Merge branch 'dev' into update/SOF-7544

Author: VsevolodX

other/materials_designer/passivate_edge.ipynb

@@ -2,14 +2,18 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "source": [],
+   "id": "759c70b8d39addc3",
    "metadata": {
     "collapsed": false
    },
-   "id": "759c70b8d39addc3"
+   "source": []
   },
   {
    "cell_type": "markdown",
+   "id": "4f5cab1ebbbe954",
+   "metadata": {
+    "collapsed": false
+   },
    "source": [
     "# Create Edge Passivation\n",
     "Passivate material edges by detecting and adding passivants to undercoordinated atoms (atoms with fewer neighbors than bulk).\n",
@@ -27,11 +31,7 @@
     "1. Coordination-based passivation finds atoms with fewer neighbors than expected\n",
     "2. Coordination threshold below which passivation is applied, must be set depending on the material\n",
     "3. Passivant atoms are placed along the direction away from existing bonds\n"
-   ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "4f5cab1ebbbe954"
+   ]
   },
   {
    "metadata": {},
@@ -44,11 +44,13 @@
     "\n",
     "<img src=\"https://github.com/Exabyte-io/documentation/raw/88451ce38b0f57f804dcb5010a1a95bb9b9e50bc/images/notebooks/coordination_based_passivation_settings.webp\" alt=\"Coordination search radius\" width=\"400\"/>"
    ],
-   "id": "b25b42e8d3da9789"
+   "id": "f63b28f159207878"
   },
   {
    "metadata": {},
    "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
    "source": [
     "# Enable interactive selection of coordination threshold\n",
     "IS_COORDINATION_SELECTION_INTERACTIVE = False\n",
@@ -71,23 +73,25 @@
     "SHOW_INTERMEDIATE_STEPS = True\n",
     "CELL_REPETITIONS_FOR_VISUALIZATION = [1, 1, 1]  # Structure repeat in view"
    ],
-   "id": "3b94d4e8623dd44f",
-   "outputs": [],
-   "execution_count": null
+   "id": "7e8d8696bb1035e5"
   },
   {
    "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`.\n"
-   ],
+   "id": "975da798561ccde8",
    "metadata": {
     "collapsed": false
    },
-   "id": "975da798561ccde8"
+   "source": [
+    "### 1.2. Install packages\n",
+    "The step executes only in Pyodide environment. For other environments, the packages should be installed via `pip install`.\n"
+   ]
   },
   {
    "cell_type": "code",
+   "id": "4b010bef5b031158",
+   "metadata": {
+    "collapsed": false
+   },
    "source": [
     "import sys\n",
     "\n",
@@ -99,25 +103,25 @@
     "\n",
     "    await install_packages(\"\")"
    ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "4b010bef5b031158",
    "outputs": [],
    "execution_count": null
   },
   {
    "cell_type": "markdown",
-   "source": [
-    "### 1.3. Load and preview input material\n"
-   ],
+   "id": "7df321ca07e11daa",
    "metadata": {
     "collapsed": false
    },
-   "id": "7df321ca07e11daa"
+   "source": [
+    "### 1.3. Load and preview input material\n"
+   ]
   },
   {
    "cell_type": "code",
+   "id": "3a53ff74253cb09a",
+   "metadata": {
+    "collapsed": false
+   },
    "source": [
     "from utils.jupyterlite import get_materials\n",
     "from utils.visualize import visualize_materials\n",
@@ -130,91 +134,101 @@
     "    visualize_materials(nanoribbon, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION)\n",
     "    visualize_materials(nanoribbon, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION, rotation=\"-90x\")"
    ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "3a53ff74253cb09a",
    "outputs": [],
    "execution_count": null
   },
   {
    "cell_type": "markdown",
-   "source": [
-    "## 2. Analyze Coordination Numbers and Select Threshold\n",
-    "### 2.1. Plot RDF to estimate coordination search radius"
-   ],
+   "id": "b5940fc50c11c7b8",
    "metadata": {
     "collapsed": false
    },
-   "id": "b5940fc50c11c7b8"
+   "source": [
+    "## 2. Analyze Coordination Numbers and Select Threshold\n",
+    "### 2.1. Plot RDF to estimate coordination search radius"
+   ]
   },
   {
    "cell_type": "code",
+   "id": "575e8fba623c06e4",
+   "metadata": {
+    "collapsed": false
+   },
    "source": [
     "from utils.plot import plot_rdf\n",
     "\n",
     "plot_rdf(nanoribbon, cutoff=10.0)"
    ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "575e8fba623c06e4",
    "outputs": [],
    "execution_count": null
   },
   {
    "cell_type": "markdown",
-   "source": [
-    "### 2.2. GEt coordination numbers and set coordination threshold"
-   ],
+   "id": "b89dc754926f1ce4",
    "metadata": {
     "collapsed": false
    },
-   "id": "b89dc754926f1ce4"
+   "source": [
+    "### 2.2. Get coordination numbers and set coordination threshold"
+   ]
   },
   {
    "cell_type": "code",
+   "id": "54c265d8ca9408af",
+   "metadata": {
+    "collapsed": false
+   },
    "source": [
     "from utils.io import select_coordination_threshold\n",
-    "from mat3ra.made.tools.build.passivation import get_unique_coordination_numbers, PassivationConfiguration\n",
+    "from mat3ra.made.tools.build.passivation import get_unique_coordination_numbers, PassivationConfiguration, \\\n",
+    "    get_coordination_numbers_distribution\n",
     "\n",
+    "coordination_search_radius = None  # Change this value according to the RDF plot if needed, Angstroms.\n",
     "config = PassivationConfiguration(\n",
     "    slab=nanoribbon,\n",
     "    passivant=PASSIVANT,\n",
     "    bond_length=BOND_LENGTH\n",
     ")\n",
-    "coordination_numbers = get_unique_coordination_numbers(config, cutoff=COORDINATION_SEARCH_RADIUS)\n",
+    "coordination_numbers = get_unique_coordination_numbers(\n",
+    "    configuration=config,\n",
+    "    cutoff=coordination_search_radius or COORDINATION_SEARCH_RADIUS\n",
+    ")\n",
     "print(f\"Unique coordination numbers: {coordination_numbers}\")\n",
     "\n",
+    "cn_distribution = get_coordination_numbers_distribution(\n",
+    "    configuration=config,\n",
+    "    cutoff=coordination_search_radius or COORDINATION_SEARCH_RADIUS\n",
+    ")\n",
+    "print(f\"Coordination numbers distribution: {cn_distribution}\")\n",
     "coordination_threshold = COORDINATION_THRESHOLD\n",
     "if IS_COORDINATION_SELECTION_INTERACTIVE:\n",
     "    coordination_threshold = await select_coordination_threshold(\n",
-    "        coordination_numbers, COORDINATION_THRESHOLD\n",
+    "        cn_distribution, COORDINATION_THRESHOLD\n",
     "    )\n",
     "\n",
     "print(f\"\\nSelected coordination threshold: {coordination_threshold}\")\n",
-    "print(f\"Atoms with coordination < {coordination_threshold} will be passivated\")"
+    "print(f\"Atoms with coordination <= {coordination_threshold} will be passivated\")"
    ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "54c265d8ca9408af",
    "outputs": [],
    "execution_count": null
   },
   {
    "cell_type": "markdown",
-   "source": [
-    "## 3. Create target material\n",
-    "### 3.1. Set up passivation configuration and builder\n"
-   ],
+   "id": "b873d2cb6eaa2bdb",
    "metadata": {
     "collapsed": false
    },
-   "id": "b873d2cb6eaa2bdb"
+   "source": [
+    "## 3. Create target material\n",
+    "### 3.1. Set up passivation configuration and builder\n"
+   ]
   },
   {
    "cell_type": "code",
+   "id": "aca1c76a52e5376a",
+   "metadata": {
+    "collapsed": false
+   },
    "source": [
     "from mat3ra.made.tools.build.passivation.builders import CoordinationBasedPassivationBuilder, \\\n",
     "    CoordinationBasedPassivationBuilderParameters\n",
@@ -228,25 +242,25 @@
     "\n",
     "builder = CoordinationBasedPassivationBuilder(build_parameters=builder_params)"
    ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "aca1c76a52e5376a",
    "outputs": [],
    "execution_count": null
   },
   {
    "cell_type": "markdown",
-   "source": [
-    "### 3.2. Generate passivated structure\n"
-   ],
+   "id": "e40b5f67ef5b54aa",
    "metadata": {
     "collapsed": false
    },
-   "id": "e40b5f67ef5b54aa"
+   "source": [
+    "### 3.2. Generate passivated structure\n"
+   ]
   },
   {
    "cell_type": "code",
+   "id": "3c36dc3654f544c1",
+   "metadata": {
+    "collapsed": false
+   },
    "source": [
     "from mat3ra.made.tools.build.passivation import create_passivation\n",
     "\n",
@@ -258,59 +272,55 @@
     "print(f\"Original atoms: {len(nanoribbon.basis.elements.ids)}\")\n",
     "print(f\"Final atoms: {len(passivated_nanoribbon.basis.elements.ids)}\")"
    ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "3c36dc3654f544c1",
    "outputs": [],
    "execution_count": null
   },
   {
    "cell_type": "markdown",
-   "source": [
-    "## 4. Visualize the result"
-   ],
+   "id": "ad96b86aef8b28f5",
    "metadata": {
     "collapsed": false
    },
-   "id": "ad96b86aef8b28f5"
+   "source": [
+    "## 4. Visualize the result"
+   ]
   },
   {
    "cell_type": "code",
+   "id": "d08ff21e3650ba5d",
+   "metadata": {
+    "collapsed": false
+   },
    "source": [
     "print(\"Final passivated structure:\")\n",
     "visualize_materials(passivated_nanoribbon, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION)\n",
     "visualize_materials(passivated_nanoribbon, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION, rotation=\"-90x\")"
    ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "d08ff21e3650ba5d",
    "outputs": [],
    "execution_count": null
   },
   {
    "cell_type": "markdown",
-   "source": [
-    "## 5. Pass data to the outside runtime\n"
-   ],
+   "id": "7151e48eae3b1886",
    "metadata": {
     "collapsed": false
    },
-   "id": "7151e48eae3b1886"
+   "source": [
+    "## 5. Pass data to the outside runtime\n"
+   ]
   },
   {
    "cell_type": "code",
+   "id": "2d69736d0c71858c",
+   "metadata": {
+    "collapsed": false
+   },
    "source": [
     "from utils.jupyterlite import set_materials\n",
     "\n",
     "passivated_nanoribbon.name = f\"{nanoribbon.name} passivated\"\n",
     "set_materials(passivated_nanoribbon)"
    ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "2d69736d0c71858c",
    "outputs": [],
    "execution_count": null
   }