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Merge pull request #140 from Exabyte-io/feature/SOF-7412
feature/SOF 7412
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‎other/materials_designer/Introduction.ipynb‎

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"\n",
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"This notebook lets user create a slab and place an adatom at specified location. [Click here to open the notebook](create_adatom_defect.ipynb).\n",
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"\n",
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"#### [1.6. Slab Perturbation](create_perturbation.ipynb)\n",
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"#### [1.6. Nanoribbon creation](create_nanoribbon.ipynb)\n",
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"\n",
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"This notebook lets user create a nanoribbon from a bulk 2D material. [Click here to open the notebook](create_nanoribbon.ipynb).\n",
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"\n",
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"#### [1.7. Slab Perturbation](create_perturbation.ipynb)\n",
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"\n",
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"This notebook lets user add a perturbation to a slab by moving atoms according to a specified function. [Click here to open the notebook](create_perturbation.ipynb).\n",
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"\n",

‎other/materials_designer/create_nanoribbon.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 Nanoribbon of a 2D material\n",
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"\n",
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"Create a nanoribbon of a 2D material with Hexagonal lattice using the `NanoribbonBuilder` tool. \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 nanoribbon 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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"## Summary\n",
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"1. Prepare the Environment: Set up the notebook and install packages, preview the input materials\n",
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"1. Create the Nanoribbon: Set nanoribbon parameters and create the nanoribbon\n",
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"2. Visualize the Perturbed Material\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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],
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"metadata": {
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"collapsed": false
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},
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"id": "367a698b29e22bd7"
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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 nanoribbon 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": "193a4e6a78fd5bd7"
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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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"# Widths and lengths are in number of unit cells\n",
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"WIDTH = 3\n",
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"VACUUM_WIDTH = 2\n",
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"LENGTH = 10\n",
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"VACUUM_LENGTH = 0\n",
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"EDGE_TYPE = \"zigzag\" # \"zigzag\" or \"armchair\""
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],
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"metadata": {
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"collapsed": false
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},
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"id": "a40d7b697c413113",
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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": "49c9f5022d50517e"
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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": "c6d9f8e57bef2f91",
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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\n",
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"Materials are loaded with `get_data()`. The first material is assigned as substrate and the second as film."
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],
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"metadata": {
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"collapsed": false
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},
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"id": "edf02101e27a2742"
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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 utils.jupyterlite import get_data\n",
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"\n",
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"# Get the list of input materials and load them into `materials_in` variable\n",
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"get_data(\"materials_in\", globals())\n",
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"materials = list(map(Material, globals()[\"materials_in\"]))"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "e0c53233ce728cc1",
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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 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": "cf29b7f6fe114d8f"
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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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"material = materials[2]\n",
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"visualize(material, repetitions=[3, 3, 1], rotation=\"0x\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "897ba7aa4e402d24",
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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 Nanoribbon\n",
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"### 2.1. Set nanoribbon 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": "39a93c4635762a83"
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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.nanoribbon import NanoribbonBuilder, NanoribbonConfiguration\n",
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"\n",
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"nanoribbon_configuration = NanoribbonConfiguration(\n",
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" material=material,\n",
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" width=WIDTH,\n",
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" vacuum_width=VACUUM_WIDTH,\n",
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" length=LENGTH,\n",
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" vacuum_length=VACUUM_LENGTH,\n",
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" edge_type=EDGE_TYPE\n",
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")\n",
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"\n",
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"\n",
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"builder = NanoribbonBuilder()"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "1991efeeebe39db4",
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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 Nanoribbon"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "d296d7287618dc0b"
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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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"nanoribbon = builder.get_material(nanoribbon_configuration)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "302f417828a8fc9c",
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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 Nanoribbon"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "eecd561cd92fb18a"
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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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"visualize([{\"material\": nanoribbon, \"title\": \"Nanoribbon\"}])"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "1ee393a7f2ec3bc8",
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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": "9e0b241366592109"
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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_data\n",
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"\n",
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"set_data(\"materials\", [nanoribbon.to_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": "29dfa0a329cca2fa",
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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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