Merge pull request #183 from Exabyte-io/feature/SOF-7526

feature/SOF 7526

Author: timurbazhirov

other/materials_designer/specific_examples/interface_2d_3d_graphene_silicon_dioxide.ipynb

@@ -0,0 +1,376 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Interface between Graphene and SiO2 (\n",
+    "\n",
+    "## Introduction\n",
+    "\n",
+    "This notebook demonstrates the creation of an interface between 2D and 3D material: Graphene on SiO2. \n",
+    "\n",
+    "Following the manuscript:\n",
+    "    > **Yong-Ju Kang, Joongoo Kang, and K. J. Chang** \n",
+    "    > \"Electronic structure of graphene and doping effect on SiO2\"\n",
+    "    > Phys. Rev. B 78, 115404 (2008)\n",
+    "    > [DOI: 10.1103/PhysRevB.78.115404](https://doi.org/10.1103/PhysRevB.78.115404)\n",
+    "\n",
+    "\n",
+    "\n",
+    "Replicating the materials from the manuscript, FIG. 1. (b):\n",
+    "\n",
+    "<img src='https://i.imgur.com/ltSj5uk.png' width='600'/>\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 1. Prepare the Environment\n",
+    "### 1.1. Set up the notebook \n",
+    "\n",
+    "Set the following flags to control the notebook behavior "
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "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",
+    "FILM_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n",
+    "FILM_USE_ORTHOGONAL_Z = True\n",
+    "\n",
+    "SUBSTRATE_INDEX = 0\n",
+    "SUBSTRATE_MILLER_INDICES = (0, 0, 1)\n",
+    "SUBSTRATE_THICKNESS = 7  # in atomic layers (for 14 bilayers -- from manuscript)\n",
+    "SUBSTRATE_VACUUM = 0.0  # in angstroms\n",
+    "SUBSTRATE_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n",
+    "SUBSTRATE_USE_ORTHOGONAL_Z = True\n",
+    "\n",
+    "# Maximum area for the superlattice search algorithm\n",
+    "MAX_AREA = 150  # in Angstrom^2\n",
+    "# Set the termination pair indices\n",
+    "TERMINATION_PAIR_INDICES = [1]  # For O-terminated\n",
+    "INTERFACE_DISTANCE = 2.58  # in Angstrom -- from manuscript\n",
+    "INTERFACE_VACUUM = 20.0  # in Angstrom -- from manuscript"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 1.2. Install Packages\n",
+    "The step executes only in Pyodide environment. For other environments, the packages should be installed via `pip install` (see [README](../../README.ipynb))."
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "\n",
+    "if sys.platform == \"emscripten\":\n",
+    "    import micropip\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": {
+    "collapsed": false
+   },
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 1.3. Get input materials and assign `substrate` and `film`"
+   ],
+   "metadata": {}
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "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_first_match(\"SiO2\"))"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 1.4. Preview Substrate and Film"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.visualize import visualize_materials as visualize\n",
+    "\n",
+    "visualize([substrate, film], repetitions=[3, 3, 1], rotation=\"0x\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 2. Configure slabs and select termination pair\n",
+    "\n",
+    "### 2.1. Create Substrate and Layer Slabs\n",
+    "Slab Configuration lets define the slab thickness, vacuum, and the Miller indices of the interfacial plane and get the slabs with possible terminations.\n",
+    "Define the substrate slab cell that will be used as a base for the interface and the film slab cell that will be placed on top of the substrate slab."
+   ],
+   "metadata": {}
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from mat3ra.made.tools.build.slab import SlabConfiguration, get_terminations, create_slab, \\\n",
+    "    PymatgenSlabGeneratorParameters\n",
+    "\n",
+    "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",
+    "    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",
+    "    xy_supercell_matrix=SUBSTRATE_XY_SUPERCELL_MATRIX,\n",
+    "    use_orthogonal_z=SUBSTRATE_USE_ORTHOGONAL_Z,\n",
+    ")\n",
+    "\n",
+    "params = PymatgenSlabGeneratorParameters(\n",
+    "    symmetrize=False)"
+   ],
+   "metadata": {},
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 2.2. Get possible terminations for the slabs"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "film_slab_terminations = get_terminations(film_slab_configuration, params)\n",
+    "substrate_slab_terminations = get_terminations(substrate_slab_configuration, params)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 2.3. Visualize slabs for all possible terminations"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "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, params) for termination in\n",
+    "                   substrate_slab_terminations]\n",
+    "\n",
+    "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
+   },
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 2.4. Print terminations for the interface"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from itertools import product\n",
+    "\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}\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 3. Create interfaces\n",
+    "\n",
+    "### 3.1. Initialize the Interface Configuration"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from mat3ra.made.tools.build.interface import InterfaceConfiguration\n",
+    "from mat3ra.made.tools.build.interface import ZSLStrainMatchingParameters\n",
+    "from mat3ra.made.tools.build.interface import ZSLStrainMatchingInterfaceBuilder, \\\n",
+    "    ZSLStrainMatchingInterfaceBuilderParameters\n",
+    "\n",
+    "interfaces = []\n",
+    "for termination_pair_idx in TERMINATION_PAIR_INDICES:\n",
+    "    termination_pair = termination_pairs[termination_pair_idx]\n",
+    "    film_termination, substrate_termination = termination_pair\n",
+    "    interface_configuration = InterfaceConfiguration(\n",
+    "        film_configuration=film_slab_configuration,\n",
+    "        substrate_configuration=substrate_slab_configuration,\n",
+    "        film_termination=film_termination,\n",
+    "        substrate_termination=substrate_termination,\n",
+    "        distance_z=INTERFACE_DISTANCE,\n",
+    "        vacuum=INTERFACE_VACUUM\n",
+    "    )\n",
+    "\n",
+    "    zsl_strain_matching_parameters = ZSLStrainMatchingParameters(\n",
+    "        max_area=MAX_AREA,\n",
+    "    )\n",
+    "\n",
+    "    matched_interfaces_builder = ZSLStrainMatchingInterfaceBuilder(\n",
+    "        build_parameters=ZSLStrainMatchingInterfaceBuilderParameters(\n",
+    "            strain_matching_parameters=zsl_strain_matching_parameters))\n",
+    "    interfaces_sorted_by_size_and_strain = matched_interfaces_builder.get_materials(\n",
+    "        configuration=interface_configuration)\n",
+    "    selected_interface = interfaces_sorted_by_size_and_strain[0]\n",
+    "    selected_interface.name = f\"Interface {termination_pair}\"\n",
+    "    interfaces.append(selected_interface)\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 4. Visualize the interfaces"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "visualize(interfaces, repetitions=[3, 3, 1])\n",
+    "visualize(interfaces, repetitions=[1, 1, 1], rotation=\"-90x\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 5. Pass data to the outside runtime"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from utils.jupyterlite import download_content_to_file\n",
+    "\n",
+    "for idx, interface in enumerate(interfaces):\n",
+    "    download_content_to_file(interfaces, f\"interface_{idx}.json\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": ".venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}