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update: restructure nb
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‎other/materials_designer/specific_examples/grain_boundary_3d_fcc_metal.ipynb‎

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{
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"cells": [
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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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"cell_type": "markdown",
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"source": [
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"# Grain Boundary 3D FCC Metal\n",
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"\n",
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"## 0. Introduction\n",
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"\n",
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"This notebook demonstrates how to create a grain boundary structure for a 3D FCC metal, Cu in particular. The grain boundary is created by combining two slabs with different orientations. \n",
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"\n",
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"Aiming to reproduce the structure from the publication:\n",
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"> **Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin**\n",
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"> \"Structural phase transformations in metallic grain boundaries\"\n",
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"> Nature Communications, volume 4, Article number: 1899 (2013)\n",
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"> DOI: [10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919) \n",
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"\n",
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"Focusing on reproducing the structures from Figure 1. b:\n",
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"\n",
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"<img src=\"https://i.imgur.com/SdIaZRD.png\" alt=\"Figure 1.\" 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": "initial_id",
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"execution_count": 0
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"id": "aa0a426af23f6def"
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},
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{
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"cell_type": "markdown",
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"source": [
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"# Enable interactive selection of terminations via UI prompt\n",
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"IS_TERMINATIONS_SELECTION_INTERACTIVE = False \n",
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"MATERIAL_NAME = \"Cu\"\n",
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"\n",
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"# Parameters for Phase 1\n",
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"PHASE_1_MILLER_INDICES = (1, 1, 1)\n",
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"PHASE_1_THICKNESS = 6 # in atomic layers\n",
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"PHASE_1_MILLER_INDICES = (3,1,0)\n",
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"PHASE_1_THICKNESS = 4 # in atomic layers\n",
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"PHASE_1_USE_ORTHOGONAL_Z = True\n",
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"\n",
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"# Parameters for Phase 2\n",
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"PHASE_2_MILLER_INDICES = (0, 0, 1)\n",
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"PHASE_2_MILLER_INDICES = (-3, -1, 0)\n",
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"PHASE_2_THICKNESS = 4 # in atomic layers\n",
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"PHASE_2_USE_ORTHOGONAL_Z = True\n",
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"\n",
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"collapsed": false
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},
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"id": "45730b0f5384262b",
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"execution_count": 0
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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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" \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(\"create_grain_boundary.ipynb\")\n"
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" await install_packages(\"specific_examples|create_grain_boundary.ipynb\")\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": "bae18ae87d3cc5ba",
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"execution_count": 0
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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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"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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"from mat3ra.standata.materials import Materials\n",
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"from mat3ra.made.material import Material\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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"material = Material(Materials.get_by_name_first_match(MATERIAL_NAME))"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "950e5bef61bbd84a",
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"execution_count": 0
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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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"collapsed": false
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},
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"id": "4ebde830102b0b94",
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"execution_count": 0
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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. Configure slabs and select termination pair\n",
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"## 2. Create grain boundary for (310) surface\n",
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"\n",
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"### 2.1. Create Phase 1 and Phase 2 Slabs\n",
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"Slab Configuration lets define the slab thickness, vacuum, and the Miller indices of the interfacial plane and get the slabs with possible terminations."
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"collapsed": false
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"id": "b7cc3daa852d868d",
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"execution_count": null
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"cell_type": "markdown",
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"collapsed": false
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},
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"id": "5bdc0e37e3ec9891",
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"execution_count": 0
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"execution_count": null
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},
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"cell_type": "markdown",
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"collapsed": false
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},
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"id": "f75092312b399f84",
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"execution_count": 0
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"execution_count": null
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"cell_type": "markdown",
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"collapsed": false
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},
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"id": "40b4ba55613d9658",
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"execution_count": 0
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"execution_count": null
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"cell_type": "markdown",
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"collapsed": false
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},
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"id": "8dfc5893f510bae4",
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"execution_count": 0
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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. Create grain boundary\n",
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"\n",
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"### 3.1. Initialize the Grain Boundary Configuration"
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"### 2.6. Initialize the Grain Boundary Configuration"
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],
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"metadata": {
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"collapsed": false
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"collapsed": false
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},
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"id": "40b6c8662d071f18",
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"execution_count": 0
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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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"### 3.2. Set Strain Matching Algorithm Parameters"
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"### 2.7. Set Strain Matching Algorithm Parameters"
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],
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"metadata": {
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"collapsed": false
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"collapsed": false
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},
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"id": "44015c5407563d4e",
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"execution_count": 0
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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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"### 3.3. Generate grain boundary with strain matcher"
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"### 2.8. Generate grain boundary with strain matcher"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "884b458236270a29",
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"execution_count": 0
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"execution_count": null
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{
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"cell_type": "markdown",
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"## 4. Preview the grain boundary"
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"## 2.9. Preview the grain boundary"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "892c0e7c932cd725",
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"execution_count": null
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},
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"cell_type": "markdown",
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"## 5. Pass data to the outside runtime"
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"## 3. Save the final material"
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],
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"metadata": {
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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(grain_boundary)"
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"from utils.jupyterlite import download_content_to_file\n",
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"\n",
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"download_content_to_file(grain_boundary, f\"{MATERIAL_NAME}-{PHASE_1_MILLER_INDICES}-{PHASE_2_MILLER_INDICES}_grain_boundary.json\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "503eff0dd5c1a160",
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"execution_count": 0
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"execution_count": null
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}
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],
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"metadata": {

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