cyrusyc commited on
Commit
05e8129
1 Parent(s): 36c27f3

add orb model to diatomic tasks

Browse files
CITATION.cff ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This CITATION.cff file was generated with cffinit.
2
+ # Visit https://bit.ly/cffinit to generate yours today!
3
+
4
+ cff-version: 1.2.0
5
+ title: MLIP Arena
6
+ message: >-
7
+ If you use this software, please cite it using the
8
+ metadata from this file.
9
+ type: software
10
+ authors:
11
+ - given-names: Yuan
12
+ family-names: Chiang
13
+ email: cyrusyc@lbl.gov
14
+ affiliation: Lawrence Berkeley National Laboratory
15
+ orcid: 'https://orcid.org/0000-0002-4017-7084'
16
+ repository-code: 'https://github.com/atomind-ai/mlip-arena'
17
+ keywords:
18
+ - Quantum Chemistry
19
+ - Foundation Model
20
+ - Interatomic Potentials
21
+ - Machine Learning
22
+ - Force Fields
23
+ license: Apache-2.0
mlip_arena/models/externals.py CHANGED
@@ -3,15 +3,16 @@ import urllib
3
  from typing import Literal
4
 
5
  import matgl
6
- import requests
7
  import torch
8
- from alignn.ff.ff import AlignnAtomwiseCalculator, get_figshare_model_ff, default_path
9
  from ase import Atoms
10
  from chgnet.model.dynamics import CHGNetCalculator
11
- from chgnet.model.model import CHGNet
12
  from fairchem.core import OCPCalculator
13
  from mace.calculators import MACECalculator
14
  from matgl.ext.ase import PESCalculator
 
 
15
  from sevenn.sevennet_calculator import SevenNetCalculator
16
 
17
 
@@ -111,7 +112,7 @@ class MACE_OFF_Medium(MACECalculator):
111
  class CHGNet(CHGNetCalculator):
112
  def __init__(
113
  self,
114
- model: CHGNet | None = None,
115
  use_device: str | None = None,
116
  stress_weight: float | None = 1 / 160.21766208,
117
  on_isolated_atoms: Literal["ignore", "warn", "error"] = "warn",
@@ -173,6 +174,7 @@ class EquiformerV2(OCPCalculator):
173
  force=atoms.get_forces(),
174
  )
175
 
 
176
  class EquiformerV2OC20(OCPCalculator):
177
  def __init__(
178
  self,
@@ -190,6 +192,7 @@ class EquiformerV2OC20(OCPCalculator):
190
  **kwargs,
191
  )
192
 
 
193
  class eSCN(OCPCalculator):
194
  def __init__(
195
  self,
@@ -217,25 +220,19 @@ class eSCN(OCPCalculator):
217
 
218
  class ALIGNN(AlignnAtomwiseCalculator):
219
  def __init__(self, dir_path: str = "/tmp/alignn/", device=None, **kwargs) -> None:
220
- model_path = get_figshare_model_ff(dir_path=dir_path)
221
  device = device or get_freer_device()
222
  super().__init__(path=dir_path, device=device, **kwargs)
223
 
224
- def calculate(self, atoms, properties=None, system_changes=None):
225
- super().calculate(atoms, properties, system_changes)
226
-
227
 
228
  class SevenNet(SevenNetCalculator):
229
  def __init__(self, device=None, **kwargs):
230
- # url = (
231
- # "https://github.com/MDIL-SNU/SevenNet/raw/main/pretrained_potentials"
232
- # "/SevenNet_0__11July2024/checkpoint_sevennet_0.pth"
233
- # )
234
- # ckpt_cache = "/tmp/sevennet_checkpoint.pth.tar"
235
- # response = requests.get(url)
236
- # with open(ckpt_cache, mode="wb") as file:
237
- # file.write(response.content)
238
-
239
  device = device or get_freer_device()
240
-
241
  super().__init__("7net-0", device=device, **kwargs)
 
 
 
 
 
 
 
 
3
  from typing import Literal
4
 
5
  import matgl
 
6
  import torch
7
+ from alignn.ff.ff import AlignnAtomwiseCalculator, get_figshare_model_ff
8
  from ase import Atoms
9
  from chgnet.model.dynamics import CHGNetCalculator
10
+ from chgnet.model.model import CHGNet as CHGNetModel
11
  from fairchem.core import OCPCalculator
12
  from mace.calculators import MACECalculator
13
  from matgl.ext.ase import PESCalculator
14
+ from orb_models.forcefield import pretrained
15
+ from orb_models.forcefield.calculator import ORBCalculator
16
  from sevenn.sevennet_calculator import SevenNetCalculator
17
 
18
 
 
112
  class CHGNet(CHGNetCalculator):
113
  def __init__(
114
  self,
115
+ model: CHGNetModel | None = None,
116
  use_device: str | None = None,
117
  stress_weight: float | None = 1 / 160.21766208,
118
  on_isolated_atoms: Literal["ignore", "warn", "error"] = "warn",
 
174
  force=atoms.get_forces(),
175
  )
176
 
177
+
178
  class EquiformerV2OC20(OCPCalculator):
179
  def __init__(
180
  self,
 
192
  **kwargs,
193
  )
194
 
195
+
196
  class eSCN(OCPCalculator):
197
  def __init__(
198
  self,
 
220
 
221
  class ALIGNN(AlignnAtomwiseCalculator):
222
  def __init__(self, dir_path: str = "/tmp/alignn/", device=None, **kwargs) -> None:
223
+ _ = get_figshare_model_ff(dir_path=dir_path)
224
  device = device or get_freer_device()
225
  super().__init__(path=dir_path, device=device, **kwargs)
226
 
 
 
 
227
 
228
  class SevenNet(SevenNetCalculator):
229
  def __init__(self, device=None, **kwargs):
 
 
 
 
 
 
 
 
 
230
  device = device or get_freer_device()
 
231
  super().__init__("7net-0", device=device, **kwargs)
232
+
233
+
234
+ class ORB(ORBCalculator):
235
+ def __init__(self, device=None, **kwargs):
236
+ device = device or get_freer_device()
237
+ orbff = pretrained.orb_v1(device=device)
238
+ super().__init__(orbff, device=device, **kwargs)
mlip_arena/models/registry.yaml CHANGED
@@ -177,4 +177,26 @@ SevenNet:
177
  date: 2024-07-11
178
  prediction: EFS
179
  nvt: true
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
180
  npt: true
 
177
  date: 2024-07-11
178
  prediction: EFS
179
  nvt: true
180
+ npt: true
181
+
182
+ ORB:
183
+ module: externals
184
+ class: ORB
185
+ family: orb
186
+ username: cyrusyc
187
+ last-update: 2024-03-25T14:30:00
188
+ datetime: 2024-03-25T14:30:00 # TODO: Fake datetime
189
+ datasets:
190
+ - atomind/mptrj # TODO: fake HF dataset repo
191
+ - atomind/alexandria
192
+ cpu-tasks:
193
+ - alexandria
194
+ - qmof
195
+ gpu-tasks:
196
+ - homonuclear-diatomics
197
+ github: https://github.com/orbital-materials/orb-models
198
+ doi:
199
+ date: 2024-09-03
200
+ prediction: EFS
201
+ nvt: true
202
  npt: true
mlip_arena/tasks/combustion/water.ipynb CHANGED
@@ -139,7 +139,7 @@
139
  "source ~/.bashrc\n",
140
  "module load python\n",
141
  "source activate /pscratch/sd/c/cyrusyc/.conda/mlip-arena\n",
142
- "/pscratch/sd/c/cyrusyc/.conda/mlip-arena/bin/python -m distributed.cli.dask_worker tcp://128.55.64.32:35601 --name dummy-name --nthreads 1 --memory-limit 59.60GiB --nanny --death-timeout 86400\n",
143
  "\n"
144
  ]
145
  }
@@ -229,11 +229,11 @@
229
  {
230
  "data": {
231
  "text/html": [
232
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:24.417 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | prefect.engine - Created flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> for flow<span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\"> 'combustion'</span>\n",
233
  "</pre>\n"
234
  ],
235
  "text/plain": [
236
- "10:53:24.417 | \u001b[36mINFO\u001b[0m | prefect.engine - Created flow run\u001b[35m 'masterful-panther'\u001b[0m for flow\u001b[1;35m 'combustion'\u001b[0m\n"
237
  ]
238
  },
239
  "metadata": {},
@@ -242,11 +242,11 @@
242
  {
243
  "data": {
244
  "text/html": [
245
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:24.422 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - 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/flow-runs/flow-run/4d0a29f8-4313-4dd3-b311-ea64abf82a83</span>\n",
246
  "</pre>\n"
247
  ],
248
  "text/plain": [
249
- "10:53:24.422 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - View at \u001b[94mhttps://app.prefect.cloud/account/f7d40474-9362-4bfa-8950-ee6a43ec00f3/workspace/d4bb0913-5f5e-49f7-bfc5-06509088baeb/flow-runs/flow-run/4d0a29f8-4313-4dd3-b311-ea64abf82a83\u001b[0m\n"
250
  ]
251
  },
252
  "metadata": {},
@@ -255,11 +255,11 @@
255
  {
256
  "data": {
257
  "text/html": [
258
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:24.423 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | prefect.task_runner.dask - Connecting to an existing Dask cluster at tcp://128.55.64.32:35601\n",
259
  "</pre>\n"
260
  ],
261
  "text/plain": [
262
- "10:53:24.423 | \u001b[36mINFO\u001b[0m | prefect.task_runner.dask - Connecting to an existing Dask cluster at tcp://128.55.64.32:35601\n"
263
  ]
264
  },
265
  "metadata": {},
@@ -268,11 +268,11 @@
268
  {
269
  "data": {
270
  "text/html": [
271
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:24.430 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | prefect.task_runner.dask - The Dask dashboard is available at <span style=\"color: #0000ff; text-decoration-color: #0000ff\">http://128.55.64.32:8787/status</span>\n",
272
  "</pre>\n"
273
  ],
274
  "text/plain": [
275
- "10:53:24.430 | \u001b[36mINFO\u001b[0m | prefect.task_runner.dask - The Dask dashboard is available at \u001b[94mhttp://128.55.64.32:8787/status\u001b[0m\n"
276
  ]
277
  },
278
  "metadata": {},
@@ -281,11 +281,11 @@
281
  {
282
  "data": {
283
  "text/html": [
284
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:24.927 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Created task run 'md-4' for task 'md'\n",
285
  "</pre>\n"
286
  ],
287
  "text/plain": [
288
- "10:53:24.927 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Created task run 'md-4' for task 'md'\n"
289
  ]
290
  },
291
  "metadata": {},
@@ -294,11 +294,11 @@
294
  {
295
  "data": {
296
  "text/html": [
297
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:24.975 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Created task run 'md-6' for task 'md'\n",
298
  "</pre>\n"
299
  ],
300
  "text/plain": [
301
- "10:53:24.975 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Created task run 'md-6' for task 'md'\n"
302
  ]
303
  },
304
  "metadata": {},
@@ -307,11 +307,11 @@
307
  {
308
  "data": {
309
  "text/html": [
310
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:24.981 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Created task run 'md-0' for task 'md'\n",
311
  "</pre>\n"
312
  ],
313
  "text/plain": [
314
- "10:53:24.981 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Created task run 'md-0' for task 'md'\n"
315
  ]
316
  },
317
  "metadata": {},
@@ -320,11 +320,11 @@
320
  {
321
  "data": {
322
  "text/html": [
323
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:24.989 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Created task run 'md-1' for task 'md'\n",
324
  "</pre>\n"
325
  ],
326
  "text/plain": [
327
- "10:53:24.989 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Created task run 'md-1' for task 'md'\n"
328
  ]
329
  },
330
  "metadata": {},
@@ -333,11 +333,11 @@
333
  {
334
  "data": {
335
  "text/html": [
336
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:24.995 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Created task run 'md-5' for task 'md'\n",
337
  "</pre>\n"
338
  ],
339
  "text/plain": [
340
- "10:53:24.995 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Created task run 'md-5' for task 'md'\n"
341
  ]
342
  },
343
  "metadata": {},
@@ -346,11 +346,11 @@
346
  {
347
  "data": {
348
  "text/html": [
349
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:24.999 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Created task run 'md-7' for task 'md'\n",
350
  "</pre>\n"
351
  ],
352
  "text/plain": [
353
- "10:53:24.999 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Created task run 'md-7' for task 'md'\n"
354
  ]
355
  },
356
  "metadata": {},
@@ -359,11 +359,11 @@
359
  {
360
  "data": {
361
  "text/html": [
362
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:25.002 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Created task run 'md-8' for task 'md'\n",
363
  "</pre>\n"
364
  ],
365
  "text/plain": [
366
- "10:53:25.002 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Created task run 'md-8' for task 'md'\n"
367
  ]
368
  },
369
  "metadata": {},
@@ -372,11 +372,11 @@
372
  {
373
  "data": {
374
  "text/html": [
375
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:25.005 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Created task run 'md-3' for task 'md'\n",
376
  "</pre>\n"
377
  ],
378
  "text/plain": [
379
- "10:53:25.005 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Created task run 'md-3' for task 'md'\n"
380
  ]
381
  },
382
  "metadata": {},
@@ -385,11 +385,11 @@
385
  {
386
  "data": {
387
  "text/html": [
388
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:25.008 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Created task run 'md-2' for task 'md'\n",
389
  "</pre>\n"
390
  ],
391
  "text/plain": [
392
- "10:53:25.008 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Created task run 'md-2' for task 'md'\n"
393
  ]
394
  },
395
  "metadata": {},
@@ -398,11 +398,11 @@
398
  {
399
  "data": {
400
  "text/html": [
401
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:25.577 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Submitted task run 'md-0' for execution.\n",
402
  "</pre>\n"
403
  ],
404
  "text/plain": [
405
- "10:53:25.577 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Submitted task run 'md-0' for execution.\n"
406
  ]
407
  },
408
  "metadata": {},
@@ -411,11 +411,11 @@
411
  {
412
  "data": {
413
  "text/html": [
414
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:25.592 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Submitted task run 'md-1' for execution.\n",
415
  "</pre>\n"
416
  ],
417
  "text/plain": [
418
- "10:53:25.592 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Submitted task run 'md-1' for execution.\n"
419
  ]
420
  },
421
  "metadata": {},
@@ -424,11 +424,11 @@
424
  {
425
  "data": {
426
  "text/html": [
427
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:25.606 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Submitted task run 'md-8' for execution.\n",
428
  "</pre>\n"
429
  ],
430
  "text/plain": [
431
- "10:53:25.606 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Submitted task run 'md-8' for execution.\n"
432
  ]
433
  },
434
  "metadata": {},
@@ -437,11 +437,11 @@
437
  {
438
  "data": {
439
  "text/html": [
440
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:25.613 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Submitted task run 'md-3' for execution.\n",
441
  "</pre>\n"
442
  ],
443
  "text/plain": [
444
- "10:53:25.613 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Submitted task run 'md-3' for execution.\n"
445
  ]
446
  },
447
  "metadata": {},
@@ -450,11 +450,11 @@
450
  {
451
  "data": {
452
  "text/html": [
453
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:25.623 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Submitted task run 'md-2' for execution.\n",
454
  "</pre>\n"
455
  ],
456
  "text/plain": [
457
- "10:53:25.623 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Submitted task run 'md-2' for execution.\n"
458
  ]
459
  },
460
  "metadata": {},
@@ -463,11 +463,11 @@
463
  {
464
  "data": {
465
  "text/html": [
466
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:25.638 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Submitted task run 'md-4' for execution.\n",
467
  "</pre>\n"
468
  ],
469
  "text/plain": [
470
- "10:53:25.638 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Submitted task run 'md-4' for execution.\n"
471
  ]
472
  },
473
  "metadata": {},
@@ -476,11 +476,11 @@
476
  {
477
  "data": {
478
  "text/html": [
479
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:25.713 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Submitted task run 'md-5' for execution.\n",
480
  "</pre>\n"
481
  ],
482
  "text/plain": [
483
- "10:53:25.713 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Submitted task run 'md-5' for execution.\n"
484
  ]
485
  },
486
  "metadata": {},
@@ -489,11 +489,11 @@
489
  {
490
  "data": {
491
  "text/html": [
492
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:25.831 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Submitted task run 'md-6' for execution.\n",
493
  "</pre>\n"
494
  ],
495
  "text/plain": [
496
- "10:53:25.831 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Submitted task run 'md-6' for execution.\n"
497
  ]
498
  },
499
  "metadata": {},
@@ -502,11 +502,37 @@
502
  {
503
  "data": {
504
  "text/html": [
505
- "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">10:53:25.903 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'masterful-panther'</span> - Submitted task run 'md-7' for execution.\n",
506
  "</pre>\n"
507
  ],
508
  "text/plain": [
509
- "10:53:25.903 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'masterful-panther'\u001b[0m - Submitted task run 'md-7' for execution.\n"
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
510
  ]
511
  },
512
  "metadata": {},
 
139
  "source ~/.bashrc\n",
140
  "module load python\n",
141
  "source activate /pscratch/sd/c/cyrusyc/.conda/mlip-arena\n",
142
+ "/pscratch/sd/c/cyrusyc/.conda/mlip-arena/bin/python -m distributed.cli.dask_worker tcp://128.55.64.16:40657 --name dummy-name --nthreads 1 --memory-limit 59.60GiB --nanny --death-timeout 86400\n",
143
  "\n"
144
  ]
145
  }
 
229
  {
230
  "data": {
231
  "text/html": [
232
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:32.556 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | prefect.engine - Created flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> for flow<span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\"> 'combustion'</span>\n",
233
  "</pre>\n"
234
  ],
235
  "text/plain": [
236
+ "18:24:32.556 | \u001b[36mINFO\u001b[0m | prefect.engine - Created flow run\u001b[35m 'airborne-chupacabra'\u001b[0m for flow\u001b[1;35m 'combustion'\u001b[0m\n"
237
  ]
238
  },
239
  "metadata": {},
 
242
  {
243
  "data": {
244
  "text/html": [
245
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:32.563 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - 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/flow-runs/flow-run/fb8616ef-5579-49a7-81ce-0306180ca401</span>\n",
246
  "</pre>\n"
247
  ],
248
  "text/plain": [
249
+ "18:24:32.563 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - View at \u001b[94mhttps://app.prefect.cloud/account/f7d40474-9362-4bfa-8950-ee6a43ec00f3/workspace/d4bb0913-5f5e-49f7-bfc5-06509088baeb/flow-runs/flow-run/fb8616ef-5579-49a7-81ce-0306180ca401\u001b[0m\n"
250
  ]
251
  },
252
  "metadata": {},
 
255
  {
256
  "data": {
257
  "text/html": [
258
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:32.565 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | prefect.task_runner.dask - Connecting to an existing Dask cluster at tcp://128.55.64.16:40657\n",
259
  "</pre>\n"
260
  ],
261
  "text/plain": [
262
+ "18:24:32.565 | \u001b[36mINFO\u001b[0m | prefect.task_runner.dask - Connecting to an existing Dask cluster at tcp://128.55.64.16:40657\n"
263
  ]
264
  },
265
  "metadata": {},
 
268
  {
269
  "data": {
270
  "text/html": [
271
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:32.591 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | prefect.task_runner.dask - The Dask dashboard is available at <span style=\"color: #0000ff; text-decoration-color: #0000ff\">http://128.55.64.16:8787/status</span>\n",
272
  "</pre>\n"
273
  ],
274
  "text/plain": [
275
+ "18:24:32.591 | \u001b[36mINFO\u001b[0m | prefect.task_runner.dask - The Dask dashboard is available at \u001b[94mhttp://128.55.64.16:8787/status\u001b[0m\n"
276
  ]
277
  },
278
  "metadata": {},
 
281
  {
282
  "data": {
283
  "text/html": [
284
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:33.239 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Created task run 'md-4' for task 'md'\n",
285
  "</pre>\n"
286
  ],
287
  "text/plain": [
288
+ "18:24:33.239 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Created task run 'md-4' for task 'md'\n"
289
  ]
290
  },
291
  "metadata": {},
 
294
  {
295
  "data": {
296
  "text/html": [
297
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:33.280 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Created task run 'md-7' for task 'md'\n",
298
  "</pre>\n"
299
  ],
300
  "text/plain": [
301
+ "18:24:33.280 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Created task run 'md-7' for task 'md'\n"
302
  ]
303
  },
304
  "metadata": {},
 
307
  {
308
  "data": {
309
  "text/html": [
310
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:33.286 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Created task run 'md-1' for task 'md'\n",
311
  "</pre>\n"
312
  ],
313
  "text/plain": [
314
+ "18:24:33.286 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Created task run 'md-1' for task 'md'\n"
315
  ]
316
  },
317
  "metadata": {},
 
320
  {
321
  "data": {
322
  "text/html": [
323
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:33.289 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Created task run 'md-2' for task 'md'\n",
324
  "</pre>\n"
325
  ],
326
  "text/plain": [
327
+ "18:24:33.289 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Created task run 'md-2' for task 'md'\n"
328
  ]
329
  },
330
  "metadata": {},
 
333
  {
334
  "data": {
335
  "text/html": [
336
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:33.292 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Created task run 'md-5' for task 'md'\n",
337
  "</pre>\n"
338
  ],
339
  "text/plain": [
340
+ "18:24:33.292 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Created task run 'md-5' for task 'md'\n"
341
  ]
342
  },
343
  "metadata": {},
 
346
  {
347
  "data": {
348
  "text/html": [
349
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:33.295 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Created task run 'md-6' for task 'md'\n",
350
  "</pre>\n"
351
  ],
352
  "text/plain": [
353
+ "18:24:33.295 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Created task run 'md-6' for task 'md'\n"
354
  ]
355
  },
356
  "metadata": {},
 
359
  {
360
  "data": {
361
  "text/html": [
362
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:33.298 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Created task run 'md-9' for task 'md'\n",
363
  "</pre>\n"
364
  ],
365
  "text/plain": [
366
+ "18:24:33.298 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Created task run 'md-9' for task 'md'\n"
367
  ]
368
  },
369
  "metadata": {},
 
372
  {
373
  "data": {
374
  "text/html": [
375
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:33.301 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Created task run 'md-0' for task 'md'\n",
376
  "</pre>\n"
377
  ],
378
  "text/plain": [
379
+ "18:24:33.301 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Created task run 'md-0' for task 'md'\n"
380
  ]
381
  },
382
  "metadata": {},
 
385
  {
386
  "data": {
387
  "text/html": [
388
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:33.304 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Created task run 'md-3' for task 'md'\n",
389
  "</pre>\n"
390
  ],
391
  "text/plain": [
392
+ "18:24:33.304 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Created task run 'md-3' for task 'md'\n"
393
  ]
394
  },
395
  "metadata": {},
 
398
  {
399
  "data": {
400
  "text/html": [
401
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:33.306 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Created task run 'md-8' for task 'md'\n",
402
  "</pre>\n"
403
  ],
404
  "text/plain": [
405
+ "18:24:33.306 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Created task run 'md-8' for task 'md'\n"
406
  ]
407
  },
408
  "metadata": {},
 
411
  {
412
  "data": {
413
  "text/html": [
414
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:37.559 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Submitted task run 'md-8' for execution.\n",
415
  "</pre>\n"
416
  ],
417
  "text/plain": [
418
+ "18:24:37.559 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Submitted task run 'md-8' for execution.\n"
419
  ]
420
  },
421
  "metadata": {},
 
424
  {
425
  "data": {
426
  "text/html": [
427
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:37.712 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Submitted task run 'md-5' for execution.\n",
428
  "</pre>\n"
429
  ],
430
  "text/plain": [
431
+ "18:24:37.712 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Submitted task run 'md-5' for execution.\n"
432
  ]
433
  },
434
  "metadata": {},
 
437
  {
438
  "data": {
439
  "text/html": [
440
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:37.731 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Submitted task run 'md-4' for execution.\n",
441
  "</pre>\n"
442
  ],
443
  "text/plain": [
444
+ "18:24:37.731 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Submitted task run 'md-4' for execution.\n"
445
  ]
446
  },
447
  "metadata": {},
 
450
  {
451
  "data": {
452
  "text/html": [
453
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:37.745 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Submitted task run 'md-7' for execution.\n",
454
  "</pre>\n"
455
  ],
456
  "text/plain": [
457
+ "18:24:37.745 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Submitted task run 'md-7' for execution.\n"
458
  ]
459
  },
460
  "metadata": {},
 
463
  {
464
  "data": {
465
  "text/html": [
466
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:37.755 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Submitted task run 'md-1' for execution.\n",
467
  "</pre>\n"
468
  ],
469
  "text/plain": [
470
+ "18:24:37.755 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Submitted task run 'md-1' for execution.\n"
471
  ]
472
  },
473
  "metadata": {},
 
476
  {
477
  "data": {
478
  "text/html": [
479
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:37.771 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Submitted task run 'md-3' for execution.\n",
480
  "</pre>\n"
481
  ],
482
  "text/plain": [
483
+ "18:24:37.771 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Submitted task run 'md-3' for execution.\n"
484
  ]
485
  },
486
  "metadata": {},
 
489
  {
490
  "data": {
491
  "text/html": [
492
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:37.789 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Submitted task run 'md-0' for execution.\n",
493
  "</pre>\n"
494
  ],
495
  "text/plain": [
496
+ "18:24:37.789 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Submitted task run 'md-0' for execution.\n"
497
  ]
498
  },
499
  "metadata": {},
 
502
  {
503
  "data": {
504
  "text/html": [
505
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:37.803 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Submitted task run 'md-2' for execution.\n",
506
  "</pre>\n"
507
  ],
508
  "text/plain": [
509
+ "18:24:37.803 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Submitted task run 'md-2' for execution.\n"
510
+ ]
511
+ },
512
+ "metadata": {},
513
+ "output_type": "display_data"
514
+ },
515
+ {
516
+ "data": {
517
+ "text/html": [
518
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:37.813 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Submitted task run 'md-6' for execution.\n",
519
+ "</pre>\n"
520
+ ],
521
+ "text/plain": [
522
+ "18:24:37.813 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Submitted task run 'md-6' for execution.\n"
523
+ ]
524
+ },
525
+ "metadata": {},
526
+ "output_type": "display_data"
527
+ },
528
+ {
529
+ "data": {
530
+ "text/html": [
531
+ "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">18:24:37.843 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span> | Flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'airborne-chupacabra'</span> - Submitted task run 'md-9' for execution.\n",
532
+ "</pre>\n"
533
+ ],
534
+ "text/plain": [
535
+ "18:24:37.843 | \u001b[36mINFO\u001b[0m | Flow run\u001b[35m 'airborne-chupacabra'\u001b[0m - Submitted task run 'md-9' for execution.\n"
536
  ]
537
  },
538
  "metadata": {},
mlip_arena/tasks/diatomics/orb/homonuclear-diatomics.json ADDED
The diff for this file is too large to render. See raw diff
 
mlip_arena/tasks/diatomics/run.ipynb CHANGED
The diff for this file is too large to render. See raw diff
 
mlip_arena/tasks/run.py CHANGED
@@ -240,14 +240,29 @@ def md(
240
  traj_file.parent.mkdir(parents=True, exist_ok=True)
241
 
242
  if restart and traj_file.exists():
243
- traj = read(traj_file, index=":")
244
- last_atoms = traj[-1]
245
- assert isinstance(last_atoms, Atoms)
246
- last_step = last_atoms.info.get("step", len(traj) * traj_interval)
247
- n_steps -= last_step
248
- traj = Trajectory(traj_file, "a", atoms)
249
- atoms.set_positions(last_atoms.get_positions())
250
- atoms.set_momenta(last_atoms.get_momenta())
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
251
  else:
252
  traj = Trajectory(traj_file, "w", atoms)
253
 
 
240
  traj_file.parent.mkdir(parents=True, exist_ok=True)
241
 
242
  if restart and traj_file.exists():
243
+ try:
244
+ traj = read(traj_file, index=":")
245
+ last_atoms = traj[-1]
246
+ assert isinstance(last_atoms, Atoms)
247
+ last_step = last_atoms.info.get("step", len(traj) * traj_interval)
248
+ n_steps -= last_step
249
+ traj = Trajectory(traj_file, "a", atoms)
250
+ atoms.set_positions(last_atoms.get_positions())
251
+ atoms.set_momenta(last_atoms.get_momenta())
252
+ except Exception:
253
+ traj = Trajectory(traj_file, "w", atoms)
254
+
255
+ if not np.isnan(t_schedule).any():
256
+ MaxwellBoltzmannDistribution(
257
+ atoms=atoms,
258
+ temperature_K=t_schedule[last_step],
259
+ rng=np.random.default_rng(seed=mb_velocity_seed),
260
+ )
261
+
262
+ if zero_linear_momentum:
263
+ Stationary(atoms)
264
+ if zero_angular_momentum:
265
+ ZeroRotation(atoms)
266
  else:
267
  traj = Trajectory(traj_file, "w", atoms)
268
 
pyproject.toml CHANGED
@@ -30,6 +30,7 @@ dependencies=[
30
  "torch",
31
  "torch_dftd>=0.4.0",
32
  "huggingface_hub",
 
33
  "torch-geometric",
34
  "safetensors",
35
  "pymatgen"
 
30
  "torch",
31
  "torch_dftd>=0.4.0",
32
  "huggingface_hub",
33
+ "datasets",
34
  "torch-geometric",
35
  "safetensors",
36
  "pymatgen"
serve/tasks/homonuclear-diatomics.py CHANGED
@@ -30,7 +30,7 @@ valid_models = [
30
  mlip_methods = container.multiselect(
31
  "MLIPs",
32
  valid_models,
33
- ["EquiformerV2(OC22)", "CHGNet", "M3GNet", "SevenNet", "MACE-MP(M)"],
34
  )
35
  dft_methods = container.multiselect("DFT Methods", ["GPAW"], [])
36
 
@@ -171,6 +171,16 @@ for i, symbol in enumerate(chemical_symbols[1:]):
171
 
172
  fig.update_layout(
173
  showlegend=True,
 
 
 
 
 
 
 
 
 
 
174
  title_text=f"{name}",
175
  title_x=0.5,
176
  )
 
30
  mlip_methods = container.multiselect(
31
  "MLIPs",
32
  valid_models,
33
+ ["EquiformerV2(OC22)", "CHGNet", "M3GNet", "SevenNet", "MACE-MP(M)", "ORB"],
34
  )
35
  dft_methods = container.multiselect("DFT Methods", ["GPAW"], [])
36
 
 
171
 
172
  fig.update_layout(
173
  showlegend=True,
174
+ legend=dict(
175
+ orientation="v",
176
+ x=0.95,
177
+ xanchor="right",
178
+ y=1,
179
+ yanchor="top",
180
+ bgcolor="rgba(0, 0, 0, 0)"
181
+ # entrywidth=0.3,
182
+ # entrywidthmode='fraction',
183
+ ),
184
  title_text=f"{name}",
185
  title_x=0.5,
186
  )