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VsevolodXVsevolodX
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Merge pull request #169 from Exabyte-io/feature/SOF-7494
feature/SOF-7494) feat: terrace NB
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‎other/materials_designer/Introduction.ipynb‎

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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",
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"#### [3.2.2. Terrace Defect on a Slab](create_terrace_defect.ipynb)\n",
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"\n",
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"### 3.3. Planar Defects\n",
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"#### [3.3.1. Grain Boundary in a 3D Crystal](create_grain_boundary_crystal.ipynb)\n",

‎other/materials_designer/create_cutout_box.ipynb‎

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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 mat3ra.made.tools.build.slab import create_slab_if_not, SlabConfiguration\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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"default_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)"
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"slab = create_slab_if_not(materials[0], default_slab_config)"
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],
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"metadata": {
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"collapsed": false

‎other/materials_designer/create_terrace_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 a Terrace Defect on a Slab\n",
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"\n",
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"Create a terrace defect by adding layers to a portion of a slab, defined by a cutting plane and number of additional layers.\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 (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. 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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"1. The input material must be a Slab, or slab will be generated with provided 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": "f5ca6879c3872454"
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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 the notebook\n",
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"The cut direction, pivot coordinate, and number of added layers define the terrace defect, shown in the image below.\n",
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"<img src=\"https://i.imgur.com/XA2F55Q.png\" alt=\"Terrace parameters visualized\" width=\"400\"/>"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "ff0f33c4e6ac1303"
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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 selection\n",
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"MATERIAL_INDEX = 0 # Which material to use from input list\n",
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"\n",
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"# Terrace parameters\n",
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"CUT_DIRECTION = [1, 0, 0] # Normal vector describing a plane that cuts the terrace from added layers (Miller indices)\n",
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"PIVOT_COORDINATE = [0.5, 0.5, 0.5] # Point the cutting plane passes through, in crystal coordinates\n",
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"NUMBER_OF_ADDED_LAYERS = 1 # Height of terrace in atomic layers\n",
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"USE_CARTESIAN_COORDINATES = False # Use cartesian instead of crystal coordinates\n",
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"ROTATE_TO_MATCH_PBC = True # Rotate to match periodic boundary conditions\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\": 6,\n",
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" \"vacuum\": 10.0,\n",
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" \"use_orthogonal_z\": True,\n",
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" \"xy_supercell_matrix\": [[5, 0], [0, 5]]\n",
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"}\n",
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"\n",
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"# Visualization parameters\n",
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"SHOW_INTERMEDIATE_STEPS = True\n",
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"CELL_REPETITIONS_FOR_VISUALIZATION = [3, 3, 1] # Structure repeat in view"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "dd6ca344ae34a2d6",
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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`."
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],
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"metadata": {
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"collapsed": false
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},
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"id": "ac4ec25db74d75f4"
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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(\"\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "38574beae9a769cd",
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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. Load 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": "c0eab57550f40708"
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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": "f2479655b99cca48",
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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 a slab if the input material is not a slab"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "4282a853c29a1501"
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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_if_not, SlabConfiguration\n",
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"\n",
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"default_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_if_not(materials[0], default_slab_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": "80b7b827c2b390c3",
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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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"### 1.5. Visualize slab"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "916c8b16e01f86ff"
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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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"if SHOW_INTERMEDIATE_STEPS:\n",
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" print(\"Initial slab structure:\")\n",
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" visualize_materials(slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION)\n",
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" visualize_materials(slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION, 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": "16bb968a93de4b9",
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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 target material\n",
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"### 2.1. Set up terrace configuration and builder\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": "9edaa3afb28ee0ad"
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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 TerraceSlabDefectConfiguration, TerraceSlabDefectBuilder\n",
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"\n",
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"config = TerraceSlabDefectConfiguration(\n",
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" crystal=slab,\n",
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" cut_direction=CUT_DIRECTION,\n",
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" pivot_coordinate=PIVOT_COORDINATE,\n",
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" number_of_added_layers=NUMBER_OF_ADDED_LAYERS,\n",
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" use_cartesian_coordinates=USE_CARTESIAN_COORDINATES,\n",
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" rotate_to_match_pbc=ROTATE_TO_MATCH_PBC\n",
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")\n",
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"\n",
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"builder = TerraceSlabDefectBuilder()"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "c318fd03c7e667df",
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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. Generate terrace defect\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": "b9df79c67a870181"
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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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"terrace_slab = builder.get_material(config)\n",
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"\n",
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"print(\"\\nTerrace defect created with:\")\n",
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"print(f\"Cut direction: {CUT_DIRECTION}\")\n",
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"print(f\"Pivot point: {PIVOT_COORDINATE}\")\n",
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"print(f\"Added layers: {NUMBER_OF_ADDED_LAYERS}\")\n",
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"print(f\"Number of atoms: {len(terrace_slab.basis.elements.ids)}\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "256bc04ff0aa1810",
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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"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "9bee7a912a90e33c"
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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(\"Final structure with terrace:\")\n",
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"visualize_materials(terrace_slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION)\n",
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"visualize_materials(terrace_slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION, 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": "4ffdd8589b02de16",
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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\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": "d65865cbab99478"
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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(terrace_slab)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "e292358fe4803b4f",
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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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