Merge pull request #161 from Exabyte-io/feature/SOF-7490

feature/SOF 7490

other/materials_designer/Introduction.ipynb

@@ -18,7 +18,8 @@
     "#### [1.1.1. Supercells. Create supercells from 3D crystals.](create_supercell.ipynb)\n",
     "\n",
     "### 1.2. 2D Structures.\n",
-    "#### [1.2.1. Slabs. Create slabs from bulk materials.](create_slab.ipynb)\n",
+    "#### [1.2.1. Slabs. Create a slab from a bulk material.](create_slab.ipynb)\n",
+    "#### [1.2.2. Monolayers. Create a monolayer from a bulk material.](create_monolayer.ipynb)\n",
     "\n",
     "### 1.3. 1D Structures.\n",
     "#### [1.3.1. Nanoribbons. Create nanoribbons from 2D materials.](create_nanoribbon.ipynb)\n",
@@ -92,6 +93,14 @@
     "\n",
     "#### [7.1.1. More info about the conventions used](under_the_hood.ipynb)."
    ]
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [],
+   "metadata": {
+    "collapsed": false
+   }
   }
  ],
  "metadata": {

other/materials_designer/create_monolayer.ipynb

@@ -0,0 +1,274 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# Create a Monolayer\n",
+    "\n",
+    "Create a Monolayer of the original structure. \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. Click “Run” > “Run All” to run all cells. \n",
+    "1. Scroll down to view results. "
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "a79609c9bc772c5c"
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 1. Prepare the Environment\n",
+    "### 1.1. Set up transformation parameters "
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "47d31d9834478007"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "XY_SUPERCELL_MATRIX = [\n",
+    "    [3, 0],\n",
+    "    [0, 3],\n",
+    "]\n",
+    "\n",
+    "VACUUM = 10.0  # Angstrom"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "a2c8922a4e627887",
+   "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": "6fab076ea1d7a223"
+  },
+  {
+   "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(\"\", \"../../config.yml\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "b0c332f1c1f451fd",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 1.3. Get input materials"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "3e9934b458d6cb4"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.jupyterlite import get_materials\n",
+    "\n",
+    "materials = get_materials(globals())\n",
+    "material = materials[0]"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "74cd0d5a3881ab47",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 1.4. Preview the material"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "d4535caf6debb8d4"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.visualize import visualize_materials as visualize\n",
+    "\n",
+    "visualize(material, repetitions=[3, 3, 1], rotation=\"0x\")\n",
+    "visualize(material, repetitions=[3, 3, 1], rotation=\"-90x\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "d6bea39864c23ab5",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 2. Create Monolayer"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "5473c36cd254aa89"
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 2.1. Create slab configuration\n",
+    "Slab Configuration lets define the slab thickness, vacuum, and the Miller indices of the interfacial plane and get the slabs with possible terminations.\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "ee17958872d03410"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from mat3ra.made.tools.build.slab import SlabConfiguration\n",
+    "\n",
+    "slab_configuration = SlabConfiguration(\n",
+    "    bulk=material,\n",
+    "    miller_indices=(0, 0, 1),\n",
+    "    thickness=1,\n",
+    "    vacuum=VACUUM,\n",
+    "    xy_supercell_matrix=XY_SUPERCELL_MATRIX,\n",
+    "    use_orthogonal_z=True,\n",
+    "    use_conventional_cell=True,\n",
+    ")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "b8dc56881543c16c",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 2.2 Create the slab of Single Layer"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "661c76f9bab9f743"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from mat3ra.made.tools.modify import translate_to_z_level, filter_by_box\n",
+    "from mat3ra.made.tools.build.slab import create_slab\n",
+    "\n",
+    "slab = create_slab(slab_configuration)\n",
+    "\n",
+    "# Get only the top layer of two -- for AB stacked bilayers forming a 3D bulk basis\n",
+    "if any(substring in material.name for substring in [\"3D\", \"Bulk\"]):\n",
+    "    centered_slab = translate_to_z_level(slab, z_level=\"center\")\n",
+    "    half_filtered_slab = filter_by_box(centered_slab, [0, 0, 0.5], [1, 1, 1])\n",
+    "    monolayer = translate_to_z_level(half_filtered_slab, z_level=\"center\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "cf27e53c85adc447",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 3. Visualize the result"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "527829d64a542d10"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "visualize(monolayer, repetitions=[1, 1, 1], rotation=\"0x\")\n",
+    "visualize(monolayer, repetitions=[1, 1, 1], rotation=\"-90x\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "ee12ab13c210b953",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# 4. Pass material to the outside runtime"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "6ce5f7dd9a919a08"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.jupyterlite import set_materials\n",
+    "\n",
+    "set_materials(monolayer)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "865c71d008d87beb",
+   "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
+}