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Merge pull request #175 from Exabyte-io/feature/SOF-7510
Feature/SOF-7510 Gold clusters
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‎other/materials_designer/Introduction.ipynb‎

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"\n",
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"### 1.4. 0D Structures.\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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"#### [1.4.2. Custom Shape Cluster. Create a cluster by cutting it out of a slab.](create_cluster_custom_shape.ipynb)\n",
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"#### [1.4.3. Specific Shape Cluster. Create a cluster by building up a specific shape.](create_cluster_specific_shape.ipynb)\n",
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"#### [1.4.4. Box-cutout. Create a slab with a box cutout](create_cutout_box.ipynb)\n",
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"#### [1.4.5. 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",

‎other/materials_designer/create_cluster_custom_shape.ipynb‎

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" return False\n",
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" return True\n",
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" \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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{
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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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"## 2. Create the Target Material\n",
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"### 2.1. Set the cluster configuration\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": "a132fe0ef8bbf0d0"
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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.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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"from mat3ra.made.tools.build.nanoparticle import ASEBasedNanoparticleConfiguration\n",
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"from mat3ra.made.tools.build.nanoparticle.enums import ASENanoparticleShapesEnum\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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"config = ASEBasedNanoparticleConfiguration(\n",
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" material=materials[0],\n",
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" supercell_size=SUPERCELL_SIZE,\n",
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" vacuum=VACUUM,\n",
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" z_orientation=Z_ORIENTATION,\n",
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" coordinate_condition=condition\n",
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")\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": "7fcb1e02e84c5f35",
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"execution_count": null
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"id": "8fbe260fa14db47a"
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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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"#### 2.2. Create 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": "690241d87e7bbbe0"
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"id": "10799f3efede924d"
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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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"from mat3ra.made.tools.build.nanoparticle import ASEBasedNanoparticleBuilder"
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],
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"metadata": {
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"collapsed": false

‎other/materials_designer/create_cluster_specific_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 nanocluster with a specific shape.\n",
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"\n",
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"Create a nanocluster using the ASE-based nanoparticle builder.\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 1.2. 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(\"\")"
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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\n",
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"Parameters for the cuboctahedron and icosahedron shapes can be found at [ASE Clusters](https://wiki.fysik.dtu.dk/ase/ase/cluster/cluster.html#ase.cluster.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": "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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"from mat3ra.made.tools.build.nanoparticle.enums import ASENanoparticleShapesEnum\n",
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"\n",
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"shape = ASENanoparticleShapesEnum.OCTAHEDRON\n",
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"parameters = {\n",
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" \"length\": 5,\n",
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" \"cutoff\": 2\n",
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"}"
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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. 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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"## 2. Create the Target Material\n",
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"### 2.1. Set the cluster configuration\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.build.nanoparticle import ASEBasedNanoparticleConfiguration, ASEBasedNanoparticleBuilder\n",
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"\n",
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"config = ASEBasedNanoparticleConfiguration(\n",
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" material=materials[0],\n",
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" shape=shape,\n",
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" parameters=parameters\n",
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")\n",
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"\n",
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"builder = ASEBasedNanoparticleBuilder()\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": "8fbe260fa14db47a",
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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. Create 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": "10799f3efede924d"
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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.nanoparticle import create_nanoparticle\n",
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"\n",
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"cluster = create_nanoparticle(config, builder)"
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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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"## 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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"from utils.visualize import visualize_materials\n",
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"\n",
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"visualize_materials([{\"material\": cluster}, {\"material\": 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} {shape.name.capitalize()} cluster\"\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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}

‎other/materials_designer/create_cluster_sphere.ipynb‎

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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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"materials = get_materials(globals())\n"
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],
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"metadata": {
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"collapsed": false

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