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Merge pull request #167 from Exabyte-io/feature/SOF-7493
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‎other/materials_designer/Introduction.ipynb‎

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"\n",
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"### 3.1. Point Defects\n",
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"#### [3.1.1. Point Defects: vacancy, substitution, interstitial](create_point_defect.ipynb)\n",
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"#### [3.1.2. Point Defects Pair](create_point_defect_pair.ipynb)\n",
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"\n",
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"### 3.2. Surface Defects\n",
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"#### [3.2.1. Adatom Defect on a Slab](create_adatom_defect.ipynb)\n",

‎other/materials_designer/create_point_defect_pair.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"source": [
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"# Create a point defect pair in a bulk material\n",
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"\n",
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"Create a pair of point defects: substitution, vacancy, or interstitial in a bulk material.\n",
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"\n",
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"<h2 style=\"color:green\">Usage</h2>\n",
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"\n",
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"1. Make sure to select Input Materials (in the outer runtime) before running the notebook. \n",
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"1. Set notebook parameters in cell 1.1. below (or use the default values) -- to create multiple defects, fill `DEFECT_CONFIGS` with a list of dictionaries. \n",
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"1. Click “Run” > “Run All” to run all cells. \n",
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"1. Scroll down to view results. \n",
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"\n",
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"## Notes\n",
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"\n",
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"1. For more information, see [Introduction](Introduction.ipynb)\n",
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"<!-- # TODO: use a hashtag-based anchor link to interface creation documention above -->\n"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "f2e1e795020d7b3f"
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},
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{
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"cell_type": "markdown",
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"source": [
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"## 1. Prepare the Environment\n",
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"### 1.1. Set up defects parameters \n",
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"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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],
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"metadata": {
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"collapsed": false
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},
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"id": "5e43ff288847b784"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"DEFECT_TYPE = \"substitution\" # (e.g. \"vacancy\", \"substitution\", \"interstitial\")\n",
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"SITE_ID = None # Site index of the defect\n",
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"COORDINATE = None # Position of the defect in crystal coordinates\n",
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"APPROXIMATE_COORDINATE = None # Approximate coordinates of the defect in crystal coordinates\n",
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"CHEMICAL_ELEMENT = \"C\" # Element to be placed at the site (ignored for vacancy)\n",
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"\n",
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"SUPERCELL_MATRIX = [[3, 0, 0], [0, 3, 0], [0, 0, 3]]\n",
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"\n",
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"# List of dictionaries with defect parameters\n",
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"PRIMARY_DEFECT_CONFIG = {\n",
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" \"defect_type\": \"vacancy\",\n",
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" \"approximate_coordinate\": [0.5, 0.5, 0.5],\n",
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" # \"site_id\": 0,\n",
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" # \"coordinate\": None,\n",
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"}\n",
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"\n",
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"SECONDARY_DEFECT_CONFIG = {\n",
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" \"defect_type\": \"substitution\",\n",
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" \"approximate_coordinate\": [0.55, 0.55, 0.55],\n",
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" \"chemical_element\": \"C\",\n",
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" # \"site_id\": 0,\n",
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" # \"coordinate\": None,\n",
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"}"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "9d8b1890b34d850a",
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 1.2. Install Packages\n",
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"The step executes only in Pyodide environment. For other environments, the packages should be installed via `pip install` (see [README](../../README.ipynb))."
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],
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"metadata": {
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"collapsed": false
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},
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"id": "bb64de5ff32649f8"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"import sys\n",
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"\n",
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"if sys.platform == \"emscripten\":\n",
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" import micropip\n",
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"\n",
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" await micropip.install('mat3ra-api-examples', deps=False)\n",
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" from utils.jupyterlite import install_packages\n",
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"\n",
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" await install_packages(\"create_point_defect.ipynb\", \"../../config.yml\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "ef664b14457530fd",
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 1.3. Get input materials\n",
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"Materials are loaded with `get_materials()`."
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],
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"metadata": {
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"collapsed": false
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},
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"id": "919ad7af8dceeedd"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from utils.jupyterlite import get_materials\n",
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"\n",
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"materials = get_materials(globals())"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "be38fdda1984c654",
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 1.4. Create and preview Supercell"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "a132fe0ef8bbf0d0"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from utils.visualize import visualize_materials as visualize\n",
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"from mat3ra.made.tools.build.supercell import create_supercell\n",
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"\n",
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"unit_cell = materials[0]\n",
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"supercell = create_supercell(unit_cell, supercell_matrix=SUPERCELL_MATRIX)\n",
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"visualize(supercell, repetitions=[1, 1, 1], rotation=\"0x\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "e2d24109d3068c9e",
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"source": [
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"## 2. Create the Defect\n",
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"### 2.1. Initialize Configuration and Builder parameters"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "5da5b0380583c952"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from mat3ra.made.tools.build.defect.configuration import PointDefectPairConfiguration, PointDefectConfiguration\n",
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"from mat3ra.made.tools.build.defect.builders import PointDefectBuilderParameters\n",
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"\n",
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"primary_defect_configuration = PointDefectConfiguration.from_dict(supercell, PRIMARY_DEFECT_CONFIG)\n",
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"secondary_defect_configuration = PointDefectConfiguration.from_dict(supercell, SECONDARY_DEFECT_CONFIG)\n",
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"\n",
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"point_defect_pair_configuration = PointDefectPairConfiguration(\n",
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" primary_defect_configuration=primary_defect_configuration,\n",
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" secondary_defect_configuration=secondary_defect_configuration\n",
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")\n",
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"\n",
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"defect_builder_parameters = PointDefectBuilderParameters(center_defect=False)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "e385e50ae11ed2b9",
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 2.2. Create the defects"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "489b51f0ee122c48"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from mat3ra.made.tools.build.defect.builders import PointDefectPairBuilder\n",
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"\n",
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"material_with_defect = PointDefectPairBuilder(defect_builder_parameters).get_material(point_defect_pair_configuration)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "a990fa35742d7269",
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"source": [
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"## 3. Visualize Result(s)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "462549d016073446"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from utils.visualize import visualize_materials as visualize\n",
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"\n",
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"visualize([{\"material\": supercell, \"title\": \"Original material\"},\n",
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" {\"material\": material_with_defect, \"title\": f\"Material with defect\"}],\n",
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" rotation=\"-90x\")\n",
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"visualize([{\"material\": supercell, \"title\": \"Original material\"},\n",
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" {\"material\": material_with_defect, \"title\": f\"Material with defect\"}])"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "509b18661a069e42",
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"source": [
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"## 4. Pass data to the outside runtime"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "d381df29a6bbdd82"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from utils.jupyterlite import set_materials\n",
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"\n",
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"set_materials([material_with_defect])"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "61daa5afcbc078a9",
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"execution_count": null
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 2
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.6"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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