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VsevolodX merged 6 commits into from
Dec 19, 2024
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feature/SOF-7521 feature: slab tutorial #176

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a7a7ac2
update: add slab tutorial nb
VsevolodX Dec 18, 2024
96e84dc
feat: add slab tutorial
VsevolodX Dec 18, 2024
b3961e2
update: use standata
VsevolodX Dec 18, 2024
7046db0
chore: cleanup
VsevolodX Dec 18, 2024
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chore: cleanup
VsevolodX Dec 18, 2024
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chore: adjsut wording
VsevolodX Dec 19, 2024
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278 changes: 278 additions & 0 deletions other/materials_designer/specific_examples/slab_strontium_titanate.ipynb
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@timurbazhirov timurbazhirov Dec 19, 2024 •
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The comment is cryptic, let's instead put:

Rotate material to correctly identify multiple terminations. Without the rotation, the current implementation only finds a single termination (as of 2024-12).


Reply via ReviewNB

"cells": [
{
"cell_type": "markdown",
"source": [
"# Slabs of SrTiO3(011) with specified terminations\n",
"\n",
"## 0. Introduction\n",
"\n",
"This notebook demonstrates how to create slabs of SrTiO3(011) with specified terminations following the manuscript:\n",
"\n",
"> **R. I. Eglitis and David Vanderbilt**\n",
"> *First-principles calculations of atomic and electronic structure of SrTiO3 (001) and (011) surfaces*\n",
"> Phys. Rev. B 77, 195408 (2008)\n",
"> [DOI: 10.1103/PhysRevB.77.195408](https://doi.org/10.1103/PhysRevB.77.195408)\n",
"\n",
"Replicating the material from the FIG. 2. with 2 different terminations:\n",
"\n",
" ![FIG. 2.](https://i.imgur.com/W3dPmWK.png)\n",
"\n"
],
"metadata": {
"collapsed": false
},
"id": "95a274d80df28ccd"
},
{
"cell_type": "markdown",
"source": [
"## 1. Prepare the Environment\n",
"### 1.1. Set up defect parameters "
],
"metadata": {
"collapsed": false
},
"id": "d55eaee8bc55bffd"
},
{
"cell_type": "code",
"outputs": [],
"source": [
"MILLER_INDICES = (0, 1, 1)\n",
"THICKNESS = 3 # in atomic layers\n",
"VACUUM = 10.0 # in angstroms\n",
"XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n",
"USE_ORTHOGONAL_Z = True\n",
"USE_CONVENTIONAL_CELL = True\n"
],
"metadata": {
"collapsed": false
},
"id": "4b64735060047bec",
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"### 1.2. Install Packages\n",
"The step executes only in Pyodide environment. For other environments, the packages should be installed via `pip install` (see [README](../../README.ipynb))."
],
"metadata": {
"collapsed": false
},
"id": "5e0ce05f6f031b3f"
},
{
"cell_type": "code",
"outputs": [],
"source": [
"import sys\n",
"\n",
"if sys.platform == \"emscripten\":\n",
" import micropip\n",
"\n",
" await micropip.install('mat3ra-api-examples', deps=False)\n",
" from utils.jupyterlite import install_packages\n",
"\n",
" await install_packages(\"\")"
],
"metadata": {
"collapsed": false
},
"id": "b457673560550933",
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"### 1.3. Get input materials"
],
"metadata": {
"collapsed": false
},
"id": "1659a8e9afe434fb"
},
{
"cell_type": "code",
"outputs": [],
"source": [
"from mat3ra.made.material import Material\n",
"from mat3ra.standata.materials import Materials\n",
"from mat3ra.made.tools.modify import rotate\n",
"\n",
"material = Material(Materials.get_by_name_first_match(\"SrTiO3\"))\n",
"# Rotate material to correctly identify multiple terminations.\n",
"# Without the rotation, the current implementation only finds a single termination (as of 2024-12).\n",
"material = rotate(material, axis=[1, 0, 0], angle=10)"
],
"metadata": {
"collapsed": false
},
"id": "b588ccfe51967a86",
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"### 1.4. Preview the material"
],
"metadata": {
"collapsed": false
},
"id": "8c13970a869adfa9"
},
{
"cell_type": "code",
"outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"\n",
"visualize(material, repetitions=[3, 3, 3], rotation=\"0x\")\n",
"visualize(material, repetitions=[3, 3, 3], rotation=\"-90x\")"
],
"metadata": {
"collapsed": false
},
"id": "c4f6e2697f97965f",
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"## 2. Configure slab\n",
"\n",
"### 2.1. Create slab configuration\n",
"Slab Configuration lets define the slab thickness, vacuum, and the Miller indices of the interfacial plane and get the slabs with possible terminations.\n"
],
"metadata": {
"collapsed": false
},
"id": "6634dae92a6c07b9"
},
{
"cell_type": "code",
"outputs": [],
"source": [
"\n",
"from mat3ra.made.tools.build.slab import SlabConfiguration\n",
"\n",
"slab_configuration = SlabConfiguration(\n",
" bulk=material,\n",
" miller_indices=MILLER_INDICES,\n",
" thickness=THICKNESS, # in atomic layers\n",
" vacuum=VACUUM, # in angstroms\n",
" xy_supercell_matrix=XY_SUPERCELL_MATRIX,\n",
" use_orthogonal_z=USE_ORTHOGONAL_Z,\n",
" use_conventional_cell=USE_CONVENTIONAL_CELL,\n",
")"
],
"metadata": {
"collapsed": false
},
"id": "3ad6765249610aa4",
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"### 2.2. Get possible terminations for the slabs"
],
"metadata": {
"collapsed": false
},
"id": "afb4c9bb89c8690b"
},
{
"cell_type": "code",
"outputs": [],
"source": [
"from mat3ra.made.tools.build.slab import get_terminations\n",
"\n",
"slab_terminations = get_terminations(slab_configuration)\n",
"print(\"Terminations\")\n",
"for idx, termination in enumerate(slab_terminations):\n",
" print(f\" {idx}: {termination}\")"
],
"metadata": {
"collapsed": false
},
"id": "70bec9d69d58b28a",
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"## 3. Visualize slabs for all possible terminations"
],
"metadata": {
"collapsed": false
},
"id": "c6e2e18452972b21"
},
{
"cell_type": "code",
"outputs": [],
"source": [
"from mat3ra.made.tools.build.slab import create_slab\n",
"\n",
"slabs = [create_slab(slab_configuration, termination) for termination in slab_terminations]\n",
"\n",
"visualize([{\"material\": slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in slabs], repetitions=[3, 3, 1])\n",
"visualize([{\"material\": slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in slabs], repetitions=[3, 3, 1],\n",
" rotation=\"-90x\")"
],
"metadata": {
"collapsed": false
},
"id": "246cb1f0437dbde0",
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"## 4. Download materials"
],
"metadata": {
"collapsed": false
},
"id": "d667623ad5f2e061"
},
{
"cell_type": "code",
"outputs": [],
"source": [
"from utils.jupyterlite import download_content_to_file\n",
"\n",
"for slab in slabs:\n",
" download_content_to_file(slab, f\"{slab.name}.json\")"
],
"metadata": {
"collapsed": false
},
"id": "3705115f04ac0010",
"execution_count": null
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.6"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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