Prototype: Bandgap Workflow NB #231
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There was a problem hiding this comment. Line #1. from mat3ra.wode.analyzers.electronic import KPointAnalyzer, CutoffAnalyzer, SmearingAnalyzer, BandsAnalyzer These are called context providers at current, not analyzers, but the concept is similar Reply via ReviewNB |
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| "cells": [ | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "# Bandgap Workflow Example\n", | ||
| " This notebook demonstrates how to build and run a bandgap workflow for a material.\n", | ||
| "\n", | ||
| "## Process Overview\n", | ||
| "### 1. Set up the environment and parameters.\n", | ||
| "### 1. Log in to get the API token\n", | ||
| "### 1. Load the target material.\n", | ||
| "### 1. Import workflow builder and related analyzers.\n", | ||
| "### 1. Analyze material to get parameters for the workflow configuration.\n", | ||
| "### 1. Create the workflow configuration.\n", | ||
| "### 1. Create a job with material and workflow configuration.\n", | ||
| "### 1. Submit the job to the server.\n", | ||
| "### 1. Monitor the job status and retrieve results." | ||
| ], | ||
| "id": "ed24b225263ae3c3" | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "markdown", | ||
| "source": "## 1. Set up the environment and parameters", | ||
| "id": "598da5f8c4f507ec" | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "markdown", | ||
| "source": "## 2. Log in to get the API token", | ||
| "id": "51105b005c535ca" | ||
| }, | ||
| { | ||
| "metadata": { | ||
| "ExecuteTime": { | ||
| "end_time": "2025-06-30T17:49:35.443494Z", | ||
| "start_time": "2025-06-30T17:49:35.381267Z" | ||
| } | ||
| }, | ||
| "cell_type": "code", | ||
| "source": [ | ||
| "from mat3ra.api import ApiClient\n", | ||
| "# Log in to get the API token\n", | ||
| "auth_config = await ApiClient().login()" | ||
| ], | ||
| "id": "23626cb27f6e7206", | ||
| "outputs": [ | ||
| { | ||
| "ename": "ModuleNotFoundError", | ||
| "evalue": "No module named 'mat3ra.api'", | ||
| "output_type": "error", | ||
| "traceback": [ | ||
| "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m", | ||
| "\u001B[0;31mModuleNotFoundError\u001B[0m Traceback (most recent call last)", | ||
| "Cell \u001B[0;32mIn[2], line 1\u001B[0m\n\u001B[0;32m----> 1\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m\u001B[38;5;250m \u001B[39m\u001B[38;5;21;01mmat3ra\u001B[39;00m\u001B[38;5;21;01m.\u001B[39;00m\u001B[38;5;21;01mapi\u001B[39;00m\u001B[38;5;250m \u001B[39m\u001B[38;5;28;01mimport\u001B[39;00m ApiClient\n\u001B[1;32m 2\u001B[0m \u001B[38;5;66;03m# Log in to get the API token\u001B[39;00m\n\u001B[1;32m 3\u001B[0m auth_config \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;01mawait\u001B[39;00m ApiClient()\u001B[38;5;241m.\u001B[39mlogin()\n", | ||
| "\u001B[0;31mModuleNotFoundError\u001B[0m: No module named 'mat3ra.api'" | ||
| ] | ||
| } | ||
| ], | ||
| "execution_count": 2 | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "markdown", | ||
| "source": "## 3. Load the target material", | ||
| "id": "ba816c64f28f6a3d" | ||
| }, | ||
| { | ||
| "metadata": { | ||
| "collapsed": true | ||
| }, | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "execution_count": null, | ||
| "source": [ | ||
| "from utils.visualize import visualize_materials as visualize\n", | ||
| "from utils.jupyterlite import load_material_from_folder\n", | ||
| "\n", | ||
| "material = load_material_from_folder(\"/uploads\", \"MoS2_twisted_interface_60_degrees.json\")\n", | ||
| "visualize(material)" | ||
| ], | ||
| "id": "initial_id" | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "markdown", | ||
| "source": "## 4. Import workflow builder and related analyzers", | ||
| "id": "f8d7e25a7c9cc2e" | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "execution_count": null, | ||
| "source": [ | ||
| "from mat3ra.wode.analyzers.electronic import KPointAnalyzer, CutoffAnalyzer, SmearingAnalyzer, BandsAnalyzer\n", | ||
| "\n", | ||
| "kpoint_analyzer = KPointAnalyzer(material=material)\n", | ||
| "cutoff_analyzer = CutoffAnalyzer(material=material)\n", | ||
| "smearing_analyzer = SmearingAnalyzer(material=material)\n", | ||
| "bands_analyzer = BandsAnalyzer(material=material)\n", | ||
| "\n", | ||
| "kpoints = kpoint_analyzer.get_kpoints()\n", | ||
| "cutoff = cutoff_analyzer.get_cutoff()\n", | ||
| "smearing = smearing_analyzer.get_smearing()\n", | ||
| "number_of_bands = bands_analyzer.get_number_of_bands()\n", | ||
| "\n" | ||
| ], | ||
| "id": "5ead702c417eff62" | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "markdown", | ||
| "source": "## 5. Get workflow and adjust its parameters", | ||
| "id": "9bdd00f870caaeeb" | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "execution_count": null, | ||
| "source": [ | ||
| "from mat3ra.wode.workflow.vasp.band_structure import BandStructureWorkflow\n", | ||
| "from mat3ra.wode.pseudopotentials import PseudopotentialEnum\n", | ||
| "\n", | ||
| "workflow = BandStructureWorkflow()\n", | ||
| "workflow.set_kpoints(kpoints)\n", | ||
| "workflow.set_pseudopotential(PseudopotentialEnum.PAW_HSE) # elements will be set automatically based on the material" | ||
| ], | ||
| "id": "68d43f6c797f2fc4" | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "markdown", | ||
| "source": "## 6. Create the job configuration", | ||
| "id": "1f15e054ddb9a08c" | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "execution_count": null, | ||
| "source": [ | ||
| "from mat3ra.wode.compute import ComputeConfiguration, QueueEnum\n", | ||
| "compute_config = ComputeConfiguration(\n", | ||
| " queue = QueueEnum.OR8,\n", | ||
| " nodes = 1,\n", | ||
| " cores = 8,\n", | ||
| ")" | ||
| ], | ||
| "id": "60e880dc581dafe1" | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "markdown", | ||
| "source": "## 7. Submit the job and monitor the status", | ||
| "id": "8d5740e099512107" | ||
| }, | ||
| { | ||
| "metadata": {}, | ||
| "cell_type": "code", | ||
| "outputs": [], | ||
| "execution_count": null, | ||
| "source": [ | ||
| "from mat3ra.wode.job import create_job\n", | ||
| "job = create_job(workflow=workflow, material=material, compute = compute_config, auth_config=auth_config)\n", | ||
| "job.run()\n", | ||
| "job.wait_for_complete()\n", | ||
| "# job.check_status()\n", | ||
| "# job.get_current_output()\n", | ||
| "# AFTER Finished\n", | ||
| "job.get_results(PropertyEnum.BANDGAP)" | ||
| ], | ||
| "id": "53c8a2cd99e5c26d" | ||
| } | ||
| ], | ||
| "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 | ||
| } | ||
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We may want to import compute from
mat3ra.ideand create amat3ra.jodefor job designReply via ReviewNB