Merge pull request #173 from Exabyte-io/feature/SOF-7508

Feature/sof 7508

Author: VsevolodX

config.yml

@@ -9,6 +9,7 @@ default:
     - pandas==1.5.3
     - ase==3.22.1
     - ipywidgets
+    - plotly==5.18
   packages_python:
     - pymatgen==2024.4.13
   packages_pyodide:

other/materials_designer/Introduction.ipynb

@@ -72,7 +72,7 @@
     "#### [4.1.1. Slab Passivation](passivate_slab.ipynb) \n",
     "\n",
     "### 4.2. Edge Passivation\n",
-    "#### [4.2.1. Nanoribbon Passivation](passivate_nanoribbon.ipynb) (COMING SOON)\n",
+    "#### [4.2.1. Edge Passivation](passivate_edge.ipynb)\n",
     "\n",
     "\n",
     "## 5. Perturbations.\n",

…ials_designer/passivate_nanoribbon.ipynb …/materials_designer/passivate_edge.ipynbother/materials_designer/passivate_nanoribbon.ipynb renamed to other/materials_designer/passivate_edge.ipynb other/materials_designer/passivate_nanoribbon.ipynb renamed to other/materials_designer/passivate_edge.ipynb

@@ -11,8 +11,8 @@
   {
    "cell_type": "markdown",
    "source": [
-    "# Create Nanoribbon Edge Passivation\n",
-    "Passivate nanoribbon edges by detecting and adding passivants to undercoordinated atoms (atoms with fewer neighbors than bulk).\n",
+    "# Create Edge Passivation\n",
+    "Passivate material edges by detecting and adding passivants to undercoordinated atoms (atoms with fewer neighbors than bulk).\n",
     "\n",
     "<h2 style=\"color:green\">Usage</h2>\n",
     "\n",
@@ -60,12 +60,14 @@
     "\n",
     "# Passivation parameters\n",
     "PASSIVANT = \"H\"  # Chemical element for passivating atom\n",
-    "BOND_LENGTH = 1.0  # Distance from atom to passivant, in Angstroms\n",
+    "BOND_LENGTH = 1.09  # Distance from atom to passivant, in Angstroms\n",
     "\n",
     "# Undercoordinated atoms search algorithm parameters\n",
-    "COORDINATION_THRESHOLD = 5  # Coordination threshold, below which passivation is applied to the atom\n",
-    "COORDINATION_SEARCH_RADIUS = 2.5  # Distance to look for neighbors for coordination, in Angstroms\n",
-    "SEARCH_DEPTH = 5.0  # How deep to look for surface atoms, in Angstroms. Ignored for 2D materials\n",
+    "COORDINATION_THRESHOLD = 2  # Coordination threshold, below which passivation is applied to the atom\n",
+    "COORDINATION_SEARCH_RADIUS = 3.0  # Distance to look for neighbors for coordination, in Angstroms\n",
+    "MAX_BONDS_TO_PASSIVATE = 1  # Maximum number of bonds to passivate\n",
+    "\n",
+    "SYMMETRY_TOLERANCE = 0.1  # Tolerance for symmetry analysis of existing bonds\n",
     "\n",
     "# Visualization parameters\n",
     "SHOW_INTERMEDIATE_STEPS = True\n",
@@ -142,13 +144,38 @@
   {
    "cell_type": "markdown",
    "source": [
-    "## 2. Analyze Coordination Numbers and Select Threshold\n"
+    "## 2. Analyze Coordination Numbers and Select Threshold\n",
+    "### 2.1. Plot RDF to estimate coordination search radius"
    ],
    "metadata": {
     "collapsed": false
    },
    "id": "b5940fc50c11c7b8"
   },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.plot import plot_rdf\n",
+    "\n",
+    "plot_rdf(nanoribbon, cutoff=10.0)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "575e8fba623c06e4",
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 2.2. GEt coordination numbers and set coordination threshold"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "b89dc754926f1ce4"
+  },
   {
    "cell_type": "code",
    "outputs": [],
@@ -161,15 +188,15 @@
     "    passivant=PASSIVANT,\n",
     "    bond_length=BOND_LENGTH\n",
     ")\n",
-    "coordination_numbers = sorted(list(get_unique_coordination_numbers(config)))\n",
+    "coordination_numbers = get_unique_coordination_numbers(config, cutoff=COORDINATION_SEARCH_RADIUS)\n",
     "print(f\"Unique coordination numbers: {coordination_numbers}\")\n",
     "\n",
     "coordination_threshold = COORDINATION_THRESHOLD\n",
     "if IS_COORDINATION_SELECTION_INTERACTIVE:\n",
     "    coordination_threshold = await select_coordination_threshold(\n",
     "        coordination_numbers, COORDINATION_THRESHOLD\n",
-    "    )   \n",
-    "        \n",
+    "    )\n",
+    "\n",
     "print(f\"\\nSelected coordination threshold: {coordination_threshold}\")\n",
     "print(f\"Atoms with coordination < {coordination_threshold} will be passivated\")"
    ],
@@ -199,8 +226,9 @@
     "\n",
     "builder_params = CoordinationBasedPassivationBuilderParameters(\n",
     "    shadowing_radius=COORDINATION_SEARCH_RADIUS,\n",
-    "    depth=SEARCH_DEPTH,\n",
-    "    coordination_threshold=coordination_threshold\n",
+    "    coordination_threshold=coordination_threshold,\n",
+    "    bonds_to_passivate=MAX_BONDS_TO_PASSIVATE,\n",
+    "    symmetry_tolerance=SYMMETRY_TOLERANCE\n",
     ")\n",
     "\n",
     "builder = CoordinationBasedPassivationBuilder(build_parameters=builder_params)"
@@ -268,7 +296,7 @@
   {
    "cell_type": "markdown",
    "source": [
-    "### 5. Pass data to the outside runtime\n"
+    "## 5. Pass data to the outside runtime\n"
    ],
    "metadata": {
     "collapsed": false
@@ -281,6 +309,7 @@
    "source": [
     "from utils.jupyterlite import set_materials\n",
     "\n",
+    "passivated_nanoribbon.name = f\"{nanoribbon.name} passivated\"\n",
     "set_materials(passivated_nanoribbon)"
    ],
    "metadata": {