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Merge pull request #150 from Exabyte-io/feature/SOF-7472
feature/SOF-7472 feat: create island defect nb
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‎other/materials_designer/create_island_defect.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 island defect on a slab\n",
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"\n",
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"Create an island defect on a slab\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. \n",
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"\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 defect 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": "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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"# Shape-specific parameters\n",
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"# Choose the island shape: 'cylinder', 'sphere', 'box', or 'triangular_prism'\n",
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"# and the corresponding parameters\n",
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"SHAPE_PARAMETERS = {\n",
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" 'shape': 'cylinder',\n",
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" 'radius': 0.25,\n",
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" 'min_z': 0,\n",
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" 'max_z': 1\n",
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"}\n",
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"\n",
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"# Common parameters\n",
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"CENTER_POSITION = [0.5, 0.5, 0.5] # Center of the island\n",
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"USE_CARTESIAN_COORDINATES = False # Use Cartesian coordinates for the island\n",
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"NUMBER_OF_ADDED_LAYERS = 1 # Number of layers to add to the island\n",
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"\n",
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"# Vacuum parameters for builder\n",
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"AUTO_ADD_VACUUM = True # Automatically add vacuum to the slab\n",
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"VACUUM_THICKNESS = 10.0 # Thickness of the vacuum\n",
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"\n",
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"# Slab parameters for creating a new slab if provided material is not a slab\n",
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"DEFAULT_SLAB_PARAMETERS = {\n",
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" \"miller_indices\": (0,0,1),\n",
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" \"thickness\": 3,\n",
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" \"vacuum\": 5.0,\n",
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" \"use_orthogonal_z\": True,\n",
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" \"xy_supercell_matrix\": [[3, 0], [0, 3]]\n",
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"}\n",
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"\n",
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"\n",
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"# Uncomment and set the parameters for other shapes if needed\n",
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"# SHAPE_PARAMETERS = {\n",
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"# 'shape': 'sphere',\n",
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"# 'radius': 0.25\n",
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"# }\n",
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"# \n",
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"# SHAPE_PARAMETERS = {\n",
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"# 'shape': 'box',\n",
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"# 'min_coordinate': [0.25, 0.25, 0],\n",
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"# 'max_coordinate': [0.75, 0.75, 1]\n",
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"# }\n",
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"# \n",
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"# SHAPE_PARAMETERS = {\n",
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"# 'shape': 'triangular_prism',\n",
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"# 'position_on_surface_1': [0.25, 0.25],\n",
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"# 'position_on_surface_2': [0.75, 0.25],\n",
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"# 'position_on_surface_3': [0.5, 0.75],\n",
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"# 'min_z': 0,\n",
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"# 'max_z': 1\n",
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"# }\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": "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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" 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": "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 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": "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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"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. Preview Slab or create a new one"
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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 mat3ra.made.tools.build.slab import create_slab, SlabConfiguration\n",
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"from utils.visualize import visualize_materials as visualize\n",
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"\n",
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"slab = materials[0]\n",
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"if not slab.metadata or slab.metadata[\"build\"][\"configuration\"][\"type\"] != SlabConfiguration.__name__:\n",
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" print(\"The material is not a slab. Creating a new slab...\")\n",
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" slab_config = SlabConfiguration(\n",
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" bulk=materials[0],\n",
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" miller_indices=DEFAULT_SLAB_PARAMETERS[\"miller_indices\"],\n",
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" thickness=DEFAULT_SLAB_PARAMETERS[\"thickness\"],\n",
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" vacuum= DEFAULT_SLAB_PARAMETERS[\"vacuum\"],\n",
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" use_orthogonal_z=DEFAULT_SLAB_PARAMETERS[\"use_orthogonal_z\"],\n",
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" xy_supercell_matrix=DEFAULT_SLAB_PARAMETERS[\"xy_supercell_matrix\"]\n",
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" )\n",
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" \n",
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" slab = create_slab(slab_config)\n",
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"\n",
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"visualize([{\"material\": slab, \"title\": \"Original material\"}])\n",
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"visualize([{\"material\": slab, \"title\": \"Original material\"}], 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": "7fcb1e02e84c5f35",
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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 Target Material\n",
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"### 2.1. Initialize the defect configuration and builder"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "690241d87e7bbbe0"
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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 import IslandSlabDefectConfiguration\n",
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"\n",
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"\n",
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"island_config = IslandSlabDefectConfiguration.from_dict(\n",
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" crystal=slab,\n",
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" condition=SHAPE_PARAMETERS,\n",
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" number_of_added_layers = NUMBER_OF_ADDED_LAYERS\n",
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")\n",
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"\n",
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"from mat3ra.made.tools.build.defect import IslandSlabDefectBuilder, SlabDefectBuilderParameters\n",
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"params = SlabDefectBuilderParameters(\n",
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" auto_add_vacuum=AUTO_ADD_VACUUM,\n",
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" vacuum_thickness=VACUUM_THICKNESS,\n",
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")\n",
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"builder = IslandSlabDefectBuilder(build_parameters=params)"
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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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"### 2.2. Create the island"
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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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"slab_with_island = builder.get_material(island_config)"
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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 the 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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"visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
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" {\"material\": slab_with_island, \"title\": f\"Material with Island Defect ({SHAPE_PARAMETERS['shape']})\"}] ,\n",
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"rotation=\"-90x\")\n",
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"\n",
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"visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
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" {\"material\": slab_with_island, \"title\": f\"Material with Island Defect ({SHAPE_PARAMETERS['shape']})\"}], 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": "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(slab_with_island)"
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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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