Feature/SOF-7759 Jode Mock NB

other/materials_designer/workflows/run_bandgap_workflow_max.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# Bandgap Workflow Example\n",
+    " This notebook demonstrates how to build and run a bandgap workflow for a material.\n",
+    " Example of building and running a bandgap workflow for twisted MoS2 interface from specific_examples.\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."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
+   "source": [
+    "## 1. Set up the environment and parameters"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2",
+   "metadata": {},
+   "source": [
+    "## 2. Log in to get the API token"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mat3ra.api import ApiClient\n",
+    "\n",
+    "# Log in to get the API token\n",
+    "auth_config = await ApiClient().login()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4",
+   "metadata": {},
+   "source": [
+    "## 3. Load the target material"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5",
+   "metadata": {},
+   "outputs": [],
+   "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)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6",
+   "metadata": {},
+   "source": [
+    "## 5. Create workflow and set its parameters\n",
+    "### 5.1. Get list of applications and select one"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mat3ra.standata.applications import Applications\n",
+    "\n",
+    "# Get Applications list (with versions, build)\n",
+    "apps_list = Applications.list_all()\n",
+    "# returns apps_list[0] = [{\"name\" : \"espresso\", \"version\": \"7.2\", \"build\": \"GNU\"}]\n",
+    "\n",
+    "app = Applications.get_by_name_first_match(\"espresso\")\n",
+    "# returns name, version, build config"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8",
+   "metadata": {},
+   "source": [
+    "### 5.2. Create workflow from standard workflows and preview it"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mat3ra.standata.workflows import Workflows\n",
+    "from mat3ra.wode.workflows import Workflow\n",
+    "from utils.visualize import visualize_workflow\n",
+    "\n",
+    "# Search WF by name and application\n",
+    "workflow_config = Workflows.filter_by_application(app).get_by_name_first_match(\"band_gap\")\n",
+    "workflow = Workflow.create(workflow_config)\n",
+    "\n",
+    "# View workflow to understand its structure\n",
+    "visualize_workflow(workflow)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "10",
+   "metadata": {},
+   "source": [
+    "### 5.3. Add relaxation subworkflow"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "11",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "workflow.add_relaxation()\n",
+    "visualize_workflow(workflow)\n",
+    "# Relaxation subworkflow is added as the first subworkflow"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "12",
+   "metadata": {},
+   "source": [
+    "### 5.4. Change subworkflow details (Model subtype)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "13",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mat3ra.standata.model_tree import ModelTreeStandata\n",
+    "\n",
+    "swf_0 = workflow.subworkflows[0]  # relaxation subworkflow\n",
+    "swf_1 = workflow.subworkflows[1]  # band structure subworkflow\n",
+    "\n",
+    "# Change model subtype for relaxation subworkflow\n",
+    "# For preview:\n",
+    "subtypes = ModelTreeStandata.get_subtypes_by_model_type(\"dft\")  # [\"gga\", \"lda\"] as enum\n",
+    "functionals = ModelTreeStandata.get_functionals_by_subtype(\"dft\", \"lda\")  # [\"pz\", ...] as enum\n",
+    "\n",
+    "model = ModelTreeStandata.get_model_by_parameters(\n",
+    "    model_type=\"dft\",\n",
+    "    subtype=subtypes.LDA,\n",
+    "    functional=functionals.PZ,\n",
+    ")\n",
+    "swf_0.model = model\n",
+    "swf_1.model = model"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "14",
+   "metadata": {},
+   "source": [
+    "### 5.5. Modify workflow units found in preview"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "15",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mat3ra.wode.context_providers import PointsGridFormDataProvider\n",
+    "\n",
+    "# Values from publication\n",
+    "kgrid_scf = [6, 6, 1]\n",
+    "kgrid_nscf = [12, 12, 1]\n",
+    "kgrid_relax = kgrid_scf\n",
+    "\n",
+    "kgrid_context_provider = PointsGridFormDataProvider(material=material)\n",
+    "\n",
+    "new_context_relax = kgrid_context_provider.get_data(dimensions=kgrid_relax)\n",
+    "new_context_scf = kgrid_context_provider.get_data(dimensions=kgrid_scf)\n",
+    "new_context_nscf = kgrid_context_provider.get_data(dimensions=kgrid_nscf)\n",
+    "\n",
+    "# Get workflow's specific unit that needs to be modified\n",
+    "# Option 1: search is done by unit name regex across the entire workflow\n",
+    "unit_to_modify_relax = workflow.get_unit_by_name(name_regex=\"relax\")\n",
+    "unit_to_modify_relax.context.add_context(new_context_relax)\n",
+    "\n",
+    "# Option 2: search is done by unit name within a specific subworkflow\n",
+    "unit_to_modify_scf = workflow.subworkflows[1].get_unit_by_name(name=\"pw_scf\")\n",
+    "unit_to_modify_scf.context.add_context(new_context_scf)\n",
+    "unit_to_modify_nscf = workflow.subworkflows[1].get_unit_by_name(name=\"pw_nscf\")\n",
+    "unit_to_modify_nscf.context.add_context(new_context_nscf)\n",
+    "\n",
+    "# Set the modified unit back to the workflow\n",
+    "# Option 1: direct set by unit object, replacing the existing one\n",
+    "workflow.set_unit(unit_to_modify_relax)\n",
+    "\n",
+    "# Option 2: set by unit flowchart id and new unit object\n",
+    "workflow.set_unit(unit_flowchart_id=unit_to_modify_scf.flowchart_id, new_unit=unit_to_modify_scf)\n",
+    "workflow.set_unit(unit_flowchart_id=unit_to_modify_nscf.flowchart_id, new_unit=unit_to_modify_nscf)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "16",
+   "metadata": {},
+   "source": [
+    "## 6. Create the compute configuration\n",
+    "### 6.1. View available clusters and providers"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "17",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# List available compute providers and clusters\n",
+    "from mat3ra.ide.compute import ComputeProvider, ComputeCluster\n",
+    "\n",
+    "providers = ComputeProvider.list_all()\n",
+    "clusters = ComputeCluster.list_all()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "18",
+   "metadata": {},
+   "source": [
+    "### 6.2. Create compute configuration"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "19",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mat3ra.ide.compute import ComputeConfiguration, QueueTypesEnum\n",
+    "\n",
+    "compute_config = ComputeConfiguration(\n",
+    "    queue=QueueTypesEnum.OR8,\n",
+    "    nodes=1,\n",
+    "    ppn=8,\n",
+    "    cluster=clusters[0],  # select first available cluster\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "20",
+   "metadata": {},
+   "source": [
+    "## 7. Create the job with material and workflow configuration"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "21",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mat3ra.jode.job import create_job\n",
+    "\n",
+    "job = create_job(\n",
+    "    workflow=workflow,\n",
+    "    material=material,\n",
+    "    compute=compute_config,\n",
+    "    auth_config=auth_config\n",
+    ")\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "22",
+   "metadata": {},
+   "source": [
+    "## 8. Submit the job and monitor the status"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "23",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mat3ra.prode import PropertyEnum\n",
+    "\n",
+    "job.run()\n",
+    "job.wait_for_complete()\n",
+    "# job.check_status()\n",
+    "# job.get_current_output()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "24",
+   "metadata": {},
+   "source": [
+    "## 9. Retrieve results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "25",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# AFTER Finished\n",
+    "# A class from Prode to handle results\n",
+    "results = job.get_results(PropertyEnum.BAND_GAP, PropertyEnum.BAND_STRUCTURE)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "26",
+   "metadata": {},
+   "source": [
+    "## 10. Display results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "27",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Visual library that can visualize any property defined in Prode\n",
+    "from mat3ra.prove import visualize_property\n",
+    "\n",
+    "visualize_property(results.band_structure)\n",
+    "print(results.band_gap)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "28",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
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+   "file_extension": ".py",
+   "mimetype": "text/x-python",
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+}