{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "7362d9ac-c021-4ca6-8d31-b365ad8e5722",
   "metadata": {},
   "source": [
    "## Initial Imports \n",
    "Import PLAMS components and set up to run jobs in tandem."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "f374ae87-bf97-4f0c-b089-0c5d6b12210a",
   "metadata": {},
   "outputs": [],
   "source": [
    "from scm.plams import Settings, AMSJob, Molecule, Atom, FCFJob, config, JobRunner, init\n",
    "from scm.plams.recipes.fcf_dos import FCFDOS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "7f720674-0fbf-4133-afda-190f4ff4c4e5",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "PLAMS working folder: /path/plams/examples/ADFVibronicDOS/plams_workdir\n"
     ]
    }
   ],
   "source": [
    "config.default_jobrunner.parallel = JobRunner(parallel=True, maxjobs=2)\n",
    "\n",
    "# this line is not required in AMS2025+\n",
    "init()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cc8ff96a-5a22-45f5-806d-c6523a8e17e8",
   "metadata": {},
   "source": [
    "## Setup Molecules\n",
    "Create the NO2 molecules using pre-optimized geometries (usually the geometry optimization step would come first)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "e1b8fb64-c210-4691-9dd0-604e3ce921b3",
   "metadata": {},
   "outputs": [],
   "source": [
    "no2_radical = Molecule()\n",
    "no2_radical.add_atom(Atom(atnum=7, coords=(0.0, 0.0, -0.01857566)))\n",
    "no2_radical.add_atom(Atom(atnum=8, coords=(0.0, 1.09915770, -0.49171967)))\n",
    "no2_radical.add_atom(Atom(atnum=8, coords=(0.0, -1.09915770, -0.49171967)))\n",
    "\n",
    "no2_anion = Molecule()\n",
    "no2_anion.add_atom(Atom(atnum=7, coords=(0.0, 0.0, 0.12041)))\n",
    "no2_anion.add_atom(Atom(atnum=8, coords=(0.0, 1.070642, -0.555172)))\n",
    "no2_anion.add_atom(Atom(atnum=8, coords=(0.0, -1.070642, -0.555172)))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a424725a-1beb-4eb1-b3c0-0aeac432b9e1",
   "metadata": {},
   "source": [
    "## Calculate Vibrational Frequencies\n",
    "Create the settings objects for the ADF donor/acceptor vibrational frequencies calculations. Run the calculations in parallel."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "0711fd28-a8f7-4f53-86c3-e7aa27fc7b1e",
   "metadata": {},
   "outputs": [],
   "source": [
    "settings_freq = Settings()\n",
    "settings_freq.input.adf.symmetry = \"NoSym\"\n",
    "settings_freq.input.adf.basis.type = \"DZP\"\n",
    "settings_freq.input.adf.basis.core = \"None\"\n",
    "settings_freq.input.adf.xc.lda = \"SCF VWN\"\n",
    "settings_freq.input.ams.Task = \"SinglePoint\"\n",
    "settings_freq.input.ams.Properties.NormalModes = \"Yes\"\n",
    "settings_freq.input.adf.title = \"Vibrational frequencies\"\n",
    "\n",
    "settings_freq_radical = settings_freq.copy()\n",
    "settings_freq_radical.input.ams.system.charge = 0\n",
    "settings_freq_radical.input.adf.spinpolarization = 1\n",
    "settings_freq_radical.input.adf.unrestricted = \"Yes\"\n",
    "\n",
    "settings_freq_anion = settings_freq.copy()\n",
    "settings_freq_anion.input.ams.system.charge = -1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "c6e7e4db-8a1e-44d6-aab2-78239865ba22",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[10.02|14:22:57] JOB fsradical STARTED\n",
      "[10.02|14:22:57] JOB fsradical RUNNING\n",
      "[10.02|14:23:08] JOB fsradical FINISHED\n",
      "[10.02|14:23:08] JOB fsradical SUCCESSFUL\n",
      "[10.02|14:23:08] JOB fsanion STARTED\n",
      "[10.02|14:23:08] JOB fsanion RUNNING\n",
      "[10.02|14:23:17] JOB fsanion FINISHED\n",
      "[10.02|14:23:17] JOB fsanion SUCCESSFUL\n"
     ]
    }
   ],
   "source": [
    "freq_job_radical = AMSJob(molecule=no2_radical, settings=settings_freq_radical, name=\"fsradical\")\n",
    "freq_job_anion = AMSJob(molecule=no2_anion, settings=settings_freq_anion, name=\"fsanion\")\n",
    "\n",
    "freq_results = (freq_job_radical.run(), freq_job_anion.run())"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ddfbeb12-765d-4dda-b387-2e433b952b06",
   "metadata": {},
   "source": [
    "## Calculate Vibronic Spectra\n",
    "Use Frank-Condon jobs to calculate the vibronic spectra."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "16d4ea89-77f2-48b4-b6bc-dd1e81e01737",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[10.02|14:23:17] JOB fcfabs STARTED\n",
      "[10.02|14:23:17] JOB fcfabs RUNNING\n",
      "[10.02|14:23:19] JOB fcfabs FINISHED\n",
      "[10.02|14:23:19] JOB fcfabs SUCCESSFUL\n",
      "[10.02|14:23:19] JOB fcfemi STARTED\n",
      "[10.02|14:23:19] JOB fcfemi RUNNING\n",
      "[10.02|14:23:20] JOB fcfemi FINISHED\n",
      "[10.02|14:23:20] JOB fcfemi SUCCESSFUL\n"
     ]
    }
   ],
   "source": [
    "def fcf_job(state1, state2, spctype, name):\n",
    "    settings_fcf = Settings()\n",
    "    settings_fcf.input.spectrum.type = spctype\n",
    "    settings_fcf.input.state1 = state1\n",
    "    settings_fcf.input.state2 = state2\n",
    "    return FCFJob(inputjob1=state1, inputjob2=state2, settings=settings_fcf, name=name)\n",
    "\n",
    "\n",
    "freq_radical = freq_results[0].rkfpath(file=\"adf\")\n",
    "freq_anion = freq_results[1].rkfpath(file=\"adf\")\n",
    "\n",
    "fc_abs = fcf_job(freq_radical, freq_anion, \"absorption\", \"fcfabs\")\n",
    "fc_emi = fcf_job(freq_anion, freq_radical, \"emission\", \"fcfemi\")\n",
    "\n",
    "fc_results = (fc_abs.run(), fc_emi.run())"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c65d3b27-7f98-44af-a608-768b7cce82e1",
   "metadata": {},
   "source": [
    "## Calculate Density of States\n",
    "\n",
    "Calculate the DOS by computing the overlap of the absorption and emission FCF spectra."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "891fd21a-ddae-4b3a-b4f5-8404aad29d3a",
   "metadata": {},
   "outputs": [],
   "source": [
    "job = FCFDOS(fc_results[0].kfpath(), fc_results[1].kfpath(), 10000.0, 10000.0)\n",
    "dos = job.dos()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "340ab36d-ff8b-4b04-bd55-f780f9ca581e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The density of states is 1.30090295e-08\n"
     ]
    }
   ],
   "source": [
    "print(f\"The density of states is {dos:.8e}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a9b68f1a-684e-4401-b14a-f85bd23e83d4",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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