update: add nb to generate interfaces

other/media_generation/create_materials.ipynb

@@ -0,0 +1,125 @@
+{
+ "cells": [
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
+    "import os\n",
+    "from pymatgen.ext.matproj import MPRester\n",
+    "from mat3ra.made.tools.build.slab import SlabConfiguration, get_terminations, create_slab\n",
+    "from mat3ra.made.tools.build.interface import InterfaceConfiguration, ZSLStrainMatchingParameters, \\\n",
+    "    ZSLStrainMatchingInterfaceBuilder, ZSLStrainMatchingInterfaceBuilderParameters\n",
+    "from utils.visualize import visualize_materials\n",
+    "from utils.jupyterlite import set_materials\n",
+    "\n",
+    "from mat3ra.standata.materials import Materials\n",
+    "from mat3ra.made.material import Material\n",
+    "\n",
+    "materials = Materials.get_by_categories(\"3D\")\n",
+    "\n",
+    "# Map lattice type to Miller Index\n",
+    "\n",
+    "lattice_to_miller = {\n",
+    "    \"CUB\": (1, 1, 1),\n",
+    "    \"FCC\": (1, 1, 1),\n",
+    "    \"HEX\": (0, 0, 1),\n",
+    "    \"TRI\": (1, 1, 1)\n",
+    "}\n",
+    "\n",
+    "# Create interfaces\n",
+    "for i, substrate_json in enumerate(materials):\n",
+    "    for j, film_json in enumerate(materials):\n",
+    "        if i != j:\n",
+    "            print(f\"Creating interface between {substrate_json['name']} and {film_json['name']}\")\n",
+    "\n",
+    "            substrate = Material(substrate_json)\n",
+    "            film = Material(film_json)\n",
+    "            # Define slab and interface parameters\n",
+    "            slab_params = {\n",
+    "                \"miller_indices\": lattice_to_miller[substrate.lattice.type],\n",
+    "                \"thickness\": 3,\n",
+    "                \"vacuum\": 15.0,\n",
+    "                \"xy_supercell_matrix\": [[1, 0], [0, 1]],\n",
+    "                \"use_conventional_cell\": True,\n",
+    "                \"use_orthogonal_z\": True\n",
+    "            }\n",
+    "\n",
+    "            interface_params = {\n",
+    "                \"distance_z\": 3.0,\n",
+    "                \"vacuum\": 0.0,\n",
+    "                \"max_area\": 150,\n",
+    "                \"max_area_tol\": 0.10,\n",
+    "                \"max_angle_tol\": 0.04,\n",
+    "                \"max_length_tol\": 0.04\n",
+    "            }\n",
+    "\n",
+    "\n",
+    "            # Create slab configurations\n",
+    "            substrate_slab_config = SlabConfiguration(bulk=substrate, **slab_params)\n",
+    "            film_slab_config = SlabConfiguration(bulk=film, **slab_params)\n",
+    "            try:\n",
+    "                # Get terminations\n",
+    "                substrate_terminations = get_terminations(substrate_slab_config)\n",
+    "                film_terminations = get_terminations(film_slab_config)\n",
+    "\n",
+    "                # Create slabs\n",
+    "                substrate_slabs = [create_slab(substrate_slab_config, t) for t in substrate_terminations]\n",
+    "                film_slabs = [create_slab(film_slab_config, t) for t in film_terminations]\n",
+    "\n",
+    "                # Select termination pair (example: first pair)\n",
+    "                termination_pair = (film_terminations[0], substrate_terminations[0])\n",
+    "\n",
+    "                # Create interface configuration\n",
+    "                interface_config = InterfaceConfiguration(\n",
+    "                    film_configuration=film_slab_config,\n",
+    "                    substrate_configuration=substrate_slab_config,\n",
+    "                    film_termination=termination_pair[0],\n",
+    "                    substrate_termination=termination_pair[1],\n",
+    "                    distance_z=interface_params[\"distance_z\"],\n",
+    "                    vacuum=interface_params[\"vacuum\"]\n",
+    "                )\n",
+    "\n",
+    "                # Set strain matching parameters\n",
+    "                zsl_params = ZSLStrainMatchingParameters(\n",
+    "                    max_area=interface_params[\"max_area\"],\n",
+    "                    max_area_tol=interface_params[\"max_area_tol\"],\n",
+    "                    max_angle_tol=interface_params[\"max_angle_tol\"],\n",
+    "                    max_length_tol=interface_params[\"max_length_tol\"]\n",
+    "                )\n",
+    "\n",
+    "                # Generate interfaces\n",
+    "                builder = ZSLStrainMatchingInterfaceBuilder(\n",
+    "                    build_parameters=ZSLStrainMatchingInterfaceBuilderParameters(strain_matching_parameters=zsl_params)\n",
+    "                )\n",
+    "                interfaces = builder.get_materials(configuration=interface_config)\n",
+    "\n",
+    "                # Visualize and save the interfaces\n",
+    "                interface = interfaces[0]\n",
+    "                visualize_materials(interface, repetitions=[1, 1, 1])\n",
+    "                # set_materials(interface)\n",
+    "            except Exception as e:\n",
+    "                print(f\"Error creating interface between {substrate.name} and {film.name}: {e}\")"
+   ],
+   "id": "2774de5c47160056",
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": "",
+   "id": "3572ccacbb4fd25f",
+   "outputs": [],
+   "execution_count": null
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "name": "python3",
+   "language": "python",
+   "display_name": "Python 3 (ipykernel)"
+  }
+ },
+ "nbformat": 5,
+ "nbformat_minor": 9
+}