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   "source": [
    "# Run a Template Job\n",
    "\n",
    "This notebook demonstrates how to run a customizable job using a template.\n",
    "\n",
    "## Imports\n",
    "\n",
    "As in every notebook we make, first import the various packages needed for the rest of the notebook function."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e4618ffa-130c-4982-bc71-9dc4790e3397",
   "metadata": {
    "tags": []
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   "outputs": [],
   "source": [
    "import webmo            # to run the job itself and download the results\n",
    "from webmo.util import xyz_from_name # to get molecular geometries by name\n",
    "from webmo.gui import JupyterGUI #alternative we can use a GUI to specify the job options"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "96682f6c-6bce-462e-98d2-54066e572285",
   "metadata": {},
   "source": [
    "## User Setup\n",
    "\n",
    "Set up the user-supplied information that defines the job."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f4add38f-5515-4d26-832b-b421e7c3f2ef",
   "metadata": {
    "tags": []
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   "source": [
    "## BOOKKEEPING PARAMETERS\n",
    "# the URL of your WebMO instance\n",
    "URL = \"https://server.university.edu/~webmo/cgi-bin/webmo/rest.cgi\"\n",
    "\n",
    "# your username on the above WebMO instance\n",
    "username = \"smith\"\n",
    "\n",
    "## JOB PARAMETERS\n",
    "# name of the molecule to run a job on\n",
    "molecule = \"formaldehyde\"\n",
    "\n",
    "# job type to run\n",
    "job_type = \"Geometry Optimization\"\n",
    "\n",
    "# theory of the theory/basis pair to run the job at\n",
    "theory = \"HF\"\n",
    "\n",
    "# basis of the theory/basis pair to run the job at\n",
    "basis = \"STO-3G\"\n",
    "\n",
    "# charge of the molecule\n",
    "charge = 0\n",
    "\n",
    "# multiplicity of the molecule\n",
    "multiplicity = 1\n",
    "\n",
    "# job title as it will show up in WebMO\n",
    "title = \"formaldehyde\""
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8c9e7bf5-7022-4171-ba32-2cf18b7b0872",
   "metadata": {},
   "source": [
    "## Initializaiton\n",
    "\n",
    "Open a REST session."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5a749ebb-b5d4-4065-bd98-033c862415e6",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "rest = webmo.WebMOREST(URL, username=username)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5aa8f4ab-c13d-4273-87a0-4c298f50c9f1",
   "metadata": {},
   "source": [
    "## Geometry\n",
    "\n",
    "Grab the 3D geometry from PubChem."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "170ea260-3711-4390-93f7-5239cdd5ed39",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "geom = xyz_from_name(molecule)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "099507cd-76b4-44fa-a3d4-b541b50b6867",
   "metadata": {
    "tags": []
   },
   "source": [
    "## Template\n",
    "\n",
    "Using the geometry (in `geom`), fill in a string template for the job. Alternatively, a GUI can be used to specify job options interactively!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "84d0d0c4-961b-448f-9466-a10715ce326c",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "templates = rest.get_templates('gaussian')\n",
    "template = templates[job_type]\n",
    "\n",
    "template_variables = {\n",
    "    'jobName' : title,\n",
    "    'geometry' : geom,\n",
    "    'theory' : theory,\n",
    "    'basisSet' : basis\n",
    "}\n",
    "\n",
    "#alternatively a Jupyter-based GUI can be used to query for the job options interactively\n",
    "#gui = JupyterGUI(template, query_vars=['jobName', 'theory', 'basisSet'], additional_vars={'geometry':geom})\n",
    "#gui.display()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "822cd1a3-a326-46bd-985e-93550f9ff390",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "#...if GUI was used\n",
    "#template_variables = gui.get_variables()\n",
    "\n",
    "input_file_contents = rest.generate_input(template, variables=template_variables)\n",
    "print(\"The job that will be submitted:\")\n",
    "print(input_file_contents)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1e627a47-4250-4c6c-b503-81dee83623e0",
   "metadata": {},
   "source": [
    "## Job Submission\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "463b2b04-3f1b-422c-ab33-89b3e0d4542c",
   "metadata": {},
   "source": [
    "Submit the job through that REST session and wait for it to complete."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c8097303-ab66-4325-a091-782cbd0a06cf",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "n = rest.submit_job(title, input_file_contents, \"gaussian\")\n",
    "rest.wait_for_job(n)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "386be75a-70be-4f19-85c6-fb96efae3fc4",
   "metadata": {},
   "source": [
    "After the job is finished, get some of its output."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "0a47a3fe-7c40-4c6b-9bce-93e172639e54",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "print(rest.get_job_output(n)[:400])"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f7446dd9-739c-4049-95f7-3b6080a8a2f3",
   "metadata": {},
   "source": [
    "We can also get numeric results through the WebMO library, such as the energy."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "89c96c8c-6dee-42d3-b685-49e6d709f5fc",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "results = rest.get_job_results(n)\n",
    "energy = results['properties']['rhf_energy']['value']\n",
    "units = results['properties']['rhf_energy']['units']\n",
    "print(\"Energy: {} {}\".format(energy, units))"
   ]
  }
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