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8bb6c0b
feat: add perturbation nb
VsevolodX 05cfc0a
wip: waves across x
VsevolodX 3243992
update: make work
VsevolodX a31ebd0
update: add description
VsevolodX fc73fef
chore: rename to match docs
VsevolodX 7533baa
chore: rename title
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other/materials_designer/specific_examples/perturbation_ripple_graphene.ipynb
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| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "# Ripple perturbation of a graphene sheet.\n", | ||
| "\n", | ||
| "## 0. Introduction\n", | ||
| "\n", | ||
| "This notebook demonstrates how to recreate a material from the following manuscript:\n", | ||
| "\n", | ||
| "> Thompson-Flagg, R. C., Moura, M. J. B., & Marder, M.\n", | ||
| "> Rippling of graphene. \n", | ||
| "> EPL (Europhysics Letters), 85(4), 46002. 2009\n", | ||
| "> [DOI: 10.1209/0295-5075/85/46002](https://doi.org/10.1209/0295-5075/85/46002)\n", | ||
| "\n", | ||
| "\n", | ||
| "Recreating material from Fig. 1:\n", | ||
| "\n", | ||
| "<img src=\"https://i.imgur.com/p1Tvz5t.png\" alt=\"Rippling of graphene\" width=\"400\"/>\n" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "367a698b29e22bd7" | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "## 1. Prepare the Environment" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "193a4e6a78fd5bd7" | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "### 1.1. 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": "f38b2711726e5859" | ||
| }, | ||
| { | ||
| "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(\"specific-examples\")" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "7a6e28cfae1a7b46", | ||
| "execution_count": null | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "### 1.2. Set Nanoribbon and Perturbation Parameters" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "11db992e02891067" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Set whether to preserve geodesic distance and scale the cell accordingly to match PBC\n", | ||
| "PRESERVE_GEODESIC_DISTANCE = False\n", | ||
| "\n", | ||
| "NANORIBBON_SIZE = 40 # in unit cells, lateral width and length of the nanoribbon\n", | ||
| "VACUUM_SIZE = 10 # in unit cells, lateral width and length of the vacuum region\n", | ||
| "\n", | ||
| "# Set whether to use Cartesian coordinates for the perturbation function\n", | ||
| "USE_CARTESIAN_COORDINATES = False\n", | ||
| "MATERIAL_NAME = \"Graphene\"" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "a40d7b697c413113", | ||
| "execution_count": null | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "### 1.3. Define Custom Perturbation Function\n", | ||
| "Provide a [SymPy](https://docs.sympy.org/latest/tutorials/intro-tutorial/intro.html) expression for the perturbation function. The expression should be a function of `x`, `y` and `z` variables." | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "e6a19c741406eafe" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "source": [ | ||
| "import sympy as sp\n", | ||
| "\n", | ||
| "# Variables for the perturbation function (for SymPy)\n", | ||
| "variable_names = [\"x\", \"y\", \"z\"]\n", | ||
| "x, y, z = sp.symbols(variable_names)\n", | ||
| "\n", | ||
| "# Set the parameters for the perturbation function\n", | ||
| "AMPLITUDE = 0.09 # Ripple amplitude\n", | ||
| "WAVELENGTH = 0.2 # Wavelength of ripples\n", | ||
| "EDGE_WIDTH = 0.25 # Width of edge effect\n", | ||
| "PHASE_X = 0.0 # Phase shift for x direction\n", | ||
| "PHASE_Y = sp.pi/2 # Phase shift for y direction\n", | ||
| "\n", | ||
| "# Create edge masks for both x and y using polynomial functions\n", | ||
| "left_edge_x = sp.Max(0, (EDGE_WIDTH - x) / EDGE_WIDTH)\n", | ||
| "right_edge_x = sp.Max(0, (x - (1 - EDGE_WIDTH)) / EDGE_WIDTH)\n", | ||
| "left_edge_y = sp.Max(0, (EDGE_WIDTH - y) / EDGE_WIDTH)\n", | ||
| "right_edge_y = sp.Max(0, (y - (1 - EDGE_WIDTH)) / EDGE_WIDTH)\n", | ||
| "\n", | ||
| "# Combine edge masks\n", | ||
| "edge_mask_x = left_edge_x + right_edge_x\n", | ||
| "edge_mask_y = left_edge_y + right_edge_y\n", | ||
| "edge_mask = edge_mask_x + edge_mask_y\n", | ||
| "\n", | ||
| "# Wave pattern\n", | ||
| "wave_pattern = (\n", | ||
| " sp.sin(2 * sp.pi * x / WAVELENGTH + PHASE_X) * \n", | ||
| " sp.sin(2 * sp.pi * y / WAVELENGTH + PHASE_Y)\n", | ||
| ")\n", | ||
| "\n", | ||
| "# Combine waves with edge mask\n", | ||
| "custom_sympy_function = AMPLITUDE * wave_pattern * edge_mask" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "203911c2413c7447", | ||
| "execution_count": null | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "### 1.4. Get input materials" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "edf02101e27a2742" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "source": [ | ||
| "from mat3ra.standata.materials import Materials\n", | ||
| "from mat3ra.made.material import Material\n", | ||
| "\n", | ||
| "material = Material(Materials.get_by_name_first_match(MATERIAL_NAME))" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "e0c53233ce728cc1", | ||
| "execution_count": null | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "### 1.5. Create and preview Nanoribbon" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "cf29b7f6fe114d8f" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "source": [ | ||
| "from mat3ra.made.tools.build.nanoribbon import create_nanoribbon, NanoribbonConfiguration\n", | ||
| "from utils.visualize import visualize_materials as visualize\n", | ||
| "\n", | ||
| "config = NanoribbonConfiguration(material=material, width=NANORIBBON_SIZE, length=NANORIBBON_SIZE, vacuum_width=VACUUM_SIZE, vacuum_length=VACUUM_SIZE)\n", | ||
| "\n", | ||
| "supercell = create_nanoribbon(config)\n", | ||
| "visualize(supercell, repetitions=[1, 1, 1], rotation=\"0x\")" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "897ba7aa4e402d24", | ||
| "execution_count": null | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "## 2. Create a target material\n", | ||
| "### 2.1. Set custom perturbation parameters\n" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "6d4adf0d580e0340" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "source": [ | ||
| "from mat3ra.made.tools.build.perturbation import CellMatchingDistancePreservingSlabPerturbationBuilder, \\\n", | ||
| " PerturbationConfiguration, SlabPerturbationBuilder\n", | ||
| "from mat3ra.made.tools.utils.perturbation import PerturbationFunctionHolder\n", | ||
| "\n", | ||
| "custom_perturbation_function = PerturbationFunctionHolder(function=custom_sympy_function,\n", | ||
| " variables=variable_names)\n", | ||
| "configuration_custom = PerturbationConfiguration(\n", | ||
| " material=supercell,\n", | ||
| " perturbation_function_holder=custom_perturbation_function,\n", | ||
| " use_cartesian_coordinates=USE_CARTESIAN_COORDINATES)\n", | ||
| "\n", | ||
| "if PRESERVE_GEODESIC_DISTANCE:\n", | ||
| " builder = CellMatchingDistancePreservingSlabPerturbationBuilder()\n", | ||
| "else:\n", | ||
| " builder = SlabPerturbationBuilder()" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "8d90932312c418ee", | ||
| "execution_count": null | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "### 2.2. Apply perturbation to the material" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "7695d5d1df6be2e3" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "source": [ | ||
| "from mat3ra.made.tools.build.perturbation import create_perturbation\n", | ||
| "\n", | ||
| "material_with_custom_perturbation = create_perturbation(configuration=configuration_custom, builder=builder)" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "69ccc90b8c5c1191", | ||
| "execution_count": null | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "### 3. Visualize the Material" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "10e7ca8950839991" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "source": [ | ||
| "visualize([\n", | ||
| " {\"material\": material_with_custom_perturbation, \"title\": f\"Material with custom perturbation\"},\n", | ||
| " {\"material\": material_with_custom_perturbation, \"title\": f\"Material with custom perturbation\", \"rotation\": \"-90x\"}\n", | ||
| "])" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "cbfe0878a16f6c83", | ||
| "execution_count": null | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "## 4. Pass data to the outside runtime" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "9e0b241366592109" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "source": [ | ||
| "from utils.jupyterlite import download_content_to_file\n", | ||
| "\n", | ||
| "download_content_to_file(material_with_custom_perturbation, f\"{MATERIAL_NAME}_edge_perturbation.json\")" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "29dfa0a329cca2fa", | ||
| "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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Ripple perturbation of a graphene sheet
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Renamed in docs as well