fix typo; add diatomic, combustion notebooks

mlip_arena/tasks/combustion/water.ipynb

@@ -0,0 +1,763 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "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.utils import REGISTRY, MLIPEnum\n",
+    "from mlip_arena.tasks import MD"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "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": null,
+   "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": null,
+   "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": null,
+   "metadata": {},
+   "outputs": [],
+   "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": "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 01:50:00\n",
+      "#SBATCH -J combustion-water\n",
+      "#SBATCH -q regular\n",
+      "#SBATCH -N 1\n",
+      "#SBATCH -C gpu\n",
+      "#SBATCH -G 4\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://128.55.64.49:34761 --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 33279 instead\n",
+      "  warnings.warn(\n",
+      "2024-08-29 07:01:08,914 - distributed.scheduler - ERROR - Task md-7-bdc25b05525842028653d9bf609a5611-1 marked as failed because 4 workers died while trying to run it\n",
+      "2024-08-29 07:01:09,223 - distributed.scheduler - ERROR - Task md-1-0dcbdd94b5ca46f7bdd90131bae6f396-1 marked as failed because 4 workers died while trying to run it\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=\"01:50:00\",\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",
+    "        # \"--time-min=00:30:00\",\n",
+    "        # \"--comment=1-00:00:00\",\n",
+    "        # \"--signal=B:USR1@60\",\n",
+    "        # \"--requeue\",\n",
+    "        # \"--open-mode=append\"\n",
+    "    ],\n",
+    "    death_timeout=86400\n",
+    ")\n",
+    "\n",
+    "\n",
+    "cluster = SLURMCluster(**cluster_kwargs)\n",
+    "print(cluster.job_script())\n",
+    "cluster.adapt(minimum_jobs=5, maximum_jobs=50)\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",
+    "            mb_velocity_seed=0,\n",
+    "            traj_file=Path(REGISTRY[model.name][\"family\"])\n",
+    "            / f\"{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": [
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:55.749 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | prefect.engine - Created flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> for flow<span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\"> 'combustion'</span>\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:55.749 | \u001b[36mINFO\u001b[0m    | prefect.engine - Created flow run\u001b[35m 'sly-yak'\u001b[0m for flow\u001b[1;35m 'combustion'\u001b[0m\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
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+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:55.759 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - View at \u001b[94mhttps://app.prefect.cloud/account/f7d40474-9362-4bfa-8950-ee6a43ec00f3/workspace/d4bb0913-5f5e-49f7-bfc5-06509088baeb/flow-runs/flow-run/248fe963-31c9-4459-9c68-79fbd7418003\u001b[0m\n"
+      ]
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+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:55.761 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | prefect.task_runner.dask - Connecting to an existing Dask cluster at tcp://128.55.64.49:34761\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:55.761 | \u001b[36mINFO\u001b[0m    | prefect.task_runner.dask - Connecting to an existing Dask cluster at tcp://128.55.64.49:34761\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
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+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:55.774 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | prefect.task_runner.dask - The Dask dashboard is available at <span style=\"color: #0000ff; text-decoration-color: #0000ff\">http://128.55.64.49:33279/status</span>\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:55.774 | \u001b[36mINFO\u001b[0m    | prefect.task_runner.dask - The Dask dashboard is available at \u001b[94mhttp://128.55.64.49:33279/status\u001b[0m\n"
+      ]
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+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:56.291 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Created task run 'md-0' for task 'md'\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:56.291 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Created task run 'md-0' for task 'md'\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:56.506 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Created task run 'md-1' for task 'md'\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:56.506 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Created task run 'md-1' for task 'md'\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:56.544 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Created task run 'md-2' for task 'md'\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:56.544 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Created task run 'md-2' for task 'md'\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:56.556 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Created task run 'md-3' for task 'md'\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:56.556 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Created task run 'md-3' for task 'md'\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:56.570 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Created task run 'md-6' for task 'md'\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:56.570 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Created task run 'md-6' for task 'md'\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:56.596 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Created task run 'md-7' for task 'md'\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:56.596 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Created task run 'md-7' for task 'md'\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:56.604 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Created task run 'md-8' for task 'md'\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:56.604 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Created task run 'md-8' for task 'md'\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:56.617 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Created task run 'md-5' for task 'md'\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:56.617 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Created task run 'md-5' for task 'md'\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:56.622 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Created task run 'md-4' for task 'md'\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:56.622 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Created task run 'md-4' for task 'md'\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:57.147 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Submitted task run 'md-0' for execution.\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:57.147 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Submitted task run 'md-0' for execution.\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:57.160 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Submitted task run 'md-5' for execution.\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:57.160 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Submitted task run 'md-5' for execution.\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:57.176 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Submitted task run 'md-3' for execution.\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:57.176 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Submitted task run 'md-3' for execution.\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:57.196 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Submitted task run 'md-2' for execution.\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:57.196 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Submitted task run 'md-2' for execution.\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:57.213 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Submitted task run 'md-6' for execution.\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:57.213 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Submitted task run 'md-6' for execution.\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:57.230 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Submitted task run 'md-8' for execution.\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:57.230 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Submitted task run 'md-8' for execution.\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:57.245 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Submitted task run 'md-1' for execution.\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:57.245 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Submitted task run 'md-1' for execution.\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:57.256 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Submitted task run 'md-4' for execution.\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:57.256 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Submitted task run 'md-4' for execution.\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">00:42:57.607 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Submitted task run 'md-7' for execution.\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "00:42:57.607 | \u001b[36mINFO\u001b[0m    | Flow run\u001b[35m 'sly-yak'\u001b[0m - Submitted task run 'md-7' for execution.\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">07:01:09.228 | <span style=\"color: #d70000; text-decoration-color: #d70000\">ERROR</span>   | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Encountered exception during execution:\n",
+       "Traceback (most recent call last):\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/engine.py\", line 867, in orchestrate_flow_run\n",
+       "    result = await flow_call.aresult()\n",
+       "             ^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 327, in aresult\n",
+       "    return await asyncio.wrap_future(self.future)\n",
+       "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 352, in _run_sync\n",
+       "    result = self.fn(*self.args, **self.kwargs)\n",
+       "             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/tmp/ipykernel_699788/2249827672.py\", line 26, in combustion\n",
+       "    return [future.result() for future in futures]\n",
+       "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/tmp/ipykernel_699788/2249827672.py\", line 26, in &lt;listcomp&gt;\n",
+       "    return [future.result() for future in futures]\n",
+       "            ^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/futures.py\", line 228, in result\n",
+       "    return from_sync.call_soon_in_loop_thread(result).result()\n",
+       "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 318, in result\n",
+       "    return self.future.result(timeout=timeout)\n",
+       "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 188, in result\n",
+       "    return self.__get_result()\n",
+       "           ^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/concurrent/futures/_base.py\", line 401, in __get_result\n",
+       "    raise self._exception\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 389, in _run_async\n",
+       "    result = await coro\n",
+       "             ^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/futures.py\", line 237, in _result\n",
+       "    return await final_state.result(raise_on_failure=raise_on_failure, fetch=True)\n",
+       "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/states.py\", line 91, in _get_state_result\n",
+       "    raise await get_state_exception(state)\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect_dask/task_runners.py\", line 311, in wait\n",
+       "    return await future.result(timeout=timeout)\n",
+       "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/distributed/client.py\", line 336, in _result\n",
+       "    raise exc.with_traceback(tb)\n",
+       "distributed.scheduler.KilledWorker: Attempted to run task 'md-1-0dcbdd94b5ca46f7bdd90131bae6f396-1' on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://128.55.69.212:43073. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see <span style=\"color: #0000ff; text-decoration-color: #0000ff\">https://distributed.dask.org/en/stable/killed.html.</span>\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "07:01:09.228 | \u001b[38;5;160mERROR\u001b[0m   | Flow run\u001b[35m 'sly-yak'\u001b[0m - Encountered exception during execution:\n",
+       "Traceback (most recent call last):\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/engine.py\", line 867, in orchestrate_flow_run\n",
+       "    result = await flow_call.aresult()\n",
+       "             ^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 327, in aresult\n",
+       "    return await asyncio.wrap_future(self.future)\n",
+       "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 352, in _run_sync\n",
+       "    result = self.fn(*self.args, **self.kwargs)\n",
+       "             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/tmp/ipykernel_699788/2249827672.py\", line 26, in combustion\n",
+       "    return [future.result() for future in futures]\n",
+       "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/tmp/ipykernel_699788/2249827672.py\", line 26, in <listcomp>\n",
+       "    return [future.result() for future in futures]\n",
+       "            ^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/futures.py\", line 228, in result\n",
+       "    return from_sync.call_soon_in_loop_thread(result).result()\n",
+       "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 318, in result\n",
+       "    return self.future.result(timeout=timeout)\n",
+       "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 188, in result\n",
+       "    return self.__get_result()\n",
+       "           ^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/concurrent/futures/_base.py\", line 401, in __get_result\n",
+       "    raise self._exception\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 389, in _run_async\n",
+       "    result = await coro\n",
+       "             ^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/futures.py\", line 237, in _result\n",
+       "    return await final_state.result(raise_on_failure=raise_on_failure, fetch=True)\n",
+       "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/states.py\", line 91, in _get_state_result\n",
+       "    raise await get_state_exception(state)\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect_dask/task_runners.py\", line 311, in wait\n",
+       "    return await future.result(timeout=timeout)\n",
+       "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+       "  File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/distributed/client.py\", line 336, in _result\n",
+       "    raise exc.with_traceback(tb)\n",
+       "distributed.scheduler.KilledWorker: Attempted to run task 'md-1-0dcbdd94b5ca46f7bdd90131bae6f396-1' on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://128.55.69.212:43073. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see \u001b[94mhttps://distributed.dask.org/en/stable/killed.html.\u001b[0m\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">07:01:21.168 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Task run 'md-1' - Crash detected! Execution was interrupted by an unexpected exception: KilledWorker: Attempted to run task 'md-1-0dcbdd94b5ca46f7bdd90131bae6f396-1' on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://128.55.69.212:43073. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see <span style=\"color: #0000ff; text-decoration-color: #0000ff\">https://distributed.dask.org/en/stable/killed.html.</span>\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "07:01:21.168 | \u001b[36mINFO\u001b[0m    | Task run 'md-1' - Crash detected! Execution was interrupted by an unexpected exception: KilledWorker: Attempted to run task 'md-1-0dcbdd94b5ca46f7bdd90131bae6f396-1' on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://128.55.69.212:43073. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see \u001b[94mhttps://distributed.dask.org/en/stable/killed.html.\u001b[0m\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">07:01:21.625 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Task run 'md-2' - Crash detected! Execution was interrupted by an unexpected exception: KilledWorker: Attempted to run task 'md-2-1d496defb0564717b104fdbe3301ba7f-1' on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://128.55.82.214:37797. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see <span style=\"color: #0000ff; text-decoration-color: #0000ff\">https://distributed.dask.org/en/stable/killed.html.</span>\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "07:01:21.625 | \u001b[36mINFO\u001b[0m    | Task run 'md-2' - Crash detected! Execution was interrupted by an unexpected exception: KilledWorker: Attempted to run task 'md-2-1d496defb0564717b104fdbe3301ba7f-1' on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://128.55.82.214:37797. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see \u001b[94mhttps://distributed.dask.org/en/stable/killed.html.\u001b[0m\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">07:01:22.243 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Task run 'md-5' - Crash detected! Execution was interrupted by an unexpected exception: KilledWorker: Attempted to run task 'md-5-957565e01bfc458f8802ff6ed33304d4-1' on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://128.55.82.215:36457. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see <span style=\"color: #0000ff; text-decoration-color: #0000ff\">https://distributed.dask.org/en/stable/killed.html.</span>\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "07:01:22.243 | \u001b[36mINFO\u001b[0m    | Task run 'md-5' - Crash detected! Execution was interrupted by an unexpected exception: KilledWorker: Attempted to run task 'md-5-957565e01bfc458f8802ff6ed33304d4-1' on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://128.55.82.215:36457. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see \u001b[94mhttps://distributed.dask.org/en/stable/killed.html.\u001b[0m\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">07:01:23.569 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Task run 'md-7' - Crash detected! Execution was interrupted by an unexpected exception: KilledWorker: Attempted to run task 'md-7-bdc25b05525842028653d9bf609a5611-1' on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://128.55.65.191:43365. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see <span style=\"color: #0000ff; text-decoration-color: #0000ff\">https://distributed.dask.org/en/stable/killed.html.</span>\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "07:01:23.569 | \u001b[36mINFO\u001b[0m    | Task run 'md-7' - Crash detected! Execution was interrupted by an unexpected exception: KilledWorker: Attempted to run task 'md-7-bdc25b05525842028653d9bf609a5611-1' on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://128.55.65.191:43365. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see \u001b[94mhttps://distributed.dask.org/en/stable/killed.html.\u001b[0m\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">07:01:24.000 | <span style=\"color: #d70000; text-decoration-color: #d70000\">ERROR</span>   | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-yak'</span> - Finished in state <span style=\"color: #d70000; text-decoration-color: #d70000\">Failed</span>(\"Flow run encountered an exception. KilledWorker: Attempted to run task 'md-1-0dcbdd94b5ca46f7bdd90131bae6f396-1' on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://128.55.69.212:43073. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see <span style=\"color: #0000ff; text-decoration-color: #0000ff\">https://distributed.dask.org/en/stable/killed.html.</span>\")\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "07:01:24.000 | \u001b[38;5;160mERROR\u001b[0m   | Flow run\u001b[35m 'sly-yak'\u001b[0m - Finished in state \u001b[38;5;160mFailed\u001b[0m(\"Flow run encountered an exception. KilledWorker: Attempted to run task 'md-1-0dcbdd94b5ca46f7bdd90131bae6f396-1' on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://128.55.69.212:43073. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see \u001b[94mhttps://distributed.dask.org/en/stable/killed.html.\u001b[0m\")\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "ename": "KilledWorker",
+     "evalue": "Attempted to run task 'md-1-0dcbdd94b5ca46f7bdd90131bae6f396-1' on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://128.55.69.212:43073. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see https://distributed.dask.org/en/stable/killed.html.",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mKilledWorker\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:1224\u001b[0m, in \u001b[0;36mFlow.__call__\u001b[0;34m(self, return_state, wait_for, *args, **kwargs)\u001b[0m\n\u001b[1;32m   1219\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m task_viz_tracker:\n\u001b[1;32m   1220\u001b[0m     \u001b[38;5;66;03m# this is a subflow, for now return a single task and do not go further\u001b[39;00m\n\u001b[1;32m   1221\u001b[0m     \u001b[38;5;66;03m# we can add support for exploring subflows for tasks in the future.\u001b[39;00m\n\u001b[1;32m   1222\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[0;32m-> 1224\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43menter_flow_run_engine_from_flow_call\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m   1225\u001b[0m \u001b[43m    \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1226\u001b[0m \u001b[43m    \u001b[49m\u001b[43mparameters\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m   1227\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   1228\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   1229\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/engine.py:297\u001b[0m, in \u001b[0;36menter_flow_run_engine_from_flow_call\u001b[0;34m(flow, parameters, wait_for, return_type)\u001b[0m\n\u001b[1;32m    290\u001b[0m     retval \u001b[38;5;241m=\u001b[39m from_async\u001b[38;5;241m.\u001b[39mwait_for_call_in_loop_thread(\n\u001b[1;32m    291\u001b[0m         begin_run,\n\u001b[1;32m    292\u001b[0m         done_callbacks\u001b[38;5;241m=\u001b[39mdone_callbacks,\n\u001b[1;32m    293\u001b[0m         contexts\u001b[38;5;241m=\u001b[39mcontexts,\n\u001b[1;32m    294\u001b[0m     )\n\u001b[1;32m    296\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 297\u001b[0m     retval \u001b[38;5;241m=\u001b[39m \u001b[43mfrom_sync\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mwait_for_call_in_loop_thread\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    298\u001b[0m \u001b[43m        \u001b[49m\u001b[43mbegin_run\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    299\u001b[0m \u001b[43m        \u001b[49m\u001b[43mdone_callbacks\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdone_callbacks\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    300\u001b[0m \u001b[43m        \u001b[49m\u001b[43mcontexts\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcontexts\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    301\u001b[0m \u001b[43m    \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    303\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m retval\n",
+      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/api.py:243\u001b[0m, in \u001b[0;36mfrom_sync.wait_for_call_in_loop_thread\u001b[0;34m(_from_sync__call, timeout, done_callbacks, contexts)\u001b[0m\n\u001b[1;32m    241\u001b[0m     stack\u001b[38;5;241m.\u001b[39menter_context(context)\n\u001b[1;32m    242\u001b[0m waiter\u001b[38;5;241m.\u001b[39mwait()\n\u001b[0;32m--> 243\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mcall\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\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/site-packages/prefect/_internal/concurrency/calls.py:318\u001b[0m, in \u001b[0;36mCall.result\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m    312\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mresult\u001b[39m(\u001b[38;5;28mself\u001b[39m, timeout: Optional[\u001b[38;5;28mfloat\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m T:\n\u001b[1;32m    313\u001b[0m \u001b[38;5;250m    \u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m    314\u001b[0m \u001b[38;5;124;03m    Wait for the result of the call.\u001b[39;00m\n\u001b[1;32m    315\u001b[0m \n\u001b[1;32m    316\u001b[0m \u001b[38;5;124;03m    Not safe for use from asynchronous contexts.\u001b[39;00m\n\u001b[1;32m    317\u001b[0m \u001b[38;5;124;03m    \"\"\"\u001b[39;00m\n\u001b[0;32m--> 318\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[43mfuture\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\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",
+      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py:179\u001b[0m, in \u001b[0;36mFuture.result\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m    177\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m CancelledError()\n\u001b[1;32m    178\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_state \u001b[38;5;241m==\u001b[39m FINISHED:\n\u001b[0;32m--> 179\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[43m__get_result\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    181\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_condition\u001b[38;5;241m.\u001b[39mwait(timeout)\n\u001b[1;32m    183\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_state \u001b[38;5;129;01min\u001b[39;00m [CANCELLED, CANCELLED_AND_NOTIFIED]:\n\u001b[1;32m    184\u001b[0m     \u001b[38;5;66;03m# Raise Prefect cancelled error instead of\u001b[39;00m\n\u001b[1;32m    185\u001b[0m     \u001b[38;5;66;03m# `concurrent.futures._base.CancelledError`\u001b[39;00m\n",
+      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/concurrent/futures/_base.py:401\u001b[0m, in \u001b[0;36mFuture.__get_result\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    399\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception:\n\u001b[1;32m    400\u001b[0m     \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 401\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception\n\u001b[1;32m    402\u001b[0m     \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m    403\u001b[0m         \u001b[38;5;66;03m# Break a reference cycle with the exception in self._exception\u001b[39;00m\n\u001b[1;32m    404\u001b[0m         \u001b[38;5;28mself\u001b[39m \u001b[38;5;241m=\u001b[39m \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/_internal/concurrency/calls.py:389\u001b[0m, in \u001b[0;36mCall._run_async\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m    387\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfuture\u001b[38;5;241m.\u001b[39menforce_async_deadline() \u001b[38;5;28;01mas\u001b[39;00m cancel_scope:\n\u001b[1;32m    388\u001b[0m     \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 389\u001b[0m         result \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m coro\n\u001b[1;32m    390\u001b[0m     \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m    391\u001b[0m         \u001b[38;5;66;03m# Forget this call's arguments in order to free up any memory\u001b[39;00m\n\u001b[1;32m    392\u001b[0m         \u001b[38;5;66;03m# that may be referenced by them; after a call has happened,\u001b[39;00m\n\u001b[1;32m    393\u001b[0m         \u001b[38;5;66;03m# there's no need to keep a reference to them\u001b[39;00m\n\u001b[1;32m    394\u001b[0m         \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39margs \u001b[38;5;241m=\u001b[39m \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/client/utilities.py:78\u001b[0m, in \u001b[0;36minject_client.<locals>.with_injected_client\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m     76\u001b[0m \u001b[38;5;28;01masync\u001b[39;00m \u001b[38;5;28;01mwith\u001b[39;00m context \u001b[38;5;28;01mas\u001b[39;00m new_client:\n\u001b[1;32m     77\u001b[0m     kwargs\u001b[38;5;241m.\u001b[39msetdefault(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mclient\u001b[39m\u001b[38;5;124m\"\u001b[39m, new_client \u001b[38;5;129;01mor\u001b[39;00m client)\n\u001b[0;32m---> 78\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m fn(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n",
+      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/engine.py:400\u001b[0m, in \u001b[0;36mcreate_then_begin_flow_run\u001b[0;34m(flow, parameters, wait_for, return_type, client, user_thread)\u001b[0m\n\u001b[1;32m    398\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m state\n\u001b[1;32m    399\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m return_type \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[0;32m--> 400\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m state\u001b[38;5;241m.\u001b[39mresult(fetch\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[1;32m    401\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    402\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mInvalid return type for flow engine \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mreturn_type\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m.\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/states.py:91\u001b[0m, in \u001b[0;36m_get_state_result\u001b[0;34m(state, raise_on_failure)\u001b[0m\n\u001b[1;32m     84\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m UnfinishedRun(\n\u001b[1;32m     85\u001b[0m         \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mRun is in \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mstate\u001b[38;5;241m.\u001b[39mtype\u001b[38;5;241m.\u001b[39mname\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m state, its result is not available.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m     86\u001b[0m     )\n\u001b[1;32m     88\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m raise_on_failure \u001b[38;5;129;01mand\u001b[39;00m (\n\u001b[1;32m     89\u001b[0m     state\u001b[38;5;241m.\u001b[39mis_crashed() \u001b[38;5;129;01mor\u001b[39;00m state\u001b[38;5;241m.\u001b[39mis_failed() \u001b[38;5;129;01mor\u001b[39;00m state\u001b[38;5;241m.\u001b[39mis_cancelled()\n\u001b[1;32m     90\u001b[0m ):\n\u001b[0;32m---> 91\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m get_state_exception(state)\n\u001b[1;32m     93\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(state\u001b[38;5;241m.\u001b[39mdata, DataDocument):\n\u001b[1;32m     94\u001b[0m     result \u001b[38;5;241m=\u001b[39m result_from_state_with_data_document(\n\u001b[1;32m     95\u001b[0m         state, raise_on_failure\u001b[38;5;241m=\u001b[39mraise_on_failure\n\u001b[1;32m     96\u001b[0m     )\n",
+      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/engine.py:867\u001b[0m, in \u001b[0;36morchestrate_flow_run\u001b[0;34m(flow, flow_run, parameters, wait_for, interruptible, client, partial_flow_run_context, user_thread)\u001b[0m\n\u001b[1;32m    862\u001b[0m         \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    863\u001b[0m             from_async\u001b[38;5;241m.\u001b[39mcall_soon_in_new_thread(\n\u001b[1;32m    864\u001b[0m                 flow_call, timeout\u001b[38;5;241m=\u001b[39mflow\u001b[38;5;241m.\u001b[39mtimeout_seconds\n\u001b[1;32m    865\u001b[0m             )\n\u001b[0;32m--> 867\u001b[0m         result \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m flow_call\u001b[38;5;241m.\u001b[39maresult()\n\u001b[1;32m    869\u001b[0m         waited_for_task_runs \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m wait_for_task_runs_and_report_crashes(\n\u001b[1;32m    870\u001b[0m             flow_run_context\u001b[38;5;241m.\u001b[39mtask_run_futures, client\u001b[38;5;241m=\u001b[39mclient\n\u001b[1;32m    871\u001b[0m         )\n\u001b[1;32m    872\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m PausedRun \u001b[38;5;28;01mas\u001b[39;00m exc:\n\u001b[1;32m    873\u001b[0m     \u001b[38;5;66;03m# could get raised either via utility or by returning Paused from a task run\u001b[39;00m\n\u001b[1;32m    874\u001b[0m     \u001b[38;5;66;03m# if a task run pauses, we set its state as the flow's state\u001b[39;00m\n\u001b[1;32m    875\u001b[0m     \u001b[38;5;66;03m# to preserve reschedule and timeout behavior\u001b[39;00m\n",
+      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py:327\u001b[0m, in \u001b[0;36mCall.aresult\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    321\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m    322\u001b[0m \u001b[38;5;124;03mWait for the result of the call.\u001b[39;00m\n\u001b[1;32m    323\u001b[0m \n\u001b[1;32m    324\u001b[0m \u001b[38;5;124;03mFor use from asynchronous contexts.\u001b[39;00m\n\u001b[1;32m    325\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m    326\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 327\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m asyncio\u001b[38;5;241m.\u001b[39mwrap_future(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfuture)\n\u001b[1;32m    328\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m asyncio\u001b[38;5;241m.\u001b[39mCancelledError \u001b[38;5;28;01mas\u001b[39;00m exc:\n\u001b[1;32m    329\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m CancelledError() \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mexc\u001b[39;00m\n",
+      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py:352\u001b[0m, in \u001b[0;36mCall._run_sync\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m    350\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfuture\u001b[38;5;241m.\u001b[39menforce_sync_deadline() \u001b[38;5;28;01mas\u001b[39;00m cancel_scope:\n\u001b[1;32m    351\u001b[0m     \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 352\u001b[0m         result \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfn\u001b[49m\u001b[43m(\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[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;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[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    353\u001b[0m     \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m    354\u001b[0m         \u001b[38;5;66;03m# Forget this call's arguments in order to free up any memory\u001b[39;00m\n\u001b[1;32m    355\u001b[0m         \u001b[38;5;66;03m# that may be referenced by them; after a call has happened,\u001b[39;00m\n\u001b[1;32m    356\u001b[0m         \u001b[38;5;66;03m# there's no need to keep a reference to them\u001b[39;00m\n\u001b[1;32m    357\u001b[0m         \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39margs \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n",
+      "Cell \u001b[0;32mIn[4], line 26\u001b[0m, in \u001b[0;36mcombustion\u001b[0;34m(atoms)\u001b[0m\n\u001b[1;32m      6\u001b[0m     future \u001b[38;5;241m=\u001b[39m MD\u001b[38;5;241m.\u001b[39msubmit(\n\u001b[1;32m      7\u001b[0m         atoms\u001b[38;5;241m=\u001b[39matoms,\n\u001b[1;32m      8\u001b[0m         calculator_name\u001b[38;5;241m=\u001b[39mmodel,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     21\u001b[0m         restart\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m     22\u001b[0m     )\n\u001b[1;32m     24\u001b[0m     futures\u001b[38;5;241m.\u001b[39mappend(future)\n\u001b[0;32m---> 26\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m[\u001b[49m\u001b[43mfuture\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mfor\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mfuture\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01min\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mfutures\u001b[49m\u001b[43m]\u001b[49m\n",
+      "Cell \u001b[0;32mIn[4], line 26\u001b[0m, in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m      6\u001b[0m     future \u001b[38;5;241m=\u001b[39m MD\u001b[38;5;241m.\u001b[39msubmit(\n\u001b[1;32m      7\u001b[0m         atoms\u001b[38;5;241m=\u001b[39matoms,\n\u001b[1;32m      8\u001b[0m         calculator_name\u001b[38;5;241m=\u001b[39mmodel,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     21\u001b[0m         restart\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m     22\u001b[0m     )\n\u001b[1;32m     24\u001b[0m     futures\u001b[38;5;241m.\u001b[39mappend(future)\n\u001b[0;32m---> 26\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m [\u001b[43mfuture\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m future \u001b[38;5;129;01min\u001b[39;00m futures]\n",
+      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/futures.py:228\u001b[0m, in \u001b[0;36mPrefectFuture.result\u001b[0;34m(self, timeout, raise_on_failure)\u001b[0m\n\u001b[1;32m    226\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m from_async\u001b[38;5;241m.\u001b[39mcall_soon_in_loop_thread(result)\u001b[38;5;241m.\u001b[39maresult()\n\u001b[1;32m    227\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 228\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfrom_sync\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcall_soon_in_loop_thread\u001b[49m\u001b[43m(\u001b[49m\u001b[43mresult\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\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/site-packages/prefect/_internal/concurrency/calls.py:318\u001b[0m, in \u001b[0;36mCall.result\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m    312\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mresult\u001b[39m(\u001b[38;5;28mself\u001b[39m, timeout: Optional[\u001b[38;5;28mfloat\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m T:\n\u001b[1;32m    313\u001b[0m \u001b[38;5;250m    \u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m    314\u001b[0m \u001b[38;5;124;03m    Wait for the result of the call.\u001b[39;00m\n\u001b[1;32m    315\u001b[0m \n\u001b[1;32m    316\u001b[0m \u001b[38;5;124;03m    Not safe for use from asynchronous contexts.\u001b[39;00m\n\u001b[1;32m    317\u001b[0m \u001b[38;5;124;03m    \"\"\"\u001b[39;00m\n\u001b[0;32m--> 318\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[43mfuture\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\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",
+      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py:188\u001b[0m, in \u001b[0;36mFuture.result\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m    186\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m CancelledError()\n\u001b[1;32m    187\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_state \u001b[38;5;241m==\u001b[39m FINISHED:\n\u001b[0;32m--> 188\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[43m__get_result\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    189\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    190\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTimeoutError\u001b[39;00m()\n",
+      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/concurrent/futures/_base.py:401\u001b[0m, in \u001b[0;36mFuture.__get_result\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    399\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception:\n\u001b[1;32m    400\u001b[0m     \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 401\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception\n\u001b[1;32m    402\u001b[0m     \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m    403\u001b[0m         \u001b[38;5;66;03m# Break a reference cycle with the exception in self._exception\u001b[39;00m\n\u001b[1;32m    404\u001b[0m         \u001b[38;5;28mself\u001b[39m \u001b[38;5;241m=\u001b[39m \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/_internal/concurrency/calls.py:389\u001b[0m, in \u001b[0;36mCall._run_async\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m    387\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfuture\u001b[38;5;241m.\u001b[39menforce_async_deadline() \u001b[38;5;28;01mas\u001b[39;00m cancel_scope:\n\u001b[1;32m    388\u001b[0m     \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 389\u001b[0m         result \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m coro\n\u001b[1;32m    390\u001b[0m     \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m    391\u001b[0m         \u001b[38;5;66;03m# Forget this call's arguments in order to free up any memory\u001b[39;00m\n\u001b[1;32m    392\u001b[0m         \u001b[38;5;66;03m# that may be referenced by them; after a call has happened,\u001b[39;00m\n\u001b[1;32m    393\u001b[0m         \u001b[38;5;66;03m# there's no need to keep a reference to them\u001b[39;00m\n\u001b[1;32m    394\u001b[0m         \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39margs \u001b[38;5;241m=\u001b[39m \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/futures.py:237\u001b[0m, in \u001b[0;36mPrefectFuture._result\u001b[0;34m(self, timeout, raise_on_failure)\u001b[0m\n\u001b[1;32m    235\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m final_state:\n\u001b[1;32m    236\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTimeoutError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCall timed out before task finished.\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 237\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m final_state\u001b[38;5;241m.\u001b[39mresult(raise_on_failure\u001b[38;5;241m=\u001b[39mraise_on_failure, fetch\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n",
+      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/states.py:91\u001b[0m, in \u001b[0;36m_get_state_result\u001b[0;34m(state, raise_on_failure)\u001b[0m\n\u001b[1;32m     84\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m UnfinishedRun(\n\u001b[1;32m     85\u001b[0m         \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mRun is in \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mstate\u001b[38;5;241m.\u001b[39mtype\u001b[38;5;241m.\u001b[39mname\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m state, its result is not available.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m     86\u001b[0m     )\n\u001b[1;32m     88\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m raise_on_failure \u001b[38;5;129;01mand\u001b[39;00m (\n\u001b[1;32m     89\u001b[0m     state\u001b[38;5;241m.\u001b[39mis_crashed() \u001b[38;5;129;01mor\u001b[39;00m state\u001b[38;5;241m.\u001b[39mis_failed() \u001b[38;5;129;01mor\u001b[39;00m state\u001b[38;5;241m.\u001b[39mis_cancelled()\n\u001b[1;32m     90\u001b[0m ):\n\u001b[0;32m---> 91\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m get_state_exception(state)\n\u001b[1;32m     93\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(state\u001b[38;5;241m.\u001b[39mdata, DataDocument):\n\u001b[1;32m     94\u001b[0m     result \u001b[38;5;241m=\u001b[39m result_from_state_with_data_document(\n\u001b[1;32m     95\u001b[0m         state, raise_on_failure\u001b[38;5;241m=\u001b[39mraise_on_failure\n\u001b[1;32m     96\u001b[0m     )\n",
+      "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect_dask/task_runners.py:311\u001b[0m, in \u001b[0;36mDaskTaskRunner.wait\u001b[0;34m(self, key, timeout)\u001b[0m\n\u001b[1;32m    309\u001b[0m future \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_dask_future(key)\n\u001b[1;32m    310\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 311\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m future\u001b[38;5;241m.\u001b[39mresult(timeout\u001b[38;5;241m=\u001b[39mtimeout)\n\u001b[1;32m    312\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m distributed\u001b[38;5;241m.\u001b[39mTimeoutError:\n\u001b[1;32m    313\u001b[0m     \u001b[38;5;28;01mreturn\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/distributed/client.py:336\u001b[0m, in \u001b[0;36mFuture._result\u001b[0;34m(self, raiseit)\u001b[0m\n\u001b[1;32m    334\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m raiseit:\n\u001b[1;32m    335\u001b[0m     typ, exc, tb \u001b[38;5;241m=\u001b[39m exc\n\u001b[0;32m--> 336\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m exc\u001b[38;5;241m.\u001b[39mwith_traceback(tb)\n\u001b[1;32m    337\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    338\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m exc\n",
+      "\u001b[0;31mKilledWorker\u001b[0m: Attempted to run task 'md-1-0dcbdd94b5ca46f7bdd90131bae6f396-1' on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://128.55.69.212:43073. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see https://distributed.dask.org/en/stable/killed.html."
+     ]
+    }
+   ],
+   "source": [
+    "results = combustion(atoms)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "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
+}

serve/tasks/combustion.py

@@ -74,7 +74,7 @@ for method in df["method"].unique():
     )
 
 fig.update_layout(
-    title="Hydrogen Combusiton (2H2 + O2 -> 2H2O, 64 units)",
+    title="Hydrogen Combustion (2H2 + O2 -> 2H2O, 64 units)",
     xaxis_title="Timesteps",
     yaxis_title="Number of water molecules",
 )
@@ -113,7 +113,7 @@ fig.add_trace(
 )
 
 fig.update_layout(
-    title="Hydrogen Combusiton (2H2 + O2 -> 2H2O, 64 units)",
+    title="Hydrogen Combustion (2H2 + O2 -> 2H2O, 64 units)",
     xaxis_title="Timesteps",
     yaxis_title="Temperatures",
     yaxis2=dict(