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Merge pull request #171 from Exabyte-io/feature/SOF-7499
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feature/SOF-7499 update: two perturbation notebooks
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@VsevolodX
VsevolodX authored Nov 28, 2024
2 parents dae6f3f + 6789f88 commit 2ba468e
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3 changes: 2 additions & 1 deletion other/materials_designer/Introduction.ipynb
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"## 5. Perturbations.\n",
"\n",
"### 5.1. Slab Perturbations\n",
"#### [5.1.1. Perturbation using sine wave, custom planar (XY) functions](create_perturbation.ipynb)\n",
"#### [5.1.1. Perturbation using sine wave](create_perturbation.ipynb)\n",
"#### [5.1.2. Perturbation using custom function](create_perturbation_custom.ipynb)\n",
"\n",
"\n",
"## 6. Other.\n",
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140 changes: 33 additions & 107 deletions other/materials_designer/create_perturbation.ipynb
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"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",
"Create a perturbation in a material with a specified smooth function (SineWave by default)\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"
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"cell_type": "markdown",
"source": [
"## 1. Prepare the Environment\n",
"### 1.1. Set up supercell parameters "
"### 1.1. Set up perturbation parameters"
],
"metadata": {
"collapsed": false
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"cell_type": "code",
"outputs": [],
"source": [
"SUPERCELL_MATRIX = [[30, 0, 0], [0, 30, 0], [0, 0, 1]] "
"# Sine wave perturbation parameters\n",
"AMPLITUDE = 0.5\n",
"WAVELENGTH = 1.0\n",
"PHASE = 0.0\n",
"AXIS = \"y\"\n",
"\n",
"USE_CARTESIAN_COORDINATES = False\n",
"\n",
"SUPERCELL_MATRIX = [[30, 0, 0], [0, 30, 0], [0, 0, 1]]\n",
"\n",
"PRESERVE_GEODESIC_DISTANCE = False"
],
"metadata": {
"collapsed": false
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"\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(\"\")"
],
"metadata": {
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"outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
"materials = get_materials(globals())"
],
"metadata": {
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"cell_type": "code",
"outputs": [],
"source": [
"from mat3ra.made.tools.build.perturbation import PerturbationConfiguration, SlabPerturbationBuilder\n",
"from mat3ra.made.tools.build.perturbation import PerturbationConfiguration, SlabPerturbationBuilder, CellMatchingDistancePreservingSlabPerturbationBuilder\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",
"perturbation_function = SineWavePerturbationFunctionHolder(\n",
" 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",
"configuration = PerturbationConfiguration(\n",
" material=supercell,\n",
" perturbation_function_holder=perturbation_function,\n",
" use_cartesian_coordinates=USE_CARTESIAN_COORDINATES)\n",
"\n",
"builder = SlabPerturbationBuilder()"
"if PRESERVE_GEODESIC_DISTANCE:\n",
" builder = CellMatchingDistancePreservingSlabPerturbationBuilder()\n",
"else:\n",
" builder = SlabPerturbationBuilder()"
],
"metadata": {
"collapsed": false
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{
"cell_type": "markdown",
"source": [
"### 2.3. Visualize the Material"
"### 3. Visualize the Result"
],
"metadata": {
"collapsed": false
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"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",
"execution_count": null
},
{
"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",
"execution_count": null
},
{
"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",
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
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"source": [
"from utils.jupyterlite import set_materials\n",
"\n",
"set_materials([material_with_perturbation, material_with_custom_perturbation])"
"set_materials(material_with_perturbation)"
],
"metadata": {
"collapsed": false
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