{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "05a81f03-503e-414a-877b-4f8837d37eb5",
   "metadata": {},
   "source": "## Initial imports"
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "3fe257a7-2374-49d6-94a2-d648a30c3ad4",
   "metadata": {
    "execution": {
     "iopub.status.busy": "2024-05-31T12:23:03.063079Z",
     "iopub.execute_input": "2024-05-31T12:23:03.063238Z",
     "iopub.status.idle": "2024-05-31T12:23:05.147695Z",
     "shell.execute_reply": "2024-05-31T12:23:05.147135Z"
    }
   },
   "outputs": [],
   "source": [
    "import scm.plams as plams\n",
    "from scm.params import ResultsImporter\n",
    "from scm.plams import Settings, AMSJob, log, Molecule, packmol_on_slab\n",
    "from pathlib import Path\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "# common_ru_h.py must exist in the current working directory\n",
    "from common_ru_h import (\n",
    "    rotation,\n",
    "    dft_settings,\n",
    "    QEKPointsConfig,\n",
    "    m3gnet_up_settings,\n",
    "    replay_settings,\n",
    "    slice_slab,\n",
    "    check_installation,\n",
    ")\n",
    "\n",
    "# register dependencies for AMSjobs, to support submitting this notebook directly to a cluster in AMS2025+ \n",
    "# dependency: {}  common_ru_h.py\n",
    "# dependency: {}  reference_data_2"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2c19c0f9-001b-4ced-96ce-19a0878f9806",
   "metadata": {},
   "source": "## Initialize PLAMS working directory"
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "81d242b7-b776-491d-a463-cca1b62a70c0",
   "metadata": {
    "execution": {
     "iopub.status.busy": "2024-05-31T12:23:05.151046Z",
     "iopub.execute_input": "2024-05-31T12:23:05.151250Z",
     "iopub.status.idle": "2024-05-31T12:23:07.427804Z",
     "shell.execute_reply": "2024-05-31T12:23:07.426505Z"
    }
   },
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": "Current AMS version: 2024.102\n05-31 14:23:05 m3gnet is installed: M3GNet ML Backend v[0.2.4] - build:0 [06668e0a45ce742d8f66ff23484b8a1e]\n05-31 14:23:06 qe is installed: Quantum ESPRESSO (AMSPIPE) v[7.1] - build:115 [777d72eb480fe4d632a003cc62e9c1cb]\nPLAMS working folder: /home/hellstrom/SALRuH/fix2024/plams_workdir.003\n"
    }
   ],
   "source": "old_ref_dir = \"reference_data_2\"\ncheck_installation(old_ref_dir)\nnew_ref_dir = \"reference_data_3\"\nri = ResultsImporter.from_yaml(old_ref_dir)\nplams.init()"
  },
  {
   "cell_type": "markdown",
   "id": "31ab389e-ad8d-4753-b0a2-ea8d434ad794",
   "metadata": {},
   "source": "## Construct the Ru(10-10)/H2(gas) interface\n\nFor details about the construction of the slab, see the previous notebook."
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "380b978e-ee27-493e-ad72-61e59c719c6f",
   "metadata": {
    "execution": {
     "iopub.status.busy": "2024-05-31T12:23:07.433072Z",
     "iopub.execute_input": "2024-05-31T12:23:07.433431Z",
     "shell.execute_reply": "2024-05-31T12:23:08.084862Z",
     "iopub.status.idle": "2024-05-31T12:23:08.085851Z"
    }
   },
   "outputs": [
    {
     "output_type": "display_data",
     "metadata": {
      "needs_background": "light"
     },
     "data": {
      "text/plain": "<Figure size 144x144 with 1 Axes>",
      "image/png": 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\n"
     }
    }
   ],
   "source": "optimized_bulk = ri.job_collection[\"hcp_lattopt_Ru_dft\"].molecule\nslab_100 = slice_slab(\n    optimized_bulk, miller=(1, 0, 0), thickness=7.0, cell_z=15, ref_atom=0\n)\nslab_100 = slab_100.supercell(3, 2, 1)\nfor at in slab_100:\n    at.properties = Settings()  # remove details about supercell generation\nplams.plot_molecule(slab_100, rotation=rotation)\nplt.title(\"Ru(10-10)\");"
  },
  {
   "cell_type": "markdown",
   "id": "3e8bc326",
   "metadata": {},
   "source": "Now use the ``packmol_slab`` function to add hydrogen molecules:"
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "8965d84c-e662-4dd4-aef0-d99f9460ea41",
   "metadata": {
    "execution": {
     "iopub.status.busy": "2024-05-31T12:23:08.089688Z",
     "iopub.execute_input": "2024-05-31T12:23:08.089820Z",
     "shell.execute_reply": "2024-05-31T12:23:34.527995Z",
     "iopub.status.idle": "2024-05-31T12:23:34.529332Z"
    }
   },
   "outputs": [],
   "source": "from scm.plams import packmol_on_slab\n\nh2_mol = plams.from_smiles(\"[HH]\")\ndensity = 0.3  # approximate density of the gas phase in g/cm^3\nslab_100_H2_gas_raw = packmol_on_slab(slab_100, h2_mol, density=density)\nslab_100_H2_gas = plams.preoptimize(\n    slab_100_H2_gas_raw, settings=m3gnet_up_settings(), maxiterations=100\n)"
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "ee06a313-36af-4ca6-944d-b02c94eb3b75",
   "metadata": {
    "execution": {
     "iopub.status.busy": "2024-05-31T12:23:34.534127Z",
     "iopub.execute_input": "2024-05-31T12:23:34.534370Z",
     "shell.execute_reply": "2024-05-31T12:23:35.212795Z",
     "iopub.status.idle": "2024-05-31T12:23:35.213795Z"
    }
   },
   "outputs": [
    {
     "output_type": "display_data",
     "metadata": {
      "needs_background": "light"
     },
     "data": {
      "text/plain": "<Figure size 144x144 with 1 Axes>",
      "image/png": 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\n"
     }
    }
   ],
   "source": "plams.plot_molecule(slab_100_H2_gas, rotation=rotation, radii=0.8)"
  },
  {
   "cell_type": "markdown",
   "id": "cfa49bac-c717-46c3-92cf-66122c111564",
   "metadata": {},
   "source": "Now let's run some MD:"
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "ca15cd63-1daa-4b63-b444-958d153a699c",
   "metadata": {
    "execution": {
     "iopub.status.busy": "2024-05-31T12:23:35.218018Z",
     "iopub.execute_input": "2024-05-31T12:23:35.218246Z",
     "iopub.status.idle": "2024-05-31T13:08:28.369092Z",
     "shell.execute_reply": "2024-05-31T13:08:28.368018Z"
    }
   },
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": "[31.05|14:23:35] JOB md_ru10-10_h2_m3gnet STARTED\n[31.05|14:23:35] JOB md_ru10-10_h2_m3gnet RUNNING\n[31.05|15:08:27] JOB md_ru10-10_h2_m3gnet FINISHED\n[31.05|15:08:28] JOB md_ru10-10_h2_m3gnet SUCCESSFUL\n"
    }
   ],
   "source": "mdjob = plams.AMSNVTJob(\n    settings=m3gnet_up_settings(),\n    name=\"md_ru10-10_h2_m3gnet\",\n    temperature=501,\n    nsteps=10000,\n    molecule=slab_100_H2_gas,\n    samplingfreq=100,\n)\nmdjob.run();"
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "e1be713a-337c-4741-80fd-41cf5fa2038e",
   "metadata": {
    "execution": {
     "iopub.status.busy": "2024-05-31T13:08:28.372220Z",
     "iopub.execute_input": "2024-05-31T13:08:28.372569Z",
     "shell.execute_reply": "2024-05-31T13:08:28.852576Z",
     "iopub.status.idle": "2024-05-31T13:08:28.853117Z"
    }
   },
   "outputs": [],
   "source": "from scm.params import ResultsImporter\n\nri = ResultsImporter.from_yaml(old_ref_dir)"
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "97daf2eb-5f73-4f22-8fd1-8fbed3286cab",
   "metadata": {
    "execution": {
     "iopub.status.busy": "2024-05-31T13:08:28.855711Z",
     "iopub.execute_input": "2024-05-31T13:08:28.855826Z",
     "iopub.status.idle": "2024-05-31T13:46:36.826972Z",
     "shell.execute_reply": "2024-05-31T13:46:36.826155Z"
    },
    "scrolled": true
   },
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": "[31.05|15:08:28] JOB snapshots_from_md_ru10-10_h2_dft STARTED\n[31.05|15:08:28] JOB snapshots_from_md_ru10-10_h2_dft RUNNING\n[31.05|15:08:29] snapshots_from_md_ru10-10_h2_dft: AMS 2024.102  RunTime: May31-2024 15:08:29  ShM Nodes: 1  Procs: 1\n[31.05|15:08:29] snapshots_from_md_ru10-10_h2_dft: Starting trajectory replay ...\n[31.05|15:08:29] snapshots_from_md_ru10-10_h2_dft: Replaying frame #1/5 (#10 in original trajectory)\n[31.05|15:08:29] snapshots_from_md_ru10-10_h2_dft:     NOTE: a single QE.Label is assigned to atoms of different species.\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:     AMS Pseudopotentials Finder\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:     ---------------------------\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:       PP library: /home/hellstrom/.scm/packages/AMS2024.1.packages/qe-_5399rm6/content/upf_files\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:       * Ru\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:         Path: GGA/PBE/SR/SSSP_Efficiency_v1.3.0/UPFs\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:         File: Ru_ONCV_PBE-1.0.oncvpsp.upf\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:       * H\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:         Path: GGA/PBE/SR/SSSP_Efficiency_v1.3.0/UPFs\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:         File: H.pbe-rrkjus_psl.1.0.0.UPF\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:       recommended ecutwfc:     60.0 Ry\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:       recommended ecutrho:    480.0 Ry\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:       recommended ratio:        8.0x\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:       NOTE: System%ecutwfc (40.0 Ry) is below the recommended threshold (60.0 Ry)\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:       NOTE: System%ecutrho not specified in input. Using recommended ecutrho to ecutwfc ratio: ecutrho = 8.0 * ecutwfc = 320.0 Ry\n[31.05|15:08:30] snapshots_from_md_ru10-10_h2_dft:     Starting QuantumEspresso worker ... (see output file for progress information)\n[31.05|15:14:14] snapshots_from_md_ru10-10_h2_dft: Replaying frame #2/5 (#30 in original trajectory)\n[31.05|15:20:39] snapshots_from_md_ru10-10_h2_dft: Replaying frame #3/5 (#50 in original trajectory)\n[31.05|15:28:07] snapshots_from_md_ru10-10_h2_dft: Replaying frame #4/5 (#70 in original trajectory)\n[31.05|15:37:02] snapshots_from_md_ru10-10_h2_dft: Replaying frame #5/5 (#90 in original trajectory)\n[31.05|15:45:36] snapshots_from_md_ru10-10_h2_dft: Trajectory replay complete.\n[31.05|15:46:36] snapshots_from_md_ru10-10_h2_dft: Number of QE evaluations: 5\n[31.05|15:46:36] snapshots_from_md_ru10-10_h2_dft: NORMAL TERMINATION\n[31.05|15:46:36] JOB snapshots_from_md_ru10-10_h2_dft FINISHED\n[31.05|15:46:36] JOB snapshots_from_md_ru10-10_h2_dft SUCCESSFUL\n"
    },
    {
     "output_type": "execute_result",
     "metadata": {},
     "data": {
      "text/plain": "<scm.plams.interfaces.adfsuite.ams.AMSResults at 0x14c005cbf7c0>"
     },
     "execution_count": 8
    }
   ],
   "source": "settings = dft_settings(QEKPointsConfig(3, 3, 1))\nsettings += replay_settings(mdjob.results.rkfpath(), frames=[10, 30, 50, 70, 90])\n\ndft_replay_job = plams.AMSJob(\n    settings=settings,\n    name=\"snapshots_from_md_ru10-10_h2_dft\",\n)\ndft_replay_job.run(watch=True)"
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "26f350af",
   "metadata": {
    "execution": {
     "iopub.status.busy": "2024-05-31T13:46:36.831595Z",
     "iopub.execute_input": "2024-05-31T13:46:36.831886Z",
     "shell.execute_reply": "2024-05-31T13:46:37.120352Z",
     "iopub.status.idle": "2024-05-31T13:46:37.121330Z"
    }
   },
   "outputs": [
    {
     "output_type": "execute_result",
     "metadata": {},
     "data": {
      "text/plain": "['reference_data_3/job_collection.yaml',\n 'reference_data_3/results_importer_settings.yaml',\n 'reference_data_3/training_set.yaml']"
     },
     "execution_count": 9
    }
   ],
   "source": "ri.add_trajectory_singlepoints(dft_replay_job, properties=[\"energy\", \"forces\"])\nri.store(new_ref_dir)"
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "name": "python",
   "version": "3.8.12",
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