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other/shapes #208

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9c38d70
feat: add heart shape cutout
VsevolodX Feb 10, 2025
2863c7c
chore: rename
VsevolodX Feb 10, 2025
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313 changes: 313 additions & 0 deletions other/materials_designer/create_cutout_heart_shape.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"source": [
"# Create a heart-shape cutout\n",
"\n",
"Create a slab with a complex cutout pattern.\n",
"By default, this notebook generates a structure of etching pattern:\n",
"- Two vertical side walls\n",
"- Two parallel channels at the top\n",
"- A deeper central cavity\n",
"\n",
"<h2 style=\"color:green\">Usage</h2>\n",
"\n",
"1. Make sure to select Input Material (in the outer runtime) before running the notebook.\n",
"2. Set structural parameters in cell 1.2 below\n",
"4. Click \"Run\" > \"Run All\" to create the structure\n",
"5. Scroll down to view the resulting structure from multiple angles\n",
"\n",
"## Resulting structure:\n",
"<img src=\"https://i.imgur.com/j9YDJ1X.png\">"
],
"metadata": {
"collapsed": false
},
"id": "f2e1e795020d7b3f"
},
{
"cell_type": "markdown",
"source": [
"## 1. Prepare the Environment\n",
"### 1.1. Install Packages\n",
"The step executes only in Pyodide environment. For other environments, the packages should be installed via `pip install` (see [README](../../README.ipynb))."
],
"metadata": {
"collapsed": false
},
"id": "98aa134f51746218"
},
{
"cell_type": "code",
"source": [
"import sys\n",
"\n",
"if sys.platform == \"emscripten\":\n",
" import micropip\n",
"\n",
" await micropip.install('mat3ra-api-examples', deps=False)\n",
" from utils.jupyterlite import install_packages\n",
"\n",
" await install_packages(\"\")"
],
"metadata": {
"collapsed": false
},
"id": "280f9794a876678b",
"outputs": [],
"execution_count": null
},
{
"metadata": {},
"cell_type": "markdown",
"source": "### 1.2. Set up structure parameters",
"id": "b3d4d3ea7b589f89"
},
{
"metadata": {
"collapsed": false
},
"cell_type": "code",
"source": [
"# Slab parameters\n",
"MILLER_INDICES = (0, 0, 1)\n",
"THICKNESS = 10 # unit cell layers\n",
"VACUUM = 6.0 # Angstrom\n",
"XY_SUPERCELL_MATRIX = [[10, 0], [0, 10]]\n",
"\n",
"# Heart shape parameters in crystal units\n",
"HEART_WIDTH = 0.75 # Width of heart relative to cell\n",
"HEART_HEIGHT = 0.8 # Height of heart relative to cell\n",
"NAME = \"Diamond Heart Y-taper - C\""
],
"id": "5177e239254e3601",
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"### 1.3. Create a condition on coordinates\n"
],
"metadata": {
"collapsed": false
},
"id": "361c291aaf3feb2a"
},
{
"cell_type": "code",
"source": [
"\n",
"\n",
"from typing import List\n",
"from mat3ra.made.tools.utils.coordinate import CoordinateCondition\n",
"\n",
"class YTaperedHeartShapeCondition(CoordinateCondition):\n",
" \"\"\"\n",
" Defines a heart-shaped structure with y-direction tapering applied.\n",
" All dimensions are specified as fractions of the total size (0.0 to 1.0).\n",
" \"\"\"\n",
" width: float = 0.75 # Heart width relative to cell size\n",
" height: float = 0.8 # Heart height relative to cell size\n",
" max_thickness: float = 0.4 # Maximum thickness (y-direction) at the top\n",
"\n",
" def condition(self, coordinate: List[float]) -> bool:\n",
" \"\"\"\n",
" Returns True for positions that should be removed.\n",
" Creates a heart shape with y-direction tapering.\n",
" \"\"\"\n",
" x, y, z = coordinate\n",
"\n",
" # Center and scale coordinates\n",
" x = (x - 0.5) * 2 / self.width\n",
" y = (y - 0.5) * 2 / self.width\n",
" z = (z - 0.5) * 2 / self.height\n",
"\n",
" # Heart shape equation (in xz-plane)\n",
" heart_equation = (x**2 + z**2 - 1)**3 - x**2 * z**3\n",
" in_heart = heart_equation <= 0 # True if within heart shape\n",
"\n",
" # Apply tapering: dynamically reduce thickness in the y-direction\n",
" taper_factor = 1 - max(0, -z * 0.7) # Adjust tapering intensity\n",
" dynamic_thickness = self.max_thickness * taper_factor\n",
"\n",
" in_thickness = abs(y) <= dynamic_thickness # Adjust thickness dynamically\n",
"\n",
" # Return True to remove atoms OUTSIDE the heart shape\n",
" return not (in_heart and in_thickness)\n",
"\n",
"# Create the condition\n",
"condition = YTaperedHeartShapeCondition(\n",
" width=HEART_WIDTH,\n",
" height=HEART_HEIGHT,\n",
" max_thickness=0.4 # Adjustable max thickness\n",
").condition\n"
],
"metadata": {
"collapsed": false
},
"id": "56c8227695643174",
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"### 1.3. Get input materials"
],
"metadata": {
"collapsed": false
},
"id": "91724db55eddad60"
},
{
"cell_type": "code",
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
"materials = get_materials(globals())\n",
"material = materials[0]"
],
"metadata": {
"collapsed": false
},
"id": "ceebf2a5229da67c",
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"### 1.4. Preview the material"
],
"metadata": {
"collapsed": false
},
"id": "13964644436b4156"
},
{
"cell_type": "code",
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"\n",
"visualize(material, repetitions=[1, 1, 1], rotation=\"0x\")\n",
"visualize(material, repetitions=[1, 1, 1], rotation=\"-90x\")"
],
"metadata": {
"collapsed": false
},
"id": "45f0c424ece00186",
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"## 2. Create target material\n",
"### 2.1. Create a slab and apply the cutout condition"
],
"metadata": {
"collapsed": false
},
"id": "615800437b2ef7a"
},
{
"cell_type": "code",
"source": [
"from mat3ra.made.tools.modify import filter_by_condition_on_coordinates, add_vacuum\n",
"from mat3ra.made.tools.build.slab import create_slab, SlabConfiguration\n",
"\n",
"slab_config = SlabConfiguration(\n",
" bulk=material,\n",
" miller_indices=MILLER_INDICES,\n",
" thickness=THICKNESS,\n",
" vacuum=0,\n",
" xy_supercell_matrix=XY_SUPERCELL_MATRIX,\n",
" use_orthogonal_z=True,\n",
" use_conventional_cell=True,\n",
")\n",
"\n",
"slab_unit_cell = create_slab(slab_config)\n",
"resulting_material = filter_by_condition_on_coordinates(slab_unit_cell, condition, invert_selection=True)\n",
"resulting_material = add_vacuum(resulting_material, VACUUM)"
],
"metadata": {
"collapsed": false
},
"id": "422815d29aa347a1",
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"## 3. Visualize the result"
],
"metadata": {
"collapsed": false
},
"id": "57cc38ec0df3c1f7"
},
{
"cell_type": "code",
"source": [
"visualize(resulting_material, repetitions=[1, 1, 1], rotation=\"0x\")\n",
"visualize(resulting_material, repetitions=[1, 1, 1], rotation=\"-90x\")\n",
"visualize(resulting_material, repetitions=[1, 1, 1], rotation=\"-90x,-90y\")"
],
"metadata": {
"collapsed": false
},
"id": "2a9627cd4a261067",
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"# 4. Pass material to the outside runtime"
],
"metadata": {
"collapsed": false
},
"id": "c67e6f5363e80942"
},
{
"cell_type": "code",
"source": [
"from utils.jupyterlite import set_materials\n",
"\n",
"resulting_material.name = NAME\n",
"set_materials(resulting_material)"
],
"metadata": {
"collapsed": false
},
"id": "cbee60d4b936e5cb",
"outputs": [],
"execution_count": null
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.6"
}
},
"nbformat": 4,
"nbformat_minor": 5
}