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Merge pull request #172 from Exabyte-io/feature/SOF-7507
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feature/SOF-7507 feat: Mg in GaN defect tutorial
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@VsevolodX
VsevolodX authored Nov 28, 2024
2 parents c37ece6 + 48a6b4b commit 8a1d506
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6 changes: 0 additions & 6 deletions other/materials_designer/create_point_defect_pair.ipynb
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"cell_type": "code",
"outputs": [],
"source": [
"DEFECT_TYPE = \"substitution\" # (e.g. \"vacancy\", \"substitution\", \"interstitial\")\n",
"SITE_ID = None # Site index of the defect\n",
"COORDINATE = None # Position of the defect in crystal coordinates\n",
"APPROXIMATE_COORDINATE = None # Approximate coordinates of the defect in crystal coordinates\n",
"CHEMICAL_ELEMENT = \"C\" # Element to be placed at the site (ignored for vacancy)\n",
"\n",
"SUPERCELL_MATRIX = [[3, 0, 0], [0, 3, 0], [0, 0, 3]]\n",
"\n",
"# List of dictionaries with defect parameters\n",
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269 changes: 269 additions & 0 deletions other/materials_designer/specific_examples/defect_point_pair_gallium_nitride.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"source": [
"# Vacancy and Substitutional defect pair in GaN\n",
"\n",
"Focusing on recreating the defect pair in GaN from the Figure 1. c) in the publication:\n",
"\n",
"<img src=\"https://i.imgur.com/1JsDwXO.png\" width=\"400\" />"
],
"metadata": {
"collapsed": false
},
"id": "4f901763903359e6"
},
{
"cell_type": "markdown",
"source": [
"## 1. Prepare the Environment\n",
"### 1.1. Set up defects parameters \n",
"Defect Configuration parameters are described in [Defect Configuration](https://github.com/Exabyte-io/made/blob/8196b759242551c77d1791bf5bd2f4150763cfef/src/py/mat3ra/made/tools/build/defect/configuration.py#L102)."
],
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{
"cell_type": "code",
"outputs": [],
"source": [
"SUPERCELL_MATRIX = [[3, 0, 0], [0, 3, 0], [0, 0, 2]]\n",
"\n",
"# List of dictionaries with defect parameters\n",
"PRIMARY_DEFECT_CONFIG = {\n",
" \"defect_type\": \"substitution\",\n",
" \"approximate_coordinate\": [0.5, 0.5, 0.5],\n",
" \"chemical_element\": \"Mg\",\n",
"}\n",
"\n",
"SECONDARY_DEFECT_CONFIG = {\n",
" \"defect_type\": \"vacancy\",\n",
" \"approximate_coordinate\": [0.5, 0.5, 0.65],\n",
"}"
],
"metadata": {
"collapsed": false
},
"id": "2719b1a0b211ce20",
"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
},
"id": "5626829bece625b"
},
{
"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(\"create_point_defect.ipynb\")"
],
"metadata": {
"collapsed": false
},
"id": "f4994342ac9f2cbd",
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"### 1.3. Get input materials\n",
"Materials are loaded with `get_materials()`."
],
"metadata": {
"collapsed": false
},
"id": "683ce558645b4465"
},
{
"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(\"GaN\"))"
],
"metadata": {
"collapsed": false
},
"id": "4a6bab14f63024d1",
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"### 1.4. Create and preview Supercell"
],
"metadata": {
"collapsed": false
},
"id": "acfef1aa207eb977"
},
{
"cell_type": "code",
"outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"from mat3ra.made.tools.build.supercell import create_supercell\n",
"\n",
"unit_cell = material\n",
"supercell = create_supercell(unit_cell, supercell_matrix=SUPERCELL_MATRIX)\n",
"visualize(supercell, repetitions=[1, 1, 1], rotation=\"0x\")"
],
"metadata": {
"collapsed": false
},
"id": "4580fda63efa927e",
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"## 2. Create the Defect\n",
"### 2.1. Initialize Configuration and Builder parameters"
],
"metadata": {
"collapsed": false
},
"id": "4391a0f444f4b64a"
},
{
"cell_type": "code",
"outputs": [],
"source": [
"from mat3ra.made.tools.build.defect.configuration import PointDefectPairConfiguration, PointDefectConfiguration\n",
"from mat3ra.made.tools.build.defect.builders import PointDefectBuilderParameters\n",
"\n",
"primary_defect_configuration = PointDefectConfiguration.from_dict(supercell, PRIMARY_DEFECT_CONFIG)\n",
"secondary_defect_configuration = PointDefectConfiguration.from_dict(supercell, SECONDARY_DEFECT_CONFIG)\n",
"\n",
"point_defect_pair_configuration = PointDefectPairConfiguration(\n",
" primary_defect_configuration=primary_defect_configuration,\n",
" secondary_defect_configuration=secondary_defect_configuration\n",
")\n",
"\n",
"defect_builder_parameters = PointDefectBuilderParameters(center_defect=False)"
],
"metadata": {
"collapsed": false
},
"id": "c686498fc4419e3c",
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"### 2.2. Create the defects"
],
"metadata": {
"collapsed": false
},
"id": "358ae5cd995c821f"
},
{
"cell_type": "code",
"outputs": [],
"source": [
"from mat3ra.made.tools.build.defect.builders import PointDefectPairBuilder\n",
"\n",
"material_with_defect = PointDefectPairBuilder(defect_builder_parameters).get_material(point_defect_pair_configuration)"
],
"metadata": {
"collapsed": false
},
"id": "7a584be241ab1548",
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"## 3. Visualize Result(s)"
],
"metadata": {
"collapsed": false
},
"id": "f99753a31e0123a"
},
{
"cell_type": "code",
"outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"\n",
"visualize([{\"material\": supercell, \"title\": \"Original material\"},\n",
" {\"material\": material_with_defect, \"title\": f\"Material with defect\"}],\n",
" rotation=\"-90x\")\n",
"visualize([{\"material\": supercell, \"title\": \"Original material\"},\n",
" {\"material\": material_with_defect, \"title\": f\"Material with defect\"}])"
],
"metadata": {
"collapsed": false
},
"id": "951f0cffe9389d5e",
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"## 4. Pass data to the outside runtime"
],
"metadata": {
"collapsed": false
},
"id": "1c5d8e66b5b105ee"
},
{
"cell_type": "code",
"outputs": [],
"source": [
"from utils.jupyterlite import download_content_to_file\n",
"\n",
"download_content_to_file(material_with_defect, \"Mg substitution and vacancy in GaN.json\")"
],
"metadata": {
"collapsed": false
},
"id": "b9e1aba13faf1bf0",
"execution_count": null
}
],
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"nbformat_minor": 5
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