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Merge branch 'dev' into feature/SOF-7493
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‎config.yml‎

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packages_pyodide:
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- mat3ra-esse
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- mat3ra-made
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- name: create_cluster_custom_shape.ipynb
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packages_common:
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- icosphere
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packages_python:
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packages_pyodide:
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- name: specific_examples
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packages_common:
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- mat3ra-standata

‎other/materials_designer/Introduction.ipynb‎

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"\n",
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"### 1.3. 1D Structures.\n",
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"#### [1.3.1. Nanoribbons. Create nanoribbons from 2D materials.](create_nanoribbon.ipynb)\n",
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"#### [1.3.2. Nanowires. Create a nanowire from a bulk material.](create_nanowire.ipynb)\n",
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"#### [1.3.3. Nanowires with custom shape. Create a nanowire with a custom cross-section.](create_nanowire_custom_shape.ipynb)\n",
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"\n",
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"### 1.4. 0D Structures.\n",
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"#### [1.4.1. Spherical. Create clusters or spherical structures.](create_cluster_sphere.ipynb)\n",
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"#### [1.4.1. Spherical Cluster. Create a spherical cluster from a bulk material.](create_cluster_sphere.ipynb)\n",
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"#### [1.4.2. Custom Shape Cluster. Create a cluster with a custom shape.](create_cluster_custom_shape.ipynb)\n",
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"#### [1.4.3. Box-cutout. Create a slab with a box cutout](create_cutout_box.ipynb)\n",
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"#### [1.4.4. Custom Shape Cutout. Create a slab with a custom shape cutout.](create_cutout_custom_shape.ipynb)\n",
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"\n",
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"\n",
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"## 2. Multi-Material Structures.\n",
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"\n",
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"### 2.1. Interfaces\n",
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"#### [2.1.1. Interface with Zur and McGill Superlattice (ZSL) straing matching](create_interface_with_min_strain_zsl.ipynb)\n",
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"#### [2.1.1. Interface with Zur and McGill Superlattice (ZSL) strain matching](create_interface_with_min_strain_zsl.ipynb)\n",
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"\n",
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"#### [2.1.3. Interface without strain matching](create_interface_with_no_strain_matching.ipynb)\n",
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"\n",

‎other/materials_designer/create_cluster_custom_shape.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"source": [
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"# Create a cluster of custom shape from a bulk material\n",
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"\n",
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"Create a cluster with shape provided by condition on coordinates and crystal orientation along the z-axis from a bulk material.\n",
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"\n",
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"<h2 style=\"color:green\">Usage</h2>\n",
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"\n",
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"1. Make sure to select Input Materials (in the outer runtime) before running the notebook.\n",
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"1. Set notebook parameters in cell 1.1. below (or use the default values).\n",
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"1. Click “Run” > “Run All” to run all cells. \n",
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"1. Scroll down to view results. \n",
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"\n",
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"\n",
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"## Notes\n",
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"\n",
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"1. For more information, see [Introduction](Introduction.ipynb)\n",
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"<!-- # TODO: use a hashtag-based anchor link to interface creation documention above -->\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": "f2e1e795020d7b3f"
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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. Prepare the Environment\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": "5e43ff288847b784"
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 1.1. 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` (see [README](../../README.ipynb))."
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],
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"metadata": {
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"collapsed": false
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},
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"id": "9adf37a8d2620dc4"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"import sys\n",
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"\n",
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"if sys.platform == \"emscripten\":\n",
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" import micropip\n",
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"\n",
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" await micropip.install('mat3ra-api-examples', deps=False)\n",
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" from utils.jupyterlite import install_packages\n",
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"\n",
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" await install_packages(\"create_cluster_custom_shape.ipynb\", \"../../config.yml\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "d9e6be14343d00a1",
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"execution_count": null
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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. Set up cluster parameters"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "26066db067a41c93"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"RADIUS = 0.3 # in crystal units\n",
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"VACUUM = 10.0 # in Angstroms on each side\n",
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"SUPERCELL_SIZE = 10 # in crystal units\n",
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"Z_ORIENTATION = (0, 0, 1) # Miller indices of the slab orientation along the z-axis for the cluster\n",
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"NAME = \"Icosahedron\" # Name of the cluster"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "9d8b1890b34d850a",
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"execution_count": null
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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. Set coordinates condition"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "3aae932e71fa71a9"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"import numpy as np\n",
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"from typing import List\n",
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"from icosphere import icosphere\n",
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"from mat3ra.made.tools.utils.coordinate import CoordinateCondition\n",
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"\n",
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"\n",
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"# Example of a custom coordinate condition (icosahedron). Adapt coordinate conditions to your needs.\n",
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"class CustomCoordinateCondition(CoordinateCondition):\n",
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" \"\"\"Creates an icosahedron shape using the icosphere module\"\"\"\n",
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" radius: float = 1\n",
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" frequency: int = 1\n",
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" vertices: List[List[float]] = icosphere(1)[0]\n",
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" faces: List[List[int]] = icosphere(1)[1]\n",
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" center: List[float] = [0.5, 0.5, 0.5]\n",
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"\n",
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" def condition(self, coordinate: List[float]) -> bool:\n",
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" \"\"\"Returns True if point is inside icosahedron\"\"\"\n",
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" coordinate = np.array(coordinate) - self.center\n",
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" for face in self.faces:\n",
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" a, b, c = face\n",
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" normal = np.cross(self.vertices[b] - self.vertices[a], self.vertices[c] - self.vertices[a])\n",
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" normal = normal / np.linalg.norm(normal)\n",
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" if np.dot(normal, coordinate) > self.radius:\n",
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" return False\n",
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" return True\n",
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" \n",
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"condition = CustomCoordinateCondition(radius=RADIUS).condition"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "8e382d5ab459e2d",
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"execution_count": null
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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. Get input material"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "919ad7af8dceeedd"
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},
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{
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"cell_type": "code",
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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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"\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": "be38fdda1984c654",
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"execution_count": null
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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 of sufficient size"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "a132fe0ef8bbf0d0"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from mat3ra.made.tools.build.supercell import create_supercell\n",
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"from mat3ra.made.tools.build.slab import create_slab, SlabConfiguration\n",
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"from utils.visualize import visualize_materials as visualize\n",
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"\n",
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"slab_config = SlabConfiguration(\n",
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" bulk=materials[0],\n",
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" miller_indices=Z_ORIENTATION,\n",
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" thickness=SUPERCELL_SIZE,\n",
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" vacuum=0,\n",
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" use_orthogonal_z=True,\n",
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" xy_supercell_matrix=[[SUPERCELL_SIZE, 0], [0, SUPERCELL_SIZE]],\n",
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")\n",
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"\n",
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"slab = create_slab(slab_config)\n",
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"\n",
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"visualize([{\"material\": slab, \"title\": \"Original material\"}])\n",
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"visualize([{\"material\": slab, \"title\": \"Original material\"}], 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": "7fcb1e02e84c5f35",
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"execution_count": null
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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 the Target Material\n",
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"### 2.1. Create spherical cluster\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": "690241d87e7bbbe0"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from mat3ra.made.tools.modify import add_vacuum, add_vacuum_sides, filter_by_condition_on_coordinates\n",
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"\n",
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"cluster = filter_by_condition_on_coordinates(slab, condition)\n",
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"cluster = add_vacuum(cluster, VACUUM, to_bottom=True, on_top=True)\n",
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"cluster = add_vacuum_sides(cluster, VACUUM, on_x=True, on_y=True)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "a990fa35742d7269",
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"execution_count": null
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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. Set lattice to Cubic"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "a01018588e6e55fc"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from mat3ra.made.lattice import Lattice\n",
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"\n",
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"current_vector_1, current_vector_2, current_vector_3 = cluster.lattice.vectors\n",
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"cubic_vector_1 = [current_vector_1[0], 0, 0]\n",
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"cubic_vector_2 = [0, current_vector_2[1], 0]\n",
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"cubic_vector_3 = [0, 0, current_vector_3[2]]\n",
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"cluster.lattice = Lattice.from_vectors_array([cubic_vector_1, cubic_vector_2, cubic_vector_3], type=\"CUB\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "4f78c4743b370c3b",
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"execution_count": null
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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(s)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "462549d016073446"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
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" {\"material\": cluster, \"title\": f\"Cluster\"}])\n",
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"\n",
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"visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
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" {\"material\": cluster, \"title\": f\"Cluster\"}], 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": "509b18661a069e42",
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"execution_count": null
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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"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "d381df29a6bbdd82"
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},
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{
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"cell_type": "code",
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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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"cluster.name = f\"{materials[0].name} {NAME}\"\n",
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"set_materials(cluster)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "61daa5afcbc078a9",
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"execution_count": null
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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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"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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},
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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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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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