Merge pull request #190 from Exabyte-io/feature/SOF-7523

Feature/SOF-7523 GB 2D h-BN NB

Author: VsevolodX

other/materials_designer/specific_examples/grain_boundary_2d_boron_nitride.ipynb

@@ -0,0 +1,316 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# A 2D grain boundary in Boron Nitride\n",
+    "\n",
+    "## 0. Introduction\n",
+    "\n",
+    "This notebook demonstrates how to generate a 2D grain boundary in Boron Nitride, following the example in the manuscript:\n",
+    "\n",
+    "> **Qiucheng Li, Xiaolong Zou, Mengxi Liu, Jingyu Sun, Yabo Gao, Yue Qi, Xiebo Zhou, Boris I. Yakobson, Yanfeng Zhang, and Zhongfan Liu**\n",
+    "> \"Grain Boundary Structures and Electronic Properties of Hexagonal Boron Nitride on Cu(111)\"\n",
+    "> *ACS Nano* **2015** 9 (6), 6308-6315\n",
+    "> [DOI: 10.1021/acs.nanolett.5b01852](https://doi.org/10.1021/acs.nanolett.5b01852)\n",
+    "\n",
+    "Reproducing the material from Figure 2. c:\n",
+    "\n",
+    "<img src=\"https://i.imgur.com/NF79OUq.png\" alt=\"Grain Boundary in Boron Nitride\" width=\"400\"/>"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "415ed707e27a6c8e"
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 1. Prepare the Environment\n",
+    "### 1.1. Set up the notebook\n",
+    "Set the following flags to control the notebook behavior\n",
+    "For more information on the parameters and algorithm, refer to [Grain Boundary Builder Source](https://github.com/Exabyte-io/made/blob/35b9f318f5d667e0f5af023f3178bc4404317ab0/src/py/mat3ra/made/tools/build/grain_boundary/builders.py#L103)\n",
+    "`EDGE_INCLUSION_TOLERANCE` is a fine-tuning parameter that controls the inclusion of the edge atoms for both orientations in the gap.\n",
+    "For example of Graphene at 17.9 degrees: orange and green atoms are present with the value of 0.5 Angstroms, with value of 0, they will not be included.\n",
+    "<img src=\"https://i.imgur.com/QRgotXS.png\" alt=\"Edge Inclusion Tolerance\" width=\"400\"/>\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "a080006df3785cc5"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "# Material selection\n",
+    "MATERIAL_NAME = \"Boron_Nitride\"  # Name of the material to import from Standata\n",
+    "\n",
+    "# Grain boundary parameters\n",
+    "TARGET_TWIST_ANGLE = 9.0  # in degrees\n",
+    "BOUNDARY_GAP = 0.0  # Gap between two orientations in X direction, in Angstroms\n",
+    "XY_SUPERCELL_MATRIX = [[1, 0], [0, 2]] # Supercell matrix to be applied to each of the orientations before matching\n",
+    "\n",
+    "# Search algorithm parameters\n",
+    "MAX_REPETITION = None  # Maximum supercell matrix element value\n",
+    "ANGLE_TOLERANCE = 0.5  # in degrees\n",
+    "RETURN_FIRST_MATCH = True  # If True, returns first solution within tolerance\n",
+    "\n",
+    "# Distance tolerance for two atoms to be considered too close. \n",
+    "# Used when merging two orientations to remove the atoms of the first one. \n",
+    "# Should be less than the expected bond length\n",
+    "DISTANCE_TOLERANCE = 1.43  # in Angstroms\n",
+    "\n",
+    "# How much to expand inclusion of the edge atoms for both orientations and fill in the gap region.\n",
+    "# A fine-tuning parameter\n",
+    "EDGE_INCLUSION_TOLERANCE = 0.0  # in Angstroms\n",
+    "\n",
+    "# Visualization parameters\n",
+    "SHOW_INTERMEDIATE_STEPS = True\n",
+    "CELL_REPETITIONS_FOR_VISUALIZATION = [3, 3, 1]"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "338ee3c51155e086",
+   "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`."
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "6463f9bbcd3be7c7"
+  },
+  {
+   "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\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "7e22d1f4da825575",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 1.3. Load and preview input material"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "4a1cfe15caa44c3e"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from mat3ra.standata.materials import Materials\n",
+    "from mat3ra.made.material import Material\n",
+    "\n",
+    "material = Material(Materials.get_by_name_first_match(MATERIAL_NAME))"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "a1635c31132962f6",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 2. Prepare Material\n",
+    "### 2.1. Select and visualize initial material"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "32b3ad775543b06f"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.visualize import visualize_materials\n",
+    "\n",
+    "if SHOW_INTERMEDIATE_STEPS:\n",
+    "    visualize_materials(material, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "61f0870d8104cd21",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 3. Generate Surface Grain Boundary\n",
+    "### 3.1. Set up grain boundary configuration and builder\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "34d6c7a337f1e40b"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from mat3ra.made.tools.build.grain_boundary import (\n",
+    "    SurfaceGrainBoundaryConfiguration,\n",
+    "    SurfaceGrainBoundaryBuilderParameters,\n",
+    "    SurfaceGrainBoundaryBuilder\n",
+    ")\n",
+    "\n",
+    "config = SurfaceGrainBoundaryConfiguration(\n",
+    "    film=material,\n",
+    "    twist_angle=TARGET_TWIST_ANGLE,\n",
+    "    distance_z=BOUNDARY_GAP,\n",
+    "    gap=BOUNDARY_GAP,\n",
+    "    xy_supercell_matrix=XY_SUPERCELL_MATRIX\n",
+    ")\n",
+    "\n",
+    "params = SurfaceGrainBoundaryBuilderParameters(\n",
+    "    max_supercell_matrix_int=MAX_REPETITION,\n",
+    "    angle_tolerance=ANGLE_TOLERANCE,\n",
+    "    return_first_match=RETURN_FIRST_MATCH,\n",
+    "    edge_inclusion_tolerance=EDGE_INCLUSION_TOLERANCE,\n",
+    "    distance_tolerance=DISTANCE_TOLERANCE\n",
+    ")\n",
+    "\n",
+    "builder = SurfaceGrainBoundaryBuilder(build_parameters=params)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "33a2c8a9be436745",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 3.2. Generate and analyze grain boundaries\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "79e9378bf5e144d4"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.plot import plot_twisted_interface_solutions\n",
+    "\n",
+    "grain_boundaries = builder.get_materials(config)\n",
+    "\n",
+    "print(f\"\\nFound {len(grain_boundaries)} possible structures\")\n",
+    "for i, gb in enumerate(grain_boundaries):\n",
+    "    actual_angle = gb.metadata.get(\"actual_twist_angle\", \"unknown\")\n",
+    "    print(f\"\\nGrain Boundary {i + 1}:\")\n",
+    "    print(f\"Actual twist angle: {actual_angle}°\")\n",
+    "    print(f\"Number of atoms: {len(gb.basis.elements.ids)}\")\n",
+    "\n",
+    "if len(grain_boundaries) > 0:\n",
+    "    plot_twisted_interface_solutions(grain_boundaries)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "d7007fe825463e5a",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 4. Preview the selected grain boundary\n",
+    "By default, the first grain boundary is selected. You can change the selection by changing the `selected_structure` index."
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "8b2f0574a20089a5"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "selected_structure = grain_boundaries[0]\n",
+    "\n",
+    "actual_angle = selected_structure.metadata.get(\"build\").get(\"configuration\").get(\"actual_twist_angle\")\n",
+    "print(f\"Target angle: {TARGET_TWIST_ANGLE}°\")\n",
+    "print(f\"Actual angle: {actual_angle}°\")\n",
+    "print(f\"Number of atoms: {len(selected_structure.basis.elements.ids)}\")\n",
+    "\n",
+    "visualize_materials(selected_structure, repetitions=[1, 1, 1])\n",
+    "visualize_materials(selected_structure, repetitions=[1, 1, 1], rotation=\"-90x\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "7f558a8e9d417cef",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 5. Pass data to the outside runtime\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "afcc004c5878b56f"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.jupyterlite import download_content_to_file\n",
+    "\n",
+    "download_content_to_file(selected_structure, \"grain_boundary_2d_boron_nitride.json\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "20e46167358d63",
+   "execution_count": null
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}