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Merge pull request #176 from Exabyte-io/feature/SOF-7521
feature/SOF-7521 feature: slab tutorial
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‎other/materials_designer/specific_examples/slab_strontium_titanate.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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"# Slabs of SrTiO3(011) with specified terminations\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 slabs of SrTiO3(011) with specified terminations following the manuscript:\n",
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"\n",
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"> **R. I. Eglitis and David Vanderbilt**\n",
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"> *First-principles calculations of atomic and electronic structure of SrTiO3 (001) and (011) surfaces*\n",
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"> Phys. Rev. B 77, 195408 (2008)\n",
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"> [DOI: 10.1103/PhysRevB.77.195408](https://doi.org/10.1103/PhysRevB.77.195408)\n",
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"\n",
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"Replicating the material from the FIG. 2. with 2 different terminations:\n",
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"\n",
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" ![FIG. 2.](https://i.imgur.com/W3dPmWK.png)\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": "95a274d80df28ccd"
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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": "d55eaee8bc55bffd"
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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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"MILLER_INDICES = (0, 1, 1)\n",
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"THICKNESS = 3 # in atomic layers\n",
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"VACUUM = 10.0 # in angstroms\n",
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"XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n",
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"USE_ORTHOGONAL_Z = True\n",
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"USE_CONVENTIONAL_CELL = True\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": "4b64735060047bec",
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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": "5e0ce05f6f031b3f"
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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": "b457673560550933",
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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 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": "1659a8e9afe434fb"
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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.material import Material\n",
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"from mat3ra.standata.materials import Materials\n",
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"from mat3ra.made.tools.modify import rotate\n",
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"\n",
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"material = Material(Materials.get_by_name_first_match(\"SrTiO3\"))\n",
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"# Rotate material to correctly identify multiple terminations.\n",
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"# Without the rotation, the current implementation only finds a single termination (as of 2024-12).\n",
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"material = rotate(material, axis=[1, 0, 0], angle=10)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "b588ccfe51967a86",
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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 the 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": "8c13970a869adfa9"
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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 as visualize\n",
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"\n",
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"visualize(material, repetitions=[3, 3, 3], rotation=\"0x\")\n",
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"visualize(material, repetitions=[3, 3, 3], 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": "c4f6e2697f97965f",
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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 slab\n",
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"\n",
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"### 2.1. Create slab configuration\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.\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": "6634dae92a6c07b9"
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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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"\n",
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"from mat3ra.made.tools.build.slab import SlabConfiguration\n",
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"\n",
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"slab_configuration = SlabConfiguration(\n",
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" bulk=material,\n",
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" miller_indices=MILLER_INDICES,\n",
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" thickness=THICKNESS, # in atomic layers\n",
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" vacuum=VACUUM, # in angstroms\n",
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" xy_supercell_matrix=XY_SUPERCELL_MATRIX,\n",
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" use_orthogonal_z=USE_ORTHOGONAL_Z,\n",
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" use_conventional_cell=USE_CONVENTIONAL_CELL,\n",
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")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "3ad6765249610aa4",
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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. Get possible terminations for the slabs"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "afb4c9bb89c8690b"
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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 get_terminations\n",
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"\n",
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"slab_terminations = get_terminations(slab_configuration)\n",
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"print(\"Terminations\")\n",
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"for idx, termination in enumerate(slab_terminations):\n",
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" print(f\" {idx}: {termination}\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "70bec9d69d58b28a",
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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 slabs for all possible terminations"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "c6e2e18452972b21"
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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\n",
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"\n",
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"slabs = [create_slab(slab_configuration, termination) for termination in slab_terminations]\n",
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"\n",
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"visualize([{\"material\": slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in slabs], repetitions=[3, 3, 1])\n",
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"visualize([{\"material\": slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in slabs], repetitions=[3, 3, 1],\n",
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" 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": "246cb1f0437dbde0",
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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. Download 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": "d667623ad5f2e061"
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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 download_content_to_file\n",
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"\n",
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"for slab in slabs:\n",
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" download_content_to_file(slab, f\"{slab.name}.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": "3705115f04ac0010",
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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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