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,
)Warp DeprecationWarning: The symbol `warp.vec` will soon be removed from the public API. Use `warp.types.vector` instead.
/home/runner/work/_tool/Python/3.12.13/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/3.12.13/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/3.12.13/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/3.12.13/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()) Step Time Energy fmax
BFGS: 0 06:40:01 -300.669832 4.057402
BFGS: 1 06:40:01 -301.117666 3.636506
BFGS: 2 06:40:02 -302.442126 3.530596
BFGS: 3 06:40:02 -302.046084 10.665651
BFGS: 4 06:40:03 -302.706844 3.185683
BFGS: 5 06:40:03 -302.850571 2.651552
BFGS: 6 06:40:03 -303.023578 2.702729
BFGS: 7 06:40:03 -303.094696 0.741182
BFGS: 8 06:40:04 -303.109065 0.620272
BFGS: 9 06:40:04 -303.150267 0.392556
BFGS: 10 06:40:04 -303.166885 0.305782
BFGS: 11 06:40:04 -303.169881 0.189501
BFGS: 12 06:40:05 -303.171285 0.148943
BFGS: 13 06:40:05 -303.173966 0.191422
BFGS: 14 06:40:05 -303.175806 0.185996
BFGS: 15 06:40:06 -303.177526 0.107098
BFGS: 16 06:40:06 -303.178360 0.097968
BFGS: 17 06:40:07 -303.178926 0.136089
BFGS: 18 06:40:07 -303.179625 0.142373
BFGS: 19 06:40:08 -303.180502 0.107468
BFGS: 20 06:40:08 -303.181203 0.078547
BFGS: 21 06:40:09 -303.181553 0.047268
Step Time Energy fmax
BFGS: 0 06:40:09 -302.865761 3.887334
BFGS: 1 06:40:10 -303.207566 2.777662
BFGS: 2 06:40:10 -303.922210 2.963684
BFGS: 3 06:40:11 -304.056764 2.416744
BFGS: 4 06:40:11 -304.260163 3.221604
BFGS: 5 06:40:12 -304.347202 1.002221
BFGS: 6 06:40:12 -304.416934 0.647811
BFGS: 7 06:40:13 -304.572089 1.049561
BFGS: 8 06:40:13 -304.595973 0.711055
BFGS: 9 06:40:14 -304.642854 0.751361
BFGS: 10 06:40:14 -304.655800 0.508461
BFGS: 11 06:40:14 -304.665413 0.141205
BFGS: 12 06:40:15 -304.666593 0.146119
BFGS: 13 06:40:15 -304.668662 0.148031
BFGS: 14 06:40:16 -304.670773 0.127357
BFGS: 15 06:40:16 -304.672700 0.098606
BFGS: 16 06:40:17 -304.673870 0.090407
BFGS: 17 06:40:17 -304.674904 0.090627
BFGS: 18 06:40:18 -304.676335 0.090028
BFGS: 19 06:40:18 -304.677933 0.078571
BFGS: 20 06:40:19 -304.679117 0.100554
BFGS: 21 06:40:19 -304.679830 0.090567
BFGS: 22 06:40:20 -304.680376 0.066797
BFGS: 23 06:40:20 -304.680838 0.046809
Step Time Energy fmax
BFGS: 0 06:40:21 -301.427868 4.177003
BFGS: 1 06:40:21 -301.819453 3.242165
BFGS: 2 06:40:22 -302.794189 3.378193
BFGS: 3 06:40:22 -302.930279 3.218719
BFGS: 4 06:40:22 -303.203129 1.995319
BFGS: 5 06:40:23 -303.325745 3.366588
BFGS: 6 06:40:23 -303.424101 1.745212
BFGS: 7 06:40:24 -303.581967 1.113382
BFGS: 8 06:40:25 -303.867550 1.890098
BFGS: 9 06:40:26 -303.919176 1.589475
BFGS: 10 06:40:26 -304.020870 1.059312
BFGS: 11 06:40:27 -304.053555 0.853703
BFGS: 12 06:40:27 -304.164627 0.645113
BFGS: 13 06:40:27 -304.181682 0.524471
BFGS: 14 06:40:28 -304.248559 0.746930
BFGS: 15 06:40:28 -304.285432 0.870430
BFGS: 16 06:40:28 -304.338468 0.898412
BFGS: 17 06:40:29 -304.377015 0.839733
BFGS: 18 06:40:29 -304.457946 0.610331
BFGS: 19 06:40:30 -304.471201 0.998175
BFGS: 20 06:40:30 -304.522923 0.440037
BFGS: 21 06:40:31 -304.539227 0.437232
BFGS: 22 06:40:31 -304.551649 0.423837
BFGS: 23 06:40:32 -304.573528 0.541730
BFGS: 24 06:40:32 -304.598985 0.537734
BFGS: 25 06:40:33 -304.620422 0.395289
BFGS: 26 06:40:33 -304.633568 0.371281
BFGS: 27 06:40:34 -304.643257 0.328585
BFGS: 28 06:40:34 -304.653530 0.257557
BFGS: 29 06:40:35 -304.664108 0.269069
BFGS: 30 06:40:35 -304.671219 0.180978
BFGS: 31 06:40:36 -304.674196 0.121060
BFGS: 32 06:40:36 -304.675720 0.132017
BFGS: 33 06:40:37 -304.677435 0.115327
BFGS: 34 06:40:37 -304.679243 0.083005
BFGS: 35 06:40:38 -304.680429 0.056264
BFGS: 36 06:40:38 -304.680867 0.035132
Step Time Energy fmax
BFGS: 0 06:40:38 -301.408543 4.106341
BFGS: 1 06:40:39 -301.794703 3.086684
BFGS: 2 06:40:39 -302.774400 3.453887
BFGS: 3 06:40:40 -302.917919 3.244348
BFGS: 4 06:40:40 -303.210139 1.664848
BFGS: 5 06:40:41 -303.299227 2.613860
BFGS: 6 06:40:41 -303.368114 1.721701
BFGS: 7 06:40:42 -303.626560 1.316861
BFGS: 8 06:40:42 -303.909468 2.347876
BFGS: 9 06:40:43 -303.967463 2.545415
BFGS: 10 06:40:43 -304.113203 1.824166
BFGS: 11 06:40:44 -304.256102 0.823383
BFGS: 12 06:40:44 -304.350968 1.695638
BFGS: 13 06:40:45 -304.460638 1.666567
BFGS: 14 06:40:45 -304.526524 0.901419
BFGS: 15 06:40:46 -304.567415 0.498315
BFGS: 16 06:40:46 -304.586270 0.408686
BFGS: 17 06:40:46 -304.600487 0.423887
BFGS: 18 06:40:47 -304.612956 0.393750
BFGS: 19 06:40:47 -304.620918 0.295555
BFGS: 20 06:40:48 -304.627751 0.273367
BFGS: 21 06:40:48 -304.635767 0.338635
BFGS: 22 06:40:49 -304.645395 0.365507
BFGS: 23 06:40:49 -304.654846 0.278460
BFGS: 24 06:40:50 -304.661366 0.187313
BFGS: 25 06:40:50 -304.665470 0.177990
BFGS: 26 06:40:51 -304.669658 0.199804
BFGS: 27 06:40:51 -304.674311 0.181681
BFGS: 28 06:40:51 -304.677960 0.118381
BFGS: 29 06:40:52 -304.679646 0.056190
BFGS: 30 06:40:52 -304.680125 0.046457
Step Time Energy fmax
BFGS: 0 06:40:53 -302.049963 4.080652
BFGS: 1 06:40:53 -302.438818 3.185993
BFGS: 2 06:40:54 -303.398287 3.185292
BFGS: 3 06:40:54 -303.570078 2.939557
BFGS: 4 06:40:55 -303.798251 1.698832
BFGS: 5 06:40:55 -303.901872 1.750116
BFGS: 6 06:40:56 -303.942354 1.043139
BFGS: 7 06:40:56 -304.036892 0.789878
BFGS: 8 06:40:57 -304.077581 0.946938
BFGS: 9 06:40:57 -304.111043 0.766835
BFGS: 10 06:40:58 -304.149190 0.422517
BFGS: 11 06:40:58 -304.173132 0.411047
BFGS: 12 06:40:58 -304.187889 0.340337
BFGS: 13 06:40:59 -304.199449 0.305526
BFGS: 14 06:41:00 -304.206545 0.301827
BFGS: 15 06:41:00 -304.215890 0.372634
BFGS: 16 06:41:00 -304.231632 0.512337
BFGS: 17 06:41:01 -304.261342 0.949052
BFGS: 18 06:41:01 -304.239850 1.878635
BFGS: 19 06:41:02 -304.315105 0.923296
BFGS: 20 06:41:03 -304.353192 0.821512
BFGS: 21 06:41:03 -304.444244 1.000400
BFGS: 22 06:41:03 -304.490584 0.595628
BFGS: 23 06:41:04 -304.513488 0.484730
BFGS: 24 06:41:04 -304.544422 0.455529
BFGS: 25 06:41:05 -304.562190 0.417102
BFGS: 26 06:41:05 -304.591305 0.428699
BFGS: 27 06:41:06 -304.606768 0.373691
BFGS: 28 06:41:06 -304.624274 0.391253
BFGS: 29 06:41:07 -304.641178 0.338292
BFGS: 30 06:41:07 -304.654292 0.280536
BFGS: 31 06:41:08 -304.661528 0.197356
BFGS: 32 06:41:08 -304.665333 0.194998
BFGS: 33 06:41:08 -304.669096 0.199859
BFGS: 34 06:41:09 -304.673363 0.203327
BFGS: 35 06:41:09 -304.677082 0.151460
BFGS: 36 06:41:10 -304.679030 0.085895
BFGS: 37 06:41:10 -304.679710 0.079341
BFGS: 38 06:41:11 -304.680118 0.064394
BFGS: 39 06:41:11 -304.680557 0.052724
BFGS: 40 06:41:12 -304.681010 0.049805
Step Time Energy fmax
BFGS: 0 06:41:12 -302.228771 4.090677
BFGS: 1 06:41:13 -302.611178 2.876842
BFGS: 2 06:41:13 -303.477400 3.312972
BFGS: 3 06:41:13 -303.640289 2.914748
BFGS: 4 06:41:14 -303.906182 2.311315
BFGS: 5 06:41:14 -303.970276 0.946206
BFGS: 6 06:41:15 -304.024630 0.745434
BFGS: 7 06:41:15 -304.217600 1.010455
BFGS: 8 06:41:16 -304.275667 0.879691
BFGS: 9 06:41:16 -304.370600 1.112031
BFGS: 10 06:41:16 -304.454235 0.945876
BFGS: 11 06:41:17 -304.519414 0.903302
BFGS: 12 06:41:17 -304.553655 0.844939
BFGS: 13 06:41:18 -304.586950 0.555833
BFGS: 14 06:41:18 -304.601219 0.331064
BFGS: 15 06:41:19 -304.611429 0.359580
BFGS: 16 06:41:19 -304.619227 0.252925
BFGS: 17 06:41:20 -304.626152 0.295950
BFGS: 18 06:41:20 -304.636848 0.271820
BFGS: 19 06:41:21 -304.645122 0.251053
BFGS: 20 06:41:21 -304.651532 0.245745
BFGS: 21 06:41:22 -304.656851 0.242207
BFGS: 22 06:41:22 -304.663520 0.231414
BFGS: 23 06:41:23 -304.670262 0.194474
BFGS: 24 06:41:23 -304.674831 0.123495
BFGS: 25 06:41:24 -304.676855 0.099367
BFGS: 26 06:41:24 -304.677979 0.106237
BFGS: 27 06:41:25 -304.679271 0.089909
BFGS: 28 06:41:25 -304.680460 0.061315
BFGS: 29 06:41:26 -304.681128 0.034995
Step Time Energy fmax
BFGS: 0 06:41:26 -300.881694 4.014250
BFGS: 1 06:41:26 -301.306720 3.430809
BFGS: 2 06:41:27 -302.564284 3.510761
BFGS: 3 06:41:27 -302.387824 8.442128
BFGS: 4 06:41:28 -302.871875 2.880102
BFGS: 5 06:41:28 -303.021928 1.867590
BFGS: 6 06:41:28 -303.103621 1.809275
BFGS: 7 06:41:29 -303.127143 0.561728
BFGS: 8 06:41:29 -303.137616 0.420432
BFGS: 9 06:41:30 -303.164977 0.758480
BFGS: 10 06:41:30 -303.179335 0.596624
BFGS: 11 06:41:31 -303.187782 0.263171
BFGS: 12 06:41:31 -303.191372 0.279801
BFGS: 13 06:41:32 -303.197479 0.595976
BFGS: 14 06:41:32 -303.206534 0.796026
BFGS: 15 06:41:33 -303.216548 0.715533
BFGS: 16 06:41:33 -303.224339 0.453242
BFGS: 17 06:41:34 -303.231438 0.400835
BFGS: 18 06:41:34 -303.242950 0.803781
BFGS: 19 06:41:35 -303.281076 1.949626
BFGS: 20 06:41:35 -303.304452 2.953175
BFGS: 21 06:41:36 -303.352681 2.802921
BFGS: 22 06:41:36 -303.546814 2.360905
BFGS: 23 06:41:36 -303.766232 1.453714
BFGS: 24 06:41:37 -303.384446 6.088501
BFGS: 25 06:41:37 -303.921114 0.661543
BFGS: 26 06:41:38 -303.972290 0.477825
BFGS: 27 06:41:39 -304.038079 0.537089
BFGS: 28 06:41:39 -304.047443 0.571461
BFGS: 29 06:41:39 -304.064005 0.390512
BFGS: 30 06:41:40 -304.096814 0.388349
BFGS: 31 06:41:40 -304.109399 0.386329
BFGS: 32 06:41:41 -304.123023 0.325135
BFGS: 33 06:41:41 -304.132429 0.284337
BFGS: 34 06:41:42 -304.146278 0.250912
BFGS: 35 06:41:42 -304.159013 0.321371
BFGS: 36 06:41:43 -304.166834 0.254373
BFGS: 37 06:41:43 -304.171199 0.225979
BFGS: 38 06:41:44 -304.174575 0.182510
BFGS: 39 06:41:44 -304.178159 0.188786
BFGS: 40 06:41:44 -304.182767 0.281713
BFGS: 41 06:41:45 -304.187343 0.283700
BFGS: 42 06:41:45 -304.192135 0.247699
BFGS: 43 06:41:46 -304.199600 0.258046
BFGS: 44 06:41:46 -304.190774 0.616110
BFGS: 45 06:41:47 -304.210747 0.307268
BFGS: 46 06:41:47 -304.217462 0.300576
BFGS: 47 06:41:47 -304.151883 1.659465
BFGS: 48 06:41:48 -304.235129 0.323085
BFGS: 49 06:41:48 -304.243436 0.329754
BFGS: 50 06:41:49 -304.251073 0.779124
BFGS: 51 06:41:49 -304.268187 0.335145
BFGS: 52 06:41:50 -304.276627 0.314808
BFGS: 53 06:41:50 -304.315974 0.296033
BFGS: 54 06:41:50 -304.323782 0.342955
BFGS: 55 06:41:51 -304.340268 0.345497
BFGS: 56 06:41:51 -304.346961 0.202256
BFGS: 57 06:41:52 -304.349841 0.095681
BFGS: 58 06:41:52 -304.350863 0.084168
BFGS: 59 06:41:53 -304.351565 0.080868
BFGS: 60 06:41:53 -304.352108 0.091210
BFGS: 61 06:41:54 -304.352547 0.065862
BFGS: 62 06:41:54 -304.352748 0.025460
Step Time Energy fmax
BFGS: 0 06:41:54 -301.096227 4.169443
BFGS: 1 06:41:55 -301.488985 3.485670
BFGS: 2 06:41:55 -302.517550 3.293029
BFGS: 3 06:41:56 -302.563137 4.719507
BFGS: 4 06:41:56 -302.833311 2.459081
BFGS: 5 06:41:57 -302.988008 1.361170
BFGS: 6 06:41:57 -303.028077 1.199725
BFGS: 7 06:41:58 -303.105203 1.482998
BFGS: 8 06:41:58 -303.157311 1.352914
BFGS: 9 06:41:59 -303.218492 0.585401
BFGS: 10 06:41:59 -303.231822 0.464385
BFGS: 11 06:42:00 -303.252188 0.456894
BFGS: 12 06:42:00 -303.268500 0.472086
BFGS: 13 06:42:01 -303.280683 0.489671
BFGS: 14 06:42:01 -303.292284 0.613268
BFGS: 15 06:42:02 -303.316759 0.946915
BFGS: 16 06:42:02 -303.381447 1.629288
BFGS: 17 06:42:03 -303.450039 2.209926
BFGS: 18 06:42:03 -303.499388 2.408330
BFGS: 19 06:42:04 -303.564894 2.192691
BFGS: 20 06:42:04 -303.844336 1.560562
BFGS: 21 06:42:05 -304.020386 1.106003
BFGS: 22 06:42:05 -304.042486 2.103258
BFGS: 23 06:42:05 -304.221163 0.901016
BFGS: 24 06:42:06 -304.253121 0.440740
BFGS: 25 06:42:06 -304.276046 0.381404
BFGS: 26 06:42:07 -304.287821 0.364032
BFGS: 27 06:42:07 -304.306028 0.276686
BFGS: 28 06:42:07 -304.313839 0.283220
BFGS: 29 06:42:08 -304.320548 0.228256
BFGS: 30 06:42:09 -304.325104 0.181427
BFGS: 31 06:42:09 -304.329068 0.200896
BFGS: 32 06:42:09 -304.333447 0.241288
BFGS: 33 06:42:10 -304.338290 0.222054
BFGS: 34 06:42:10 -304.341802 0.143360
BFGS: 35 06:42:11 -304.343861 0.117798
BFGS: 36 06:42:11 -304.345659 0.176596
BFGS: 37 06:42:12 -304.347734 0.194049
BFGS: 38 06:42:12 -304.349568 0.122010
BFGS: 39 06:42:13 -304.350502 0.071135
BFGS: 40 06:42:13 -304.350912 0.061239
BFGS: 41 06:42:14 -304.351339 0.083817
BFGS: 42 06:42:14 -304.351854 0.088654
BFGS: 43 06:42:15 -304.352263 0.055153
BFGS: 44 06:42:15 -304.352445 0.027742
Step Time Energy fmax
BFGS: 0 06:42:15 -302.242213 4.159501
BFGS: 1 06:42:16 -302.637670 3.295594
BFGS: 2 06:42:16 -303.513807 2.976815
BFGS: 3 06:42:17 -303.666937 2.560078
BFGS: 4 06:42:17 -303.903505 1.167625
BFGS: 5 06:42:18 -303.944480 0.877497
BFGS: 6 06:42:18 -304.061726 0.498523
BFGS: 7 06:42:19 -304.079905 0.539046
BFGS: 8 06:42:19 -304.121486 0.485916
BFGS: 9 06:42:20 -304.144232 0.345119
BFGS: 10 06:42:20 -304.153034 0.244708
BFGS: 11 06:42:21 -304.156690 0.183382
BFGS: 12 06:42:21 -304.159809 0.127624
BFGS: 13 06:42:21 -304.161970 0.088980
BFGS: 14 06:42:22 -304.163635 0.107381
BFGS: 15 06:42:22 -304.164676 0.100821
BFGS: 16 06:42:23 -304.165532 0.094086
BFGS: 17 06:42:24 -304.166407 0.085332
BFGS: 18 06:42:24 -304.167256 0.084292
BFGS: 19 06:42:24 -304.168064 0.098002
BFGS: 20 06:42:25 -304.168940 0.105197
BFGS: 21 06:42:26 -304.169978 0.089522
BFGS: 22 06:42:26 -304.171139 0.108124
BFGS: 23 06:42:27 -304.172272 0.125734
BFGS: 24 06:42:27 -304.173601 0.144960
BFGS: 25 06:42:27 -304.176758 0.236147
BFGS: 26 06:42:28 -304.201838 0.680089
BFGS: 27 06:42:28 -304.314289 0.964519
BFGS: 28 06:42:29 -304.251446 1.633499
BFGS: 29 06:42:29 -304.364748 0.926212
BFGS: 30 06:42:30 -304.391006 0.725387
BFGS: 31 06:42:30 -304.474381 0.599541
BFGS: 32 06:42:31 -304.508699 0.477551
BFGS: 33 06:42:31 -304.566951 0.425000
BFGS: 34 06:42:32 -304.595517 0.341490
BFGS: 35 06:42:32 -304.613681 0.335969
BFGS: 36 06:42:33 -304.627233 0.385257
BFGS: 37 06:42:33 -304.642800 0.356137
BFGS: 38 06:42:34 -304.654564 0.235466
BFGS: 39 06:42:34 -304.661026 0.157156
BFGS: 40 06:42:35 -304.664576 0.160125
BFGS: 41 06:42:35 -304.667761 0.147751
BFGS: 42 06:42:36 -304.671774 0.104835
BFGS: 43 06:42:36 -304.675765 0.131890
BFGS: 44 06:42:36 -304.678145 0.107655
BFGS: 45 06:42:37 -304.679067 0.069846
BFGS: 46 06:42:38 -304.679585 0.061059
BFGS: 47 06:42:38 -304.680176 0.054509
BFGS: 48 06:42:39 -304.680850 0.066047
BFGS: 49 06:42:39 -304.681338 0.052537
BFGS: 50 06:42:39 -304.681523 0.026763
Step Time Energy fmax
BFGS: 0 06:42:40 -302.314115 4.012722
BFGS: 1 06:42:40 -302.696866 2.979915
BFGS: 2 06:42:41 -303.537752 3.119355
BFGS: 3 06:42:41 -303.681877 2.590130
BFGS: 4 06:42:42 -303.786735 4.549155
BFGS: 5 06:42:42 -303.927526 1.111575
BFGS: 6 06:42:43 -303.959806 0.725051
BFGS: 7 06:42:43 -304.035334 1.161072
BFGS: 8 06:42:44 -304.071766 0.840423
BFGS: 9 06:42:44 -304.100633 0.607636
BFGS: 10 06:42:44 -304.123479 0.454408
BFGS: 11 06:42:45 -304.143838 0.574670
BFGS: 12 06:42:45 -304.153925 0.393180
BFGS: 13 06:42:46 -304.157910 0.164729
BFGS: 14 06:42:47 -304.159344 0.149788
BFGS: 15 06:42:47 -304.161508 0.177557
BFGS: 16 06:42:48 -304.163189 0.141608
BFGS: 17 06:42:48 -304.164158 0.090860
BFGS: 18 06:42:49 -304.164830 0.089712
BFGS: 19 06:42:49 -304.165565 0.129724
BFGS: 20 06:42:50 -304.166307 0.136790
BFGS: 21 06:42:50 -304.167088 0.112001
BFGS: 22 06:42:51 -304.167903 0.111703
BFGS: 23 06:42:51 -304.168773 0.134605
BFGS: 24 06:42:52 -304.169693 0.145691
BFGS: 25 06:42:52 -304.170502 0.114522
BFGS: 26 06:42:53 -304.171273 0.108542
BFGS: 27 06:42:53 -304.172613 0.191385
BFGS: 28 06:42:53 -304.176148 0.399169
BFGS: 29 06:42:54 -304.189826 0.917682
BFGS: 30 06:42:54 -304.205096 1.404750
BFGS: 31 06:42:55 -304.190482 2.002685
BFGS: 32 06:42:55 -304.222336 1.284210
BFGS: 33 06:42:56 -304.229467 1.269633
BFGS: 34 06:42:56 -304.284670 1.330475
BFGS: 35 06:42:57 -304.305021 1.304185
BFGS: 36 06:42:57 -304.330808 1.320835
BFGS: 37 06:42:57 -304.357602 1.362415
BFGS: 38 06:42:58 -304.383114 1.424762
BFGS: 39 06:42:58 -304.405279 1.394462
BFGS: 40 06:42:59 -304.447425 1.269753
BFGS: 41 06:42:59 -304.483181 1.089070
BFGS: 42 06:43:00 -304.519623 0.682807
BFGS: 43 06:43:01 -304.546319 0.566625
BFGS: 44 06:43:01 -304.573752 0.491069
BFGS: 45 06:43:02 -304.605079 0.477111
BFGS: 46 06:43:02 -304.631799 0.414055
BFGS: 47 06:43:03 -304.644162 0.305963
BFGS: 48 06:43:03 -304.651528 0.270471
BFGS: 49 06:43:04 -304.661540 0.295204
BFGS: 50 06:43:04 -304.670204 0.296760
BFGS: 51 06:43:05 -304.675712 0.252595
BFGS: 52 06:43:05 -304.677925 0.194017
BFGS: 53 06:43:06 -304.678919 0.172159
BFGS: 54 06:43:06 -304.679782 0.129312
BFGS: 55 06:43:07 -304.680568 0.072397
BFGS: 56 06:43:07 -304.681049 0.048419
# 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()) Step Time Energy fmax
BFGS: 0 06:43:08 -297.260781 4.648768
BFGS: 1 06:43:08 -297.715194 4.789542
BFGS: 2 06:43:09 -298.961212 3.978128
BFGS: 3 06:43:09 -299.405684 4.000692
BFGS: 4 06:43:10 -299.580591 2.056505
BFGS: 5 06:43:11 -299.861988 2.075075
BFGS: 6 06:43:11 -299.984473 1.952827
BFGS: 7 06:43:11 -300.038856 1.531133
BFGS: 8 06:43:12 -300.072187 1.527146
BFGS: 9 06:43:12 -300.127106 2.031699
BFGS: 10 06:43:13 -300.157287 1.259421
BFGS: 11 06:43:13 -300.164364 1.196406
BFGS: 12 06:43:14 -300.181878 1.310960
BFGS: 13 06:43:14 -300.196997 1.234517
BFGS: 14 06:43:15 -300.218023 1.111798
BFGS: 15 06:43:15 -300.229072 1.143710
BFGS: 16 06:43:16 -300.249101 1.142887
BFGS: 17 06:43:16 -300.270355 1.181741
BFGS: 18 06:43:17 -300.292522 1.148504
BFGS: 19 06:43:17 -300.310318 1.041262
BFGS: 20 06:43:18 -300.323950 0.957459
BFGS: 21 06:43:18 -300.342900 0.916943
BFGS: 22 06:43:18 -300.377192 0.960144
BFGS: 23 06:43:19 -300.409508 0.701790
BFGS: 24 06:43:20 -300.429857 0.618997
BFGS: 25 06:43:20 -300.453195 0.584094
BFGS: 26 06:43:21 -300.487170 0.648604
BFGS: 27 06:43:21 -300.520178 0.658738
BFGS: 28 06:43:22 -300.545471 0.533325
BFGS: 29 06:43:22 -300.562972 0.283703
BFGS: 30 06:43:23 -300.568639 0.125447
BFGS: 31 06:43:23 -300.570339 0.166002
BFGS: 32 06:43:23 -300.572855 0.191566
BFGS: 33 06:43:24 -300.575312 0.154269
BFGS: 34 06:43:24 -300.577120 0.089662
BFGS: 35 06:43:25 -300.577859 0.050787
BFGS: 36 06:43:25 -300.578129 0.041607
Step Time Energy fmax
BFGS: 0 06:43:25 -296.310805 4.362776
BFGS: 1 06:43:26 -296.795866 4.613985
BFGS: 2 06:43:26 -298.268089 3.126469
BFGS: 3 06:43:26 -297.508641 12.149985
BFGS: 4 06:43:27 -298.480858 1.854388
BFGS: 5 06:43:27 -298.547562 1.102616
BFGS: 6 06:43:28 -298.600162 1.134620
BFGS: 7 06:43:28 -298.620465 1.051965
BFGS: 8 06:43:29 -298.736291 1.474740
BFGS: 9 06:43:29 -298.787715 1.534871
BFGS: 10 06:43:29 -299.312877 2.052804
BFGS: 11 06:43:30 -299.557863 2.512784
BFGS: 12 06:43:30 -299.763401 1.823385
BFGS: 13 06:43:31 -299.911827 1.925583
BFGS: 14 06:43:31 -300.043303 1.812835
BFGS: 15 06:43:32 -300.133070 1.831681
BFGS: 16 06:43:32 -300.293987 1.721907
BFGS: 17 06:43:33 -300.391364 1.161632
BFGS: 18 06:43:33 -300.466703 0.592432
BFGS: 19 06:43:34 -300.484550 0.811466
BFGS: 20 06:43:34 -300.510379 0.586709
BFGS: 21 06:43:35 -300.539132 0.459751
BFGS: 22 06:43:35 -300.548147 0.467090
BFGS: 23 06:43:35 -300.556390 0.405680
BFGS: 24 06:43:36 -300.564556 0.283952
BFGS: 25 06:43:36 -300.571471 0.134269
BFGS: 26 06:43:37 -300.574828 0.075688
BFGS: 27 06:43:37 -300.575909 0.066493
BFGS: 28 06:43:38 -300.576407 0.068301
BFGS: 29 06:43:38 -300.577085 0.056992
BFGS: 30 06:43:38 -300.577805 0.033526
Step Time Energy fmax
BFGS: 0 06:43:39 -296.040969 4.440882
BFGS: 1 06:43:39 -296.593465 4.762483
BFGS: 2 06:43:40 -298.249568 2.813155
BFGS: 3 06:43:41 -296.635433 18.260473
BFGS: 4 06:43:41 -298.402432 1.745038
BFGS: 5 06:43:42 -298.459505 0.994407
BFGS: 6 06:43:42 -298.495385 0.553305
BFGS: 7 06:43:42 -298.499843 0.293977
BFGS: 8 06:43:43 -298.506509 0.098952
BFGS: 9 06:43:44 -298.508135 0.119849
BFGS: 10 06:43:44 -298.508435 0.075067
BFGS: 11 06:43:45 -298.508567 0.054658
BFGS: 12 06:43:45 -298.508895 0.098774
BFGS: 13 06:43:45 -298.509543 0.155316
BFGS: 14 06:43:46 -298.510837 0.215551
BFGS: 15 06:43:46 -298.513231 0.271862
BFGS: 16 06:43:47 -298.521444 0.453904
BFGS: 17 06:43:47 -298.528237 1.100009
BFGS: 18 06:43:48 -298.534578 1.165942
BFGS: 19 06:43:48 -298.546626 1.994663
BFGS: 20 06:43:49 -298.564625 2.705089
BFGS: 21 06:43:49 -298.577617 2.420919
BFGS: 22 06:43:49 -298.600239 3.300372
BFGS: 23 06:43:50 -298.658783 2.846666
BFGS: 24 06:43:50 -298.697350 2.798524
BFGS: 25 06:43:51 -298.708717 2.645519
BFGS: 26 06:43:51 -298.744280 2.410953
BFGS: 27 06:43:52 -298.812940 2.079385
BFGS: 28 06:43:52 -298.898517 1.804377
BFGS: 29 06:43:53 -298.965660 1.879389
BFGS: 30 06:43:54 -299.025331 1.694632
BFGS: 31 06:43:54 -299.106831 1.885398
BFGS: 32 06:43:54 -299.196360 2.018108
BFGS: 33 06:43:55 -299.305886 2.113712
BFGS: 34 06:43:55 -299.433322 2.060446
BFGS: 35 06:43:56 -299.538674 1.575072
BFGS: 36 06:43:57 -299.625153 0.851932
BFGS: 37 06:43:57 -299.702606 0.720112
BFGS: 38 06:43:58 -299.766521 0.869447
BFGS: 39 06:43:58 -299.795272 0.787929
BFGS: 40 06:43:58 -299.827148 0.534165
BFGS: 41 06:43:59 -299.850812 0.238769
BFGS: 42 06:43:59 -299.862543 0.195755
BFGS: 43 06:44:00 -299.869297 0.250310
BFGS: 44 06:44:00 -299.873639 0.344402
BFGS: 45 06:44:01 -299.879508 0.428246
BFGS: 46 06:44:01 -299.888761 0.512993
BFGS: 47 06:44:02 -299.901027 0.548662
BFGS: 48 06:44:02 -299.919308 0.691166
BFGS: 49 06:44:03 -299.966532 1.241384
BFGS: 50 06:44:03 -299.989185 2.076889
BFGS: 51 06:44:04 -300.055186 1.739977
BFGS: 52 06:44:04 -300.197599 1.569593
BFGS: 53 06:44:05 -300.404705 0.884791
BFGS: 54 06:44:05 -300.399459 1.066453
BFGS: 55 06:44:06 -300.488213 0.659762
BFGS: 56 06:44:06 -300.511907 0.620301
BFGS: 57 06:44:07 -300.537242 0.447973
BFGS: 58 06:44:07 -300.562336 0.187038
BFGS: 59 06:44:08 -300.568283 0.141736
BFGS: 60 06:44:08 -300.571601 0.121238
BFGS: 61 06:44:09 -300.572987 0.110725
BFGS: 62 06:44:09 -300.573987 0.104004
BFGS: 63 06:44:10 -300.575155 0.097838
BFGS: 64 06:44:10 -300.576379 0.086386
BFGS: 65 06:44:10 -300.577287 0.063588
BFGS: 66 06:44:11 -300.577761 0.040757
Step Time Energy fmax
BFGS: 0 06:44:11 -296.086264 4.419667
BFGS: 1 06:44:12 -296.623654 4.724507
BFGS: 2 06:44:12 -298.244030 2.867041
BFGS: 3 06:44:13 -296.802100 17.043173
BFGS: 4 06:44:13 -298.405383 1.765785
BFGS: 5 06:44:14 -298.463896 1.002477
BFGS: 6 06:44:14 -298.500259 0.613991
BFGS: 7 06:44:14 -298.505296 0.363452
BFGS: 8 06:44:15 -298.513806 0.167631
BFGS: 9 06:44:16 -298.515565 0.182077
BFGS: 10 06:44:16 -298.516215 0.145181
BFGS: 11 06:44:17 -298.517074 0.121190
BFGS: 12 06:44:17 -298.519614 0.226848
BFGS: 13 06:44:17 -298.530093 0.502294
BFGS: 14 06:44:18 -298.558153 0.933422
BFGS: 15 06:44:18 -298.641108 1.980965
BFGS: 16 06:44:19 -298.821109 2.371119
BFGS: 17 06:44:19 -299.113622 4.208669
BFGS: 18 06:44:20 -299.370317 5.928053
BFGS: 19 06:44:20 -299.519762 6.625398
BFGS: 20 06:44:21 -299.752766 5.384173
BFGS: 21 06:44:21 -300.091565 2.427188
BFGS: 22 06:44:21 -300.164129 1.537911
BFGS: 23 06:44:22 -300.213939 1.549290
BFGS: 24 06:44:23 -300.250763 1.674431
BFGS: 25 06:44:23 -300.283524 1.770931
BFGS: 26 06:44:23 -300.317088 1.744711
BFGS: 27 06:44:24 -300.327997 1.690324
BFGS: 28 06:44:24 -300.337984 1.653002
BFGS: 29 06:44:25 -300.349033 1.628195
BFGS: 30 06:44:25 -300.359392 1.612956
BFGS: 31 06:44:26 -300.366867 1.611680
BFGS: 32 06:44:26 -300.372470 1.619603
BFGS: 33 06:44:27 -300.377882 1.615621
BFGS: 34 06:44:27 -300.383444 1.576388
BFGS: 35 06:44:28 -300.387569 1.508426
BFGS: 36 06:44:28 -300.389789 1.466862
BFGS: 37 06:44:28 -300.391283 1.469357
BFGS: 38 06:44:29 -300.392783 1.480814
BFGS: 39 06:44:29 -300.394174 1.500256
BFGS: 40 06:44:30 -300.395269 1.519669
BFGS: 41 06:44:30 -300.396113 1.530547
BFGS: 42 06:44:31 -300.396894 1.529944
BFGS: 43 06:44:31 -300.397580 1.516642
BFGS: 44 06:44:32 -300.398092 1.497338
BFGS: 45 06:44:32 -300.398427 1.481329
BFGS: 46 06:44:33 -300.398685 1.470296
BFGS: 47 06:44:33 -300.398953 1.461789
BFGS: 48 06:44:33 -300.399218 1.456109
BFGS: 49 06:44:34 -300.399424 1.453185
BFGS: 50 06:44:34 -300.399570 1.450309
BFGS: 51 06:44:35 -300.399715 1.454177
BFGS: 52 06:44:35 -300.399866 1.452932
BFGS: 53 06:44:36 -300.399999 1.443265
BFGS: 54 06:44:36 -300.400096 1.431749
BFGS: 55 06:44:37 -300.400173 1.422868
BFGS: 56 06:44:37 -300.400264 1.416527
BFGS: 57 06:44:38 -300.400364 1.415263
BFGS: 58 06:44:38 -300.400432 1.419912
BFGS: 59 06:44:39 -300.400460 1.425448
BFGS: 60 06:44:39 -300.400481 1.429197
BFGS: 61 06:44:39 -300.400503 1.431840
BFGS: 62 06:44:40 -300.400521 1.432749
BFGS: 63 06:44:40 -300.400534 1.431361
BFGS: 64 06:44:41 -300.400543 1.429245
BFGS: 65 06:44:41 -300.400548 1.427687
BFGS: 66 06:44:42 -300.400553 1.426678
BFGS: 67 06:44:42 -300.400557 1.426395
BFGS: 68 06:44:43 -300.400560 1.427086
BFGS: 69 06:44:43 -300.400562 1.428222
BFGS: 70 06:44:43 -300.400562 1.429077
BFGS: 71 06:44:44 -300.400564 1.429729
BFGS: 72 06:44:44 -300.400568 1.430225
BFGS: 73 06:44:45 -300.400567 1.430382
BFGS: 74 06:44:45 -300.400567 1.430049
BFGS: 75 06:44:46 -300.400569 1.429623
BFGS: 76 06:44:46 -300.400569 1.429329
BFGS: 77 06:44:47 -300.400569 1.429092
BFGS: 78 06:44:47 -300.400566 1.429085
BFGS: 79 06:44:48 -300.400568 1.429287
BFGS: 80 06:44:48 -300.400568 1.429533
BFGS: 81 06:44:49 -300.400570 1.429752
BFGS: 82 06:44:49 -300.400571 1.429924
BFGS: 83 06:44:50 -300.400568 1.430044
BFGS: 84 06:44:50 -300.400571 1.430059
BFGS: 85 06:44:51 -300.400570 1.430000
BFGS: 86 06:44:51 -300.400570 1.429922
BFGS: 87 06:44:52 -300.400572 1.429833
BFGS: 88 06:44:52 -300.400570 1.429791
BFGS: 89 06:44:53 -300.400569 1.429807
BFGS: 90 06:44:53 -300.400569 1.429834
BFGS: 91 06:44:54 -300.400571 1.429877
BFGS: 92 06:44:54 -300.400571 1.429927
BFGS: 93 06:44:55 -300.400569 1.429972
BFGS: 94 06:44:55 -300.400571 1.429954
BFGS: 95 06:44:56 -300.400569 1.429942
BFGS: 96 06:44:56 -300.400571 1.429940
BFGS: 97 06:44:57 -300.400567 1.429913
BFGS: 98 06:44:57 -300.400572 1.429892
BFGS: 99 06:44:58 -300.400570 1.429857
BFGS: 100 06:44:58 -300.400570 1.429861
BFGS: 101 06:44:59 -300.400569 1.429908
BFGS: 102 06:44:59 -300.400570 1.429917
BFGS: 103 06:45:00 -300.400570 1.429895
BFGS: 104 06:45:00 -300.400571 1.429888
BFGS: 105 06:45:01 -300.400569 1.429931
BFGS: 106 06:45:01 -300.400569 1.429928
BFGS: 107 06:45:02 -300.400570 1.429903
BFGS: 108 06:45:02 -300.400570 1.429911
BFGS: 109 06:45:03 -300.400570 1.429905
BFGS: 110 06:45:03 -300.400570 1.429923
BFGS: 111 06:45:04 -300.400570 1.429898
BFGS: 112 06:45:04 -300.400570 1.429905
BFGS: 113 06:45:05 -300.400569 1.429909
BFGS: 114 06:45:05 -300.400568 1.429920
BFGS: 115 06:45:06 -300.400570 1.429916
BFGS: 116 06:45:06 -300.400572 1.429909
BFGS: 117 06:45:07 -300.400571 1.429900
BFGS: 118 06:45:07 -300.400571 1.429918
BFGS: 119 06:45:08 -300.400570 1.429918
BFGS: 120 06:45:08 -300.400567 1.429907
BFGS: 121 06:45:09 -300.400569 1.429919
BFGS: 122 06:45:09 -300.400572 1.429907
BFGS: 123 06:45:09 -300.400571 1.429915
BFGS: 124 06:45:10 -300.400567 1.429916
BFGS: 125 06:45:10 -300.400569 1.429900
BFGS: 126 06:45:11 -300.400570 1.429913
BFGS: 127 06:45:11 -300.400569 1.429913
BFGS: 128 06:45:12 -300.400568 1.429920
BFGS: 129 06:45:13 -300.400571 1.429898
BFGS: 130 06:45:13 -300.400571 1.429919
BFGS: 131 06:45:14 -300.400569 1.429914
BFGS: 132 06:45:14 -300.400571 1.429908
BFGS: 133 06:45:14 -300.400571 1.429896
BFGS: 134 06:45:15 -300.400572 1.429895
BFGS: 135 06:45:15 -300.400573 1.429918
BFGS: 136 06:45:16 -300.400569 1.429933
BFGS: 137 06:45:16 -300.400571 1.429863
BFGS: 138 06:45:17 -300.400571 1.429924
BFGS: 139 06:45:17 -300.400567 1.429917
BFGS: 140 06:45:18 -300.400571 1.429921
BFGS: 141 06:45:18 -300.400568 1.429916
BFGS: 142 06:45:19 -300.400571 1.429913
BFGS: 143 06:45:19 -300.400571 1.429918
BFGS: 144 06:45:20 -300.400567 1.429912
BFGS: 145 06:45:20 -300.400570 1.429919
BFGS: 146 06:45:21 -300.400571 1.429914
BFGS: 147 06:45:21 -300.400570 1.429912
BFGS: 148 06:45:22 -300.400571 1.429887
BFGS: 149 06:45:22 -300.400567 1.429914
BFGS: 150 06:45:23 -300.400571 1.429914
BFGS: 151 06:45:23 -300.400568 1.429914
BFGS: 152 06:45:23 -300.400572 1.429868
BFGS: 153 06:45:24 -300.400569 1.429910
BFGS: 154 06:45:24 -300.400570 1.429913
BFGS: 155 06:45:25 -300.400568 1.429919
BFGS: 156 06:45:25 -300.400569 1.429917
BFGS: 157 06:45:26 -300.400570 1.429903
BFGS: 158 06:45:26 -300.400572 1.429909
BFGS: 159 06:45:27 -300.400571 1.429912
BFGS: 160 06:45:27 -300.400568 1.429925
BFGS: 161 06:45:28 -300.400572 1.429898
BFGS: 162 06:45:28 -300.400570 1.429914
BFGS: 163 06:45:29 -300.400569 1.429915
BFGS: 164 06:45:29 -300.400570 1.429906
BFGS: 165 06:45:29 -300.400570 1.429919
BFGS: 166 06:45:30 -300.400572 1.429918
BFGS: 167 06:45:30 -300.400569 1.429904
BFGS: 168 06:45:30 -300.400570 1.429904
BFGS: 169 06:45:31 -300.400568 1.429929
BFGS: 170 06:45:32 -300.400571 1.429922
BFGS: 171 06:45:32 -300.400569 1.429903
BFGS: 172 06:45:33 -300.400570 1.429907
BFGS: 173 06:45:33 -300.400571 1.429930
BFGS: 174 06:45:33 -300.400572 1.429919
BFGS: 175 06:45:34 -300.400567 1.429909
BFGS: 176 06:45:34 -300.400569 1.429902
BFGS: 177 06:45:34 -300.400569 1.429955
BFGS: 178 06:45:35 -300.400573 1.429918
BFGS: 179 06:45:36 -300.400568 1.429905
BFGS: 180 06:45:36 -300.400575 1.429901
BFGS: 181 06:45:37 -300.400571 1.429914
BFGS: 182 06:45:37 -300.400573 1.429901
BFGS: 183 06:45:38 -300.400570 1.429910
BFGS: 184 06:45:38 -300.400572 1.429892
BFGS: 185 06:45:39 -300.400571 1.429922
BFGS: 186 06:45:39 -300.400571 1.429920
BFGS: 187 06:45:39 -300.400571 1.429897
BFGS: 188 06:45:40 -300.400568 1.429916
BFGS: 189 06:45:40 -300.400573 1.429909
BFGS: 190 06:45:41 -300.400573 1.429914
BFGS: 191 06:45:41 -300.400568 1.429917
BFGS: 192 06:45:42 -300.400571 1.429902
BFGS: 193 06:45:42 -300.400572 1.429909
BFGS: 194 06:45:43 -300.400574 1.429901
BFGS: 195 06:45:43 -300.400570 1.429896
BFGS: 196 06:45:43 -300.400569 1.429932
BFGS: 197 06:45:44 -300.400570 1.429934
BFGS: 198 06:45:44 -300.400570 1.429920
BFGS: 199 06:45:45 -300.400572 1.429910
BFGS: 200 06:45:45 -300.400568 1.429906
BFGS: 201 06:45:46 -300.400572 1.429902
BFGS: 202 06:45:46 -300.400573 1.429904
BFGS: 203 06:45:47 -300.400572 1.429904
BFGS: 204 06:45:47 -300.400571 1.429902
BFGS: 205 06:45:48 -300.400570 1.429900
BFGS: 206 06:45:48 -300.400571 1.429925
BFGS: 207 06:45:49 -300.400570 1.429926
BFGS: 208 06:45:50 -300.400571 1.429862
BFGS: 209 06:45:50 -300.400568 1.429906
BFGS: 210 06:45:50 -300.400570 1.429927
BFGS: 211 06:45:51 -300.400571 1.429912
BFGS: 212 06:45:52 -300.400569 1.429906
BFGS: 213 06:45:52 -300.400571 1.429900
BFGS: 214 06:45:53 -300.400569 1.429942
BFGS: 215 06:45:53 -300.400570 1.429926
BFGS: 216 06:45:54 -300.400569 1.429902
BFGS: 217 06:45:54 -300.400572 1.429914
BFGS: 218 06:45:55 -300.400573 1.429902
BFGS: 219 06:45:55 -300.400573 1.429900
BFGS: 220 06:45:56 -300.400570 1.429932
BFGS: 221 06:45:56 -300.400570 1.429925
BFGS: 222 06:45:57 -300.400572 1.429898
BFGS: 223 06:45:57 -300.400570 1.429906
BFGS: 224 06:45:58 -300.400570 1.429936
BFGS: 225 06:45:58 -300.400572 1.429906
BFGS: 226 06:45:59 -300.400568 1.429905
BFGS: 227 06:45:59 -300.400572 1.429903
BFGS: 228 06:46:00 -300.400570 1.429928
BFGS: 229 06:46:00 -300.400573 1.429904
BFGS: 230 06:46:01 -300.400569 1.429899
BFGS: 231 06:46:01 -300.400570 1.429899
BFGS: 232 06:46:01 -300.400569 1.429950
BFGS: 233 06:46:02 -300.400570 1.429926
BFGS: 234 06:46:02 -300.400569 1.429905
BFGS: 235 06:46:02 -300.400574 1.429899
BFGS: 236 06:46:03 -300.400572 1.429902
BFGS: 237 06:46:03 -300.400572 1.429907
BFGS: 238 06:46:03 -300.400572 1.429905
BFGS: 239 06:46:04 -300.400574 1.429900
BFGS: 240 06:46:04 -300.400572 1.429900
BFGS: 241 06:46:04 -300.400570 1.429897
BFGS: 242 06:46:05 -300.400572 1.429922
BFGS: 243 06:46:05 -300.400573 1.429904
BFGS: 244 06:46:06 -300.400571 1.429898
BFGS: 245 06:46:06 -300.400574 1.429907
BFGS: 246 06:46:07 -300.400570 1.429914
BFGS: 247 06:46:07 -300.400573 1.429903
BFGS: 248 06:46:08 -300.400572 1.429897
BFGS: 249 06:46:08 -300.400570 1.429902
BFGS: 250 06:46:09 -300.400571 1.429910
BFGS: 251 06:46:09 -300.400572 1.429908
BFGS: 252 06:46:10 -300.400571 1.429913
BFGS: 253 06:46:10 -300.400569 1.429935
BFGS: 254 06:46:11 -300.400571 1.429905
BFGS: 255 06:46:11 -300.400569 1.429931
BFGS: 256 06:46:11 -300.400570 1.429927
BFGS: 257 06:46:12 -300.400572 1.429905
BFGS: 258 06:46:12 -300.400572 1.429909
BFGS: 259 06:46:12 -300.400570 1.429891
BFGS: 260 06:46:13 -300.400575 1.429908
BFGS: 261 06:46:13 -300.400570 1.429916
BFGS: 262 06:46:14 -300.400571 1.429899
BFGS: 263 06:46:14 -300.400570 1.429922
BFGS: 264 06:46:14 -300.400575 1.429904
BFGS: 265 06:46:15 -300.400569 1.429916
BFGS: 266 06:46:15 -300.400573 1.429905
BFGS: 267 06:46:16 -300.400574 1.429899
BFGS: 268 06:46:16 -300.400571 1.429908
BFGS: 269 06:46:17 -300.400569 1.429898
BFGS: 270 06:46:17 -300.400568 1.429931
BFGS: 271 06:46:18 -300.400569 1.429931
BFGS: 272 06:46:18 -300.400571 1.429900
BFGS: 273 06:46:18 -300.400572 1.429906
BFGS: 274 06:46:19 -300.400571 1.429921
BFGS: 275 06:46:19 -300.400570 1.429910
BFGS: 276 06:46:20 -300.400573 1.429900
BFGS: 277 06:46:20 -300.400573 1.429910
BFGS: 278 06:46:21 -300.400570 1.429908
BFGS: 279 06:46:21 -300.400571 1.429908
BFGS: 280 06:46:22 -300.400572 1.429903
BFGS: 281 06:46:22 -300.400571 1.429907
BFGS: 282 06:46:22 -300.400570 1.429912
BFGS: 283 06:46:23 -300.400573 1.429905
BFGS: 284 06:46:23 -300.400572 1.429900
BFGS: 285 06:46:24 -300.400572 1.429916
BFGS: 286 06:46:24 -300.400571 1.429916
BFGS: 287 06:46:25 -300.400572 1.429901
BFGS: 288 06:46:25 -300.400573 1.429903
BFGS: 289 06:46:26 -300.400571 1.429904
BFGS: 290 06:46:26 -300.400567 1.429926
BFGS: 291 06:46:27 -300.400572 1.429909
BFGS: 292 06:46:27 -300.400571 1.429900
BFGS: 293 06:46:27 -300.400572 1.429899
BFGS: 294 06:46:28 -300.400570 1.429900
BFGS: 295 06:46:29 -300.400572 1.429904
BFGS: 296 06:46:29 -300.400573 1.429901
BFGS: 297 06:46:30 -300.400569 1.429913
BFGS: 298 06:46:30 -300.400571 1.429917
BFGS: 299 06:46:30 -300.400571 1.429911
BFGS: 300 06:46:31 -300.400572 1.429899
Step Time Energy fmax
BFGS: 0 06:46:31 -296.953181 4.494010
BFGS: 1 06:46:32 -297.406025 4.662019
BFGS: 2 06:46:32 -298.680975 3.796108
BFGS: 3 06:46:32 -299.016016 4.708933
BFGS: 4 06:46:33 -299.222445 1.950965
BFGS: 5 06:46:33 -299.390986 1.979934
BFGS: 6 06:46:34 -299.813175 1.191265
BFGS: 7 06:46:34 -299.832226 2.284256
BFGS: 8 06:46:34 -299.923569 0.928736
BFGS: 9 06:46:35 -299.985072 1.045057
BFGS: 10 06:46:35 -300.237228 1.445582
BFGS: 11 06:46:36 -300.306440 2.045743
BFGS: 12 06:46:36 -300.384210 1.288280
BFGS: 13 06:46:37 -300.481443 0.881653
BFGS: 14 06:46:37 -300.498404 0.758439
BFGS: 15 06:46:38 -300.539456 0.417855
BFGS: 16 06:46:38 -300.548754 0.335900
BFGS: 17 06:46:39 -300.554641 0.260106
BFGS: 18 06:46:39 -300.562465 0.241220
BFGS: 19 06:46:39 -300.569113 0.231704
BFGS: 20 06:46:40 -300.572891 0.169274
BFGS: 21 06:46:40 -300.574577 0.094866
BFGS: 22 06:46:41 -300.575476 0.076487
BFGS: 23 06:46:41 -300.576183 0.072286
BFGS: 24 06:46:42 -300.577017 0.077695
BFGS: 25 06:46:42 -300.577776 0.061345
BFGS: 26 06:46:43 -300.578189 0.042519
Step Time Energy fmax
BFGS: 0 06:46:43 -296.442996 4.359473
BFGS: 1 06:46:44 -296.914381 4.587648
BFGS: 2 06:46:44 -298.327466 3.204618
BFGS: 3 06:46:44 -297.775963 10.691521
BFGS: 4 06:46:45 -298.562867 1.879821
BFGS: 5 06:46:45 -298.633403 1.201440
BFGS: 6 06:46:46 -298.705725 1.396345
BFGS: 7 06:46:46 -298.746554 1.424209
BFGS: 8 06:46:47 -298.931557 1.324053
BFGS: 9 06:46:47 -299.055739 1.834472
BFGS: 10 06:46:47 -299.173671 2.079437
BFGS: 11 06:46:48 -299.307435 1.894761
BFGS: 12 06:46:48 -299.619099 1.496285
BFGS: 13 06:46:49 -299.906410 0.633471
BFGS: 14 06:46:49 -299.923254 1.208580
BFGS: 15 06:46:50 -299.949700 0.783068
BFGS: 16 06:46:50 -299.995604 0.350247
BFGS: 17 06:46:51 -300.009731 0.233565
BFGS: 18 06:46:51 -300.013654 0.249279
BFGS: 19 06:46:51 -300.020178 0.214982
BFGS: 20 06:46:52 -300.027263 0.200448
BFGS: 21 06:46:52 -300.033786 0.190507
BFGS: 22 06:46:52 -300.037224 0.158895
BFGS: 23 06:46:53 -300.039039 0.134233
BFGS: 24 06:46:53 -300.040418 0.114688
BFGS: 25 06:46:54 -300.042005 0.090241
BFGS: 26 06:46:54 -300.043089 0.057312
BFGS: 27 06:46:55 -300.043460 0.034857
Step Time Energy fmax
BFGS: 0 06:46:55 -297.098995 4.562378
BFGS: 1 06:46:56 -297.551657 4.717636
BFGS: 2 06:46:56 -298.783986 3.950336
BFGS: 3 06:46:57 -299.275406 3.474867
BFGS: 4 06:46:57 -299.443518 1.912815
BFGS: 5 06:46:57 -299.896451 1.845970
BFGS: 6 06:46:58 -300.021707 1.683182
BFGS: 7 06:46:58 -300.099442 1.334667
BFGS: 8 06:46:58 -300.203505 1.330201
BFGS: 9 06:46:59 -300.457090 1.208753
BFGS: 10 06:46:59 -300.494890 0.876557
BFGS: 11 06:47:00 -300.524899 0.466452
BFGS: 12 06:47:00 -300.537701 0.267022
BFGS: 13 06:47:01 -300.546675 0.287710
BFGS: 14 06:47:01 -300.556596 0.270228
BFGS: 15 06:47:02 -300.564245 0.234510
BFGS: 16 06:47:02 -300.568333 0.170069
BFGS: 17 06:47:02 -300.571171 0.127667
BFGS: 18 06:47:03 -300.573139 0.140819
BFGS: 19 06:47:03 -300.574703 0.138765
BFGS: 20 06:47:04 -300.576074 0.095274
BFGS: 21 06:47:04 -300.576911 0.062060
BFGS: 22 06:47:05 -300.577374 0.051869
BFGS: 23 06:47:05 -300.577755 0.061139
BFGS: 24 06:47:06 -300.578105 0.054239
BFGS: 25 06:47:06 -300.578352 0.041157
Step Time Energy fmax
BFGS: 0 06:47:06 -297.368307 4.615770
BFGS: 1 06:47:07 -297.841858 4.708762
BFGS: 2 06:47:07 -299.079594 3.565629
BFGS: 3 06:47:08 -299.389093 3.781331
BFGS: 4 06:47:08 -299.555975 1.401737
BFGS: 5 06:47:09 -299.662422 1.231977
BFGS: 6 06:47:09 -299.870256 1.016984
BFGS: 7 06:47:10 -299.908377 1.043727
BFGS: 8 06:47:10 -300.108894 1.164161
BFGS: 9 06:47:11 -300.225646 1.672896
BFGS: 10 06:47:11 -300.311731 1.350775
BFGS: 11 06:47:11 -300.429574 1.273825
BFGS: 12 06:47:12 -300.469871 0.916143
BFGS: 13 06:47:12 -300.502022 0.585450
BFGS: 14 06:47:12 -300.519377 0.589836
BFGS: 15 06:47:13 -300.537364 0.542437
BFGS: 16 06:47:13 -300.548835 0.441940
BFGS: 17 06:47:14 -300.564432 0.158939
BFGS: 18 06:47:14 -300.567516 0.135772
BFGS: 19 06:47:15 -300.569587 0.130723
BFGS: 20 06:47:15 -300.572163 0.169568
BFGS: 21 06:47:16 -300.574931 0.150069
BFGS: 22 06:47:16 -300.576668 0.085894
BFGS: 23 06:47:17 -300.577332 0.043473
Step Time Energy fmax
BFGS: 0 06:47:17 -296.268504 4.370613
BFGS: 1 06:47:17 -296.761523 4.630105
BFGS: 2 06:47:17 -298.257809 3.080525
BFGS: 3 06:47:18 -297.390566 12.884114
BFGS: 4 06:47:18 -298.459577 1.839271
BFGS: 5 06:47:19 -298.524409 1.071671
BFGS: 6 06:47:19 -298.571058 1.001248
BFGS: 7 06:47:20 -298.585494 0.865041
BFGS: 8 06:47:20 -298.653850 0.994358
BFGS: 9 06:47:21 -298.675871 1.060312
BFGS: 10 06:47:21 -299.018006 1.669684
BFGS: 11 06:47:22 -299.460011 2.191538
BFGS: 12 06:47:22 -299.885755 1.505231
BFGS: 13 06:47:23 -299.906106 3.015288
BFGS: 14 06:47:23 -300.018432 1.176361
BFGS: 15 06:47:24 -300.073060 1.094910
BFGS: 16 06:47:24 -300.268232 1.381227
BFGS: 17 06:47:25 -300.426602 1.150365
BFGS: 18 06:47:25 -300.467101 0.844674
BFGS: 19 06:47:25 -300.496651 0.519531
BFGS: 20 06:47:26 -300.515357 0.496994
BFGS: 21 06:47:26 -300.540987 0.472135
BFGS: 22 06:47:27 -300.555275 0.299829
BFGS: 23 06:47:27 -300.561600 0.273392
BFGS: 24 06:47:28 -300.565012 0.232613
BFGS: 25 06:47:28 -300.567976 0.199027
BFGS: 26 06:47:29 -300.572035 0.174249
BFGS: 27 06:47:29 -300.575276 0.148579
BFGS: 28 06:47:30 -300.576701 0.083723
BFGS: 29 06:47:30 -300.577092 0.054258
BFGS: 30 06:47:30 -300.577426 0.051820
BFGS: 31 06:47:31 -300.577822 0.063138
BFGS: 32 06:47:31 -300.578192 0.059372
BFGS: 33 06:47:31 -300.578432 0.039636
Step Time Energy fmax
BFGS: 0 06:47:32 -296.080504 4.428673
BFGS: 1 06:47:32 -296.620956 4.736194
BFGS: 2 06:47:32 -298.245600 2.866040
BFGS: 3 06:47:33 -296.789065 17.154991
BFGS: 4 06:47:33 -298.406282 1.765815
BFGS: 5 06:47:34 -298.464666 1.002578
BFGS: 6 06:47:34 -298.500935 0.604714
BFGS: 7 06:47:34 -298.505916 0.353568
BFGS: 8 06:47:35 -298.514305 0.166523
BFGS: 9 06:47:35 -298.516095 0.181365
BFGS: 10 06:47:36 -298.516745 0.145108
BFGS: 11 06:47:36 -298.517583 0.122771
BFGS: 12 06:47:37 -298.520019 0.219557
BFGS: 13 06:47:37 -298.529087 0.480438
BFGS: 14 06:47:38 -298.557323 0.897609
BFGS: 15 06:47:38 -298.481963 5.454338
BFGS: 16 06:47:39 -298.751925 3.235533
BFGS: 17 06:47:39 -299.127100 2.365367
BFGS: 18 06:47:39 -299.317732 2.059252
BFGS: 19 06:47:40 -299.400615 3.816838
BFGS: 20 06:47:40 -299.710856 1.096506
BFGS: 21 06:47:41 -299.768926 0.655415
BFGS: 22 06:47:41 -299.823321 0.931076
BFGS: 23 06:47:42 -299.842131 0.589799
BFGS: 24 06:47:42 -299.860050 0.217363
BFGS: 25 06:47:43 -299.862141 0.169683
BFGS: 26 06:47:43 -299.863813 0.117635
BFGS: 27 06:47:43 -299.865521 0.100923
BFGS: 28 06:47:44 -299.867156 0.087160
BFGS: 29 06:47:44 -299.867896 0.059023
BFGS: 30 06:47:45 -299.868137 0.050737
BFGS: 31 06:47:45 -299.868306 0.052025
BFGS: 32 06:47:46 -299.868546 0.063389
BFGS: 33 06:47:46 -299.868777 0.059969
BFGS: 34 06:47:47 -299.868927 0.045008
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 06:47:47 -295.636827 0.729905
BFGS: 1 06:47:48 -295.686846 0.700306
BFGS: 2 06:47:48 -295.877850 0.444734
BFGS: 3 06:47:49 -295.890425 0.475590
BFGS: 4 06:47:49 -295.896386 0.466168
BFGS: 5 06:47:50 -295.941517 0.295774
BFGS: 6 06:47:50 -295.945711 0.292658
BFGS: 7 06:47:50 -295.952430 0.189930
BFGS: 8 06:47:51 -295.955515 0.195069
BFGS: 9 06:47:51 -295.958867 0.196280
BFGS: 10 06:47:52 -295.960421 0.176884
BFGS: 11 06:47:52 -295.961845 0.142310
BFGS: 12 06:47:53 -295.963412 0.096610
BFGS: 13 06:47:53 -295.964776 0.087358
BFGS: 14 06:47:54 -295.965516 0.091362
BFGS: 15 06:47:54 -295.965963 0.084998
BFGS: 16 06:47:55 -295.966433 0.060910
BFGS: 17 06:47:55 -295.966843 0.026019
Step Time Energy fmax
BFGS: 0 06:47:56 -295.387889 1.158277
BFGS: 1 06:47:56 -295.455786 1.064008
BFGS: 2 06:47:57 -295.668633 1.074010
BFGS: 3 06:47:57 -295.690611 0.586618
BFGS: 4 06:47:58 -295.702943 0.478173
BFGS: 5 06:47:58 -295.742928 0.587613
BFGS: 6 06:47:59 -295.752632 0.563573
BFGS: 7 06:47:59 -295.793371 0.568121
BFGS: 8 06:48:00 -295.822003 0.527949
BFGS: 9 06:48:00 -295.846865 0.477274
BFGS: 10 06:48:01 -295.857705 0.430107
BFGS: 11 06:48:01 -295.865761 0.356693
BFGS: 12 06:48:02 -295.876759 0.266255
BFGS: 13 06:48:02 -295.887153 0.224726
BFGS: 14 06:48:02 -295.892623 0.254992
BFGS: 15 06:48:03 -295.895775 0.239752
BFGS: 16 06:48:03 -295.900331 0.222186
BFGS: 17 06:48:04 -295.907444 0.213149
BFGS: 18 06:48:04 -295.915019 0.169418
BFGS: 19 06:48:05 -295.919776 0.170494
BFGS: 20 06:48:05 -295.922434 0.150944
BFGS: 21 06:48:06 -295.924070 0.116140
BFGS: 22 06:48:06 -295.926695 0.103366
BFGS: 23 06:48:07 -295.929223 0.086777
BFGS: 24 06:48:07 -295.930749 0.069926
BFGS: 25 06:48:08 -295.931346 0.053136
BFGS: 26 06:48:08 -295.931680 0.042216
Step Time Energy fmax
BFGS: 0 06:48:09 -295.405519 1.150589
BFGS: 1 06:48:09 -295.471562 1.062479
BFGS: 2 06:48:09 -295.690680 1.035618
BFGS: 3 06:48:10 -295.712622 0.569799
BFGS: 4 06:48:10 -295.724870 0.505067
BFGS: 5 06:48:11 -295.768790 0.609493
BFGS: 6 06:48:11 -295.780282 0.589459
BFGS: 7 06:48:11 -295.832448 0.782839
BFGS: 8 06:48:12 -295.865548 0.702657
BFGS: 9 06:48:12 -295.896912 0.526933
BFGS: 10 06:48:13 -295.907744 0.464081
BFGS: 11 06:48:13 -295.919626 0.367799
BFGS: 12 06:48:13 -295.930635 0.283676
BFGS: 13 06:48:14 -295.940158 0.248155
BFGS: 14 06:48:14 -295.944665 0.258567
BFGS: 15 06:48:15 -295.948022 0.231074
BFGS: 16 06:48:15 -295.952751 0.184688
BFGS: 17 06:48:16 -295.958349 0.138808
BFGS: 18 06:48:16 -295.962348 0.100672
BFGS: 19 06:48:17 -295.963935 0.087139
BFGS: 20 06:48:17 -295.964542 0.073951
BFGS: 21 06:48:17 -295.965035 0.068208
BFGS: 22 06:48:18 -295.965721 0.062016
BFGS: 23 06:48:18 -295.966360 0.048108
Step Time Energy fmax
BFGS: 0 06:48:19 -295.551112 0.782204
BFGS: 1 06:48:19 -295.606564 0.726685
BFGS: 2 06:48:20 -295.798871 0.513599
BFGS: 3 06:48:20 -295.810997 0.324641
BFGS: 4 06:48:21 -295.815738 0.327802
BFGS: 5 06:48:21 -295.833135 0.272897
BFGS: 6 06:48:22 -295.835365 0.225523
BFGS: 7 06:48:22 -295.839193 0.161153
BFGS: 8 06:48:22 -295.840927 0.095844
BFGS: 9 06:48:23 -295.841727 0.071966
BFGS: 10 06:48:23 -295.841971 0.065091
BFGS: 11 06:48:24 -295.842226 0.049092
Step Time Energy fmax
BFGS: 0 06:48:24 -295.297832 1.309652
BFGS: 1 06:48:25 -295.374830 1.195428
BFGS: 2 06:48:25 -295.589153 1.426767
BFGS: 3 06:48:25 -295.623846 0.587331
BFGS: 4 06:48:26 -295.634736 0.509731
BFGS: 5 06:48:26 -295.669988 0.460563
BFGS: 6 06:48:27 -295.675562 0.458484
BFGS: 7 06:48:27 -295.734560 0.729198
BFGS: 8 06:48:28 -295.755973 0.707453
BFGS: 9 06:48:28 -295.797688 1.006606
BFGS: 10 06:48:29 -295.835347 1.015573
BFGS: 11 06:48:29 -295.886001 0.844323
BFGS: 12 06:48:30 -295.933467 0.462567
BFGS: 13 06:48:30 -295.945357 0.269103
BFGS: 14 06:48:30 -295.950120 0.291082
BFGS: 15 06:48:31 -295.953906 0.307233
BFGS: 16 06:48:32 -295.959379 0.256009
BFGS: 17 06:48:32 -295.963004 0.154097
BFGS: 18 06:48:32 -295.964736 0.059354
BFGS: 19 06:48:33 -295.965433 0.048183
Step Time Energy fmax
BFGS: 0 06:48:33 -295.622473 0.732476
BFGS: 1 06:48:34 -295.672276 0.649751
BFGS: 2 06:48:34 -295.851568 0.364532
BFGS: 3 06:48:35 -295.862868 0.403272
BFGS: 4 06:48:35 -295.867669 0.399115
BFGS: 5 06:48:36 -295.898744 0.289203
BFGS: 6 06:48:36 -295.902610 0.286203
BFGS: 7 06:48:37 -295.912759 0.189202
BFGS: 8 06:48:37 -295.916387 0.205880
BFGS: 9 06:48:37 -295.919391 0.217996
BFGS: 10 06:48:38 -295.921017 0.204868
BFGS: 11 06:48:38 -295.923645 0.164797
BFGS: 12 06:48:39 -295.926057 0.114997
BFGS: 13 06:48:40 -295.927733 0.119818
BFGS: 14 06:48:40 -295.928683 0.131696
BFGS: 15 06:48:40 -295.929682 0.121488
BFGS: 16 06:48:41 -295.931042 0.085163
BFGS: 17 06:48:41 -295.932182 0.044924
Step Time Energy fmax
BFGS: 0 06:48:42 -295.685759 0.699674
BFGS: 1 06:48:42 -295.732633 0.623217
BFGS: 2 06:48:43 -295.900014 0.351793
BFGS: 3 06:48:43 -295.909728 0.354087
BFGS: 4 06:48:44 -295.912102 0.341643
BFGS: 5 06:48:44 -295.938710 0.267792
BFGS: 6 06:48:44 -295.940768 0.261614
BFGS: 7 06:48:45 -295.955869 0.171179
BFGS: 8 06:48:45 -295.957571 0.160112
BFGS: 9 06:48:45 -295.959907 0.142632
BFGS: 10 06:48:46 -295.962690 0.109704
BFGS: 11 06:48:46 -295.964203 0.097708
BFGS: 12 06:48:47 -295.965050 0.088652
BFGS: 13 06:48:47 -295.965789 0.070677
BFGS: 14 06:48:48 -295.966522 0.047632
Step Time Energy fmax
BFGS: 0 06:48:48 -295.460848 1.039960
BFGS: 1 06:48:49 -295.522157 0.964141
BFGS: 2 06:48:49 -295.730562 0.856329
BFGS: 3 06:48:50 -295.747803 0.528530
BFGS: 4 06:48:50 -295.760713 0.514212
BFGS: 5 06:48:50 -295.800293 0.598476
BFGS: 6 06:48:51 -295.814464 0.569605
BFGS: 7 06:48:51 -295.840144 0.638887
BFGS: 8 06:48:52 -295.868563 0.573687
BFGS: 9 06:48:52 -295.893669 0.343125
BFGS: 10 06:48:53 -295.906559 0.351523
BFGS: 11 06:48:53 -295.912128 0.303388
BFGS: 12 06:48:54 -295.916287 0.244003
BFGS: 13 06:48:54 -295.921593 0.162428
BFGS: 14 06:48:55 -295.925606 0.139830
BFGS: 15 06:48:55 -295.927406 0.150087
BFGS: 16 06:48:56 -295.928370 0.134666
BFGS: 17 06:48:56 -295.929610 0.098093
BFGS: 18 06:48:57 -295.931135 0.059778
BFGS: 19 06:48:57 -295.932302 0.051804
BFGS: 20 06:48:57 -295.932729 0.030120
Step Time Energy fmax
BFGS: 0 06:48:58 -295.391384 1.150746
BFGS: 1 06:48:58 -295.460248 1.057109
BFGS: 2 06:48:59 -295.676922 1.071570
BFGS: 3 06:48:59 -295.699114 0.587252
BFGS: 4 06:48:59 -295.711590 0.487320
BFGS: 5 06:49:00 -295.751570 0.577649
BFGS: 6 06:49:01 -295.761125 0.545584
BFGS: 7 06:49:01 -295.793665 0.520566
BFGS: 8 06:49:01 -295.811773 0.385442
BFGS: 9 06:49:02 -295.826606 0.289316
BFGS: 10 06:49:02 -295.830142 0.248728
BFGS: 11 06:49:03 -295.833716 0.183155
BFGS: 12 06:49:03 -295.837230 0.114990
BFGS: 13 06:49:04 -295.840036 0.103953
BFGS: 14 06:49:04 -295.841029 0.108836
BFGS: 15 06:49:05 -295.841433 0.093973
BFGS: 16 06:49:05 -295.841868 0.068967
BFGS: 17 06:49:06 -295.842456 0.052745
BFGS: 18 06:49:06 -295.842965 0.045003
Step Time Energy fmax
BFGS: 0 06:49:06 -295.458781 1.031938
BFGS: 1 06:49:06 -295.521177 0.955061
BFGS: 2 06:49:07 -295.731649 0.861759
BFGS: 3 06:49:07 -295.749035 0.524687
BFGS: 4 06:49:07 -295.760996 0.492019
BFGS: 5 06:49:08 -295.796946 0.541594
BFGS: 6 06:49:08 -295.807421 0.490328
BFGS: 7 06:49:09 -295.824673 0.469526
BFGS: 8 06:49:09 -295.838364 0.332655
BFGS: 9 06:49:09 -295.848943 0.216942
BFGS: 10 06:49:10 -295.853195 0.216452
BFGS: 11 06:49:10 -295.855468 0.198280
BFGS: 12 06:49:11 -295.858571 0.173940
BFGS: 13 06:49:11 -295.862439 0.163182
BFGS: 14 06:49:12 -295.865575 0.174070
BFGS: 15 06:49:12 -295.867583 0.186079
BFGS: 16 06:49:13 -295.869857 0.198145
BFGS: 17 06:49:13 -295.874407 0.220070
BFGS: 18 06:49:14 -295.883084 0.251147
BFGS: 19 06:49:14 -295.892894 0.273705
BFGS: 20 06:49:15 -295.902082 0.263136
BFGS: 21 06:49:15 -295.909751 0.227470
BFGS: 22 06:49:16 -295.913501 0.199735
BFGS: 23 06:49:16 -295.920172 0.151078
BFGS: 24 06:49:16 -295.925496 0.124325
BFGS: 25 06:49:17 -295.928446 0.105709
BFGS: 26 06:49:17 -295.929445 0.078460
BFGS: 27 06:49:18 -295.930235 0.071466
BFGS: 28 06:49:18 -295.931445 0.064014
BFGS: 29 06:49:19 -295.932232 0.053523
BFGS: 30 06:49:19 -295.932615 0.046500
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 06:49:19 -304.385518 0.261465
BFGS: 1 06:49:20 -304.389441 0.243338
BFGS: 2 06:49:20 -304.405620 0.151552
BFGS: 3 06:49:21 -304.408983 0.153405
BFGS: 4 06:49:21 -304.410792 0.109865
BFGS: 5 06:49:22 -304.411647 0.069337
BFGS: 6 06:49:22 -304.412540 0.059284
BFGS: 7 06:49:23 -304.413225 0.086057
BFGS: 8 06:49:23 -304.413881 0.099502
BFGS: 9 06:49:24 -304.414412 0.074806
BFGS: 10 06:49:24 -304.414756 0.054269
BFGS: 11 06:49:25 -304.414937 0.046569
Step Time Energy fmax
BFGS: 0 06:49:25 -304.388906 0.297781
BFGS: 1 06:49:26 -304.392971 0.237971
BFGS: 2 06:49:26 -304.407244 0.152351
BFGS: 3 06:49:27 -304.410276 0.167354
BFGS: 4 06:49:27 -304.412560 0.131589
BFGS: 5 06:49:27 -304.413776 0.101467
BFGS: 6 06:49:28 -304.414806 0.088638
BFGS: 7 06:49:28 -304.415585 0.073675
BFGS: 8 06:49:29 -304.416155 0.083902
BFGS: 9 06:49:30 -304.416637 0.062312
BFGS: 10 06:49:30 -304.417057 0.062539
BFGS: 11 06:49:30 -304.417336 0.052093
BFGS: 12 06:49:31 -304.417518 0.036648
Step Time Energy fmax
BFGS: 0 06:49:31 -304.363753 0.266991
BFGS: 1 06:49:32 -304.366006 0.238196
BFGS: 2 06:49:32 -304.373868 0.144718
BFGS: 3 06:49:33 -304.375564 0.178188
BFGS: 4 06:49:33 -304.378089 0.174755
BFGS: 5 06:49:34 -304.379543 0.127613
BFGS: 6 06:49:34 -304.380755 0.088988
BFGS: 7 06:49:35 -304.381599 0.091339
BFGS: 8 06:49:35 -304.382427 0.099266
BFGS: 9 06:49:36 -304.383212 0.104670
BFGS: 10 06:49:36 -304.384059 0.103708
BFGS: 11 06:49:36 -304.385291 0.147622
BFGS: 12 06:49:37 -304.387310 0.207527
BFGS: 13 06:49:37 -304.390074 0.226389
BFGS: 14 06:49:38 -304.393399 0.250614
BFGS: 15 06:49:38 -304.397592 0.287201
BFGS: 16 06:49:39 -304.404326 0.323940
BFGS: 17 06:49:39 -304.418586 0.660606
BFGS: 18 06:49:40 -304.436039 1.011608
BFGS: 19 06:49:40 -304.461002 0.844023
BFGS: 20 06:49:41 -304.482659 0.334892
BFGS: 21 06:49:41 -304.487673 0.327131
BFGS: 22 06:49:42 -304.494914 0.233351
BFGS: 23 06:49:42 -304.499514 0.121006
BFGS: 24 06:49:42 -304.501667 0.091436
BFGS: 25 06:49:43 -304.502701 0.102889
BFGS: 26 06:49:43 -304.503511 0.099739
BFGS: 27 06:49:44 -304.504632 0.071299
BFGS: 28 06:49:44 -304.505450 0.039569
Step Time Energy fmax
BFGS: 0 06:49:44 -303.900198 0.331468
BFGS: 1 06:49:45 -303.905682 0.257405
BFGS: 2 06:49:45 -303.918805 0.167268
BFGS: 3 06:49:46 -303.921542 0.145156
BFGS: 4 06:49:46 -303.923876 0.100241
BFGS: 5 06:49:47 -303.925227 0.095938
BFGS: 6 06:49:47 -303.926372 0.069621
BFGS: 7 06:49:48 -303.927093 0.081012
BFGS: 8 06:49:48 -303.927501 0.062969
BFGS: 9 06:49:49 -303.927762 0.045444
Step Time Energy fmax
BFGS: 0 06:49:49 -303.904669 0.338673
BFGS: 1 06:49:50 -303.910316 0.258105
BFGS: 2 06:49:50 -303.922550 0.154924
BFGS: 3 06:49:51 -303.924880 0.133620
BFGS: 4 06:49:51 -303.926896 0.111238
BFGS: 5 06:49:52 -303.928212 0.108814
BFGS: 6 06:49:52 -303.929301 0.090063
BFGS: 7 06:49:53 -303.929960 0.074636
BFGS: 8 06:49:53 -303.930289 0.058231
BFGS: 9 06:49:54 -303.930467 0.034153
Step Time Energy fmax
BFGS: 0 06:49:54 -303.118345 1.002873
BFGS: 1 06:49:54 -303.147244 0.772662
BFGS: 2 06:49:55 -303.213491 0.664802
BFGS: 3 06:49:55 -303.243370 0.660520
BFGS: 4 06:49:56 -303.276716 0.732485
BFGS: 5 06:49:56 -303.306382 0.607438
BFGS: 6 06:49:57 -303.352377 0.545157
BFGS: 7 06:49:57 -303.364105 0.342244
BFGS: 8 06:49:58 -303.368862 0.212140
BFGS: 9 06:49:58 -303.377054 0.182928
BFGS: 10 06:49:59 -303.380090 0.166833
BFGS: 11 06:49:59 -303.382595 0.198431
BFGS: 12 06:50:00 -303.385015 0.167005
BFGS: 13 06:50:00 -303.387426 0.154258
BFGS: 14 06:50:00 -303.389695 0.169695
BFGS: 15 06:50:01 -303.391461 0.145801
BFGS: 16 06:50:01 -303.393163 0.138939
BFGS: 17 06:50:02 -303.395699 0.138297
BFGS: 18 06:50:02 -303.398923 0.208209
BFGS: 19 06:50:03 -303.402335 0.241720
BFGS: 20 06:50:03 -303.405742 0.214597
BFGS: 21 06:50:04 -303.409795 0.262689
BFGS: 22 06:50:04 -303.416241 0.386243
BFGS: 23 06:50:05 -303.428989 0.686868
BFGS: 24 06:50:05 -303.450093 0.863825
BFGS: 25 06:50:06 -303.483229 0.797775
BFGS: 26 06:50:06 -303.515899 0.603008
BFGS: 27 06:50:06 -303.550353 0.757581
BFGS: 28 06:50:07 -303.597254 0.865824
BFGS: 29 06:50:07 -303.642314 0.860773
BFGS: 30 06:50:08 -303.725698 0.793247
BFGS: 31 06:50:08 -303.793541 0.764675
BFGS: 32 06:50:09 -303.826204 0.523173
BFGS: 33 06:50:09 -303.851220 0.766243
BFGS: 34 06:50:10 -303.880013 0.669464
BFGS: 35 06:50:10 -303.908936 0.281566
BFGS: 36 06:50:11 -303.914588 0.207088
BFGS: 37 06:50:11 -303.918425 0.172158
BFGS: 38 06:50:12 -303.923070 0.115517
BFGS: 39 06:50:12 -303.925501 0.074771
BFGS: 40 06:50:12 -303.926449 0.071909
BFGS: 41 06:50:13 -303.926983 0.055148
BFGS: 42 06:50:14 -303.927430 0.042950
Step Time Energy fmax
BFGS: 0 06:50:14 -303.102865 1.014970
BFGS: 1 06:50:14 -303.133779 0.762876
BFGS: 2 06:50:15 -303.196639 0.675811
BFGS: 3 06:50:15 -303.226341 0.669076
BFGS: 4 06:50:15 -303.263267 0.747226
BFGS: 5 06:50:16 -303.293985 0.646379
BFGS: 6 06:50:17 -303.344263 0.612416
BFGS: 7 06:50:17 -303.361523 0.395618
BFGS: 8 06:50:17 -303.366546 0.270488
BFGS: 9 06:50:18 -303.376673 0.180160
BFGS: 10 06:50:18 -303.380015 0.167427
BFGS: 11 06:50:19 -303.382575 0.204451
BFGS: 12 06:50:19 -303.385221 0.175672
BFGS: 13 06:50:20 -303.387945 0.157628
BFGS: 14 06:50:20 -303.390348 0.162194
BFGS: 15 06:50:21 -303.392125 0.144867
BFGS: 16 06:50:21 -303.393867 0.148771
BFGS: 17 06:50:22 -303.396735 0.151555
BFGS: 18 06:50:22 -303.400717 0.224499
BFGS: 19 06:50:22 -303.405114 0.272844
BFGS: 20 06:50:23 -303.409505 0.244716
BFGS: 21 06:50:23 -303.414958 0.294760
BFGS: 22 06:50:24 -303.423474 0.449464
BFGS: 23 06:50:24 -303.440673 0.780622
BFGS: 24 06:50:25 -303.467768 0.927210
BFGS: 25 06:50:25 -303.504500 0.773191
BFGS: 26 06:50:26 -303.537705 0.644238
BFGS: 27 06:50:26 -303.569381 0.792148
BFGS: 28 06:50:26 -303.619079 0.787590
BFGS: 29 06:50:27 -303.670964 0.789964
BFGS: 30 06:50:27 -303.742315 0.787771
BFGS: 31 06:50:28 -303.805472 0.706299
BFGS: 32 06:50:28 -303.839142 0.527151
BFGS: 33 06:50:29 -303.860445 0.671603
BFGS: 34 06:50:29 -303.891165 0.498170
BFGS: 35 06:50:30 -303.910798 0.274809
BFGS: 36 06:50:30 -303.917411 0.184439
BFGS: 37 06:50:30 -303.921057 0.138788
BFGS: 38 06:50:31 -303.923593 0.107056
BFGS: 39 06:50:31 -303.925597 0.071432
BFGS: 40 06:50:32 -303.926715 0.068123
BFGS: 41 06:50:32 -303.927250 0.047577
/home/runner/work/_tool/Python/3.12.13/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/3.12.13/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 06:51:36 -302.737821 3.440152
BFGS: 1 06:51:40 -302.908683 2.966908
BFGS: 2 06:51:43 -303.370321 8.204193
BFGS: 3 06:51:49 -303.394309 1.859982
BFGS: 4 06:51:53 -303.522668 1.569385
BFGS: 5 06:51:57 -303.663726 0.967571
BFGS: 6 06:52:01 -303.685191 0.759134
BFGS: 7 06:52:04 -303.730044 0.640002
BFGS: 8 06:52:08 -303.740905 0.601992
BFGS: 9 06:52:12 -303.759618 0.430183
BFGS: 10 06:52:16 -303.763750 0.413684
BFGS: 11 06:52:20 -303.766525 0.397658
BFGS: 12 06:52:24 -303.766371 0.374378
BFGS: 13 06:52:29 -303.764261 0.376502
BFGS: 14 06:52:35 -303.761279 0.346730
BFGS: 15 06:52:40 -303.758450 0.305750
BFGS: 16 06:52:44 -303.758094 0.329650
BFGS: 17 06:52:48 -303.761431 0.359402
BFGS: 18 06:52:52 -303.766629 0.352895
BFGS: 19 06:52:56 -303.773227 0.314632
BFGS: 20 06:53:00 -303.782445 0.445806
BFGS: 21 06:53:06 -303.792641 0.573454
BFGS: 22 06:53:11 -303.798258 0.454908
BFGS: 23 06:53:15 -303.798332 0.335186
BFGS: 24 06:53:18 -303.796454 0.403480
BFGS: 25 06:53:23 -303.795700 0.432950
BFGS: 26 06:53:28 -303.796340 0.574143
BFGS: 27 06:53:34 -303.796120 0.494708
BFGS: 28 06:53:37 -303.794778 0.371395
BFGS: 29 06:53:41 -303.796221 0.363392
BFGS: 30 06:53:44 -303.800719 0.376954
BFGS: 31 06:53:49 -303.804438 0.440321
BFGS: 32 06:53:53 -303.806474 0.308202
BFGS: 33 06:53:57 -303.808166 0.292372
BFGS: 34 06:54:01 -303.812847 0.360602
BFGS: 35 06:54:05 -303.812478 0.324823
BFGS: 36 06:54:09 -303.809384 0.308615
BFGS: 37 06:54:13 -303.806674 0.277973
BFGS: 38 06:54:17 -303.805828 0.277510
BFGS: 39 06:54:21 -303.804302 0.274127
BFGS: 40 06:54:24 -303.800923 0.317482
BFGS: 41 06:54:29 -303.796976 0.363057
BFGS: 42 06:54:34 -303.795390 0.366434
BFGS: 43 06:54:38 -303.792901 0.360124
BFGS: 44 06:54:40 -303.796787 0.298160
BFGS: 45 06:54:44 -303.798273 0.245186
BFGS: 46 06:54:47 -303.800113 0.202864
BFGS: 47 06:54:50 -303.801425 0.186305
BFGS: 48 06:54:53 -303.801982 0.182247
BFGS: 49 06:54:57 -303.801358 0.126945
BFGS: 50 06:55:02 -303.802390 0.119515
BFGS: 51 06:55:05 -303.803357 0.115679
BFGS: 52 06:55:08 -303.804332 0.105025
BFGS: 53 06:55:10 -303.805494 0.105745
BFGS: 54 06:55:13 -303.806066 0.095936
BFGS: 55 06:55:16 -303.807205 0.065077
BFGS: 56 06:55:19 -303.807205 0.075680
BFGS: 57 06:55:22 -303.807205 0.070328
BFGS: 58 06:55:26 -303.807205 0.070492
BFGS: 59 06:55:28 -303.807205 0.065581
BFGS: 60 06:55:29 -303.807205 0.066634
BFGS: 61 06:55:30 -303.807205 0.065222
BFGS: 62 06:55:33 -303.807205 0.104269
BFGS: 63 06:55:35 -303.807205 0.065212
BFGS: 64 06:55:37 -303.807205 0.060769
BFGS: 65 06:55:39 -303.807205 0.071453
BFGS: 66 06:55:41 -303.807205 0.065839
BFGS: 67 06:55:43 -303.807205 0.048936
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_13237/3247994494.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")