{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "No module named 'deepmd'\n"
     ]
    }
   ],
   "source": [
    "from pathlib import Path\n",
    "\n",
    "from ase import units, Atoms\n",
    "from ase.build import molecule\n",
    "from ase.io import read, write\n",
    "from dask.distributed import Client\n",
    "from dask_jobqueue import SLURMCluster\n",
    "from prefect import flow\n",
    "from prefect_dask import DaskTaskRunner\n",
    "from pymatgen.core import Molecule\n",
    "from pymatgen.io.packmol import PackmolBoxGen\n",
    "\n",
    "from mlip_arena.models import REGISTRY, MLIPEnum\n",
    "\n",
    "from mlip_arena.tasks.md import run as MD"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "# Intial configuration"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "h2 = molecule(\"H2\")\n",
    "o2 = molecule(\"O2\")\n",
    "h2o = molecule(\"H2O\")\n",
    "\n",
    "write(\"h2.xyz\", h2)\n",
    "write(\"o2.xyz\", o2)\n",
    "write(\"h2o.xyz\", h2o)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "h2 = Molecule.from_file(\"h2.xyz\")\n",
    "o2 = Molecule.from_file(\"o2.xyz\")\n",
    "h2o = Molecule.from_file(\"h2o.xyz\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "molecules = []\n",
    "\n",
    "for m, number in zip([h2, o2], [128, 64]):\n",
    "    molecules.append(\n",
    "        {\n",
    "            \"name\": m.composition.to_pretty_string(),\n",
    "            \"number\": number,\n",
    "            \"coords\": m,\n",
    "        }\n",
    "    )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Atoms(symbols='H256O128', pbc=True, cell=[30.0, 30.0, 30.0])\n"
     ]
    }
   ],
   "source": [
    "tolerance = 2.0\n",
    "input_gen = PackmolBoxGen(\n",
    "    tolerance=tolerance,\n",
    "    seed=1,\n",
    ")\n",
    "margin = 0.5 * tolerance\n",
    "\n",
    "a = 30\n",
    "\n",
    "packmol_set = input_gen.get_input_set(\n",
    "    molecules=molecules,\n",
    "    box=[margin, margin, margin, a - margin, a - margin, a - margin],\n",
    ")\n",
    "packmol_set.write_input(\".\")\n",
    "packmol_set.run(\".\")\n",
    "\n",
    "atoms = read(\"packmol_out.xyz\")\n",
    "atoms.cell = [a, a, a]\n",
    "atoms.pbc = True\n",
    "\n",
    "print(atoms)\n",
    "\n",
    "write(f'{atoms.get_chemical_formula()}.extxyz', atoms)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Run workflow"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Atoms(symbols='H256O128', pbc=True, cell=[30.0, 30.0, 30.0])\n"
     ]
    }
   ],
   "source": [
    "atoms = read(\"H256O128.extxyz\")\n",
    "print(atoms)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "#!/bin/bash\n",
      "\n",
      "#SBATCH -A matgen\n",
      "#SBATCH --mem=0\n",
      "#SBATCH -t 02:00:00\n",
      "#SBATCH -J combustion-water\n",
      "#SBATCH -q regular\n",
      "#SBATCH -N 1\n",
      "#SBATCH -C gpu\n",
      "#SBATCH -G 4\n",
      "#SBATCH --exclusive\n",
      "source ~/.bashrc\n",
      "module load python\n",
      "source activate /pscratch/sd/c/cyrusyc/.conda/mlip-arena\n",
      "/pscratch/sd/c/cyrusyc/.conda/mlip-arena/bin/python -m distributed.cli.dask_worker tcp://128.55.64.26:43909 --name dummy-name --nthreads 1 --memory-limit 59.60GiB --nanny --death-timeout 86400\n",
      "\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/distributed/node.py:182: UserWarning: Port 8787 is already in use.\n",
      "Perhaps you already have a cluster running?\n",
      "Hosting the HTTP server on port 36977 instead\n",
      "  warnings.warn(\n"
     ]
    }
   ],
   "source": [
    "nodes_per_alloc = 1\n",
    "gpus_per_alloc = 4\n",
    "ntasks = 1\n",
    "\n",
    "cluster_kwargs = dict(\n",
    "    cores=1,\n",
    "    memory=\"64 GB\",\n",
    "    shebang=\"#!/bin/bash\",\n",
    "    account=\"matgen\",\n",
    "    walltime=\"02:00:00\",\n",
    "    job_mem=\"0\",\n",
    "    job_script_prologue=[\n",
    "        \"source ~/.bashrc\",\n",
    "        \"module load python\",\n",
    "        \"source activate /pscratch/sd/c/cyrusyc/.conda/mlip-arena\",\n",
    "    ],\n",
    "    job_directives_skip=[\"-n\", \"--cpus-per-task\", \"-J\"],\n",
    "    job_extra_directives=[\n",
    "        \"-J combustion-water\",\n",
    "        \"-q regular\",\n",
    "        f\"-N {nodes_per_alloc}\",\n",
    "        \"-C gpu\",\n",
    "        f\"-G {gpus_per_alloc}\",\n",
    "        f\"--exclusive\",\n",
    "    ],\n",
    "    death_timeout=86400\n",
    ")\n",
    "\n",
    "cluster = SLURMCluster(**cluster_kwargs)\n",
    "\n",
    "# cluster_kwargs = {\n",
    "#     \"cores\": 1,\n",
    "#     \"memory\": \"64 GB\",\n",
    "#     \"shebang\": \"#!/bin/bash\",\n",
    "#     \"account\": \"matgen\",\n",
    "#     \"walltime\": \"00:30:00\",\n",
    "#     \"job_mem\": \"0\",\n",
    "#     \"job_script_prologue\": [\n",
    "#         \"source ~/.bashrc\",\n",
    "#         \"module load python\",\n",
    "#         \"source activate /pscratch/sd/c/cyrusyc/.conda/mlip-arena\",\n",
    "#     ],\n",
    "#     \"job_directives_skip\": [\"-n\", \"--cpus-per-task\", \"-J\"],\n",
    "#     \"job_extra_directives\": [f\"-N {nodes_per_alloc}\", \"-q debug\", \"-C gpu\", \"-J combustion-water\"],\n",
    "# }\n",
    "# cluster = SLURMCluster(**cluster_kwargs)\n",
    "\n",
    "print(cluster.job_script())\n",
    "cluster.adapt(minimum_jobs=2, maximum_jobs=2)\n",
    "client = Client(cluster)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "@flow(task_runner=DaskTaskRunner(address=client.scheduler.address), log_prints=True)\n",
    "def combustion(atoms: Atoms):\n",
    "    futures = []\n",
    "\n",
    "    for model in MLIPEnum:\n",
    "        future = MD.submit(\n",
    "            atoms=atoms,\n",
    "            calculator_name=model,\n",
    "            calculator_kwargs=None,\n",
    "            ensemble=\"nvt\",\n",
    "            dynamics=\"nose-hoover\",\n",
    "            time_step=None,\n",
    "            ase_md_kwargs=dict(ttime=25 * units.fs, pfactor=None),\n",
    "            total_time=1000_000,\n",
    "            temperature=[300, 3000, 3000, 300],\n",
    "            pressure=None,\n",
    "            md_velocity_seed=0,\n",
    "            traj_file=Path(REGISTRY[model.name][\"family\"])\n",
    "            / f\"{model.name}_{atoms.get_chemical_formula()}.traj\",\n",
    "            traj_interval=1000,\n",
    "            restart=True,\n",
    "        )\n",
    "\n",
    "        futures.append(future)\n",
    "    \n",
    "    return [future.result() for future in futures]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "ename": "PrefectHTTPStatusError",
     "evalue": "Client error '401 Unauthorized' for url 'https://api.prefect.cloud/api/accounts/f7d40474-9362-4bfa-8950-ee6a43ec00f3/workspaces/d4bb0913-5f5e-49f7-bfc5-06509088baeb/flows/'\nResponse: {'detail': 'Invalid authentication credentials'}\nFor more information check: https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/401",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mPrefectHTTPStatusError\u001b[0m                    Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[5], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m results \u001b[38;5;241m=\u001b[39m \u001b[43mcombustion\u001b[49m\u001b[43m(\u001b[49m\u001b[43matoms\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flows.py:1355\u001b[0m, in \u001b[0;36mFlow.__call__\u001b[0;34m(self, return_state, wait_for, *args, **kwargs)\u001b[0m\n\u001b[1;32m   1351\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m track_viz_task(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39misasync, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mname, parameters)\n\u001b[1;32m   1353\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mprefect\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mflow_engine\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m run_flow\n\u001b[0;32m-> 1355\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrun_flow\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m   1356\u001b[0m \u001b[43m    \u001b[49m\u001b[43mflow\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1357\u001b[0m \u001b[43m    \u001b[49m\u001b[43mparameters\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mparameters\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1358\u001b[0m \u001b[43m    \u001b[49m\u001b[43mwait_for\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mwait_for\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1359\u001b[0m \u001b[43m    \u001b[49m\u001b[43mreturn_type\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mreturn_type\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1360\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:821\u001b[0m, in \u001b[0;36mrun_flow\u001b[0;34m(flow, flow_run, parameters, wait_for, return_type)\u001b[0m\n\u001b[1;32m    819\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m run_flow_async(\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m    820\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 821\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrun_flow_sync\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:696\u001b[0m, in \u001b[0;36mrun_flow_sync\u001b[0;34m(flow, flow_run, parameters, wait_for, return_type)\u001b[0m\n\u001b[1;32m    682\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mrun_flow_sync\u001b[39m(\n\u001b[1;32m    683\u001b[0m     flow: Flow[P, R],\n\u001b[1;32m    684\u001b[0m     flow_run: Optional[FlowRun] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    687\u001b[0m     return_type: Literal[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mstate\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mresult\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mresult\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m    688\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m Union[R, State, \u001b[38;5;28;01mNone\u001b[39;00m]:\n\u001b[1;32m    689\u001b[0m     engine \u001b[38;5;241m=\u001b[39m FlowRunEngine[P, R](\n\u001b[1;32m    690\u001b[0m         flow\u001b[38;5;241m=\u001b[39mflow,\n\u001b[1;32m    691\u001b[0m         parameters\u001b[38;5;241m=\u001b[39mparameters,\n\u001b[1;32m    692\u001b[0m         flow_run\u001b[38;5;241m=\u001b[39mflow_run,\n\u001b[1;32m    693\u001b[0m         wait_for\u001b[38;5;241m=\u001b[39mwait_for,\n\u001b[1;32m    694\u001b[0m     )\n\u001b[0;32m--> 696\u001b[0m \u001b[43m    \u001b[49m\u001b[38;5;28;43;01mwith\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mengine\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mstart\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m:\u001b[49m\n\u001b[1;32m    697\u001b[0m \u001b[43m        \u001b[49m\u001b[38;5;28;43;01mwhile\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mengine\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mis_running\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m:\u001b[49m\n\u001b[1;32m    698\u001b[0m \u001b[43m            \u001b[49m\u001b[38;5;28;43;01mwith\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mengine\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrun_context\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m:\u001b[49m\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/contextlib.py:137\u001b[0m, in \u001b[0;36m_GeneratorContextManager.__enter__\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    135\u001b[0m \u001b[38;5;28;01mdel\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39margs, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mkwds, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfunc\n\u001b[1;32m    136\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 137\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mnext\u001b[39m(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgen)\n\u001b[1;32m    138\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mStopIteration\u001b[39;00m:\n\u001b[1;32m    139\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgenerator didn\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mt yield\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:635\u001b[0m, in \u001b[0;36mFlowRunEngine.start\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    633\u001b[0m \u001b[38;5;129m@contextmanager\u001b[39m\n\u001b[1;32m    634\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mstart\u001b[39m(\u001b[38;5;28mself\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m Generator[\u001b[38;5;28;01mNone\u001b[39;00m, \u001b[38;5;28;01mNone\u001b[39;00m, \u001b[38;5;28;01mNone\u001b[39;00m]:\n\u001b[0;32m--> 635\u001b[0m \u001b[43m    \u001b[49m\u001b[38;5;28;43;01mwith\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43minitialize_run\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m:\u001b[49m\n\u001b[1;32m    636\u001b[0m \u001b[43m        \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mbegin_run\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    638\u001b[0m \u001b[43m        \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mstate\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mis_running\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m:\u001b[49m\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/contextlib.py:137\u001b[0m, in \u001b[0;36m_GeneratorContextManager.__enter__\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    135\u001b[0m \u001b[38;5;28;01mdel\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39margs, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mkwds, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfunc\n\u001b[1;32m    136\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 137\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mnext\u001b[39m(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgen)\n\u001b[1;32m    138\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mStopIteration\u001b[39;00m:\n\u001b[1;32m    139\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgenerator didn\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mt yield\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:559\u001b[0m, in \u001b[0;36mFlowRunEngine.initialize_run\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    556\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_is_started \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[1;32m    558\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mflow_run:\n\u001b[0;32m--> 559\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mflow_run \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_flow_run\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mclient\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    560\u001b[0m     flow_run_url \u001b[38;5;241m=\u001b[39m url_for(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mflow_run)\n\u001b[1;32m    562\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m flow_run_url:\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:415\u001b[0m, in \u001b[0;36mFlowRunEngine.create_flow_run\u001b[0;34m(self, client)\u001b[0m\n\u001b[1;32m    410\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m subflow_run \u001b[38;5;241m:=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mload_subflow_run(\n\u001b[1;32m    411\u001b[0m         parent_task_run\u001b[38;5;241m=\u001b[39mparent_task_run, client\u001b[38;5;241m=\u001b[39mclient, context\u001b[38;5;241m=\u001b[39mflow_run_ctx\n\u001b[1;32m    412\u001b[0m     ):\n\u001b[1;32m    413\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m subflow_run\n\u001b[0;32m--> 415\u001b[0m flow_run \u001b[38;5;241m=\u001b[39m \u001b[43mclient\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_flow_run\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    416\u001b[0m \u001b[43m    \u001b[49m\u001b[43mflow\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mflow\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    417\u001b[0m \u001b[43m    \u001b[49m\u001b[43mparameters\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mflow\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mserialize_parameters\u001b[49m\u001b[43m(\u001b[49m\u001b[43mparameters\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    418\u001b[0m \u001b[43m    \u001b[49m\u001b[43mstate\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mPending\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    419\u001b[0m \u001b[43m    \u001b[49m\u001b[43mparent_task_run_id\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mgetattr\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mparent_task_run\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mid\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    420\u001b[0m \u001b[43m    \u001b[49m\u001b[43mtags\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mTagsContext\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcurrent_tags\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    421\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    422\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m flow_run_ctx:\n\u001b[1;32m    423\u001b[0m     parent_logger \u001b[38;5;241m=\u001b[39m get_run_logger(flow_run_ctx)\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/client/orchestration.py:3824\u001b[0m, in \u001b[0;36mSyncPrefectClient.create_flow_run\u001b[0;34m(self, flow, name, parameters, context, tags, parent_task_run_id, state)\u001b[0m\n\u001b[1;32m   3821\u001b[0m     state \u001b[38;5;241m=\u001b[39m prefect\u001b[38;5;241m.\u001b[39mstates\u001b[38;5;241m.\u001b[39mPending()\n\u001b[1;32m   3823\u001b[0m \u001b[38;5;66;03m# Retrieve the flow id\u001b[39;00m\n\u001b[0;32m-> 3824\u001b[0m flow_id \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_flow\u001b[49m\u001b[43m(\u001b[49m\u001b[43mflow\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m   3826\u001b[0m flow_run_create \u001b[38;5;241m=\u001b[39m FlowRunCreate(\n\u001b[1;32m   3827\u001b[0m     flow_id\u001b[38;5;241m=\u001b[39mflow_id,\n\u001b[1;32m   3828\u001b[0m     flow_version\u001b[38;5;241m=\u001b[39mflow\u001b[38;5;241m.\u001b[39mversion,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m   3838\u001b[0m     ),\n\u001b[1;32m   3839\u001b[0m )\n\u001b[1;32m   3841\u001b[0m flow_run_create_json \u001b[38;5;241m=\u001b[39m flow_run_create\u001b[38;5;241m.\u001b[39mmodel_dump(mode\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mjson\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/client/orchestration.py:3762\u001b[0m, in \u001b[0;36mSyncPrefectClient.create_flow\u001b[0;34m(self, flow)\u001b[0m\n\u001b[1;32m   3749\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcreate_flow\u001b[39m(\u001b[38;5;28mself\u001b[39m, flow: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mFlowObject\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m UUID:\n\u001b[1;32m   3750\u001b[0m \u001b[38;5;250m    \u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m   3751\u001b[0m \u001b[38;5;124;03m    Create a flow in the Prefect API.\u001b[39;00m\n\u001b[1;32m   3752\u001b[0m \n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m   3760\u001b[0m \u001b[38;5;124;03m        the ID of the flow in the backend\u001b[39;00m\n\u001b[1;32m   3761\u001b[0m \u001b[38;5;124;03m    \"\"\"\u001b[39;00m\n\u001b[0;32m-> 3762\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_flow_from_name\u001b[49m\u001b[43m(\u001b[49m\u001b[43mflow\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/client/orchestration.py:3778\u001b[0m, in \u001b[0;36mSyncPrefectClient.create_flow_from_name\u001b[0;34m(self, flow_name)\u001b[0m\n\u001b[1;32m   3765\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m   3766\u001b[0m \u001b[38;5;124;03mCreate a flow in the Prefect API.\u001b[39;00m\n\u001b[1;32m   3767\u001b[0m \n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m   3775\u001b[0m \u001b[38;5;124;03m    the ID of the flow in the backend\u001b[39;00m\n\u001b[1;32m   3776\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m   3777\u001b[0m flow_data \u001b[38;5;241m=\u001b[39m FlowCreate(name\u001b[38;5;241m=\u001b[39mflow_name)\n\u001b[0;32m-> 3778\u001b[0m response \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_client\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpost\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m/flows/\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mjson\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mflow_data\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmodel_dump\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mjson\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m   3780\u001b[0m flow_id \u001b[38;5;241m=\u001b[39m response\u001b[38;5;241m.\u001b[39mjson()\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mid\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m   3781\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m flow_id:\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/httpx/_client.py:1145\u001b[0m, in \u001b[0;36mClient.post\u001b[0;34m(self, url, content, data, files, json, params, headers, cookies, auth, follow_redirects, timeout, extensions)\u001b[0m\n\u001b[1;32m   1124\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mpost\u001b[39m(\n\u001b[1;32m   1125\u001b[0m     \u001b[38;5;28mself\u001b[39m,\n\u001b[1;32m   1126\u001b[0m     url: URLTypes,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m   1138\u001b[0m     extensions: RequestExtensions \u001b[38;5;241m|\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m   1139\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m Response:\n\u001b[1;32m   1140\u001b[0m \u001b[38;5;250m    \u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m   1141\u001b[0m \u001b[38;5;124;03m    Send a `POST` request.\u001b[39;00m\n\u001b[1;32m   1142\u001b[0m \n\u001b[1;32m   1143\u001b[0m \u001b[38;5;124;03m    **Parameters**: See `httpx.request`.\u001b[39;00m\n\u001b[1;32m   1144\u001b[0m \u001b[38;5;124;03m    \"\"\"\u001b[39;00m\n\u001b[0;32m-> 1145\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrequest\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m   1146\u001b[0m \u001b[43m        \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mPOST\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1147\u001b[0m \u001b[43m        \u001b[49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1148\u001b[0m \u001b[43m        \u001b[49m\u001b[43mcontent\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcontent\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1149\u001b[0m \u001b[43m        \u001b[49m\u001b[43mdata\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1150\u001b[0m \u001b[43m        \u001b[49m\u001b[43mfiles\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfiles\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1151\u001b[0m \u001b[43m        \u001b[49m\u001b[43mjson\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mjson\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1152\u001b[0m \u001b[43m        \u001b[49m\u001b[43mparams\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mparams\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1153\u001b[0m \u001b[43m        \u001b[49m\u001b[43mheaders\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mheaders\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1154\u001b[0m \u001b[43m        \u001b[49m\u001b[43mcookies\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcookies\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1155\u001b[0m \u001b[43m        \u001b[49m\u001b[43mauth\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mauth\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1156\u001b[0m \u001b[43m        \u001b[49m\u001b[43mfollow_redirects\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfollow_redirects\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1157\u001b[0m \u001b[43m        \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1158\u001b[0m \u001b[43m        \u001b[49m\u001b[43mextensions\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mextensions\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1159\u001b[0m \u001b[43m    \u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/httpx/_client.py:827\u001b[0m, in \u001b[0;36mClient.request\u001b[0;34m(self, method, url, content, data, files, json, params, headers, cookies, auth, follow_redirects, timeout, extensions)\u001b[0m\n\u001b[1;32m    812\u001b[0m     warnings\u001b[38;5;241m.\u001b[39mwarn(message, \u001b[38;5;167;01mDeprecationWarning\u001b[39;00m)\n\u001b[1;32m    814\u001b[0m request \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mbuild_request(\n\u001b[1;32m    815\u001b[0m     method\u001b[38;5;241m=\u001b[39mmethod,\n\u001b[1;32m    816\u001b[0m     url\u001b[38;5;241m=\u001b[39murl,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    825\u001b[0m     extensions\u001b[38;5;241m=\u001b[39mextensions,\n\u001b[1;32m    826\u001b[0m )\n\u001b[0;32m--> 827\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msend\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrequest\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mauth\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mauth\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfollow_redirects\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfollow_redirects\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/client/base.py:575\u001b[0m, in \u001b[0;36mPrefectHttpxSyncClient.send\u001b[0;34m(self, request, *args, **kwargs)\u001b[0m\n\u001b[1;32m    572\u001b[0m response \u001b[38;5;241m=\u001b[39m PrefectResponse\u001b[38;5;241m.\u001b[39mfrom_httpx_response(response)\n\u001b[1;32m    574\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mraise_on_all_errors:\n\u001b[0;32m--> 575\u001b[0m     \u001b[43mresponse\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mraise_for_status\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    577\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m response\n",
      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/client/base.py:174\u001b[0m, in \u001b[0;36mPrefectResponse.raise_for_status\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    172\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28msuper\u001b[39m()\u001b[38;5;241m.\u001b[39mraise_for_status()\n\u001b[1;32m    173\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m HTTPStatusError \u001b[38;5;28;01mas\u001b[39;00m exc:\n\u001b[0;32m--> 174\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m PrefectHTTPStatusError\u001b[38;5;241m.\u001b[39mfrom_httpx_error(exc) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mexc\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m__cause__\u001b[39;00m\n",
      "\u001b[0;31mPrefectHTTPStatusError\u001b[0m: Client error '401 Unauthorized' for url 'https://api.prefect.cloud/api/accounts/f7d40474-9362-4bfa-8950-ee6a43ec00f3/workspaces/d4bb0913-5f5e-49f7-bfc5-06509088baeb/flows/'\nResponse: {'detail': 'Invalid authentication credentials'}\nFor more information check: https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/401"
     ]
    }
   ],
   "source": [
    "results = combustion(atoms)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "mlip_arena"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "mlip-arena",
   "language": "python",
   "name": "mlip-arena"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.11.8"
  },
  "widgets": {
   "application/vnd.jupyter.widget-state+json": {
    "state": {},
    "version_major": 2,
    "version_minor": 0
   }
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}