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Merge pull request #224 from Exabyte-io/feature/2-example-notebooks
update: add etched cell + heterostack to specific examples
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‎.github/workflows/cicd.yml

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jobs:
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run-linter:
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runs-on: ubuntu-20.04
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runs-on: ubuntu-24.04
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strategy:
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matrix:
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python-version: ["3.10.13"]
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# TODO: Add back when when fixed.
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# build-and-deploy-docs:
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# runs-on: ubuntu-20.04
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# runs-on: ubuntu-24.04
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# strategy:
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# matrix:
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# python-version: ["3.8.6"]

‎other/materials_designer/specific_examples/custom_cutout_etched_silicon.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 custom-shape cutout (Si)\n",
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"\n",
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"Create a slab with a complex cutout pattern.\n",
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"By default, this notebook generates a structure of etching pattern:\n",
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"- Two vertical side walls\n",
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"- Two parallel channels at the top\n",
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"- A deeper central cavity\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 Material (in the outer runtime) before running the notebook.\n",
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"2. Set structural parameters in cell 1.2 below\n",
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"4. Click \"Run\" > \"Run All\" to create the structure\n",
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"5. Scroll down to view the resulting structure from multiple angles\n",
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"\n",
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"## Resulting structure:\n",
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"<img src=\"https://objects.mat3ra.com/images/notebooks/cutout_custom_shape_silicon.png\" width=\"400\">"
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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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"### 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": "98aa134f51746218"
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},
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{
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"cell_type": "code",
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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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" await micropip.install('mat3ra-utils')\n",
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" from mat3ra.utils.jupyterlite.packages import install_packages\n",
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"\n",
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" await install_packages(\"specific_examples\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "280f9794a876678b",
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"outputs": [],
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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 structure 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": "b3d4d3ea7b589f89"
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},
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{
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"cell_type": "code",
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"source": [
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"# Slab parameters\n",
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"MILLER_INDICES = (0, 0, 1)\n",
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"THICKNESS = 6 # unit cell layers\n",
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"VACUUM = 10.0 # Angstrom\n",
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"XY_SUPERCELL_MATRIX = [[10, 0], [0, 10]]\n",
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"\n",
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"# Custom shape parameters in crystal units of the slab\n",
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"LEFT_WALL_POSITION = 0.2\n",
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"RIGHT_WALL_POSITION = 0.8\n",
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"LEFT_CHANNEL_POSITION = 0.25\n",
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"RIGHT_CHANNEL_POSITION = 0.75\n",
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"CHANNEL_TOP_Z = 0.8\n",
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"CAVITY_TOP_Z = 0.5\n",
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"\n",
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"NAME = \"Custom Shape - Etching Pattern\""
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],
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"metadata": {
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"collapsed": false
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},
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"id": "5177e239254e3601",
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"outputs": [],
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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. Create a condition on coordinates\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": "361c291aaf3feb2a"
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},
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{
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"cell_type": "code",
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"source": [
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"from typing import List\n",
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"\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. Adapt coordinate conditions to your needs.\n",
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"class CustomCoordinateCondition(CoordinateCondition):\n",
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" \"\"\"\n",
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" Defines an etched pattern structure with side walls, channels, and a central cavity.\n",
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" All dimensions are specified as fractions of the total size (0.0 to 1.0).\n",
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" \"\"\"\n",
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" left_wall_position: float = 0.2\n",
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" right_wall_position: float = 0.8\n",
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" left_channel_position: float = 0.25\n",
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" right_channel_position: float = 0.75\n",
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" channel_top_z: float = 0.8\n",
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" cavity_top_z: float = 0.5\n",
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"\n",
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" def condition(self, coordinate: List[float]) -> bool:\n",
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" \"\"\"\n",
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" Determines which atoms to filter based on the coordinate.\n",
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" Returns True for positions where atoms should be removed.\n",
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" \n",
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" The structure consists of:\n",
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" 1. Side walls: Two vertical walls running along the y-axis\n",
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" 2. Channels: Two trenches at the top running along the x-axis\n",
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" 3. Cavity: A deeper central region between the channels\n",
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" \"\"\"\n",
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" x, y, z = coordinate\n",
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"\n",
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" # Define the structural elements\n",
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" is_in_left_wall = x <= self.left_wall_position\n",
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" is_in_right_wall = x >= self.right_wall_position\n",
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"\n",
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" is_in_left_channel = y <= self.left_channel_position\n",
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" is_in_right_channel = y >= self.right_channel_position\n",
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"\n",
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" is_in_channel = (\n",
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" z < self.channel_top_z and\n",
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" (is_in_left_channel or is_in_right_channel)\n",
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" )\n",
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"\n",
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" is_below_cavity = (\n",
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" z < self.cavity_top_z and # Cavity depth\n",
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" self.left_wall_position < x < self.right_wall_position and # Between walls\n",
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" not is_in_left_channel and not is_in_right_channel # Between channels\n",
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" )\n",
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"\n",
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" return (\n",
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" is_in_left_wall or\n",
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" is_in_right_wall or\n",
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" is_in_channel or\n",
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" is_below_cavity\n",
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" )\n",
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"\n",
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"\n",
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"condition = CustomCoordinateCondition(\n",
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" left_wall_position=LEFT_WALL_POSITION,\n",
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" right_wall_position=RIGHT_WALL_POSITION,\n",
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" left_channel_position=LEFT_CHANNEL_POSITION,\n",
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" right_channel_position=RIGHT_CHANNEL_POSITION,\n",
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" channel_depth=CHANNEL_TOP_Z,\n",
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" cavity_depth=CAVITY_TOP_Z,\n",
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").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": "56c8227695643174",
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"outputs": [],
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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 materials"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "91724db55eddad60"
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},
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{
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"cell_type": "code",
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"source": [
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"from mat3ra.standata.materials import Materials\n",
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"from mat3ra.made.material import Material\n",
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"\n",
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"material_json = Materials.get_by_name_first_match(\"Si\")\n",
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"material = Material.create(material_json)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "ceebf2a5229da67c",
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"outputs": [],
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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. Preview the 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": "13964644436b4156"
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},
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{
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"cell_type": "code",
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"source": [
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"from utils.visualize import visualize_materials as visualize\n",
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"\n",
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"visualize(material, repetitions=[1, 1, 1], rotation=\"0x\")\n",
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"visualize(material, repetitions=[1, 1, 1], 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": "45f0c424ece00186",
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"outputs": [],
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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 target material\n",
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"### 2.1. Create a slab and apply the cutout 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": "615800437b2ef7a"
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},
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{
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"metadata": {},
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"cell_type": "code",
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"source": [
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"from mat3ra.made.tools.modify import filter_by_condition_on_coordinates, add_vacuum\n",
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"from mat3ra.made.tools.build.slab import create_slab, SlabConfiguration\n",
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"\n",
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"slab_config = SlabConfiguration(\n",
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" bulk=material,\n",
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" miller_indices=MILLER_INDICES,\n",
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" thickness=THICKNESS,\n",
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" vacuum=0,\n",
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" xy_supercell_matrix=XY_SUPERCELL_MATRIX,\n",
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" use_orthogonal_z=True,\n",
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" use_conventional_cell=True,\n",
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")\n",
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"\n",
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"slab_unit_cell = create_slab(slab_config)\n",
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"visualize(slab_unit_cell, viewer=\"wave\", title=\"Slab Unit Cell\")"
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],
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"id": "8938220048670941",
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"outputs": [],
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"execution_count": null
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},
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{
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"metadata": {},
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"cell_type": "markdown",
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"source": "### 2.2. Apply the cutout condition and add vacuum",
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"id": "b52118b5a4fb494c"
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},
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{
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"metadata": {},
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"cell_type": "code",
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"source": [
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"resulting_material = filter_by_condition_on_coordinates(slab_unit_cell, condition)\n",
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"resulting_material = add_vacuum(resulting_material, VACUUM)"
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],
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"id": "e1a13d9490a4d5ca",
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"outputs": [],
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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"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "57cc38ec0df3c1f7"
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},
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{
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"metadata": {},
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"cell_type": "code",
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"source": [
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"visualize(resulting_material, title=\"Resulting Material\", rotation=\"-90x\")\n",
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"visualize(resulting_material, viewer=\"wave\")"
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],
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"id": "20f499a8dd2362e0",
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"outputs": [],
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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 material 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": "c67e6f5363e80942"
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},
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{
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"cell_type": "code",
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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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"resulting_material.name = NAME\n",
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"set_materials(resulting_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": "cbee60d4b936e5cb",
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"outputs": [],
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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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