_TERMINATIONS_SELECTION_INTERACTIVE:\n",
     "    if sys.platform == \"emscripten\":\n",
-    "        termination_pair = await ui_prompt_select_array_element_by_index_pyodide(termination_pairs, element_name=\"film/substrate termination pair\")\n",
+    "        termination_pair = await ui_prompt_select_array_element_by_index_pyodide(termination_pairs,\n",
+    "                                                                                 element_name=\"film/substrate termination pair\")\n",
     "    else:\n",
-    "        termination_pair = ui_prompt_select_array_element_by_index(termination_pairs, element_name=\"film/substrate termination pair\")"
+    "        termination_pair = ui_prompt_select_array_element_by_index(termination_pairs,\n",
+    "                                                                   element_name=\"film/substrate termination pair\")"
    ],
    "metadata": {
     "collapsed": false
@@ -299,7 +307,7 @@
     "    film_termination=film_termination,\n",
     "    substrate_termination=substrate_termination,\n",
     "    distance=INTERFACE_DISTANCE,\n",
-    "    vacuum= INTERFACE_VACUUM\n",
+    "    vacuum=INTERFACE_VACUUM\n",
     ")"
    ],
    "metadata": {
@@ -322,6 +330,7 @@
    "outputs": [],
    "source": [
     "from mat3ra.made.tools.build.interface import ZSLStrainMatchingParameters\n",
+    "\n",
     "zsl_strain_matching_parameters = ZSLStrainMatchingParameters(\n",
     "    max_area=MAX_AREA\n",
     ")"
@@ -345,11 +354,14 @@
    "cell_type": "code",
    "outputs": [],
    "source": [
-    "from mat3ra.made.tools.build.interface import ZSLStrainMatchingInterfaceBuilder, ZSLStrainMatchingInterfaceBuilderParameters\n",
+    "from mat3ra.made.tools.build.interface import ZSLStrainMatchingInterfaceBuilder, \\\n",
+    "    ZSLStrainMatchingInterfaceBuilderParameters\n",
     "\n",
-    "matched_interfaces_builder = ZSLStrainMatchingInterfaceBuilder(build_parameters=ZSLStrainMatchingInterfaceBuilderParameters(strain_matching_parameters=zsl_strain_matching_parameters))\n",
+    "matched_interfaces_builder = ZSLStrainMatchingInterfaceBuilder(\n",
+    "    build_parameters=ZSLStrainMatchingInterfaceBuilderParameters(\n",
+    "        strain_matching_parameters=zsl_strain_matching_parameters))\n",
     "\n",
-    "interfaces_sorted_by_size_and_strain= matched_interfaces_builder.get_materials(configuration=interface_configuration)"
+    "interfaces_sorted_by_size_and_strain = matched_interfaces_builder.get_materials(configuration=interface_configuration)"
    ],
    "metadata": {
     "collapsed": false
@@ -445,10 +457,14 @@
    "source": [
     "import numpy as np\n",
     "from mat3ra.made.tools.modify import interface_displace_part\n",
+    "\n",
     "a = selected_interface.lattice.a\n",
     "shifted_interfaces = []\n",
-    "for n in range(7):\n",
-    "    shifted_interface= interface_displace_part(selected_interface, [0,n*a/np.sqrt(3)/2,0], use_cartesian_coordinates=True)\n",
+    "for n in range(2, 9):\n",
+    "    shifted_interface = interface_displace_part(\n",
+    "        interface=selected_interface, \n",
+    "        displacement=[0, n * a / np.sqrt(3) / 2, 0],\n",
+    "        use_cartesian_coordinates=True)\n",
     "    shifted_interfaces.append(shifted_interface)"
    ],
    "metadata": {
@@ -490,6 +506,7 @@
    "outputs": [],
    "source": [
     "from utils.jupyterlite import download_content_to_file\n",
+    "\n",
     "for idx, interface in enumerate(shifted_interfaces):\n",
     "    download_content_to_file(interface, f\"interface_{idx}.json\")"
    ]