diff --git "a/tests/oxygen_diatomics.ipynb" "b/tests/oxygen_diatomics.ipynb" --- "a/tests/oxygen_diatomics.ipynb" +++ "b/tests/oxygen_diatomics.ipynb" @@ -1,15 +1,5019 @@ { "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "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 33813 instead\n", + " warnings.warn(\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "#!/bin/bash\n", + "\n", + "#SBATCH -J dask-worker\n", + "#SBATCH -A m3828\n", + "#SBATCH --mem=0\n", + "#SBATCH -t 00:10:00\n", + "#SBATCH -q debug\n", + "#SBATCH -C gpu\n", + "source ~/.bashrc\n", + "/pscratch/sd/c/cyrusyc/.conda/mlip-arena/bin/python -m distributed.cli.dask_worker tcp://128.55.64.14:40709 --name dummy-name --nthreads 8 --memory-limit 3.73GiB --nworkers 16 --nanny --death-timeout 60\n", + "\n" + ] + } + ], + "source": [ + "from dask.distributed import Client\n", + "from dask_jobqueue import SLURMCluster\n", + "\n", + "cluster_kwargs = {\n", + " \"cores\": 128, \n", + " \"memory\": \"64 GB\",\n", + " \"shebang\": \"#!/bin/bash\",\n", + " \"account\": \"m3828\",\n", + " \"walltime\": \"00:10:00\",\n", + " \"job_mem\": \"0\",\n", + " \"job_script_prologue\": [\"source ~/.bashrc\"],\n", + " \"job_directives_skip\": [\"-n\", \"--cpus-per-task\"], \n", + " \"job_extra_directives\": [\"-q debug\", \"-C gpu\"], \n", + "}\n", + "\n", + "cluster = SLURMCluster(**cluster_kwargs)\n", + "print(cluster.job_script())\n", + "\n", + "slurm_jobs = 1\n", + "cluster.scale(jobs=slurm_jobs)\n", + "client = Client(cluster)" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "True\n" + ] + } + ], + "source": [ + "from mlip_arena.models.utils import EXTMLIPEnum\n", + "\n", + "print(EXTMLIPEnum.MACE in EXTMLIPEnum)" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", + " from .autonotebook import tqdm as notebook_tqdm\n" + ] + } + ], + "source": [ + "from typing import Union\n", + "\n", + "import covalent as ct\n", + "import numpy as np\n", + "import pandas as pd\n", + "import torch\n", + "from ase import Atoms\n", + "from ase.calculators.calculator import Calculator\n", + "from ase.data import chemical_symbols\n", + "from matplotlib import pyplot as plt\n", + "from prefect import flow, task\n", + "from prefect_dask import DaskTaskRunner\n", + "\n", + "from mlip_arena.models import MLIPCalculator\n", + "from mlip_arena.models.utils import EXTMLIPEnum, MLIPMap, external_ase_calculator\n", + "\n", + "# chemical_symbols.remove(\"X\")\n", + "\n", + "\n", + "@task\n", + "def calculate_single_diatomic(\n", + " calculator_name: str,\n", + " calculator_kwargs: dict | None,\n", + " atom1: str,\n", + " atom2: str,\n", + " rmin: float = 0.1,\n", + " rmax: float = 6.5,\n", + " npts: int = int(1e3),\n", + ") -> dict:\n", + "\n", + " calculator_kwargs = calculator_kwargs or {}\n", + "\n", + " if calculator_name in EXTMLIPEnum:\n", + " calc = external_ase_calculator(calculator_name, **calculator_kwargs)\n", + " elif calculator_name in MLIPMap:\n", + " calc = MLIPMap[calculator_name](**calculator_kwargs)\n", + "\n", + " a = 2 * rmax\n", + "\n", + " rs = np.linspace(rmin, rmax, npts)\n", + " e = np.zeros_like(rs)\n", + " f = np.zeros_like(rs)\n", + "\n", + " da = atom1 + atom2\n", + "\n", + " for i, r in enumerate(rs):\n", + "\n", + " positions = [\n", + " [0, 0, 0],\n", + " [r, 0, 0],\n", + " ]\n", + "\n", + " # Create the unit cell with two atoms\n", + " atoms = Atoms(da, positions=positions, cell=[a, a, a])\n", + "\n", + " atoms.calc = calc\n", + "\n", + " e[i] = atoms.get_potential_energy()\n", + " f[i] = np.inner(np.array([1, 0, 0]), atoms.get_forces()[1])\n", + "\n", + " return {\"r\": rs, \"E\": e, \"F\": f, \"da\": da}\n", + "\n", + "\n", + "from dask.distributed import Client\n", + "from dask_jobqueue import SLURMCluster\n", + "\n", + "\n", + "@flow(\n", + " task_runner=DaskTaskRunner(\n", + " cluster_class=SLURMCluster, cluster_kwargs=cluster_kwargs\n", + " ),\n", + " log_prints=True\n", + ")\n", + "def calculate_homonuclear_diatomics(calculator_name, calculator_kwargs):\n", + "\n", + "\n", + " results = {}\n", + "\n", + " for atom in chemical_symbols:\n", + " output = calculate_single_diatomic.submit(\n", + " calculator_name, calculator_kwargs, atom, atom\n", + " )\n", + " print(output)\n", + " da = output.pop(\"da\")\n", + " results[da] = output\n", + " \n", + "\n", + " return results" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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23:20:07.070 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-4' for task 'calculate_single_diatomic'\n",
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23:20:07.071 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-69')\n",
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23:20:07.075 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-4' for execution.\n",
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23:20:07.082 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-70')\n",
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23:20:07.087 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-5' for task 'calculate_single_diatomic'\n",
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23:20:07.093 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-5' for execution.\n",
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23:20:07.096 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-71')\n",
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23:20:07.108 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-72')\n",
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23:20:07.113 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-7' for task 'calculate_single_diatomic'\n",
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23:20:07.118 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-7' for execution.\n",
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23:20:07.120 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-73')\n",
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23:20:07.125 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-8' for task 'calculate_single_diatomic'\n",
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23:20:07.130 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-8' for execution.\n",
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23:20:07.133 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-74')\n",
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23:20:07.135 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-9' for task 'calculate_single_diatomic'\n",
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23:20:07.139 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-9' for execution.\n",
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23:20:07.145 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-75')\n",
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23:20:07.151 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-10' for task 'calculate_single_diatomic'\n",
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23:20:07.155 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-10' for execution.\n",
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23:20:07.156 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-76')\n",
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23:20:07.162 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-11' for task 'calculate_single_diatomic'\n",
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23:20:07.166 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-11' for execution.\n",
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23:20:07.168 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-77')\n",
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23:20:07.170 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-12' for task 'calculate_single_diatomic'\n",
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23:20:07.175 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-12' for execution.\n",
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23:20:07.178 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-78')\n",
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23:20:07.184 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-13' for task 'calculate_single_diatomic'\n",
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23:20:07.189 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-13' for execution.\n",
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23:20:07.191 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-79')\n",
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23:20:07.198 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-80')\n",
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23:20:07.203 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-81')\n",
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23:20:07.207 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-16' for task 'calculate_single_diatomic'\n",
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23:20:07.211 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-16' for execution.\n",
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23:20:07.213 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-82')\n",
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23:20:07.219 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-17' for task 'calculate_single_diatomic'\n",
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23:20:07.224 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-17' for execution.\n",
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23:20:07.227 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-83')\n",
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23:20:07.232 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-18' for task 'calculate_single_diatomic'\n",
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23:20:07.237 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-18' for execution.\n",
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23:20:07.240 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-84')\n",
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23:20:07.246 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-85')\n",
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23:20:07.248 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-19' for task 'calculate_single_diatomic'\n",
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23:20:07.254 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-19' for execution.\n",
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23:20:07.256 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-86')\n",
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23:20:07.261 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-20' for task 'calculate_single_diatomic'\n",
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23:20:07.266 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-20' for execution.\n",
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23:20:07.270 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-87')\n",
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23:20:07.274 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-21' for task 'calculate_single_diatomic'\n",
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23:20:07.280 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-21' for execution.\n",
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23:20:07.287 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-22' for task 'calculate_single_diatomic'\n",
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23:20:07.292 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-22' for execution.\n",
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23:20:07.298 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-89')\n",
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23:20:07.307 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-90')\n",
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23:20:07.309 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-23' for task 'calculate_single_diatomic'\n",
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23:20:07.315 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-23' for execution.\n",
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23:20:07.317 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-91')\n",
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23:20:07.325 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-92')\n",
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23:20:07.329 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-24' for task 'calculate_single_diatomic'\n",
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23:20:07.334 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-24' for execution.\n",
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23:20:07.336 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-93')\n",
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23:20:07.343 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-94')\n",
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23:20:07.346 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-26' for task 'calculate_single_diatomic'\n",
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23:20:07.351 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-26' for execution.\n",
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23:20:07.354 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-95')\n",
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23:20:07.355 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-27' for task 'calculate_single_diatomic'\n",
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23:20:07.360 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-27' for execution.\n",
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23:20:07.366 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-96')\n",
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23:20:07.370 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-28' for task 'calculate_single_diatomic'\n",
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23:20:07.375 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-28' for execution.\n",
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23:20:07.377 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-29' for task 'calculate_single_diatomic'\n",
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23:20:07.381 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-29' for execution.\n",
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23:20:07.382 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-97')\n",
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23:20:07.388 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-30' for task 'calculate_single_diatomic'\n",
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23:20:07.392 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-30' for execution.\n",
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23:20:07.396 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-98')\n",
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23:20:07.400 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-32' for task 'calculate_single_diatomic'\n",
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23:20:07.404 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-32' for execution.\n",
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23:20:07.408 | INFO    | Flow run 'bizarre-mantis' - PrefectFuture('calculate_single_diatomic-99')\n",
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23:20:07.419 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-33' for execution.\n",
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23:20:07.424 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-35' for task 'calculate_single_diatomic'\n",
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23:20:07.538 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-14' for task 'calculate_single_diatomic'\n",
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23:20:07.678 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-54' for task 'calculate_single_diatomic'\n",
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23:20:07.682 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-54' for execution.\n",
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23:20:07.688 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-56' for task 'calculate_single_diatomic'\n",
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23:20:07.692 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-56' for execution.\n",
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23:20:07.694 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-58' for task 'calculate_single_diatomic'\n",
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23:20:07.698 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-58' for execution.\n",
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23:20:07.713 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-44' for task 'calculate_single_diatomic'\n",
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23:20:07.719 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-44' for execution.\n",
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23:20:07.722 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-61' for task 'calculate_single_diatomic'\n",
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23:20:07.726 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-61' for execution.\n",
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23:20:07.733 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-49' for task 'calculate_single_diatomic'\n",
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23:20:07.737 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-49' for execution.\n",
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23:20:07.740 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-50' for task 'calculate_single_diatomic'\n",
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23:20:07.745 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-50' for execution.\n",
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23:20:07.753 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-62' for task 'calculate_single_diatomic'\n",
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23:20:07.757 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-62' for execution.\n",
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23:20:07.760 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-55' for task 'calculate_single_diatomic'\n",
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23:20:07.765 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-55' for execution.\n",
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23:20:07.772 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-64' for task 'calculate_single_diatomic'\n",
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23:20:07.776 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-64' for execution.\n",
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23:20:07.782 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-65' for task 'calculate_single_diatomic'\n",
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23:20:07.787 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-65' for execution.\n",
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23:20:07.790 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-66' for task 'calculate_single_diatomic'\n",
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23:20:07.795 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-66' for execution.\n",
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23:20:07.804 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-60' for task 'calculate_single_diatomic'\n",
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23:20:07.808 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-60' for execution.\n",
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23:20:07.821 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-63' for task 'calculate_single_diatomic'\n",
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23:20:07.915 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-74' for execution.\n",
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23:20:07.917 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-75' for task 'calculate_single_diatomic'\n",
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23:20:07.921 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-75' for execution.\n",
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23:20:07.929 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-76' for task 'calculate_single_diatomic'\n",
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23:20:07.933 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-76' for execution.\n",
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23:20:07.938 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-77' for task 'calculate_single_diatomic'\n",
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23:20:07.942 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-77' for execution.\n",
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23:20:07.947 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-78' for task 'calculate_single_diatomic'\n",
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23:20:07.951 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-78' for execution.\n",
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23:20:07.955 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-79' for task 'calculate_single_diatomic'\n",
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23:20:07.959 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-79' for execution.\n",
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23:20:07.964 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-80' for task 'calculate_single_diatomic'\n",
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23:20:07.969 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-80' for execution.\n",
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23:20:07.972 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-81' for task 'calculate_single_diatomic'\n",
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23:20:07.976 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-81' for execution.\n",
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23:20:07.980 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-82' for task 'calculate_single_diatomic'\n",
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23:20:07.984 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-82' for execution.\n",
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23:20:07.989 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-83' for task 'calculate_single_diatomic'\n",
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23:20:07.993 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-83' for execution.\n",
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23:20:08.000 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-84' for task 'calculate_single_diatomic'\n",
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23:20:08.004 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-84' for execution.\n",
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23:20:08.006 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-85' for task 'calculate_single_diatomic'\n",
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23:20:08.011 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-85' for execution.\n",
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23:20:08.015 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-86' for task 'calculate_single_diatomic'\n",
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23:20:08.019 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-86' for execution.\n",
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23:20:08.028 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-87' for execution.\n",
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23:20:08.037 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-88' for execution.\n",
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23:20:08.044 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-89' for execution.\n",
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23:20:08.053 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-90' for execution.\n",
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23:20:08.061 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-91' for execution.\n",
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23:20:08.073 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-92' for execution.\n",
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23:20:08.109 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-97' for execution.\n",
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23:20:08.111 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-98' for task 'calculate_single_diatomic'\n",
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23:20:08.115 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-98' for execution.\n",
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23:20:08.118 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-99' for task 'calculate_single_diatomic'\n",
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23:20:08.123 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-99' for execution.\n",
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23:20:08.126 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-100' for task 'calculate_single_diatomic'\n",
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23:20:08.130 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-100' for execution.\n",
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23:20:08.136 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-104' for task 'calculate_single_diatomic'\n",
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23:20:08.140 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-104' for execution.\n",
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23:20:08.142 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-105' for task 'calculate_single_diatomic'\n",
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23:20:08.146 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-105' for execution.\n",
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23:20:08.152 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-109' for task 'calculate_single_diatomic'\n",
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23:20:08.156 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-109' for execution.\n",
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23:20:08.159 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-111' for task 'calculate_single_diatomic'\n",
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23:20:08.163 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-111' for execution.\n",
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23:20:08.172 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-101' for task 'calculate_single_diatomic'\n",
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23:20:08.176 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-101' for execution.\n",
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23:20:08.179 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-103' for task 'calculate_single_diatomic'\n",
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23:20:08.183 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-103' for execution.\n",
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23:20:08.187 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-107' for task 'calculate_single_diatomic'\n",
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23:20:08.191 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-107' for execution.\n",
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23:20:08.195 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-108' for task 'calculate_single_diatomic'\n",
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23:20:08.199 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-108' for execution.\n",
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23:20:08.205 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-113' for task 'calculate_single_diatomic'\n",
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23:20:08.209 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-113' for execution.\n",
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23:20:08.212 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-115' for task 'calculate_single_diatomic'\n",
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23:20:08.216 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-115' for execution.\n",
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23:20:08.219 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-116' for task 'calculate_single_diatomic'\n",
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23:20:08.223 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-116' for execution.\n",
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23:20:08.229 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-102' for task 'calculate_single_diatomic'\n",
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23:20:08.234 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-102' for execution.\n",
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23:20:08.237 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-106' for task 'calculate_single_diatomic'\n",
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23:20:08.242 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-106' for execution.\n",
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23:20:08.250 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-112' for task 'calculate_single_diatomic'\n",
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23:20:08.254 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-112' for execution.\n",
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23:20:08.256 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-114' for task 'calculate_single_diatomic'\n",
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23:20:08.260 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-114' for execution.\n",
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23:20:08.262 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-117' for task 'calculate_single_diatomic'\n",
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23:20:08.267 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-117' for execution.\n",
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23:20:08.271 | INFO    | Flow run 'bizarre-mantis' - Created task run 'calculate_single_diatomic-118' for task 'calculate_single_diatomic'\n",
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23:20:08.275 | INFO    | Flow run 'bizarre-mantis' - Submitted task run 'calculate_single_diatomic-118' for execution.\n",
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23:27:44.390 | ERROR   | Flow run 'bizarre-mantis' - Crash detected! Execution was cancelled by the runtime environment.\n",
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\n" + ], + "text/plain": [ + "23:27:44.390 | \u001b[38;5;160mERROR\u001b[0m | Flow run\u001b[35m 'bizarre-mantis'\u001b[0m - Crash detected! Execution was cancelled by the runtime environment.\n" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "ename": "KeyboardInterrupt", + "evalue": "", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[3], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mcalculate_homonuclear_diatomics\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mMACE\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m{\u001b[49m\u001b[43m}\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mresult()\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 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\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 240\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m context \u001b[38;5;129;01min\u001b[39;00m contexts \u001b[38;5;129;01mor\u001b[39;00m []:\n\u001b[1;32m 241\u001b[0m stack\u001b[38;5;241m.\u001b[39menter_context(context)\n\u001b[0;32m--> 242\u001b[0m \u001b[43mwaiter\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mwait\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 243\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m call\u001b[38;5;241m.\u001b[39mresult()\n", + "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/waiters.py:170\u001b[0m, in \u001b[0;36mSyncWaiter.wait\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 167\u001b[0m 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\u001b[0;36mSyncWaiter._handle_waiting_callbacks\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 135\u001b[0m logger\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mWaiter \u001b[39m\u001b[38;5;132;01m%r\u001b[39;00m\u001b[38;5;124m watching for callbacks\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28mself\u001b[39m)\n\u001b[1;32m 136\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m \u001b[38;5;28;01mTrue\u001b[39;00m:\n\u001b[0;32m--> 137\u001b[0m callback: Call \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_queue\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 138\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m callback \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 139\u001b[0m \u001b[38;5;28;01mbreak\u001b[39;00m\n", + "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/queue.py:171\u001b[0m, in \u001b[0;36mQueue.get\u001b[0;34m(self, block, timeout)\u001b[0m\n\u001b[1;32m 169\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m timeout \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 170\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_qsize():\n\u001b[0;32m--> 171\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mnot_empty\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mwait\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 172\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m timeout \u001b[38;5;241m<\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 173\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtimeout\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m must be a non-negative number\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", + "File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/threading.py:327\u001b[0m, in \u001b[0;36mCondition.wait\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 325\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m: \u001b[38;5;66;03m# restore state no matter what (e.g., KeyboardInterrupt)\u001b[39;00m\n\u001b[1;32m 326\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m timeout \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m--> 327\u001b[0m \u001b[43mwaiter\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43macquire\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 328\u001b[0m gotit \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[1;32m 329\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n", + "\u001b[0;31mKeyboardInterrupt\u001b[0m: " + ] + } + ], + "source": [ + "calculate_homonuclear_diatomics(\"MACE\", {}).result()" + ] + }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ - "from mace.calculators import mace_mp\n", - "from mlip_arena.tasks.diatomics import calculate_single_diatomic, calculate_homonuclear_diatomics\n", + "from typing import Union\n", + "\n", + "import covalent as ct\n", + "import numpy as np\n", + "import pandas as pd\n", + "import torch\n", + "from ase import Atoms\n", + "from ase.calculators.calculator import Calculator\n", + "from ase.data import chemical_symbols\n", + "from matplotlib import pyplot as plt\n", + "\n", + "from mlip_arena.models import MLIPCalculator\n", + "from mlip_arena.models.utils import EXTMLIPEnum, MLIPMap, external_ase_calculator\n", + "\n", + "local = ct.executor.LocalExecutor()\n", + "\n", + "\n", + "@ct.electron\n", + "def calculate_single_diatomic(\n", + " calculator_name: str,\n", + " calculator_kwargs: dict | None,\n", + " atom1: str,\n", + " atom2: str,\n", + " rmin: float = 0.1,\n", + " rmax: float = 6.5,\n", + " npts: int = int(1e3),\n", + "):\n", + "\n", + " calculator_kwargs = calculator_kwargs or {}\n", + "\n", + " if calculator_name in EXTMLIPEnum:\n", + " calc = external_ase_calculator(calculator_name, **calculator_kwargs)\n", + " elif calculator_name in MLIPMap:\n", + " calc = MLIPMap[calculator_name](**calculator_kwargs)\n", + "\n", + " a = 2 * rmax\n", + "\n", + " rs = np.linspace(rmin, rmax, npts)\n", + " e = np.zeros_like(rs)\n", + " f = np.zeros_like(rs)\n", + "\n", + " da = atom1 + atom2\n", + "\n", + " for i, r in enumerate(rs):\n", + "\n", + " positions = [\n", + " [0, 0, 0],\n", + " [r, 0, 0],\n", + " ]\n", + "\n", + " # Create the unit cell with two atoms\n", + " atoms = Atoms(da, positions=positions, cell=[a, a, a])\n", + "\n", + " atoms.calc = calc\n", + "\n", + " e[i] = atoms.get_potential_energy()\n", + " f[i] = np.inner(np.array([1, 0, 0]), atoms.get_forces()[1])\n", + "\n", + " return rs, e, f, da\n", + "\n", + "\n", + "@ct.lattice\n", + "def calculate_homonuclear_diatomics(\n", + " calculator_name: str, calculator_kwargs: dict | None = None\n", + "):\n", + "\n", + " chemical_symbols.remove(\"X\")\n", "\n", - "calc = mace_mp()" + " results = {}\n", + "\n", + " for atom in chemical_symbols:\n", + " rs, e, f, da = calculate_single_diatomic(\n", + " calculator_name, calculator_kwargs, atom, atom\n", + " )\n", + " results[da] = {\"r\": rs, \"E\": e, \"F\": f}\n", + "\n", + " return results\n", + "\n", + "\n", + "\n", + "dispatch_id = ct.dispatch(calculate_homonuclear_diatomics)(calculator_name=\"MACE\", calculator_kwargs={})\n", + "\n", + "result = ct.get_result(dispatch_id)" ] }, { @@ -31,26 +5035,31 @@ "execution_count": null, "metadata": {}, "outputs": [], - "source": [] + "source": [ + "from mlip_arena.models.utils import external_ase_calculator, EXTMLIPEnum\n", + "\n", + "external_ase_calculator(EXTMLIPEnum.MACE)" + ] }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "MACE_MP_Medium \n" - ] - } - ], + "outputs": [], "source": [ "from mlip_arena.models.utils import MLIPEnum\n", "\n", - "for i in MLIPEnum:\n", - " print(i.name, i.value)" + "for model in MLIPEnum:\n", + " print(type(model.name), model.value)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "type(EXTMLIPEnum.MACE.value)" ] }, { @@ -60,9 +5069,14 @@ "outputs": [], "source": [ "import covalent as ct\n", + "\n", + "from mace.calculators import mace_mp\n", + "from mlip_arena.tasks.diatomics import calculate_homonuclear_diatomics\n", + "from mlip_arena.models.utils import EXTMLIPEnum\n", + "\n", "local = ct.executor.LocalExecutor()\n", "\n", - "dispatch_id = ct.dispatch(calculate_homonuclear_diatomics)(mace_mp)\n", + "dispatch_id = ct.dispatch(calculate_homonuclear_diatomics)(calculator_name=\"MACE\")\n", "\n", "result = ct.get_result(dispatch_id)\n", "print(result)"