{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "e676a8e1-8c9d-4e06-975b-bdca2e8647fd",
   "metadata": {},
   "source": [
    "## Initial imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "e7d55482-7a63-4d9f-a720-2dbd198d6521",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "PLAMS working folder: /path/plams/examples/COSMORSConformers/plams_workdir\n"
     ]
    }
   ],
   "source": [
    "from scm.plams.recipes.adfcosmorsconformers import ADFCOSMORSConfJob, ADFCOSMORSConfFilter\n",
    "from scm.plams import Molecule, from_smiles, Settings, init, config, JobRunner\n",
    "from scm.conformers import ConformersJob\n",
    "\n",
    "# this line is not required in AMS2025+\n",
    "init();"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "24541907-e64a-40ba-bcde-077b3484bf5c",
   "metadata": {},
   "outputs": [],
   "source": [
    "config.default_jobrunner = JobRunner(parallel=True, maxjobs=8)  # Set the default jobrunner to be parallel\n",
    "config.default_jobmanager.settings.hashing = None  # Disable rerun prevention\n",
    "config.job.runscript.nproc = 1  # Number of cores for each job\n",
    "config.log.stdout = 1  # Suppress plams output"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ae03f386-2f8f-4fb5-9dcb-4e5529de98d0",
   "metadata": {},
   "source": [
    "## Set up conformer generator"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "47bc1ee7-def3-43f2-8cf9-9a89f99988d6",
   "metadata": {},
   "source": [
    "First, we input the acetic acid molecule with the `from_smiles` function"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "1c873e27-0231-42c6-8253-ca0236b78c88",
   "metadata": {},
   "outputs": [],
   "source": [
    "mol = from_smiles(\"CC(=O)O\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "db87c8f7-7e0f-47ca-a372-64417d35b7bf",
   "metadata": {},
   "source": [
    "Now, we'll specify a conformer generator (identical to the default) that generates only 50 initial structures:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "213cfc46-e2ee-4544-b8f8-6cf132e7f91e",
   "metadata": {},
   "outputs": [],
   "source": [
    "conf_sett = Settings()\n",
    "conf_sett.input.AMS.Generator.RDKit\n",
    "conf_sett.input.AMS.Generator.RDKit.InitialNConformers = 50\n",
    "conf_job = ConformersJob(name=\"conformers_uff\", molecule=mol, settings=conf_sett)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5bb08dec-a93e-472b-a8ce-37816c01e1c9",
   "metadata": {},
   "source": [
    "Let's also specify an additional step to add to the default workflow.  Here, we'll add a DFTB geometry optimization."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "7c358881-cc56-4851-ab4d-a357105128cf",
   "metadata": {},
   "outputs": [],
   "source": [
    "dftb_sett = Settings()\n",
    "dftb_sett.input.DFTB\n",
    "dftb_sett.input.AMS.Task = \"Optimize\""
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5ebc8c6d-e951-4c1a-a9c8-c7b5b3e7d51a",
   "metadata": {},
   "source": [
    "The final thing we need to specify are filters.  Let's make three filters, the first to take a maximum of 20 conformers with a maximum energy range of 22 kcal/mol, the second with 10 conformers and 12 kcal/mol and the third with 5 conformers and 7 kcal/mol."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "ab44876a-9ee6-4009-b51f-bdb8073bf2e8",
   "metadata": {},
   "outputs": [],
   "source": [
    "# ADFCOSMORSConfFilter(max number of conformers, max energy range)\n",
    "fil1 = ADFCOSMORSConfFilter(20, 22)  # applied to UFF\n",
    "fil2 = ADFCOSMORSConfFilter(10, 12)  # applied to DFTB\n",
    "fil3 = ADFCOSMORSConfFilter(5, 7)  # applied to ADF gas phase"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "09e070fc-be09-4cff-a09a-bd6ff5f4a000",
   "metadata": {},
   "source": [
    "## Run COSMO-RS conformers job"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e3f91ae0-1518-4185-80c4-2779703a2df5",
   "metadata": {},
   "source": [
    "Finally, we give this information to the `ADFCOSMORSConfJob` class.  We also specify the name of the coskf files as well as the directory in which we'll find them after the calculations complete."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "a778760d-0d80-44a8-9068-0183c5b6fd51",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[19.03|15:33:37] JOB plamsjob STARTED\n",
      "[19.03|15:33:37] Waiting for job plamsjob to finish\n",
      "[19.03|15:33:37] JOB plamsjob/conformers_uff STARTED\n",
      "[19.03|15:33:37] JOB plamsjob/additional_1 STARTED\n",
      "[19.03|15:33:37] JOB plamsjob/adf_conformers STARTED\n",
      "[19.03|15:33:37] JOB plamsjob/adf_filter STARTED\n",
      "[19.03|15:33:37] Waiting for job conformers_uff to finish\n",
      "[19.03|15:33:37] Waiting for job adf_filter to finish\n",
      "[19.03|15:33:37] Waiting for job additional_1 to finish\n",
      "[19.03|15:33:37] Waiting for job adf_conformers to finish\n",
      "[19.03|15:33:44] JOB plamsjob/conformers_uff SUCCESSFUL\n",
      "[19.03|15:33:45] JOB plamsjob/additional_1 SUCCESSFUL\n",
      "[19.03|15:43:18] JOB plamsjob/adf_conformers SUCCESSFUL\n",
      "[19.03|15:43:19] JOB plamsjob/adf_filter SUCCESSFUL\n",
      "[19.03|15:43:19] JOB plamsjob/replay STARTED\n",
      "[19.03|15:44:08] JOB plamsjob/replay SUCCESSFUL\n",
      "[19.03|15:44:10] JOB plamsjob SUCCESSFUL\n"
     ]
    }
   ],
   "source": [
    "job = ADFCOSMORSConfJob(\n",
    "    mol,\n",
    "    conf_gen=conf_job,\n",
    "    first_filter=fil1,\n",
    "    additional=[(dftb_sett, fil2)],\n",
    "    final_filter=fil3,\n",
    "    coskf_name=\"acetic_acid\",\n",
    "    coskf_dir=\"test_coskfs\",\n",
    ")\n",
    "job.run()\n",
    "job.results.wait()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "fa86e6a5-4098-4d31-96a4-5a338d62ccfc",
   "metadata": {},
   "outputs": [],
   "source": [
    "!amsview test_coskfs/acetic_acid_0.coskf"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "96fae9f9-5465-494c-accf-23bcb3783843",
   "metadata": {},
   "outputs": [],
   "source": [
    "!amsview test_coskfs/acetic_acid_1.coskf"
   ]
  }
 ],
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