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hoomd example update #54

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hoomd example update #54

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497963d
first draft
ychihmei Aug 1, 2022
0624d83
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 1, 2022
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304 changes: 304 additions & 0 deletions projects/flow.hoomd.lj/src/project_2.ipynb
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Original file line number Diff line number Diff line change
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/ychihmei/opt/anaconda3/envs/RS/lib/python3.10/site-packages/tqdm/auto.py:22: 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": [
"import flow\n",
"import hoomd\n",
"import numpy as np\n",
"import signac\n",
"\n",
"cpu = hoomd.device.CPU()\n",
"# Initialize the HOOMD-blue execution context\n",
"# hoomd.context.initialize(\"\")\n",
"\n",
"project_root = \"projects/tutorial-signac-flow-hoomd\"\n",
"\n",
"\n",
"class MyProject(flow.FlowProject):\n",
" pass"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"from math import ceil\n",
"\n",
"\n",
"def init(N):\n",
" with hoomd.Simulation(device=cpu, seed=job.statepoint.seed):\n",
" n = ceil(pow(N, 1 / 3))\n",
" assert n**3 == N\n",
" hoomd.init.create_lattice(unitcell=hoomd.lattice.sc(a=1.0), n=n)\n",
" hoomd.dump.gsd(\"init.gsd\", period=None, group=hoomd.group.all())\n",
"\n",
"\n",
"def sample_lj(N, sigma, seed, kT, tau, p, tauP, steps, r_cut):\n",
" from hoomd import md\n",
"\n",
" hoomd.init.read_gsd(\"init.gsd\", restart=\"restart.gsd\")\n",
" group = hoomd.group.all()\n",
" hoomd.dump.gsd(\"restart.gsd\", truncate=True, period=100, phase=0, group=group)\n",
" lj = md.pair.lj(r_cut=r_cut, nlist=md.nlist.cell())\n",
" lj.pair_coeff.set(\"A\", \"A\", epsilon=1.0, sigma=sigma)\n",
" md.integrate.mode_standard(dt=0.005)\n",
" md.integrate.npt(group=group, kT=kT, tau=tau, P=p, tauP=tauP)\n",
" hoomd.analyze.log(\"dump.log\", [\"V\"], 100, phase=0)\n",
" hoomd.run_upto(steps)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"@MyProject.label\n",
"def estimated(job):\n",
" return \"V\" in job.document\n",
"\n",
"\n",
"@MyProject.label\n",
"def sampled(job):\n",
" return job.document.get(\"sample_step\", 0) >= 5000\n",
"\n",
"\n",
"@MyProject.operation\n",
"@MyProject.post(estimated)\n",
"def estimate(job):\n",
" job.document[\"V\"] = job.sp.N * job.sp.kT / job.sp.p\n",
" # sp = job.statepoint()\n",
" # job.document[\"V\"] = sp[\"N\"] * sp[\"kT\"] / sp[\"p\"]\n",
"\n",
"\n",
"@MyProject.operation\n",
"@MyProject.post(sampled)\n",
"def sample(job):\n",
" import hoomd\n",
"\n",
" with job:\n",
" with hoomd.Simulation(device=cpu, seed=job.statepoint.seed):\n",
" try:\n",
" sample_lj(steps=5000, **job.statepoint())\n",
" finally:\n",
" job.document[\"sample_step\"] = hoomd.get_step()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/ychihmei/opt/anaconda3/envs/RS/lib/python3.10/site-packages/signac/synced_collections/numpy_utils.py:46: NumpyConversionWarning: Any numpy types provided will be transparently converted to the closest base Python equivalents.\n",
" warnings.warn(NUMPY_CONVERSION_WARNING, NumpyConversionWarning)\n"
]
}
],
"source": [
"project = MyProject.init_project(name=\"FlowTutorialHOOMDProject\", root=project_root)\n",
"\n",
"# Uncomment the following two lines if you want to start over!\n",
"# for job in project:\n",
"# job.remove()\n",
"\n",
"for p in np.linspace(0.5, 5.0, 10):\n",
" sp = dict(N=512, sigma=1.0, seed=42, kT=1.0, p=p, tau=1.0, tauP=1.0, r_cut=2.5)\n",
" job = project.open_job(sp).init()\n",
" with job:\n",
" hoomd.Simulation(device=sp[\"N\"], seed=None)"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Fetching status: 100%|██████████| 20/20 [00:00<00:00, 7722.18it/s]\n",
"Fetching labels: 100%|██████████| 10/10 [00:00<00:00, 39568.91it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"Overview: 10 jobs/aggregates, 10 jobs/aggregates with eligible operations.\n",
"\n",
"label ratio\n",
"--------- --------------------------------------------------------\n",
"estimated |████ | 1/10 (10.00%)\n",
"\n",
"operation number of eligible jobs submission status\n",
"----------- ------------------------- -------------------\n",
"sample 10 [U]: 10\n",
"estimate 9 [U]: 10\n",
"\n",
"Detailed View:\n",
"\n",
"job id operation p V labels\n",
"-------------------------------- ------------ --- ---- ---------\n",
"18c063206c37ab03d06de130c6ae2b70 estimate [U] 1 None\n",
" sample [U] 1 None\n",
"2a05a487f254db90b08f576d199a83b7 sample [U] 5 None estimated\n",
"4ef567c185064a4b27b73f62124991c0 estimate [U] 3 None\n",
" sample [U] 3 None\n",
"5b3c8f0fbd9458a304222d83bb82bc30 estimate [U] 3.5 None\n",
" sample [U] 3.5 None\n",
"6681f083e2b03f5b9816f35502e411f7 estimate [U] 1.5 None\n",
" sample [U] 1.5 None\n",
"6ff6b952b42f0ad3e1315e137cf67cdb estimate [U] 4 None\n",
" sample [U] 4 None\n",
"99f5397cf2f6250afe34927606aa2f37 estimate [U] 4.5 None\n",
" sample [U] 4.5 None\n",
"a5d4427e8d285c78239005f740a2625b estimate [U] 2 None\n",
" sample [U] 2 None\n",
"a89bc9f5cceaf268f18efed936a70333 estimate [U] 0.5 None\n",
" sample [U] 0.5 None\n",
"c342fff540bfa0a2128efac700fc5aef estimate [U] 2.5 None\n",
" sample [U] 2.5 None\n",
"\n",
"[U]:unknown [R]:registered [I]:inactive [S]:submitted [H]:held [Q]:queued [A]:active [E]:error\n",
"\n",
"\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
}
],
"source": [
"project.print_status(detailed=True, parameters=[\"p\", \"V\"])"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"ename": "NameError",
"evalue": "name 'V' is not defined",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[1;32m/Users/ychihmei/Code/signac-examples/projects/flow.hoomd.lj/src/project_2.ipynb Cell 6\u001b[0m in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> <a href='vscode-notebook-cell:/Users/ychihmei/Code/signac-examples/projects/flow.hoomd.lj/src/project_2.ipynb#ch0000010?line=0'>1</a>\u001b[0m \u001b[39mprint\u001b[39m(V)\n",
"\u001b[0;31mNameError\u001b[0m: name 'V' is not defined"
]
}
],
"source": [
"print(V)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"ename": "UserOperationError",
"evalue": "An exception was raised during operation sample for job or aggregate with id 2a05a487f254db90b08f576d199a83b7.",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
"File \u001b[0;32m~/opt/anaconda3/envs/RS/lib/python3.10/site-packages/flow/project.py:3190\u001b[0m, in \u001b[0;36mFlowProject._execute_operation\u001b[0;34m(self, operation, timeout, pretend)\u001b[0m\n\u001b[1;32m 3189\u001b[0m \u001b[39mtry\u001b[39;00m:\n\u001b[0;32m-> 3190\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_operations[operation\u001b[39m.\u001b[39;49mname](\u001b[39m*\u001b[39;49moperation\u001b[39m.\u001b[39;49m_jobs)\n\u001b[1;32m 3191\u001b[0m \u001b[39mexcept\u001b[39;00m \u001b[39mException\u001b[39;00m \u001b[39mas\u001b[39;00m error:\n",
"File \u001b[0;32m~/opt/anaconda3/envs/RS/lib/python3.10/site-packages/flow/project.py:622\u001b[0m, in \u001b[0;36mFlowOperation.__call__\u001b[0;34m(self, *jobs)\u001b[0m\n\u001b[1;32m 609\u001b[0m \u001b[39mr\u001b[39m\u001b[39m\"\"\"Call the operation on the provided jobs.\u001b[39;00m\n\u001b[1;32m 610\u001b[0m \n\u001b[1;32m 611\u001b[0m \u001b[39mParameters\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 620\u001b[0m \n\u001b[1;32m 621\u001b[0m \u001b[39m\"\"\"\u001b[39;00m\n\u001b[0;32m--> 622\u001b[0m \u001b[39mreturn\u001b[39;00m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_op_func(\u001b[39m*\u001b[39;49mjobs)\n",
"\u001b[1;32m/Users/ychihmei/Code/signac-examples/projects/flow.hoomd.lj/src/project_2.ipynb Cell 6\u001b[0m in \u001b[0;36msample\u001b[0;34m(job)\u001b[0m\n\u001b[1;32m <a href='vscode-notebook-cell:/Users/ychihmei/Code/signac-examples/projects/flow.hoomd.lj/src/project_2.ipynb#ch0000006?line=22'>23</a>\u001b[0m \u001b[39mwith\u001b[39;00m job:\n\u001b[0;32m---> <a href='vscode-notebook-cell:/Users/ychihmei/Code/signac-examples/projects/flow.hoomd.lj/src/project_2.ipynb#ch0000006?line=23'>24</a>\u001b[0m \u001b[39mwith\u001b[39;00m hoomd\u001b[39m.\u001b[39mSimulation(device\u001b[39m=\u001b[39mcpu, seed\u001b[39m=\u001b[39mjob\u001b[39m.\u001b[39mstatepoint\u001b[39m.\u001b[39mseed):\n\u001b[1;32m <a href='vscode-notebook-cell:/Users/ychihmei/Code/signac-examples/projects/flow.hoomd.lj/src/project_2.ipynb#ch0000006?line=24'>25</a>\u001b[0m \u001b[39mtry\u001b[39;00m:\n",
"\u001b[0;31mAttributeError\u001b[0m: __enter__",
"\nThe above exception was the direct cause of the following exception:\n",
"\u001b[0;31mUserOperationError\u001b[0m Traceback (most recent call last)",
"\u001b[1;32m/Users/ychihmei/Code/signac-examples/projects/flow.hoomd.lj/src/project_2.ipynb Cell 6\u001b[0m in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> <a href='vscode-notebook-cell:/Users/ychihmei/Code/signac-examples/projects/flow.hoomd.lj/src/project_2.ipynb#ch0000006?line=0'>1</a>\u001b[0m project\u001b[39m.\u001b[39;49mrun()\n",
"File \u001b[0;32m~/opt/anaconda3/envs/RS/lib/python3.10/site-packages/flow/project.py:3438\u001b[0m, in \u001b[0;36mFlowProject.run\u001b[0;34m(self, jobs, names, pretend, np, timeout, num, num_passes, progress, order, ignore_conditions)\u001b[0m\n\u001b[1;32m 3428\u001b[0m \u001b[39mraise\u001b[39;00m \u001b[39mValueError\u001b[39;00m(\n\u001b[1;32m 3429\u001b[0m \u001b[39m\"\u001b[39m\u001b[39mInvalid value for the \u001b[39m\u001b[39m'\u001b[39m\u001b[39morder\u001b[39m\u001b[39m'\u001b[39m\u001b[39m argument, valid arguments are \u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m 3430\u001b[0m \u001b[39m\"\u001b[39m\u001b[39m'\u001b[39m\u001b[39mnone\u001b[39m\u001b[39m'\u001b[39m\u001b[39m, \u001b[39m\u001b[39m'\u001b[39m\u001b[39mby-job\u001b[39m\u001b[39m'\u001b[39m\u001b[39m, \u001b[39m\u001b[39m'\u001b[39m\u001b[39mcyclic\u001b[39m\u001b[39m'\u001b[39m\u001b[39m, \u001b[39m\u001b[39m'\u001b[39m\u001b[39mrandom\u001b[39m\u001b[39m'\u001b[39m\u001b[39m, None, or a callable.\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m 3431\u001b[0m )\n\u001b[1;32m 3433\u001b[0m logger\u001b[39m.\u001b[39minfo(\n\u001b[1;32m 3434\u001b[0m \u001b[39m\"\u001b[39m\u001b[39mExecuting \u001b[39m\u001b[39m%i\u001b[39;00m\u001b[39m operation(s) (Pass #\u001b[39m\u001b[39m%02d\u001b[39;00m\u001b[39m)...\u001b[39m\u001b[39m\"\u001b[39m,\n\u001b[1;32m 3435\u001b[0m \u001b[39mlen\u001b[39m(operations),\n\u001b[1;32m 3436\u001b[0m i_pass,\n\u001b[1;32m 3437\u001b[0m )\n\u001b[0;32m-> 3438\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_run_operations(\n\u001b[1;32m 3439\u001b[0m operations, pretend\u001b[39m=\u001b[39;49mpretend, np\u001b[39m=\u001b[39;49mnp, timeout\u001b[39m=\u001b[39;49mtimeout, progress\u001b[39m=\u001b[39;49mprogress\n\u001b[1;32m 3440\u001b[0m )\n",
"File \u001b[0;32m~/opt/anaconda3/envs/RS/lib/python3.10/site-packages/flow/project.py:3058\u001b[0m, in \u001b[0;36mFlowProject._run_operations\u001b[0;34m(self, operations, pretend, np, timeout, progress)\u001b[0m\n\u001b[1;32m 3056\u001b[0m operations \u001b[39m=\u001b[39m tqdm(operations)\n\u001b[1;32m 3057\u001b[0m \u001b[39mfor\u001b[39;00m operation \u001b[39min\u001b[39;00m operations:\n\u001b[0;32m-> 3058\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_execute_operation(operation, timeout, pretend)\n\u001b[1;32m 3059\u001b[0m \u001b[39melse\u001b[39;00m:\n\u001b[1;32m 3060\u001b[0m logger\u001b[39m.\u001b[39mdebug(\u001b[39m\"\u001b[39m\u001b[39mParallelized execution of \u001b[39m\u001b[39m%i\u001b[39;00m\u001b[39m operation(s).\u001b[39m\u001b[39m\"\u001b[39m, \u001b[39mlen\u001b[39m(operations))\n",
"File \u001b[0;32m~/opt/anaconda3/envs/RS/lib/python3.10/site-packages/flow/project.py:3192\u001b[0m, in \u001b[0;36mFlowProject._execute_operation\u001b[0;34m(self, operation, timeout, pretend)\u001b[0m\n\u001b[1;32m 3190\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_operations[operation\u001b[39m.\u001b[39mname](\u001b[39m*\u001b[39moperation\u001b[39m.\u001b[39m_jobs)\n\u001b[1;32m 3191\u001b[0m \u001b[39mexcept\u001b[39;00m \u001b[39mException\u001b[39;00m \u001b[39mas\u001b[39;00m error:\n\u001b[0;32m-> 3192\u001b[0m \u001b[39mraise\u001b[39;00m UserOperationError(\n\u001b[1;32m 3193\u001b[0m \u001b[39mf\u001b[39m\u001b[39m\"\u001b[39m\u001b[39mAn exception was raised during operation \u001b[39m\u001b[39m{\u001b[39;00moperation\u001b[39m.\u001b[39mname\u001b[39m}\u001b[39;00m\u001b[39m \u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m 3194\u001b[0m \u001b[39mf\u001b[39m\u001b[39m\"\u001b[39m\u001b[39mfor job or aggregate with id \u001b[39m\u001b[39m{\u001b[39;00mget_aggregate_id(operation\u001b[39m.\u001b[39m_jobs)\u001b[39m}\u001b[39;00m\u001b[39m.\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m 3195\u001b[0m ) \u001b[39mfrom\u001b[39;00m \u001b[39merror\u001b[39;00m\n",
"\u001b[0;31mUserOperationError\u001b[0m: An exception was raised during operation sample for job or aggregate with id 2a05a487f254db90b08f576d199a83b7."
]
}
],
"source": [
"project.run()"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"ename": "NameError",
"evalue": "name 'V' is not defined",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[1;32m/Users/ychihmei/Code/signac-examples/projects/flow.hoomd.lj/src/project_2.ipynb Cell 8\u001b[0m in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> <a href='vscode-notebook-cell:/Users/ychihmei/Code/signac-examples/projects/flow.hoomd.lj/src/project_2.ipynb#ch0000007?line=0'>1</a>\u001b[0m \u001b[39mprint\u001b[39m(V)\n",
"\u001b[0;31mNameError\u001b[0m: name 'V' is not defined"
]
}
],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3.10.4 ('RS')",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.4"
},
"vscode": {
"interpreter": {
"hash": "d0f6f30aa31cd7031202ef1611dc07a0ec742865e629d88081a44390ddef9294"
}
}
},
"nbformat": 4,
"nbformat_minor": 2
}