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VsevolodXVsevolodX
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Merge pull request #159 from Exabyte-io/feature/SOF-7489
feature/SOF-7489 supercell nb
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‎other/materials_designer/Introduction.ipynb‎

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"## 1. Single-Material Structures.\n",
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"\n",
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"### 1.1. 3D Structures.\n",
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"#### [1.1.1. Supercells. Create supercells from 3D crystals.](create_supercell.ipynb)(COMING SOON)\n",
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"#### [1.1.1. Supercells. Create supercells from 3D crystals.](create_supercell.ipynb)\n",
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"\n",
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"### 1.2. 2D Structures.\n",
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"#### [1.2.1. Slabs. Create slabs from bulk materials.](create_slab.ipynb)\n",

‎other/materials_designer/create_slab.ipynb‎

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"from utils.jupyterlite import get_materials\n",
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"\n",
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"materials = get_materials(globals())\n",
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"material = materials[26]"
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"material = materials[0]"
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],
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"metadata": {
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"collapsed": false

‎other/materials_designer/create_supercell.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 supercell\n",
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"\n",
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"Create a supercell of the original structure. The supercell is set either with the supercell matrix or the number of repetitions in each direction.\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).\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. "
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],
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"metadata": {
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"collapsed": false
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},
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"id": "bfcbf5c3f9adb668"
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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 transformation 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": "e3702ff2a5270ce6"
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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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"SUPERCELL_MATRIX = [\n",
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" [3, 0, 0], \n",
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" [0, 3, 0], \n",
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" [0, 0, 1]\n",
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"] \n",
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"\n",
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"# or use the scaling factor\n",
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"SCALING_FACTOR = None # [3, 3, 1]"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "e93f72e7c37dea10",
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"execution_count": 0
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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": "9f3ffe460d75942f"
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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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" await install_packages(\"\", \"../../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": "9eb0650f7183279c",
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"execution_count": 0
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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"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "f348991bf39a14e7"
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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())\n",
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"material = materials[0]"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "4b72580121ca40d0",
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"execution_count": 0
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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. Preview the material"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "aa183a2ac1a6993"
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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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"repetitions = SCALING_FACTOR if SCALING_FACTOR else [3, 3, 1]\n",
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"visualize(material, repetitions=repetitions, rotation=\"0x\")\n",
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"visualize(material, repetitions=repetitions, rotation=\"-90x\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "d3cba46f185c1a1b",
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"execution_count": 0
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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 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": "ba9e20ebe63ffda7"
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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.supercell import create_supercell\n",
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"\n",
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"if SUPERCELL_MATRIX:\n",
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" supercell = create_supercell(material, supercell_matrix=SUPERCELL_MATRIX)\n",
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"elif SCALING_FACTOR:\n",
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" supercell = create_supercell(material, scaling_factor=SCALING_FACTOR)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "2795d5bdbbaafbe6",
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"execution_count": 0
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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 the result"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "d8f41816d0b48edc"
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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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"visualize(supercell, repetitions=[1, 1, 1], rotation=\"0x\")\n",
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"visualize(supercell, repetitions=[1, 1, 1], rotation=\"-90x\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "aea078560283ca95",
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"execution_count": 0
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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 material 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": "a212abe25bf59b4f"
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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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"set_materials(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": "cdaf612bc6198546",
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"execution_count": 0
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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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