Tutorial Overview
| Property | Value |
|---|---|
| Difficulty | Advanced |
| Time | 30-45 minutes |
| Prerequisites | Understanding of NEB, ASE, catalysis |
| Goal | Find transition states using CatTsunami tools |
FAIR chemistry models can be used to enumerate and study reaction pathways via transition state search tools built into ASE or in packages like Sella via the ASE interface.
Since the NEB calculations here can be a bit time consuming, we’ll use a small number of steps during the documentation testing, and otherwise use a reasonable guess.
import os
# Use a small number of steps here to keep the docs fast during CI, but otherwise do quite reasonable settings.
fast_docs = os.environ.get("FAST_DOCS", "false").lower() == "true"
if fast_docs:
optimization_steps = 20
else:
optimization_steps = 300Need to install fairchem-core or get UMA access or getting permissions/401 errors?
Install the necessary packages using pip, uv etc
! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunamiGet access to any necessary huggingface gated models
Get and login to your Huggingface account
Request access to https://
huggingface .co /facebook /UMA Create a Huggingface token at https://
huggingface .co /settings /tokens/ with the permission “Permissions: Read access to contents of all public gated repos you can access” Add the token as an environment variable using
huggingface-cli loginor by setting the HF_TOKEN environment variable.
# Login using the huggingface-cli utility
! huggingface-cli login
# alternatively,
import os
os.environ['HF_TOKEN'] = 'MY_TOKEN'Do enumerations in an AdsorbML style¶
from __future__ import annotations
import matplotlib.pyplot as plt
from ase.io import read
from ase.mep import DyNEB
from ase.optimize import BFGS
from fairchem.applications.cattsunami.core import Reaction
from fairchem.applications.cattsunami.core.autoframe import AutoFrameDissociation
from fairchem.applications.cattsunami.databases import DISSOCIATION_REACTION_DB_PATH
from fairchem.core import FAIRChemCalculator, pretrained_mlip
from fairchem.data.oc.core import Adsorbate, AdsorbateSlabConfig, Bulk, Slab
from fairchem.data.oc.databases.pkls import ADSORBATE_PKL_PATH, BULK_PKL_PATH
from x3dase.x3d import X3D
# Instantiate the reaction class for the reaction of interest
reaction = Reaction(
reaction_str_from_db="*CH -> *C + *H",
reaction_db_path=DISSOCIATION_REACTION_DB_PATH,
adsorbate_db_path=ADSORBATE_PKL_PATH,
)/home/runner/work/_tool/Python/3.12.14/x64/lib/python3.12/site-packages/fairchem/applications/cattsunami/core/reaction.py:29: UserWarning: Loading data from a pickle file. Pickle files can execute arbitrary code and should only be loaded from trusted sources. Consider migrating to a safer format such as Parquet, CSV, or JSON.
reaction_db = safe_pickle_load(reaction_db_path)
/home/runner/work/_tool/Python/3.12.14/x64/lib/python3.12/site-packages/fairchem/applications/cattsunami/core/reaction.py:30: UserWarning: Loading data from a pickle file. Pickle files can execute arbitrary code and should only be loaded from trusted sources. Consider migrating to a safer format such as Parquet, CSV, or JSON.
adsorbate_db = safe_pickle_load(adsorbate_db_path)
# Instantiate our adsorbate class for the reactant and product
reactant = Adsorbate(
adsorbate_id_from_db=reaction.reactant1_idx, adsorbate_db_path=ADSORBATE_PKL_PATH
)
product1 = Adsorbate(
adsorbate_id_from_db=reaction.product1_idx, adsorbate_db_path=ADSORBATE_PKL_PATH
)
product2 = Adsorbate(
adsorbate_id_from_db=reaction.product2_idx, adsorbate_db_path=ADSORBATE_PKL_PATH
)/home/runner/work/_tool/Python/3.12.14/x64/lib/python3.12/site-packages/fairchem/data/oc/core/adsorbate.py:79: UserWarning: Loading data from a pickle file. Pickle files can execute arbitrary code and should only be loaded from trusted sources. Consider migrating to a safer format such as Parquet, CSV, or JSON.
adsorbate_db = safe_pickle_load(fp)
# Grab the bulk and cut the slab we are interested in
bulk = Bulk(bulk_src_id_from_db="mp-33", bulk_db_path=BULK_PKL_PATH)
slab = Slab.from_bulk_get_specific_millers(bulk=bulk, specific_millers=(0, 0, 1))/home/runner/work/_tool/Python/3.12.14/x64/lib/python3.12/site-packages/fairchem/data/oc/core/bulk.py:66: UserWarning: Loading data from a pickle file. Pickle files can execute arbitrary code and should only be loaded from trusted sources. Consider migrating to a safer format such as Parquet, CSV, or JSON.
bulk_db = safe_pickle_load(fp)
# Perform site enumeration
# For AdsorbML num_sites = 100, but we use 5 here for brevity. This should be increased for practical use.
reactant_configs = AdsorbateSlabConfig(
slab=slab[0],
adsorbate=reactant,
mode="random_site_heuristic_placement",
num_sites=10,
).atoms_list
product1_configs = AdsorbateSlabConfig(
slab=slab[0],
adsorbate=product1,
mode="random_site_heuristic_placement",
num_sites=10,
).atoms_list
product2_configs = AdsorbateSlabConfig(
slab=slab[0],
adsorbate=product2,
mode="random_site_heuristic_placement",
num_sites=10,
).atoms_list# Instantiate the calculator
predictor = pretrained_mlip.get_predict_unit("uma-s-1p2")
calc = FAIRChemCalculator(predictor, task_name="oc20")WARNING:root:device was not explicitly set, using device='cuda'.
# Relax the reactant systems
reactant_energies = []
for config in reactant_configs:
config.calc = calc
config.pbc = True
opt = BFGS(config)
opt.run(fmax=0.05, steps=optimization_steps)
reactant_energies.append(config.get_potential_energy())WARNING:root:Model is being compiled this might take a while for the first time
W0916 12:38:44.741000 9931 site-packages/torch/_logging/_internal.py:1345] [0/0] Profiler record function <class 'torch.autograd.profiler.record_function'> will be ignored
Step Time Energy fmax
BFGS: 0 12:39:21 -300.933261 4.077974
BFGS: 1 12:39:23 -301.337736 3.517650
BFGS: 2 12:39:23 -302.493299 3.329638
BFGS: 3 12:39:23 -302.249258 8.844289
BFGS: 4 12:39:23 -302.793132 2.773703
BFGS: 5 12:39:23 -302.933644 1.974363
BFGS: 6 12:39:23 -303.058115 1.989273
BFGS: 7 12:39:23 -303.096158 0.702294
BFGS: 8 12:39:23 -303.123328 0.671407
BFGS: 9 12:39:24 -303.178025 1.098177
BFGS: 10 12:39:24 -303.194164 0.722759
BFGS: 11 12:39:24 -303.208954 0.232813
BFGS: 12 12:39:24 -303.212442 0.291844
BFGS: 13 12:39:24 -303.220217 0.347695
BFGS: 14 12:39:25 -303.225474 0.327028
BFGS: 15 12:39:25 -303.229920 0.302810
BFGS: 16 12:39:25 -303.234062 0.303851
BFGS: 17 12:39:26 -303.241095 0.377533
BFGS: 18 12:39:26 -303.264506 0.721592
BFGS: 19 12:39:26 -303.329918 1.497553
BFGS: 20 12:39:26 -303.486169 1.671594
BFGS: 21 12:39:27 -303.522710 2.252730
BFGS: 22 12:39:27 -303.574064 1.549645
BFGS: 23 12:39:27 -303.609133 1.408270
BFGS: 24 12:39:27 -303.733084 1.457965
BFGS: 25 12:39:28 -303.802392 0.977771
BFGS: 26 12:39:28 -303.876327 1.219008
BFGS: 27 12:39:28 -303.985030 1.204698
BFGS: 28 12:39:28 -304.060475 0.655859
BFGS: 29 12:39:29 -304.092155 0.480082
BFGS: 30 12:39:29 -304.119933 0.439830
BFGS: 31 12:39:29 -304.141051 0.429950
BFGS: 32 12:39:29 -304.158554 0.428387
BFGS: 33 12:39:29 -304.169634 0.436618
BFGS: 34 12:39:30 -304.186882 0.430070
BFGS: 35 12:39:30 -304.202046 0.381558
BFGS: 36 12:39:30 -304.213158 0.314232
BFGS: 37 12:39:30 -304.222288 0.269737
BFGS: 38 12:39:31 -304.238167 0.280133
BFGS: 39 12:39:31 -304.260379 0.388076
BFGS: 40 12:39:31 -304.284831 0.427060
BFGS: 41 12:39:32 -304.297862 0.398017
BFGS: 42 12:39:32 -304.310270 0.388781
BFGS: 43 12:39:32 -304.321778 0.302665
BFGS: 44 12:39:32 -304.330549 0.337481
BFGS: 45 12:39:33 -304.338691 0.257514
BFGS: 46 12:39:33 -304.342122 0.153752
BFGS: 47 12:39:33 -304.344120 0.117182
BFGS: 48 12:39:33 -304.345672 0.140594
BFGS: 49 12:39:34 -304.347189 0.139465
BFGS: 50 12:39:34 -304.348557 0.124314
BFGS: 51 12:39:34 -304.349632 0.101765
BFGS: 52 12:39:34 -304.350366 0.086007
BFGS: 53 12:39:34 -304.350873 0.086371
BFGS: 54 12:39:35 -304.351257 0.072562
BFGS: 55 12:39:35 -304.351504 0.051462
BFGS: 56 12:39:35 -304.351682 0.046224
Step Time Energy fmax
BFGS: 0 12:39:35 -302.799723 3.924140
BFGS: 1 12:39:35 -303.147906 2.772141
BFGS: 2 12:39:36 -303.894792 3.051433
BFGS: 3 12:39:36 -304.039739 2.545936
BFGS: 4 12:39:36 -304.256458 3.532021
BFGS: 5 12:39:36 -304.356203 1.034413
BFGS: 6 12:39:37 -304.422270 0.795706
BFGS: 7 12:39:37 -304.591387 0.866481
BFGS: 8 12:39:37 -304.613256 0.608649
BFGS: 9 12:39:37 -304.657189 0.669367
BFGS: 10 12:39:37 -304.669169 0.431179
BFGS: 11 12:39:37 -304.674312 0.113867
BFGS: 12 12:39:38 -304.675109 0.107986
BFGS: 13 12:39:38 -304.676968 0.154879
BFGS: 14 12:39:38 -304.677902 0.118480
BFGS: 15 12:39:39 -304.678385 0.067274
BFGS: 16 12:39:39 -304.678639 0.058357
BFGS: 17 12:39:39 -304.679039 0.087622
BFGS: 18 12:39:39 -304.679577 0.117350
BFGS: 19 12:39:40 -304.680078 0.086755
BFGS: 20 12:39:40 -304.680399 0.052537
BFGS: 21 12:39:40 -304.680666 0.059553
BFGS: 22 12:39:40 -304.680975 0.095094
BFGS: 23 12:39:41 -304.681274 0.092153
BFGS: 24 12:39:41 -304.681459 0.049946
Step Time Energy fmax
BFGS: 0 12:39:41 -302.755273 3.638026
BFGS: 1 12:39:41 -303.092903 2.522356
BFGS: 2 12:39:41 -303.798164 3.060422
BFGS: 3 12:39:42 -303.932994 2.352438
BFGS: 4 12:39:42 -304.100990 2.273485
BFGS: 5 12:39:42 -304.152872 1.187963
BFGS: 6 12:39:42 -304.225797 0.719586
BFGS: 7 12:39:42 -304.273385 0.610548
BFGS: 8 12:39:43 -304.303683 0.478572
BFGS: 9 12:39:43 -304.315777 0.431939
BFGS: 10 12:39:43 -304.330146 0.333386
BFGS: 11 12:39:43 -304.336754 0.242563
BFGS: 12 12:39:44 -304.339532 0.143328
BFGS: 13 12:39:44 -304.340575 0.123498
BFGS: 14 12:39:44 -304.342540 0.193296
BFGS: 15 12:39:44 -304.344243 0.201074
BFGS: 16 12:39:44 -304.345627 0.112916
BFGS: 17 12:39:44 -304.346552 0.093576
BFGS: 18 12:39:45 -304.347668 0.112954
BFGS: 19 12:39:45 -304.349297 0.194717
BFGS: 20 12:39:45 -304.350918 0.185420
BFGS: 21 12:39:45 -304.351757 0.101840
BFGS: 22 12:39:45 -304.352113 0.063159
BFGS: 23 12:39:46 -304.352339 0.061208
BFGS: 24 12:39:46 -304.352555 0.065262
BFGS: 25 12:39:46 -304.352714 0.043502
Step Time Energy fmax
BFGS: 0 12:39:46 -301.330009 4.077147
BFGS: 1 12:39:47 -301.712100 3.183848
BFGS: 2 12:39:47 -302.733028 3.428428
BFGS: 3 12:39:47 -302.833995 4.308837
BFGS: 4 12:39:47 -303.110870 2.367737
BFGS: 5 12:39:48 -303.255667 2.786512
BFGS: 6 12:39:48 -303.316763 1.263978
BFGS: 7 12:39:48 -303.410269 1.101161
BFGS: 8 12:39:48 -303.681352 2.129463
BFGS: 9 12:39:49 -303.783894 3.013467
BFGS: 10 12:39:49 -303.876058 2.114043
BFGS: 11 12:39:49 -304.017608 0.940643
BFGS: 12 12:39:49 -304.073481 0.831674
BFGS: 13 12:39:49 -304.101858 0.566605
BFGS: 14 12:39:50 -304.121387 0.472989
BFGS: 15 12:39:50 -304.138079 0.249569
BFGS: 16 12:39:50 -304.143180 0.217053
BFGS: 17 12:39:50 -304.152560 0.255824
BFGS: 18 12:39:51 -304.159078 0.290933
BFGS: 19 12:39:51 -304.165357 0.195281
BFGS: 20 12:39:51 -304.169884 0.153909
BFGS: 21 12:39:51 -304.174655 0.161042
BFGS: 22 12:39:51 -304.180000 0.272315
BFGS: 23 12:39:52 -304.185728 0.286067
BFGS: 24 12:39:52 -304.190638 0.202803
BFGS: 25 12:39:52 -304.194754 0.223966
BFGS: 26 12:39:52 -304.199208 0.244612
BFGS: 27 12:39:52 -304.207228 0.456370
BFGS: 28 12:39:52 -304.219048 0.589108
BFGS: 29 12:39:53 -304.234046 0.504418
BFGS: 30 12:39:53 -304.251465 0.418767
BFGS: 31 12:39:53 -304.263173 0.457475
BFGS: 32 12:39:53 -304.277697 0.348780
BFGS: 33 12:39:53 -304.297474 0.339770
BFGS: 34 12:39:54 -304.314430 0.281037
BFGS: 35 12:39:54 -304.329810 0.194504
BFGS: 36 12:39:54 -304.333118 0.209229
BFGS: 37 12:39:54 -304.336718 0.219449
BFGS: 38 12:39:54 -304.340541 0.184748
BFGS: 39 12:39:54 -304.345133 0.171529
BFGS: 40 12:39:54 -304.348469 0.095942
BFGS: 41 12:39:55 -304.349875 0.071959
BFGS: 42 12:39:55 -304.350565 0.071330
BFGS: 43 12:39:55 -304.351325 0.057450
BFGS: 44 12:39:55 -304.352036 0.036609
Step Time Energy fmax
BFGS: 0 12:39:55 -302.180323 3.995883
BFGS: 1 12:39:56 -302.547258 2.910801
BFGS: 2 12:39:56 -303.415478 3.302213
BFGS: 3 12:39:56 -303.581185 2.951794
BFGS: 4 12:39:56 -303.917861 1.715449
BFGS: 5 12:39:56 -303.985927 1.291115
BFGS: 6 12:39:56 -304.174400 0.768794
BFGS: 7 12:39:56 -304.204897 0.755307
BFGS: 8 12:39:56 -304.272957 0.890627
BFGS: 9 12:39:57 -304.299045 0.607818
BFGS: 10 12:39:57 -304.316504 0.212507
BFGS: 11 12:39:57 -304.319798 0.201666
BFGS: 12 12:39:57 -304.331371 0.178097
BFGS: 13 12:39:57 -304.334579 0.168470
BFGS: 14 12:39:58 -304.336432 0.157817
BFGS: 15 12:39:58 -304.338395 0.145187
BFGS: 16 12:39:58 -304.341557 0.192409
BFGS: 17 12:39:58 -304.345028 0.210012
BFGS: 18 12:39:59 -304.347630 0.152998
BFGS: 19 12:39:59 -304.349214 0.135272
BFGS: 20 12:39:59 -304.350143 0.124589
BFGS: 21 12:39:59 -304.351027 0.087471
BFGS: 22 12:40:00 -304.351846 0.068547
BFGS: 23 12:40:00 -304.352202 0.046807
Step Time Energy fmax
BFGS: 0 12:40:00 -302.313933 4.102683
BFGS: 1 12:40:00 -302.688545 3.022457
BFGS: 2 12:40:00 -303.552043 3.217132
BFGS: 3 12:40:01 -303.725947 2.904352
BFGS: 4 12:40:01 -304.046589 1.814781
BFGS: 5 12:40:01 -304.141804 1.785493
BFGS: 6 12:40:01 -304.305827 2.196127
BFGS: 7 12:40:01 -304.492745 1.319373
BFGS: 8 12:40:01 -304.535402 1.016113
BFGS: 9 12:40:02 -304.615789 0.706365
BFGS: 10 12:40:02 -304.643447 0.571533
BFGS: 11 12:40:02 -304.655615 0.311876
BFGS: 12 12:40:02 -304.661529 0.266039
BFGS: 13 12:40:02 -304.666071 0.268359
BFGS: 14 12:40:03 -304.670009 0.232908
BFGS: 15 12:40:03 -304.671739 0.134902
BFGS: 16 12:40:03 -304.672418 0.108893
BFGS: 17 12:40:03 -304.673291 0.141769
BFGS: 18 12:40:04 -304.674641 0.207318
BFGS: 19 12:40:04 -304.676254 0.218810
BFGS: 20 12:40:04 -304.677508 0.134805
BFGS: 21 12:40:04 -304.678228 0.077922
BFGS: 22 12:40:05 -304.678884 0.101407
BFGS: 23 12:40:05 -304.679865 0.159283
BFGS: 24 12:40:05 -304.680845 0.145708
BFGS: 25 12:40:05 -304.681318 0.065644
BFGS: 26 12:40:06 -304.681454 0.021090
Step Time Energy fmax
BFGS: 0 12:40:06 -301.835126 4.175792
BFGS: 1 12:40:06 -302.227337 3.243359
BFGS: 2 12:40:06 -303.194969 3.267767
BFGS: 3 12:40:07 -303.375024 3.140050
BFGS: 4 12:40:07 -303.651369 2.115311
BFGS: 5 12:40:07 -303.849632 2.838721
BFGS: 6 12:40:08 -303.942139 1.339166
BFGS: 7 12:40:08 -304.042880 0.658711
BFGS: 8 12:40:08 -304.141877 1.270535
BFGS: 9 12:40:09 -304.207469 1.293554
BFGS: 10 12:40:09 -304.380757 1.741893
BFGS: 11 12:40:09 -304.493333 1.498580
BFGS: 12 12:40:09 -304.580709 0.891493
BFGS: 13 12:40:09 -304.596308 0.325496
BFGS: 14 12:40:10 -304.604613 0.327426
BFGS: 15 12:40:10 -304.615810 0.441894
BFGS: 16 12:40:10 -304.626741 0.470515
BFGS: 17 12:40:11 -304.633842 0.341443
BFGS: 18 12:40:11 -304.638136 0.248541
BFGS: 19 12:40:11 -304.643716 0.316015
BFGS: 20 12:40:11 -304.652197 0.449995
BFGS: 21 12:40:12 -304.663994 0.408404
BFGS: 22 12:40:12 -304.672425 0.182421
BFGS: 23 12:40:12 -304.675257 0.131050
BFGS: 24 12:40:12 -304.677066 0.113435
BFGS: 25 12:40:13 -304.678492 0.095419
BFGS: 26 12:40:13 -304.680012 0.083569
BFGS: 27 12:40:13 -304.680975 0.063000
BFGS: 28 12:40:13 -304.681327 0.034764
Step Time Energy fmax
BFGS: 0 12:40:13 -302.038786 4.137260
BFGS: 1 12:40:14 -302.435938 3.021382
BFGS: 2 12:40:14 -303.364331 3.320685
BFGS: 3 12:40:14 -303.537911 2.994631
BFGS: 4 12:40:14 -303.848666 1.468166
BFGS: 5 12:40:14 -303.895561 1.089170
BFGS: 6 12:40:15 -303.983265 1.181513
BFGS: 7 12:40:15 -304.039419 0.817720
BFGS: 8 12:40:15 -304.071324 0.786789
BFGS: 9 12:40:16 -304.119491 0.610645
BFGS: 10 12:40:16 -304.151088 0.523149
BFGS: 11 12:40:16 -304.160118 0.264836
BFGS: 12 12:40:16 -304.164346 0.147312
BFGS: 13 12:40:17 -304.166832 0.189871
BFGS: 14 12:40:17 -304.169416 0.201500
BFGS: 15 12:40:17 -304.170771 0.125146
BFGS: 16 12:40:17 -304.171329 0.087582
BFGS: 17 12:40:18 -304.171864 0.113637
BFGS: 18 12:40:18 -304.172802 0.169256
BFGS: 19 12:40:18 -304.174114 0.192353
BFGS: 20 12:40:18 -304.175585 0.146971
BFGS: 21 12:40:19 -304.177368 0.148939
BFGS: 22 12:40:19 -304.180418 0.210527
BFGS: 23 12:40:19 -304.189212 0.477879
BFGS: 24 12:40:20 -304.183533 0.614744
BFGS: 25 12:40:20 -304.198926 0.741659
BFGS: 26 12:40:20 -304.205193 0.719323
BFGS: 27 12:40:20 -304.200029 0.923376
BFGS: 28 12:40:21 -304.230639 0.432760
BFGS: 29 12:40:21 -304.243575 0.337720
BFGS: 30 12:40:21 -304.273396 0.727625
BFGS: 31 12:40:21 -304.290845 0.417743
BFGS: 32 12:40:22 -304.300173 0.369795
BFGS: 33 12:40:22 -304.327121 0.203429
BFGS: 34 12:40:22 -304.330854 0.186374
BFGS: 35 12:40:23 -304.335632 0.175284
BFGS: 36 12:40:23 -304.338653 0.181907
BFGS: 37 12:40:23 -304.342530 0.142508
BFGS: 38 12:40:23 -304.345378 0.083782
BFGS: 39 12:40:24 -304.346897 0.075615
BFGS: 40 12:40:24 -304.347873 0.085513
BFGS: 41 12:40:24 -304.349013 0.082199
BFGS: 42 12:40:25 -304.350139 0.073896
BFGS: 43 12:40:25 -304.350847 0.046700
Step Time Energy fmax
BFGS: 0 12:40:25 -302.042526 4.066749
BFGS: 1 12:40:25 -302.416318 3.336354
BFGS: 2 12:40:25 -303.339140 3.041060
BFGS: 3 12:40:26 -303.502168 2.891173
BFGS: 4 12:40:26 -303.753197 1.952085
BFGS: 5 12:40:26 -303.970051 2.670398
BFGS: 6 12:40:27 -304.063107 1.541974
BFGS: 7 12:40:27 -304.179829 0.665665
BFGS: 8 12:40:27 -304.204327 0.730383
BFGS: 9 12:40:27 -304.245057 0.671387
BFGS: 10 12:40:27 -304.276930 0.487598
BFGS: 11 12:40:27 -304.290621 0.273566
BFGS: 12 12:40:28 -304.296915 0.295754
BFGS: 13 12:40:28 -304.303730 0.268147
BFGS: 14 12:40:28 -304.313083 0.321577
BFGS: 15 12:40:28 -304.320211 0.263709
BFGS: 16 12:40:29 -304.324712 0.194112
BFGS: 17 12:40:29 -304.329541 0.209670
BFGS: 18 12:40:29 -304.335713 0.281863
BFGS: 19 12:40:30 -304.341536 0.281872
BFGS: 20 12:40:30 -304.345366 0.179538
BFGS: 21 12:40:30 -304.347826 0.145845
BFGS: 22 12:40:30 -304.349346 0.121611
BFGS: 23 12:40:31 -304.350671 0.133153
BFGS: 24 12:40:31 -304.351753 0.099758
BFGS: 25 12:40:31 -304.352149 0.045967
Step Time Energy fmax
BFGS: 0 12:40:31 -301.311670 4.061924
BFGS: 1 12:40:32 -301.695326 3.477868
BFGS: 2 12:40:32 -302.740969 3.160937
BFGS: 3 12:40:32 -302.755271 5.633437
BFGS: 4 12:40:32 -303.084875 2.427977
BFGS: 5 12:40:33 -303.240861 1.125175
BFGS: 6 12:40:33 -303.356087 2.353412
BFGS: 7 12:40:33 -303.480528 2.388218
BFGS: 8 12:40:34 -303.792508 2.061522
BFGS: 9 12:40:34 -304.028258 1.643184
BFGS: 10 12:40:34 -304.093601 1.653288
BFGS: 11 12:40:34 -304.217526 1.478998
BFGS: 12 12:40:35 -304.547571 1.208829
BFGS: 13 12:40:35 -304.578483 0.925169
BFGS: 14 12:40:35 -304.604352 0.471188
BFGS: 15 12:40:35 -304.619966 0.458198
BFGS: 16 12:40:35 -304.634712 0.518492
BFGS: 17 12:40:36 -304.644142 0.354296
BFGS: 18 12:40:36 -304.649071 0.203518
BFGS: 19 12:40:36 -304.652814 0.201449
BFGS: 20 12:40:36 -304.657124 0.284581
BFGS: 21 12:40:36 -304.662263 0.318917
BFGS: 22 12:40:37 -304.667233 0.241399
BFGS: 23 12:40:37 -304.670214 0.129811
BFGS: 24 12:40:37 -304.671812 0.166988
BFGS: 25 12:40:37 -304.673466 0.210465
BFGS: 26 12:40:37 -304.675549 0.209870
BFGS: 27 12:40:38 -304.677580 0.149992
BFGS: 28 12:40:38 -304.678889 0.086475
BFGS: 29 12:40:38 -304.679592 0.072746
BFGS: 30 12:40:38 -304.680105 0.059603
BFGS: 31 12:40:38 -304.680610 0.056093
BFGS: 32 12:40:39 -304.681096 0.051087
BFGS: 33 12:40:39 -304.681401 0.038658
# Relax the product systems
product1_energies = []
for config in product1_configs:
config.calc = calc
config.pbc = True
opt = BFGS(config)
opt.run(fmax=0.05, steps=optimization_steps)
product1_energies.append(config.get_potential_energy())WARNING:root:The UMA fast path (merge_mole + compile) is only available for fixed composition, task, charge, and spin. This is optimized for MD applications. Falling back to a less optimized version for subsequent evaluations. Reason: 'Compositions differ from merged model'.
Use inference_settings='batch' for heterogeneous batched evaluations.
Step Time Energy fmax
BFGS: 0 12:40:44 -296.634585 4.343764
BFGS: 1 12:40:44 -297.088550 4.546995
BFGS: 2 12:40:45 -298.433492 3.330889
BFGS: 3 12:40:45 -298.168337 8.707155
BFGS: 4 12:40:45 -298.719296 1.918039
BFGS: 5 12:40:46 -298.799661 1.407149
BFGS: 6 12:40:46 -298.948666 2.041668
BFGS: 7 12:40:46 -299.108325 2.372886
BFGS: 8 12:40:47 -299.361351 2.296872
BFGS: 9 12:40:47 -299.513875 1.361330
BFGS: 10 12:40:47 -299.593408 1.143540
BFGS: 11 12:40:48 -299.879289 1.176412
BFGS: 12 12:40:48 -299.922273 1.139829
BFGS: 13 12:40:48 -299.970493 0.690932
BFGS: 14 12:40:48 -299.990568 0.300916
BFGS: 15 12:40:49 -299.999426 0.374683
BFGS: 16 12:40:49 -300.009434 0.440200
BFGS: 17 12:40:49 -300.022595 0.400425
BFGS: 18 12:40:49 -300.030524 0.265497
BFGS: 19 12:40:50 -300.033936 0.186907
BFGS: 20 12:40:50 -300.036592 0.189137
BFGS: 21 12:40:50 -300.038832 0.175297
BFGS: 22 12:40:51 -300.040937 0.150229
BFGS: 23 12:40:51 -300.042193 0.076556
BFGS: 24 12:40:51 -300.042742 0.065387
BFGS: 25 12:40:52 -300.043039 0.059473
BFGS: 26 12:40:52 -300.043317 0.048496
Step Time Energy fmax
BFGS: 0 12:40:52 -297.188645 4.353011
BFGS: 1 12:40:52 -297.629994 4.484883
BFGS: 2 12:40:53 -298.875245 3.392899
BFGS: 3 12:40:53 -298.982796 5.654070
BFGS: 4 12:40:54 -299.271571 1.818629
BFGS: 5 12:40:54 -299.380076 1.675193
BFGS: 6 12:40:54 -299.719659 1.034707
BFGS: 7 12:40:55 -299.773652 1.678572
BFGS: 8 12:40:55 -299.827854 1.071474
BFGS: 9 12:40:55 -299.916640 1.030296
BFGS: 10 12:40:56 -299.959366 0.951661
BFGS: 11 12:40:56 -299.990774 0.619856
BFGS: 12 12:40:56 -300.009994 0.521462
BFGS: 13 12:40:57 -300.021331 0.534428
BFGS: 14 12:40:57 -300.028731 0.434383
BFGS: 15 12:40:57 -300.036359 0.215102
BFGS: 16 12:40:57 -300.039120 0.136701
BFGS: 17 12:40:58 -300.040021 0.102242
BFGS: 18 12:40:58 -300.040728 0.099225
BFGS: 19 12:40:58 -300.041763 0.100451
BFGS: 20 12:40:59 -300.042612 0.103830
BFGS: 21 12:40:59 -300.043026 0.068269
BFGS: 22 12:40:59 -300.043209 0.040595
Step Time Energy fmax
BFGS: 0 12:41:00 -297.107967 4.344697
BFGS: 1 12:41:00 -297.547742 4.488832
BFGS: 2 12:41:00 -298.825524 3.324205
BFGS: 3 12:41:01 -298.777886 6.638970
BFGS: 4 12:41:01 -299.165741 1.940009
BFGS: 5 12:41:01 -299.291201 1.722284
BFGS: 6 12:41:01 -299.691626 1.415510
BFGS: 7 12:41:02 -299.908680 0.802632
BFGS: 8 12:41:02 -299.943269 0.850037
BFGS: 9 12:41:03 -299.982784 0.573367
BFGS: 10 12:41:03 -300.012470 0.593417
BFGS: 11 12:41:03 -300.022532 0.465292
BFGS: 12 12:41:03 -300.031223 0.205713
BFGS: 13 12:41:04 -300.033996 0.148234
BFGS: 14 12:41:04 -300.036334 0.176976
BFGS: 15 12:41:04 -300.038543 0.197643
BFGS: 16 12:41:05 -300.040285 0.169737
BFGS: 17 12:41:05 -300.041253 0.123936
BFGS: 18 12:41:06 -300.041880 0.102233
BFGS: 19 12:41:06 -300.042596 0.092559
BFGS: 20 12:41:06 -300.043222 0.074653
BFGS: 21 12:41:06 -300.043528 0.050549
BFGS: 22 12:41:07 -300.043630 0.024444
Step Time Energy fmax
BFGS: 0 12:41:07 -296.721095 4.367717
BFGS: 1 12:41:07 -297.175050 4.557409
BFGS: 2 12:41:07 -298.501327 3.427800
BFGS: 3 12:41:08 -298.405421 7.594419
BFGS: 4 12:41:08 -298.837871 1.949119
BFGS: 5 12:41:08 -298.930805 1.596106
BFGS: 6 12:41:09 -299.235980 2.589260
BFGS: 7 12:41:09 -299.467082 2.744796
BFGS: 8 12:41:09 -299.555192 1.658764
BFGS: 9 12:41:09 -299.701593 0.874861
BFGS: 10 12:41:10 -299.767599 0.784568
BFGS: 11 12:41:10 -299.808280 0.820020
BFGS: 12 12:41:10 -299.840445 0.679711
BFGS: 13 12:41:11 -299.860035 0.472873
BFGS: 14 12:41:11 -299.872852 0.398916
BFGS: 15 12:41:11 -299.883919 0.374207
BFGS: 16 12:41:12 -299.896897 0.433422
BFGS: 17 12:41:12 -299.904457 0.380192
BFGS: 18 12:41:12 -299.909098 0.333769
BFGS: 19 12:41:13 -299.917861 0.379017
BFGS: 20 12:41:13 -299.932825 0.706232
BFGS: 21 12:41:13 -299.950944 0.875061
BFGS: 22 12:41:14 -299.971168 0.712671
BFGS: 23 12:41:14 -299.994674 0.516144
BFGS: 24 12:41:14 -300.003986 0.342570
BFGS: 25 12:41:15 -300.015465 0.448844
BFGS: 26 12:41:15 -300.026820 0.418901
BFGS: 27 12:41:15 -300.038023 0.154489
BFGS: 28 12:41:15 -300.040761 0.101910
BFGS: 29 12:41:16 -300.041524 0.075595
BFGS: 30 12:41:16 -300.042196 0.069209
BFGS: 31 12:41:17 -300.042918 0.044965
Step Time Energy fmax
BFGS: 0 12:41:17 -296.651746 4.386670
BFGS: 1 12:41:17 -297.109317 4.585930
BFGS: 2 12:41:17 -298.452883 3.476456
BFGS: 3 12:41:18 -298.377554 7.540644
BFGS: 4 12:41:18 -298.801589 1.968553
BFGS: 5 12:41:18 -298.896938 1.617601
BFGS: 6 12:41:19 -299.215346 2.705618
BFGS: 7 12:41:19 -299.446800 2.905724
BFGS: 8 12:41:19 -299.554351 1.863676
BFGS: 9 12:41:20 -299.712125 0.900559
BFGS: 10 12:41:20 -299.770708 0.896434
BFGS: 11 12:41:20 -299.814571 0.848100
BFGS: 12 12:41:21 -299.846260 0.749990
BFGS: 13 12:41:21 -299.871185 0.553638
BFGS: 14 12:41:21 -299.890750 0.486547
BFGS: 15 12:41:22 -299.914529 0.714539
BFGS: 16 12:41:22 -299.958999 1.190801
BFGS: 17 12:41:22 -300.013990 1.554913
BFGS: 18 12:41:22 -300.068761 1.451573
BFGS: 19 12:41:23 -300.202704 1.595647
BFGS: 20 12:41:23 -300.278561 1.563336
BFGS: 21 12:41:23 -300.408211 1.060067
BFGS: 22 12:41:24 -300.453959 0.851206
BFGS: 23 12:41:24 -300.494410 0.793079
BFGS: 24 12:41:24 -300.519005 0.674104
BFGS: 25 12:41:24 -300.538467 0.438421
BFGS: 26 12:41:25 -300.552842 0.329764
BFGS: 27 12:41:25 -300.562038 0.222654
BFGS: 28 12:41:25 -300.566507 0.175947
BFGS: 29 12:41:26 -300.569342 0.163514
BFGS: 30 12:41:26 -300.572358 0.142100
BFGS: 31 12:41:26 -300.575169 0.096442
BFGS: 32 12:41:27 -300.576904 0.054555
BFGS: 33 12:41:27 -300.577593 0.048648
Step Time Energy fmax
BFGS: 0 12:41:27 -297.574143 4.789163
BFGS: 1 12:41:27 -298.043497 4.878800
BFGS: 2 12:41:28 -299.248322 3.998758
BFGS: 3 12:41:28 -299.805991 2.799015
BFGS: 4 12:41:28 -299.967311 2.363569
BFGS: 5 12:41:29 -300.366270 1.291998
BFGS: 6 12:41:29 -300.432062 0.828364
BFGS: 7 12:41:29 -300.478332 0.767530
BFGS: 8 12:41:30 -300.527486 0.657607
BFGS: 9 12:41:30 -300.554864 0.366645
BFGS: 10 12:41:30 -300.567970 0.251813
BFGS: 11 12:41:30 -300.571821 0.176570
BFGS: 12 12:41:31 -300.574042 0.139409
BFGS: 13 12:41:31 -300.576173 0.094368
BFGS: 14 12:41:32 -300.576791 0.068073
BFGS: 15 12:41:32 -300.577093 0.052672
BFGS: 16 12:41:32 -300.577389 0.067885
BFGS: 17 12:41:33 -300.577780 0.078787
BFGS: 18 12:41:33 -300.578093 0.057060
BFGS: 19 12:41:33 -300.578248 0.035853
Step Time Energy fmax
BFGS: 0 12:41:33 -296.421607 4.363081
BFGS: 1 12:41:33 -296.893188 4.594826
BFGS: 2 12:41:34 -298.312732 3.254643
BFGS: 3 12:41:34 -297.821186 10.347977
BFGS: 4 12:41:34 -298.562406 1.897959
BFGS: 5 12:41:35 -298.635968 1.236667
BFGS: 6 12:41:35 -298.719877 1.587363
BFGS: 7 12:41:35 -298.780156 1.777329
BFGS: 8 12:41:36 -299.021462 1.901924
BFGS: 9 12:41:36 -299.193936 1.853811
BFGS: 10 12:41:36 -299.255967 1.771612
BFGS: 11 12:41:37 -299.409696 1.441653
BFGS: 12 12:41:37 -299.830908 0.977495
BFGS: 13 12:41:38 -299.909829 0.755940
BFGS: 14 12:41:38 -299.929030 0.647857
BFGS: 15 12:41:38 -299.997926 0.906475
BFGS: 16 12:41:38 -300.122224 1.464879
BFGS: 17 12:41:39 -300.163439 1.584284
BFGS: 18 12:41:39 -300.294562 1.209065
BFGS: 19 12:41:39 -300.368406 0.911656
BFGS: 20 12:41:39 -300.428267 0.783541
BFGS: 21 12:41:40 -300.476928 0.624722
BFGS: 22 12:41:40 -300.521622 0.479197
BFGS: 23 12:41:40 -300.536797 0.422606
BFGS: 24 12:41:40 -300.547089 0.280255
BFGS: 25 12:41:41 -300.557545 0.266356
BFGS: 26 12:41:41 -300.566223 0.221065
BFGS: 27 12:41:41 -300.571579 0.157684
BFGS: 28 12:41:42 -300.573873 0.090774
BFGS: 29 12:41:42 -300.574929 0.068799
BFGS: 30 12:41:42 -300.575873 0.065890
BFGS: 31 12:41:43 -300.576664 0.076390
BFGS: 32 12:41:43 -300.577285 0.085567
BFGS: 33 12:41:43 -300.577772 0.086844
BFGS: 34 12:41:44 -300.578150 0.061951
BFGS: 35 12:41:44 -300.578384 0.028762
Step Time Energy fmax
BFGS: 0 12:41:44 -297.448440 4.596669
BFGS: 1 12:41:44 -297.928829 4.659143
BFGS: 2 12:41:45 -299.150122 3.278952
BFGS: 3 12:41:45 -299.330703 3.813217
BFGS: 4 12:41:46 -299.539822 1.156191
BFGS: 5 12:41:46 -299.617634 0.978226
BFGS: 6 12:41:46 -299.811416 0.679097
BFGS: 7 12:41:47 -299.840973 0.673616
BFGS: 8 12:41:47 -299.901485 0.687003
BFGS: 9 12:41:47 -299.980471 0.830927
BFGS: 10 12:41:47 -300.071184 1.253019
BFGS: 11 12:41:48 -300.156508 1.639996
BFGS: 12 12:41:48 -300.239506 1.608109
BFGS: 13 12:41:48 -300.331931 1.210937
BFGS: 14 12:41:48 -300.418189 0.928055
BFGS: 15 12:41:49 -300.446214 1.065263
BFGS: 16 12:41:49 -300.505249 0.610587
BFGS: 17 12:41:49 -300.517904 0.547267
BFGS: 18 12:41:50 -300.544642 0.311365
BFGS: 19 12:41:50 -300.553386 0.234534
BFGS: 20 12:41:50 -300.562551 0.240640
BFGS: 21 12:41:50 -300.567343 0.202934
BFGS: 22 12:41:51 -300.571417 0.144531
BFGS: 23 12:41:51 -300.573929 0.113915
BFGS: 24 12:41:51 -300.575128 0.105524
BFGS: 25 12:41:51 -300.575991 0.091381
BFGS: 26 12:41:52 -300.576965 0.077064
BFGS: 27 12:41:52 -300.577734 0.063188
BFGS: 28 12:41:52 -300.578128 0.035727
Step Time Energy fmax
BFGS: 0 12:41:53 -297.139810 4.407565
BFGS: 1 12:41:53 -297.592848 4.545385
BFGS: 2 12:41:53 -298.872713 3.432026
BFGS: 3 12:41:54 -298.947223 5.901813
BFGS: 4 12:41:54 -299.263065 1.811376
BFGS: 5 12:41:54 -299.360057 1.550492
BFGS: 6 12:41:54 -299.532356 2.134272
BFGS: 7 12:41:55 -299.585648 0.802806
BFGS: 8 12:41:55 -299.606276 0.837627
BFGS: 9 12:41:55 -299.654955 1.101199
BFGS: 10 12:41:56 -299.684404 1.230496
BFGS: 11 12:41:56 -299.737626 1.287485
BFGS: 12 12:41:56 -299.776748 1.086375
BFGS: 13 12:41:57 -299.827044 1.067140
BFGS: 14 12:41:57 -299.864785 1.052937
BFGS: 15 12:41:57 -299.909537 1.011091
BFGS: 16 12:41:57 -299.976145 0.780751
BFGS: 17 12:41:58 -299.993600 0.389271
BFGS: 18 12:41:58 -299.997841 0.558655
BFGS: 19 12:41:58 -300.005228 0.374383
BFGS: 20 12:41:59 -300.014108 0.381110
BFGS: 21 12:41:59 -300.017192 0.348804
BFGS: 22 12:41:59 -300.019556 0.283651
BFGS: 23 12:41:59 -300.020525 0.244620
BFGS: 24 12:42:00 -300.021372 0.219027
BFGS: 25 12:42:00 -300.022365 0.212617
BFGS: 26 12:42:00 -300.023393 0.197691
BFGS: 27 12:42:01 -300.024051 0.200217
BFGS: 28 12:42:01 -300.024427 0.209765
BFGS: 29 12:42:01 -300.024760 0.219590
BFGS: 30 12:42:02 -300.025185 0.227169
BFGS: 31 12:42:02 -300.025596 0.225262
BFGS: 32 12:42:02 -300.025837 0.214420
BFGS: 33 12:42:03 -300.025947 0.204315
BFGS: 34 12:42:03 -300.026044 0.196021
BFGS: 35 12:42:03 -300.026180 0.188931
BFGS: 36 12:42:04 -300.026350 0.186068
BFGS: 37 12:42:04 -300.026490 0.190075
BFGS: 38 12:42:04 -300.026565 0.196789
BFGS: 39 12:42:05 -300.026611 0.201966
BFGS: 40 12:42:05 -300.026676 0.206111
BFGS: 41 12:42:05 -300.026758 0.206967
BFGS: 42 12:42:06 -300.026836 0.202144
BFGS: 43 12:42:06 -300.026879 0.195338
BFGS: 44 12:42:06 -300.026902 0.190860
BFGS: 45 12:42:07 -300.026923 0.187749
BFGS: 46 12:42:07 -300.026951 0.185874
BFGS: 47 12:42:08 -300.026978 0.186527
BFGS: 48 12:42:08 -300.026994 0.189281
BFGS: 49 12:42:08 -300.027001 0.191710
BFGS: 50 12:42:09 -300.027007 0.193648
BFGS: 51 12:42:09 -300.027013 0.195181
BFGS: 52 12:42:09 -300.027026 0.195705
BFGS: 53 12:42:10 -300.027033 0.194535
BFGS: 54 12:42:10 -300.027036 0.192742
BFGS: 55 12:42:10 -300.027037 0.191462
BFGS: 56 12:42:11 -300.027042 0.190485
BFGS: 57 12:42:11 -300.027045 0.189982
BFGS: 58 12:42:11 -300.027048 0.190529
BFGS: 59 12:42:12 -300.027052 0.191906
BFGS: 60 12:42:12 -300.027053 0.193041
BFGS: 61 12:42:12 -300.027053 0.193814
BFGS: 62 12:42:12 -300.027054 0.194479
BFGS: 63 12:42:13 -300.027056 0.194665
BFGS: 64 12:42:13 -300.027058 0.194212
BFGS: 65 12:42:13 -300.027058 0.193580
BFGS: 66 12:42:14 -300.027059 0.193110
BFGS: 67 12:42:14 -300.027059 0.192736
BFGS: 68 12:42:14 -300.027062 0.192575
BFGS: 69 12:42:14 -300.027061 0.192872
BFGS: 70 12:42:15 -300.027063 0.193403
BFGS: 71 12:42:15 -300.027063 0.193804
BFGS: 72 12:42:15 -300.027061 0.194073
BFGS: 73 12:42:16 -300.027062 0.194255
BFGS: 74 12:42:16 -300.027063 0.194157
BFGS: 75 12:42:16 -300.027062 0.193912
BFGS: 76 12:42:17 -300.027061 0.193716
BFGS: 77 12:42:17 -300.027065 0.193588
BFGS: 78 12:42:17 -300.027063 0.193513
BFGS: 79 12:42:17 -300.027064 0.193542
BFGS: 80 12:42:18 -300.027063 0.193660
BFGS: 81 12:42:18 -300.027063 0.193824
BFGS: 82 12:42:18 -300.027063 0.193896
BFGS: 83 12:42:18 -300.027063 0.193981
BFGS: 84 12:42:19 -300.027063 0.194015
BFGS: 85 12:42:19 -300.027063 0.194029
BFGS: 86 12:42:19 -300.027062 0.194015
BFGS: 87 12:42:20 -300.027064 0.193993
BFGS: 88 12:42:20 -300.027063 0.193961
BFGS: 89 12:42:20 -300.027064 0.193956
BFGS: 90 12:42:21 -300.027064 0.193923
BFGS: 91 12:42:21 -300.027063 0.193922
BFGS: 92 12:42:21 -300.027063 0.193910
BFGS: 93 12:42:21 -300.027062 0.193933
BFGS: 94 12:42:22 -300.027062 0.193946
BFGS: 95 12:42:22 -300.027062 0.193930
BFGS: 96 12:42:22 -300.027063 0.193915
BFGS: 97 12:42:23 -300.027063 0.193922
BFGS: 98 12:42:23 -300.027064 0.193930
BFGS: 99 12:42:23 -300.027064 0.193914
BFGS: 100 12:42:24 -300.027063 0.193918
BFGS: 101 12:42:24 -300.027062 0.193919
BFGS: 102 12:42:24 -300.027061 0.193916
BFGS: 103 12:42:25 -300.027063 0.193922
BFGS: 104 12:42:25 -300.027064 0.193921
BFGS: 105 12:42:25 -300.027063 0.193915
BFGS: 106 12:42:25 -300.027063 0.193919
BFGS: 107 12:42:26 -300.027063 0.193916
BFGS: 108 12:42:26 -300.027062 0.193920
BFGS: 109 12:42:26 -300.027062 0.193916
BFGS: 110 12:42:26 -300.027062 0.193914
BFGS: 111 12:42:27 -300.027064 0.193915
BFGS: 112 12:42:27 -300.027065 0.193940
BFGS: 113 12:42:27 -300.027064 0.193921
BFGS: 114 12:42:27 -300.027063 0.193917
BFGS: 115 12:42:28 -300.027064 0.193915
BFGS: 116 12:42:28 -300.027062 0.193943
BFGS: 117 12:42:29 -300.027063 0.193925
BFGS: 118 12:42:29 -300.027062 0.193924
BFGS: 119 12:42:29 -300.027063 0.193915
BFGS: 120 12:42:30 -300.027063 0.193944
BFGS: 121 12:42:30 -300.027061 0.193924
BFGS: 122 12:42:30 -300.027063 0.193915
BFGS: 123 12:42:30 -300.027062 0.193920
BFGS: 124 12:42:31 -300.027063 0.193924
BFGS: 125 12:42:31 -300.027062 0.193919
BFGS: 126 12:42:32 -300.027062 0.193921
BFGS: 127 12:42:32 -300.027062 0.193919
BFGS: 128 12:42:32 -300.027063 0.193917
BFGS: 129 12:42:32 -300.027063 0.193916
BFGS: 130 12:42:33 -300.027063 0.193926
BFGS: 131 12:42:33 -300.027063 0.193922
BFGS: 132 12:42:33 -300.027063 0.193916
BFGS: 133 12:42:34 -300.027062 0.193915
BFGS: 134 12:42:34 -300.027064 0.193928
BFGS: 135 12:42:35 -300.027063 0.193919
BFGS: 136 12:42:35 -300.027063 0.193916
BFGS: 137 12:42:35 -300.027064 0.193917
BFGS: 138 12:42:35 -300.027063 0.193923
BFGS: 139 12:42:36 -300.027063 0.193919
BFGS: 140 12:42:36 -300.027062 0.193927
BFGS: 141 12:42:36 -300.027063 0.193915
BFGS: 142 12:42:36 -300.027063 0.193924
BFGS: 143 12:42:37 -300.027063 0.193922
BFGS: 144 12:42:37 -300.027063 0.193924
BFGS: 145 12:42:37 -300.027063 0.193916
BFGS: 146 12:42:37 -300.027063 0.193921
BFGS: 147 12:42:38 -300.027064 0.193919
BFGS: 148 12:42:38 -300.027064 0.193932
BFGS: 149 12:42:38 -300.027062 0.193919
BFGS: 150 12:42:38 -300.027062 0.193917
BFGS: 151 12:42:39 -300.027064 0.193934
BFGS: 152 12:42:39 -300.027064 0.193931
BFGS: 153 12:42:39 -300.027063 0.193918
BFGS: 154 12:42:39 -300.027062 0.193918
BFGS: 155 12:42:40 -300.027063 0.193921
BFGS: 156 12:42:40 -300.027062 0.193928
BFGS: 157 12:42:40 -300.027064 0.193917
BFGS: 158 12:42:41 -300.027062 0.193918
BFGS: 159 12:42:41 -300.027064 0.193933
BFGS: 160 12:42:41 -300.027062 0.193914
BFGS: 161 12:42:42 -300.027063 0.193918
BFGS: 162 12:42:42 -300.027063 0.193917
BFGS: 163 12:42:42 -300.027064 0.193914
BFGS: 164 12:42:43 -300.027063 0.193919
BFGS: 165 12:42:43 -300.027065 0.193917
BFGS: 166 12:42:43 -300.027063 0.193919
BFGS: 167 12:42:43 -300.027062 0.193920
BFGS: 168 12:42:44 -300.027062 0.193916
BFGS: 169 12:42:44 -300.027064 0.193916
BFGS: 170 12:42:44 -300.027064 0.193921
BFGS: 171 12:42:45 -300.027063 0.193917
BFGS: 172 12:42:45 -300.027062 0.193919
BFGS: 173 12:42:45 -300.027064 0.193914
BFGS: 174 12:42:46 -300.027062 0.193919
BFGS: 175 12:42:46 -300.027064 0.193933
BFGS: 176 12:42:47 -300.027063 0.193917
BFGS: 177 12:42:47 -300.027063 0.193918
BFGS: 178 12:42:47 -300.027063 0.193919
BFGS: 179 12:42:47 -300.027063 0.193922
BFGS: 180 12:42:48 -300.027064 0.193916
BFGS: 181 12:42:48 -300.027063 0.193918
BFGS: 182 12:42:48 -300.027062 0.193916
BFGS: 183 12:42:49 -300.027064 0.193919
BFGS: 184 12:42:49 -300.027064 0.193923
BFGS: 185 12:42:50 -300.027064 0.193920
BFGS: 186 12:42:50 -300.027063 0.193917
BFGS: 187 12:42:50 -300.027063 0.193916
BFGS: 188 12:42:50 -300.027064 0.193920
BFGS: 189 12:42:51 -300.027064 0.193921
BFGS: 190 12:42:51 -300.027064 0.193917
BFGS: 191 12:42:51 -300.027063 0.193922
BFGS: 192 12:42:51 -300.027064 0.193919
BFGS: 193 12:42:52 -300.027062 0.193917
BFGS: 194 12:42:52 -300.027064 0.193917
BFGS: 195 12:42:52 -300.027064 0.193922
BFGS: 196 12:42:53 -300.027065 0.193923
BFGS: 197 12:42:53 -300.027062 0.193921
BFGS: 198 12:42:53 -300.027064 0.193930
BFGS: 199 12:42:54 -300.027062 0.193925
BFGS: 200 12:42:54 -300.027064 0.193932
BFGS: 201 12:42:54 -300.027064 0.193941
BFGS: 202 12:42:55 -300.027062 0.193921
BFGS: 203 12:42:55 -300.027065 0.193933
BFGS: 204 12:42:55 -300.027064 0.193937
BFGS: 205 12:42:56 -300.027064 0.193917
BFGS: 206 12:42:56 -300.027063 0.193933
BFGS: 207 12:42:56 -300.027064 0.193932
BFGS: 208 12:42:56 -300.027063 0.193932
BFGS: 209 12:42:57 -300.027063 0.193922
BFGS: 210 12:42:57 -300.027064 0.193920
BFGS: 211 12:42:58 -300.027063 0.193914
BFGS: 212 12:42:58 -300.027062 0.193913
BFGS: 213 12:42:58 -300.027063 0.193933
BFGS: 214 12:42:58 -300.027063 0.193918
BFGS: 215 12:42:59 -300.027063 0.193920
BFGS: 216 12:42:59 -300.027063 0.193918
BFGS: 217 12:42:59 -300.027066 0.193918
BFGS: 218 12:43:00 -300.027063 0.193920
BFGS: 219 12:43:00 -300.027062 0.193915
BFGS: 220 12:43:00 -300.027064 0.193918
BFGS: 221 12:43:01 -300.027065 0.193922
BFGS: 222 12:43:01 -300.027063 0.193921
BFGS: 223 12:43:01 -300.027063 0.193933
BFGS: 224 12:43:02 -300.027063 0.193932
BFGS: 225 12:43:02 -300.027062 0.193926
BFGS: 226 12:43:02 -300.027062 0.193914
BFGS: 227 12:43:03 -300.027063 0.193920
BFGS: 228 12:43:03 -300.027063 0.193918
BFGS: 229 12:43:03 -300.027064 0.193919
BFGS: 230 12:43:03 -300.027063 0.193915
BFGS: 231 12:43:04 -300.027063 0.193927
BFGS: 232 12:43:04 -300.027063 0.193932
BFGS: 233 12:43:04 -300.027063 0.193931
BFGS: 234 12:43:04 -300.027064 0.193914
BFGS: 235 12:43:05 -300.027063 0.193923
BFGS: 236 12:43:05 -300.027063 0.193918
BFGS: 237 12:43:05 -300.027063 0.193925
BFGS: 238 12:43:06 -300.027062 0.193925
BFGS: 239 12:43:06 -300.027063 0.193919
BFGS: 240 12:43:06 -300.027062 0.193915
BFGS: 241 12:43:06 -300.027064 0.193921
BFGS: 242 12:43:07 -300.027064 0.193918
BFGS: 243 12:43:07 -300.027062 0.193932
BFGS: 244 12:43:07 -300.027064 0.193914
BFGS: 245 12:43:08 -300.027062 0.193930
BFGS: 246 12:43:08 -300.027062 0.193914
BFGS: 247 12:43:08 -300.027063 0.193918
BFGS: 248 12:43:09 -300.027062 0.193927
BFGS: 249 12:43:09 -300.027062 0.193923
BFGS: 250 12:43:09 -300.027064 0.193917
BFGS: 251 12:43:10 -300.027063 0.193913
BFGS: 252 12:43:10 -300.027064 0.193921
BFGS: 253 12:43:11 -300.027063 0.193921
BFGS: 254 12:43:11 -300.027064 0.193934
BFGS: 255 12:43:11 -300.027063 0.193934
BFGS: 256 12:43:11 -300.027062 0.193921
BFGS: 257 12:43:12 -300.027063 0.193918
BFGS: 258 12:43:12 -300.027063 0.193913
BFGS: 259 12:43:12 -300.027062 0.193932
BFGS: 260 12:43:12 -300.027062 0.193918
BFGS: 261 12:43:13 -300.027065 0.193918
BFGS: 262 12:43:13 -300.027064 0.193913
BFGS: 263 12:43:13 -300.027062 0.193931
BFGS: 264 12:43:13 -300.027063 0.193918
BFGS: 265 12:43:14 -300.027063 0.193913
BFGS: 266 12:43:14 -300.027062 0.193920
BFGS: 267 12:43:14 -300.027062 0.193922
BFGS: 268 12:43:14 -300.027065 0.193916
BFGS: 269 12:43:14 -300.027062 0.193921
BFGS: 270 12:43:15 -300.027063 0.193919
BFGS: 271 12:43:15 -300.027062 0.193922
BFGS: 272 12:43:15 -300.027062 0.193910
BFGS: 273 12:43:15 -300.027064 0.193915
BFGS: 274 12:43:15 -300.027065 0.193922
BFGS: 275 12:43:15 -300.027063 0.193923
BFGS: 276 12:43:16 -300.027061 0.193926
BFGS: 277 12:43:16 -300.027064 0.193918
BFGS: 278 12:43:16 -300.027064 0.193919
BFGS: 279 12:43:17 -300.027063 0.193910
BFGS: 280 12:43:17 -300.027062 0.193918
BFGS: 281 12:43:17 -300.027063 0.193918
BFGS: 282 12:43:18 -300.027062 0.193918
BFGS: 283 12:43:18 -300.027063 0.193920
BFGS: 284 12:43:18 -300.027063 0.193931
BFGS: 285 12:43:19 -300.027063 0.193920
BFGS: 286 12:43:19 -300.027064 0.193916
BFGS: 287 12:43:19 -300.027062 0.193918
BFGS: 288 12:43:20 -300.027062 0.193929
BFGS: 289 12:43:20 -300.027063 0.193929
BFGS: 290 12:43:20 -300.027064 0.193914
BFGS: 291 12:43:21 -300.027064 0.193931
BFGS: 292 12:43:21 -300.027063 0.193927
BFGS: 293 12:43:22 -300.027064 0.193923
BFGS: 294 12:43:22 -300.027065 0.193918
BFGS: 295 12:43:22 -300.027062 0.193919
BFGS: 296 12:43:22 -300.027063 0.193920
BFGS: 297 12:43:23 -300.027065 0.193918
BFGS: 298 12:43:23 -300.027061 0.193920
BFGS: 299 12:43:23 -300.027064 0.193920
BFGS: 300 12:43:24 -300.027063 0.193927
Step Time Energy fmax
BFGS: 0 12:43:24 -296.457832 4.364251
BFGS: 1 12:43:24 -296.925389 4.592269
BFGS: 2 12:43:25 -298.330349 3.294118
BFGS: 3 12:43:25 -297.910978 9.880319
BFGS: 4 12:43:25 -298.593194 1.914579
BFGS: 5 12:43:26 -298.669721 1.290046
BFGS: 6 12:43:26 -298.771316 1.786528
BFGS: 7 12:43:26 -298.858622 2.099129
BFGS: 8 12:43:27 -299.113494 2.236785
BFGS: 9 12:43:27 -299.294308 1.898197
BFGS: 10 12:43:27 -299.359309 1.629525
BFGS: 11 12:43:28 -299.505701 1.412447
BFGS: 12 12:43:28 -299.992543 0.895435
BFGS: 13 12:43:28 -300.034455 0.959066
BFGS: 14 12:43:28 -300.110640 1.189035
BFGS: 15 12:43:29 -300.222949 1.255494
BFGS: 16 12:43:29 -300.316011 1.135269
BFGS: 17 12:43:29 -300.465350 0.617064
BFGS: 18 12:43:30 -300.481301 0.579812
BFGS: 19 12:43:30 -300.516344 0.727600
BFGS: 20 12:43:31 -300.538015 0.568277
BFGS: 21 12:43:31 -300.547405 0.423558
BFGS: 22 12:43:31 -300.556640 0.248056
BFGS: 23 12:43:32 -300.567606 0.124821
BFGS: 24 12:43:32 -300.570529 0.116412
BFGS: 25 12:43:32 -300.572003 0.116312
BFGS: 26 12:43:32 -300.573588 0.095523
BFGS: 27 12:43:33 -300.575738 0.096378
BFGS: 28 12:43:33 -300.577287 0.057839
BFGS: 29 12:43:33 -300.577801 0.039046
product2_energies = []
for config in product2_configs:
config.calc = calc
config.pbc = True
opt = BFGS(config)
opt.run(fmax=0.05, steps=optimization_steps)
product2_energies.append(config.get_potential_energy()) Step Time Energy fmax
BFGS: 0 12:43:34 -295.438469 1.067848
BFGS: 1 12:43:34 -295.503217 0.985476
BFGS: 2 12:43:34 -295.716988 0.925001
BFGS: 3 12:43:35 -295.735687 0.546410
BFGS: 4 12:43:35 -295.747767 0.489735
BFGS: 5 12:43:35 -295.784117 0.545078
BFGS: 6 12:43:36 -295.793960 0.496093
BFGS: 7 12:43:36 -295.812345 0.455514
BFGS: 8 12:43:36 -295.825442 0.318873
BFGS: 9 12:43:37 -295.835239 0.187250
BFGS: 10 12:43:37 -295.838440 0.176035
BFGS: 11 12:43:37 -295.840026 0.150545
BFGS: 12 12:43:38 -295.842001 0.113959
BFGS: 13 12:43:38 -295.844023 0.083454
BFGS: 14 12:43:38 -295.845166 0.083998
BFGS: 15 12:43:38 -295.845637 0.079399
BFGS: 16 12:43:39 -295.846057 0.078685
BFGS: 17 12:43:39 -295.846778 0.081897
BFGS: 18 12:43:39 -295.847809 0.086223
BFGS: 19 12:43:40 -295.848833 0.096019
BFGS: 20 12:43:40 -295.849608 0.111345
BFGS: 21 12:43:40 -295.850408 0.129948
BFGS: 22 12:43:40 -295.851987 0.163361
BFGS: 23 12:43:40 -295.856457 0.244996
BFGS: 24 12:43:41 -295.865232 0.354941
BFGS: 25 12:43:41 -295.868158 0.468784
BFGS: 26 12:43:41 -295.882200 0.363718
BFGS: 27 12:43:42 -295.900463 0.268585
BFGS: 28 12:43:42 -295.913350 0.222883
BFGS: 29 12:43:42 -295.918547 0.217608
BFGS: 30 12:43:43 -295.925406 0.187303
BFGS: 31 12:43:43 -295.929581 0.121523
BFGS: 32 12:43:43 -295.931226 0.085264
BFGS: 33 12:43:44 -295.931779 0.066990
BFGS: 34 12:43:44 -295.932217 0.049422
Step Time Energy fmax
BFGS: 0 12:43:44 -295.541744 0.812125
BFGS: 1 12:43:44 -295.597974 0.754239
BFGS: 2 12:43:45 -295.792829 0.557625
BFGS: 3 12:43:45 -295.805477 0.350730
BFGS: 4 12:43:45 -295.810939 0.348188
BFGS: 5 12:43:46 -295.830097 0.297529
BFGS: 6 12:43:46 -295.832783 0.245417
BFGS: 7 12:43:46 -295.837174 0.178079
BFGS: 8 12:43:47 -295.839298 0.107107
BFGS: 9 12:43:47 -295.840348 0.082946
BFGS: 10 12:43:47 -295.840643 0.074408
BFGS: 11 12:43:48 -295.840895 0.054431
BFGS: 12 12:43:48 -295.841197 0.032957
Step Time Energy fmax
BFGS: 0 12:43:48 -295.574144 0.802457
BFGS: 1 12:43:49 -295.627275 0.755922
BFGS: 2 12:43:49 -295.818976 0.497977
BFGS: 3 12:43:49 -295.831745 0.447782
BFGS: 4 12:43:50 -295.839447 0.453935
BFGS: 5 12:43:50 -295.873763 0.416719
BFGS: 6 12:43:50 -295.882115 0.389563
BFGS: 7 12:43:51 -295.893552 0.387195
BFGS: 8 12:43:51 -295.902081 0.256713
BFGS: 9 12:43:51 -295.909064 0.246329
BFGS: 10 12:43:51 -295.912579 0.253366
BFGS: 11 12:43:51 -295.915065 0.235029
BFGS: 12 12:43:52 -295.918293 0.196615
BFGS: 13 12:43:52 -295.922023 0.142438
BFGS: 14 12:43:52 -295.924731 0.147308
BFGS: 15 12:43:53 -295.926296 0.162774
BFGS: 16 12:43:53 -295.927622 0.144474
BFGS: 17 12:43:53 -295.929459 0.096275
BFGS: 18 12:43:53 -295.931250 0.062225
BFGS: 19 12:43:54 -295.932157 0.039963
Step Time Energy fmax
BFGS: 0 12:43:54 -295.648691 0.702920
BFGS: 1 12:43:54 -295.698128 0.676539
BFGS: 2 12:43:54 -295.886525 0.443951
BFGS: 3 12:43:55 -295.898880 0.470853
BFGS: 4 12:43:55 -295.904445 0.459601
BFGS: 5 12:43:55 -295.948632 0.267454
BFGS: 6 12:43:56 -295.951725 0.247742
BFGS: 7 12:43:56 -295.957183 0.162249
BFGS: 8 12:43:56 -295.959428 0.162364
BFGS: 9 12:43:57 -295.961792 0.158468
BFGS: 10 12:43:57 -295.962812 0.141188
BFGS: 11 12:43:57 -295.963742 0.112451
BFGS: 12 12:43:58 -295.964748 0.075755
BFGS: 13 12:43:58 -295.965628 0.071370
BFGS: 14 12:43:58 -295.966116 0.072663
BFGS: 15 12:43:59 -295.966421 0.066333
BFGS: 16 12:43:59 -295.966736 0.045997
Step Time Energy fmax
BFGS: 0 12:43:59 -295.741991 0.690075
BFGS: 1 12:44:00 -295.788841 0.617170
BFGS: 2 12:44:00 -295.944996 0.302064
BFGS: 3 12:44:00 -295.952510 0.267894
BFGS: 4 12:44:00 -295.953933 0.248346
BFGS: 5 12:44:01 -295.960162 0.127468
BFGS: 6 12:44:01 -295.961305 0.123647
BFGS: 7 12:44:02 -295.963087 0.104707
BFGS: 8 12:44:02 -295.964509 0.076508
BFGS: 9 12:44:02 -295.965711 0.060658
BFGS: 10 12:44:03 -295.966132 0.050232
BFGS: 11 12:44:03 -295.966295 0.045581
Step Time Energy fmax
BFGS: 0 12:44:03 -295.114999 1.665812
BFGS: 1 12:44:04 -295.222763 1.504297
BFGS: 2 12:44:04 -295.409736 2.362785
BFGS: 3 12:44:04 -295.492765 0.472077
BFGS: 4 12:44:04 -295.508252 0.607772
BFGS: 5 12:44:05 -295.533646 0.634469
BFGS: 6 12:44:05 -295.546047 0.393558
BFGS: 7 12:44:05 -295.552882 0.253226
BFGS: 8 12:44:06 -295.557141 0.300104
BFGS: 9 12:44:06 -295.562682 0.277344
BFGS: 10 12:44:06 -295.566178 0.173460
BFGS: 11 12:44:06 -295.567384 0.059945
BFGS: 12 12:44:07 -295.567579 0.055362
BFGS: 13 12:44:07 -295.567694 0.060682
BFGS: 14 12:44:08 -295.567931 0.069773
BFGS: 15 12:44:08 -295.568351 0.078286
BFGS: 16 12:44:08 -295.568945 0.078517
BFGS: 17 12:44:09 -295.569558 0.073116
BFGS: 18 12:44:09 -295.570290 0.105694
BFGS: 19 12:44:09 -295.571877 0.197177
BFGS: 20 12:44:10 -295.578466 0.538136
BFGS: 21 12:44:10 -295.589193 0.900098
BFGS: 22 12:44:10 -295.612238 1.173580
BFGS: 23 12:44:11 -295.626995 1.231291
BFGS: 24 12:44:11 -295.639650 1.171221
BFGS: 25 12:44:11 -295.670142 1.124731
BFGS: 26 12:44:12 -295.687947 1.003605
BFGS: 27 12:44:12 -295.698766 0.993883
BFGS: 28 12:44:12 -295.733179 0.849746
BFGS: 29 12:44:13 -295.751521 0.724306
BFGS: 30 12:44:13 -295.772825 0.594060
BFGS: 31 12:44:13 -295.802969 0.425548
BFGS: 32 12:44:14 -295.822120 0.400612
BFGS: 33 12:44:14 -295.834777 0.212315
BFGS: 34 12:44:14 -295.838071 0.130103
BFGS: 35 12:44:15 -295.839343 0.098012
BFGS: 36 12:44:15 -295.840349 0.070239
BFGS: 37 12:44:15 -295.841519 0.060481
BFGS: 38 12:44:16 -295.842266 0.045593
Step Time Energy fmax
BFGS: 0 12:44:16 -295.396081 1.151965
BFGS: 1 12:44:16 -295.463991 1.060879
BFGS: 2 12:44:17 -295.682561 1.067344
BFGS: 3 12:44:17 -295.705180 0.579350
BFGS: 4 12:44:17 -295.717431 0.496372
BFGS: 5 12:44:17 -295.759719 0.588318
BFGS: 6 12:44:18 -295.769942 0.560786
BFGS: 7 12:44:18 -295.810233 0.632227
BFGS: 8 12:44:18 -295.830744 0.452443
BFGS: 9 12:44:19 -295.848377 0.344874
BFGS: 10 12:44:19 -295.852371 0.308657
BFGS: 11 12:44:19 -295.858843 0.229429
BFGS: 12 12:44:20 -295.864380 0.189638
BFGS: 13 12:44:20 -295.868734 0.178583
BFGS: 14 12:44:20 -295.870683 0.185700
BFGS: 15 12:44:20 -295.872901 0.190253
BFGS: 16 12:44:21 -295.876878 0.204813
BFGS: 17 12:44:21 -295.883996 0.234637
BFGS: 18 12:44:21 -295.893085 0.300733
BFGS: 19 12:44:22 -295.902293 0.400043
BFGS: 20 12:44:22 -295.912622 0.404474
BFGS: 21 12:44:22 -295.922658 0.347417
BFGS: 22 12:44:22 -295.935855 0.289389
BFGS: 23 12:44:23 -295.949484 0.218213
BFGS: 24 12:44:23 -295.958757 0.134334
BFGS: 25 12:44:23 -295.960805 0.104975
BFGS: 26 12:44:23 -295.962956 0.088045
BFGS: 27 12:44:24 -295.963720 0.072271
BFGS: 28 12:44:24 -295.965627 0.067056
BFGS: 29 12:44:24 -295.966384 0.048501
Step Time Energy fmax
BFGS: 0 12:44:25 -295.199426 1.474976
BFGS: 1 12:44:25 -295.290836 1.336642
BFGS: 2 12:44:25 -295.493857 1.862446
BFGS: 3 12:44:25 -295.548670 0.537400
BFGS: 4 12:44:26 -295.560776 0.568526
BFGS: 5 12:44:26 -295.589445 0.354443
BFGS: 6 12:44:26 -295.595677 0.291166
BFGS: 7 12:44:26 -295.602119 0.339798
BFGS: 8 12:44:27 -295.609149 0.341257
BFGS: 9 12:44:27 -295.617202 0.354914
BFGS: 10 12:44:27 -295.623236 0.276917
BFGS: 11 12:44:28 -295.627230 0.370277
BFGS: 12 12:44:28 -295.633845 0.531512
BFGS: 13 12:44:28 -295.673510 1.085548
BFGS: 14 12:44:29 -295.473267 2.595040
BFGS: 15 12:44:29 -295.775106 0.591349
BFGS: 16 12:44:29 -295.801974 0.455997
BFGS: 17 12:44:30 -295.813778 0.364458
BFGS: 18 12:44:30 -295.828086 0.319980
BFGS: 19 12:44:30 -295.833061 0.222175
BFGS: 20 12:44:30 -295.835903 0.190564
BFGS: 21 12:44:31 -295.838139 0.201092
BFGS: 22 12:44:31 -295.840204 0.135606
BFGS: 23 12:44:32 -295.841315 0.055017
BFGS: 24 12:44:32 -295.841688 0.046018
Step Time Energy fmax
BFGS: 0 12:44:32 -295.689491 0.720572
BFGS: 1 12:44:32 -295.735782 0.641567
BFGS: 2 12:44:33 -295.895730 0.320492
BFGS: 3 12:44:33 -295.904890 0.314699
BFGS: 4 12:44:33 -295.906763 0.302482
BFGS: 5 12:44:33 -295.924179 0.123000
BFGS: 6 12:44:34 -295.924990 0.120377
BFGS: 7 12:44:34 -295.929749 0.086468
BFGS: 8 12:44:34 -295.930329 0.075300
BFGS: 9 12:44:35 -295.930601 0.070061
BFGS: 10 12:44:35 -295.930937 0.065323
BFGS: 11 12:44:35 -295.931519 0.058077
BFGS: 12 12:44:36 -295.932120 0.047828
Step Time Energy fmax
BFGS: 0 12:44:36 -295.301579 1.297158
BFGS: 1 12:44:36 -295.378892 1.183546
BFGS: 2 12:44:36 -295.593618 1.397917
BFGS: 3 12:44:37 -295.627101 0.592102
BFGS: 4 12:44:37 -295.638260 0.503269
BFGS: 5 12:44:37 -295.675311 0.485489
BFGS: 6 12:44:38 -295.681361 0.480141
BFGS: 7 12:44:38 -295.746952 0.632941
BFGS: 8 12:44:38 -295.766086 0.676932
BFGS: 9 12:44:38 -295.783482 0.709384
BFGS: 10 12:44:39 -295.817312 0.629355
BFGS: 11 12:44:39 -295.841149 0.394892
BFGS: 12 12:44:40 -295.850970 0.269299
BFGS: 13 12:44:40 -295.855552 0.235979
BFGS: 14 12:44:40 -295.857596 0.233682
BFGS: 15 12:44:41 -295.862979 0.233439
BFGS: 16 12:44:41 -295.866896 0.184482
BFGS: 17 12:44:41 -295.870076 0.198122
BFGS: 18 12:44:42 -295.872030 0.201768
BFGS: 19 12:44:42 -295.874372 0.202146
BFGS: 20 12:44:42 -295.878581 0.298041
BFGS: 21 12:44:43 -295.888198 0.473191
BFGS: 22 12:44:43 -295.901953 0.603670
BFGS: 23 12:44:43 -295.916265 0.491608
BFGS: 24 12:44:43 -295.938223 0.237337
BFGS: 25 12:44:44 -295.945159 0.217667
BFGS: 26 12:44:44 -295.955625 0.183282
BFGS: 27 12:44:44 -295.959920 0.144566
BFGS: 28 12:44:44 -295.963332 0.074377
BFGS: 29 12:44:45 -295.964184 0.076420
BFGS: 30 12:44:45 -295.964910 0.065515
BFGS: 31 12:44:46 -295.965972 0.046698
Enumerate NEBs¶
af = AutoFrameDissociation(
reaction=reaction,
reactant_system=reactant_configs[reactant_energies.index(min(reactant_energies))],
product1_systems=product1_configs,
product1_energies=product1_energies,
product2_systems=product2_configs,
product2_energies=product2_energies,
r_product1_max=2, # r1 in the above fig
r_product2_max=3, # r3 in the above fig
r_product2_min=1, # r2 in the above fig
)import random
nframes = 10
random.seed(
42
) # set the seed to make the random generation deterministic for the tutorial!
frame_sets, mapping_idxs = af.get_neb_frames(
calc,
n_frames=nframes,
n_pdt1_sites=4, # = 5 in the above fig (step 1)
n_pdt2_sites=4, # = 5 in the above fig (step 2)
) Step Time Energy fmax
BFGS: 0 12:44:46 -303.903946 0.356111
BFGS: 1 12:44:46 -303.909655 0.268339
BFGS: 2 12:44:46 -303.922378 0.152186
BFGS: 3 12:44:47 -303.924758 0.126300
BFGS: 4 12:44:47 -303.926579 0.108416
BFGS: 5 12:44:47 -303.927915 0.105317
BFGS: 6 12:44:47 -303.929110 0.083218
BFGS: 7 12:44:48 -303.929789 0.071835
BFGS: 8 12:44:48 -303.930121 0.054210
BFGS: 9 12:44:48 -303.930328 0.039644
Step Time Energy fmax
BFGS: 0 12:44:48 -303.897974 0.346346
BFGS: 1 12:44:49 -303.904189 0.269149
BFGS: 2 12:44:49 -303.918641 0.157529
BFGS: 3 12:44:49 -303.921364 0.136228
BFGS: 4 12:44:49 -303.923647 0.110580
BFGS: 5 12:44:49 -303.925146 0.105103
BFGS: 6 12:44:50 -303.926405 0.080926
BFGS: 7 12:44:50 -303.927145 0.079479
BFGS: 8 12:44:50 -303.927524 0.062482
BFGS: 9 12:44:51 -303.927778 0.044647
Step Time Energy fmax
BFGS: 0 12:44:51 -303.896192 0.435509
BFGS: 1 12:44:51 -303.903643 0.323561
BFGS: 2 12:44:52 -303.918733 0.167705
BFGS: 3 12:44:52 -303.921652 0.141424
BFGS: 4 12:44:52 -303.923885 0.131325
BFGS: 5 12:44:53 -303.925480 0.125523
BFGS: 6 12:44:53 -303.926839 0.096016
BFGS: 7 12:44:53 -303.927562 0.066268
BFGS: 8 12:44:54 -303.927875 0.049767
Step Time Energy fmax
BFGS: 0 12:44:54 -303.904549 0.306709
BFGS: 1 12:44:54 -303.909840 0.250994
BFGS: 2 12:44:55 -303.922306 0.149197
BFGS: 3 12:44:55 -303.924604 0.122482
BFGS: 4 12:44:55 -303.926428 0.108732
BFGS: 5 12:44:56 -303.927758 0.107561
BFGS: 6 12:44:56 -303.928943 0.086079
BFGS: 7 12:44:56 -303.929659 0.076226
BFGS: 8 12:44:56 -303.930020 0.057202
BFGS: 9 12:44:57 -303.930241 0.041250
Step Time Energy fmax
BFGS: 0 12:44:57 -303.862783 0.535818
BFGS: 1 12:44:57 -303.876799 0.417730
BFGS: 2 12:44:58 -303.907231 0.202748
BFGS: 3 12:44:58 -303.913452 0.177200
BFGS: 4 12:44:58 -303.917937 0.153001
BFGS: 5 12:44:59 -303.920884 0.140603
BFGS: 6 12:44:59 -303.923863 0.112888
BFGS: 7 12:44:59 -303.925757 0.090990
BFGS: 8 12:45:00 -303.926608 0.075259
BFGS: 9 12:45:00 -303.927084 0.062412
BFGS: 10 12:45:00 -303.927638 0.051340
BFGS: 11 12:45:01 -303.928003 0.047457
Step Time Energy fmax
BFGS: 0 12:45:01 -303.892458 0.380187
BFGS: 1 12:45:01 -303.898853 0.329891
BFGS: 2 12:45:02 -303.918432 0.144236
BFGS: 3 12:45:02 -303.920688 0.164479
BFGS: 4 12:45:02 -303.922212 0.142480
BFGS: 5 12:45:03 -303.923853 0.091666
BFGS: 6 12:45:03 -303.925488 0.082443
BFGS: 7 12:45:03 -303.926502 0.092369
BFGS: 8 12:45:04 -303.927059 0.090521
BFGS: 9 12:45:04 -303.927495 0.060712
BFGS: 10 12:45:04 -303.927916 0.060482
BFGS: 11 12:45:05 -303.928175 0.050505
BFGS: 12 12:45:05 -303.928305 0.033507
Step Time Energy fmax
BFGS: 0 12:45:05 -303.094758 1.042558
BFGS: 1 12:45:05 -303.133839 0.780733
BFGS: 2 12:45:06 -303.206507 0.676171
BFGS: 3 12:45:06 -303.238489 0.675182
BFGS: 4 12:45:06 -303.274609 0.762264
BFGS: 5 12:45:07 -303.303886 0.634454
BFGS: 6 12:45:07 -303.346403 0.562910
BFGS: 7 12:45:07 -303.362416 0.396265
BFGS: 8 12:45:08 -303.367834 0.259992
BFGS: 9 12:45:08 -303.375814 0.196884
BFGS: 10 12:45:09 -303.379448 0.213684
BFGS: 11 12:45:09 -303.381980 0.163634
BFGS: 12 12:45:09 -303.383988 0.153838
BFGS: 13 12:45:09 -303.385627 0.132578
BFGS: 14 12:45:10 -303.387208 0.138578
BFGS: 15 12:45:10 -303.388542 0.132138
BFGS: 16 12:45:10 -303.389568 0.097245
BFGS: 17 12:45:11 -303.390657 0.088972
BFGS: 18 12:45:11 -303.391807 0.118628
BFGS: 19 12:45:12 -303.392820 0.130081
BFGS: 20 12:45:12 -303.393537 0.085634
BFGS: 21 12:45:12 -303.393965 0.066678
BFGS: 22 12:45:13 -303.394327 0.068108
BFGS: 23 12:45:13 -303.394837 0.095024
BFGS: 24 12:45:13 -303.395506 0.098811
BFGS: 25 12:45:13 -303.396239 0.099907
BFGS: 26 12:45:13 -303.397052 0.124214
BFGS: 27 12:45:14 -303.398630 0.173172
BFGS: 28 12:45:14 -303.403172 0.417148
BFGS: 29 12:45:14 -303.409740 0.507834
BFGS: 30 12:45:14 -303.432951 0.699518
BFGS: 31 12:45:15 -303.467262 0.869468
BFGS: 32 12:45:15 -303.500675 0.934103
BFGS: 33 12:45:15 -303.551214 0.869262
BFGS: 34 12:45:16 -303.609802 0.662988
BFGS: 35 12:45:16 -303.706147 0.867978
BFGS: 36 12:45:16 -303.746839 0.822757
BFGS: 37 12:45:16 -303.815209 0.550172
BFGS: 38 12:45:17 -303.846130 0.494135
BFGS: 39 12:45:17 -303.873099 0.459179
BFGS: 40 12:45:17 -303.898435 0.319241
BFGS: 41 12:45:18 -303.913405 0.156185
BFGS: 42 12:45:18 -303.918514 0.150814
BFGS: 43 12:45:18 -303.920653 0.109014
BFGS: 44 12:45:19 -303.922195 0.112691
BFGS: 45 12:45:19 -303.924232 0.131185
BFGS: 46 12:45:19 -303.925996 0.106449
BFGS: 47 12:45:19 -303.927018 0.060340
BFGS: 48 12:45:20 -303.927467 0.055636
BFGS: 49 12:45:20 -303.927771 0.045126
Step Time Energy fmax
BFGS: 0 12:45:20 -303.114498 0.886160
BFGS: 1 12:45:21 -303.149410 0.815022
BFGS: 2 12:45:21 -303.220477 0.703177
BFGS: 3 12:45:21 -303.250801 0.660426
BFGS: 4 12:45:21 -303.285104 0.701773
BFGS: 5 12:45:22 -303.312344 0.570341
BFGS: 6 12:45:22 -303.348881 0.511060
BFGS: 7 12:45:22 -303.362551 0.365122
BFGS: 8 12:45:22 -303.367804 0.238733
BFGS: 9 12:45:23 -303.375399 0.207233
BFGS: 10 12:45:23 -303.379171 0.239953
BFGS: 11 12:45:23 -303.382212 0.184498
BFGS: 12 12:45:24 -303.384707 0.172942
BFGS: 13 12:45:24 -303.386659 0.140310
BFGS: 14 12:45:24 -303.388634 0.165836
BFGS: 15 12:45:25 -303.390664 0.176980
BFGS: 16 12:45:25 -303.392357 0.130768
BFGS: 17 12:45:25 -303.394112 0.132347
BFGS: 18 12:45:26 -303.396198 0.140196
BFGS: 19 12:45:26 -303.398516 0.193613
BFGS: 20 12:45:26 -303.400954 0.176588
BFGS: 21 12:45:27 -303.403575 0.198458
BFGS: 22 12:45:27 -303.407154 0.256153
BFGS: 23 12:45:27 -303.414033 0.426437
BFGS: 24 12:45:28 -303.426471 0.701970
BFGS: 25 12:45:28 -303.448589 0.837097
BFGS: 26 12:45:28 -303.484491 0.667548
BFGS: 27 12:45:28 -303.516868 0.598397
BFGS: 28 12:45:29 -303.557680 0.642387
BFGS: 29 12:45:29 -303.596356 0.865545
BFGS: 30 12:45:29 -303.643721 0.857487
BFGS: 31 12:45:30 -303.722374 0.760846
BFGS: 32 12:45:30 -303.795809 0.674667
BFGS: 33 12:45:31 -303.831379 0.521552
BFGS: 34 12:45:31 -303.852549 0.639919
BFGS: 35 12:45:31 -303.887952 0.507315
BFGS: 36 12:45:31 -303.911401 0.231013
BFGS: 37 12:45:31 -303.916777 0.202549
BFGS: 38 12:45:32 -303.920086 0.148296
BFGS: 39 12:45:32 -303.923082 0.099814
BFGS: 40 12:45:32 -303.925379 0.071423
BFGS: 41 12:45:33 -303.926379 0.066110
BFGS: 42 12:45:33 -303.926883 0.065140
BFGS: 43 12:45:33 -303.927376 0.050745
BFGS: 44 12:45:34 -303.927882 0.033292
/home/runner/work/_tool/Python/3.12.14/x64/lib/python3.12/site-packages/fairchem/applications/cattsunami/core/autoframe.py:1551: UserWarning: torch.range is deprecated and will be removed in a future release because its behavior is inconsistent with Python's range builtin. Instead, use torch.arange, which produces values in [start, end).
alpha = torch.range(0, num_frames - 1, device=device) / (num_frames - 1)
Run NEBs¶
## This will run all NEBs enumerated - to just run one, run the code cell below.
# On GPU, each NEB takes an average of ~1 minute so this could take around a half hour on GPU
# But much longer on CPU
# Remember that not all NEBs will converge -- the k, nframes would be adjusted to achieve convergence
fmax = 0.05 # [eV / ang**2]
delta_fmax_climb = 0.4
converged_idxs = []
for idx, frame_set in enumerate(frame_sets):
neb = DyNEB(frame_set, k=1)
for image in frame_set:
image.calc = FAIRChemCalculator(predictor, task_name="oc20")
optimizer = BFGS(
neb,
trajectory=f"ch_dissoc_on_Ru_{idx}.traj",
)
conv = optimizer.run(fmax=fmax + delta_fmax_climb, steps=optimization_steps)
if conv:
neb.climb = True
conv = optimizer.run(fmax=fmax, steps=optimization_steps)
if conv:
converged_idxs.append(idx)
print(converged_idxs)This cell will run a shorter calculations for just a single one of the enumerated transition state pathways. You can adapt this code to run transition state searches via nudged elastic band (NEB) calculations for any reaction.
# If you run the above cell -- dont run this one
fmax = 0.05 # [eV / ang**2]
delta_fmax_climb = 0.4
images = frame_sets[0]
neb = DyNEB(images, k=1)
for image in images:
image.calc = FAIRChemCalculator(predictor, task_name="oc20")
optimizer = BFGS(
neb,
trajectory="ch_dissoc_on_Ru_0.traj",
)
conv = optimizer.run(fmax=fmax + delta_fmax_climb, steps=optimization_steps)
if conv:
neb.climb = True
conv = optimizer.run(fmax=fmax, steps=optimization_steps)/home/runner/work/_tool/Python/3.12.14/x64/lib/python3.12/site-packages/ase/mep/neb.py:329: UserWarning: The default method has changed from 'aseneb' to 'improvedtangent'. The 'aseneb' method is an unpublished, custom implementation that is not recommended as it frequently results in very poor bands. Please explicitly set method='improvedtangent' to silence this warning, or set method='aseneb' if you strictly require the old behavior (results may vary). See: https://gitlab.com/ase/ase/-/merge_requests/3952
warnings.warn(
Step Time Energy fmax
BFGS: 0 12:46:40 -301.892087 4.162920
BFGS: 1 12:46:46 -302.189186 3.363860
BFGS: 2 12:46:48 -302.776115 5.157551
BFGS: 3 12:46:52 -302.881887 1.532153
BFGS: 4 12:46:57 -303.026695 0.911838
BFGS: 5 12:47:00 -303.048421 0.788612
BFGS: 6 12:47:03 -303.056144 0.658713
BFGS: 7 12:47:06 -303.074027 0.803922
BFGS: 8 12:47:08 -303.095266 0.807425
BFGS: 9 12:47:10 -303.124864 0.799484
BFGS: 10 12:47:12 -303.164958 0.790380
BFGS: 11 12:47:15 -303.233702 1.029137
BFGS: 12 12:47:19 -303.269005 1.245382
BFGS: 13 12:47:26 -303.272104 1.262173
BFGS: 14 12:47:28 -303.282738 0.876635
BFGS: 15 12:47:31 -303.297063 0.794051
BFGS: 16 12:47:32 -303.314492 1.517072
BFGS: 17 12:47:34 -303.307621 1.006812
BFGS: 18 12:47:36 -303.326598 0.829684
BFGS: 19 12:47:43 -303.376124 1.221661
BFGS: 20 12:47:46 -303.403535 0.970300
BFGS: 21 12:47:52 -303.469743 1.081192
BFGS: 22 12:47:55 -303.484513 1.221862
BFGS: 23 12:47:57 -303.568051 1.449625
BFGS: 24 12:48:04 -303.591639 1.012761
BFGS: 25 12:48:05 -303.618445 0.665300
BFGS: 26 12:48:07 -303.652776 0.537110
BFGS: 27 12:48:09 -303.672139 0.452960
BFGS: 28 12:48:11 -303.688900 0.641773
BFGS: 29 12:48:16 -303.697934 0.429889
BFGS: 30 12:48:21 -303.690300 0.561891
BFGS: 31 12:48:28 -303.691196 0.480535
BFGS: 32 12:48:30 -303.684410 0.485156
BFGS: 33 12:48:34 -303.677125 0.439541
BFGS: 34 12:48:37 -303.662755 0.351531
BFGS: 35 12:48:41 -303.653327 0.324588
BFGS: 36 12:48:46 -303.646966 0.258005
BFGS: 37 12:48:51 -303.646332 0.247865
BFGS: 38 12:48:53 -303.647433 0.279245
BFGS: 39 12:49:00 -303.647576 0.319143
BFGS: 40 12:49:04 -303.647449 0.290459
BFGS: 41 12:49:11 -303.648477 0.244981
BFGS: 42 12:49:16 -303.650747 0.304838
BFGS: 43 12:49:20 -303.651991 0.251222
BFGS: 44 12:49:28 -303.652367 0.203631
BFGS: 45 12:49:33 -303.652184 0.230731
BFGS: 46 12:49:36 -303.651760 0.250271
BFGS: 47 12:49:39 -303.651305 0.259584
BFGS: 48 12:49:47 -303.651318 0.265086
BFGS: 49 12:49:53 -303.652075 0.255211
BFGS: 50 12:49:55 -303.653440 0.244079
BFGS: 51 12:49:59 -303.655140 0.258285
BFGS: 52 12:50:06 -303.657219 0.316012
BFGS: 53 12:50:14 -303.659488 0.336321
BFGS: 54 12:50:17 -303.661886 0.437796
BFGS: 55 12:50:21 -303.666092 0.547878
BFGS: 56 12:50:23 -303.669229 0.965533
BFGS: 57 12:50:27 -303.661144 1.994202
BFGS: 58 12:50:31 -303.636013 3.571147
BFGS: 59 12:50:33 -303.643780 1.636926
BFGS: 60 12:50:41 -303.684819 0.617541
BFGS: 61 12:50:46 -303.693766 0.489680
BFGS: 62 12:50:48 -303.695691 0.445618
BFGS: 63 12:50:52 -303.701300 0.418511
BFGS: 64 12:50:58 -303.705007 0.375254
BFGS: 65 12:51:02 -303.711444 0.300564
BFGS: 66 12:51:06 -303.713186 0.278620
BFGS: 67 12:51:09 -303.715955 0.345490
BFGS: 68 12:51:13 -303.715078 0.609769
BFGS: 69 12:51:18 -303.710853 0.497927
BFGS: 70 12:51:25 -303.712107 0.463766
BFGS: 71 12:51:28 -303.717700 0.398189
BFGS: 72 12:51:34 -303.720791 0.297131
BFGS: 73 12:51:39 -303.720670 0.185998
BFGS: 74 12:51:43 -303.720412 0.157543
BFGS: 75 12:51:46 -303.720239 0.243350
BFGS: 76 12:51:55 -303.719361 0.191991
BFGS: 77 12:52:00 -303.718496 0.210298
BFGS: 78 12:52:04 -303.717466 0.293461
BFGS: 79 12:52:06 -303.716462 0.298481
BFGS: 80 12:52:09 -303.716973 0.241598
BFGS: 81 12:52:13 -303.716572 0.252956
BFGS: 82 12:52:18 -303.709163 0.635442
BFGS: 83 12:52:22 -303.678596 1.130270
BFGS: 84 12:52:28 -303.710771 0.576320
BFGS: 85 12:52:32 -303.710105 0.618966
BFGS: 86 12:52:40 -303.699276 0.885645
BFGS: 87 12:52:41 -303.710956 0.526609
BFGS: 88 12:52:44 -303.710634 0.509614
BFGS: 89 12:52:45 -303.706416 0.659716
BFGS: 90 12:52:46 -303.713378 0.424526
BFGS: 91 12:52:48 -303.718372 0.285147
BFGS: 92 12:52:49 -303.720182 0.242179
BFGS: 93 12:52:50 -303.720379 0.253582
BFGS: 94 12:52:51 -303.720025 0.183182
BFGS: 95 12:52:52 -303.719294 0.240105
BFGS: 96 12:52:54 -303.719123 0.282609
BFGS: 97 12:52:55 -303.719425 0.313596
BFGS: 98 12:52:57 -303.720144 0.300008
BFGS: 99 12:52:58 -303.720648 0.255428
BFGS: 100 12:52:59 -303.720618 0.211268
BFGS: 101 12:53:01 -303.720589 0.237024
BFGS: 102 12:53:02 -303.720857 0.176790
BFGS: 103 12:53:06 -303.721120 0.138847
BFGS: 104 12:53:06 -303.721120 0.132074
BFGS: 105 12:53:08 -303.721120 0.144910
BFGS: 106 12:53:09 -303.721120 0.663345
BFGS: 107 12:53:10 -303.721120 0.621107
BFGS: 108 12:53:11 -303.721120 0.705833
BFGS: 109 12:53:12 -303.721120 0.677008
BFGS: 110 12:53:14 -303.721120 0.168764
BFGS: 111 12:53:15 -303.721120 0.394679
BFGS: 112 12:53:16 -303.721120 0.467690
BFGS: 113 12:53:17 -303.721120 0.323483
BFGS: 114 12:53:18 -303.721120 0.255721
BFGS: 115 12:53:22 -303.721120 0.324453
BFGS: 116 12:53:23 -303.721120 0.223595
BFGS: 117 12:53:23 -303.721120 0.413734
BFGS: 118 12:53:24 -303.721120 0.358224
BFGS: 119 12:53:25 -303.721120 0.349709
BFGS: 120 12:53:26 -303.721120 0.323854
BFGS: 121 12:53:29 -303.721120 0.350953
BFGS: 122 12:53:29 -303.721120 0.356604
BFGS: 123 12:53:31 -303.721120 0.381873
BFGS: 124 12:53:32 -303.721120 0.385128
BFGS: 125 12:53:32 -303.721120 0.598993
BFGS: 126 12:53:32 -303.721120 0.343557
BFGS: 127 12:53:33 -303.721120 0.324263
BFGS: 128 12:53:36 -303.721120 0.248453
BFGS: 129 12:53:36 -303.721120 0.236417
BFGS: 130 12:53:37 -303.721120 0.232606
BFGS: 131 12:53:37 -303.721120 0.674098
BFGS: 132 12:53:38 -303.721120 0.387068
BFGS: 133 12:53:39 -303.721120 0.337734
BFGS: 134 12:53:40 -303.721120 0.334503
BFGS: 135 12:53:40 -303.721120 0.363366
BFGS: 136 12:53:41 -303.721120 0.450528
BFGS: 137 12:53:43 -303.721120 0.515347
BFGS: 138 12:53:43 -303.721120 0.407999
BFGS: 139 12:53:44 -303.721120 0.663369
BFGS: 140 12:53:45 -303.721120 0.367749
BFGS: 141 12:53:47 -303.721120 0.296827
BFGS: 142 12:53:48 -303.721120 0.229252
BFGS: 143 12:53:49 -303.721120 0.261895
BFGS: 144 12:53:53 -303.721120 0.300487
BFGS: 145 12:53:53 -303.721120 0.325936
BFGS: 146 12:53:54 -303.721120 0.496866
BFGS: 147 12:53:56 -303.721120 0.311353
BFGS: 148 12:53:57 -303.721120 0.345901
BFGS: 149 12:53:58 -303.721120 0.417665
BFGS: 150 12:54:00 -303.721120 0.454911
BFGS: 151 12:54:01 -303.721120 0.758504
BFGS: 152 12:54:02 -303.721120 0.607849
BFGS: 153 12:54:03 -303.721120 0.575673
BFGS: 154 12:54:04 -303.721120 0.579829
BFGS: 155 12:54:04 -303.721120 0.557497
BFGS: 156 12:54:05 -303.721120 0.335952
BFGS: 157 12:54:06 -303.721120 0.308168
BFGS: 158 12:54:07 -303.721120 0.329988
BFGS: 159 12:54:10 -303.721120 0.610356
BFGS: 160 12:54:11 -303.721120 1.097694
BFGS: 161 12:54:12 -303.721120 0.443570
BFGS: 162 12:54:14 -303.721120 0.537948
BFGS: 163 12:54:15 -303.721120 1.319563
BFGS: 164 12:54:16 -303.721120 1.092209
BFGS: 165 12:54:17 -303.721120 0.376619
BFGS: 166 12:54:18 -303.721120 0.320050
BFGS: 167 12:54:21 -303.721120 0.128238
BFGS: 168 12:54:22 -303.721120 0.190802
BFGS: 169 12:54:24 -303.721120 0.386922
BFGS: 170 12:54:25 -303.721120 0.610597
BFGS: 171 12:54:27 -303.721120 0.562601
BFGS: 172 12:54:28 -303.721120 0.411875
BFGS: 173 12:54:28 -303.721120 0.280945
BFGS: 174 12:54:30 -303.721120 0.297386
BFGS: 175 12:54:31 -303.721120 0.247550
BFGS: 176 12:54:32 -303.721120 0.171512
BFGS: 177 12:54:32 -303.721120 0.137729
BFGS: 178 12:54:34 -303.721120 0.219682
BFGS: 179 12:54:35 -303.721120 0.170134
BFGS: 180 12:54:36 -303.721120 0.325367
BFGS: 181 12:54:36 -303.721120 0.320823
BFGS: 182 12:54:37 -303.721120 0.220443
BFGS: 183 12:54:39 -303.721120 0.265328
BFGS: 184 12:54:40 -303.721120 0.199882
BFGS: 185 12:54:40 -303.721120 0.255585
BFGS: 186 12:54:41 -303.721120 0.239659
BFGS: 187 12:54:42 -303.721120 0.267279
BFGS: 188 12:54:43 -303.721120 0.513861
BFGS: 189 12:54:44 -303.721120 0.295417
BFGS: 190 12:54:45 -303.721120 0.257591
BFGS: 191 12:54:47 -303.721120 0.183295
BFGS: 192 12:54:48 -303.721120 0.227780
BFGS: 193 12:54:49 -303.721120 0.313388
BFGS: 194 12:54:50 -303.721120 0.241518
BFGS: 195 12:54:54 -303.721120 0.345599
BFGS: 196 12:54:55 -303.721120 0.198894
BFGS: 197 12:54:56 -303.721120 0.147963
BFGS: 198 12:54:57 -303.721120 0.156340
BFGS: 199 12:55:00 -303.721120 0.168712
BFGS: 200 12:55:03 -303.721120 0.153101
BFGS: 201 12:55:03 -303.721120 0.148803
BFGS: 202 12:55:05 -303.721120 0.145508
BFGS: 203 12:55:06 -303.721120 0.106321
BFGS: 204 12:55:06 -303.721120 0.075908
BFGS: 205 12:55:07 -303.721120 0.071539
BFGS: 206 12:55:08 -303.721120 0.060187
BFGS: 207 12:55:09 -303.721120 0.089313
BFGS: 208 12:55:10 -303.721120 0.064555
BFGS: 209 12:55:11 -303.721120 0.038981
Visualize the results¶
Finally, let’s visualize the results!
optimized_neb = read("ch_dissoc_on_Ru_0.traj", ":")[-1 * nframes :]es = []
for frame in optimized_neb:
frame.set_calculator(calc)
es.append(frame.get_potential_energy())/tmp/ipykernel_9931/3247994494.py:3: FutureWarning: Please use atoms.calc = calc
frame.set_calculator(calc)
# Plot the reaction coordinate
es = [e - es[0] for e in es]
plt.plot(es)
plt.xlabel("frame number")
plt.ylabel("relative energy [eV]")
plt.title(f"CH dissociation on Ru(0001), Ea = {max(es):1.2f} eV")
plt.savefig("CH_dissoc_on_Ru_0001.png")
To generalize an interactive visualization, use ase gui from the command line or the X3D package
# Make an interative html file of the optimized neb trajectory
x3d = X3D(optimized_neb)
x3d.write("optimized_neb_ch_disoc_on_Ru0001.html")