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Merge pull request #192 from Exabyte-io/feature/SOF-7509
feature/SOF-7509 optimize film nb
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‎other/materials_designer/Introduction.ipynb‎

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"\n",
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"This notebook demonstrates a workflow for converting materials data from the [JARVIS](https://jarvis.nist.gov/) database into ESSE format for use with the Mat3ra.com platform.\n",
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"\n",
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"#### [6.1.4. Optimize film position on interface](optimize_film_position.ipynb).\n",
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"\n",
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"## 7. Read more\n",
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"\n",
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"### 7.1. Under the hood.\n",

‎other/materials_designer/optimize_film_position.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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"# Optimize Interface Film Position\n",
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"\n",
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"Find most optimal position of the film on the substrate interface.\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 Material from the list of available materials. Must be an interface.\n",
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"1. Set notebook parameters in cell 1.2. 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. Wait for the run to complete.\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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"- The optimization is performed on a 2D grid of x,y translations.\n",
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"- Interface material must have atoms labeled \"0\" for the substrate and \"1\" for the film.\n",
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"\n",
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"\n",
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"## 1. Prepare the Environment\n",
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"### 1.1. Install Packages\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": "4dc7b2ed495d66e0"
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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(\"\")\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": "dd86bee2985f1b50",
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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. Set optimization parameters\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": "cca70ab27ef1d01d"
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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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"MATERIAL_INDEX = 0 # Index of the material to optimize\n",
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"# Grid parameters\n",
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"GRID_SIZE = (20, 20) # Resolution of the x-y grid\n",
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"GRID_RANGE_X = (-0.5, 0.5) # Range to search in x direction\n",
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"GRID_RANGE_Y = (-0.5, 0.5) # Range to search in y direction\n",
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"USE_CARTESIAN = False # Whether to use Cartesian coordinates\n",
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"\n",
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"# Visualization parameters\n",
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"SHOW_3D_LANDSCAPE = False # Whether to show 3D energy landscape\n",
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"STRUCTURE_REPETITIONS = [3, 3, 1] # Repetitions for structure visualization\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": "12878fd61f5a6b13",
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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. Load Material\n",
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"### 3.1. Make sure that loaded material is an interface material (atoms must have labels \"0\" for the substrate and \"1\" for the film)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "463af646361cd982"
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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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"interface_material = materials[MATERIAL_INDEX]\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": "3d982a1ca641f0d8"
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 3.2. Visualize the Material\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": "e920a6dd4906d8e8"
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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\n",
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"\n",
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"visualize_materials([interface_material], repetitions=STRUCTURE_REPETITIONS)\n",
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"visualize_materials([interface_material], repetitions=STRUCTURE_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": "5f4afdb7ac0c865b"
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 3.3. Optimize Film Position"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "90255d774f62d1da"
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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.interface import get_optimal_film_displacement\n",
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"from mat3ra.made.tools.modify import interface_displace_part\n",
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"from mat3ra.made.tools.calculate.calculators import InterfaceMaterialCalculator\n",
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"from mat3ra.made.tools.optimize import evaluate_calculator_on_xy_grid\n",
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"calculator = InterfaceMaterialCalculator()\n",
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"\n",
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"# Calculate energy landscape\n",
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"xy_matrix, energy_matrix = evaluate_calculator_on_xy_grid(\n",
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" material=interface_material,\n",
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" calculator_function=calculator.get_energy,\n",
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" modifier=interface_displace_part,\n",
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" grid_size_xy=GRID_SIZE,\n",
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" grid_range_x=GRID_RANGE_X,\n",
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" grid_range_y=GRID_RANGE_Y,\n",
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" use_cartesian_coordinates=USE_CARTESIAN\n",
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")\n",
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"\n",
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"# Find optimal position\n",
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"optimal_displacement = get_optimal_film_displacement(\n",
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" material=interface_material,\n",
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" calculator=calculator,\n",
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" grid_size_xy=GRID_SIZE,\n",
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" grid_range_x=GRID_RANGE_X,\n",
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" grid_range_y=GRID_RANGE_Y,\n",
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" use_cartesian_coordinates=USE_CARTESIAN\n",
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")\n",
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"\n",
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"print(f\"\\nOptimal displacement vector: {optimal_displacement}\")\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": "eb0b6e59c24dda4"
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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. Visualize Results\n",
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"### 4.1. Plot Energy Landscape"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "2945179d3729935d"
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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.plot import plot_energy_heatmap, plot_energy_landscape\n",
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"# Plot energy landscape\n",
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"plot_energy_heatmap(xy_matrix, energy_matrix, optimal_position=optimal_displacement[:2])\n",
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"\n",
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"if SHOW_3D_LANDSCAPE:\n",
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" plot_energy_landscape(xy_matrix, energy_matrix, optimal_position=optimal_displacement[:2])\n",
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"\n",
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"# Create optimized material\n",
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"optimized_material = interface_displace_part(\n",
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" interface_material,\n",
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" displacement=optimal_displacement,\n",
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" use_cartesian_coordinates=USE_CARTESIAN\n",
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")\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": "41ac6b383001db6b",
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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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"### 4.1. Visualize Original and Optimized 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": "82a1af573c6ca0e9"
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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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"print(\"\\nVisualization of original and optimized materials:\")\n",
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"visualize_materials([interface_material, optimized_material],\n",
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" repetitions=STRUCTURE_REPETITIONS)\n",
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"visualize_materials([interface_material, optimized_material],\n",
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" repetitions=STRUCTURE_REPETITIONS,\n",
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" rotation='-90x')\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": "e7972543ae747b68",
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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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"## 5. Save Results\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": "b4f6308e795e4f3c"
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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(optimized_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": "c81ec652fbb64316",
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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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