{
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  {
   "cell_type": "markdown",
   "id": "a92f9abe-116b-4afb-b2e7-53dc45ba488c",
   "metadata": {},
   "source": [
    "## Initial Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "ea87db27-0f82-41c7-8e7f-5dfe9fef669b",
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "from scm.plams import AMSJob, Settings, from_smiles"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e5e7849e-730d-46ff-8536-f5cb19eb3174",
   "metadata": {},
   "source": [
    "## Run/Load Job with ForceField Information"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a6b5a174-741b-4366-96cf-739bc90cfbab",
   "metadata": {},
   "source": [
    "First run a reference calculation where charges are guessed (using DFTB by default):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "2d3fb20f-31f1-4317-96ff-fe8e05d25963",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[25.03|09:47:58] JOB plamsjob STARTED\n",
      "[25.03|09:47:58] JOB plamsjob RUNNING\n",
      "[25.03|09:47:59] JOB plamsjob FINISHED\n",
      "[25.03|09:47:59] JOB plamsjob SUCCESSFUL\n"
     ]
    }
   ],
   "source": [
    "ref_job = AMSJob.from_input(\n",
    "    \"\"\"\n",
    "Task GeometryOptimization\n",
    "\n",
    "GeometryOptimization\n",
    "   Convergence Step=1.0e-3\n",
    "End\n",
    "\n",
    "System\n",
    "   Atoms\n",
    "      C 0.0 0.0 0.0\n",
    "      O 1.13 0.0 0.0\n",
    "      C 0.0 0.0 2.1\n",
    "      O 1.13 0.0 1.9\n",
    "   End\n",
    "End\n",
    "\n",
    "Engine ForceField\n",
    "   Verbosity Verbose\n",
    "   GuessCharges True\n",
    "EndEngine\n",
    "\"\"\"\n",
    ")\n",
    "\n",
    "# Alternatively, load a previously run calculation\n",
    "# ref_job = AMSJob.load_external(\"./plams_workdir/plamsjob/ams.rkf\")\n",
    "\n",
    "ref_job.run();"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f589a951-1dd0-4e98-a837-8eabfa71c42c",
   "metadata": {},
   "source": [
    "## Reuse ForceField Parameters"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4f4ab593-cbbb-4a2d-bb19-0d0b17412d82",
   "metadata": {},
   "source": [
    "Extract the charges and types from the job results and add them as properties on the molecule:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "685756e8-c9da-4c53-9ec0-494b1c883e6c",
   "metadata": {},
   "outputs": [],
   "source": [
    "charges, types, patch = ref_job.results.get_forcefield_params()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "0d79278c-ef3e-41a4-a39b-489a62b2fb01",
   "metadata": {},
   "outputs": [],
   "source": [
    "mol = ref_job.molecule[\"\"].copy()\n",
    "\n",
    "for i, at in enumerate(mol.atoms):\n",
    "    at.properties.ForceField.Charge = charges[i]\n",
    "    at.properties.ForceField.Type = types[i]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "34a5b1ba-bdc3-4e3b-abd2-2e96ead16f00",
   "metadata": {},
   "outputs": [],
   "source": [
    "sett = Settings()\n",
    "sett.input.AMS.Task = \"SinglePoint\"\n",
    "sett.input.ForceField.Type = \"UFF\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "0f9c454d-f41b-425b-8f36-4c64fcd5137f",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Create a patch file if required\n",
    "if patch:\n",
    "    with open(\"patch.dat\", \"w\") as outfile:\n",
    "        outfile.write(str(patch))\n",
    "        outfile.close()\n",
    "    # For example with:\n",
    "    # sett.input.ForceField.GAFF.ForceFieldPatchFile = \"patch.dat\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "06813554-f47b-457e-ba1d-735abea20cce",
   "metadata": {},
   "outputs": [],
   "source": [
    "job = AMSJob(molecule=mol, settings=sett)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "8c78410b-c361-4931-9087-65af6aa8c4b2",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Task SinglePoint\n",
      "\n",
      "System\n",
      "  Atoms\n",
      "              C       0.0000000000       0.0000000000       0.0000000000 ForceField.Charge=0.2881959744167275 ForceField.Type=C_1\n",
      "              O       1.1300000000       0.0000000000       0.0000000000 ForceField.Charge=-0.2676126103828702 ForceField.Type=O_2\n",
      "              C       0.0000000000       0.0000000000       2.1000000000 ForceField.Charge=0.2536150412119178 ForceField.Type=C_1\n",
      "              O       1.1300000000       0.0000000000       1.9000000000 ForceField.Charge=-0.27419840524497996 ForceField.Type=O_2\n",
      "  End\n",
      "End\n",
      "\n",
      "Engine ForceField\n",
      "  Type UFF\n",
      "EndEngine\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(job.get_input())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "c6b469a5-70f7-4db6-a163-2ea4093717ce",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[25.03|09:47:59] JOB plamsjob STARTED\n",
      "[25.03|09:47:59] Renaming job plamsjob to plamsjob.002\n",
      "[25.03|09:47:59] JOB plamsjob.002 RUNNING\n",
      "[25.03|09:48:00] JOB plamsjob.002 FINISHED\n",
      "[25.03|09:48:00] JOB plamsjob.002 SUCCESSFUL\n"
     ]
    }
   ],
   "source": [
    "job.run();"
   ]
  }
 ],
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