Merge pull request #171 from Exabyte-io/feature/SOF-7499

feature/SOF-7499 update: two perturbation notebooks

Author: VsevolodX

other/materials_designer/Introduction.ipynb

@@ -78,7 +78,8 @@
     "## 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",

other/materials_designer/create_perturbation.ipynb

@@ -5,22 +5,16 @@
    "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"
@@ -34,7 +28,7 @@
    "cell_type": "markdown",
    "source": [
     "## 1. Prepare the Environment\n",
-    "### 1.1. Set up supercell parameters "
+    "### 1.1. Set up perturbation parameters"
    ],
    "metadata": {
     "collapsed": false
@@ -45,7 +39,17 @@
    "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
@@ -72,8 +76,10 @@
     "\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": {
@@ -98,6 +104,7 @@
    "outputs": [],
    "source": [
     "from utils.jupyterlite import get_materials\n",
+    "\n",
     "materials = get_materials(globals())"
    ],
    "metadata": {
@@ -149,23 +156,24 @@
    "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
@@ -200,7 +208,7 @@
   {
    "cell_type": "markdown",
    "source": [
-    "### 2.3. Visualize the Material"
+    "### 3. Visualize the Result"
    ],
    "metadata": {
     "collapsed": false
@@ -216,96 +224,14 @@
     "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": [
@@ -322,7 +248,7 @@
    "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