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VsevolodXVsevolodX
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Merge pull request #162 from Exabyte-io/feature/SOF-7491
feat: add nanowire nb
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‎other/materials_designer/Introduction.ipynb‎

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"\n",
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"### 1.3. 1D Structures.\n",
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"#### [1.3.1. Nanoribbons. Create nanoribbons from 2D materials.](create_nanoribbon.ipynb)\n",
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"#### [1.3.2. Nanowires. Create a nanowire from a bulk material.](create_nanowire.ipynb)\n",
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"#### [1.3.3. Nanowires with custom shape. Create a nanowire with a custom cross-section.](create_nanowire_custom_shape.ipynb)\n",
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"\n",
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"### 1.4. 0D Structures.\n",
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"#### [1.4.1. Spherical. Create clusters or spherical structures.](create_cluster_sphere.ipynb)\n",

‎other/materials_designer/create_nanowire.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 nanowire\n",
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"\n",
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"Create a nanowire from original material by creating a slab (with specific Miller indices) and cutting a cylinder along its Z axis, then, optionally, rotating to align along X axis.\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 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. Scroll down to view results. "
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],
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"metadata": {
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"collapsed": false
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},
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"id": "c9f342d4ac1988c6"
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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 nanowire 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": "cbcd112c418fcaa4"
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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= (0,0,1) # Miller indices of the nanowire direction\n",
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"RADIUS = 5.0 # Wire radius in Angstroms\n",
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"LENGTH = 30.0 # Wire length in Angstroms\n",
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"VACUUM = 10.0 # Vacuum thickness on the sides in Angstroms\n",
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"ALIGN_ALONG_X = True"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "2269749714d81b93"
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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": "65c906791f69bac9"
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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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" 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": "6dac92b719d539ec"
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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": "2fe1d71e1b02aed9"
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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())\n",
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"material = materials[0] "
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],
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"metadata": {
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"collapsed": false
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},
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"id": "b95701d7a0e593fe"
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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": "a8ebe61794b2e803"
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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, 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": "c98ec170f3ee6d24"
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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 nanowire\n",
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"### 2.1. Create a slab and cut a cylinder"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "38ecf94e650e268d"
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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 math\n",
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"from mat3ra.made.tools.build.supercell import create_supercell\n",
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"from mat3ra.made.tools.modify import filter_by_cylinder, add_vacuum_sides\n",
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"from mat3ra.made.tools.build.slab import create_slab, SlabConfiguration\n",
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"\n",
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"slab_config = SlabConfiguration(\n",
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" bulk=material,\n",
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" miller_indices=MILLER_INDICES,\n",
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" thickness=1,\n",
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" vacuum=0,\n",
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" use_orthogonal_z=True,\n",
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")\n",
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"\n",
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"slab_unit_cell = create_slab(slab_config)\n",
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"n_for_x = math.ceil(int(2*RADIUS / slab_unit_cell.lattice.a)) + 1\n",
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"n_for_y = math.ceil(int(2*RADIUS / slab_unit_cell.lattice.b)) + 1\n",
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"n_for_z = int(LENGTH / slab_unit_cell.lattice.c)\n",
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"supercell = create_supercell(slab_unit_cell, supercell_matrix=[[n_for_x, 0, 0], [0, n_for_y, 0], [0, 0, n_for_z]])\n",
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"nanowire_z = filter_by_cylinder(supercell, radius=RADIUS, use_cartesian_coordinates=True)\n",
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"nanowire_z = add_vacuum_sides(nanowire_z, vacuum=VACUUM, on_x=True, on_y=True) "
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],
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"metadata": {
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"collapsed": false
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},
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"id": "c4b34b3287960dcc"
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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. Rotate to align along X axis (optional)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "ae940638396f93a6"
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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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"rotate_90_degree_matrix = [[0, 0, 1], [0, 1, 0], [-1, 0, 0]]\n",
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"nanowire_x = create_supercell(nanowire_z, supercell_matrix=rotate_90_degree_matrix)\n",
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"nanowire = nanowire_x if ALIGN_ALONG_X else nanowire_z"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "7401ab24726bf4e5"
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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": "d8f41816d0b48edc"
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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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"visualize(nanowire, repetitions=[1, 1, 1], rotation=\"0x\")\n",
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"visualize(nanowire, repetitions=[1, 1, 1], rotation=\"-90x\")\n",
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"visualize(nanowire, repetitions=[1, 1, 1], rotation=\"-90y\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "aea078560283ca95",
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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 material 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": "a212abe25bf59b4f"
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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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"set_materials(nanowire)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "cdaf612bc6198546",
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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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