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())WARNING:root:Model is being compiled this might take a while for the first time
W0807 06:01:11.913000 10250 site-packages/torch/_logging/_internal.py:1345] [0/0] Profiler record function <class 'torch.autograd.profiler.record_function'> will be ignored
Step Time Energy fmax
BFGS: 0 06:01:52 -300.838022 4.023417
BFGS: 1 06:01:52 -301.273258 3.538600
BFGS: 2 06:01:52 -302.558064 3.552249
BFGS: 3 06:01:53 -302.432381 7.988595
BFGS: 4 06:01:53 -302.876054 2.871682
BFGS: 5 06:01:53 -303.037015 1.669553
BFGS: 6 06:01:53 -303.105178 1.642590
BFGS: 7 06:01:53 -303.124400 0.601689
BFGS: 8 06:01:53 -303.135510 0.459521
BFGS: 9 06:01:54 -303.152861 0.707976
BFGS: 10 06:01:54 -303.167659 0.590608
BFGS: 11 06:01:54 -303.175391 0.297577
BFGS: 12 06:01:54 -303.178629 0.211325
BFGS: 13 06:01:54 -303.182392 0.474062
BFGS: 14 06:01:55 -303.189093 0.712708
BFGS: 15 06:01:55 -303.196966 0.698255
BFGS: 16 06:01:55 -303.202902 0.425558
BFGS: 17 06:01:55 -303.206493 0.215972
BFGS: 18 06:01:56 -303.209868 0.337431
BFGS: 19 06:01:56 -303.215348 0.577856
BFGS: 20 06:01:56 -303.224070 0.727325
BFGS: 21 06:01:56 -303.232891 0.624229
BFGS: 22 06:01:57 -303.244600 0.467837
BFGS: 23 06:01:57 -303.293469 1.368284
BFGS: 24 06:01:57 -303.297295 3.649530
BFGS: 25 06:01:57 -303.513140 4.534250
BFGS: 26 06:01:58 -303.504336 3.371482
BFGS: 27 06:01:58 -303.751547 1.363859
BFGS: 28 06:01:58 -303.797578 1.478744
BFGS: 29 06:01:58 -304.001085 1.632236
BFGS: 30 06:01:58 -304.093217 1.560257
BFGS: 31 06:01:58 -304.148551 1.020475
BFGS: 32 06:01:58 -304.234445 0.866132
BFGS: 33 06:01:59 -304.286498 1.356217
BFGS: 34 06:01:59 -304.378216 1.949559
BFGS: 35 06:01:59 -304.435151 1.645145
BFGS: 36 06:01:59 -304.534643 0.500014
BFGS: 37 06:02:00 -304.557297 0.536073
BFGS: 38 06:02:00 -304.583996 0.423930
BFGS: 39 06:02:00 -304.593829 0.339243
BFGS: 40 06:02:00 -304.611276 0.342454
BFGS: 41 06:02:00 -304.625231 0.333284
BFGS: 42 06:02:00 -304.631628 0.309478
BFGS: 43 06:02:01 -304.635931 0.294951
BFGS: 44 06:02:01 -304.640720 0.286561
BFGS: 45 06:02:01 -304.646815 0.269148
BFGS: 46 06:02:01 -304.652131 0.244239
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BFGS: 48 06:02:02 -304.656979 0.248033
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BFGS: 50 06:02:02 -304.662473 0.244234
BFGS: 51 06:02:02 -304.665532 0.222609
BFGS: 52 06:02:02 -304.667344 0.199626
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BFGS: 54 06:02:02 -304.668754 0.176084
BFGS: 55 06:02:03 -304.669559 0.166649
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BFGS: 57 06:02:03 -304.671124 0.149531
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BFGS: 60 06:02:04 -304.671642 0.149706
BFGS: 61 06:02:04 -304.671858 0.150525
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BFGS: 63 06:02:04 -304.672201 0.148300
BFGS: 64 06:02:04 -304.672244 0.148016
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BFGS: 291 06:02:52 -304.672452 0.154014
BFGS: 292 06:02:52 -304.672451 0.154031
BFGS: 293 06:02:52 -304.672452 0.154011
BFGS: 294 06:02:52 -304.672452 0.154032
BFGS: 295 06:02:53 -304.672452 0.154035
BFGS: 296 06:02:53 -304.672452 0.154030
BFGS: 297 06:02:53 -304.672451 0.154032
BFGS: 298 06:02:53 -304.672451 0.154032
BFGS: 299 06:02:54 -304.672452 0.154033
BFGS: 300 06:02:54 -304.672452 0.154034
Step Time Energy fmax
BFGS: 0 06:02:54 -300.910567 4.028409
BFGS: 1 06:02:54 -301.333176 3.389309
BFGS: 2 06:02:54 -302.563259 3.540238
BFGS: 3 06:02:54 -302.512792 7.001301
BFGS: 4 06:02:55 -302.898336 2.743906
BFGS: 5 06:02:55 -303.064188 1.131793
BFGS: 6 06:02:55 -303.107116 1.306989
BFGS: 7 06:02:55 -303.124334 0.646400
BFGS: 8 06:02:55 -303.144994 0.816525
BFGS: 9 06:02:55 -303.164295 0.881376
BFGS: 10 06:02:56 -303.183148 0.531376
BFGS: 11 06:02:56 -303.189440 0.251408
BFGS: 12 06:02:56 -303.193702 0.337449
BFGS: 13 06:02:56 -303.199049 0.600099
BFGS: 14 06:02:56 -303.207739 0.746184
BFGS: 15 06:02:56 -303.215701 0.608257
BFGS: 16 06:02:56 -303.221559 0.367534
BFGS: 17 06:02:56 -303.227287 0.390609
BFGS: 18 06:02:56 -303.237884 0.792698
BFGS: 19 06:02:57 -303.275169 1.758985
BFGS: 20 06:02:57 -303.318673 2.857349
BFGS: 21 06:02:57 -303.311640 3.478317
BFGS: 22 06:02:57 -303.351615 3.096053
BFGS: 23 06:02:57 -303.376018 3.174458
BFGS: 24 06:02:57 -303.483490 3.145168
BFGS: 25 06:02:57 -303.434989 2.888582
BFGS: 26 06:02:58 -303.608950 2.381844
BFGS: 27 06:02:58 -303.681610 2.252091
BFGS: 28 06:02:58 -303.868926 1.449035
BFGS: 29 06:02:58 -303.905032 1.698607
BFGS: 30 06:02:58 -303.964853 1.863614
BFGS: 31 06:02:58 -304.030282 2.432426
BFGS: 32 06:02:58 -304.103455 1.863308
BFGS: 33 06:02:58 -304.136819 1.663710
BFGS: 34 06:02:58 -304.188013 1.450668
BFGS: 35 06:02:58 -304.226963 1.306616
BFGS: 36 06:02:58 -304.331865 0.993405
BFGS: 37 06:02:58 -304.374656 1.107978
BFGS: 38 06:02:59 -304.424308 1.475304
BFGS: 39 06:02:59 -304.451951 1.690536
BFGS: 40 06:02:59 -304.484413 1.881930
BFGS: 41 06:03:00 -304.508809 1.927338
BFGS: 42 06:03:00 -304.523170 1.869796
BFGS: 43 06:03:00 -304.529782 1.805146
BFGS: 44 06:03:00 -304.537834 1.698215
BFGS: 45 06:03:00 -304.543186 1.597008
BFGS: 46 06:03:01 -304.546371 1.530934
BFGS: 47 06:03:01 -304.548508 1.499949
BFGS: 48 06:03:01 -304.550610 1.483238
BFGS: 49 06:03:01 -304.552966 1.470053
BFGS: 50 06:03:02 -304.555383 1.456789
BFGS: 51 06:03:02 -304.557269 1.443870
BFGS: 52 06:03:02 -304.558756 1.426984
BFGS: 53 06:03:03 -304.560452 1.396486
BFGS: 54 06:03:03 -304.562529 1.344517
BFGS: 55 06:03:03 -304.564321 1.288577
BFGS: 56 06:03:03 -304.565401 1.256626
BFGS: 57 06:03:04 -304.566122 1.245967
BFGS: 58 06:03:04 -304.566875 1.242585
BFGS: 59 06:03:04 -304.567635 1.240198
BFGS: 60 06:03:05 -304.568166 1.234728
BFGS: 61 06:03:05 -304.568443 1.225842
BFGS: 62 06:03:05 -304.568639 1.214561
BFGS: 63 06:03:05 -304.568855 1.199059
BFGS: 64 06:03:06 -304.569088 1.181301
BFGS: 65 06:03:06 -304.569270 1.169922
BFGS: 66 06:03:06 -304.569376 1.169043
BFGS: 67 06:03:06 -304.569447 1.174409
BFGS: 68 06:03:07 -304.569525 1.183782
BFGS: 69 06:03:07 -304.569612 1.195953
BFGS: 70 06:03:07 -304.569688 1.205832
BFGS: 71 06:03:07 -304.569728 1.208699
BFGS: 72 06:03:07 -304.569754 1.207131
BFGS: 73 06:03:08 -304.569772 1.204671
BFGS: 74 06:03:08 -304.569790 1.202154
BFGS: 75 06:03:08 -304.569805 1.200988
BFGS: 76 06:03:08 -304.569818 1.201524
BFGS: 77 06:03:09 -304.569823 1.203000
BFGS: 78 06:03:09 -304.569826 1.204573
BFGS: 79 06:03:09 -304.569831 1.206151
BFGS: 80 06:03:09 -304.569838 1.207607
BFGS: 81 06:03:10 -304.569843 1.208145
BFGS: 82 06:03:10 -304.569845 1.207645
BFGS: 83 06:03:10 -304.569849 1.206740
BFGS: 84 06:03:10 -304.569851 1.206017
BFGS: 85 06:03:11 -304.569851 1.205129
BFGS: 86 06:03:11 -304.569855 1.204586
BFGS: 87 06:03:11 -304.569860 1.204712
BFGS: 88 06:03:11 -304.569858 1.205152
BFGS: 89 06:03:11 -304.569858 1.205531
BFGS: 90 06:03:12 -304.569857 1.205811
BFGS: 91 06:03:12 -304.569860 1.205956
BFGS: 92 06:03:12 -304.569860 1.205922
BFGS: 93 06:03:12 -304.569861 1.205767
BFGS: 94 06:03:12 -304.569860 1.205675
BFGS: 95 06:03:13 -304.569859 1.205568
BFGS: 96 06:03:13 -304.569861 1.205433
BFGS: 97 06:03:13 -304.569860 1.205462
BFGS: 98 06:03:13 -304.569860 1.205488
BFGS: 99 06:03:14 -304.569860 1.205499
BFGS: 100 06:03:14 -304.569860 1.205526
BFGS: 101 06:03:14 -304.569859 1.205547
BFGS: 102 06:03:14 -304.569859 1.205567
BFGS: 103 06:03:14 -304.569859 1.205499
BFGS: 104 06:03:14 -304.569859 1.205531
BFGS: 105 06:03:15 -304.569860 1.205509
BFGS: 106 06:03:15 -304.569861 1.205417
BFGS: 107 06:03:15 -304.569860 1.205479
BFGS: 108 06:03:15 -304.569860 1.205467
BFGS: 109 06:03:15 -304.569859 1.205462
BFGS: 110 06:03:15 -304.569861 1.205412
BFGS: 111 06:03:15 -304.569860 1.205454
BFGS: 112 06:03:16 -304.569859 1.205515
BFGS: 113 06:03:16 -304.569859 1.205470
BFGS: 114 06:03:16 -304.569860 1.205462
BFGS: 115 06:03:16 -304.569861 1.205450
BFGS: 116 06:03:16 -304.569860 1.205566
BFGS: 117 06:03:16 -304.569860 1.205521
BFGS: 118 06:03:17 -304.569859 1.205513
BFGS: 119 06:03:17 -304.569860 1.205455
BFGS: 120 06:03:17 -304.569858 1.205516
BFGS: 121 06:03:17 -304.569860 1.205476
BFGS: 122 06:03:17 -304.569859 1.205456
BFGS: 123 06:03:17 -304.569859 1.205452
BFGS: 124 06:03:18 -304.569858 1.205480
BFGS: 125 06:03:18 -304.569859 1.205490
BFGS: 126 06:03:18 -304.569859 1.205409
BFGS: 127 06:03:18 -304.569859 1.205445
BFGS: 128 06:03:19 -304.569860 1.205486
BFGS: 129 06:03:19 -304.569860 1.205474
BFGS: 130 06:03:19 -304.569860 1.205447
BFGS: 131 06:03:19 -304.569859 1.205465
BFGS: 132 06:03:19 -304.569860 1.205481
BFGS: 133 06:03:19 -304.569860 1.205426
BFGS: 134 06:03:20 -304.569860 1.205447
BFGS: 135 06:03:20 -304.569860 1.205450
BFGS: 136 06:03:20 -304.569860 1.205469
BFGS: 137 06:03:20 -304.569861 1.205417
BFGS: 138 06:03:21 -304.569860 1.205452
BFGS: 139 06:03:21 -304.569860 1.205426
BFGS: 140 06:03:21 -304.569860 1.205454
BFGS: 141 06:03:21 -304.569860 1.205455
BFGS: 142 06:03:22 -304.569860 1.205489
BFGS: 143 06:03:22 -304.569859 1.205485
BFGS: 144 06:03:22 -304.569859 1.205461
BFGS: 145 06:03:22 -304.569861 1.205457
BFGS: 146 06:03:22 -304.569861 1.205440
BFGS: 147 06:03:22 -304.569859 1.205483
BFGS: 148 06:03:23 -304.569860 1.205430
BFGS: 149 06:03:23 -304.569860 1.205449
BFGS: 150 06:03:23 -304.569859 1.205480
BFGS: 151 06:03:23 -304.569860 1.205478
BFGS: 152 06:03:23 -304.569857 1.205499
BFGS: 153 06:03:23 -304.569860 1.205450
BFGS: 154 06:03:24 -304.569859 1.205511
BFGS: 155 06:03:24 -304.569859 1.205488
BFGS: 156 06:03:24 -304.569858 1.205485
BFGS: 157 06:03:24 -304.569860 1.205453
BFGS: 158 06:03:25 -304.569859 1.205484
BFGS: 159 06:03:25 -304.569858 1.205521
BFGS: 160 06:03:25 -304.569859 1.205455
BFGS: 161 06:03:25 -304.569860 1.205444
BFGS: 162 06:03:25 -304.569860 1.205643
BFGS: 163 06:03:26 -304.569860 1.205486
BFGS: 164 06:03:26 -304.569860 1.205444
BFGS: 165 06:03:26 -304.569860 1.205460
BFGS: 166 06:03:26 -304.569860 1.205472
BFGS: 167 06:03:27 -304.569860 1.205468
BFGS: 168 06:03:27 -304.569860 1.205446
BFGS: 169 06:03:27 -304.569861 1.205462
BFGS: 170 06:03:27 -304.569860 1.205466
BFGS: 171 06:03:28 -304.569860 1.205451
BFGS: 172 06:03:28 -304.569859 1.205467
BFGS: 173 06:03:28 -304.569861 1.205469
BFGS: 174 06:03:28 -304.569860 1.205464
BFGS: 175 06:03:29 -304.569861 1.205453
BFGS: 176 06:03:29 -304.569858 1.205510
BFGS: 177 06:03:29 -304.569860 1.205464
BFGS: 178 06:03:29 -304.569860 1.205465
BFGS: 179 06:03:30 -304.569859 1.205465
BFGS: 180 06:03:30 -304.569860 1.205455
BFGS: 181 06:03:30 -304.569861 1.205474
BFGS: 182 06:03:31 -304.569860 1.205486
BFGS: 183 06:03:31 -304.569860 1.205452
BFGS: 184 06:03:31 -304.569860 1.205449
BFGS: 185 06:03:32 -304.569860 1.205469
BFGS: 186 06:03:32 -304.569860 1.205474
BFGS: 187 06:03:32 -304.569858 1.205507
BFGS: 188 06:03:32 -304.569860 1.205450
BFGS: 189 06:03:32 -304.569859 1.205480
BFGS: 190 06:03:33 -304.569860 1.205475
BFGS: 191 06:03:33 -304.569860 1.205450
BFGS: 192 06:03:33 -304.569858 1.205508
BFGS: 193 06:03:33 -304.569858 1.205516
BFGS: 194 06:03:34 -304.569861 1.205421
BFGS: 195 06:03:34 -304.569860 1.205488
BFGS: 196 06:03:34 -304.569859 1.205509
BFGS: 197 06:03:34 -304.569860 1.205448
BFGS: 198 06:03:35 -304.569859 1.205488
BFGS: 199 06:03:35 -304.569862 1.205413
BFGS: 200 06:03:35 -304.569858 1.205510
BFGS: 201 06:03:35 -304.569861 1.205465
BFGS: 202 06:03:36 -304.569861 1.205458
BFGS: 203 06:03:36 -304.569860 1.205466
BFGS: 204 06:03:36 -304.569860 1.205487
BFGS: 205 06:03:36 -304.569860 1.205460
BFGS: 206 06:03:36 -304.569860 1.205465
BFGS: 207 06:03:36 -304.569859 1.205480
BFGS: 208 06:03:37 -304.569861 1.205454
BFGS: 209 06:03:37 -304.569860 1.205450
BFGS: 210 06:03:37 -304.569859 1.205526
BFGS: 211 06:03:37 -304.569860 1.205486
BFGS: 212 06:03:38 -304.569860 1.205487
BFGS: 213 06:03:38 -304.569860 1.205452
BFGS: 214 06:03:38 -304.569860 1.205450
BFGS: 215 06:03:38 -304.569859 1.205478
BFGS: 216 06:03:38 -304.569859 1.205487
BFGS: 217 06:03:39 -304.569859 1.205479
BFGS: 218 06:03:39 -304.569860 1.205453
BFGS: 219 06:03:39 -304.569860 1.205482
BFGS: 220 06:03:39 -304.569859 1.205488
BFGS: 221 06:03:39 -304.569859 1.205466
BFGS: 222 06:03:39 -304.569861 1.205453
BFGS: 223 06:03:40 -304.569859 1.205486
BFGS: 224 06:03:40 -304.569860 1.205463
BFGS: 225 06:03:40 -304.569860 1.205461
BFGS: 226 06:03:40 -304.569860 1.205476
BFGS: 227 06:03:40 -304.569861 1.205477
BFGS: 228 06:03:40 -304.569859 1.205476
BFGS: 229 06:03:40 -304.569860 1.205452
BFGS: 230 06:03:41 -304.569860 1.205486
BFGS: 231 06:03:41 -304.569861 1.205465
BFGS: 232 06:03:41 -304.569860 1.205454
BFGS: 233 06:03:41 -304.569861 1.205453
BFGS: 234 06:03:41 -304.569859 1.205493
BFGS: 235 06:03:41 -304.569859 1.205479
BFGS: 236 06:03:42 -304.569860 1.205452
BFGS: 237 06:03:42 -304.569860 1.205460
BFGS: 238 06:03:42 -304.569859 1.205487
BFGS: 239 06:03:42 -304.569859 1.205514
BFGS: 240 06:03:43 -304.569860 1.205454
BFGS: 241 06:03:43 -304.569861 1.205453
BFGS: 242 06:03:43 -304.569858 1.205505
BFGS: 243 06:03:43 -304.569859 1.205488
BFGS: 244 06:03:43 -304.569860 1.205450
BFGS: 245 06:03:43 -304.569860 1.205465
BFGS: 246 06:03:44 -304.569860 1.205474
BFGS: 247 06:03:44 -304.569858 1.205521
BFGS: 248 06:03:44 -304.569861 1.205454
BFGS: 249 06:03:44 -304.569860 1.205450
BFGS: 250 06:03:44 -304.569860 1.205487
BFGS: 251 06:03:44 -304.569859 1.205490
BFGS: 252 06:03:45 -304.569861 1.205373
BFGS: 253 06:03:45 -304.569860 1.205454
BFGS: 254 06:03:45 -304.569859 1.205479
BFGS: 255 06:03:45 -304.569860 1.205450
BFGS: 256 06:03:45 -304.569860 1.205464
BFGS: 257 06:03:46 -304.569859 1.205487
BFGS: 258 06:03:46 -304.569859 1.205476
BFGS: 259 06:03:46 -304.569860 1.205449
BFGS: 260 06:03:46 -304.569860 1.205461
BFGS: 261 06:03:47 -304.569860 1.205480
BFGS: 262 06:03:47 -304.569859 1.205488
BFGS: 263 06:03:47 -304.569861 1.205425
BFGS: 264 06:03:47 -304.569860 1.205461
BFGS: 265 06:03:48 -304.569860 1.205476
BFGS: 266 06:03:48 -304.569860 1.205461
BFGS: 267 06:03:48 -304.569860 1.205454
BFGS: 268 06:03:48 -304.569858 1.205508
BFGS: 269 06:03:48 -304.569860 1.205479
BFGS: 270 06:03:49 -304.569859 1.205458
BFGS: 271 06:03:49 -304.569860 1.205450
BFGS: 272 06:03:49 -304.569860 1.205624
BFGS: 273 06:03:49 -304.569860 1.205471
BFGS: 274 06:03:49 -304.569860 1.205461
BFGS: 275 06:03:49 -304.569860 1.205476
BFGS: 276 06:03:49 -304.569860 1.205450
BFGS: 277 06:03:49 -304.569859 1.205513
BFGS: 278 06:03:50 -304.569861 1.205451
BFGS: 279 06:03:50 -304.569859 1.205479
BFGS: 280 06:03:50 -304.569859 1.205489
BFGS: 281 06:03:51 -304.569860 1.205484
BFGS: 282 06:03:51 -304.569860 1.205462
BFGS: 283 06:03:51 -304.569860 1.205462
BFGS: 284 06:03:52 -304.569860 1.205479
BFGS: 285 06:03:52 -304.569860 1.205488
BFGS: 286 06:03:52 -304.569860 1.205455
BFGS: 287 06:03:52 -304.569859 1.205460
BFGS: 288 06:03:52 -304.569860 1.205477
BFGS: 289 06:03:53 -304.569860 1.205460
BFGS: 290 06:03:53 -304.569860 1.205463
BFGS: 291 06:03:53 -304.569860 1.205478
BFGS: 292 06:03:53 -304.569861 1.205456
BFGS: 293 06:03:54 -304.569860 1.205459
BFGS: 294 06:03:54 -304.569857 1.205524
BFGS: 295 06:03:54 -304.569860 1.205492
BFGS: 296 06:03:54 -304.569860 1.205482
BFGS: 297 06:03:54 -304.569861 1.205442
BFGS: 298 06:03:55 -304.569859 1.205451
BFGS: 299 06:03:55 -304.569859 1.205485
BFGS: 300 06:03:55 -304.569860 1.205482
Step Time Energy fmax
BFGS: 0 06:03:55 -302.025906 4.113877
BFGS: 1 06:03:55 -302.400766 3.419341
BFGS: 2 06:03:56 -303.353894 3.034330
BFGS: 3 06:03:56 -303.549521 3.643747
BFGS: 4 06:03:56 -303.804604 2.225130
BFGS: 5 06:03:57 -304.063229 2.005272
BFGS: 6 06:03:57 -304.136304 1.337155
BFGS: 7 06:03:57 -304.318577 1.343392
BFGS: 8 06:03:57 -304.374679 1.198864
BFGS: 9 06:03:58 -304.479103 0.881998
BFGS: 10 06:03:58 -304.551071 1.079744
BFGS: 11 06:03:58 -304.590019 0.837057
BFGS: 12 06:03:58 -304.609186 0.396832
BFGS: 13 06:03:59 -304.620440 0.406863
BFGS: 14 06:03:59 -304.631227 0.380543
BFGS: 15 06:03:59 -304.641518 0.299389
BFGS: 16 06:03:59 -304.646718 0.200116
BFGS: 17 06:03:59 -304.650582 0.223963
BFGS: 18 06:03:59 -304.656050 0.198787
BFGS: 19 06:04:00 -304.661910 0.231445
BFGS: 20 06:04:00 -304.667053 0.223631
BFGS: 21 06:04:00 -304.670556 0.154980
BFGS: 22 06:04:00 -304.672757 0.152607
BFGS: 23 06:04:00 -304.674682 0.144859
BFGS: 24 06:04:01 -304.676856 0.146920
BFGS: 25 06:04:01 -304.678578 0.119697
BFGS: 26 06:04:01 -304.679372 0.078134
BFGS: 27 06:04:01 -304.679832 0.049260
Step Time Energy fmax
BFGS: 0 06:04:01 -301.047873 3.942823
BFGS: 1 06:04:01 -301.451043 3.414082
BFGS: 2 06:04:02 -302.647691 3.311024
BFGS: 3 06:04:02 -302.413780 8.696511
BFGS: 4 06:04:02 -302.945255 2.696805
BFGS: 5 06:04:02 -303.069912 1.866902
BFGS: 6 06:04:02 -303.163904 1.655128
BFGS: 7 06:04:03 -303.187699 0.647405
BFGS: 8 06:04:03 -303.211482 0.741645
BFGS: 9 06:04:03 -303.276804 1.224751
BFGS: 10 06:04:03 -303.327988 1.490158
BFGS: 11 06:04:03 -303.399523 1.320032
BFGS: 12 06:04:04 -303.538042 1.529983
BFGS: 13 06:04:04 -303.726881 2.306975
BFGS: 14 06:04:04 -303.894174 2.875420
BFGS: 15 06:04:04 -303.982264 1.032227
BFGS: 16 06:04:05 -304.107527 1.231407
BFGS: 17 06:04:05 -304.141529 0.808409
BFGS: 18 06:04:05 -304.174224 0.450053
BFGS: 19 06:04:06 -304.196928 0.388990
BFGS: 20 06:04:06 -304.213057 0.391286
BFGS: 21 06:04:06 -304.225677 0.406526
BFGS: 22 06:04:06 -304.240410 0.422982
BFGS: 23 06:04:07 -304.253870 0.375636
BFGS: 24 06:04:07 -304.270199 0.362865
BFGS: 25 06:04:07 -304.291109 0.447887
BFGS: 26 06:04:07 -304.315614 0.505572
BFGS: 27 06:04:07 -304.331744 0.350960
BFGS: 28 06:04:07 -304.339491 0.170123
BFGS: 29 06:04:07 -304.342964 0.143671
BFGS: 30 06:04:08 -304.346420 0.142930
BFGS: 31 06:04:08 -304.348839 0.116816
BFGS: 32 06:04:08 -304.349993 0.093167
BFGS: 33 06:04:08 -304.350468 0.064676
BFGS: 34 06:04:09 -304.350776 0.053567
BFGS: 35 06:04:09 -304.351140 0.047620
Step Time Energy fmax
BFGS: 0 06:04:09 -301.769321 4.059536
BFGS: 1 06:04:09 -302.152683 3.103932
BFGS: 2 06:04:09 -303.147904 3.366969
BFGS: 3 06:04:09 -303.330555 3.646605
BFGS: 4 06:04:10 -303.629621 2.183524
BFGS: 5 06:04:10 -303.821471 2.540524
BFGS: 6 06:04:10 -303.907458 1.120971
BFGS: 7 06:04:11 -303.971179 0.628765
BFGS: 8 06:04:11 -304.037287 0.965302
BFGS: 9 06:04:11 -304.065462 0.859786
BFGS: 10 06:04:11 -304.124772 0.650437
BFGS: 11 06:04:12 -304.153480 0.621901
BFGS: 12 06:04:12 -304.168608 0.287734
BFGS: 13 06:04:12 -304.172744 0.257206
BFGS: 14 06:04:12 -304.178369 0.256655
BFGS: 15 06:04:13 -304.182860 0.295840
BFGS: 16 06:04:13 -304.186056 0.225321
BFGS: 17 06:04:13 -304.187723 0.168653
BFGS: 18 06:04:13 -304.189811 0.207086
BFGS: 19 06:04:13 -304.194263 0.336868
BFGS: 20 06:04:14 -304.206328 0.473758
BFGS: 21 06:04:14 -304.169662 0.784737
BFGS: 22 06:04:14 -304.218104 0.504974
BFGS: 23 06:04:14 -304.224779 0.376389
BFGS: 24 06:04:14 -304.230570 0.980599
BFGS: 25 06:04:14 -304.251430 0.406837
BFGS: 26 06:04:15 -304.259321 0.452267
BFGS: 27 06:04:15 -304.285957 0.596199
BFGS: 28 06:04:15 -304.299905 0.414816
BFGS: 29 06:04:16 -304.308590 0.287249
BFGS: 30 06:04:16 -304.321116 0.366262
BFGS: 31 06:04:16 -304.327310 0.388160
BFGS: 32 06:04:16 -304.334863 0.270310
BFGS: 33 06:04:17 -304.340172 0.173091
BFGS: 34 06:04:17 -304.343925 0.142284
BFGS: 35 06:04:17 -304.346347 0.144111
BFGS: 36 06:04:17 -304.348725 0.127295
BFGS: 37 06:04:18 -304.350704 0.093319
BFGS: 38 06:04:18 -304.351632 0.087106
BFGS: 39 06:04:18 -304.351995 0.066315
BFGS: 40 06:04:18 -304.352231 0.044475
Step Time Energy fmax
BFGS: 0 06:04:18 -302.289282 4.013744
BFGS: 1 06:04:19 -302.660151 2.987756
BFGS: 2 06:04:19 -303.505510 3.183205
BFGS: 3 06:04:19 -303.654528 2.750792
BFGS: 4 06:04:20 -303.861576 3.183772
BFGS: 5 06:04:20 -303.950228 0.985463
BFGS: 6 06:04:20 -303.988121 0.765927
BFGS: 7 06:04:20 -304.092514 0.641555
BFGS: 8 06:04:21 -304.108988 0.564908
BFGS: 9 06:04:21 -304.148047 0.466100
BFGS: 10 06:04:21 -304.160055 0.237813
BFGS: 11 06:04:21 -304.165963 0.295305
BFGS: 12 06:04:22 -304.170449 0.296317
BFGS: 13 06:04:22 -304.176246 0.243129
BFGS: 14 06:04:22 -304.180852 0.211019
BFGS: 15 06:04:22 -304.184712 0.240420
BFGS: 16 06:04:23 -304.189118 0.281412
BFGS: 17 06:04:23 -304.195983 0.302350
BFGS: 18 06:04:23 -304.205559 0.332896
BFGS: 19 06:04:23 -304.216178 0.393826
BFGS: 20 06:04:23 -304.229538 0.357986
BFGS: 21 06:04:24 -304.241774 0.341578
BFGS: 22 06:04:24 -304.252983 0.366865
BFGS: 23 06:04:24 -304.265058 0.364449
BFGS: 24 06:04:24 -304.273949 0.354510
BFGS: 25 06:04:24 -304.278064 0.458135
BFGS: 26 06:04:24 -304.291031 0.314672
BFGS: 27 06:04:24 -304.304095 0.309503
BFGS: 28 06:04:24 -304.325970 0.265964
BFGS: 29 06:04:24 -304.333424 0.194205
BFGS: 30 06:04:25 -304.337256 0.167376
BFGS: 31 06:04:25 -304.340564 0.170111
BFGS: 32 06:04:25 -304.345212 0.207818
BFGS: 33 06:04:25 -304.348749 0.187889
BFGS: 34 06:04:25 -304.350494 0.089084
BFGS: 35 06:04:26 -304.351097 0.043908
Step Time Energy fmax
BFGS: 0 06:04:26 -300.800787 4.121179
BFGS: 1 06:04:26 -301.237382 3.462191
BFGS: 2 06:04:26 -302.482758 3.567736
BFGS: 3 06:04:27 -302.420692 7.358453
BFGS: 4 06:04:27 -302.828711 2.817835
BFGS: 5 06:04:27 -303.017830 1.216388
BFGS: 6 06:04:27 -303.076861 1.571333
BFGS: 7 06:04:27 -303.101557 0.780421
BFGS: 8 06:04:28 -303.129493 0.872613
BFGS: 9 06:04:28 -303.151300 0.893813
BFGS: 10 06:04:28 -303.168881 0.547549
BFGS: 11 06:04:28 -303.173229 0.202443
BFGS: 12 06:04:29 -303.174721 0.173196
BFGS: 13 06:04:29 -303.176496 0.328419
BFGS: 14 06:04:29 -303.179407 0.404459
BFGS: 15 06:04:29 -303.181487 0.283696
BFGS: 16 06:04:29 -303.182490 0.116172
BFGS: 17 06:04:30 -303.183136 0.114343
BFGS: 18 06:04:30 -303.184057 0.166999
BFGS: 19 06:04:30 -303.185365 0.230079
BFGS: 20 06:04:30 -303.186533 0.167246
BFGS: 21 06:04:30 -303.187052 0.070845
BFGS: 22 06:04:31 -303.187281 0.059475
BFGS: 23 06:04:31 -303.187541 0.113966
BFGS: 24 06:04:31 -303.187972 0.161062
BFGS: 25 06:04:31 -303.188477 0.144014
BFGS: 26 06:04:32 -303.188825 0.065327
BFGS: 27 06:04:32 -303.188998 0.043485
Step Time Energy fmax
BFGS: 0 06:04:32 -301.416120 4.086193
BFGS: 1 06:04:32 -301.802232 3.010670
BFGS: 2 06:04:32 -302.790446 3.503050
BFGS: 3 06:04:33 -302.941459 3.279169
BFGS: 4 06:04:33 -303.257996 1.675472
BFGS: 5 06:04:33 -303.346625 2.626103
BFGS: 6 06:04:33 -303.424444 2.001003
BFGS: 7 06:04:33 -303.830131 1.435999
BFGS: 8 06:04:33 -303.925942 2.179024
BFGS: 9 06:04:34 -304.009284 1.477225
BFGS: 10 06:04:34 -304.072730 0.821377
BFGS: 11 06:04:34 -304.175492 1.444009
BFGS: 12 06:04:34 -304.213441 1.057112
BFGS: 13 06:04:35 -304.318007 0.910095
BFGS: 14 06:04:35 -304.351287 0.997354
BFGS: 15 06:04:35 -304.422819 1.181865
BFGS: 16 06:04:35 -304.478234 0.996168
BFGS: 17 06:04:36 -304.536629 0.650104
BFGS: 18 06:04:36 -304.549117 0.667181
BFGS: 19 06:04:36 -304.566548 0.434377
BFGS: 20 06:04:36 -304.598579 0.425833
BFGS: 21 06:04:37 -304.606947 0.327104
BFGS: 22 06:04:37 -304.615688 0.306691
BFGS: 23 06:04:37 -304.624967 0.310458
BFGS: 24 06:04:37 -304.639438 0.412035
BFGS: 25 06:04:38 -304.653240 0.372208
BFGS: 26 06:04:38 -304.662343 0.246436
BFGS: 27 06:04:38 -304.666856 0.194110
BFGS: 28 06:04:38 -304.670053 0.143268
BFGS: 29 06:04:38 -304.673589 0.209811
BFGS: 30 06:04:39 -304.677131 0.180671
BFGS: 31 06:04:39 -304.679006 0.089486
BFGS: 32 06:04:39 -304.679670 0.060632
BFGS: 33 06:04:39 -304.680130 0.056901
BFGS: 34 06:04:40 -304.680684 0.084827
BFGS: 35 06:04:40 -304.681221 0.076163
BFGS: 36 06:04:40 -304.681552 0.036814
Step Time Energy fmax
BFGS: 0 06:04:40 -302.548731 4.023789
BFGS: 1 06:04:40 -302.916215 3.084215
BFGS: 2 06:04:41 -303.736672 2.959367
BFGS: 3 06:04:41 -303.894076 2.519997
BFGS: 4 06:04:41 -304.159273 1.693313
BFGS: 5 06:04:41 -304.233885 1.321023
BFGS: 6 06:04:42 -304.516063 0.872872
BFGS: 7 06:04:42 -304.551282 0.921178
BFGS: 8 06:04:42 -304.604433 0.754346
BFGS: 9 06:04:42 -304.643327 0.468161
BFGS: 10 06:04:43 -304.658486 0.352713
BFGS: 11 06:04:43 -304.663756 0.241846
BFGS: 12 06:04:43 -304.667318 0.174625
BFGS: 13 06:04:43 -304.671250 0.140421
BFGS: 14 06:04:43 -304.673271 0.116229
BFGS: 15 06:04:43 -304.674060 0.089801
BFGS: 16 06:04:43 -304.674687 0.091035
BFGS: 17 06:04:44 -304.675722 0.120579
BFGS: 18 06:04:44 -304.677029 0.114259
BFGS: 19 06:04:44 -304.678120 0.090089
BFGS: 20 06:04:44 -304.678741 0.079343
BFGS: 21 06:04:44 -304.679229 0.078983
BFGS: 22 06:04:45 -304.679864 0.103294
BFGS: 23 06:04:45 -304.680563 0.096900
BFGS: 24 06:04:45 -304.681027 0.061776
BFGS: 25 06:04:45 -304.681226 0.036388
Step Time Energy fmax
BFGS: 0 06:04:45 -301.295804 4.135736
BFGS: 1 06:04:46 -301.683974 3.121443
BFGS: 2 06:04:46 -302.689656 3.497726
BFGS: 3 06:04:46 -302.814954 3.578759
BFGS: 4 06:04:46 -303.095802 2.080769
BFGS: 5 06:04:47 -303.171454 2.801183
BFGS: 6 06:04:47 -303.241115 0.913376
BFGS: 7 06:04:47 -303.283670 0.823726
BFGS: 8 06:04:47 -303.587857 1.281790
BFGS: 9 06:04:47 -303.723504 1.796911
BFGS: 10 06:04:48 -303.811537 1.450887
BFGS: 11 06:04:48 -303.999528 0.788779
BFGS: 12 06:04:48 -304.034222 1.142282
BFGS: 13 06:04:48 -304.085956 0.526633
BFGS: 14 06:04:48 -304.105520 0.412226
BFGS: 15 06:04:49 -304.112893 0.392760
BFGS: 16 06:04:49 -304.131738 0.235831
BFGS: 17 06:04:49 -304.142710 0.222770
BFGS: 18 06:04:49 -304.149404 0.209283
BFGS: 19 06:04:50 -304.153734 0.201720
BFGS: 20 06:04:50 -304.159743 0.177478
BFGS: 21 06:04:50 -304.166910 0.200689
BFGS: 22 06:04:50 -304.172804 0.196762
BFGS: 23 06:04:51 -304.175916 0.151695
BFGS: 24 06:04:51 -304.177732 0.160789
BFGS: 25 06:04:51 -304.180241 0.174889
BFGS: 26 06:04:52 -304.184252 0.203243
BFGS: 27 06:04:52 -304.188334 0.176955
BFGS: 28 06:04:52 -304.191790 0.196930
BFGS: 29 06:04:52 -304.196685 0.252631
BFGS: 30 06:04:53 -304.207993 0.484348
BFGS: 31 06:04:53 -304.222466 1.016738
BFGS: 32 06:04:53 -304.248534 0.696081
BFGS: 33 06:04:53 -304.285528 0.499536
BFGS: 34 06:04:54 -304.310928 0.369457
BFGS: 35 06:04:54 -304.314075 0.237051
BFGS: 36 06:04:54 -304.321037 0.216005
BFGS: 37 06:04:54 -304.329478 0.226549
BFGS: 38 06:04:55 -304.335525 0.196154
BFGS: 39 06:04:55 -304.341335 0.136327
BFGS: 40 06:04:55 -304.344150 0.113019
BFGS: 41 06:04:55 -304.346571 0.111746
BFGS: 42 06:04:55 -304.348765 0.107240
BFGS: 43 06:04:56 -304.350910 0.093598
BFGS: 44 06:04:56 -304.352103 0.049282
# Relax the product systems
product1_energies = []
for config in product1_configs:
config.calc = calc
config.pbc = True
opt = BFGS(config)
opt.run(fmax=0.05, steps=optimization_steps)
product1_energies.append(config.get_potential_energy())WARNING:root:The UMA fast path (merge_mole + compile) is only available for fixed composition, task, charge, and spin. This is optimized for MD applications. Falling back to a less optimized version for subsequent evaluations. Reason: 'Compositions differ from merged model'.
Use inference_settings='batch' for heterogeneous batched evaluations.
Step Time Energy fmax
BFGS: 0 06:05:01 -298.044453 4.913280
BFGS: 1 06:05:01 -298.527654 4.877915
BFGS: 2 06:05:02 -299.662953 3.591141
BFGS: 3 06:05:02 -300.123347 2.131020
BFGS: 4 06:05:02 -300.237642 1.610209
BFGS: 5 06:05:03 -300.491555 0.541613
BFGS: 6 06:05:03 -300.511974 0.456094
BFGS: 7 06:05:03 -300.542016 0.447046
BFGS: 8 06:05:04 -300.561108 0.331348
BFGS: 9 06:05:04 -300.572169 0.157956
BFGS: 10 06:05:04 -300.576212 0.068206
BFGS: 11 06:05:05 -300.577211 0.068407
BFGS: 12 06:05:05 -300.577570 0.051512
BFGS: 13 06:05:05 -300.577999 0.035409
Step Time Energy fmax
BFGS: 0 06:05:05 -297.034667 4.417434
BFGS: 1 06:05:06 -297.490400 4.567255
BFGS: 2 06:05:06 -298.739908 3.606078
BFGS: 3 06:05:06 -299.030309 4.609652
BFGS: 4 06:05:06 -299.229282 1.771748
BFGS: 5 06:05:07 -299.358639 1.689947
BFGS: 6 06:05:07 -299.696027 0.800340
BFGS: 7 06:05:07 -299.730814 1.112673
BFGS: 8 06:05:08 -299.772648 0.550692
BFGS: 9 06:05:08 -299.803851 0.643467
BFGS: 10 06:05:08 -299.837987 0.459499
BFGS: 11 06:05:09 -299.858111 0.287776
BFGS: 12 06:05:09 -299.866726 0.196597
BFGS: 13 06:05:09 -299.870286 0.189166
BFGS: 14 06:05:10 -299.873112 0.168417
BFGS: 15 06:05:10 -299.875093 0.167318
BFGS: 16 06:05:10 -299.876936 0.198409
BFGS: 17 06:05:11 -299.879482 0.234592
BFGS: 18 06:05:11 -299.882897 0.252863
BFGS: 19 06:05:11 -299.888121 0.281923
BFGS: 20 06:05:12 -299.899427 0.406386
BFGS: 21 06:05:12 -299.899174 0.605228
BFGS: 22 06:05:12 -299.927814 0.592773
BFGS: 23 06:05:12 -299.947580 0.538427
BFGS: 24 06:05:13 -299.983887 0.776821
BFGS: 25 06:05:13 -300.013234 0.236260
BFGS: 26 06:05:13 -300.020878 0.252867
BFGS: 27 06:05:13 -300.028140 0.263056
BFGS: 28 06:05:14 -300.033103 0.227546
BFGS: 29 06:05:14 -300.040669 0.113255
BFGS: 30 06:05:14 -300.041814 0.066254
BFGS: 31 06:05:15 -300.042363 0.062656
BFGS: 32 06:05:15 -300.042793 0.060915
BFGS: 33 06:05:15 -300.043253 0.066925
BFGS: 34 06:05:15 -300.043538 0.042057
Step Time Energy fmax
BFGS: 0 06:05:16 -297.347607 4.413886
BFGS: 1 06:05:16 -297.804249 4.516747
BFGS: 2 06:05:16 -299.036569 3.294221
BFGS: 3 06:05:16 -299.177684 4.848364
BFGS: 4 06:05:17 -299.423693 1.433797
BFGS: 5 06:05:17 -299.511458 1.224286
BFGS: 6 06:05:18 -299.730800 1.490847
BFGS: 7 06:05:18 -299.768060 0.831608
BFGS: 8 06:05:18 -299.821257 0.933181
BFGS: 9 06:05:18 -299.875746 1.013842
BFGS: 10 06:05:19 -299.912196 0.804900
BFGS: 11 06:05:19 -299.938616 0.564929
BFGS: 12 06:05:19 -299.951760 0.451781
BFGS: 13 06:05:19 -299.958602 0.487172
BFGS: 14 06:05:20 -299.971211 0.537989
BFGS: 15 06:05:20 -299.986521 0.470832
BFGS: 16 06:05:20 -299.999599 0.375738
BFGS: 17 06:05:20 -300.010618 0.416689
BFGS: 18 06:05:21 -300.023074 0.347183
BFGS: 19 06:05:21 -300.033912 0.213037
BFGS: 20 06:05:21 -300.037815 0.161349
BFGS: 21 06:05:21 -300.039432 0.136471
BFGS: 22 06:05:22 -300.041349 0.102899
BFGS: 23 06:05:22 -300.042376 0.079440
BFGS: 24 06:05:22 -300.043156 0.062193
BFGS: 25 06:05:23 -300.043558 0.030162
Step Time Energy fmax
BFGS: 0 06:05:23 -297.088990 4.397096
BFGS: 1 06:05:23 -297.539862 4.542645
BFGS: 2 06:05:23 -298.837351 3.015498
BFGS: 3 06:05:24 -299.042644 4.949129
BFGS: 4 06:05:24 -299.313629 1.644208
BFGS: 5 06:05:24 -299.427656 1.616403
BFGS: 6 06:05:25 -299.722427 0.609182
BFGS: 7 06:05:25 -299.754458 1.060370
BFGS: 8 06:05:25 -299.786071 0.800943
BFGS: 9 06:05:26 -299.838058 0.466673
BFGS: 10 06:05:26 -299.858849 0.495491
BFGS: 11 06:05:26 -299.879360 0.400336
BFGS: 12 06:05:26 -299.888278 0.292120
BFGS: 13 06:05:27 -299.894333 0.303065
BFGS: 14 06:05:27 -299.898622 0.370421
BFGS: 15 06:05:27 -299.907953 0.477309
BFGS: 16 06:05:28 -299.918931 0.493467
BFGS: 17 06:05:28 -299.931012 0.386656
BFGS: 18 06:05:28 -299.948290 0.384214
BFGS: 19 06:05:28 -299.968643 0.436815
BFGS: 20 06:05:29 -299.992954 0.573044
BFGS: 21 06:05:29 -300.009465 0.468758
BFGS: 22 06:05:29 -300.015360 0.492321
BFGS: 23 06:05:29 -300.029772 0.293192
BFGS: 24 06:05:30 -300.033824 0.178795
BFGS: 25 06:05:30 -300.036914 0.168185
BFGS: 26 06:05:30 -300.039820 0.152279
BFGS: 27 06:05:30 -300.042075 0.111017
BFGS: 28 06:05:31 -300.042847 0.045186
Step Time Energy fmax
BFGS: 0 06:05:31 -296.118003 4.412352
BFGS: 1 06:05:31 -296.646561 4.707732
BFGS: 2 06:05:32 -298.242424 2.914358
BFGS: 3 06:05:32 -296.924249 16.156649
BFGS: 4 06:05:32 -298.410872 1.783935
BFGS: 5 06:05:32 -298.470488 1.010364
BFGS: 6 06:05:33 -298.507343 0.660450
BFGS: 7 06:05:33 -298.513016 0.420033
BFGS: 8 06:05:33 -298.524103 0.243140
BFGS: 9 06:05:34 -298.526281 0.259330
BFGS: 10 06:05:34 -298.527933 0.232789
BFGS: 11 06:05:34 -298.531523 0.224966
BFGS: 12 06:05:34 -298.545203 0.406186
BFGS: 13 06:05:35 -298.586136 0.960372
BFGS: 14 06:05:35 -297.662908 11.479668
BFGS: 15 06:05:35 -298.727570 1.494608
BFGS: 16 06:05:35 -298.850139 1.521973
BFGS: 17 06:05:36 -299.266268 1.962473
BFGS: 18 06:05:36 -299.711750 1.656393
BFGS: 19 06:05:36 -299.733791 3.084519
BFGS: 20 06:05:37 -299.846617 1.008162
BFGS: 21 06:05:37 -299.877554 0.873425
BFGS: 22 06:05:37 -299.957588 1.230787
BFGS: 23 06:05:38 -300.024635 1.468626
BFGS: 24 06:05:38 -300.181970 1.614106
BFGS: 25 06:05:38 -300.235011 1.882012
BFGS: 26 06:05:39 -300.333694 1.092991
BFGS: 27 06:05:39 -300.393935 0.961710
BFGS: 28 06:05:40 -300.466625 0.743328
BFGS: 29 06:05:40 -300.508351 0.616661
BFGS: 30 06:05:40 -300.528848 0.501860
BFGS: 31 06:05:41 -300.540227 0.398841
BFGS: 32 06:05:41 -300.550450 0.340551
BFGS: 33 06:05:41 -300.560808 0.328766
BFGS: 34 06:05:42 -300.569171 0.225209
BFGS: 35 06:05:42 -300.573585 0.142869
BFGS: 36 06:05:42 -300.574836 0.093932
BFGS: 37 06:05:42 -300.575411 0.080739
BFGS: 38 06:05:43 -300.576254 0.091397
BFGS: 39 06:05:43 -300.577143 0.102148
BFGS: 40 06:05:43 -300.577903 0.080238
BFGS: 41 06:05:44 -300.578240 0.041155
Step Time Energy fmax
BFGS: 0 06:05:44 -297.199086 4.351346
BFGS: 1 06:05:44 -297.640047 4.481640
BFGS: 2 06:05:45 -298.881897 3.390386
BFGS: 3 06:05:45 -298.996665 5.592293
BFGS: 4 06:05:45 -299.280317 1.812728
BFGS: 5 06:05:46 -299.390053 1.679447
BFGS: 6 06:05:46 -299.738191 0.997349
BFGS: 7 06:05:46 -299.793221 1.728549
BFGS: 8 06:05:47 -299.848098 1.029534
BFGS: 9 06:05:47 -299.921604 0.953642
BFGS: 10 06:05:47 -299.970773 0.934911
BFGS: 11 06:05:48 -299.999124 0.631667
BFGS: 12 06:05:48 -300.017128 0.430388
BFGS: 13 06:05:48 -300.027678 0.473175
BFGS: 14 06:05:48 -300.032942 0.384012
BFGS: 15 06:05:49 -300.038287 0.192534
BFGS: 16 06:05:49 -300.040380 0.111174
BFGS: 17 06:05:49 -300.041013 0.091573
BFGS: 18 06:05:50 -300.041559 0.085603
BFGS: 19 06:05:50 -300.042356 0.079422
BFGS: 20 06:05:50 -300.042970 0.084225
BFGS: 21 06:05:50 -300.043249 0.056675
BFGS: 22 06:05:51 -300.043375 0.037496
Step Time Energy fmax
BFGS: 0 06:05:51 -296.625100 4.385537
BFGS: 1 06:05:51 -297.078159 4.593209
BFGS: 2 06:05:52 -298.420980 3.500142
BFGS: 3 06:05:52 -298.333745 7.651015
BFGS: 4 06:05:52 -298.764358 1.978179
BFGS: 5 06:05:52 -298.857265 1.581369
BFGS: 6 06:05:53 -299.152865 2.844175
BFGS: 7 06:05:53 -299.440694 3.099005
BFGS: 8 06:05:53 -299.591381 2.311103
BFGS: 9 06:05:54 -299.725115 1.824131
BFGS: 10 06:05:54 -300.040224 1.212444
BFGS: 11 06:05:54 -300.144428 1.443179
BFGS: 12 06:05:54 -300.269860 1.610008
BFGS: 13 06:05:55 -300.351689 1.269442
BFGS: 14 06:05:55 -300.449104 0.725786
BFGS: 15 06:05:55 -300.500187 0.627727
BFGS: 16 06:05:56 -300.518252 0.600294
BFGS: 17 06:05:56 -300.543128 0.348649
BFGS: 18 06:05:56 -300.549727 0.262106
BFGS: 19 06:05:56 -300.556497 0.338043
BFGS: 20 06:05:57 -300.563771 0.321908
BFGS: 21 06:05:57 -300.570361 0.213855
BFGS: 22 06:05:57 -300.573607 0.117785
BFGS: 23 06:05:58 -300.574592 0.073734
BFGS: 24 06:05:58 -300.575280 0.080867
BFGS: 25 06:05:58 -300.576365 0.102415
BFGS: 26 06:05:58 -300.577494 0.088269
BFGS: 27 06:05:59 -300.578158 0.049933
Step Time Energy fmax
BFGS: 0 06:05:59 -296.356115 4.370898
BFGS: 1 06:05:59 -296.837954 4.613164
BFGS: 2 06:05:59 -298.290267 3.171428
BFGS: 3 06:06:00 -297.634810 11.459598
BFGS: 4 06:06:00 -298.516113 1.871013
BFGS: 5 06:06:01 -298.585447 1.156910
BFGS: 6 06:06:01 -298.648832 1.301530
BFGS: 7 06:06:01 -298.680717 1.309300
BFGS: 8 06:06:01 -298.867730 1.403987
BFGS: 9 06:06:02 -298.971830 2.082212
BFGS: 10 06:06:02 -299.123115 2.186022
BFGS: 11 06:06:02 -299.283692 2.034731
BFGS: 12 06:06:02 -299.724535 1.050628
BFGS: 13 06:06:03 -299.857143 1.100165
BFGS: 14 06:06:03 -299.876874 0.661664
BFGS: 15 06:06:03 -299.914157 0.711645
BFGS: 16 06:06:04 -300.006219 1.183643
BFGS: 17 06:06:04 -300.068570 1.540056
BFGS: 18 06:06:04 -300.141243 1.967920
BFGS: 19 06:06:04 -300.240226 1.158219
BFGS: 20 06:06:05 -300.350417 1.390543
BFGS: 21 06:06:05 -300.416355 1.282973
BFGS: 22 06:06:05 -300.473396 0.796019
BFGS: 23 06:06:06 -300.502274 0.593471
BFGS: 24 06:06:06 -300.530530 0.383077
BFGS: 25 06:06:06 -300.542663 0.374370
BFGS: 26 06:06:07 -300.555715 0.349690
BFGS: 27 06:06:07 -300.564720 0.301048
BFGS: 28 06:06:07 -300.569873 0.194724
BFGS: 29 06:06:08 -300.572780 0.119374
BFGS: 30 06:06:08 -300.574726 0.094071
BFGS: 31 06:06:08 -300.575620 0.073964
BFGS: 32 06:06:08 -300.576219 0.075693
BFGS: 33 06:06:09 -300.576864 0.072134
BFGS: 34 06:06:09 -300.577570 0.091232
BFGS: 35 06:06:09 -300.578159 0.070183
BFGS: 36 06:06:09 -300.578425 0.027269
Step Time Energy fmax
BFGS: 0 06:06:10 -296.885485 4.456937
BFGS: 1 06:06:10 -297.343468 4.625489
BFGS: 2 06:06:10 -298.640892 3.679171
BFGS: 3 06:06:10 -298.875905 5.393155
BFGS: 4 06:06:11 -299.122803 1.947275
BFGS: 5 06:06:11 -299.254913 1.857775
BFGS: 6 06:06:11 -299.663064 1.068655
BFGS: 7 06:06:12 -299.654815 2.575855
BFGS: 8 06:06:12 -299.761968 0.678065
BFGS: 9 06:06:13 -299.793230 0.604694
BFGS: 10 06:06:13 -299.916600 1.001306
BFGS: 11 06:06:13 -299.951832 0.918361
BFGS: 12 06:06:14 -300.048179 1.314410
BFGS: 13 06:06:14 -300.093101 1.573217
BFGS: 14 06:06:14 -300.199016 1.821655
BFGS: 15 06:06:14 -300.284384 1.904582
BFGS: 16 06:06:15 -300.365081 1.327738
BFGS: 17 06:06:15 -300.431095 0.884427
BFGS: 18 06:06:15 -300.467834 0.563195
BFGS: 19 06:06:15 -300.494959 0.584264
BFGS: 20 06:06:16 -300.538967 0.393013
BFGS: 21 06:06:16 -300.554934 0.270289
BFGS: 22 06:06:16 -300.561625 0.154073
BFGS: 23 06:06:17 -300.565162 0.136793
BFGS: 24 06:06:17 -300.568393 0.154987
BFGS: 25 06:06:17 -300.571642 0.181701
BFGS: 26 06:06:18 -300.574740 0.146297
BFGS: 27 06:06:18 -300.576535 0.076102
BFGS: 28 06:06:18 -300.577267 0.055267
BFGS: 29 06:06:18 -300.577589 0.042580
Step Time Energy fmax
BFGS: 0 06:06:19 -296.354407 4.363421
BFGS: 1 06:06:19 -296.833943 4.606462
BFGS: 2 06:06:19 -298.284317 3.179519
BFGS: 3 06:06:20 -297.637756 11.390439
BFGS: 4 06:06:20 -298.511032 1.872075
BFGS: 5 06:06:20 -298.580209 1.150270
BFGS: 6 06:06:21 -298.642298 1.293567
BFGS: 7 06:06:21 -298.673242 1.298442
BFGS: 8 06:06:21 -298.860298 1.415850
BFGS: 9 06:06:21 -298.963098 2.148211
BFGS: 10 06:06:22 -299.118237 2.318374
BFGS: 11 06:06:22 -299.297351 2.239151
BFGS: 12 06:06:23 -299.715673 1.369557
BFGS: 13 06:06:23 -299.922594 1.191751
BFGS: 14 06:06:23 -299.947894 0.813827
BFGS: 15 06:06:23 -299.988871 0.873736
BFGS: 16 06:06:24 -300.211672 1.274652
BFGS: 17 06:06:24 -300.292396 1.023962
BFGS: 18 06:06:24 -300.336366 1.096014
BFGS: 19 06:06:25 -300.385174 1.027690
BFGS: 20 06:06:25 -300.482530 0.523362
BFGS: 21 06:06:25 -300.503539 0.494494
BFGS: 22 06:06:26 -300.533188 0.390999
BFGS: 23 06:06:26 -300.547574 0.315970
BFGS: 24 06:06:26 -300.556716 0.225298
BFGS: 25 06:06:27 -300.562862 0.239819
BFGS: 26 06:06:27 -300.567566 0.251068
BFGS: 27 06:06:27 -300.571687 0.219877
BFGS: 28 06:06:27 -300.574969 0.135360
BFGS: 29 06:06:28 -300.576463 0.049281
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 06:06:28 -295.479929 0.993816
BFGS: 1 06:06:28 -295.541410 0.922052
BFGS: 2 06:06:28 -295.753737 0.797664
BFGS: 3 06:06:29 -295.770399 0.485646
BFGS: 4 06:06:29 -295.780708 0.471826
BFGS: 5 06:06:29 -295.813873 0.475564
BFGS: 6 06:06:30 -295.821931 0.408808
BFGS: 7 06:06:30 -295.833533 0.377921
BFGS: 8 06:06:30 -295.841257 0.238536
BFGS: 9 06:06:30 -295.846449 0.150982
BFGS: 10 06:06:31 -295.848181 0.148639
BFGS: 11 06:06:31 -295.849253 0.136422
BFGS: 12 06:06:31 -295.850759 0.119764
BFGS: 13 06:06:32 -295.852522 0.111345
BFGS: 14 06:06:32 -295.853902 0.116448
BFGS: 15 06:06:32 -295.854848 0.124259
BFGS: 16 06:06:33 -295.856028 0.135041
BFGS: 17 06:06:33 -295.858459 0.159025
BFGS: 18 06:06:33 -295.863449 0.213812
BFGS: 19 06:06:33 -295.871521 0.305793
BFGS: 20 06:06:34 -295.882023 0.445598
BFGS: 21 06:06:34 -295.894354 0.506238
BFGS: 22 06:06:34 -295.908492 0.383448
BFGS: 23 06:06:34 -295.922412 0.325315
BFGS: 24 06:06:35 -295.941068 0.289683
BFGS: 25 06:06:35 -295.951028 0.178867
BFGS: 26 06:06:35 -295.957351 0.144152
BFGS: 27 06:06:35 -295.959040 0.124080
BFGS: 28 06:06:35 -295.962002 0.125332
BFGS: 29 06:06:36 -295.964299 0.120528
BFGS: 30 06:06:36 -295.966016 0.082388
BFGS: 31 06:06:36 -295.966562 0.053165
BFGS: 32 06:06:36 -295.966768 0.040470
Step Time Energy fmax
BFGS: 0 06:06:36 -295.603037 0.745748
BFGS: 1 06:06:36 -295.652752 0.663968
BFGS: 2 06:06:37 -295.821723 0.225953
BFGS: 3 06:06:37 -295.831235 0.207001
BFGS: 4 06:06:37 -295.832695 0.201544
BFGS: 5 06:06:37 -295.840203 0.131313
BFGS: 6 06:06:38 -295.840716 0.108772
BFGS: 7 06:06:38 -295.841834 0.059146
BFGS: 8 06:06:38 -295.842152 0.044670
Step Time Energy fmax
BFGS: 0 06:06:38 -295.530557 0.906169
BFGS: 1 06:06:38 -295.586740 0.848345
BFGS: 2 06:06:39 -295.787239 0.646057
BFGS: 3 06:06:39 -295.801588 0.477956
BFGS: 4 06:06:39 -295.812148 0.495617
BFGS: 5 06:06:39 -295.849289 0.510999
BFGS: 6 06:06:40 -295.861728 0.473761
BFGS: 7 06:06:40 -295.877828 0.519710
BFGS: 8 06:06:40 -295.892121 0.377797
BFGS: 9 06:06:40 -295.903588 0.259961
BFGS: 10 06:06:41 -295.909465 0.272556
BFGS: 11 06:06:41 -295.912576 0.252546
BFGS: 12 06:06:41 -295.915855 0.216557
BFGS: 13 06:06:41 -295.920131 0.162585
BFGS: 14 06:06:42 -295.923512 0.120067
BFGS: 15 06:06:42 -295.925380 0.150015
BFGS: 16 06:06:42 -295.926663 0.139348
BFGS: 17 06:06:42 -295.928346 0.101811
BFGS: 18 06:06:42 -295.930364 0.071145
BFGS: 19 06:06:43 -295.931745 0.054311
BFGS: 20 06:06:43 -295.932225 0.037206
Step Time Energy fmax
BFGS: 0 06:06:43 -295.295279 1.306716
BFGS: 1 06:06:43 -295.373353 1.191635
BFGS: 2 06:06:43 -295.587585 1.422176
BFGS: 3 06:06:44 -295.622027 0.590411
BFGS: 4 06:06:44 -295.633161 0.508127
BFGS: 5 06:06:44 -295.669689 0.475133
BFGS: 6 06:06:45 -295.675508 0.470668
BFGS: 7 06:06:45 -295.738051 0.654269
BFGS: 8 06:06:45 -295.756250 0.644990
BFGS: 9 06:06:45 -295.776650 0.744438
BFGS: 10 06:06:45 -295.805636 0.693872
BFGS: 11 06:06:46 -295.833738 0.459052
BFGS: 12 06:06:46 -295.846923 0.288008
BFGS: 13 06:06:46 -295.851629 0.247274
BFGS: 14 06:06:46 -295.853823 0.233118
BFGS: 15 06:06:47 -295.857905 0.209266
BFGS: 16 06:06:47 -295.861625 0.171311
BFGS: 17 06:06:47 -295.865331 0.181840
BFGS: 18 06:06:47 -295.867094 0.181501
BFGS: 19 06:06:47 -295.868739 0.178745
BFGS: 20 06:06:48 -295.871400 0.185339
BFGS: 21 06:06:48 -295.877131 0.295346
BFGS: 22 06:06:48 -295.887098 0.402748
BFGS: 23 06:06:48 -295.900226 0.434873
BFGS: 24 06:06:48 -295.916911 0.346546
BFGS: 25 06:06:49 -295.932164 0.269509
BFGS: 26 06:06:49 -295.942262 0.223895
BFGS: 27 06:06:49 -295.955567 0.150796
BFGS: 28 06:06:49 -295.960060 0.092395
BFGS: 29 06:06:49 -295.962569 0.085650
BFGS: 30 06:06:49 -295.963545 0.073177
BFGS: 31 06:06:49 -295.964627 0.063654
BFGS: 32 06:06:50 -295.965870 0.044279
Step Time Energy fmax
BFGS: 0 06:06:50 -295.555602 0.915733
BFGS: 1 06:06:50 -295.610372 0.865740
BFGS: 2 06:06:50 -295.819567 0.559606
BFGS: 3 06:06:50 -295.834507 0.530578
BFGS: 4 06:06:51 -295.845112 0.539925
BFGS: 5 06:06:51 -295.895363 0.507689
BFGS: 6 06:06:51 -295.910895 0.595450
BFGS: 7 06:06:51 -295.929318 0.588834
BFGS: 8 06:06:52 -295.942207 0.367368
BFGS: 9 06:06:52 -295.951183 0.244774
BFGS: 10 06:06:52 -295.955400 0.235779
BFGS: 11 06:06:52 -295.957665 0.207447
BFGS: 12 06:06:52 -295.959808 0.165662
BFGS: 13 06:06:53 -295.962262 0.111094
BFGS: 14 06:06:53 -295.963962 0.103818
BFGS: 15 06:06:53 -295.964770 0.102887
BFGS: 16 06:06:53 -295.965322 0.086151
BFGS: 17 06:06:54 -295.966005 0.052851
BFGS: 18 06:06:54 -295.966634 0.034814
Step Time Energy fmax
BFGS: 0 06:06:54 -295.465877 1.029337
BFGS: 1 06:06:54 -295.528414 0.954453
BFGS: 2 06:06:54 -295.743680 0.842922
BFGS: 3 06:06:54 -295.761224 0.508195
BFGS: 4 06:06:55 -295.772422 0.490224
BFGS: 5 06:06:55 -295.808414 0.512259
BFGS: 6 06:06:55 -295.817869 0.450732
BFGS: 7 06:06:55 -295.832631 0.441331
BFGS: 8 06:06:56 -295.842845 0.288417
BFGS: 9 06:06:56 -295.850007 0.186372
BFGS: 10 06:06:56 -295.852445 0.181935
BFGS: 11 06:06:56 -295.853960 0.166610
BFGS: 12 06:06:57 -295.856065 0.146713
BFGS: 13 06:06:57 -295.858615 0.138711
BFGS: 14 06:06:57 -295.860682 0.148608
BFGS: 15 06:06:57 -295.862180 0.160332
BFGS: 16 06:06:57 -295.864107 0.175100
BFGS: 17 06:06:57 -295.868155 0.207302
BFGS: 18 06:06:58 -295.876727 0.278884
BFGS: 19 06:06:58 -295.889427 0.364026
BFGS: 20 06:06:58 -295.902687 0.463488
BFGS: 21 06:06:58 -295.920499 0.388150
BFGS: 22 06:06:59 -295.927887 0.332573
BFGS: 23 06:06:59 -295.944584 0.270519
BFGS: 24 06:06:59 -295.953471 0.181583
BFGS: 25 06:06:59 -295.957982 0.169714
BFGS: 26 06:07:00 -295.960990 0.112856
BFGS: 27 06:07:00 -295.962348 0.092581
BFGS: 28 06:07:00 -295.963770 0.096573
BFGS: 29 06:07:00 -295.965374 0.095902
BFGS: 30 06:07:01 -295.966454 0.064165
BFGS: 31 06:07:01 -295.966833 0.038667
Step Time Energy fmax
BFGS: 0 06:07:01 -295.141816 1.598512
BFGS: 1 06:07:01 -295.243704 1.445233
BFGS: 2 06:07:02 -295.435553 2.202140
BFGS: 3 06:07:02 -295.509378 0.488575
BFGS: 4 06:07:02 -295.523586 0.594469
BFGS: 5 06:07:03 -295.548829 0.568926
BFGS: 6 06:07:03 -295.559136 0.320666
BFGS: 7 06:07:03 -295.564975 0.263877
BFGS: 8 06:07:03 -295.569317 0.300082
BFGS: 9 06:07:03 -295.574627 0.264470
BFGS: 10 06:07:04 -295.578075 0.175366
BFGS: 11 06:07:04 -295.579346 0.108957
BFGS: 12 06:07:04 -295.579759 0.122289
BFGS: 13 06:07:04 -295.580460 0.152276
BFGS: 14 06:07:04 -295.582143 0.209567
BFGS: 15 06:07:05 -295.587274 0.317440
BFGS: 16 06:07:05 -295.607356 0.447565
BFGS: 17 06:07:05 -295.518670 1.470730
BFGS: 18 06:07:05 -295.697094 0.576102
BFGS: 19 06:07:06 -295.768812 0.473704
BFGS: 20 06:07:06 -295.782966 0.839495
BFGS: 21 06:07:06 -295.816313 0.525204
BFGS: 22 06:07:06 -295.828970 0.408887
BFGS: 23 06:07:07 -295.849952 0.253063
BFGS: 24 06:07:07 -295.855074 0.242044
BFGS: 25 06:07:07 -295.859925 0.215405
BFGS: 26 06:07:07 -295.863147 0.192702
BFGS: 27 06:07:07 -295.868416 0.178506
BFGS: 28 06:07:07 -295.873469 0.195424
BFGS: 29 06:07:08 -295.877513 0.212950
BFGS: 30 06:07:08 -295.880582 0.226236
BFGS: 31 06:07:08 -295.885197 0.238503
BFGS: 32 06:07:08 -295.892655 0.266328
BFGS: 33 06:07:09 -295.900897 0.271629
BFGS: 34 06:07:09 -295.907701 0.208624
BFGS: 35 06:07:09 -295.913408 0.200800
BFGS: 36 06:07:09 -295.918811 0.171102
BFGS: 37 06:07:10 -295.924457 0.154818
BFGS: 38 06:07:10 -295.928129 0.118496
BFGS: 39 06:07:10 -295.929867 0.091574
BFGS: 40 06:07:10 -295.930783 0.091360
BFGS: 41 06:07:11 -295.931683 0.075285
BFGS: 42 06:07:11 -295.932431 0.046406
Step Time Energy fmax
BFGS: 0 06:07:11 -295.109724 1.680892
BFGS: 1 06:07:11 -295.218722 1.517395
BFGS: 2 06:07:12 -295.404784 2.392639
BFGS: 3 06:07:12 -295.489504 0.469472
BFGS: 4 06:07:12 -295.505236 0.610415
BFGS: 5 06:07:12 -295.530803 0.645934
BFGS: 6 06:07:12 -295.543639 0.407297
BFGS: 7 06:07:13 -295.550734 0.253205
BFGS: 8 06:07:13 -295.555032 0.301830
BFGS: 9 06:07:13 -295.560724 0.281206
BFGS: 10 06:07:13 -295.564285 0.174813
BFGS: 11 06:07:13 -295.565514 0.056996
BFGS: 12 06:07:14 -295.565691 0.044699
Step Time Energy fmax
BFGS: 0 06:07:14 -295.124088 1.641512
BFGS: 1 06:07:14 -295.229731 1.482944
BFGS: 2 06:07:14 -295.417982 2.308638
BFGS: 3 06:07:14 -295.498049 0.474741
BFGS: 4 06:07:15 -295.513062 0.601609
BFGS: 5 06:07:15 -295.538065 0.613800
BFGS: 6 06:07:15 -295.549741 0.371411
BFGS: 7 06:07:15 -295.556180 0.253273
BFGS: 8 06:07:16 -295.560372 0.297111
BFGS: 9 06:07:16 -295.565719 0.271235
BFGS: 10 06:07:16 -295.569125 0.171503
BFGS: 11 06:07:16 -295.570315 0.070343
BFGS: 12 06:07:16 -295.570543 0.071037
BFGS: 13 06:07:17 -295.570737 0.080157
BFGS: 14 06:07:17 -295.571167 0.096828
BFGS: 15 06:07:17 -295.572004 0.116384
BFGS: 16 06:07:17 -295.573426 0.126985
BFGS: 17 06:07:18 -295.575336 0.129973
BFGS: 18 06:07:18 -295.578302 0.239242
BFGS: 19 06:07:18 -295.588556 0.630019
BFGS: 20 06:07:18 -295.593863 1.032473
BFGS: 21 06:07:19 -295.612529 0.715826
BFGS: 22 06:07:19 -295.642298 0.932651
BFGS: 23 06:07:19 -295.681310 1.198828
BFGS: 24 06:07:19 -295.710379 1.211784
BFGS: 25 06:07:20 -295.731259 0.882168
BFGS: 26 06:07:20 -295.752194 0.874982
BFGS: 27 06:07:20 -295.775634 0.778597
BFGS: 28 06:07:21 -295.792327 0.643424
BFGS: 29 06:07:21 -295.818807 0.513555
BFGS: 30 06:07:21 -295.835886 0.476444
BFGS: 31 06:07:21 -295.849071 0.541286
BFGS: 32 06:07:21 -295.865017 0.533167
BFGS: 33 06:07:21 -295.885195 0.393854
BFGS: 34 06:07:22 -295.897922 0.209107
BFGS: 35 06:07:22 -295.902943 0.262486
BFGS: 36 06:07:22 -295.907931 0.230909
BFGS: 37 06:07:22 -295.912262 0.201655
BFGS: 38 06:07:23 -295.920698 0.145059
BFGS: 39 06:07:23 -295.923867 0.127192
BFGS: 40 06:07:23 -295.925518 0.120905
BFGS: 41 06:07:23 -295.926619 0.115154
BFGS: 42 06:07:24 -295.928322 0.100183
BFGS: 43 06:07:24 -295.930046 0.076600
BFGS: 44 06:07:24 -295.931161 0.053388
BFGS: 45 06:07:24 -295.931564 0.042664
Step Time Energy fmax
BFGS: 0 06:07:25 -295.159501 1.556252
BFGS: 1 06:07:25 -295.257974 1.408706
BFGS: 2 06:07:25 -295.453688 2.111979
BFGS: 3 06:07:25 -295.522381 0.505125
BFGS: 4 06:07:25 -295.535963 0.589758
BFGS: 5 06:07:25 -295.561755 0.519734
BFGS: 6 06:07:26 -295.570853 0.270431
BFGS: 7 06:07:26 -295.576409 0.280814
BFGS: 8 06:07:26 -295.581211 0.309965
BFGS: 9 06:07:27 -295.586833 0.267396
BFGS: 10 06:07:27 -295.590700 0.192822
BFGS: 11 06:07:27 -295.592369 0.168834
BFGS: 12 06:07:27 -295.593284 0.201125
BFGS: 13 06:07:28 -295.595663 0.284110
BFGS: 14 06:07:28 -295.602907 0.469510
BFGS: 15 06:07:28 -295.636261 0.813833
BFGS: 16 06:07:29 -295.710781 0.819367
BFGS: 17 06:07:29 -295.786607 0.586548
BFGS: 18 06:07:29 -295.775310 0.954981
BFGS: 19 06:07:29 -295.818412 0.531531
BFGS: 20 06:07:30 -295.834879 0.451147
BFGS: 21 06:07:30 -295.869279 0.274107
BFGS: 22 06:07:30 -295.873426 0.247490
BFGS: 23 06:07:30 -295.878432 0.257178
BFGS: 24 06:07:30 -295.885249 0.290989
BFGS: 25 06:07:30 -295.895381 0.318586
BFGS: 26 06:07:31 -295.902383 0.302674
BFGS: 27 06:07:31 -295.907163 0.280287
BFGS: 28 06:07:31 -295.913033 0.268342
BFGS: 29 06:07:32 -295.921752 0.292921
BFGS: 30 06:07:32 -295.934201 0.317143
BFGS: 31 06:07:32 -295.943897 0.266238
BFGS: 32 06:07:32 -295.951078 0.194069
BFGS: 33 06:07:33 -295.955616 0.163201
BFGS: 34 06:07:33 -295.958697 0.147638
BFGS: 35 06:07:33 -295.962324 0.114446
BFGS: 36 06:07:33 -295.964798 0.080620
BFGS: 37 06:07:34 -295.965782 0.067392
BFGS: 38 06:07:34 -295.966200 0.049106
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 06:07:34 -303.652922 0.905978
BFGS: 1 06:07:35 -303.673763 0.699606
BFGS: 2 06:07:35 -303.722812 0.571739
BFGS: 3 06:07:35 -303.744790 0.595330
BFGS: 4 06:07:35 -303.774248 0.669779
BFGS: 5 06:07:36 -303.800179 0.512799
BFGS: 6 06:07:36 -303.844218 0.513870
BFGS: 7 06:07:36 -303.851649 0.340615
BFGS: 8 06:07:36 -303.859596 0.209965
BFGS: 9 06:07:37 -303.866694 0.151373
BFGS: 10 06:07:37 -303.869243 0.160555
BFGS: 11 06:07:37 -303.870691 0.163590
BFGS: 12 06:07:37 -303.872618 0.154075
BFGS: 13 06:07:38 -303.874714 0.157011
BFGS: 14 06:07:38 -303.876400 0.124002
BFGS: 15 06:07:38 -303.877418 0.127071
BFGS: 16 06:07:39 -303.878365 0.120905
BFGS: 17 06:07:39 -303.880117 0.113121
BFGS: 18 06:07:39 -303.883426 0.178917
BFGS: 19 06:07:39 -303.888826 0.196320
BFGS: 20 06:07:40 -303.895260 0.315370
BFGS: 21 06:07:40 -303.901312 0.286544
BFGS: 22 06:07:40 -303.912131 0.443231
BFGS: 23 06:07:40 -303.917973 0.570772
BFGS: 24 06:07:40 -303.935601 0.651698
BFGS: 25 06:07:41 -303.952289 0.502270
BFGS: 26 06:07:41 -303.979546 0.347886
BFGS: 27 06:07:41 -303.980967 0.472497
BFGS: 28 06:07:41 -303.998081 0.346500
BFGS: 29 06:07:42 -304.008676 0.313435
BFGS: 30 06:07:42 -304.029473 0.290382
BFGS: 31 06:07:42 -304.047709 0.269587
BFGS: 32 06:07:42 -304.065470 0.442573
BFGS: 33 06:07:43 -304.086373 0.505355
BFGS: 34 06:07:43 -304.110895 0.467422
BFGS: 35 06:07:43 -304.134436 0.558593
BFGS: 36 06:07:43 -304.163747 0.696009
BFGS: 37 06:07:44 -304.195702 0.795991
BFGS: 38 06:07:44 -304.237677 0.861225
BFGS: 39 06:07:44 -304.272008 0.638604
BFGS: 40 06:07:44 -304.299861 0.730787
BFGS: 41 06:07:45 -304.340311 0.546403
BFGS: 42 06:07:45 -304.357619 0.383676
BFGS: 43 06:07:45 -304.377696 0.288965
BFGS: 44 06:07:45 -304.383754 0.241922
BFGS: 45 06:07:45 -304.387449 0.185318
BFGS: 46 06:07:45 -304.390410 0.108116
BFGS: 47 06:07:46 -304.392089 0.084621
BFGS: 48 06:07:46 -304.393140 0.083246
BFGS: 49 06:07:46 -304.393971 0.094827
BFGS: 50 06:07:46 -304.394875 0.078565
BFGS: 51 06:07:47 -304.395871 0.093157
BFGS: 52 06:07:47 -304.396787 0.108032
BFGS: 53 06:07:47 -304.397573 0.118234
BFGS: 54 06:07:47 -304.398629 0.130080
BFGS: 55 06:07:48 -304.400774 0.154796
BFGS: 56 06:07:48 -304.405147 0.201041
BFGS: 57 06:07:48 -304.412325 0.246080
BFGS: 58 06:07:49 -304.422666 0.336137
BFGS: 59 06:07:49 -304.435004 0.306639
BFGS: 60 06:07:49 -304.443179 0.309493
BFGS: 61 06:07:49 -304.452428 0.186434
BFGS: 62 06:07:49 -304.457979 0.114361
BFGS: 63 06:07:50 -304.461385 0.101967
BFGS: 64 06:07:50 -304.463244 0.098198
BFGS: 65 06:07:50 -304.464614 0.084223
BFGS: 66 06:07:51 -304.465865 0.075425
BFGS: 67 06:07:51 -304.466915 0.066511
BFGS: 68 06:07:51 -304.467564 0.042023
Step Time Energy fmax
BFGS: 0 06:07:51 -303.674220 0.863259
BFGS: 1 06:07:52 -303.693794 0.675455
BFGS: 2 06:07:52 -303.745423 0.576087
BFGS: 3 06:07:52 -303.766517 0.591224
BFGS: 4 06:07:52 -303.793321 0.628094
BFGS: 5 06:07:53 -303.817860 0.498814
BFGS: 6 06:07:53 -303.851207 0.430895
BFGS: 7 06:07:53 -303.856780 0.289191
BFGS: 8 06:07:53 -303.862666 0.191652
BFGS: 9 06:07:54 -303.867670 0.143422
BFGS: 10 06:07:54 -303.869728 0.160298
BFGS: 11 06:07:54 -303.871052 0.166295
BFGS: 12 06:07:54 -303.872947 0.155701
BFGS: 13 06:07:55 -303.875135 0.161597
BFGS: 14 06:07:55 -303.877050 0.128000
BFGS: 15 06:07:55 -303.878339 0.137264
BFGS: 16 06:07:56 -303.879557 0.135780
BFGS: 17 06:07:56 -303.881878 0.135598
BFGS: 18 06:07:56 -303.886899 0.245543
BFGS: 19 06:07:56 -303.895653 0.372363
BFGS: 20 06:07:56 -303.903227 0.324845
BFGS: 21 06:07:56 -303.913428 0.332088
BFGS: 22 06:07:57 -303.916612 0.390224
BFGS: 23 06:07:57 -303.923578 0.312815
BFGS: 24 06:07:57 -303.942753 0.224641
BFGS: 25 06:07:57 -303.964641 0.307378
BFGS: 26 06:07:57 -303.983866 0.358611
BFGS: 27 06:07:57 -303.999446 0.341086
BFGS: 28 06:07:58 -304.009007 0.415119
BFGS: 29 06:07:58 -304.026105 0.333553
BFGS: 30 06:07:58 -304.054187 0.296339
BFGS: 31 06:07:58 -304.079794 0.498393
BFGS: 32 06:07:59 -304.104482 0.604765
BFGS: 33 06:07:59 -304.129728 0.680355
BFGS: 34 06:07:59 -304.163727 0.826381
BFGS: 35 06:07:59 -304.205038 0.843342
BFGS: 36 06:07:59 -304.256792 0.700203
BFGS: 37 06:08:00 -304.280860 0.638251
BFGS: 38 06:08:00 -304.311675 0.730500
BFGS: 39 06:08:00 -304.340141 0.511139
BFGS: 40 06:08:00 -304.365282 0.316288
BFGS: 41 06:08:01 -304.373703 0.260730
BFGS: 42 06:08:01 -304.380328 0.284325
BFGS: 43 06:08:01 -304.385887 0.186697
BFGS: 44 06:08:01 -304.388785 0.076165
BFGS: 45 06:08:02 -304.390714 0.066139
BFGS: 46 06:08:02 -304.391656 0.069222
BFGS: 47 06:08:02 -304.392290 0.070276
BFGS: 48 06:08:02 -304.392989 0.071483
BFGS: 49 06:08:03 -304.393804 0.075971
BFGS: 50 06:08:03 -304.394680 0.084192
BFGS: 51 06:08:04 -304.395558 0.092108
BFGS: 52 06:08:04 -304.396403 0.096818
BFGS: 53 06:08:04 -304.397414 0.100656
BFGS: 54 06:08:04 -304.398953 0.108181
BFGS: 55 06:08:04 -304.401459 0.158495
BFGS: 56 06:08:05 -304.405851 0.257256
BFGS: 57 06:08:05 -304.413821 0.349734
BFGS: 58 06:08:05 -304.428966 0.582540
BFGS: 59 06:08:05 -304.450804 0.518251
BFGS: 60 06:08:05 -304.468247 0.185894
BFGS: 61 06:08:06 -304.469915 0.272250
BFGS: 62 06:08:06 -304.480837 0.205150
BFGS: 63 06:08:06 -304.485255 0.177144
BFGS: 64 06:08:06 -304.490835 0.139392
BFGS: 65 06:08:07 -304.492797 0.120324
BFGS: 66 06:08:07 -304.494545 0.086182
BFGS: 67 06:08:07 -304.495759 0.076152
BFGS: 68 06:08:07 -304.496654 0.072011
BFGS: 69 06:08:08 -304.497256 0.058460
BFGS: 70 06:08:08 -304.497675 0.045168
Step Time Energy fmax
BFGS: 0 06:08:08 -304.388420 0.284625
BFGS: 1 06:08:08 -304.392448 0.223948
BFGS: 2 06:08:08 -304.405265 0.166002
BFGS: 3 06:08:08 -304.408247 0.169201
BFGS: 4 06:08:09 -304.410637 0.129497
BFGS: 5 06:08:09 -304.411636 0.094644
BFGS: 6 06:08:09 -304.412367 0.086339
BFGS: 7 06:08:09 -304.412994 0.077714
BFGS: 8 06:08:09 -304.413611 0.097797
BFGS: 9 06:08:09 -304.414155 0.082195
BFGS: 10 06:08:09 -304.414523 0.054476
BFGS: 11 06:08:10 -304.414741 0.054802
BFGS: 12 06:08:10 -304.414898 0.037733
Step Time Energy fmax
BFGS: 0 06:08:10 -304.390028 0.295007
BFGS: 1 06:08:10 -304.394766 0.219880
BFGS: 2 06:08:11 -304.406888 0.170539
BFGS: 3 06:08:11 -304.409839 0.154110
BFGS: 4 06:08:11 -304.412365 0.120368
BFGS: 5 06:08:11 -304.413636 0.102521
BFGS: 6 06:08:12 -304.414559 0.091078
BFGS: 7 06:08:12 -304.415373 0.072867
BFGS: 8 06:08:12 -304.416019 0.086189
BFGS: 9 06:08:12 -304.416482 0.064627
BFGS: 10 06:08:13 -304.416831 0.049191
Step Time Energy fmax
BFGS: 0 06:08:13 -303.900881 0.305683
BFGS: 1 06:08:13 -303.906620 0.245423
BFGS: 2 06:08:13 -303.920605 0.140511
BFGS: 3 06:08:13 -303.923042 0.114083
BFGS: 4 06:08:14 -303.924770 0.106838
BFGS: 5 06:08:14 -303.925931 0.099491
BFGS: 6 06:08:14 -303.926952 0.075175
BFGS: 7 06:08:14 -303.927544 0.069747
BFGS: 8 06:08:15 -303.927849 0.052089
BFGS: 9 06:08:15 -303.928043 0.041047
Step Time Energy fmax
BFGS: 0 06:08:15 -303.906855 0.270999
BFGS: 1 06:08:15 -303.911602 0.230934
BFGS: 2 06:08:15 -303.923695 0.134359
BFGS: 3 06:08:16 -303.925757 0.105258
BFGS: 4 06:08:16 -303.927244 0.103224
BFGS: 5 06:08:16 -303.928315 0.098915
BFGS: 6 06:08:16 -303.929281 0.076845
BFGS: 7 06:08:17 -303.929862 0.070766
BFGS: 8 06:08:17 -303.930170 0.052531
BFGS: 9 06:08:17 -303.930363 0.038689
Step Time Energy fmax
BFGS: 0 06:08:17 -303.129045 1.021112
BFGS: 1 06:08:18 -303.157890 0.790684
BFGS: 2 06:08:18 -303.225807 0.661014
BFGS: 3 06:08:18 -303.255193 0.650082
BFGS: 4 06:08:18 -303.285974 0.694138
BFGS: 5 06:08:19 -303.314376 0.552201
BFGS: 6 06:08:19 -303.355651 0.509702
BFGS: 7 06:08:19 -303.365594 0.313421
BFGS: 8 06:08:20 -303.370167 0.201942
BFGS: 9 06:08:20 -303.377189 0.188484
BFGS: 10 06:08:20 -303.380039 0.176817
BFGS: 11 06:08:20 -303.382448 0.187120
BFGS: 12 06:08:20 -303.384609 0.156389
BFGS: 13 06:08:21 -303.386655 0.144309
BFGS: 14 06:08:21 -303.388648 0.169089
BFGS: 15 06:08:21 -303.390239 0.147477
BFGS: 16 06:08:22 -303.391709 0.120758
BFGS: 17 06:08:22 -303.393654 0.115091
BFGS: 18 06:08:22 -303.395859 0.173579
BFGS: 19 06:08:22 -303.397994 0.186538
BFGS: 20 06:08:22 -303.399905 0.148595
BFGS: 21 06:08:23 -303.401841 0.179528
BFGS: 22 06:08:23 -303.404872 0.250037
BFGS: 23 06:08:23 -303.411573 0.484791
BFGS: 24 06:08:23 -303.421970 0.717419
BFGS: 25 06:08:23 -303.441057 0.731401
BFGS: 26 06:08:24 -303.475399 0.534759
BFGS: 27 06:08:24 -303.506178 0.613653
BFGS: 28 06:08:24 -303.559044 0.818219
BFGS: 29 06:08:24 -303.591606 0.975242
BFGS: 30 06:08:24 -303.644279 0.919328
BFGS: 31 06:08:25 -303.725935 0.953870
BFGS: 32 06:08:25 -303.789961 0.721571
BFGS: 33 06:08:25 -303.828897 0.694737
BFGS: 34 06:08:25 -303.852701 0.797949
BFGS: 35 06:08:25 -303.888531 0.575480
BFGS: 36 06:08:26 -303.904090 0.326917
BFGS: 37 06:08:26 -303.913139 0.213145
BFGS: 38 06:08:26 -303.917584 0.164674
BFGS: 39 06:08:27 -303.922056 0.106636
BFGS: 40 06:08:27 -303.924552 0.097557
BFGS: 41 06:08:27 -303.926124 0.081413
BFGS: 42 06:08:27 -303.926699 0.054854
BFGS: 43 06:08:27 -303.927158 0.045366
Step Time Energy fmax
BFGS: 0 06:08:28 -303.121390 1.051775
BFGS: 1 06:08:28 -303.154301 0.796705
BFGS: 2 06:08:28 -303.223163 0.679211
BFGS: 3 06:08:28 -303.252517 0.635725
BFGS: 4 06:08:29 -303.285592 0.696972
BFGS: 5 06:08:29 -303.314428 0.572057
BFGS: 6 06:08:29 -303.353615 0.513377
BFGS: 7 06:08:29 -303.366505 0.330877
BFGS: 8 06:08:30 -303.370664 0.209413
BFGS: 9 06:08:30 -303.378069 0.176262
BFGS: 10 06:08:30 -303.381418 0.171613
BFGS: 11 06:08:30 -303.383899 0.209518
BFGS: 12 06:08:30 -303.386306 0.177698
BFGS: 13 06:08:31 -303.388745 0.155905
BFGS: 14 06:08:31 -303.391204 0.172447
BFGS: 15 06:08:31 -303.393301 0.163024
BFGS: 16 06:08:31 -303.395356 0.160068
BFGS: 17 06:08:32 -303.398621 0.164823
BFGS: 18 06:08:32 -303.403394 0.227700
BFGS: 19 06:08:32 -303.408797 0.299866
BFGS: 20 06:08:32 -303.414355 0.293992
BFGS: 21 06:08:32 -303.421473 0.348382
BFGS: 22 06:08:32 -303.431665 0.449038
BFGS: 23 06:08:32 -303.452693 0.792493
BFGS: 24 06:08:32 -303.485195 0.952124
BFGS: 25 06:08:32 -303.525766 0.825941
BFGS: 26 06:08:32 -303.565796 0.636950
BFGS: 27 06:08:32 -303.597504 0.706202
BFGS: 28 06:08:33 -303.659550 0.890237
BFGS: 29 06:08:33 -303.707523 0.895960
BFGS: 30 06:08:33 -303.768265 0.856473
BFGS: 31 06:08:33 -303.832733 0.697607
BFGS: 32 06:08:33 -303.860884 0.514215
BFGS: 33 06:08:33 -303.879730 0.441397
BFGS: 34 06:08:33 -303.892697 0.300199
BFGS: 35 06:08:33 -303.910249 0.174693
BFGS: 36 06:08:34 -303.919143 0.141133
BFGS: 37 06:08:34 -303.923276 0.118165
BFGS: 38 06:08:34 -303.924710 0.090855
BFGS: 39 06:08:34 -303.925789 0.068005
BFGS: 40 06:08:34 -303.926799 0.053695
BFGS: 41 06:08:34 -303.927520 0.048100
/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 06:10:05 -301.965038 4.569569
BFGS: 1 06:10:09 -302.079981 3.477206
BFGS: 2 06:10:18 -302.288844 2.466897
BFGS: 3 06:10:22 -302.375733 3.623812
BFGS: 4 06:10:28 -302.559941 3.311402
BFGS: 5 06:10:32 -302.589644 1.706402
BFGS: 6 06:10:36 -302.746908 1.638543
BFGS: 7 06:10:39 -302.961487 1.710057
BFGS: 8 06:10:44 -303.133233 1.457178
BFGS: 9 06:10:49 -303.369784 1.474317
BFGS: 10 06:10:52 -303.500694 1.354368
BFGS: 11 06:10:57 -303.563883 1.189554
BFGS: 12 06:11:00 -303.614524 0.799442
BFGS: 13 06:11:05 -303.646097 0.587609
BFGS: 14 06:11:13 -303.662077 0.323888
BFGS: 15 06:11:16 -303.661576 0.554354
BFGS: 16 06:11:23 -303.653351 0.483997
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BFGS: 163 06:15:24 -303.563666 2.951868
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BFGS: 174 06:15:43 -303.254152 3.330443
BFGS: 175 06:15:46 -303.280850 3.301249
BFGS: 176 06:15:47 -303.042628 4.574649
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BFGS: 182 06:15:57 -303.761079 2.860660
BFGS: 183 06:16:00 -303.888755 1.817398
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BFGS: 221 06:17:03 -303.723850 0.477014
BFGS: 222 06:17:05 -303.690962 0.918051
BFGS: 223 06:17:06 -303.677944 0.309674
BFGS: 224 06:17:07 -303.688825 0.616816
BFGS: 225 06:17:09 -303.723626 1.248052
BFGS: 226 06:17:10 -303.733338 0.647517
BFGS: 227 06:17:11 -303.715058 0.768783
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BFGS: 229 06:17:13 -303.702338 0.510592
BFGS: 230 06:17:15 -303.714450 1.286804
BFGS: 231 06:17:16 -303.731848 2.064393
BFGS: 232 06:17:19 -303.736960 2.270542
BFGS: 233 06:17:20 -303.714374 2.422226
BFGS: 234 06:17:21 -303.770212 1.480152
BFGS: 235 06:17:23 -303.761879 0.942910
BFGS: 236 06:17:24 -303.762224 0.716329
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BFGS: 275 06:18:28 -303.988029 1.347372
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BFGS: 288 06:18:46 -303.671717 1.466649
BFGS: 289 06:18:48 -303.690049 1.723710
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BFGS: 292 06:18:53 -303.756984 1.666107
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BFGS: 294 06:18:55 -303.739566 1.236866
BFGS: 295 06:18:57 -303.732454 1.102312
BFGS: 296 06:18:58 -303.729112 1.009878
BFGS: 297 06:18:59 -303.725731 0.894297
BFGS: 298 06:19:01 -303.719562 0.745545
BFGS: 299 06:19:03 -303.702412 0.593838
BFGS: 300 06:19:05 -303.696606 0.585832
BFGS: 301 06:19:06 -303.702417 0.600124
BFGS: 302 06:19:09 -303.722211 0.622624
BFGS: 303 06:19:11 -303.756830 0.652946
BFGS: 304 06:19:12 -303.773955 0.681866
BFGS: 305 06:19:15 -303.782162 1.448558
BFGS: 306 06:19:17 -303.783515 0.689474
BFGS: 307 06:19:20 -303.802949 0.639966
BFGS: 308 06:19:23 -303.813820 0.699175
BFGS: 309 06:19:24 -303.804632 0.702766
BFGS: 310 06:19:26 -303.765036 0.662532
BFGS: 311 06:19:27 -303.729134 0.803057
BFGS: 312 06:19:29 -303.715465 0.897058
BFGS: 313 06:19:30 -303.726940 0.665408
BFGS: 314 06:19:31 -303.743774 0.611981
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_10250/3247994494.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")