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VsevolodXVsevolodX
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Merge pull request #199 from Exabyte-io/update/SOF-7544
update/SOF-7544 various cleanups for tutorials
2 parents 11ed434 + 315238a commit 3f6fb9c

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‎config.yml‎

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- pandas==1.5.3
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- ase==3.22.1
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- ipywidgets
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- plotly==5.18
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- plotly>=5.18
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- nbformat>=4.2.0
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packages_python:
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- pymatgen==2024.4.13
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packages_pyodide:
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notebooks:
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- name: create_interface_with_min_strain_zsl.ipynb
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packages_common:
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- plotly==5.18
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- plotly>=5.18
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- nbformat>=4.2.0
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packages_python:
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packages_pyodide:

‎other/materials_designer/Introduction.ipynb‎

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"\n",
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"This notebook demonstrates a workflow for converting materials data from the [JARVIS](https://jarvis.nist.gov/) database into ESSE format for use with the Mat3ra.com platform.\n",
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"\n",
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"#### [6.1.4. Optimize film position on interface](optimize_film_position.ipynb).\n",
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"## 6.2. Optimize.\n",
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"\n",
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"#### [6.2.1. Optimize film position on interface](optimize_film_position.ipynb).\n",
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"\n",
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"## 6.3. Development.\n",
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"\n",
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"#### [6.3.1. Custom Transformation](custom_transformation.ipynb). Notebook setup for development of custom transformations on materials.\n",
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"\n",
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"## 7. Read more\n",
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"\n",
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"source": [],
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"metadata": {
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"collapsed": false
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}
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},
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"execution_count": null
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}
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],
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"metadata": {

‎other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb‎

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"cell_type": "code",
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"outputs": [],
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"source": [
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"MATERIAL_INDEX = 0 # Index of the material in the list of materials\n",
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"# Maximum force tolerance for the relaxation to stop, in eV/Å\n",
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"FMAX = 0.05"
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],
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"from utils.jupyterlite import get_materials\n",
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"\n",
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"materials = get_materials(globals())\n",
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"interface = materials[0]"
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"interface = materials[MATERIAL_INDEX]"
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]
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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.plot import create_realtime_plot, plot_update_callback\n",
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"from mat3ra.utils.jupyterlite.plot import create_realtime_plot, create_update_callback\n",
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"from mat3ra.made.tools.convert import from_ase\n",
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"from mat3ra.made.material import Material\n",
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"\n",
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"# Add calculator to the interface for relaxation\n",
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"ase_interface = to_ase(interface)\n",
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"ase_interface.set_calculator(calculator)\n",
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"ase_interface.calc = calculator\n",
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"\n",
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"dyn = optimizer(ase_interface)\n",
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"\n",
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"\n",
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"# Create the real-time plot\n",
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"fig = create_realtime_plot(\n",
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" title=\"Optimization Progress\",\n",
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" x_label=\"Step\",\n",
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" y_label=\"Energy (eV)\"\n",
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")\n",
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"\n",
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"steps = []\n",
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"energies = []\n",
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"\n",
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"fig = create_realtime_plot()\n",
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"\n",
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"# Run the relaxation\n",
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"dyn.attach(plot_update_callback(dyn, ase_interface, fig, steps, energies), interval=1)\n",
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"dyn.attach(\n",
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" create_update_callback(\n",
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" dynamic_object=dyn,\n",
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" value_getter= ase_interface.get_potential_energy,\n",
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" figure=fig,\n",
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" steps=steps,\n",
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" values=energies\n",
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" ),\n",
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" interval=1\n",
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")\n",
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"dyn.run(fmax=OPTIMIZATION_PARAMETERS[\"FMAX\"])\n",
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"\n",
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"ase_final_interface = ase_interface\n",

‎other/materials_designer/create_terrace_defect.ipynb‎

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"## 1. Prepare the Environment\n",
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"### 1.1. Set up the notebook\n",
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"The cut direction, pivot coordinate, and number of added layers define the terrace defect, shown in the image below.\n",
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"<img src=\"https://i.imgur.com/XA2F55Q.png\" alt=\"Terrace parameters visualized\" width=\"400\"/>"
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"\n",
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"<img src=\"https://github.com/Exabyte-io/documentation/raw/88451ce38b0f57f804dcb5010a1a95bb9b9e50bc/images/notebooks/terrace_settings.webp\" alt=\"Terrace parameters visualized\" width=\"400\"/>"
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],
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"metadata": {
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"collapsed": false

‎other/materials_designer/custom_transformation.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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"# Development Notebook\n",
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"\n",
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"This notebook enables loading materials and performing custom transformations with Python. The transformed materials can then be passed to the Materials Designer or saved to a folder. Necessary packages are installed and imported below.\n",
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"## 1. Setup Notebook\n",
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"### 1.1 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": "36708f17f40b64cb"
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "initial_id",
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"# Install packages for JupyterLite\n",
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"from mat3ra.utils.jupyterlite.packages import install_packages\n",
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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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" # Import the mat3ra api-examples package to allow for relative imports\n",
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" await micropip.install('mat3ra-api-examples', deps=False)\n",
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"\n",
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"await install_packages(\"\")"
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]
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 1.2 Import necessary 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": "8185aca94726dc8f"
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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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"# Material class to hold structural data\n",
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"from mat3ra.made.material import Material\n",
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"# Materials class with JSONs of selected materials\n",
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"from mat3ra.standata.materials import 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": "b2fa69b96b195d30"
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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. Load 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": "c783d38d94a627e4"
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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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"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": "54e68de6c6cc3e03"
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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. Transform 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": "6ca73dec2609be4a"
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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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"new_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": "91069f5712a65dbb"
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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. Save transformed 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": "296f89e8dde270ed"
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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, download_content_to_file\n",
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"\n",
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"set_materials(new_materials)\n",
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"# for idx, material in enumerate(new_materials):\n",
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"# download_content_to_file(new_materials, f\"new_material_{idx}.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": "7973f7ee67bdc42a"
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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/mat3ra.ipynb‎

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‎other/materials_designer/optimize_film_position.ipynb‎

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"metadata": {
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"collapsed": false
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},
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"id": "3d982a1ca641f0d8"
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"id": "3d982a1ca641f0d8",
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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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"metadata": {
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"collapsed": false
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},
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"id": "5f4afdb7ac0c865b"
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"id": "5f4afdb7ac0c865b",
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"execution_count": null
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{
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"cell_type": "markdown",
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"from mat3ra.made.tools.modify import interface_displace_part\n",
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"from mat3ra.made.tools.calculate.calculators import InterfaceMaterialCalculator\n",
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"from mat3ra.made.tools.optimize import evaluate_calculator_on_xy_grid\n",
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"\n",
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"calculator = InterfaceMaterialCalculator()\n",
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"\n",
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"# Calculate energy landscape\n",
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"metadata": {
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"collapsed": false
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},
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"id": "eb0b6e59c24dda4"
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"id": "eb0b6e59c24dda4",
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"execution_count": null
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},
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"cell_type": "markdown",
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from utils.plot import plot_energy_heatmap, plot_energy_landscape\n",
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"from mat3ra.utils.jupyterlite.plot import plot_2d_heatmap, plot_3d_surface\n",
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"\n",
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"# Plot energy landscape\n",
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"plot_energy_heatmap(xy_matrix, energy_matrix, optimal_position=optimal_displacement[:2])\n",
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"x_values, y_values = xy_matrix\n",
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"plot_2d_heatmap(x_values, y_values, energy_matrix, optimal_displacement[:2])\n",
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"\n",
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"if SHOW_3D_LANDSCAPE:\n",
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" plot_energy_landscape(xy_matrix, energy_matrix, optimal_position=optimal_displacement[:2])\n",
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" plot_3d_surface(x_values, y_values, energy_matrix, optimal_displacement[:2])\n",
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"\n",
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"# Create optimized material\n",
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"optimized_material = interface_displace_part(\n",

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