Feature/SOF-7759 Jode Mock NB

other/materials_designer/specific_examples/run_bandgap_workflow.ipynb

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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",
+    "### 2. Log in to get the API token\n",
+    "### 3. Load the target material.\n",
+    "### 4. Import workflow builder and related analyzers.\n",
+    "### 5. Analyze material to get parameters for the workflow configuration.\n",
+    "### 6. Create the workflow configuration.\n",
+    "### 7. Create a job with material and workflow configuration.\n",
+    "### 8. Submit the job to the server.\n",
+    "### 9. Monitor the job status and retrieve results.\n",
+    "### 10. Display the 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": {},
+   "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": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## 3. Load the target material",
+   "id": "ba816c64f28f6a3d"
+  },
+  {
+   "metadata": {
+    "collapsed": true
+   },
+   "cell_type": "code",
+   "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",
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## 4. Import workflow builder and related analyzers",
+   "id": "f8d7e25a7c9cc2e"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
+    "from mat3ra.wode.context_providers import (\n",
+    "    PointsGridFormDataProvider,  # exists - for k-points\n",
+    "    PlanewaveCutoffsContextProvider,  # exists - for cutoffs\n",
+    "    SmearingContextProvider, # no JS implementation yet\n",
+    "    BandsContextProvider # no JS implementation yet\n",
+    ")\n",
+    "\n",
+    "\n",
+    "kgrid_provider = PointsGridFormDataProvider(material=material)\n",
+    "cutoffs_provider = PlanewaveCutoffsContextProvider(material=material)\n",
+    "smearing_provider = SmearingContextProvider(material=material)\n",
+    "bands_provider = BandsContextProvider(material=material)\n",
+    "\n",
+    "kpoints = kgrid_provider.get_dimensions()  # or calculate_dimensions()\n",
+    "cutoff = cutoffs_provider.get_cutoff()  # defaultECUTWFC, defaultECUTRHO\n",
+    "smearing = smearing_provider.get_smearing()\n",
+    "number_of_bands = bands_provider.get_number_of_bands()"
+   ],
+   "id": "5ead702c417eff62",
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## 5. Create workflow and set its parameters",
+   "id": "9bdd00f870caaeeb"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
+    "from mat3ra.standata.workflows import Workflows\n",
+    "from mat3ra.wode.workflows import Workflow\n",
+    "from mat3ra.wode.pseudopotentials import PseudopotentialEnum\n",
+    "\n",
+    "workflow_config = Workflows.get_by_name_first_match(\"band_structure\")\n",
+    "workflow = Workflow.create(workflow_config)\n",
+    "workflow.set_kpoints(kpoints)\n",
+    "workflow.set_pseudopotential(PseudopotentialEnum.PAW_HSE) # elements will be set automatically based on the material"
+   ],
+   "id": "68d43f6c797f2fc4",
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## 6. Create the compute configuration",
+   "id": "1f15e054ddb9a08c"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
+    "from mat3ra.ide.compute import ComputeConfiguration, QueueEnum\n",
+    "compute_config = ComputeConfiguration(\n",
+    "    queue = QueueEnum.OR8,\n",
+    "    nodes = 1,\n",
+    "    cores = 8,\n",
+    ")"
+   ],
+   "id": "60e880dc581dafe1",
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## 7. Create the job with material and workflow configuration",
+   "id": "cbc16438ad5b0ce0"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "from mat3ra.jode.job import create_job\n",
+    "job = create_job(workflow=workflow, material=material, compute = compute_config, auth_config=auth_config)"
+   ],
+   "id": "20b3bf702b6e084c"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## 8. Submit the job and monitor the status",
+   "id": "8d5740e099512107"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "from mat3ra.prode import PropertyEnum\n",
+    "job.run()\n",
+    "job.wait_for_complete()\n",
+    "# job.check_status()\n",
+    "# job.get_current_output()"
+   ],
+   "id": "df29a9065e8b5eae"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## 9. Retrieve results",
+   "id": "349d46228a98bcd9"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "# AFTER Finished\n",
+    "# A class from Prode to handle results\n",
+    "results = job.get_results(PropertyEnum.BAND_GAP, PropertyEnum.BAND_STRUCTURE)"
+   ],
+   "id": "ce79fc805900503a"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## 10. Display results",
+   "id": "6f864b5134b53eac"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "# Visual library that can visualize any property defined in Prode\n",
+    "from mat3ra.prove import visualize_property\n",
+    "visualize_property(results.band_structure)\n",
+    "print(results.band_gap)"
+   ],
+   "id": "978bb38b10c15976"
+  }
+ ],
+ "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
+}