Spaces:
Running
Running
File size: 73,667 Bytes
f0fdb88 b22d49d f0fdb88 b22d49d f0fdb88 c1d2139 1effaf5 8b028aa 1effaf5 8b028aa f0fdb88 c7922c2 f0fdb88 c7922c2 f0fdb88 c7922c2 f0fdb88 c7922c2 f0fdb88 c7922c2 f0fdb88 1effaf5 f0fdb88 b22d49d f0fdb88 b22d49d f0fdb88 c1d2139 f0fdb88 c1d2139 f0fdb88 8b028aa f0fdb88 b22d49d 8b028aa b22d49d 8b028aa b22d49d f0fdb88 c1d2139 f0fdb88 c1d2139 f0fdb88 1effaf5 c1d2139 f0fdb88 1effaf5 f0fdb88 b22d49d f0fdb88 c7922c2 f0fdb88 cf512f3 f0fdb88 b22d49d f0fdb88 b22d49d 8b028aa b22d49d 8b028aa b22d49d 8b028aa b22d49d f0fdb88 c1d2139 f0fdb88 8b028aa f0fdb88 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 |
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"No module named 'deepmd'\n"
]
}
],
"source": [
"from pathlib import Path\n",
"\n",
"from ase import units, Atoms\n",
"from ase.build import molecule\n",
"from ase.io import read, write\n",
"from dask.distributed import Client\n",
"from dask_jobqueue import SLURMCluster\n",
"from prefect import flow\n",
"from prefect_dask import DaskTaskRunner\n",
"from pymatgen.core import Molecule\n",
"from pymatgen.io.packmol import PackmolBoxGen\n",
"\n",
"from mlip_arena.models import REGISTRY, MLIPEnum\n",
"\n",
"from mlip_arena.tasks.md import run as MD"
]
},
{
"cell_type": "markdown",
"metadata": {
"jp-MarkdownHeadingCollapsed": true,
"tags": []
},
"source": [
"## Intial configuration"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"h2 = molecule(\"H2\")\n",
"o2 = molecule(\"O2\")\n",
"h2o = molecule(\"H2O\")\n",
"\n",
"write(\"h2.xyz\", h2)\n",
"write(\"o2.xyz\", o2)\n",
"write(\"h2o.xyz\", h2o)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"h2 = Molecule.from_file(\"h2.xyz\")\n",
"o2 = Molecule.from_file(\"o2.xyz\")\n",
"h2o = Molecule.from_file(\"h2o.xyz\")"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"molecules = []\n",
"\n",
"for m, number in zip([h2, o2], [128, 64]):\n",
" molecules.append(\n",
" {\n",
" \"name\": m.composition.to_pretty_string(),\n",
" \"number\": number,\n",
" \"coords\": m,\n",
" }\n",
" )"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Atoms(symbols='H256O128', pbc=True, cell=[30.0, 30.0, 30.0])\n"
]
}
],
"source": [
"tolerance = 2.0\n",
"input_gen = PackmolBoxGen(\n",
" tolerance=tolerance,\n",
" seed=1,\n",
")\n",
"margin = 0.5 * tolerance\n",
"\n",
"a = 30\n",
"\n",
"packmol_set = input_gen.get_input_set(\n",
" molecules=molecules,\n",
" box=[margin, margin, margin, a - margin, a - margin, a - margin],\n",
")\n",
"packmol_set.write_input(\".\")\n",
"packmol_set.run(\".\")\n",
"\n",
"atoms = read(\"packmol_out.xyz\")\n",
"atoms.cell = [a, a, a]\n",
"atoms.pbc = True\n",
"\n",
"print(atoms)\n",
"\n",
"write(f'{atoms.get_chemical_formula()}.extxyz', atoms)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Run workflow"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Atoms(symbols='H256O128', pbc=True, cell=[30.0, 30.0, 30.0])\n"
]
}
],
"source": [
"atoms = read(\"H256O128.extxyz\")\n",
"print(atoms)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"#!/bin/bash\n",
"\n",
"#SBATCH -A matgen\n",
"#SBATCH --mem=0\n",
"#SBATCH -t 02:00:00\n",
"#SBATCH -J combustion-water\n",
"#SBATCH -q regular\n",
"#SBATCH -N 1\n",
"#SBATCH -C gpu\n",
"#SBATCH -G 4\n",
"#SBATCH --exclusive\n",
"source ~/.bashrc\n",
"module load python\n",
"source activate /pscratch/sd/c/cyrusyc/.conda/mlip-arena\n",
"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/bin/python -m distributed.cli.dask_worker tcp://128.55.64.15:38781 --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:187: UserWarning: Port 8787 is already in use.\n",
"Perhaps you already have a cluster running?\n",
"Hosting the HTTP server on port 44831 instead\n",
" warnings.warn(\n"
]
}
],
"source": [
"nodes_per_alloc = 1\n",
"gpus_per_alloc = 4\n",
"ntasks = 1\n",
"\n",
"cluster_kwargs = dict(\n",
" cores=1,\n",
" memory=\"64 GB\",\n",
" shebang=\"#!/bin/bash\",\n",
" account=\"matgen\",\n",
" walltime=\"02:00:00\",\n",
" job_mem=\"0\",\n",
" job_script_prologue=[\n",
" \"source ~/.bashrc\",\n",
" \"module load python\",\n",
" \"source activate /pscratch/sd/c/cyrusyc/.conda/mlip-arena\",\n",
" ],\n",
" job_directives_skip=[\"-n\", \"--cpus-per-task\", \"-J\"],\n",
" job_extra_directives=[\n",
" \"-J combustion-water\",\n",
" \"-q regular\",\n",
" f\"-N {nodes_per_alloc}\",\n",
" \"-C gpu\",\n",
" f\"-G {gpus_per_alloc}\",\n",
" f\"--exclusive\",\n",
" ],\n",
" death_timeout=86400\n",
")\n",
"\n",
"cluster = SLURMCluster(**cluster_kwargs)\n",
"\n",
"# cluster_kwargs = {\n",
"# \"cores\": 1,\n",
"# \"memory\": \"64 GB\",\n",
"# \"shebang\": \"#!/bin/bash\",\n",
"# \"account\": \"matgen\",\n",
"# \"walltime\": \"00:30:00\",\n",
"# \"job_mem\": \"0\",\n",
"# \"job_script_prologue\": [\n",
"# \"source ~/.bashrc\",\n",
"# \"module load python\",\n",
"# \"source activate /pscratch/sd/c/cyrusyc/.conda/mlip-arena\",\n",
"# ],\n",
"# \"job_directives_skip\": [\"-n\", \"--cpus-per-task\", \"-J\"],\n",
"# \"job_extra_directives\": [f\"-N {nodes_per_alloc}\", \"-q debug\", \"-C gpu\", \"-J combustion-water\"],\n",
"# }\n",
"# cluster = SLURMCluster(**cluster_kwargs)\n",
"\n",
"print(cluster.job_script())\n",
"cluster.adapt(minimum_jobs=2, maximum_jobs=2)\n",
"client = Client(cluster)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"@flow(task_runner=DaskTaskRunner(address=client.scheduler.address), log_prints=True)\n",
"def combustion(atoms: Atoms):\n",
" futures = []\n",
"\n",
" for model in MLIPEnum:\n",
" future = MD.submit(\n",
" atoms=atoms,\n",
" calculator_name=model,\n",
" calculator_kwargs=None,\n",
" ensemble=\"nvt\",\n",
" dynamics=\"nose-hoover\",\n",
" time_step=None,\n",
" ase_md_kwargs=dict(ttime=25 * units.fs, pfactor=None),\n",
" total_time=1000_000,\n",
" temperature=[300, 3000, 3000, 300],\n",
" pressure=None,\n",
" md_velocity_seed=0,\n",
" traj_file=Path(REGISTRY[model.name][\"family\"])\n",
" / f\"{model.name}_{atoms.get_chemical_formula()}.traj\",\n",
" traj_interval=1000,\n",
" restart=True,\n",
" )\n",
"\n",
" futures.append(future)\n",
" \n",
" return [future.result() for future in futures]"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"tags": []
},
"outputs": [
{
"data": {
"text/html": [
"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">12:01:53.150 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | prefect.engine - Created flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'khaki-hippo'</span> for flow<span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\"> 'combustion'</span>\n",
"</pre>\n"
],
"text/plain": [
"12:01:53.150 | \u001b[36mINFO\u001b[0m | prefect.engine - Created flow run\u001b[35m 'khaki-hippo'\u001b[0m for flow\u001b[1;35m 'combustion'\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\">12:01:53.156 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | prefect.engine - View at <span style=\"color: #0000ff; text-decoration-color: #0000ff\">https://app.prefect.cloud/account/f7d40474-9362-4bfa-8950-ee6a43ec00f3/workspace/d4bb0913-5f5e-49f7-bfc5-06509088baeb/runs/flow-run/ce836160-4f0d-49a4-90d8-227225cb8f4c</span>\n",
"</pre>\n"
],
"text/plain": [
"12:01:53.156 | \u001b[36mINFO\u001b[0m | prefect.engine - View at \u001b[94mhttps://app.prefect.cloud/account/f7d40474-9362-4bfa-8950-ee6a43ec00f3/workspace/d4bb0913-5f5e-49f7-bfc5-06509088baeb/runs/flow-run/ce836160-4f0d-49a4-90d8-227225cb8f4c\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\">12:01:53.523 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | prefect.task_runner.dask - Connecting to existing Dask cluster SLURMCluster(99282258, 'tcp://128.55.64.15:38781', workers=0, threads=0, memory=0 B)\n",
"</pre>\n"
],
"text/plain": [
"12:01:53.523 | \u001b[36mINFO\u001b[0m | prefect.task_runner.dask - Connecting to existing Dask cluster SLURMCluster(99282258, 'tcp://128.55.64.15:38781', workers=0, threads=0, memory=0 B)\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\">13:06:57.332 | <span style=\"color: #d70000; text-decoration-color: #d70000\">ERROR</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'khaki-hippo'</span> - Encountered exception during execution: IndexError('too many indices for tensor of dimension 1')\n",
"Traceback (most recent call last):\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py\", line 652, in run_context\n",
" yield self\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py\", line 696, in run_flow_sync\n",
" engine.call_flow_fn()\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py\", line 675, in call_flow_fn\n",
" result = call_with_parameters(self.flow.fn, self.parameters)\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/callables.py\", line 206, in call_with_parameters\n",
" return fn(*args, **kwargs)\n",
" ^^^^^^^^^^^^^^^^^^^\n",
" File \"/tmp/ipykernel_1849247/2043615938.py\", line 26, in combustion\n",
" return [future.result() for future in futures]\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/tmp/ipykernel_1849247/2043615938.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_dask/task_runners.py\", line 143, in result\n",
" _result = self._final_state.result(\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/client/schemas/objects.py\", line 314, in result\n",
" return get_state_result(\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/states.py\", line 75, in get_state_result\n",
" return _get_state_result(\n",
" ^^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 399, in coroutine_wrapper\n",
" return run_coro_as_sync(ctx_call())\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 243, in run_coro_as_sync\n",
" return call.result()\n",
" ^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 312, 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 182, 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 383, in _run_async\n",
" result = await coro\n",
" ^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 225, in coroutine_wrapper\n",
" return await task\n",
" ^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 389, in ctx_call\n",
" result = await async_fn(*args, **kwargs)\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/states.py\", line 138, 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/task_engine.py\", line 763, in run_context\n",
" yield self\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py\", line 1323, in run_task_sync\n",
" engine.call_task_fn(txn)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py\", line 786, in call_task_fn\n",
" result = call_with_parameters(self.task.fn, parameters)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/callables.py\", line 206, in call_with_parameters\n",
" return fn(*args, **kwargs)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/mlip-arena/mlip_arena/tasks/md.py\", line 363, in run\n",
" md_runner.run(steps=n_steps)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py\", line 277, in run\n",
" self.initialize()\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py\", line 399, in initialize\n",
" self._calculate_q_past_and_future()\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py\", line 608, in _calculate_q_past_and_future\n",
" self._calculate_q_future(self.atoms.get_forces(md=True))\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/atoms.py\", line 812, in get_forces\n",
" forces = self._calc.get_forces(self)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/calculators/abc.py\", line 30, in get_forces\n",
" return self.get_property('forces', atoms)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/calculators/calculator.py\", line 538, in get_property\n",
" self.calculate(atoms, [name], system_changes)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/mlip-arena/mlip_arena/models/externals/chgnet.py\", line 36, in calculate\n",
" super().calculate(atoms, properties, system_changes)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/dynamics.py\", line 143, in calculate\n",
" model_prediction = self.model.predict_graph(\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py\", line 627, in predict_graph\n",
" prediction = self.forward(\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py\", line 359, in forward\n",
" batched_graph = BatchedGraph.from_graphs(\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py\", line 822, in from_graphs\n",
" center=atom_cart_coords[graph.atom_graph[:, 0]],\n",
" ^^^^^^^^^^^^^^^^^\n",
"IndexError: too many indices for tensor of dimension 1\n",
"</pre>\n"
],
"text/plain": [
"13:06:57.332 | \u001b[38;5;160mERROR\u001b[0m | Flow run\u001b[35m 'khaki-hippo'\u001b[0m - Encountered exception during execution: IndexError('too many indices for tensor of dimension 1')\n",
"Traceback (most recent call last):\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py\", line 652, in run_context\n",
" yield self\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py\", line 696, in run_flow_sync\n",
" engine.call_flow_fn()\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py\", line 675, in call_flow_fn\n",
" result = call_with_parameters(self.flow.fn, self.parameters)\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/callables.py\", line 206, in call_with_parameters\n",
" return fn(*args, **kwargs)\n",
" ^^^^^^^^^^^^^^^^^^^\n",
" File \"/tmp/ipykernel_1849247/2043615938.py\", line 26, in combustion\n",
" return [future.result() for future in futures]\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/tmp/ipykernel_1849247/2043615938.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_dask/task_runners.py\", line 143, in result\n",
" _result = self._final_state.result(\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/client/schemas/objects.py\", line 314, in result\n",
" return get_state_result(\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/states.py\", line 75, in get_state_result\n",
" return _get_state_result(\n",
" ^^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 399, in coroutine_wrapper\n",
" return run_coro_as_sync(ctx_call())\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 243, in run_coro_as_sync\n",
" return call.result()\n",
" ^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py\", line 312, 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 182, 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 383, in _run_async\n",
" result = await coro\n",
" ^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 225, in coroutine_wrapper\n",
" return await task\n",
" ^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py\", line 389, in ctx_call\n",
" result = await async_fn(*args, **kwargs)\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/states.py\", line 138, 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/task_engine.py\", line 763, in run_context\n",
" yield self\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py\", line 1323, in run_task_sync\n",
" engine.call_task_fn(txn)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py\", line 786, in call_task_fn\n",
" result = call_with_parameters(self.task.fn, parameters)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/callables.py\", line 206, in call_with_parameters\n",
" return fn(*args, **kwargs)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/mlip-arena/mlip_arena/tasks/md.py\", line 363, in run\n",
" md_runner.run(steps=n_steps)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py\", line 277, in run\n",
" self.initialize()\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py\", line 399, in initialize\n",
" self._calculate_q_past_and_future()\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py\", line 608, in _calculate_q_past_and_future\n",
" self._calculate_q_future(self.atoms.get_forces(md=True))\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/atoms.py\", line 812, in get_forces\n",
" forces = self._calc.get_forces(self)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/calculators/abc.py\", line 30, in get_forces\n",
" return self.get_property('forces', atoms)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/calculators/calculator.py\", line 538, in get_property\n",
" self.calculate(atoms, [name], system_changes)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/mlip-arena/mlip_arena/models/externals/chgnet.py\", line 36, in calculate\n",
" super().calculate(atoms, properties, system_changes)\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/dynamics.py\", line 143, in calculate\n",
" model_prediction = self.model.predict_graph(\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py\", line 627, in predict_graph\n",
" prediction = self.forward(\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py\", line 359, in forward\n",
" batched_graph = BatchedGraph.from_graphs(\n",
" ^^^^^^^^^^^^^^^^^\n",
" File \"/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py\", line 822, in from_graphs\n",
" center=atom_cart_coords[graph.atom_graph[:, 0]],\n",
" ^^^^^^^^^^^^^^^^^\n",
"IndexError: too many indices for tensor of dimension 1\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\">13:06:58.009 | <span style=\"color: #d70000; text-decoration-color: #d70000\">ERROR</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'khaki-hippo'</span> - Finished in state <span style=\"color: #d70000; text-decoration-color: #d70000\">Failed</span>('Flow run encountered an exception: IndexError: too many indices for tensor of dimension 1')\n",
"</pre>\n"
],
"text/plain": [
"13:06:58.009 | \u001b[38;5;160mERROR\u001b[0m | Flow run\u001b[35m 'khaki-hippo'\u001b[0m - Finished in state \u001b[38;5;160mFailed\u001b[0m('Flow run encountered an exception: IndexError: too many indices for tensor of dimension 1')\n"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"ename": "IndexError",
"evalue": "too many indices for tensor of dimension 1",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mIndexError\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:1345\u001b[0m, in \u001b[0;36mFlow.__call__\u001b[0;34m(self, return_state, wait_for, *args, **kwargs)\u001b[0m\n\u001b[1;32m 1341\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m track_viz_task(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39misasync, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mname, parameters)\n\u001b[1;32m 1343\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mprefect\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mflow_engine\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m run_flow\n\u001b[0;32m-> 1345\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrun_flow\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1346\u001b[0m \u001b[43m \u001b[49m\u001b[43mflow\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1347\u001b[0m \u001b[43m \u001b[49m\u001b[43mparameters\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mparameters\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1348\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 1349\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 1350\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:818\u001b[0m, in \u001b[0;36mrun_flow\u001b[0;34m(flow, flow_run, parameters, wait_for, return_type)\u001b[0m\n\u001b[1;32m 816\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m run_flow_async(\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 817\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 818\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrun_flow_sync\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:698\u001b[0m, in \u001b[0;36mrun_flow_sync\u001b[0;34m(flow, flow_run, parameters, wait_for, return_type)\u001b[0m\n\u001b[1;32m 695\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mrun_context():\n\u001b[1;32m 696\u001b[0m engine\u001b[38;5;241m.\u001b[39mcall_flow_fn()\n\u001b[0;32m--> 698\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mstate \u001b[38;5;28;01mif\u001b[39;00m return_type \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mstate\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m \u001b[43mengine\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/flow_engine.py:255\u001b[0m, in \u001b[0;36mFlowRunEngine.result\u001b[0;34m(self, raise_on_failure)\u001b[0m\n\u001b[1;32m 253\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_raised \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m NotSet:\n\u001b[1;32m 254\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m raise_on_failure:\n\u001b[0;32m--> 255\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_raised\n\u001b[1;32m 256\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_raised\n\u001b[1;32m 258\u001b[0m \u001b[38;5;66;03m# This is a fall through case which leans on the existing state result mechanics to get the\u001b[39;00m\n\u001b[1;32m 259\u001b[0m \u001b[38;5;66;03m# return value. This is necessary because we currently will return a State object if the\u001b[39;00m\n\u001b[1;32m 260\u001b[0m \u001b[38;5;66;03m# the State was Prefect-created.\u001b[39;00m\n\u001b[1;32m 261\u001b[0m \u001b[38;5;66;03m# TODO: Remove the need to get the result from a State except in cases where the return value\u001b[39;00m\n\u001b[1;32m 262\u001b[0m \u001b[38;5;66;03m# is a State object.\u001b[39;00m\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:652\u001b[0m, in \u001b[0;36mFlowRunEngine.run_context\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 645\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m timeout_context(\n\u001b[1;32m 646\u001b[0m seconds\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mflow\u001b[38;5;241m.\u001b[39mtimeout_seconds,\n\u001b[1;32m 647\u001b[0m timeout_exc_type\u001b[38;5;241m=\u001b[39mFlowRunTimeoutError,\n\u001b[1;32m 648\u001b[0m ):\n\u001b[1;32m 649\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mlogger\u001b[38;5;241m.\u001b[39mdebug(\n\u001b[1;32m 650\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mExecuting flow \u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mflow\u001b[38;5;241m.\u001b[39mname\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m for flow run \u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mflow_run\u001b[38;5;241m.\u001b[39mname\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m...\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 651\u001b[0m )\n\u001b[0;32m--> 652\u001b[0m \u001b[38;5;28;01myield\u001b[39;00m \u001b[38;5;28mself\u001b[39m\n\u001b[1;32m 653\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mTimeoutError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m exc:\n\u001b[1;32m 654\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhandle_timeout(exc)\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:696\u001b[0m, in \u001b[0;36mrun_flow_sync\u001b[0;34m(flow, flow_run, parameters, wait_for, return_type)\u001b[0m\n\u001b[1;32m 694\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mis_running():\n\u001b[1;32m 695\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mrun_context():\n\u001b[0;32m--> 696\u001b[0m \u001b[43mengine\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcall_flow_fn\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 698\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mstate \u001b[38;5;28;01mif\u001b[39;00m return_type \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mstate\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mresult()\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/flow_engine.py:675\u001b[0m, in \u001b[0;36mFlowRunEngine.call_flow_fn\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 673\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m _call_flow_fn()\n\u001b[1;32m 674\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 675\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[43mcall_with_parameters\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mflow\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfn\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mparameters\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 676\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhandle_success(result)\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/callables.py:206\u001b[0m, in \u001b[0;36mcall_with_parameters\u001b[0;34m(fn, parameters)\u001b[0m\n\u001b[1;32m 198\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 199\u001b[0m \u001b[38;5;124;03mCall a function with parameters extracted with `get_call_parameters`\u001b[39;00m\n\u001b[1;32m 200\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 203\u001b[0m \u001b[38;5;124;03mthe args/kwargs using `parameters_to_positional_and_keyword` directly\u001b[39;00m\n\u001b[1;32m 204\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 205\u001b[0m args, kwargs \u001b[38;5;241m=\u001b[39m parameters_to_args_kwargs(fn, parameters)\n\u001b[0;32m--> 206\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfn\u001b[49m\u001b[43m(\u001b[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[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\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_dask/task_runners.py:143\u001b[0m, in \u001b[0;36mPrefectDaskFuture.result\u001b[0;34m(self, timeout, raise_on_failure)\u001b[0m\n\u001b[1;32m 140\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 141\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m future_result\n\u001b[0;32m--> 143\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[43m_final_state\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 144\u001b[0m \u001b[43m \u001b[49m\u001b[43mraise_on_failure\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mraise_on_failure\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfetch\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\n\u001b[1;32m 145\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 146\u001b[0m \u001b[38;5;66;03m# state.result is a `sync_compatible` function that may or may not return an awaitable\u001b[39;00m\n\u001b[1;32m 147\u001b[0m \u001b[38;5;66;03m# depending on whether the parent frame is sync or not\u001b[39;00m\n\u001b[1;32m 148\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m asyncio\u001b[38;5;241m.\u001b[39miscoroutine(_result):\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/client/schemas/objects.py:314\u001b[0m, in \u001b[0;36mState.result\u001b[0;34m(self, raise_on_failure, fetch, retry_result_failure)\u001b[0m\n\u001b[1;32m 229\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 230\u001b[0m \u001b[38;5;124;03mRetrieve the result attached to this state.\u001b[39;00m\n\u001b[1;32m 231\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 310\u001b[0m \u001b[38;5;124;03m >>> await flow_run.state.result(raise_on_failure=True, fetch=True) # Raises `ValueError(\"oh no!\")`\u001b[39;00m\n\u001b[1;32m 311\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 312\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mprefect\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mstates\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m get_state_result\n\u001b[0;32m--> 314\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mget_state_result\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 315\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 316\u001b[0m \u001b[43m \u001b[49m\u001b[43mraise_on_failure\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mraise_on_failure\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 317\u001b[0m \u001b[43m \u001b[49m\u001b[43mfetch\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfetch\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 318\u001b[0m \u001b[43m \u001b[49m\u001b[43mretry_result_failure\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mretry_result_failure\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 319\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/states.py:75\u001b[0m, in \u001b[0;36mget_state_result\u001b[0;34m(state, raise_on_failure, fetch, retry_result_failure)\u001b[0m\n\u001b[1;32m 73\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m state\u001b[38;5;241m.\u001b[39mdata\n\u001b[1;32m 74\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m---> 75\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_get_state_result\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 76\u001b[0m \u001b[43m \u001b[49m\u001b[43mstate\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 77\u001b[0m \u001b[43m \u001b[49m\u001b[43mraise_on_failure\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mraise_on_failure\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 78\u001b[0m \u001b[43m \u001b[49m\u001b[43mretry_result_failure\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mretry_result_failure\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 79\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/utilities/asyncutils.py:399\u001b[0m, in \u001b[0;36msync_compatible.<locals>.coroutine_wrapper\u001b[0;34m(_sync, *args, **kwargs)\u001b[0m\n\u001b[1;32m 397\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ctx_call()\n\u001b[1;32m 398\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 399\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrun_coro_as_sync\u001b[49m\u001b[43m(\u001b[49m\u001b[43mctx_call\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py:243\u001b[0m, in \u001b[0;36mrun_coro_as_sync\u001b[0;34m(coroutine, force_new_thread, wait_for_result)\u001b[0m\n\u001b[1;32m 241\u001b[0m runner\u001b[38;5;241m.\u001b[39msubmit(call)\n\u001b[1;32m 242\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\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\u001b[1;32m 244\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyboardInterrupt\u001b[39;00m:\n\u001b[1;32m 245\u001b[0m call\u001b[38;5;241m.\u001b[39mcancel()\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/_internal/concurrency/calls.py:312\u001b[0m, in \u001b[0;36mCall.result\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 306\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 307\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 308\u001b[0m \u001b[38;5;124;03m Wait for the result of the call.\u001b[39;00m\n\u001b[1;32m 309\u001b[0m \n\u001b[1;32m 310\u001b[0m \u001b[38;5;124;03m Not safe for use from asynchronous contexts.\u001b[39;00m\n\u001b[1;32m 311\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m--> 312\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:182\u001b[0m, in \u001b[0;36mFuture.result\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 180\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CancelledError()\n\u001b[1;32m 181\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--> 182\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 183\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 184\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:383\u001b[0m, in \u001b[0;36mCall._run_async\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 381\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 382\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 383\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m coro\n\u001b[1;32m 384\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 385\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 386\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 387\u001b[0m \u001b[38;5;66;03m# there's no need to keep a reference to them\u001b[39;00m\n\u001b[1;32m 388\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/utilities/asyncutils.py:225\u001b[0m, in \u001b[0;36mrun_coro_as_sync.<locals>.coroutine_wrapper\u001b[0;34m()\u001b[0m\n\u001b[1;32m 223\u001b[0m task \u001b[38;5;241m=\u001b[39m create_task(coroutine)\n\u001b[1;32m 224\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m wait_for_result:\n\u001b[0;32m--> 225\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m task\n\u001b[1;32m 226\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 227\u001b[0m RUNNING_IN_RUN_SYNC_LOOP_FLAG\u001b[38;5;241m.\u001b[39mreset(token1)\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/asyncutils.py:389\u001b[0m, in \u001b[0;36msync_compatible.<locals>.coroutine_wrapper.<locals>.ctx_call\u001b[0;34m()\u001b[0m\n\u001b[1;32m 387\u001b[0m token \u001b[38;5;241m=\u001b[39m RUNNING_ASYNC_FLAG\u001b[38;5;241m.\u001b[39mset(\u001b[38;5;28;01mTrue\u001b[39;00m)\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 async_fn(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 390\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 391\u001b[0m RUNNING_ASYNC_FLAG\u001b[38;5;241m.\u001b[39mreset(token)\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/states.py:138\u001b[0m, in \u001b[0;36m_get_state_result\u001b[0;34m(state, raise_on_failure, retry_result_failure)\u001b[0m\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m UnfinishedRun(\n\u001b[1;32m 132\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 133\u001b[0m )\n\u001b[1;32m 135\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 136\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 137\u001b[0m ):\n\u001b[0;32m--> 138\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 140\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(state\u001b[38;5;241m.\u001b[39mdata, (BaseResult, ResultRecordMetadata)):\n\u001b[1;32m 141\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m _get_state_result_data_with_retries(\n\u001b[1;32m 142\u001b[0m state, retry_result_failure\u001b[38;5;241m=\u001b[39mretry_result_failure\n\u001b[1;32m 143\u001b[0m )\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py:763\u001b[0m, in \u001b[0;36mrun_context\u001b[0;34m()\u001b[0m\n\u001b[1;32m 760\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mis_cancelled():\n\u001b[1;32m 761\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CancelledError(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mTask run cancelled by the task runner\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 763\u001b[0m \u001b[38;5;28;01myield\u001b[39;00m \u001b[38;5;28mself\u001b[39m\n\u001b[1;32m 764\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mTimeoutError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m exc:\n\u001b[1;32m 765\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhandle_timeout(exc)\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py:1323\u001b[0m, in \u001b[0;36mrun_task_sync\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1321\u001b[0m run_coro_as_sync(engine\u001b[38;5;241m.\u001b[39mwait_until_ready())\n\u001b[1;32m 1322\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mrun_context(), engine\u001b[38;5;241m.\u001b[39mtransaction_context() \u001b[38;5;28;01mas\u001b[39;00m txn:\n\u001b[0;32m-> 1323\u001b[0m engine\u001b[38;5;241m.\u001b[39mcall_task_fn(txn)\n\u001b[1;32m 1325\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mstate \u001b[38;5;28;01mif\u001b[39;00m return_type \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mstate\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mresult()\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/task_engine.py:786\u001b[0m, in \u001b[0;36mcall_task_fn\u001b[0;34m()\u001b[0m\n\u001b[1;32m 784\u001b[0m result \u001b[38;5;241m=\u001b[39m call_with_parameters(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtask\u001b[38;5;241m.\u001b[39mfn, parameters)\n\u001b[1;32m 785\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 786\u001b[0m result \u001b[38;5;241m=\u001b[39m call_with_parameters(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtask\u001b[38;5;241m.\u001b[39mfn, parameters)\n\u001b[1;32m 787\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhandle_success(result, transaction\u001b[38;5;241m=\u001b[39mtransaction)\n\u001b[1;32m 788\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m result\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/prefect/utilities/callables.py:206\u001b[0m, in \u001b[0;36mcall_with_parameters\u001b[0;34m()\u001b[0m\n\u001b[1;32m 198\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 199\u001b[0m \u001b[38;5;124;03mCall a function with parameters extracted with `get_call_parameters`\u001b[39;00m\n\u001b[1;32m 200\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 203\u001b[0m \u001b[38;5;124;03mthe args/kwargs using `parameters_to_positional_and_keyword` directly\u001b[39;00m\n\u001b[1;32m 204\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 205\u001b[0m args, kwargs \u001b[38;5;241m=\u001b[39m parameters_to_args_kwargs(fn, parameters)\n\u001b[0;32m--> 206\u001b[0m \u001b[38;5;28;01mreturn\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/mlip-arena/mlip_arena/tasks/md.py:363\u001b[0m, in \u001b[0;36mrun\u001b[0;34m()\u001b[0m\n\u001b[1;32m 360\u001b[0m md_runner\u001b[38;5;241m.\u001b[39mattach(_callback, interval\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1\u001b[39m)\n\u001b[1;32m 362\u001b[0m start_time \u001b[38;5;241m=\u001b[39m datetime\u001b[38;5;241m.\u001b[39mnow()\n\u001b[0;32m--> 363\u001b[0m md_runner\u001b[38;5;241m.\u001b[39mrun(steps\u001b[38;5;241m=\u001b[39mn_steps)\n\u001b[1;32m 364\u001b[0m end_time \u001b[38;5;241m=\u001b[39m datetime\u001b[38;5;241m.\u001b[39mnow()\n\u001b[1;32m 366\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m traj_file \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\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/ase/md/npt.py:277\u001b[0m, in \u001b[0;36mrun\u001b[0;34m()\u001b[0m\n\u001b[1;32m 275\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Perform a number of time steps.\"\"\"\u001b[39;00m\n\u001b[1;32m 276\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39minitialized:\n\u001b[0;32m--> 277\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39minitialize()\n\u001b[1;32m 278\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 279\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhave_the_atoms_been_changed():\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py:399\u001b[0m, in \u001b[0;36minitialize\u001b[0;34m()\u001b[0m\n\u001b[1;32m 396\u001b[0m deltazeta \u001b[38;5;241m=\u001b[39m dt \u001b[38;5;241m*\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtfact \u001b[38;5;241m*\u001b[39m (atoms\u001b[38;5;241m.\u001b[39mget_kinetic_energy() \u001b[38;5;241m-\u001b[39m\n\u001b[1;32m 397\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdesiredEkin)\n\u001b[1;32m 398\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mzeta_past \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mzeta \u001b[38;5;241m-\u001b[39m deltazeta\n\u001b[0;32m--> 399\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_calculate_q_past_and_future()\n\u001b[1;32m 400\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39minitialized \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m1\u001b[39m\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/md/npt.py:608\u001b[0m, in \u001b[0;36m_calculate_q_past_and_future\u001b[0;34m()\u001b[0m\n\u001b[1;32m 606\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m i \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mrange\u001b[39m(\u001b[38;5;241m2\u001b[39m):\n\u001b[1;32m 607\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mq_past \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mq \u001b[38;5;241m-\u001b[39m dt \u001b[38;5;241m*\u001b[39m np\u001b[38;5;241m.\u001b[39mdot(p \u001b[38;5;241m/\u001b[39m m, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39minv_h)\n\u001b[0;32m--> 608\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_calculate_q_future(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39matoms\u001b[38;5;241m.\u001b[39mget_forces(md\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m))\n\u001b[1;32m 609\u001b[0m p \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39mdot(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mq_future \u001b[38;5;241m-\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mq_past, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mh \u001b[38;5;241m/\u001b[39m (\u001b[38;5;241m2\u001b[39m \u001b[38;5;241m*\u001b[39m dt)) \u001b[38;5;241m*\u001b[39m m\n\u001b[1;32m 610\u001b[0m e \u001b[38;5;241m=\u001b[39m ekin(p)\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/atoms.py:812\u001b[0m, in \u001b[0;36mget_forces\u001b[0;34m()\u001b[0m\n\u001b[1;32m 810\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_calc \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 811\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mAtoms object has no calculator.\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[0;32m--> 812\u001b[0m forces \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_calc\u001b[38;5;241m.\u001b[39mget_forces(\u001b[38;5;28mself\u001b[39m)\n\u001b[1;32m 814\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m apply_constraint:\n\u001b[1;32m 815\u001b[0m \u001b[38;5;66;03m# We need a special md flag here because for MD we want\u001b[39;00m\n\u001b[1;32m 816\u001b[0m \u001b[38;5;66;03m# to skip real constraints but include special \"constraints\"\u001b[39;00m\n\u001b[1;32m 817\u001b[0m \u001b[38;5;66;03m# Like Hookean.\u001b[39;00m\n\u001b[1;32m 818\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m constraint \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconstraints:\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/calculators/abc.py:30\u001b[0m, in \u001b[0;36mget_forces\u001b[0;34m()\u001b[0m\n\u001b[1;32m 29\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mget_forces\u001b[39m(\u001b[38;5;28mself\u001b[39m, atoms\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m):\n\u001b[0;32m---> 30\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_property(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mforces\u001b[39m\u001b[38;5;124m'\u001b[39m, atoms)\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/ase/calculators/calculator.py:538\u001b[0m, in \u001b[0;36mget_property\u001b[0;34m()\u001b[0m\n\u001b[1;32m 535\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39muse_cache:\n\u001b[1;32m 536\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39matoms \u001b[38;5;241m=\u001b[39m atoms\u001b[38;5;241m.\u001b[39mcopy()\n\u001b[0;32m--> 538\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcalculate(atoms, [name], system_changes)\n\u001b[1;32m 540\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m name \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mresults:\n\u001b[1;32m 541\u001b[0m \u001b[38;5;66;03m# For some reason the calculator was not able to do what we want,\u001b[39;00m\n\u001b[1;32m 542\u001b[0m \u001b[38;5;66;03m# and that is OK.\u001b[39;00m\n\u001b[1;32m 543\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m PropertyNotImplementedError(\n\u001b[1;32m 544\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m not present in this \u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcalculation\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(name)\n\u001b[1;32m 545\u001b[0m )\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/mlip-arena/mlip_arena/models/externals/chgnet.py:36\u001b[0m, in \u001b[0;36mcalculate\u001b[0;34m()\u001b[0m\n\u001b[1;32m 30\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcalculate\u001b[39m(\n\u001b[1;32m 31\u001b[0m \u001b[38;5;28mself\u001b[39m,\n\u001b[1;32m 32\u001b[0m atoms: Atoms \u001b[38;5;241m|\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 33\u001b[0m properties: \u001b[38;5;28mlist\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;28;01mNone\u001b[39;00m,\n\u001b[1;32m 34\u001b[0m system_changes: \u001b[38;5;28mlist\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;28;01mNone\u001b[39;00m,\n\u001b[1;32m 35\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m---> 36\u001b[0m \u001b[38;5;28msuper\u001b[39m()\u001b[38;5;241m.\u001b[39mcalculate(atoms, properties, system_changes)\n\u001b[1;32m 38\u001b[0m \u001b[38;5;66;03m# for ase.io.write compatibility\u001b[39;00m\n\u001b[1;32m 39\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mresults\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcrystal_fea\u001b[39m\u001b[38;5;124m\"\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/chgnet/model/dynamics.py:143\u001b[0m, in \u001b[0;36mcalculate\u001b[0;34m()\u001b[0m\n\u001b[1;32m 141\u001b[0m structure \u001b[38;5;241m=\u001b[39m AseAtomsAdaptor\u001b[38;5;241m.\u001b[39mget_structure(atoms)\n\u001b[1;32m 142\u001b[0m graph \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmodel\u001b[38;5;241m.\u001b[39mgraph_converter(structure)\n\u001b[0;32m--> 143\u001b[0m model_prediction \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmodel\u001b[38;5;241m.\u001b[39mpredict_graph(\n\u001b[1;32m 144\u001b[0m graph\u001b[38;5;241m.\u001b[39mto(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdevice), task\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mefsm\u001b[39m\u001b[38;5;124m\"\u001b[39m, return_crystal_feas\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[1;32m 145\u001b[0m )\n\u001b[1;32m 147\u001b[0m \u001b[38;5;66;03m# Convert Result\u001b[39;00m\n\u001b[1;32m 148\u001b[0m factor \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m1\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmodel\u001b[38;5;241m.\u001b[39mis_intensive \u001b[38;5;28;01melse\u001b[39;00m structure\u001b[38;5;241m.\u001b[39mcomposition\u001b[38;5;241m.\u001b[39mnum_atoms\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py:627\u001b[0m, in \u001b[0;36mpredict_graph\u001b[0;34m()\u001b[0m\n\u001b[1;32m 625\u001b[0m n_steps \u001b[38;5;241m=\u001b[39m math\u001b[38;5;241m.\u001b[39mceil(\u001b[38;5;28mlen\u001b[39m(graphs) \u001b[38;5;241m/\u001b[39m batch_size)\n\u001b[1;32m 626\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m step \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mrange\u001b[39m(n_steps):\n\u001b[0;32m--> 627\u001b[0m prediction \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mforward(\n\u001b[1;32m 628\u001b[0m [\n\u001b[1;32m 629\u001b[0m g\u001b[38;5;241m.\u001b[39mto(model_device)\n\u001b[1;32m 630\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m g \u001b[38;5;129;01min\u001b[39;00m graphs[batch_size \u001b[38;5;241m*\u001b[39m step : batch_size \u001b[38;5;241m*\u001b[39m (step \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m)]\n\u001b[1;32m 631\u001b[0m ],\n\u001b[1;32m 632\u001b[0m task\u001b[38;5;241m=\u001b[39mtask,\n\u001b[1;32m 633\u001b[0m return_site_energies\u001b[38;5;241m=\u001b[39mreturn_site_energies,\n\u001b[1;32m 634\u001b[0m return_atom_feas\u001b[38;5;241m=\u001b[39mreturn_atom_feas,\n\u001b[1;32m 635\u001b[0m return_crystal_feas\u001b[38;5;241m=\u001b[39mreturn_crystal_feas,\n\u001b[1;32m 636\u001b[0m )\n\u001b[1;32m 637\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m key \u001b[38;5;129;01min\u001b[39;00m {\n\u001b[1;32m 638\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124me\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 639\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 644\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcrystal_fea\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 645\u001b[0m } \u001b[38;5;241m&\u001b[39m {\u001b[38;5;241m*\u001b[39mprediction}:\n\u001b[1;32m 646\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m idx, tensor \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28menumerate\u001b[39m(prediction[key]):\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py:359\u001b[0m, in \u001b[0;36mforward\u001b[0;34m()\u001b[0m\n\u001b[1;32m 354\u001b[0m comp_energy \u001b[38;5;241m=\u001b[39m (\n\u001b[1;32m 355\u001b[0m \u001b[38;5;241m0\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcomposition_model \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcomposition_model(graphs)\n\u001b[1;32m 356\u001b[0m )\n\u001b[1;32m 358\u001b[0m \u001b[38;5;66;03m# Make batched graph\u001b[39;00m\n\u001b[0;32m--> 359\u001b[0m batched_graph \u001b[38;5;241m=\u001b[39m BatchedGraph\u001b[38;5;241m.\u001b[39mfrom_graphs(\n\u001b[1;32m 360\u001b[0m graphs,\n\u001b[1;32m 361\u001b[0m bond_basis_expansion\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mbond_basis_expansion,\n\u001b[1;32m 362\u001b[0m angle_basis_expansion\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mangle_basis_expansion,\n\u001b[1;32m 363\u001b[0m compute_stress\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124ms\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m task,\n\u001b[1;32m 364\u001b[0m )\n\u001b[1;32m 366\u001b[0m \u001b[38;5;66;03m# Pass to model\u001b[39;00m\n\u001b[1;32m 367\u001b[0m prediction \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_compute(\n\u001b[1;32m 368\u001b[0m batched_graph,\n\u001b[1;32m 369\u001b[0m compute_force\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m task,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 374\u001b[0m return_crystal_feas\u001b[38;5;241m=\u001b[39mreturn_crystal_feas,\n\u001b[1;32m 375\u001b[0m )\n",
"File \u001b[0;32m/pscratch/sd/c/cyrusyc/.conda/mlip-arena/lib/python3.11/site-packages/chgnet/model/model.py:822\u001b[0m, in \u001b[0;36mfrom_graphs\u001b[0;34m()\u001b[0m\n\u001b[1;32m 819\u001b[0m \u001b[38;5;66;03m# Bonds\u001b[39;00m\n\u001b[1;32m 820\u001b[0m atom_cart_coords \u001b[38;5;241m=\u001b[39m graph\u001b[38;5;241m.\u001b[39matom_frac_coord \u001b[38;5;241m@\u001b[39m lattice\n\u001b[1;32m 821\u001b[0m bond_basis_ag, bond_basis_bg, bond_vectors \u001b[38;5;241m=\u001b[39m bond_basis_expansion(\n\u001b[0;32m--> 822\u001b[0m center\u001b[38;5;241m=\u001b[39matom_cart_coords[graph\u001b[38;5;241m.\u001b[39matom_graph[:, \u001b[38;5;241m0\u001b[39m]],\n\u001b[1;32m 823\u001b[0m neighbor\u001b[38;5;241m=\u001b[39matom_cart_coords[graph\u001b[38;5;241m.\u001b[39matom_graph[:, \u001b[38;5;241m1\u001b[39m]],\n\u001b[1;32m 824\u001b[0m undirected2directed\u001b[38;5;241m=\u001b[39mgraph\u001b[38;5;241m.\u001b[39mundirected2directed,\n\u001b[1;32m 825\u001b[0m image\u001b[38;5;241m=\u001b[39mgraph\u001b[38;5;241m.\u001b[39mneighbor_image,\n\u001b[1;32m 826\u001b[0m lattice\u001b[38;5;241m=\u001b[39mlattice,\n\u001b[1;32m 827\u001b[0m )\n\u001b[1;32m 828\u001b[0m atom_positions\u001b[38;5;241m.\u001b[39mappend(atom_cart_coords)\n\u001b[1;32m 829\u001b[0m bond_bases_ag\u001b[38;5;241m.\u001b[39mappend(bond_basis_ag)\n",
"\u001b[0;31mIndexError\u001b[0m: too many indices for tensor of dimension 1"
]
}
],
"source": [
"results = combustion(atoms)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"mlip_arena"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "mlip-arena",
"language": "python",
"name": "mlip-arena"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.10"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
"state": {},
"version_major": 2,
"version_minor": 0
}
}
},
"nbformat": 4,
"nbformat_minor": 4
}
|