Merge pull request #139 from Exabyte-io/feature/SOF-7398

feature/SOF 7398
Exabyte-io · Aug 17, 2024 · fe60c46 · fe60c46
2 parents ee1eacb + 20ebb48
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diff --git a/other/materials_designer/Introduction.ipynb b/other/materials_designer/Introduction.ipynb
@@ -33,6 +33,10 @@
     "\n",
     "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",
     "\n",
+    "#### [1.6. Slab Perturbation](create_perturbation.ipynb)\n",
+    "\n",
+    "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",
+    "\n",
     "### 2. Data Import\n",
     "\n",
     "#### [2.1. Materials import from files in ASE-supported formats](import_materials_from_files.ipynb)\n",

diff --git a/other/materials_designer/create_perturbation.ipynb b/other/materials_designer/create_perturbation.ipynb
@@ -0,0 +1,356 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# Create a Perturbation in a Material\n",
+    "\n",
+    "Create a perturbation in a material with a specified smooth function or a custom function described with [SymPy](https://docs.sympy.org/latest/tutorials/intro-tutorial/intro.html) expressions. \n",
+    "\n",
+    "<h2 style=\"color:green\">Usage</h2>\n",
+    "\n",
+    "1. Make sure to select Input Materials (in the outer runtime) before running the notebook.\n",
+    "1. Set notebook parameters in cell 1.1. below (or use the default values).\n",
+    "1. Set perturbation parameters in cell 2.1. (or use default).\n",
+    "1. Click “Run” > “Run All” to run all cells. \n",
+    "1. Wait for the run to complete (depending on the parameters can take a few min). \n",
+    "1. Scroll down to view results. \n",
+    "\n",
+    "## Summary\n",
+    "1. Prepare the Environment: Set up the notebook and install packages, preview the input materials\n",
+    "1. Create the Perturbation: Add a smooth perturbation to the material\n",
+    "2. Visualize the Perturbed Material\n",
+    "\n",
+    "## Notes\n",
+    "\n",
+    "1. For more information, see [Introduction](Introduction.ipynb)\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "367a698b29e22bd7"
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 1. Prepare the Environment\n",
+    "### 1.1. Set up supercell parameters "
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "193a4e6a78fd5bd7"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "SUPERCELL_MATRIX = [[5, 0, 0], [0, 5, 0], [0, 0, 1]] "
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "a40d7b697c413113",
+   "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": "49c9f5022d50517e"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "\n",
+    "if sys.platform == \"emscripten\":\n",
+    "    import micropip\n",
+    "    await micropip.install('mat3ra-api-examples', deps=False)\n",
+    "    from utils.jupyterlite import install_packages\n",
+    "    await install_packages(\"\", \"../../config.yml\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "c6d9f8e57bef2f91",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 1.3. Get input materials\n",
+    "Materials are loaded with `get_data()`. The first material is assigned as substrate and the second as film."
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "edf02101e27a2742"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from mat3ra.made.material import Material\n",
+    "from utils.jupyterlite import get_data\n",
+    "\n",
+    "# Get the list of input materials and load them into `materials_in` variable\n",
+    "get_data(\"materials_in\", globals())\n",
+    "materials = list(map(Material, globals()[\"materials_in\"]))"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "e0c53233ce728cc1",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 1.4. Create and preview Supercell"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "cf29b7f6fe114d8f"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.visualize import visualize_materials as visualize\n",
+    "from mat3ra.made.tools.build.supercell import create_supercell\n",
+    "\n",
+    "unit_cell = materials[0]\n",
+    "supercell = create_supercell(unit_cell, supercell_matrix=SUPERCELL_MATRIX)\n",
+    "visualize(supercell, repetitions=[1, 1, 1], rotation=\"0x\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "897ba7aa4e402d24",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 2. Create the SineWave Perturbation\n",
+    "### 2.1. Set sine wave perturbation parameters\n",
+    "Use perturbation function imported from `mat3ra.made.tools.utils.perturbation` folder."
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "39a93c4635762a83"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from mat3ra.made.tools.build.perturbation import PerturbationConfiguration, SlabPerturbationBuilder\n",
+    "from mat3ra.made.tools.utils.perturbation import SineWavePerturbationFunctionHolder\n",
+    "\n",
+    "amplitude = 0.05\n",
+    "wavelength = 1\n",
+    "phase = 0\n",
+    "axis = \"y\"\n",
+    "perturbation_function = SineWavePerturbationFunctionHolder(amplitude=amplitude, \n",
+    "                                                           wavelength=wavelength, \n",
+    "                                                           phase=phase,\n",
+    "                                                           axis=axis)\n",
+    "\n",
+    "configuration = PerturbationConfiguration(material=supercell, \n",
+    "                                          perturbation_function_holder=perturbation_function,\n",
+    "                                          use_cartesian_coordinates=False)\n",
+    "\n",
+    "builder = SlabPerturbationBuilder()"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "1991efeeebe39db4",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 2.2. Apply perturbation to the material"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "d296d7287618dc0b"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from mat3ra.made.tools.build.perturbation import create_perturbation\n",
+    "\n",
+    "material_with_perturbation = create_perturbation(configuration, builder)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "d77821f7d0b8c330",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 2.3. Visualize the Material"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "eecd561cd92fb18a"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.visualize import visualize_materials as visualize\n",
+    "\n",
+    "visualize([{\"material\": supercell, \"title\": \"Original material\"},\n",
+    "           {\"material\": material_with_perturbation, \"title\": f\"Material with perturbation\"},\n",
+    "           {\"material\": material_with_perturbation, \"title\": f\"Material with perturbation\", \"rotation\": \"-90x\"},\n",
+    "])"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "1ee393a7f2ec3bc8",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 3. Create a Custom Perturbation\n",
+    "### 3.1. Set custom perturbation parameters\n",
+    "Provide a SymPy expression for the perturbation function. The expression should be a function of `x`, `y` and `z` variables."
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "6d4adf0d580e0340"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "import sympy as sp\n",
+    "from mat3ra.made.tools.build.perturbation import CellMatchingDistancePreservingSlabPerturbationBuilder\n",
+    "from mat3ra.made.tools.utils.perturbation import PerturbationFunctionHolder\n",
+    "\n",
+    "x,y = sp.symbols('x y')\n",
+    "function = amplitude * sp.sin(2 * sp.pi * x / wavelength + phase) * sp.sin(2 * sp.pi * y / wavelength)\n",
+    "\n",
+    "custom_perturbation_function = PerturbationFunctionHolder(function=function, variables=[\"x\", \"y\"])\n",
+    "configuration_custom = PerturbationConfiguration(material=supercell,\n",
+    "                                                 perturbation_function_holder=custom_perturbation_function,\n",
+    "                                                 use_cartesian_coordinates=False)\n",
+    "distance_preserving_builder = CellMatchingDistancePreservingSlabPerturbationBuilder()"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "8d90932312c418ee"
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 3.2. Apply perturbation to the material"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "7695d5d1df6be2e3"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "material_with_custom_perturbation = create_perturbation(configuration_custom, distance_preserving_builder)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "69ccc90b8c5c1191"
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 3.3. 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"
+  },
+  {
+   "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 set_data\n",
+    "\n",
+    "set_data(\"materials\", [material_with_perturbation.to_json(), material_with_custom_perturbation.to_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
+}
diff --git a/other/materials_designer/create_point_defect.ipynb b/other/materials_designer/create_point_defect.ipynb
@@ -90,7 +90,7 @@
   {
    "cell_type": "markdown",
    "source": [
-    "### 1.3. Get input material and \n",
+    "### 1.3. Get input materials\n",
     "Materials are loaded with `get_data()`. The first material is assigned as substrate and the second as film."
    ],
    "metadata": {

diff --git a/utils/visualize.py b/utils/visualize.py
@@ -29,7 +29,7 @@ def get_material_image(material: Material, title: str, rotation="0x,0y,0z", repe
     # Create supercell for visualization
     supercell_matrix = [[repetitions[0], 0, 0], [0, repetitions[1], 0], [0, 0, repetitions[2]]]
     material_repeat = make_supercell(ase_atoms, supercell_matrix)
-    text = f"{ase_atoms.symbols} - {title} - rotation: {rotation}"
+    text = f"{ase_atoms.get_chemical_formula()} - {title} - rotation: {rotation}"
 
     # Write image to a buffer to display in HTML
     buf = io.BytesIO()