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/3.12.13/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 14:28:41 -302.701737 3.698806
BFGS: 1 14:28:41 -303.049661 2.782886
BFGS: 2 14:28:42 -303.813801 2.892513
BFGS: 3 14:28:42 -303.945148 2.227489
BFGS: 4 14:28:43 -304.110888 2.299642
BFGS: 5 14:28:43 -304.177744 0.939556
BFGS: 6 14:28:44 -304.227707 0.586616
BFGS: 7 14:28:44 -304.288658 0.852346
BFGS: 8 14:28:45 -304.302516 0.544933
BFGS: 9 14:28:45 -304.323619 0.373112
BFGS: 10 14:28:46 -304.332667 0.365549
BFGS: 11 14:28:46 -304.340107 0.197918
BFGS: 12 14:28:46 -304.341480 0.129867
BFGS: 13 14:28:47 -304.342473 0.120115
BFGS: 14 14:28:47 -304.344111 0.155685
BFGS: 15 14:28:48 -304.345703 0.155540
BFGS: 16 14:28:48 -304.346879 0.104707
BFGS: 17 14:28:48 -304.347732 0.079741
BFGS: 18 14:28:49 -304.348831 0.116206
BFGS: 19 14:28:49 -304.350353 0.152032
BFGS: 20 14:28:49 -304.351682 0.116118
BFGS: 21 14:28:50 -304.352271 0.075075
BFGS: 22 14:28:50 -304.352494 0.050451
BFGS: 23 14:28:51 -304.352637 0.036107
Step Time Energy fmax
BFGS: 0 14:28:51 -302.364703 4.118460
BFGS: 1 14:28:52 -302.737180 3.278638
BFGS: 2 14:28:52 -303.607831 2.992415
BFGS: 3 14:28:52 -303.777914 2.735267
BFGS: 4 14:28:53 -303.989219 1.497504
BFGS: 5 14:28:53 -304.113031 1.954233
BFGS: 6 14:28:54 -304.180624 1.542704
BFGS: 7 14:28:54 -304.399548 1.005077
BFGS: 8 14:28:54 -304.434170 0.916457
BFGS: 9 14:28:55 -304.575357 0.663494
BFGS: 10 14:28:55 -304.595171 0.448222
BFGS: 11 14:28:56 -304.604282 0.393019
BFGS: 12 14:28:56 -304.628865 0.286975
BFGS: 13 14:28:56 -304.633679 0.279511
BFGS: 14 14:28:57 -304.644163 0.231972
BFGS: 15 14:28:57 -304.651151 0.234121
BFGS: 16 14:28:58 -304.657320 0.210525
BFGS: 17 14:28:58 -304.661069 0.182839
BFGS: 18 14:28:59 -304.664998 0.175452
BFGS: 19 14:28:59 -304.669866 0.180684
BFGS: 20 14:29:00 -304.673931 0.126431
BFGS: 21 14:29:00 -304.675916 0.097398
BFGS: 22 14:29:01 -304.676944 0.079604
BFGS: 23 14:29:01 -304.677948 0.096808
BFGS: 24 14:29:02 -304.679143 0.103404
BFGS: 25 14:29:02 -304.680288 0.072482
BFGS: 26 14:29:02 -304.680967 0.044004
Step Time Energy fmax
BFGS: 0 14:29:03 -301.306118 4.077010
BFGS: 1 14:29:03 -301.696422 3.032920
BFGS: 2 14:29:03 -302.717788 3.518247
BFGS: 3 14:29:04 -302.855526 3.312151
BFGS: 4 14:29:04 -303.150654 1.743491
BFGS: 5 14:29:04 -303.221463 2.357355
BFGS: 6 14:29:05 -303.274041 1.282702
BFGS: 7 14:29:05 -303.366388 0.851202
BFGS: 8 14:29:06 -303.659502 2.143184
BFGS: 9 14:29:06 -303.801945 2.763436
BFGS: 10 14:29:07 -303.908260 2.312320
BFGS: 11 14:29:07 -304.125410 1.032413
BFGS: 12 14:29:07 -304.162288 0.885158
BFGS: 13 14:29:08 -304.211925 0.436159
BFGS: 14 14:29:08 -304.266569 0.668704
BFGS: 15 14:29:09 -304.305652 0.853020
BFGS: 16 14:29:09 -304.355133 1.045038
BFGS: 17 14:29:10 -304.404890 0.994762
BFGS: 18 14:29:10 -304.473754 0.842369
BFGS: 19 14:29:10 -304.521389 0.623354
BFGS: 20 14:29:11 -304.543735 0.371078
BFGS: 21 14:29:11 -304.560925 0.445362
BFGS: 22 14:29:12 -304.576735 0.516002
BFGS: 23 14:29:12 -304.593475 0.423995
BFGS: 24 14:29:13 -304.609855 0.325250
BFGS: 25 14:29:13 -304.617813 0.318966
BFGS: 26 14:29:13 -304.629534 0.365478
BFGS: 27 14:29:14 -304.645696 0.392604
BFGS: 28 14:29:14 -304.660008 0.291873
BFGS: 29 14:29:15 -304.667075 0.175035
BFGS: 30 14:29:15 -304.670478 0.172827
BFGS: 31 14:29:16 -304.673225 0.141218
BFGS: 32 14:29:16 -304.676213 0.150330
BFGS: 33 14:29:16 -304.678689 0.115059
BFGS: 34 14:29:17 -304.679911 0.057566
BFGS: 35 14:29:17 -304.680382 0.050954
BFGS: 36 14:29:18 -304.680699 0.048869
Step Time Energy fmax
BFGS: 0 14:29:18 -301.849580 4.140628
BFGS: 1 14:29:19 -302.233532 3.154776
BFGS: 2 14:29:19 -303.181590 3.316223
BFGS: 3 14:29:19 -303.363052 3.154531
BFGS: 4 14:29:20 -303.658423 2.032969
BFGS: 5 14:29:20 -303.866145 3.286456
BFGS: 6 14:29:21 -303.981579 1.655547
BFGS: 7 14:29:21 -304.140803 0.877243
BFGS: 8 14:29:22 -304.256066 1.422460
BFGS: 9 14:29:22 -304.344248 1.472737
BFGS: 10 14:29:22 -304.500324 1.658363
BFGS: 11 14:29:23 -304.589295 1.004789
BFGS: 12 14:29:23 -304.632773 0.430694
BFGS: 13 14:29:23 -304.639159 0.283694
BFGS: 14 14:29:24 -304.646323 0.246966
BFGS: 15 14:29:24 -304.651211 0.324237
BFGS: 16 14:29:25 -304.656933 0.296625
BFGS: 17 14:29:25 -304.659813 0.195199
BFGS: 18 14:29:26 -304.661545 0.168239
BFGS: 19 14:29:26 -304.663726 0.225159
BFGS: 20 14:29:26 -304.667736 0.308960
BFGS: 21 14:29:27 -304.673331 0.290196
BFGS: 22 14:29:27 -304.677064 0.129496
BFGS: 23 14:29:28 -304.678306 0.097040
BFGS: 24 14:29:28 -304.679337 0.082472
BFGS: 25 14:29:29 -304.680252 0.105302
BFGS: 26 14:29:29 -304.681095 0.085932
BFGS: 27 14:29:29 -304.681513 0.044488
Step Time Energy fmax
BFGS: 0 14:29:30 -301.417467 3.969568
BFGS: 1 14:29:30 -301.799182 3.210205
BFGS: 2 14:29:31 -302.860297 3.335197
BFGS: 3 14:29:31 -302.949383 5.052563
BFGS: 4 14:29:32 -303.255901 2.369630
BFGS: 5 14:29:32 -303.465001 2.168765
BFGS: 6 14:29:33 -303.567164 2.415860
BFGS: 7 14:29:33 -303.875284 1.402695
BFGS: 8 14:29:33 -303.795530 2.637029
BFGS: 9 14:29:34 -303.983168 1.045486
BFGS: 10 14:29:34 -304.024863 0.889983
BFGS: 11 14:29:35 -304.113701 0.608424
BFGS: 12 14:29:35 -304.128988 0.538536
BFGS: 13 14:29:36 -304.158816 0.302218
BFGS: 14 14:29:36 -304.166941 0.253737
BFGS: 15 14:29:36 -304.173710 0.286709
BFGS: 16 14:29:37 -304.179315 0.266865
BFGS: 17 14:29:37 -304.183476 0.172656
BFGS: 18 14:29:37 -304.185580 0.152376
BFGS: 19 14:29:38 -304.188014 0.166650
BFGS: 20 14:29:38 -304.192026 0.291995
BFGS: 21 14:29:38 -304.198054 0.365387
BFGS: 22 14:29:39 -304.204973 0.300914
BFGS: 23 14:29:39 -304.212622 0.381256
BFGS: 24 14:29:40 -304.222665 0.379552
BFGS: 25 14:29:40 -304.234876 0.493629
BFGS: 26 14:29:41 -304.254588 0.687702
BFGS: 27 14:29:41 -304.265986 0.555733
BFGS: 28 14:29:42 -304.286169 0.340034
BFGS: 29 14:29:42 -304.294562 0.337029
BFGS: 30 14:29:42 -304.311727 0.304133
BFGS: 31 14:29:43 -304.320897 0.309309
BFGS: 32 14:29:43 -304.327699 0.216095
BFGS: 33 14:29:44 -304.332227 0.211233
BFGS: 34 14:29:44 -304.336061 0.208132
BFGS: 35 14:29:44 -304.340933 0.205637
BFGS: 36 14:29:45 -304.346453 0.232491
BFGS: 37 14:29:45 -304.349712 0.125991
BFGS: 38 14:29:46 -304.350798 0.069688
BFGS: 39 14:29:46 -304.351226 0.053425
BFGS: 40 14:29:46 -304.351618 0.053126
BFGS: 41 14:29:47 -304.351999 0.051718
BFGS: 42 14:29:47 -304.352279 0.033293
Step Time Energy fmax
BFGS: 0 14:29:47 -302.132030 4.049308
BFGS: 1 14:29:48 -302.513913 3.392361
BFGS: 2 14:29:48 -303.441263 2.904974
BFGS: 3 14:29:48 -303.597703 2.680078
BFGS: 4 14:29:49 -303.826202 1.844175
BFGS: 5 14:29:49 -303.987862 2.109438
BFGS: 6 14:29:50 -304.063273 1.444405
BFGS: 7 14:29:50 -304.184152 0.940574
BFGS: 8 14:29:51 -304.211396 0.681887
BFGS: 9 14:29:51 -304.265999 0.580159
BFGS: 10 14:29:51 -304.295280 0.289698
BFGS: 11 14:29:52 -304.303717 0.281767
BFGS: 12 14:29:52 -304.312194 0.292560
BFGS: 13 14:29:52 -304.320164 0.289564
BFGS: 14 14:29:53 -304.326288 0.232844
BFGS: 15 14:29:53 -304.329482 0.192009
BFGS: 16 14:29:54 -304.332285 0.209141
BFGS: 17 14:29:54 -304.336271 0.229316
BFGS: 18 14:29:55 -304.341405 0.208166
BFGS: 19 14:29:55 -304.345906 0.174915
BFGS: 20 14:29:55 -304.348459 0.131790
BFGS: 21 14:29:56 -304.349869 0.158847
BFGS: 22 14:29:56 -304.351095 0.138883
BFGS: 23 14:29:56 -304.352037 0.080612
BFGS: 24 14:29:57 -304.352408 0.034532
Step Time Energy fmax
BFGS: 0 14:29:57 -302.540578 3.833058
BFGS: 1 14:29:58 -302.894342 2.915296
BFGS: 2 14:29:58 -303.708119 3.013088
BFGS: 3 14:29:59 -303.845048 2.520040
BFGS: 4 14:29:59 -303.989084 4.075306
BFGS: 5 14:30:00 -304.112316 0.978257
BFGS: 6 14:30:00 -304.149952 0.705637
BFGS: 7 14:30:00 -304.248092 0.480864
BFGS: 8 14:30:01 -304.263659 0.596052
BFGS: 9 14:30:01 -304.294096 0.530654
BFGS: 10 14:30:02 -304.306876 0.263093
BFGS: 11 14:30:02 -304.312978 0.200088
BFGS: 12 14:30:02 -304.316130 0.226036
BFGS: 13 14:30:03 -304.323486 0.266488
BFGS: 14 14:30:03 -304.329257 0.245799
BFGS: 15 14:30:04 -304.333420 0.191909
BFGS: 16 14:30:04 -304.336355 0.170260
BFGS: 17 14:30:05 -304.339943 0.188735
BFGS: 18 14:30:05 -304.344325 0.216060
BFGS: 19 14:30:05 -304.347997 0.161433
BFGS: 20 14:30:06 -304.350004 0.098510
BFGS: 21 14:30:06 -304.350787 0.082090
BFGS: 22 14:30:07 -304.351304 0.063817
BFGS: 23 14:30:07 -304.351976 0.075382
BFGS: 24 14:30:08 -304.352390 0.048566
Step Time Energy fmax
BFGS: 0 14:30:08 -300.941666 3.977805
BFGS: 1 14:30:08 -301.365204 3.461266
BFGS: 2 14:30:09 -302.613757 3.577566
BFGS: 3 14:30:09 -302.607825 6.356387
BFGS: 4 14:30:10 -302.955578 2.658795
BFGS: 5 14:30:10 -303.108583 0.842651
BFGS: 6 14:30:11 -303.128059 0.820029
BFGS: 7 14:30:11 -303.141696 0.598858
BFGS: 8 14:30:12 -303.151741 0.735932
BFGS: 9 14:30:12 -303.184230 0.728414
BFGS: 10 14:30:13 -303.194143 0.417781
BFGS: 11 14:30:13 -303.201573 0.301837
BFGS: 12 14:30:13 -303.215525 0.503136
BFGS: 13 14:30:14 -303.231663 0.662986
BFGS: 14 14:30:14 -303.249455 0.687465
BFGS: 15 14:30:15 -303.264485 0.637463
BFGS: 16 14:30:15 -303.282993 0.759896
BFGS: 17 14:30:15 -303.361010 1.994726
BFGS: 18 14:30:16 -303.370539 3.644912
BFGS: 19 14:30:16 -303.486170 1.493299
BFGS: 20 14:30:16 -303.565171 2.162167
BFGS: 21 14:30:17 -303.614760 2.269096
BFGS: 22 14:30:17 -303.681854 2.154656
BFGS: 23 14:30:17 -303.718647 1.529321
BFGS: 24 14:30:18 -303.777931 1.581581
BFGS: 25 14:30:18 -303.831408 1.169695
BFGS: 26 14:30:19 -303.882410 1.329204
BFGS: 27 14:30:19 -303.898370 1.210299
BFGS: 28 14:30:19 -303.928837 1.204353
BFGS: 29 14:30:20 -303.944976 1.243707
BFGS: 30 14:30:20 -303.970030 1.179093
BFGS: 31 14:30:21 -303.986462 0.994868
BFGS: 32 14:30:21 -304.001167 0.837941
BFGS: 33 14:30:22 -304.017840 0.759949
BFGS: 34 14:30:22 -304.043664 0.770030
BFGS: 35 14:30:23 -304.065203 0.689409
BFGS: 36 14:30:23 -304.076623 0.671062
BFGS: 37 14:30:23 -304.083586 0.748521
BFGS: 38 14:30:24 -304.089323 0.778010
BFGS: 39 14:30:24 -304.096839 0.797520
BFGS: 40 14:30:25 -304.103522 0.709971
BFGS: 41 14:30:25 -304.108033 0.628874
BFGS: 42 14:30:26 -304.111925 0.512967
BFGS: 43 14:30:26 -304.117278 0.464043
BFGS: 44 14:30:27 -304.124837 0.419374
BFGS: 45 14:30:27 -304.135549 0.345615
BFGS: 46 14:30:28 -304.147936 0.322891
BFGS: 47 14:30:28 -304.161486 0.323007
BFGS: 48 14:30:29 -304.189774 0.577609
BFGS: 49 14:30:29 -304.240564 0.976169
BFGS: 50 14:30:29 -304.254510 1.315777
BFGS: 51 14:30:30 -304.298334 1.191032
BFGS: 52 14:30:30 -304.362236 1.159433
BFGS: 53 14:30:31 -304.492093 0.880091
BFGS: 54 14:30:31 -304.534301 0.649419
BFGS: 55 14:30:31 -304.555931 0.937239
BFGS: 56 14:30:32 -304.567419 0.833700
BFGS: 57 14:30:32 -304.577171 0.878802
BFGS: 58 14:30:32 -304.585825 0.830761
BFGS: 59 14:30:33 -304.588830 0.783851
BFGS: 60 14:30:33 -304.590008 0.749159
BFGS: 61 14:30:34 -304.591368 0.707606
BFGS: 62 14:30:34 -304.592924 0.676572
BFGS: 63 14:30:35 -304.594251 0.674592
BFGS: 64 14:30:35 -304.595049 0.697125
BFGS: 65 14:30:36 -304.595664 0.724568
BFGS: 66 14:30:36 -304.596417 0.755054
BFGS: 67 14:30:37 -304.597386 0.781565
BFGS: 68 14:30:37 -304.598298 0.788260
BFGS: 69 14:30:38 -304.598862 0.774454
BFGS: 70 14:30:38 -304.599231 0.755891
BFGS: 71 14:30:38 -304.599606 0.737508
BFGS: 72 14:30:39 -304.600002 0.725862
BFGS: 73 14:30:39 -304.600304 0.728225
BFGS: 74 14:30:40 -304.600467 0.738854
BFGS: 75 14:30:40 -304.600571 0.748903
BFGS: 76 14:30:41 -304.600669 0.757192
BFGS: 77 14:30:41 -304.600780 0.761681
BFGS: 78 14:30:42 -304.600873 0.759530
BFGS: 79 14:30:42 -304.600934 0.753494
BFGS: 80 14:30:42 -304.600969 0.747905
BFGS: 81 14:30:43 -304.601007 0.743452
BFGS: 82 14:30:43 -304.601063 0.740474
BFGS: 83 14:30:44 -304.601129 0.741285
BFGS: 84 14:30:44 -304.601175 0.745960
BFGS: 85 14:30:45 -304.601196 0.750376
BFGS: 86 14:30:45 -304.601210 0.752834
BFGS: 87 14:30:45 -304.601221 0.754623
BFGS: 88 14:30:46 -304.601236 0.755443
BFGS: 89 14:30:46 -304.601251 0.755147
BFGS: 90 14:30:47 -304.601256 0.754265
BFGS: 91 14:30:47 -304.601259 0.753822
BFGS: 92 14:30:47 -304.601262 0.753588
BFGS: 93 14:30:48 -304.601263 0.753594
BFGS: 94 14:30:48 -304.601266 0.753762
BFGS: 95 14:30:48 -304.601268 0.753818
BFGS: 96 14:30:48 -304.601270 0.753732
BFGS: 97 14:30:49 -304.601269 0.753555
BFGS: 98 14:30:49 -304.601268 0.753338
BFGS: 99 14:30:50 -304.601270 0.753049
BFGS: 100 14:30:50 -304.601272 0.752965
BFGS: 101 14:30:51 -304.601272 0.753030
BFGS: 102 14:30:51 -304.601271 0.753236
BFGS: 103 14:30:52 -304.601271 0.753481
BFGS: 104 14:30:52 -304.601269 0.753656
BFGS: 105 14:30:53 -304.601270 0.753735
BFGS: 106 14:30:53 -304.601272 0.753774
BFGS: 107 14:30:53 -304.601272 0.753573
BFGS: 108 14:30:54 -304.601271 0.753484
BFGS: 109 14:30:54 -304.601271 0.753318
BFGS: 110 14:30:55 -304.601271 0.753289
BFGS: 111 14:30:55 -304.601273 0.753196
BFGS: 112 14:30:55 -304.601273 0.753242
BFGS: 113 14:30:56 -304.601272 0.753326
BFGS: 114 14:30:56 -304.601273 0.753325
BFGS: 115 14:30:56 -304.601272 0.753411
BFGS: 116 14:30:57 -304.601272 0.753419
BFGS: 117 14:30:57 -304.601272 0.753349
BFGS: 118 14:30:58 -304.601271 0.753362
BFGS: 119 14:30:58 -304.601271 0.753403
BFGS: 120 14:30:59 -304.601272 0.753361
BFGS: 121 14:30:59 -304.601272 0.753354
BFGS: 122 14:31:00 -304.601271 0.753353
BFGS: 123 14:31:00 -304.601272 0.753336
BFGS: 124 14:31:01 -304.601272 0.753326
BFGS: 125 14:31:01 -304.601272 0.753348
BFGS: 126 14:31:01 -304.601272 0.753404
BFGS: 127 14:31:02 -304.601270 0.753372
BFGS: 128 14:31:02 -304.601273 0.753364
BFGS: 129 14:31:03 -304.601270 0.753368
BFGS: 130 14:31:03 -304.601271 0.753325
BFGS: 131 14:31:04 -304.601273 0.753358
BFGS: 132 14:31:04 -304.601273 0.753361
BFGS: 133 14:31:04 -304.601271 0.753349
BFGS: 134 14:31:05 -304.601274 0.753328
BFGS: 135 14:31:05 -304.601272 0.753361
BFGS: 136 14:31:06 -304.601272 0.753364
BFGS: 137 14:31:06 -304.601271 0.753344
BFGS: 138 14:31:07 -304.601271 0.753360
BFGS: 139 14:31:07 -304.601273 0.753364
BFGS: 140 14:31:08 -304.601272 0.753370
BFGS: 141 14:31:08 -304.601272 0.753360
BFGS: 142 14:31:09 -304.601271 0.753369
BFGS: 143 14:31:09 -304.601272 0.753362
BFGS: 144 14:31:09 -304.601273 0.753367
BFGS: 145 14:31:10 -304.601273 0.753326
BFGS: 146 14:31:11 -304.601272 0.753368
BFGS: 147 14:31:11 -304.601273 0.753350
BFGS: 148 14:31:12 -304.601272 0.753325
BFGS: 149 14:31:12 -304.601272 0.753375
BFGS: 150 14:31:12 -304.601271 0.753362
BFGS: 151 14:31:13 -304.601272 0.753392
BFGS: 152 14:31:13 -304.601273 0.753362
BFGS: 153 14:31:14 -304.601273 0.753350
BFGS: 154 14:31:14 -304.601271 0.753375
BFGS: 155 14:31:14 -304.601271 0.753366
BFGS: 156 14:31:14 -304.601273 0.753354
BFGS: 157 14:31:15 -304.601273 0.753360
BFGS: 158 14:31:15 -304.601272 0.753362
BFGS: 159 14:31:16 -304.601271 0.753363
BFGS: 160 14:31:16 -304.601271 0.753380
BFGS: 161 14:31:16 -304.601271 0.753360
BFGS: 162 14:31:17 -304.601271 0.753362
BFGS: 163 14:31:17 -304.601273 0.753363
BFGS: 164 14:31:18 -304.601272 0.753331
BFGS: 165 14:31:18 -304.601270 0.753362
BFGS: 166 14:31:18 -304.601272 0.753362
BFGS: 167 14:31:19 -304.601273 0.753365
BFGS: 168 14:31:19 -304.601273 0.753337
BFGS: 169 14:31:19 -304.601272 0.753360
BFGS: 170 14:31:20 -304.601271 0.753365
BFGS: 171 14:31:20 -304.601272 0.753367
BFGS: 172 14:31:21 -304.601271 0.753276
BFGS: 173 14:31:21 -304.601272 0.753348
BFGS: 174 14:31:22 -304.601272 0.753367
BFGS: 175 14:31:22 -304.601271 0.753367
BFGS: 176 14:31:23 -304.601274 0.753328
BFGS: 177 14:31:23 -304.601273 0.753322
BFGS: 178 14:31:24 -304.601271 0.753365
BFGS: 179 14:31:24 -304.601273 0.753365
BFGS: 180 14:31:25 -304.601271 0.753359
BFGS: 181 14:31:25 -304.601272 0.753357
BFGS: 182 14:31:25 -304.601272 0.753366
BFGS: 183 14:31:26 -304.601271 0.753369
BFGS: 184 14:31:26 -304.601273 0.753354
BFGS: 185 14:31:27 -304.601273 0.753357
BFGS: 186 14:31:27 -304.601271 0.753364
BFGS: 187 14:31:27 -304.601271 0.753362
BFGS: 188 14:31:28 -304.601271 0.753361
BFGS: 189 14:31:28 -304.601272 0.753354
BFGS: 190 14:31:29 -304.601271 0.753360
BFGS: 191 14:31:29 -304.601271 0.753364
BFGS: 192 14:31:30 -304.601272 0.753346
BFGS: 193 14:31:30 -304.601272 0.753363
BFGS: 194 14:31:30 -304.601271 0.753365
BFGS: 195 14:31:31 -304.601270 0.753368
BFGS: 196 14:31:31 -304.601272 0.753355
BFGS: 197 14:31:32 -304.601273 0.753357
BFGS: 198 14:31:32 -304.601272 0.753379
BFGS: 199 14:31:32 -304.601271 0.753364
BFGS: 200 14:31:33 -304.601271 0.753360
BFGS: 201 14:31:33 -304.601271 0.753352
BFGS: 202 14:31:33 -304.601271 0.753365
BFGS: 203 14:31:33 -304.601271 0.753368
BFGS: 204 14:31:34 -304.601272 0.753362
BFGS: 205 14:31:34 -304.601272 0.753350
BFGS: 206 14:31:35 -304.601271 0.753363
BFGS: 207 14:31:35 -304.601272 0.753364
BFGS: 208 14:31:36 -304.601271 0.753360
BFGS: 209 14:31:36 -304.601274 0.753349
BFGS: 210 14:31:36 -304.601271 0.753378
BFGS: 211 14:31:37 -304.601271 0.753368
BFGS: 212 14:31:37 -304.601272 0.753357
BFGS: 213 14:31:38 -304.601273 0.753322
BFGS: 214 14:31:38 -304.601271 0.753391
BFGS: 215 14:31:39 -304.601272 0.753365
BFGS: 216 14:31:39 -304.601271 0.753355
BFGS: 217 14:31:39 -304.601274 0.753350
BFGS: 218 14:31:40 -304.601270 0.753364
BFGS: 219 14:31:40 -304.601271 0.753367
BFGS: 220 14:31:41 -304.601272 0.753357
BFGS: 221 14:31:41 -304.601274 0.753352
BFGS: 222 14:31:41 -304.601272 0.753368
BFGS: 223 14:31:42 -304.601272 0.753363
BFGS: 224 14:31:42 -304.601271 0.753361
BFGS: 225 14:31:42 -304.601272 0.753360
BFGS: 226 14:31:43 -304.601271 0.753363
BFGS: 227 14:31:43 -304.601274 0.753365
BFGS: 228 14:31:44 -304.601271 0.752928
BFGS: 229 14:31:44 -304.601272 0.753362
BFGS: 230 14:31:44 -304.601271 0.753362
BFGS: 231 14:31:45 -304.601272 0.753356
BFGS: 232 14:31:45 -304.601273 0.753321
BFGS: 233 14:31:46 -304.601270 0.753365
BFGS: 234 14:31:46 -304.601272 0.753363
BFGS: 235 14:31:47 -304.601271 0.753348
BFGS: 236 14:31:47 -304.601273 0.753361
BFGS: 237 14:31:47 -304.601273 0.753363
BFGS: 238 14:31:48 -304.601271 0.753366
BFGS: 239 14:31:48 -304.601272 0.753345
BFGS: 240 14:31:49 -304.601272 0.753363
BFGS: 241 14:31:49 -304.601270 0.753362
BFGS: 242 14:31:50 -304.601270 0.753364
BFGS: 243 14:31:50 -304.601273 0.753358
BFGS: 244 14:31:51 -304.601273 0.753353
BFGS: 245 14:31:51 -304.599993 0.857592
BFGS: 246 14:31:52 -304.601270 0.753345
BFGS: 247 14:31:52 -304.601270 0.753347
BFGS: 248 14:31:52 -304.601269 0.753380
BFGS: 249 14:31:53 -304.601271 0.753338
BFGS: 250 14:31:53 -304.601270 0.753347
BFGS: 251 14:31:54 -304.601272 0.753349
BFGS: 252 14:31:54 -304.601269 0.753357
BFGS: 253 14:31:55 -304.601272 0.753346
BFGS: 254 14:31:55 -304.601272 0.753349
BFGS: 255 14:31:56 -304.601271 0.753355
BFGS: 256 14:31:56 -304.601269 0.753358
BFGS: 257 14:31:56 -304.601271 0.753349
BFGS: 258 14:31:57 -304.601271 0.753350
BFGS: 259 14:31:57 -304.601270 0.753349
BFGS: 260 14:31:58 -304.601273 0.753352
BFGS: 261 14:31:58 -304.601272 0.753347
BFGS: 262 14:31:58 -304.601273 0.753313
BFGS: 263 14:31:59 -304.601272 0.753314
BFGS: 264 14:31:59 -304.601273 0.753352
BFGS: 265 14:32:00 -304.601273 0.753318
BFGS: 266 14:32:00 -304.601272 0.753318
BFGS: 267 14:32:01 -304.601272 0.753316
BFGS: 268 14:32:01 -304.601270 0.753347
BFGS: 269 14:32:01 -304.601274 0.753321
BFGS: 270 14:32:02 -304.601274 0.753342
BFGS: 271 14:32:02 -304.601273 0.753352
BFGS: 272 14:32:03 -304.601272 0.753344
BFGS: 273 14:32:03 -304.601270 0.753359
BFGS: 274 14:32:04 -304.601272 0.753319
BFGS: 275 14:32:04 -304.601272 0.753358
BFGS: 276 14:32:04 -304.601273 0.753351
BFGS: 277 14:32:05 -304.601271 0.753359
BFGS: 278 14:32:05 -304.601273 0.753352
BFGS: 279 14:32:06 -304.601272 0.753347
BFGS: 280 14:32:06 -304.601272 0.753354
BFGS: 281 14:32:07 -304.601272 0.753319
BFGS: 282 14:32:07 -304.601272 0.753321
BFGS: 283 14:32:08 -304.601273 0.753355
BFGS: 284 14:32:08 -304.601273 0.753358
BFGS: 285 14:32:09 -304.601270 0.753366
BFGS: 286 14:32:09 -304.601270 0.753327
BFGS: 287 14:32:09 -304.601273 0.753354
BFGS: 288 14:32:10 -304.601271 0.753355
BFGS: 289 14:32:10 -304.601271 0.753357
BFGS: 290 14:32:10 -304.601273 0.753321
BFGS: 291 14:32:11 -304.601272 0.753361
BFGS: 292 14:32:11 -304.601273 0.753356
BFGS: 293 14:32:12 -304.601272 0.753321
BFGS: 294 14:32:12 -304.601274 0.753318
BFGS: 295 14:32:12 -304.601270 0.753360
BFGS: 296 14:32:13 -304.601271 0.753355
BFGS: 297 14:32:13 -304.601272 0.753166
BFGS: 298 14:32:14 -304.601273 0.753322
BFGS: 299 14:32:14 -304.601272 0.753360
BFGS: 300 14:32:15 -304.601270 0.753357
Step Time Energy fmax
BFGS: 0 14:32:15 -302.525092 4.030005
BFGS: 1 14:32:15 -302.891566 2.970149
BFGS: 2 14:32:16 -303.704395 3.090902
BFGS: 3 14:32:16 -303.860590 2.659360
BFGS: 4 14:32:17 -304.125232 2.603424
BFGS: 5 14:32:17 -304.212324 1.182775
BFGS: 6 14:32:17 -304.351839 0.872387
BFGS: 7 14:32:18 -304.510750 1.751437
BFGS: 8 14:32:18 -304.555551 1.226416
BFGS: 9 14:32:19 -304.620424 0.978177
BFGS: 10 14:32:19 -304.639337 0.720358
BFGS: 11 14:32:20 -304.661739 0.275108
BFGS: 12 14:32:20 -304.665998 0.208662
BFGS: 13 14:32:21 -304.668972 0.144815
BFGS: 14 14:32:21 -304.670788 0.106800
BFGS: 15 14:32:22 -304.672523 0.096757
BFGS: 16 14:32:22 -304.673470 0.090873
BFGS: 17 14:32:22 -304.674237 0.089376
BFGS: 18 14:32:23 -304.675163 0.093357
BFGS: 19 14:32:23 -304.676469 0.087696
BFGS: 20 14:32:24 -304.677886 0.062914
BFGS: 21 14:32:24 -304.678883 0.078992
BFGS: 22 14:32:25 -304.679478 0.090996
BFGS: 23 14:32:25 -304.680050 0.083885
BFGS: 24 14:32:25 -304.680709 0.055173
BFGS: 25 14:32:26 -304.681202 0.034188
Step Time Energy fmax
BFGS: 0 14:32:26 -302.304751 3.956821
BFGS: 1 14:32:27 -302.670385 2.834756
BFGS: 2 14:32:27 -303.526839 3.284715
BFGS: 3 14:32:28 -303.686759 2.862921
BFGS: 4 14:32:28 -303.919562 2.688693
BFGS: 5 14:32:29 -303.994322 0.820504
BFGS: 6 14:32:29 -304.032975 0.653586
BFGS: 7 14:32:30 -304.156208 0.521691
BFGS: 8 14:32:30 -304.175257 0.554171
BFGS: 9 14:32:31 -304.204217 0.402962
BFGS: 10 14:32:31 -304.220072 0.322517
BFGS: 11 14:32:31 -304.230863 0.366728
BFGS: 12 14:32:32 -304.238061 0.396628
BFGS: 13 14:32:32 -304.248338 0.401004
BFGS: 14 14:32:33 -304.261124 0.371188
BFGS: 15 14:32:33 -304.273257 0.426303
BFGS: 16 14:32:33 -304.285809 0.413414
BFGS: 17 14:32:33 -304.296366 0.395581
BFGS: 18 14:32:34 -304.307115 0.260195
BFGS: 19 14:32:34 -304.314489 0.254882
BFGS: 20 14:32:35 -304.318982 0.254820
BFGS: 21 14:32:35 -304.322786 0.250363
BFGS: 22 14:32:35 -304.327883 0.228278
BFGS: 23 14:32:36 -304.333669 0.192343
BFGS: 24 14:32:36 -304.339211 0.155735
BFGS: 25 14:32:37 -304.342694 0.143942
BFGS: 26 14:32:37 -304.345304 0.148202
BFGS: 27 14:32:37 -304.348303 0.145674
BFGS: 28 14:32:38 -304.350606 0.091492
BFGS: 29 14:32:38 -304.351667 0.049658
# 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 14:32:38 -296.873642 4.468788
BFGS: 1 14:32:39 -297.316911 4.650478
BFGS: 2 14:32:39 -298.588722 3.782546
BFGS: 3 14:32:40 -298.860009 5.183795
BFGS: 4 14:32:40 -299.089000 2.033840
BFGS: 5 14:32:41 -299.236797 2.082582
BFGS: 6 14:32:41 -299.764893 2.194052
BFGS: 7 14:32:41 -300.112848 1.471609
BFGS: 8 14:32:42 -300.191841 1.512922
BFGS: 9 14:32:42 -300.295158 1.147388
BFGS: 10 14:32:43 -300.513227 0.636790
BFGS: 11 14:32:43 -300.533086 0.489786
BFGS: 12 14:32:43 -300.540714 0.388372
BFGS: 13 14:32:44 -300.562362 0.280953
BFGS: 14 14:32:44 -300.568272 0.229095
BFGS: 15 14:32:45 -300.570704 0.158864
BFGS: 16 14:32:45 -300.572021 0.123139
BFGS: 17 14:32:46 -300.573526 0.154434
BFGS: 18 14:32:46 -300.574548 0.177215
BFGS: 19 14:32:46 -300.576064 0.167664
BFGS: 20 14:32:47 -300.577282 0.109667
BFGS: 21 14:32:47 -300.577891 0.052759
BFGS: 22 14:32:48 -300.578099 0.043664
Step Time Energy fmax
BFGS: 0 14:32:48 -296.196028 4.388897
BFGS: 1 14:32:48 -296.705024 4.664083
BFGS: 2 14:32:49 -298.247119 2.994584
BFGS: 3 14:32:49 -297.169337 14.351896
BFGS: 4 14:32:50 -298.431158 1.810433
BFGS: 5 14:32:50 -298.493228 1.033385
BFGS: 6 14:32:50 -298.533676 0.818803
BFGS: 7 14:32:51 -298.542345 0.618342
BFGS: 8 14:32:51 -298.569253 0.504380
BFGS: 9 14:32:52 -298.574896 0.557685
BFGS: 10 14:32:52 -298.610379 0.922076
BFGS: 11 14:32:53 -298.682705 1.749969
BFGS: 12 14:32:53 -298.732164 2.644237
BFGS: 13 14:32:54 -298.751604 2.841883
BFGS: 14 14:32:54 -298.830487 3.194966
BFGS: 15 14:32:54 -298.921572 3.585504
BFGS: 16 14:32:55 -299.160260 3.469049
BFGS: 17 14:32:55 -299.396397 3.410427
BFGS: 18 14:32:56 -299.562587 3.026953
BFGS: 19 14:32:56 -299.987347 2.819530
BFGS: 20 14:32:57 -300.317737 2.437070
BFGS: 21 14:32:57 -300.455443 1.691896
BFGS: 22 14:32:58 -300.529394 0.574868
BFGS: 23 14:32:58 -300.542938 0.345693
BFGS: 24 14:32:59 -300.552223 0.296919
BFGS: 25 14:32:59 -300.559657 0.289050
BFGS: 26 14:32:59 -300.567106 0.159407
BFGS: 27 14:33:00 -300.570001 0.113969
BFGS: 28 14:33:00 -300.571453 0.112432
BFGS: 29 14:33:01 -300.573198 0.110589
BFGS: 30 14:33:01 -300.574851 0.123899
BFGS: 31 14:33:02 -300.575961 0.091574
BFGS: 32 14:33:02 -300.576611 0.093053
BFGS: 33 14:33:03 -300.577167 0.089929
BFGS: 34 14:33:03 -300.577805 0.074331
BFGS: 35 14:33:03 -300.578282 0.057826
BFGS: 36 14:33:04 -300.578449 0.025526
Step Time Energy fmax
BFGS: 0 14:33:04 -296.131196 4.415090
BFGS: 1 14:33:05 -296.657367 4.706502
BFGS: 2 14:33:05 -298.243293 2.931592
BFGS: 3 14:33:06 -296.973020 15.810653
BFGS: 4 14:33:06 -298.414449 1.789886
BFGS: 5 14:33:07 -298.474445 1.013911
BFGS: 6 14:33:07 -298.511568 0.677334
BFGS: 7 14:33:07 -298.517555 0.440438
BFGS: 8 14:33:08 -298.530028 0.276895
BFGS: 9 14:33:08 -298.532473 0.294670
BFGS: 10 14:33:09 -298.534919 0.274278
BFGS: 11 14:33:09 -298.540785 0.280546
BFGS: 12 14:33:09 -298.564274 0.579458
BFGS: 13 14:33:10 -298.608768 1.188589
BFGS: 14 14:33:10 -298.671731 1.520288
BFGS: 15 14:33:10 -298.908226 1.954623
BFGS: 16 14:33:11 -299.318026 2.193548
BFGS: 17 14:33:11 -299.692717 1.369095
BFGS: 18 14:33:12 -299.576820 3.823016
BFGS: 19 14:33:12 -299.781666 0.606830
BFGS: 20 14:33:12 -299.807822 0.573931
BFGS: 21 14:33:13 -299.851971 0.427783
BFGS: 22 14:33:13 -299.858001 0.281520
BFGS: 23 14:33:14 -299.863160 0.256787
BFGS: 24 14:33:14 -299.867360 0.252874
BFGS: 25 14:33:15 -299.873311 0.238487
BFGS: 26 14:33:15 -299.877168 0.205463
BFGS: 27 14:33:15 -299.879773 0.204074
BFGS: 28 14:33:16 -299.882324 0.259209
BFGS: 29 14:33:16 -299.888354 0.406187
BFGS: 30 14:33:17 -299.899905 0.613769
BFGS: 31 14:33:17 -299.911762 0.601460
BFGS: 32 14:33:18 -299.934383 0.455093
BFGS: 33 14:33:18 -299.957295 0.421077
BFGS: 34 14:33:19 -299.983650 0.489244
BFGS: 35 14:33:19 -300.000298 0.525437
BFGS: 36 14:33:19 -299.982825 0.777558
BFGS: 37 14:33:20 -300.020296 0.369489
BFGS: 38 14:33:20 -300.026677 0.256751
BFGS: 39 14:33:20 -300.035856 0.132072
BFGS: 40 14:33:21 -300.037403 0.123060
BFGS: 41 14:33:21 -300.040523 0.093505
BFGS: 42 14:33:22 -300.042045 0.069835
BFGS: 43 14:33:22 -300.042942 0.056918
BFGS: 44 14:33:23 -300.043179 0.055461
BFGS: 45 14:33:23 -300.043379 0.044381
Step Time Energy fmax
BFGS: 0 14:33:23 -296.071010 4.429381
BFGS: 1 14:33:24 -296.613551 4.739858
BFGS: 2 14:33:24 -298.245328 2.856855
BFGS: 3 14:33:25 -296.755398 17.394903
BFGS: 4 14:33:25 -298.404426 1.762663
BFGS: 5 14:33:26 -298.462568 1.000875
BFGS: 6 14:33:26 -298.498627 0.590360
BFGS: 7 14:33:26 -298.503437 0.335937
BFGS: 8 14:33:27 -298.511182 0.143886
BFGS: 9 14:33:27 -298.512888 0.159581
BFGS: 10 14:33:28 -298.513378 0.120468
BFGS: 11 14:33:28 -298.513860 0.097468
BFGS: 12 14:33:29 -298.515222 0.178785
BFGS: 13 14:33:29 -298.519177 0.335359
BFGS: 14 14:33:30 -298.543505 0.828148
BFGS: 15 14:33:30 -298.675665 1.922415
BFGS: 16 14:33:31 -298.814049 3.234471
BFGS: 17 14:33:31 -298.905339 4.270367
BFGS: 18 14:33:32 -298.978848 3.444907
BFGS: 19 14:33:32 -299.107918 1.538841
BFGS: 20 14:33:32 -299.143681 1.925723
BFGS: 21 14:33:33 -299.168530 1.818181
BFGS: 22 14:33:33 -299.198656 1.661091
BFGS: 23 14:33:34 -299.225095 1.724996
BFGS: 24 14:33:34 -299.275330 1.951321
BFGS: 25 14:33:35 -299.292965 1.839756
BFGS: 26 14:33:35 -299.354470 1.492815
BFGS: 27 14:33:36 -299.437074 1.330328
BFGS: 28 14:33:36 -299.544985 1.209271
BFGS: 29 14:33:37 -299.641815 0.968141
BFGS: 30 14:33:37 -299.720600 0.998309
BFGS: 31 14:33:38 -299.805682 1.167612
BFGS: 32 14:33:38 -300.014181 1.471032
BFGS: 33 14:33:38 -300.167471 1.393929
BFGS: 34 14:33:39 -300.295623 1.388487
BFGS: 35 14:33:39 -300.355592 1.095686
BFGS: 36 14:33:40 -300.420300 0.992905
BFGS: 37 14:33:40 -300.476658 0.799018
BFGS: 38 14:33:41 -300.511923 0.673227
BFGS: 39 14:33:41 -300.534237 0.368660
BFGS: 40 14:33:42 -300.544849 0.295325
BFGS: 41 14:33:42 -300.557761 0.302046
BFGS: 42 14:33:42 -300.566062 0.281286
BFGS: 43 14:33:43 -300.571740 0.180607
BFGS: 44 14:33:43 -300.574162 0.093597
BFGS: 45 14:33:44 -300.575520 0.080396
BFGS: 46 14:33:44 -300.576386 0.086906
BFGS: 47 14:33:45 -300.576909 0.081802
BFGS: 48 14:33:45 -300.577418 0.060581
BFGS: 49 14:33:45 -300.577948 0.031219
Step Time Energy fmax
BFGS: 0 14:33:46 -296.951530 4.492928
BFGS: 1 14:33:46 -297.404621 4.660851
BFGS: 2 14:33:46 -298.680330 3.792364
BFGS: 3 14:33:47 -299.012833 4.725702
BFGS: 4 14:33:47 -299.220083 1.949321
BFGS: 5 14:33:47 -299.386958 1.973144
BFGS: 6 14:33:48 -299.807712 1.170605
BFGS: 7 14:33:48 -299.827165 2.259909
BFGS: 8 14:33:48 -299.916253 0.910261
BFGS: 9 14:33:49 -299.976948 1.030418
BFGS: 10 14:33:50 -300.223078 1.453602
BFGS: 11 14:33:50 -300.297086 1.996053
BFGS: 12 14:33:50 -300.377247 1.337825
BFGS: 13 14:33:51 -300.471643 0.941414
BFGS: 14 14:33:51 -300.493490 0.849652
BFGS: 15 14:33:52 -300.512490 0.645428
BFGS: 16 14:33:52 -300.548084 0.263926
BFGS: 17 14:33:53 -300.552630 0.267504
BFGS: 18 14:33:53 -300.560432 0.218405
BFGS: 19 14:33:54 -300.568293 0.169567
BFGS: 20 14:33:54 -300.573133 0.110931
BFGS: 21 14:33:54 -300.574584 0.077515
BFGS: 22 14:33:55 -300.575267 0.073266
BFGS: 23 14:33:55 -300.576224 0.073291
BFGS: 24 14:33:56 -300.577283 0.067286
BFGS: 25 14:33:56 -300.577990 0.039579
Step Time Energy fmax
BFGS: 0 14:33:56 -296.020382 4.445643
BFGS: 1 14:33:57 -296.579511 4.775585
BFGS: 2 14:33:57 -298.253195 2.782350
BFGS: 3 14:33:58 -296.546910 18.890295
BFGS: 4 14:33:58 -298.401812 1.731814
BFGS: 5 14:33:58 -298.458104 0.989867
BFGS: 6 14:33:59 -298.493945 0.531373
BFGS: 7 14:33:59 -298.498215 0.270359
BFGS: 8 14:34:00 -298.504387 0.081731
BFGS: 9 14:34:00 -298.506004 0.100955
BFGS: 10 14:34:01 -298.506250 0.052060
BFGS: 11 14:34:01 -298.506303 0.032506
Step Time Energy fmax
BFGS: 0 14:34:02 -296.168922 4.404617
BFGS: 1 14:34:02 -296.686169 4.686621
BFGS: 2 14:34:03 -298.246741 2.969161
BFGS: 3 14:34:03 -297.091655 14.943246
BFGS: 4 14:34:03 -298.425268 1.801500
BFGS: 5 14:34:04 -298.486401 1.024662
BFGS: 6 14:34:04 -298.525288 0.753815
BFGS: 7 14:34:05 -298.532697 0.538219
BFGS: 8 14:34:05 -298.552480 0.406761
BFGS: 9 14:34:06 -298.556392 0.440844
BFGS: 10 14:34:06 -298.567289 0.499568
BFGS: 11 14:34:07 -298.600468 0.787774
BFGS: 12 14:34:07 -298.661238 1.465118
BFGS: 13 14:34:07 -298.699852 2.303262
BFGS: 14 14:34:08 -298.729827 2.328317
BFGS: 15 14:34:08 -299.350181 1.875943
BFGS: 16 14:34:09 -299.498319 2.154184
BFGS: 17 14:34:09 -299.604874 1.603510
BFGS: 18 14:34:10 -299.684427 1.348781
BFGS: 19 14:34:10 -299.839367 0.741737
BFGS: 20 14:34:11 -299.866961 0.466584
BFGS: 21 14:34:11 -299.877314 0.334385
BFGS: 22 14:34:12 -299.881755 0.301466
BFGS: 23 14:34:12 -299.890974 0.382973
BFGS: 24 14:34:12 -299.908743 0.662587
BFGS: 25 14:34:13 -299.948638 1.143275
BFGS: 26 14:34:13 -299.985578 1.497663
BFGS: 27 14:34:14 -300.037684 1.382714
BFGS: 28 14:34:14 -300.178860 1.519304
BFGS: 29 14:34:15 -300.338313 1.233341
BFGS: 30 14:34:15 -300.434519 0.612371
BFGS: 31 14:34:16 -300.460050 0.663711
BFGS: 32 14:34:16 -300.492292 0.710080
BFGS: 33 14:34:17 -300.535560 0.452700
BFGS: 34 14:34:17 -300.553608 0.222587
BFGS: 35 14:34:18 -300.561418 0.191676
BFGS: 36 14:34:18 -300.566198 0.158145
BFGS: 37 14:34:19 -300.569963 0.158231
BFGS: 38 14:34:19 -300.572944 0.116177
BFGS: 39 14:34:19 -300.574825 0.090361
BFGS: 40 14:34:20 -300.575867 0.078997
BFGS: 41 14:34:20 -300.576715 0.076224
BFGS: 42 14:34:20 -300.577537 0.069988
BFGS: 43 14:34:21 -300.578074 0.050138
BFGS: 44 14:34:21 -300.578307 0.026234
Step Time Energy fmax
BFGS: 0 14:34:21 -296.565424 4.367351
BFGS: 1 14:34:22 -297.018632 4.583323
BFGS: 2 14:34:22 -298.374742 3.425169
BFGS: 3 14:34:23 -298.173836 8.384219
BFGS: 4 14:34:23 -298.682421 1.946762
BFGS: 5 14:34:24 -298.766716 1.435352
BFGS: 6 14:34:24 -298.943454 2.392597
BFGS: 7 14:34:24 -299.197837 2.992369
BFGS: 8 14:34:25 -299.463500 2.892532
BFGS: 9 14:34:25 -299.587435 2.030498
BFGS: 10 14:34:26 -299.657192 2.022792
BFGS: 11 14:34:26 -300.188063 1.485182
BFGS: 12 14:34:26 -300.370226 1.492820
BFGS: 13 14:34:27 -300.420717 1.239121
BFGS: 14 14:34:27 -300.462326 1.042840
BFGS: 15 14:34:28 -300.525612 0.892099
BFGS: 16 14:34:28 -300.541513 0.736914
BFGS: 17 14:34:28 -300.558004 0.408253
BFGS: 18 14:34:29 -300.564305 0.197541
BFGS: 19 14:34:29 -300.568642 0.212075
BFGS: 20 14:34:30 -300.570322 0.239668
BFGS: 21 14:34:30 -300.572237 0.238238
BFGS: 22 14:34:30 -300.574570 0.194006
BFGS: 23 14:34:31 -300.576357 0.114920
BFGS: 24 14:34:31 -300.577087 0.062553
BFGS: 25 14:34:32 -300.577402 0.072999
BFGS: 26 14:34:32 -300.577726 0.068541
BFGS: 27 14:34:32 -300.578052 0.046534
Step Time Energy fmax
BFGS: 0 14:34:33 -297.688872 4.370208
BFGS: 1 14:34:33 -298.138001 4.408659
BFGS: 2 14:34:34 -299.287429 2.989349
BFGS: 3 14:34:34 -299.408420 4.034723
BFGS: 4 14:34:35 -299.627310 1.280714
BFGS: 5 14:34:35 -299.712751 1.116803
BFGS: 6 14:34:35 -299.954676 0.560178
BFGS: 7 14:34:36 -299.974236 0.493099
BFGS: 8 14:34:36 -300.028809 0.431856
BFGS: 9 14:34:36 -300.038992 0.245779
BFGS: 10 14:34:36 -300.042511 0.075893
BFGS: 11 14:34:37 -300.042737 0.046083
Step Time Energy fmax
BFGS: 0 14:34:37 -296.130220 4.417099
BFGS: 1 14:34:37 -296.657219 4.708614
BFGS: 2 14:34:37 -298.244030 2.927659
BFGS: 3 14:34:38 -296.965537 15.865400
BFGS: 4 14:34:38 -298.414484 1.788220
BFGS: 5 14:34:39 -298.474341 1.012972
BFGS: 6 14:34:39 -298.511419 0.672412
BFGS: 7 14:34:39 -298.517355 0.434949
BFGS: 8 14:34:40 -298.529581 0.269255
BFGS: 9 14:34:40 -298.531932 0.284851
BFGS: 10 14:34:40 -298.534167 0.261928
BFGS: 11 14:34:41 -298.539379 0.261868
BFGS: 12 14:34:41 -298.558493 0.453234
BFGS: 13 14:34:42 -298.597988 0.935606
BFGS: 14 14:34:42 -298.621870 1.529965
BFGS: 15 14:34:42 -298.667446 1.139412
BFGS: 16 14:34:43 -298.819173 1.304430
BFGS: 17 14:34:43 -299.245070 2.235253
BFGS: 18 14:34:44 -299.628337 2.458933
BFGS: 19 14:34:44 -299.618320 3.044236
BFGS: 20 14:34:45 -299.812524 1.581771
BFGS: 21 14:34:45 -299.887358 1.049643
BFGS: 22 14:34:45 -299.987202 0.498981
BFGS: 23 14:34:46 -300.004207 0.484594
BFGS: 24 14:34:46 -300.020147 0.514034
BFGS: 25 14:34:46 -300.027795 0.442813
BFGS: 26 14:34:47 -300.036593 0.228587
BFGS: 27 14:34:47 -300.039297 0.109712
BFGS: 28 14:34:47 -300.040308 0.090021
BFGS: 29 14:34:48 -300.041313 0.083954
BFGS: 30 14:34:48 -300.042452 0.086863
BFGS: 31 14:34:49 -300.043019 0.051838
BFGS: 32 14:34:49 -300.043194 0.029516
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 14:34:49 -295.595805 0.789853
BFGS: 1 14:34:50 -295.648051 0.748797
BFGS: 2 14:34:50 -295.844260 0.406762
BFGS: 3 14:34:51 -295.856883 0.450491
BFGS: 4 14:34:51 -295.863190 0.447353
BFGS: 5 14:34:52 -295.900618 0.333875
BFGS: 6 14:34:52 -295.906240 0.354311
BFGS: 7 14:34:52 -295.915417 0.281399
BFGS: 8 14:34:53 -295.921342 0.297120
BFGS: 9 14:34:53 -295.927938 0.352444
BFGS: 10 14:34:54 -295.932837 0.358186
BFGS: 11 14:34:54 -295.938948 0.325494
BFGS: 12 14:34:54 -295.946463 0.254802
BFGS: 13 14:34:55 -295.953665 0.222806
BFGS: 14 14:34:55 -295.958394 0.222515
BFGS: 15 14:34:55 -295.960575 0.214118
BFGS: 16 14:34:56 -295.962859 0.160182
BFGS: 17 14:34:56 -295.964937 0.077158
BFGS: 18 14:34:57 -295.966091 0.048974
Step Time Energy fmax
BFGS: 0 14:34:57 -295.241139 1.399029
BFGS: 1 14:34:58 -295.325841 1.270267
BFGS: 2 14:34:58 -295.532955 1.640921
BFGS: 3 14:34:58 -295.576734 0.560992
BFGS: 4 14:34:59 -295.587881 0.541932
BFGS: 5 14:34:59 -295.619367 0.344994
BFGS: 6 14:34:59 -295.623994 0.366249
BFGS: 7 14:35:00 -295.638634 0.391002
BFGS: 8 14:35:00 -295.649797 0.474295
BFGS: 9 14:35:00 -295.663985 0.428342
BFGS: 10 14:35:00 -295.675147 0.590393
BFGS: 11 14:35:01 -295.697983 0.919763
BFGS: 12 14:35:01 -295.733522 1.178751
BFGS: 13 14:35:02 -295.759709 1.079184
BFGS: 14 14:35:02 -295.809376 0.805994
BFGS: 15 14:35:03 -295.838472 0.502710
BFGS: 16 14:35:03 -295.863139 0.321772
BFGS: 17 14:35:03 -295.868579 0.393076
BFGS: 18 14:35:04 -295.877110 0.418209
BFGS: 19 14:35:04 -295.885953 0.335455
BFGS: 20 14:35:05 -295.894219 0.251305
BFGS: 21 14:35:05 -295.899917 0.237345
BFGS: 22 14:35:05 -295.903605 0.219148
BFGS: 23 14:35:06 -295.906659 0.225325
BFGS: 24 14:35:06 -295.912246 0.254174
BFGS: 25 14:35:07 -295.919225 0.206553
BFGS: 26 14:35:07 -295.923566 0.130320
BFGS: 27 14:35:08 -295.926147 0.103115
BFGS: 28 14:35:08 -295.927594 0.094404
BFGS: 29 14:35:09 -295.928921 0.090719
BFGS: 30 14:35:09 -295.930540 0.070803
BFGS: 31 14:35:10 -295.931717 0.041264
Step Time Energy fmax
BFGS: 0 14:35:10 -295.455092 1.036475
BFGS: 1 14:35:10 -295.518375 0.958084
BFGS: 2 14:35:11 -295.730213 0.872741
BFGS: 3 14:35:11 -295.747837 0.526033
BFGS: 4 14:35:11 -295.759455 0.483353
BFGS: 5 14:35:12 -295.794134 0.524956
BFGS: 6 14:35:12 -295.803607 0.470718
BFGS: 7 14:35:12 -295.819218 0.430210
BFGS: 8 14:35:13 -295.830584 0.294274
BFGS: 9 14:35:13 -295.838958 0.176218
BFGS: 10 14:35:13 -295.841845 0.164645
BFGS: 11 14:35:14 -295.843261 0.144868
BFGS: 12 14:35:14 -295.845075 0.116660
BFGS: 13 14:35:14 -295.847039 0.095871
BFGS: 14 14:35:15 -295.848290 0.093417
BFGS: 15 14:35:15 -295.848893 0.096045
BFGS: 16 14:35:16 -295.849488 0.099665
BFGS: 17 14:35:16 -295.850600 0.106884
BFGS: 18 14:35:17 -295.852473 0.120980
BFGS: 19 14:35:17 -295.854873 0.147576
BFGS: 20 14:35:17 -295.857287 0.184605
BFGS: 21 14:35:18 -295.860165 0.229572
BFGS: 22 14:35:18 -295.865542 0.295230
BFGS: 23 14:35:19 -295.873814 0.320722
BFGS: 24 14:35:19 -295.884114 0.309401
BFGS: 25 14:35:20 -295.910625 0.239451
BFGS: 26 14:35:20 -295.902389 0.268670
BFGS: 27 14:35:21 -295.919042 0.172063
BFGS: 28 14:35:21 -295.921777 0.151528
BFGS: 29 14:35:21 -295.925351 0.132088
BFGS: 30 14:35:22 -295.930176 0.120618
BFGS: 31 14:35:22 -295.931541 0.080530
BFGS: 32 14:35:23 -295.932234 0.064452
BFGS: 33 14:35:23 -295.932447 0.048757
Step Time Energy fmax
BFGS: 0 14:35:23 -295.277506 1.341173
BFGS: 1 14:35:24 -295.357066 1.222203
BFGS: 2 14:35:24 -295.569648 1.513852
BFGS: 3 14:35:25 -295.607992 0.580798
BFGS: 4 14:35:25 -295.618911 0.525367
BFGS: 5 14:35:25 -295.652511 0.419906
BFGS: 6 14:35:26 -295.657509 0.424670
BFGS: 7 14:35:26 -295.695513 0.672073
BFGS: 8 14:35:27 -295.711845 0.594733
BFGS: 9 14:35:27 -295.745482 0.897946
BFGS: 10 14:35:27 -295.785736 1.175767
BFGS: 11 14:35:28 -295.815005 1.104562
BFGS: 12 14:35:28 -295.878860 0.896834
BFGS: 13 14:35:29 -295.926794 0.520037
BFGS: 14 14:35:29 -295.943355 0.292918
BFGS: 15 14:35:29 -295.949087 0.284239
BFGS: 16 14:35:30 -295.953371 0.313751
BFGS: 17 14:35:30 -295.958146 0.279010
BFGS: 18 14:35:30 -295.962098 0.181124
BFGS: 19 14:35:31 -295.964220 0.079557
BFGS: 20 14:35:31 -295.965191 0.053296
BFGS: 21 14:35:32 -295.965589 0.049712
Step Time Energy fmax
BFGS: 0 14:35:32 -295.136860 1.607563
BFGS: 1 14:35:32 -295.239828 1.453709
BFGS: 2 14:35:33 -295.431167 2.245103
BFGS: 3 14:35:33 -295.507478 0.487176
BFGS: 4 14:35:33 -295.522034 0.599144
BFGS: 5 14:35:34 -295.547182 0.583775
BFGS: 6 14:35:34 -295.557920 0.335101
BFGS: 7 14:35:34 -295.563909 0.260722
BFGS: 8 14:35:35 -295.568241 0.299867
BFGS: 9 14:35:35 -295.573520 0.268362
BFGS: 10 14:35:36 -295.576996 0.177512
BFGS: 11 14:35:36 -295.578293 0.104898
BFGS: 12 14:35:37 -295.578669 0.115949
BFGS: 13 14:35:37 -295.579237 0.140705
BFGS: 14 14:35:37 -295.580589 0.188838
BFGS: 15 14:35:38 -295.584317 0.275516
BFGS: 16 14:35:38 -295.600269 0.414368
BFGS: 17 14:35:38 -295.614123 0.579288
BFGS: 18 14:35:39 -295.631698 0.860053
BFGS: 19 14:35:39 -295.664609 1.058763
BFGS: 20 14:35:40 -295.761539 0.861289
BFGS: 21 14:35:40 -295.858122 0.726878
BFGS: 22 14:35:40 -295.879955 0.901055
BFGS: 23 14:35:40 -295.916415 0.414385
BFGS: 24 14:35:41 -295.928412 0.334079
BFGS: 25 14:35:41 -295.946477 0.194093
BFGS: 26 14:35:41 -295.950785 0.163337
BFGS: 27 14:35:42 -295.957361 0.138500
BFGS: 28 14:35:42 -295.959948 0.122134
BFGS: 29 14:35:43 -295.961465 0.109690
BFGS: 30 14:35:43 -295.962577 0.100370
BFGS: 31 14:35:44 -295.964161 0.084539
BFGS: 32 14:35:44 -295.965552 0.063241
BFGS: 33 14:35:45 -295.966250 0.045210
Step Time Energy fmax
BFGS: 0 14:35:45 -295.653312 0.722339
BFGS: 1 14:35:45 -295.701465 0.641854
BFGS: 2 14:35:46 -295.874155 0.363371
BFGS: 3 14:35:46 -295.884978 0.389200
BFGS: 4 14:35:46 -295.888742 0.380275
BFGS: 5 14:35:47 -295.918298 0.234657
BFGS: 6 14:35:48 -295.920317 0.208140
BFGS: 7 14:35:48 -295.927855 0.128361
BFGS: 8 14:35:48 -295.928371 0.126748
BFGS: 9 14:35:49 -295.929969 0.101596
BFGS: 10 14:35:49 -295.930676 0.076376
BFGS: 11 14:35:50 -295.931122 0.057640
BFGS: 12 14:35:50 -295.931382 0.062348
BFGS: 13 14:35:51 -295.931812 0.064218
BFGS: 14 14:35:51 -295.932372 0.054602
BFGS: 15 14:35:51 -295.932803 0.029374
Step Time Energy fmax
BFGS: 0 14:35:52 -295.594756 0.745453
BFGS: 1 14:35:52 -295.645428 0.663641
BFGS: 2 14:35:53 -295.818570 0.276269
BFGS: 3 14:35:53 -295.828368 0.226006
BFGS: 4 14:35:54 -295.830316 0.222467
BFGS: 5 14:35:54 -295.839398 0.161773
BFGS: 6 14:35:54 -295.840141 0.135877
BFGS: 7 14:35:55 -295.841847 0.073487
BFGS: 8 14:35:55 -295.842279 0.050405
BFGS: 9 14:35:56 -295.842472 0.049025
Step Time Energy fmax
BFGS: 0 14:35:56 -295.576492 0.872837
BFGS: 1 14:35:56 -295.629986 0.828031
BFGS: 2 14:35:57 -295.835255 0.489556
BFGS: 3 14:35:57 -295.849564 0.521128
BFGS: 4 14:35:58 -295.858985 0.525038
BFGS: 5 14:35:58 -295.908785 0.453292
BFGS: 6 14:35:58 -295.921641 0.531124
BFGS: 7 14:35:58 -295.936094 0.482861
BFGS: 8 14:35:59 -295.945279 0.288126
BFGS: 9 14:35:59 -295.952159 0.238952
BFGS: 10 14:35:59 -295.955574 0.230563
BFGS: 11 14:36:00 -295.957672 0.203396
BFGS: 12 14:36:00 -295.959885 0.160398
BFGS: 13 14:36:01 -295.962333 0.106189
BFGS: 14 14:36:01 -295.963988 0.104827
BFGS: 15 14:36:02 -295.964789 0.098892
BFGS: 16 14:36:02 -295.965376 0.083893
BFGS: 17 14:36:02 -295.966089 0.055893
BFGS: 18 14:36:03 -295.966683 0.033767
Step Time Energy fmax
BFGS: 0 14:36:03 -295.240152 1.396312
BFGS: 1 14:36:04 -295.325338 1.268259
BFGS: 2 14:36:04 -295.533806 1.656165
BFGS: 3 14:36:04 -295.578522 0.562863
BFGS: 4 14:36:04 -295.589811 0.544516
BFGS: 5 14:36:05 -295.621648 0.351238
BFGS: 6 14:36:05 -295.626478 0.372970
BFGS: 7 14:36:05 -295.641611 0.401913
BFGS: 8 14:36:06 -295.653450 0.501030
BFGS: 9 14:36:06 -295.669195 0.466968
BFGS: 10 14:36:06 -295.682003 0.627293
BFGS: 11 14:36:07 -295.705311 0.946186
BFGS: 12 14:36:07 -295.725201 1.121480
BFGS: 13 14:36:07 -295.759991 0.956777
BFGS: 14 14:36:08 -295.798130 0.654627
BFGS: 15 14:36:08 -295.824785 0.267770
BFGS: 16 14:36:09 -295.830514 0.251148
BFGS: 17 14:36:09 -295.833769 0.283824
BFGS: 18 14:36:09 -295.836626 0.278956
BFGS: 19 14:36:10 -295.839931 0.209481
BFGS: 20 14:36:10 -295.841987 0.107659
BFGS: 21 14:36:11 -295.842842 0.047105
Step Time Energy fmax
BFGS: 0 14:36:11 -295.319049 1.265739
BFGS: 1 14:36:11 -295.394469 1.155326
BFGS: 2 14:36:12 -295.608644 1.310438
BFGS: 3 14:36:12 -295.638380 0.597891
BFGS: 4 14:36:13 -295.649796 0.484457
BFGS: 5 14:36:13 -295.688260 0.516557
BFGS: 6 14:36:13 -295.694923 0.505662
BFGS: 7 14:36:14 -295.763806 0.556287
BFGS: 8 14:36:14 -295.780408 0.589255
BFGS: 9 14:36:15 -295.791880 0.576422
BFGS: 10 14:36:15 -295.812890 0.471390
BFGS: 11 14:36:16 -295.833821 0.245208
BFGS: 12 14:36:16 -295.838786 0.209330
BFGS: 13 14:36:16 -295.840821 0.214157
BFGS: 14 14:36:17 -295.842884 0.208105
BFGS: 15 14:36:17 -295.845355 0.180169
BFGS: 16 14:36:18 -295.847882 0.125301
BFGS: 17 14:36:18 -295.849201 0.097532
BFGS: 18 14:36:18 -295.849784 0.095030
BFGS: 19 14:36:19 -295.850316 0.095969
BFGS: 20 14:36:19 -295.851307 0.108047
BFGS: 21 14:36:19 -295.852968 0.140820
BFGS: 22 14:36:20 -295.855157 0.134399
BFGS: 23 14:36:20 -295.857742 0.156270
BFGS: 24 14:36:21 -295.861910 0.208624
BFGS: 25 14:36:21 -295.870757 0.352753
BFGS: 26 14:36:21 -295.876445 0.468803
BFGS: 27 14:36:22 -295.891841 0.353340
BFGS: 28 14:36:22 -295.906292 0.243928
BFGS: 29 14:36:22 -295.920408 0.133644
BFGS: 30 14:36:23 -295.924079 0.132696
BFGS: 31 14:36:23 -295.926563 0.124697
BFGS: 32 14:36:23 -295.929067 0.079072
BFGS: 33 14:36:24 -295.930884 0.062508
BFGS: 34 14:36:24 -295.931977 0.050624
BFGS: 35 14:36:24 -295.932426 0.043802
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 14:36:25 -303.650687 0.881364
BFGS: 1 14:36:25 -303.672621 0.662847
BFGS: 2 14:36:26 -303.716897 0.572018
BFGS: 3 14:36:26 -303.738335 0.585019
BFGS: 4 14:36:27 -303.769097 0.727952
BFGS: 5 14:36:27 -303.794209 0.598358
BFGS: 6 14:36:28 -303.842982 0.598478
BFGS: 7 14:36:28 -303.852158 0.373910
BFGS: 8 14:36:28 -303.859163 0.212999
BFGS: 9 14:36:29 -303.867508 0.148556
BFGS: 10 14:36:29 -303.869855 0.131514
BFGS: 11 14:36:30 -303.871244 0.144411
BFGS: 12 14:36:30 -303.873039 0.155243
BFGS: 13 14:36:31 -303.875196 0.171906
BFGS: 14 14:36:31 -303.877078 0.123042
BFGS: 15 14:36:31 -303.878223 0.119930
BFGS: 16 14:36:32 -303.879191 0.119139
BFGS: 17 14:36:32 -303.880843 0.114174
BFGS: 18 14:36:33 -303.884037 0.198005
BFGS: 19 14:36:33 -303.890196 0.355618
BFGS: 20 14:36:34 -303.897024 0.518964
BFGS: 21 14:36:34 -303.904649 0.434484
BFGS: 22 14:36:34 -303.916508 0.387271
BFGS: 23 14:36:35 -303.921530 0.497349
BFGS: 24 14:36:35 -303.931495 0.696100
BFGS: 25 14:36:36 -303.952022 0.614198
BFGS: 26 14:36:36 -303.981904 0.355803
BFGS: 27 14:36:36 -303.985566 0.437516
BFGS: 28 14:36:37 -304.000696 0.312357
BFGS: 29 14:36:37 -304.011493 0.258282
BFGS: 30 14:36:38 -304.037404 0.378898
BFGS: 31 14:36:38 -304.059553 0.422267
BFGS: 32 14:36:39 -304.076983 0.405722
BFGS: 33 14:36:39 -304.095435 0.473074
BFGS: 34 14:36:40 -304.118812 0.608570
BFGS: 35 14:36:40 -304.146892 0.771785
BFGS: 36 14:36:41 -304.179440 0.856593
BFGS: 37 14:36:41 -304.219050 0.858593
BFGS: 38 14:36:42 -304.266717 0.777874
BFGS: 39 14:36:42 -304.298245 0.536615
BFGS: 40 14:36:42 -304.304613 0.651045
BFGS: 41 14:36:43 -304.346051 0.477821
BFGS: 42 14:36:43 -304.356868 0.359394
BFGS: 43 14:36:43 -304.376582 0.249206
BFGS: 44 14:36:44 -304.383399 0.174922
BFGS: 45 14:36:44 -304.385825 0.128683
BFGS: 46 14:36:44 -304.387084 0.079390
BFGS: 47 14:36:45 -304.387886 0.070644
BFGS: 48 14:36:45 -304.388457 0.045725
Step Time Energy fmax
BFGS: 0 14:36:46 -304.390789 0.256782
BFGS: 1 14:36:46 -304.394332 0.209232
BFGS: 2 14:36:47 -304.407522 0.136721
BFGS: 3 14:36:47 -304.410135 0.125729
BFGS: 4 14:36:48 -304.411575 0.088094
BFGS: 5 14:36:48 -304.412248 0.069896
BFGS: 6 14:36:48 -304.412947 0.060992
BFGS: 7 14:36:49 -304.413529 0.072672
BFGS: 8 14:36:49 -304.414036 0.082514
BFGS: 9 14:36:50 -304.414431 0.058296
BFGS: 10 14:36:50 -304.414711 0.039560
Step Time Energy fmax
BFGS: 0 14:36:50 -304.353154 0.300413
BFGS: 1 14:36:51 -304.355915 0.261972
BFGS: 2 14:36:51 -304.364316 0.151217
BFGS: 3 14:36:52 -304.366284 0.175987
BFGS: 4 14:36:52 -304.368664 0.187807
BFGS: 5 14:36:52 -304.370046 0.145887
BFGS: 6 14:36:53 -304.370943 0.089743
BFGS: 7 14:36:53 -304.371428 0.058419
BFGS: 8 14:36:54 -304.371709 0.043451
Step Time Energy fmax
BFGS: 0 14:36:54 -303.904416 0.280208
BFGS: 1 14:36:55 -303.909439 0.241323
BFGS: 2 14:36:55 -303.922056 0.156836
BFGS: 3 14:36:55 -303.924327 0.139311
BFGS: 4 14:36:56 -303.926419 0.101702
BFGS: 5 14:36:56 -303.927760 0.101533
BFGS: 6 14:36:57 -303.928865 0.082609
BFGS: 7 14:36:57 -303.929564 0.078368
BFGS: 8 14:36:58 -303.929949 0.064873
BFGS: 9 14:36:58 -303.930204 0.040820
Step Time Energy fmax
BFGS: 0 14:36:59 -303.108604 0.990323
BFGS: 1 14:36:59 -303.138092 0.748167
BFGS: 2 14:37:00 -303.201444 0.673760
BFGS: 3 14:37:00 -303.232650 0.661808
BFGS: 4 14:37:00 -303.270593 0.770372
BFGS: 5 14:37:01 -303.299728 0.653078
BFGS: 6 14:37:01 -303.350717 0.562165
BFGS: 7 14:37:02 -303.362934 0.353392
BFGS: 8 14:37:02 -303.367725 0.230151
BFGS: 9 14:37:03 -303.376313 0.195794
BFGS: 10 14:37:03 -303.379044 0.182984
BFGS: 11 14:37:03 -303.381550 0.181983
BFGS: 12 14:37:04 -303.383733 0.159083
BFGS: 13 14:37:04 -303.385694 0.135597
BFGS: 14 14:37:05 -303.387404 0.157069
BFGS: 15 14:37:05 -303.388640 0.124838
BFGS: 16 14:37:05 -303.389690 0.097509
BFGS: 17 14:37:06 -303.390955 0.096986
BFGS: 18 14:37:06 -303.392218 0.138708
BFGS: 19 14:37:07 -303.393239 0.125628
BFGS: 20 14:37:07 -303.393861 0.066637
BFGS: 21 14:37:07 -303.394232 0.065259
BFGS: 22 14:37:08 -303.394633 0.086136
BFGS: 23 14:37:08 -303.395247 0.108788
BFGS: 24 14:37:09 -303.396069 0.105459
BFGS: 25 14:37:09 -303.397074 0.120579
BFGS: 26 14:37:09 -303.398620 0.168561
BFGS: 27 14:37:10 -303.402708 0.288139
BFGS: 28 14:37:10 -303.405619 0.481251
BFGS: 29 14:37:11 -303.418191 0.480233
BFGS: 30 14:37:11 -303.461264 0.638913
BFGS: 31 14:37:12 -303.510873 0.756121
BFGS: 32 14:37:12 -303.545085 0.600983
BFGS: 33 14:37:12 -303.579896 0.714586
BFGS: 34 14:37:13 -303.632506 0.609384
BFGS: 35 14:37:13 -303.680340 0.634604
BFGS: 36 14:37:14 -303.742179 0.637253
BFGS: 37 14:37:15 -303.794863 0.569645
BFGS: 38 14:37:15 -303.835240 0.426363
BFGS: 39 14:37:15 -303.862984 0.351866
BFGS: 40 14:37:16 -303.891307 0.236787
BFGS: 41 14:37:16 -303.904185 0.178277
BFGS: 42 14:37:17 -303.908033 0.169961
BFGS: 43 14:37:17 -303.912152 0.138113
BFGS: 44 14:37:18 -303.916637 0.143664
BFGS: 45 14:37:18 -303.921235 0.153267
BFGS: 46 14:37:18 -303.924034 0.117978
BFGS: 47 14:37:19 -303.925365 0.083906
BFGS: 48 14:37:19 -303.926327 0.067636
BFGS: 49 14:37:20 -303.927321 0.064461
BFGS: 50 14:37:20 -303.927893 0.047135
Step Time Energy fmax
BFGS: 0 14:37:21 -303.822285 0.710690
BFGS: 1 14:37:21 -303.836076 0.546055
BFGS: 2 14:37:21 -303.854193 0.218732
BFGS: 3 14:37:22 -303.857858 0.219973
BFGS: 4 14:37:22 -303.861415 0.256817
BFGS: 5 14:37:22 -303.863992 0.228492
BFGS: 6 14:37:23 -303.866210 0.159279
BFGS: 7 14:37:23 -303.867623 0.093540
BFGS: 8 14:37:24 -303.868436 0.094197
BFGS: 9 14:37:24 -303.869026 0.078793
BFGS: 10 14:37:25 -303.869559 0.064751
BFGS: 11 14:37:25 -303.869938 0.059785
BFGS: 12 14:37:25 -303.870184 0.059529
BFGS: 13 14:37:26 -303.870360 0.046662
Step Time Energy fmax
BFGS: 0 14:37:26 -303.901564 0.310644
BFGS: 1 14:37:27 -303.906527 0.245501
BFGS: 2 14:37:27 -303.919866 0.154792
BFGS: 3 14:37:27 -303.922359 0.131051
BFGS: 4 14:37:28 -303.924303 0.098956
BFGS: 5 14:37:28 -303.925587 0.085329
BFGS: 6 14:37:29 -303.926665 0.060057
BFGS: 7 14:37:29 -303.927262 0.071048
BFGS: 8 14:37:29 -303.927594 0.053433
BFGS: 9 14:37:30 -303.927843 0.045158
Step Time Energy fmax
BFGS: 0 14:37:30 -303.885582 0.487083
BFGS: 1 14:37:31 -303.895228 0.361153
BFGS: 2 14:37:31 -303.914246 0.190885
BFGS: 3 14:37:32 -303.918084 0.160692
BFGS: 4 14:37:32 -303.921324 0.144076
BFGS: 5 14:37:32 -303.923655 0.146986
BFGS: 6 14:37:33 -303.925633 0.117376
BFGS: 7 14:37:33 -303.926770 0.077795
BFGS: 8 14:37:33 -303.927282 0.063907
BFGS: 9 14:37:34 -303.927576 0.050335
BFGS: 10 14:37:34 -303.927885 0.041419
Step Time Energy fmax
BFGS: 0 14:37:35 -303.122222 0.990883
BFGS: 1 14:37:35 -303.151935 0.754821
BFGS: 2 14:37:35 -303.220533 0.680458
BFGS: 3 14:37:36 -303.250953 0.654664
BFGS: 4 14:37:36 -303.283426 0.715642
BFGS: 5 14:37:36 -303.311541 0.581729
BFGS: 6 14:37:37 -303.353309 0.509943
BFGS: 7 14:37:37 -303.364017 0.318576
BFGS: 8 14:37:38 -303.368699 0.212785
BFGS: 9 14:37:38 -303.376295 0.195290
BFGS: 10 14:37:38 -303.379382 0.186950
BFGS: 11 14:37:39 -303.382020 0.192286
BFGS: 12 14:37:39 -303.384357 0.163420
BFGS: 13 14:37:40 -303.386502 0.149029
BFGS: 14 14:37:40 -303.388603 0.176319
BFGS: 15 14:37:40 -303.390306 0.154531
BFGS: 16 14:37:41 -303.391805 0.123578
BFGS: 17 14:37:41 -303.393725 0.117976
BFGS: 18 14:37:42 -303.395909 0.171212
BFGS: 19 14:37:42 -303.398052 0.187168
BFGS: 20 14:37:42 -303.400012 0.148358
BFGS: 21 14:37:43 -303.402001 0.179796
BFGS: 22 14:37:43 -303.405051 0.244645
BFGS: 23 14:37:44 -303.411726 0.472472
BFGS: 24 14:37:44 -303.422131 0.705564
BFGS: 25 14:37:45 -303.440751 0.725297
BFGS: 26 14:37:45 -303.476580 0.536106
BFGS: 27 14:37:45 -303.507690 0.618786
BFGS: 28 14:37:46 -303.567729 0.739738
BFGS: 29 14:37:46 -303.594174 0.857549
BFGS: 30 14:37:46 -303.658127 1.026843
BFGS: 31 14:37:47 -303.710331 0.972878
BFGS: 32 14:37:47 -303.812983 0.696257
BFGS: 33 14:37:47 -303.834226 0.783746
BFGS: 34 14:37:48 -303.865431 0.793243
BFGS: 35 14:37:48 -303.896012 0.304089
BFGS: 36 14:37:48 -303.910755 0.240384
BFGS: 37 14:37:49 -303.916067 0.201446
BFGS: 38 14:37:49 -303.920242 0.140141
BFGS: 39 14:37:49 -303.923527 0.105753
BFGS: 40 14:37:50 -303.925483 0.093942
BFGS: 41 14:37:50 -303.926311 0.063232
BFGS: 42 14:37:50 -303.926875 0.055385
BFGS: 43 14:37:51 -303.927453 0.041073
Step Time Energy fmax
BFGS: 0 14:37:51 -303.097715 1.072825
BFGS: 1 14:37:52 -303.130996 0.794980
BFGS: 2 14:37:52 -303.192063 0.674479
BFGS: 3 14:37:52 -303.221256 0.668824
BFGS: 4 14:37:53 -303.259805 0.773869
BFGS: 5 14:37:53 -303.290753 0.680109
BFGS: 6 14:37:54 -303.340003 0.616050
BFGS: 7 14:37:54 -303.361560 0.415523
BFGS: 8 14:37:55 -303.366530 0.287403
BFGS: 9 14:37:55 -303.375911 0.171863
BFGS: 10 14:37:56 -303.379661 0.157857
BFGS: 11 14:37:56 -303.382104 0.203275
BFGS: 12 14:37:56 -303.384605 0.181238
BFGS: 13 14:37:57 -303.387282 0.160446
BFGS: 14 14:37:57 -303.389685 0.151142
BFGS: 15 14:37:58 -303.391437 0.137757
BFGS: 16 14:37:58 -303.392965 0.140643
BFGS: 17 14:37:59 -303.395411 0.140607
BFGS: 18 14:37:59 -303.398875 0.183646
BFGS: 19 14:37:59 -303.402615 0.224837
BFGS: 20 14:38:00 -303.406014 0.213777
BFGS: 21 14:38:00 -303.409972 0.254870
BFGS: 22 14:38:01 -303.416503 0.372056
BFGS: 23 14:38:01 -303.429861 0.701458
BFGS: 24 14:38:02 -303.451688 0.894551
BFGS: 25 14:38:02 -303.487943 0.822061
BFGS: 26 14:38:03 -303.521939 0.618133
BFGS: 27 14:38:03 -303.558541 0.698885
BFGS: 28 14:38:04 -303.599389 0.739863
BFGS: 29 14:38:04 -303.644278 0.823747
BFGS: 30 14:38:04 -303.719660 0.842640
BFGS: 31 14:38:05 -303.779568 0.873994
BFGS: 32 14:38:05 -303.824312 0.619518
BFGS: 33 14:38:06 -303.854203 0.790167
BFGS: 34 14:38:06 -303.871065 0.669339
BFGS: 35 14:38:07 -303.905167 0.197308
BFGS: 36 14:38:07 -303.917335 0.156871
BFGS: 37 14:38:08 -303.920455 0.163821
BFGS: 38 14:38:08 -303.922795 0.131956
BFGS: 39 14:38:08 -303.925019 0.076842
BFGS: 40 14:38:09 -303.926569 0.068742
BFGS: 41 14:38:09 -303.927301 0.054711
BFGS: 42 14:38:10 -303.927628 0.036773
Step Time Energy fmax
BFGS: 0 14:38:10 -301.997503 0.990890
BFGS: 1 14:38:10 -302.025325 0.743389
BFGS: 2 14:38:11 -302.095482 0.887899
BFGS: 3 14:38:11 -302.145980 0.985680
BFGS: 4 14:38:12 -302.189734 0.793348
BFGS: 5 14:38:12 -302.212397 0.634263
BFGS: 6 14:38:13 -302.239356 0.560794
BFGS: 7 14:38:13 -302.270460 0.403398
BFGS: 8 14:38:14 -302.288453 0.420410
BFGS: 9 14:38:14 -302.300013 0.371173
BFGS: 10 14:38:14 -302.318477 0.510364
BFGS: 11 14:38:15 -302.342961 0.750627
BFGS: 12 14:38:15 -302.378739 1.112011
BFGS: 13 14:38:16 -302.446218 1.919505
BFGS: 14 14:38:16 -302.499838 2.928690
BFGS: 15 14:38:17 -302.880907 1.734035
BFGS: 16 14:38:17 -303.105450 1.745872
BFGS: 17 14:38:17 -303.197345 2.009939
BFGS: 18 14:38:18 -303.286259 1.794737
BFGS: 19 14:38:18 -303.400250 1.846168
BFGS: 20 14:38:19 -303.678694 1.418104
BFGS: 21 14:38:19 -303.777325 1.682899
BFGS: 22 14:38:19 -303.943128 1.488662
BFGS: 23 14:38:20 -304.091534 1.467880
BFGS: 24 14:38:20 -304.268312 0.879854
BFGS: 25 14:38:20 -304.321376 0.667576
BFGS: 26 14:38:21 -304.353455 0.842889
BFGS: 27 14:38:21 -304.377978 0.800102
BFGS: 28 14:38:22 -304.412819 0.573543
BFGS: 29 14:38:22 -304.423185 0.431166
BFGS: 30 14:38:23 -304.430685 0.322535
BFGS: 31 14:38:23 -304.439613 0.274996
BFGS: 32 14:38:23 -304.450392 0.280178
BFGS: 33 14:38:24 -304.459110 0.273471
BFGS: 34 14:38:24 -304.464379 0.259412
BFGS: 35 14:38:24 -304.468439 0.244183
BFGS: 36 14:38:25 -304.473754 0.244717
BFGS: 37 14:38:25 -304.481197 0.255046
BFGS: 38 14:38:26 -304.488347 0.186248
BFGS: 39 14:38:26 -304.492751 0.151922
BFGS: 40 14:38:27 -304.495196 0.111579
BFGS: 41 14:38:27 -304.497175 0.116733
BFGS: 42 14:38:27 -304.499522 0.105874
BFGS: 43 14:38:28 -304.501791 0.099621
BFGS: 44 14:38:28 -304.503293 0.085536
BFGS: 45 14:38:29 -304.503978 0.062967
BFGS: 46 14:38:29 -304.504353 0.056623
BFGS: 47 14:38:29 -304.504774 0.055308
BFGS: 48 14:38:30 -304.505309 0.042631
Step Time Energy fmax
BFGS: 0 14:38:30 -302.063078 0.886050
BFGS: 1 14:38:31 -302.083532 0.676984
BFGS: 2 14:38:31 -302.150405 0.862162
BFGS: 3 14:38:31 -302.193512 0.907791
BFGS: 4 14:38:32 -302.227603 0.689318
BFGS: 5 14:38:32 -302.245847 0.533723
BFGS: 6 14:38:33 -302.272486 0.539911
BFGS: 7 14:38:33 -302.299611 0.444299
BFGS: 8 14:38:34 -302.316443 0.403512
BFGS: 9 14:38:34 -302.329342 0.442108
BFGS: 10 14:38:35 -302.355180 0.722362
BFGS: 11 14:38:35 -302.395798 1.225877
BFGS: 12 14:38:35 -302.476331 2.139266
BFGS: 13 14:38:36 -302.552490 3.079314
BFGS: 14 14:38:36 -302.613398 3.395045
BFGS: 15 14:38:37 -302.759059 3.526127
BFGS: 16 14:38:37 -302.767344 2.795027
BFGS: 17 14:38:37 -302.831366 3.492069
BFGS: 18 14:38:38 -302.885263 3.384281
BFGS: 19 14:38:38 -303.045999 2.750587
BFGS: 20 14:38:39 -303.235632 2.010199
BFGS: 21 14:38:39 -303.398257 2.093976
BFGS: 22 14:38:39 -303.516643 2.099518
BFGS: 23 14:38:40 -303.644793 1.387948
BFGS: 24 14:38:40 -303.831441 1.416954
BFGS: 25 14:38:41 -303.999225 1.808041
BFGS: 26 14:38:41 -304.077581 1.635005
BFGS: 27 14:38:41 -304.165355 1.576398
BFGS: 28 14:38:42 -304.208572 1.220664
BFGS: 29 14:38:42 -304.256373 0.927102
BFGS: 30 14:38:42 -304.299559 0.647400
BFGS: 31 14:38:43 -304.318312 0.598038
BFGS: 32 14:38:43 -304.332055 0.531418
BFGS: 33 14:38:43 -304.351983 0.381692
BFGS: 34 14:38:44 -304.364935 0.210685
BFGS: 35 14:38:44 -304.370295 0.163325
BFGS: 36 14:38:44 -304.372588 0.134720
BFGS: 37 14:38:45 -304.374170 0.113980
BFGS: 38 14:38:45 -304.375695 0.103936
BFGS: 39 14:38:45 -304.377093 0.080994
BFGS: 40 14:38:46 -304.378072 0.049481
Step Time Energy fmax
BFGS: 0 14:38:46 -301.792413 1.292590
BFGS: 1 14:38:46 -301.833152 0.796622
BFGS: 2 14:38:47 -301.893569 0.913123
BFGS: 3 14:38:47 -301.968651 1.315026
BFGS: 4 14:38:47 -302.045521 1.261176
BFGS: 5 14:38:47 -302.090909 0.879043
BFGS: 6 14:38:48 -302.126141 0.727909
BFGS: 7 14:38:48 -302.170919 0.749468
BFGS: 8 14:38:48 -302.205032 0.455177
BFGS: 9 14:38:49 -302.216240 0.418685
BFGS: 10 14:38:49 -302.226014 0.312064
BFGS: 11 14:38:50 -302.236334 0.395817
BFGS: 12 14:38:50 -302.244991 0.413391
BFGS: 13 14:38:50 -302.253957 0.383613
BFGS: 14 14:38:50 -302.267990 0.468988
BFGS: 15 14:38:51 -302.296381 0.575772
BFGS: 16 14:38:51 -302.336692 0.879817
BFGS: 17 14:38:52 -302.377813 1.622337
BFGS: 18 14:38:52 -302.423107 2.268901
BFGS: 19 14:38:53 -302.492505 2.566045
BFGS: 20 14:38:53 -302.604507 2.544011
BFGS: 21 14:38:53 -302.729513 2.207606
BFGS: 22 14:38:54 -302.884903 2.197256
BFGS: 23 14:38:54 -302.988693 2.177725
BFGS: 24 14:38:54 -303.254745 1.802454
BFGS: 25 14:38:55 -303.654027 0.950313
BFGS: 26 14:38:55 -303.713239 0.840255
BFGS: 27 14:38:56 -303.755859 0.540389
BFGS: 28 14:38:56 -303.813317 0.737403
BFGS: 29 14:38:56 -303.849720 0.503118
BFGS: 30 14:38:57 -303.882135 0.366186
BFGS: 31 14:38:57 -303.896238 0.388399
BFGS: 32 14:38:57 -303.916154 0.356464
BFGS: 33 14:38:58 -303.927688 0.268527
BFGS: 34 14:38:58 -303.934456 0.186669
BFGS: 35 14:38:59 -303.937298 0.180750
BFGS: 36 14:38:59 -303.940613 0.230309
BFGS: 37 14:38:59 -303.944096 0.209566
BFGS: 38 14:38:59 -303.946654 0.134109
BFGS: 39 14:39:00 -303.948120 0.103130
BFGS: 40 14:39:00 -303.949148 0.096255
BFGS: 41 14:39:00 -303.950234 0.116658
BFGS: 42 14:39:01 -303.951383 0.109479
BFGS: 43 14:39:01 -303.952352 0.070243
BFGS: 44 14:39:02 -303.953001 0.073258
BFGS: 45 14:39:02 -303.953394 0.068397
BFGS: 46 14:39:02 -303.953658 0.043670
/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 14:40:52 -302.027848 3.861638
BFGS: 1 14:40:57 -302.132696 3.035465
BFGS: 2 14:40:59 -302.361480 4.677055
BFGS: 3 14:41:02 -302.437180 3.050082
BFGS: 4 14:41:09 -302.704260 2.653244
BFGS: 5 14:41:15 -302.733952 1.955491
BFGS: 6 14:41:21 -302.952850 1.754820
BFGS: 7 14:41:26 -303.240318 1.889017
BFGS: 8 14:41:29 -303.428603 1.891520
BFGS: 9 14:41:32 -303.586486 1.614780
BFGS: 10 14:41:35 -303.594469 0.896466
BFGS: 11 14:41:37 -303.614396 0.827935
BFGS: 12 14:41:40 -303.634497 0.652069
BFGS: 13 14:41:43 -303.649325 0.640359
BFGS: 14 14:41:46 -303.651440 0.429971
BFGS: 15 14:41:52 -303.654575 0.393471
BFGS: 16 14:41:55 -303.661757 0.383018
BFGS: 17 14:41:58 -303.665586 0.438979
BFGS: 18 14:42:06 -303.662918 0.405498
BFGS: 19 14:42:11 -303.656871 0.514399
BFGS: 20 14:42:15 -303.657332 0.560317
BFGS: 21 14:42:19 -303.669092 0.426420
BFGS: 22 14:42:21 -303.682420 0.473339
BFGS: 23 14:42:24 -303.694608 0.525485
BFGS: 24 14:42:30 -303.707916 0.758632
BFGS: 25 14:42:33 -303.725035 0.772365
BFGS: 26 14:42:37 -303.746564 0.697061
BFGS: 27 14:42:40 -303.768955 0.557241
BFGS: 28 14:42:43 -303.786329 0.609651
BFGS: 29 14:42:46 -303.802560 0.834109
BFGS: 30 14:42:49 -303.826465 0.706792
BFGS: 31 14:42:56 -303.834746 0.569183
BFGS: 32 14:42:59 -303.850385 0.603171
BFGS: 33 14:43:06 -303.849501 0.519760
BFGS: 34 14:43:14 -303.845257 0.515767
BFGS: 35 14:43:17 -303.834177 0.541043
BFGS: 36 14:43:22 -303.823002 0.585108
BFGS: 37 14:43:25 -303.818858 0.537403
BFGS: 38 14:43:33 -303.809356 0.496879
BFGS: 39 14:43:36 -303.785493 0.638126
BFGS: 40 14:43:40 -303.773293 0.613860
BFGS: 41 14:43:43 -303.767300 0.480851
BFGS: 42 14:43:46 -303.774030 0.516812
BFGS: 43 14:43:51 -303.806053 1.054386
BFGS: 44 14:43:55 -303.836238 0.856987
BFGS: 45 14:44:00 -303.843407 0.630899
BFGS: 46 14:44:03 -303.823073 0.568923
BFGS: 47 14:44:05 -303.810244 0.435899
BFGS: 48 14:44:08 -303.808304 0.365833
BFGS: 49 14:44:13 -303.811554 0.399260
BFGS: 50 14:44:17 -303.808831 0.447373
BFGS: 51 14:44:20 -303.792589 0.410908
BFGS: 52 14:44:23 -303.783874 0.318618
BFGS: 53 14:44:26 -303.786820 0.275229
BFGS: 54 14:44:29 -303.793996 0.272319
BFGS: 55 14:44:32 -303.800900 0.220861
BFGS: 56 14:44:35 -303.802993 0.181460
BFGS: 57 14:44:37 -303.803368 0.174288
BFGS: 58 14:44:39 -303.803004 0.215006
BFGS: 59 14:44:42 -303.803579 0.233530
BFGS: 60 14:44:48 -303.808620 0.235723
BFGS: 61 14:44:51 -303.816006 0.293806
BFGS: 62 14:44:58 -303.818168 0.330669
BFGS: 63 14:45:05 -303.809277 0.344470
BFGS: 64 14:45:11 -303.791335 0.321953
BFGS: 65 14:45:14 -303.790981 0.315044
BFGS: 66 14:45:18 -303.819595 0.466206
BFGS: 67 14:45:24 -303.794924 0.447568
BFGS: 68 14:45:31 -303.797679 0.307706
BFGS: 69 14:45:37 -303.814223 0.335722
BFGS: 70 14:45:43 -303.811291 0.277926
BFGS: 71 14:45:46 -303.803180 0.148700
BFGS: 72 14:45:52 -303.807610 0.175470
BFGS: 73 14:45:59 -303.804648 0.206165
BFGS: 74 14:46:01 -303.808746 0.293182
BFGS: 75 14:46:06 -303.831642 0.395264
BFGS: 76 14:46:13 -303.845874 0.371846
BFGS: 77 14:46:17 -303.823842 0.391829
BFGS: 78 14:46:23 -303.787821 0.540684
BFGS: 79 14:46:26 -303.851262 0.743461
BFGS: 80 14:46:28 -303.800030 0.863864
BFGS: 81 14:46:31 -303.763645 0.720983
BFGS: 82 14:46:34 -303.806600 0.600975
BFGS: 83 14:46:37 -303.856197 0.857847
BFGS: 84 14:46:40 -303.828172 0.401065
BFGS: 85 14:46:43 -303.806943 0.303652
BFGS: 86 14:46:47 -303.805090 0.187814
BFGS: 87 14:46:49 -303.803092 0.230895
BFGS: 88 14:46:52 -303.801072 0.677662
BFGS: 89 14:46:55 -303.807839 0.585589
BFGS: 90 14:47:01 -303.797745 0.297578
BFGS: 91 14:47:04 -303.803952 0.270654
BFGS: 92 14:47:10 -303.799523 0.794901
BFGS: 93 14:47:13 -303.804145 0.575943
BFGS: 94 14:47:16 -303.804107 0.435142
BFGS: 95 14:47:22 -303.803436 0.581452
BFGS: 96 14:47:25 -303.806258 0.538055
BFGS: 97 14:47:32 -303.808635 0.284298
BFGS: 98 14:47:35 -303.809229 0.226052
BFGS: 99 14:47:38 -303.809135 0.368623
BFGS: 100 14:47:40 -303.809135 0.399158
BFGS: 101 14:47:42 -303.809135 0.401495
BFGS: 102 14:47:45 -303.809135 0.250258
BFGS: 103 14:47:48 -303.809135 0.184776
BFGS: 104 14:47:49 -303.809135 0.180830
BFGS: 105 14:47:51 -303.809135 0.164363
BFGS: 106 14:47:52 -303.809135 0.171567
BFGS: 107 14:47:53 -303.809135 0.161018
BFGS: 108 14:47:54 -303.809135 0.112390
BFGS: 109 14:47:55 -303.809135 0.076098
BFGS: 110 14:47:57 -303.809135 0.073177
BFGS: 111 14:47:58 -303.809135 0.075340
BFGS: 112 14:48:02 -303.809135 0.079167
BFGS: 113 14:48:02 -303.809135 0.077145
BFGS: 114 14:48:03 -303.809135 0.074214
BFGS: 115 14:48:04 -303.809135 0.071684
BFGS: 116 14:48:06 -303.809135 0.086130
BFGS: 117 14:48:09 -303.809135 0.060826
BFGS: 118 14:48:13 -303.809135 0.052431
BFGS: 119 14:48:17 -303.809135 0.054688
BFGS: 120 14:48:20 -303.809135 0.072330
BFGS: 121 14:48:22 -303.809135 0.183119
BFGS: 122 14:48:23 -303.809135 0.083676
BFGS: 123 14:48:24 -303.809135 0.070688
BFGS: 124 14:48:29 -303.809135 0.056789
BFGS: 125 14:48:32 -303.809135 0.054949
BFGS: 126 14:48:33 -303.809135 0.092176
BFGS: 127 14:48:35 -303.809135 0.060555
BFGS: 128 14:48:36 -303.809135 0.064425
BFGS: 129 14:48:37 -303.809135 0.041264
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_9008/3247994494.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")