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update: rename flag
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‎other/materials_designer/passivate_slab.ipynb‎

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"cells": [
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{
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"cell_type": "markdown",
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"id": "7d00c63281a63fa0",
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"metadata": {
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"collapsed": false
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},
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"source": [
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"# Passivate Slab Surface\n",
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"\n",
@@ -20,14 +24,14 @@
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"1. Surface atoms are detected by analyzing atomic positions along z-axis\n",
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"1. \"Shadowing radius\" controls the exclusion of atoms below the surface ones from being passivated\n",
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"1. Passivants are added at specified bond lengths from surface atoms"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "7d00c63281a63fa0"
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]
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},
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{
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"cell_type": "markdown",
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"id": "d80280b47f767281",
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"metadata": {
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"collapsed": false
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},
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"source": [
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"## 1. Prepare the Environment\n",
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"### 1.1. Set up the notebook\n",
@@ -36,14 +40,15 @@
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"Visualization of the parameters of passivation on the image below:\n",
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"\n",
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"<img src=\"https://i.imgur.com/sVd7BWn.png\" alt=\"Passivation parameters\" width=\"600\"/>\n"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "d80280b47f767281"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"id": "92b3518bebdcf547",
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"# Material selection\n",
@@ -58,7 +63,7 @@
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"SHADOWING_RADIUS = 2.5 # Radius to exclude subsurface atoms, in Angstroms\n",
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"DEPTH = 5.0 # How deep to look for surface atoms, in Angstroms\n",
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"\n",
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"CREATE_SLAB = False # Create a slab if the input material is not a slab\n",
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"BYPASS_SLAB_CREATION = False # If True, will use input material directly\n",
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"\n",
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"# Slab parameters for creating a new slab if previous option is set to True\n",
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"DEFAULT_SLAB_PARAMETERS = {\n",
@@ -72,26 +77,26 @@
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"# Visualization parameters\n",
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"SHOW_INTERMEDIATE_STEPS = True\n",
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"CELL_REPETITIONS_FOR_VISUALIZATION = [1, 1, 1] # Structure repeat in view"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "92b3518bebdcf547",
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"execution_count": null
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]
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 1.2. Install packages\n",
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"The step executes only in Pyodide environment. For other environments, the packages should be installed via `pip install`."
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],
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"id": "11bd9b5fca1510fc",
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"metadata": {
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"collapsed": false
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},
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"id": "11bd9b5fca1510fc"
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"source": [
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"### 1.2. Install packages\n",
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"The step executes only in Pyodide environment. For other environments, the packages should be installed via `pip install`."
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"id": "42863fe84bfab53c",
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"import sys\n",
@@ -103,50 +108,50 @@
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" from utils.jupyterlite import install_packages\n",
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"\n",
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" await install_packages(\"\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "42863fe84bfab53c",
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"execution_count": null
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]
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 1.3. Load and preview input material"
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],
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"id": "6983ab284dff18c0",
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"metadata": {
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"collapsed": false
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},
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"id": "6983ab284dff18c0"
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"source": [
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"### 1.3. Load and preview input material"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "a51551f4af6456c7",
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"from utils.jupyterlite import get_materials\n",
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"from utils.visualize import visualize_materials\n",
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"\n",
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"materials = get_materials(globals())"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "a51551f4af6456c7",
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"execution_count": null
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]
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 1.4. Create a slab if the input material is not a slab"
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],
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"id": "6b929ffec7c4876e",
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"metadata": {
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"collapsed": false
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},
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"id": "6b929ffec7c4876e"
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"source": [
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"### 1.4. Create a slab if the input material is not a slab"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "ad71f877f76f0550",
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"from mat3ra.made.tools.build.slab import create_slab_if_not, SlabConfiguration\n",
@@ -161,32 +166,32 @@
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" xy_supercell_matrix=DEFAULT_SLAB_PARAMETERS[\"xy_supercell_matrix\"]\n",
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")\n",
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"\n",
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"slab = create_slab_if_not(material, default_slab_config) if CREATE_SLAB else material\n",
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"slab = material if BYPASS_SLAB_CREATION else create_slab_if_not(material, default_slab_config)\n",
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"\n",
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"if SHOW_INTERMEDIATE_STEPS:\n",
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" print(\"Initial slab structure:\")\n",
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" visualize_materials(slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION)\n",
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" visualize_materials(slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION, rotation=\"-90x\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "ad71f877f76f0550",
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"execution_count": null
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]
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},
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{
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"cell_type": "markdown",
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"source": [
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"## 2. Create target material\n",
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"### 2.1. Set up passivation configuration and builder\n"
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],
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"id": "cee250785246811a",
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"metadata": {
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"collapsed": false
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},
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"id": "cee250785246811a"
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"source": [
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"## 2. Create target material\n",
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"### 2.1. Set up passivation configuration and builder\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"id": "7e26e8e7fb8319a",
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"from mat3ra.made.tools.build.passivation import (\n",
@@ -208,25 +213,25 @@
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")\n",
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"\n",
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"builder = SurfacePassivationBuilder(build_parameters=builder_params)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "7e26e8e7fb8319a",
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"execution_count": null
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]
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 2.2. Generate passivated structure\n"
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],
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"id": "2950f29de8bc79b2",
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"metadata": {
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"collapsed": false
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},
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"id": "2950f29de8bc79b2"
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"source": [
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"### 2.2. Generate passivated structure\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "a4ed473eb2129ac4",
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"from mat3ra.made.tools.build.passivation import create_passivation\n",
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"print(f\"Bond length: {BOND_LENGTH} Å\")\n",
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"print(f\"Surfaces passivated: {SURFACE}\")\n",
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"print(f\"Number of atoms: {len(passivated_slab.basis.elements.ids)}\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "a4ed473eb2129ac4",
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"execution_count": null
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]
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},
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{
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"cell_type": "markdown",
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"source": [
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"## 3. Visualize the result"
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],
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"id": "56ec05c6ed2f91cd",
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"metadata": {
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"collapsed": false
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},
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"id": "56ec05c6ed2f91cd"
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"source": [
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"## 3. Visualize the result"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "c4b5e1e0ec0ab02a",
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"print(\"Final passivated structure:\")\n",
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"visualize_materials(passivated_slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION)\n",
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"visualize_materials(passivated_slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION, rotation=\"-90x\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "c4b5e1e0ec0ab02a",
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"execution_count": null
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]
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 4. Pass data to the outside runtime\n"
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],
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"id": "eab7e14d2c7880a5",
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"metadata": {
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"collapsed": false
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},
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"id": "eab7e14d2c7880a5"
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"source": [
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"### 4. Pass data to the outside runtime\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "d66a15a29d27c6ea",
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"from utils.jupyterlite import set_materials\n",
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"\n",
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"set_materials(passivated_slab)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "d66a15a29d27c6ea",
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"execution_count": null
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": ".venv-3.11",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 2
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.6"
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"pygments_lexer": "ipython3",
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"version": "3.11.7"
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}
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},
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"nbformat": 4,

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