Transition State Search (NEBs)#
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.
The first section of this tutorial walks through how to use the CatTsunami tools to automatically enumerate a number of hypothetical initial/final configurations for various types of reactions on a heterogeneous catalyst surface. If you already have a NEB you’re looking to optimize, you can jump straight to the last section (Run NEBs)!
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 = 300
Need to install fairchem-core or get UMA access or getting permissions/401 errors?
Install the necessary packages using pip, uv etc
Get 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.
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,
)
# 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
)
# 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))
# 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-1p1")
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 21:21:26 -301.559904 4.135691
BFGS: 1 21:21:26 -301.933976 3.385659
BFGS: 2 21:21:26 -302.881417 3.209412
BFGS: 3 21:21:26 -303.005156 3.163942
BFGS: 4 21:21:26 -303.245962 2.316478
BFGS: 5 21:21:26 -303.455943 3.825987
BFGS: 6 21:21:26 -303.580894 2.153085
BFGS: 7 21:21:26 -303.903721 1.280130
BFGS: 8 21:21:26 -304.125447 2.062244
BFGS: 9 21:21:26 -304.208176 1.729804
BFGS: 10 21:21:26 -304.493724 1.191859
BFGS: 11 21:21:26 -304.540847 1.295915
BFGS: 12 21:21:27 -304.588931 0.652929
BFGS: 13 21:21:27 -304.600759 0.379222
BFGS: 14 21:21:27 -304.613630 0.351042
BFGS: 15 21:21:27 -304.643511 0.277552
BFGS: 16 21:21:27 -304.648665 0.232640
BFGS: 17 21:21:27 -304.653575 0.228980
BFGS: 18 21:21:27 -304.659393 0.245395
BFGS: 19 21:21:27 -304.668503 0.302512
BFGS: 20 21:21:27 -304.676201 0.221255
BFGS: 21 21:21:27 -304.680271 0.149514
BFGS: 22 21:21:27 -304.682727 0.135623
BFGS: 23 21:21:28 -304.684974 0.137810
BFGS: 24 21:21:28 -304.687160 0.137113
BFGS: 25 21:21:28 -304.689043 0.107181
BFGS: 26 21:21:28 -304.690029 0.071395
BFGS: 27 21:21:28 -304.690477 0.073516
BFGS: 28 21:21:28 -304.690871 0.078368
BFGS: 29 21:21:28 -304.691328 0.077547
BFGS: 30 21:21:28 -304.691798 0.060814
BFGS: 31 21:21:28 -304.692140 0.035223
Step Time Energy fmax
BFGS: 0 21:21:28 -300.908528 4.035530
BFGS: 1 21:21:28 -301.316240 3.256709
BFGS: 2 21:21:28 -302.504168 3.643420
BFGS: 3 21:21:29 -302.490270 6.612797
BFGS: 4 21:21:29 -302.870095 2.749739
BFGS: 5 21:21:29 -303.051438 1.160766
BFGS: 6 21:21:29 -303.087604 1.199993
BFGS: 7 21:21:29 -303.117964 0.791196
BFGS: 8 21:21:29 -303.140897 0.954710
BFGS: 9 21:21:29 -303.182801 0.584174
BFGS: 10 21:21:29 -303.187724 0.218188
BFGS: 11 21:21:29 -303.189469 0.168709
BFGS: 12 21:21:29 -303.191709 0.317367
BFGS: 13 21:21:29 -303.195332 0.410030
BFGS: 14 21:21:29 -303.199034 0.355856
BFGS: 15 21:21:30 -303.201253 0.206524
BFGS: 16 21:21:30 -303.202630 0.135159
BFGS: 17 21:21:30 -303.204428 0.254485
BFGS: 18 21:21:30 -303.207141 0.334876
BFGS: 19 21:21:30 -303.210938 0.298413
BFGS: 20 21:21:30 -303.213433 0.179335
BFGS: 21 21:21:30 -303.215409 0.162885
BFGS: 22 21:21:30 -303.219890 0.354967
BFGS: 23 21:21:30 -303.264260 1.180185
BFGS: 24 21:21:30 -303.413603 1.345195
BFGS: 25 21:21:30 -303.477186 2.753227
BFGS: 26 21:21:30 -303.601005 1.894634
BFGS: 27 21:21:31 -303.822051 1.985561
BFGS: 28 21:21:31 -303.945388 3.247328
BFGS: 29 21:21:31 -304.072314 2.458534
BFGS: 30 21:21:31 -304.157518 2.167520
BFGS: 31 21:21:31 -304.382388 1.308155
BFGS: 32 21:21:31 -304.427669 1.611916
BFGS: 33 21:21:31 -304.471749 1.019780
BFGS: 34 21:21:31 -304.514530 0.525254
BFGS: 35 21:21:31 -304.539387 0.526387
BFGS: 36 21:21:31 -304.593842 0.439381
BFGS: 37 21:21:31 -304.612786 0.370549
BFGS: 38 21:21:31 -304.624491 0.365034
BFGS: 39 21:21:32 -304.635812 0.360289
BFGS: 40 21:21:32 -304.650688 0.311705
BFGS: 41 21:21:32 -304.664475 0.297381
BFGS: 42 21:21:32 -304.673950 0.236470
BFGS: 43 21:21:32 -304.681179 0.150191
BFGS: 44 21:21:32 -304.684136 0.140648
BFGS: 45 21:21:32 -304.686332 0.123198
BFGS: 46 21:21:32 -304.688079 0.104013
BFGS: 47 21:21:32 -304.689672 0.060954
BFGS: 48 21:21:32 -304.690783 0.068064
BFGS: 49 21:21:32 -304.691400 0.056187
BFGS: 50 21:21:32 -304.691672 0.034738
Step Time Energy fmax
BFGS: 0 21:21:33 -301.158751 4.084730
BFGS: 1 21:21:33 -301.534147 3.383734
BFGS: 2 21:21:33 -302.535016 3.313709
BFGS: 3 21:21:33 -302.595553 4.500926
BFGS: 4 21:21:33 -302.862223 2.441974
BFGS: 5 21:21:33 -303.017565 1.667021
BFGS: 6 21:21:33 -303.058770 1.172722
BFGS: 7 21:21:33 -303.168073 1.698970
BFGS: 8 21:21:33 -303.224875 1.412170
BFGS: 9 21:21:33 -303.297109 0.650671
BFGS: 10 21:21:33 -303.323912 0.691955
BFGS: 11 21:21:33 -303.475291 1.839907
BFGS: 12 21:21:34 -303.595099 2.288488
BFGS: 13 21:21:34 -303.690005 2.428493
BFGS: 14 21:21:34 -303.869534 1.263397
BFGS: 15 21:21:34 -303.999053 1.802495
BFGS: 16 21:21:34 -304.000353 2.645626
BFGS: 17 21:21:34 -304.118169 0.825419
BFGS: 18 21:21:34 -304.153311 0.594334
BFGS: 19 21:21:34 -304.213298 0.763528
BFGS: 20 21:21:34 -304.240677 0.982603
BFGS: 21 21:21:35 -304.302800 1.301671
BFGS: 22 21:21:35 -304.378218 1.301300
BFGS: 23 21:21:35 -304.446937 1.197630
BFGS: 24 21:21:35 -304.538828 1.014373
BFGS: 25 21:21:35 -304.564009 0.558454
BFGS: 26 21:21:35 -304.591507 0.444433
BFGS: 27 21:21:35 -304.591179 0.569601
BFGS: 28 21:21:35 -304.614446 0.334817
BFGS: 29 21:21:35 -304.625359 0.310577
BFGS: 30 21:21:35 -304.635686 0.279366
BFGS: 31 21:21:35 -304.643219 0.295205
BFGS: 32 21:21:35 -304.649397 0.334714
BFGS: 33 21:21:36 -304.660003 0.359403
BFGS: 34 21:21:36 -304.671232 0.280519
BFGS: 35 21:21:36 -304.677895 0.228776
BFGS: 36 21:21:36 -304.680824 0.170365
BFGS: 37 21:21:36 -304.682908 0.138678
BFGS: 38 21:21:36 -304.685336 0.172475
BFGS: 39 21:21:36 -304.687948 0.162861
BFGS: 40 21:21:36 -304.689890 0.095646
BFGS: 41 21:21:36 -304.690769 0.062064
BFGS: 42 21:21:36 -304.691071 0.044797
Step Time Energy fmax
BFGS: 0 21:21:36 -301.030054 4.103750
BFGS: 1 21:21:36 -301.413382 3.442569
BFGS: 2 21:21:37 -302.465662 3.354088
BFGS: 3 21:21:37 -302.442906 5.871673
BFGS: 4 21:21:37 -302.776216 2.670671
BFGS: 5 21:21:37 -302.930860 1.309724
BFGS: 6 21:21:37 -303.003370 1.642763
BFGS: 7 21:21:37 -303.042479 0.878758
BFGS: 8 21:21:37 -303.117341 1.564995
BFGS: 9 21:21:37 -303.162261 1.288289
BFGS: 10 21:21:37 -303.202652 0.495918
BFGS: 11 21:21:37 -303.210326 0.320774
BFGS: 12 21:21:37 -303.219823 0.393685
BFGS: 13 21:21:37 -303.227163 0.404738
BFGS: 14 21:21:38 -303.232022 0.307453
BFGS: 15 21:21:38 -303.235266 0.297132
BFGS: 16 21:21:38 -303.239960 0.395559
BFGS: 17 21:21:38 -303.252264 0.681297
BFGS: 18 21:21:38 -303.324811 1.484139
BFGS: 19 21:21:38 -303.533429 1.713585
BFGS: 20 21:21:38 -303.784936 1.875986
BFGS: 21 21:21:38 -303.850036 2.016882
BFGS: 22 21:21:38 -303.944447 1.264075
BFGS: 23 21:21:38 -304.029258 0.731118
BFGS: 24 21:21:38 -304.112561 0.780137
BFGS: 25 21:21:38 -304.128036 0.643778
BFGS: 26 21:21:39 -304.156817 0.411825
BFGS: 27 21:21:39 -304.170256 0.270722
BFGS: 28 21:21:39 -304.176979 0.187076
BFGS: 29 21:21:39 -304.180614 0.168000
BFGS: 30 21:21:39 -304.186058 0.251111
BFGS: 31 21:21:39 -304.191015 0.270669
BFGS: 32 21:21:39 -304.194420 0.201020
BFGS: 33 21:21:39 -304.196669 0.157859
BFGS: 34 21:21:39 -304.199937 0.227431
BFGS: 35 21:21:39 -304.204740 0.373666
BFGS: 36 21:21:39 -304.212047 0.525567
BFGS: 37 21:21:40 -304.220790 0.547595
BFGS: 38 21:21:40 -304.231696 0.432716
BFGS: 39 21:21:40 -304.255489 0.367592
BFGS: 40 21:21:40 -304.269223 0.431544
BFGS: 41 21:21:40 -304.286381 0.627448
BFGS: 42 21:21:40 -304.298550 0.719235
BFGS: 43 21:21:40 -304.311160 0.310467
BFGS: 44 21:21:40 -304.322237 0.251208
BFGS: 45 21:21:40 -304.329471 0.240775
BFGS: 46 21:21:40 -304.334492 0.223850
BFGS: 47 21:21:40 -304.339292 0.174173
BFGS: 48 21:21:40 -304.344077 0.173808
BFGS: 49 21:21:41 -304.348751 0.165504
BFGS: 50 21:21:41 -304.351840 0.104367
BFGS: 51 21:21:41 -304.353092 0.107473
BFGS: 52 21:21:41 -304.354325 0.101848
BFGS: 53 21:21:41 -304.355196 0.082066
BFGS: 54 21:21:41 -304.356041 0.066610
BFGS: 55 21:21:41 -304.356662 0.052008
BFGS: 56 21:21:41 -304.356968 0.028533
Step Time Energy fmax
BFGS: 0 21:21:41 -301.072089 4.059658
BFGS: 1 21:21:41 -301.466616 3.049848
BFGS: 2 21:21:41 -302.570351 3.653797
BFGS: 3 21:21:41 -302.650663 4.920840
BFGS: 4 21:21:42 -302.965099 2.456672
BFGS: 5 21:21:42 -303.065841 2.648247
BFGS: 6 21:21:42 -303.115338 0.576087
BFGS: 7 21:21:42 -303.132038 0.490482
BFGS: 8 21:21:42 -303.221202 0.715285
BFGS: 9 21:21:42 -303.234074 0.440692
BFGS: 10 21:21:42 -303.243181 0.307658
BFGS: 11 21:21:42 -303.259068 0.497338
BFGS: 12 21:21:42 -303.274175 0.630776
BFGS: 13 21:21:42 -303.290843 0.708316
BFGS: 14 21:21:42 -303.308347 0.812313
BFGS: 15 21:21:42 -303.352936 1.258093
BFGS: 16 21:21:43 -303.417337 2.833778
BFGS: 17 21:21:43 -303.632049 1.464014
BFGS: 18 21:21:43 -303.823583 1.760925
BFGS: 19 21:21:43 -303.881903 1.736192
BFGS: 20 21:21:43 -304.023625 1.208496
BFGS: 21 21:21:43 -304.089765 1.198233
BFGS: 22 21:21:43 -304.160937 0.811168
BFGS: 23 21:21:43 -304.184947 0.643935
BFGS: 24 21:21:43 -304.227324 0.518364
BFGS: 25 21:21:43 -304.243638 0.449169
BFGS: 26 21:21:43 -304.259099 0.394393
BFGS: 27 21:21:43 -304.276134 0.348052
BFGS: 28 21:21:44 -304.290189 0.367742
BFGS: 29 21:21:44 -304.301446 0.468103
BFGS: 30 21:21:44 -304.313170 0.459952
BFGS: 31 21:21:44 -304.323018 0.367782
BFGS: 32 21:21:44 -304.331951 0.212329
BFGS: 33 21:21:44 -304.342355 0.262987
BFGS: 34 21:21:44 -304.346003 0.220290
BFGS: 35 21:21:44 -304.349506 0.185009
BFGS: 36 21:21:44 -304.353231 0.130338
BFGS: 37 21:21:44 -304.354700 0.067786
BFGS: 38 21:21:44 -304.355394 0.069365
BFGS: 39 21:21:44 -304.355861 0.051385
BFGS: 40 21:21:45 -304.356278 0.044565
Step Time Energy fmax
BFGS: 0 21:21:45 -301.268603 4.157227
BFGS: 1 21:21:45 -301.648701 3.616933
BFGS: 2 21:21:45 -302.668828 3.146492
BFGS: 3 21:21:45 -302.640344 6.068588
BFGS: 4 21:21:45 -303.011285 2.563778
BFGS: 5 21:21:45 -303.175437 1.521618
BFGS: 6 21:21:45 -303.359544 2.826492
BFGS: 7 21:21:45 -303.488339 2.359145
BFGS: 8 21:21:45 -303.767254 1.347729
BFGS: 9 21:21:45 -303.781262 1.944742
BFGS: 10 21:21:45 -303.916013 0.862541
BFGS: 11 21:21:46 -303.982942 0.771168
BFGS: 12 21:21:46 -304.086177 0.515263
BFGS: 13 21:21:46 -304.107522 0.552642
BFGS: 14 21:21:46 -304.138116 0.762027
BFGS: 15 21:21:46 -304.177619 0.793836
BFGS: 16 21:21:46 -304.221879 0.664587
BFGS: 17 21:21:46 -304.263776 0.876856
BFGS: 18 21:21:46 -304.304467 1.015517
BFGS: 19 21:21:46 -304.350914 0.850522
BFGS: 20 21:21:46 -304.432397 0.746578
BFGS: 21 21:21:46 -304.470202 0.838785
BFGS: 22 21:21:46 -304.495915 1.049707
BFGS: 23 21:21:47 -304.527452 0.679569
BFGS: 24 21:21:47 -304.547009 0.557519
BFGS: 25 21:21:47 -304.570747 0.445707
BFGS: 26 21:21:47 -304.596468 0.598845
BFGS: 27 21:21:47 -304.623415 0.614700
BFGS: 28 21:21:47 -304.643415 0.496468
BFGS: 29 21:21:47 -304.659724 0.382007
BFGS: 30 21:21:47 -304.670166 0.347993
BFGS: 31 21:21:47 -304.678882 0.262668
BFGS: 32 21:21:47 -304.684685 0.149354
BFGS: 33 21:21:47 -304.687423 0.080496
BFGS: 34 21:21:47 -304.688462 0.072829
BFGS: 35 21:21:48 -304.689020 0.091680
BFGS: 36 21:21:48 -304.689624 0.099491
BFGS: 37 21:21:48 -304.690380 0.088799
BFGS: 38 21:21:48 -304.691171 0.056799
BFGS: 39 21:21:48 -304.691669 0.030173
Step Time Energy fmax
BFGS: 0 21:21:48 -300.754673 4.032273
BFGS: 1 21:21:48 -301.159535 3.511008
BFGS: 2 21:21:48 -302.368430 3.463815
BFGS: 3 21:21:48 -301.881196 11.340914
BFGS: 4 21:21:48 -302.656205 3.024625
BFGS: 5 21:21:48 -302.808860 2.406164
BFGS: 6 21:21:48 -302.995842 2.284701
BFGS: 7 21:21:49 -303.063845 0.848616
BFGS: 8 21:21:49 -303.091356 0.769267
BFGS: 9 21:21:49 -303.169163 0.973792
BFGS: 10 21:21:49 -303.180680 0.278799
BFGS: 11 21:21:49 -303.183430 0.114438
BFGS: 12 21:21:49 -303.185451 0.118575
BFGS: 13 21:21:49 -303.186725 0.123022
BFGS: 14 21:21:49 -303.188499 0.104059
BFGS: 15 21:21:49 -303.189486 0.062412
BFGS: 16 21:21:49 -303.189845 0.039191
Step Time Energy fmax
BFGS: 0 21:21:49 -300.929569 3.978121
BFGS: 1 21:21:50 -301.341472 3.375961
BFGS: 2 21:21:50 -302.563997 3.682356
BFGS: 3 21:21:50 -302.593104 5.955489
BFGS: 4 21:21:50 -302.941720 2.637311
BFGS: 5 21:21:50 -303.092220 1.765710
BFGS: 6 21:21:50 -303.114891 0.639904
BFGS: 7 21:21:50 -303.131652 0.559781
BFGS: 8 21:21:50 -303.150791 0.868422
BFGS: 9 21:21:50 -303.176185 0.808339
BFGS: 10 21:21:50 -303.188308 0.389436
BFGS: 11 21:21:50 -303.191546 0.184958
BFGS: 12 21:21:50 -303.196333 0.413254
BFGS: 13 21:21:51 -303.202247 0.566629
BFGS: 14 21:21:51 -303.210755 0.587472
BFGS: 15 21:21:51 -303.217758 0.441105
BFGS: 16 21:21:51 -303.222359 0.301296
BFGS: 17 21:21:51 -303.229437 0.456206
BFGS: 18 21:21:51 -303.240134 0.761767
BFGS: 19 21:21:51 -303.303423 1.802440
BFGS: 20 21:21:51 -303.496325 1.915551
BFGS: 21 21:21:51 -303.517643 3.026082
BFGS: 22 21:21:51 -303.824479 1.229313
BFGS: 23 21:21:51 -303.949428 2.220562
BFGS: 24 21:21:51 -304.033347 1.419826
BFGS: 25 21:21:52 -304.070150 1.247048
BFGS: 26 21:21:52 -304.146445 0.714145
BFGS: 27 21:21:52 -304.179262 0.715432
BFGS: 28 21:21:52 -304.351500 0.785021
BFGS: 29 21:21:52 -304.431372 1.134507
BFGS: 30 21:21:52 -304.489697 0.996566
BFGS: 31 21:21:52 -304.535931 1.054240
BFGS: 32 21:21:52 -304.579433 0.953332
BFGS: 33 21:21:52 -304.618686 0.503575
BFGS: 34 21:21:52 -304.635160 0.384837
BFGS: 35 21:21:52 -304.644271 0.302508
BFGS: 36 21:21:52 -304.651449 0.266886
BFGS: 37 21:21:53 -304.659618 0.211147
BFGS: 38 21:21:53 -304.665225 0.201583
BFGS: 39 21:21:53 -304.668338 0.190422
BFGS: 40 21:21:53 -304.670285 0.179922
BFGS: 41 21:21:53 -304.672168 0.170320
BFGS: 42 21:21:53 -304.674791 0.152876
BFGS: 43 21:21:53 -304.678113 0.180629
BFGS: 44 21:21:53 -304.681139 0.185558
BFGS: 45 21:21:53 -304.683025 0.143356
BFGS: 46 21:21:53 -304.684000 0.117135
BFGS: 47 21:21:53 -304.684858 0.134006
BFGS: 48 21:21:53 -304.685996 0.156736
BFGS: 49 21:21:54 -304.687069 0.169801
BFGS: 50 21:21:54 -304.687681 0.164748
BFGS: 51 21:21:54 -304.687916 0.151246
BFGS: 52 21:21:54 -304.688057 0.138995
BFGS: 53 21:21:54 -304.688223 0.126892
BFGS: 54 21:21:54 -304.688425 0.117730
BFGS: 55 21:21:54 -304.688609 0.116224
BFGS: 56 21:21:54 -304.688720 0.121132
BFGS: 57 21:21:54 -304.688772 0.125919
BFGS: 58 21:21:54 -304.688816 0.128835
BFGS: 59 21:21:54 -304.688867 0.131498
BFGS: 60 21:21:54 -304.688941 0.133449
BFGS: 61 21:21:55 -304.689013 0.133870
BFGS: 62 21:21:55 -304.689052 0.132686
BFGS: 63 21:21:55 -304.689072 0.131082
BFGS: 64 21:21:55 -304.689081 0.129779
BFGS: 65 21:21:55 -304.689094 0.128501
BFGS: 66 21:21:55 -304.689113 0.126977
BFGS: 67 21:21:55 -304.689143 0.125528
BFGS: 68 21:21:55 -304.689172 0.125748
BFGS: 69 21:21:55 -304.689187 0.127343
BFGS: 70 21:21:55 -304.689195 0.129462
BFGS: 71 21:21:55 -304.689197 0.130910
BFGS: 72 21:21:55 -304.689199 0.132908
BFGS: 73 21:21:56 -304.689204 0.134889
BFGS: 74 21:21:56 -304.689212 0.136946
BFGS: 75 21:21:56 -304.689221 0.136808
BFGS: 76 21:21:56 -304.689226 0.134353
BFGS: 77 21:21:56 -304.689228 0.131392
BFGS: 78 21:21:56 -304.689231 0.129829
BFGS: 79 21:21:56 -304.689231 0.128145
BFGS: 80 21:21:56 -304.689235 0.126700
BFGS: 81 21:21:56 -304.689236 0.125510
BFGS: 82 21:21:56 -304.689239 0.126123
BFGS: 83 21:21:56 -304.689238 0.127728
BFGS: 84 21:21:56 -304.689239 0.128635
BFGS: 85 21:21:57 -304.689239 0.129682
BFGS: 86 21:21:57 -304.689239 0.130325
BFGS: 87 21:21:57 -304.689239 0.131219
BFGS: 88 21:21:57 -304.689242 0.131506
BFGS: 89 21:21:57 -304.689241 0.130583
BFGS: 90 21:21:57 -304.689242 0.129577
BFGS: 91 21:21:57 -304.689244 0.128808
BFGS: 92 21:21:57 -304.689244 0.128495
BFGS: 93 21:21:57 -304.689243 0.127898
BFGS: 94 21:21:57 -304.689243 0.127501
BFGS: 95 21:21:57 -304.689244 0.127841
BFGS: 96 21:21:57 -304.689245 0.128432
BFGS: 97 21:21:58 -304.689245 0.129030
BFGS: 98 21:21:58 -304.689244 0.129325
BFGS: 99 21:21:58 -304.689246 0.129434
BFGS: 100 21:21:58 -304.689244 0.129765
BFGS: 101 21:21:58 -304.689245 0.129836
BFGS: 102 21:21:58 -304.689244 0.129576
BFGS: 103 21:21:58 -304.689245 0.129378
BFGS: 104 21:21:58 -304.689244 0.129051
BFGS: 105 21:21:58 -304.689246 0.129050
BFGS: 106 21:21:58 -304.689244 0.129012
BFGS: 107 21:21:58 -304.689244 0.128866
BFGS: 108 21:21:58 -304.689245 0.128963
BFGS: 109 21:21:59 -304.689244 0.129047
BFGS: 110 21:21:59 -304.689244 0.129133
BFGS: 111 21:21:59 -304.689246 0.129090
BFGS: 112 21:21:59 -304.689244 0.129214
BFGS: 113 21:21:59 -304.689244 0.129192
BFGS: 114 21:21:59 -304.689246 0.129155
BFGS: 115 21:21:59 -304.689246 0.129138
BFGS: 116 21:21:59 -304.689245 0.129025
BFGS: 117 21:21:59 -304.689246 0.129091
BFGS: 118 21:21:59 -304.689243 0.129134
BFGS: 119 21:21:59 -304.689244 0.129120
BFGS: 120 21:21:59 -304.689245 0.129163
BFGS: 121 21:22:00 -304.689244 0.129161
BFGS: 122 21:22:00 -304.689244 0.129077
BFGS: 123 21:22:00 -304.689245 0.129071
BFGS: 124 21:22:00 -304.689244 0.129096
BFGS: 125 21:22:00 -304.689244 0.129211
BFGS: 126 21:22:00 -304.689244 0.129210
BFGS: 127 21:22:00 -304.689244 0.129186
BFGS: 128 21:22:00 -304.689246 0.129121
BFGS: 129 21:22:00 -304.689244 0.129143
BFGS: 130 21:22:00 -304.689244 0.129223
BFGS: 131 21:22:00 -304.689243 0.129097
BFGS: 132 21:22:00 -304.689244 0.129158
BFGS: 133 21:22:01 -304.689244 0.129206
BFGS: 134 21:22:01 -304.689246 0.129138
BFGS: 135 21:22:01 -304.689245 0.129122
BFGS: 136 21:22:01 -304.689245 0.129124
BFGS: 137 21:22:01 -304.689246 0.129117
BFGS: 138 21:22:01 -304.689246 0.129174
BFGS: 139 21:22:01 -304.689244 0.129185
BFGS: 140 21:22:01 -304.689244 0.129140
BFGS: 141 21:22:01 -304.689245 0.129194
BFGS: 142 21:22:01 -304.689246 0.129140
BFGS: 143 21:22:01 -304.689245 0.129126
BFGS: 144 21:22:01 -304.689246 0.129141
BFGS: 145 21:22:02 -304.689246 0.129131
BFGS: 146 21:22:02 -304.689246 0.129135
BFGS: 147 21:22:02 -304.689244 0.129137
BFGS: 148 21:22:02 -304.689244 0.129131
BFGS: 149 21:22:02 -304.689246 0.129128
BFGS: 150 21:22:02 -304.689246 0.129124
BFGS: 151 21:22:02 -304.689245 0.129126
BFGS: 152 21:22:02 -304.689245 0.129201
BFGS: 153 21:22:02 -304.689245 0.129202
BFGS: 154 21:22:02 -304.689245 0.129130
BFGS: 155 21:22:02 -304.689243 0.129128
BFGS: 156 21:22:03 -304.689245 0.129150
BFGS: 157 21:22:03 -304.689244 0.129131
BFGS: 158 21:22:03 -304.689246 0.129129
BFGS: 159 21:22:03 -304.689244 0.129208
BFGS: 160 21:22:03 -304.689244 0.129131
BFGS: 161 21:22:03 -304.689245 0.129129
BFGS: 162 21:22:03 -304.689245 0.129130
BFGS: 163 21:22:03 -304.689243 0.129139
BFGS: 164 21:22:03 -304.689244 0.129135
BFGS: 165 21:22:03 -304.689244 0.129125
BFGS: 166 21:22:03 -304.689245 0.129133
BFGS: 167 21:22:03 -304.689245 0.129132
BFGS: 168 21:22:04 -304.689246 0.129138
BFGS: 169 21:22:04 -304.689246 0.129128
BFGS: 170 21:22:04 -304.689245 0.129128
BFGS: 171 21:22:04 -304.689244 0.129185
BFGS: 172 21:22:04 -304.689245 0.129189
BFGS: 173 21:22:04 -304.689247 0.129128
BFGS: 174 21:22:04 -304.689246 0.129131
BFGS: 175 21:22:04 -304.689246 0.129187
BFGS: 176 21:22:04 -304.689245 0.129137
BFGS: 177 21:22:04 -304.689244 0.129132
BFGS: 178 21:22:04 -304.689246 0.129180
BFGS: 179 21:22:04 -304.689244 0.129188
BFGS: 180 21:22:05 -304.689246 0.129199
BFGS: 181 21:22:05 -304.689243 0.129080
BFGS: 182 21:22:05 -304.689246 0.129136
BFGS: 183 21:22:05 -304.689245 0.129198
BFGS: 184 21:22:05 -304.689244 0.129131
BFGS: 185 21:22:05 -304.689245 0.129137
BFGS: 186 21:22:05 -304.689246 0.129134
BFGS: 187 21:22:05 -304.689244 0.129179
BFGS: 188 21:22:05 -304.689244 0.129130
BFGS: 189 21:22:05 -304.689246 0.129183
BFGS: 190 21:22:05 -304.689244 0.129185
BFGS: 191 21:22:05 -304.689245 0.129140
BFGS: 192 21:22:06 -304.689245 0.129141
BFGS: 193 21:22:06 -304.689244 0.129178
BFGS: 194 21:22:06 -304.689244 0.129127
BFGS: 195 21:22:06 -304.689245 0.129135
BFGS: 196 21:22:06 -304.689246 0.129134
BFGS: 197 21:22:06 -304.689246 0.129180
BFGS: 198 21:22:06 -304.689245 0.129182
BFGS: 199 21:22:06 -304.689246 0.129145
BFGS: 200 21:22:06 -304.689246 0.129140
BFGS: 201 21:22:06 -304.689244 0.129297
BFGS: 202 21:22:06 -304.689244 0.129129
BFGS: 203 21:22:06 -304.689246 0.129134
BFGS: 204 21:22:07 -304.689246 0.129185
BFGS: 205 21:22:07 -304.689246 0.129180
BFGS: 206 21:22:07 -304.689244 0.129047
BFGS: 207 21:22:07 -304.689244 0.129139
BFGS: 208 21:22:07 -304.689246 0.129182
BFGS: 209 21:22:07 -304.689244 0.129139
BFGS: 210 21:22:07 -304.689246 0.129141
BFGS: 211 21:22:07 -304.689245 0.129230
BFGS: 212 21:22:07 -304.689246 0.129178
BFGS: 213 21:22:07 -304.689244 0.129141
BFGS: 214 21:22:07 -304.689247 0.129139
BFGS: 215 21:22:07 -304.689244 0.129344
BFGS: 216 21:22:08 -304.689246 0.129183
BFGS: 217 21:22:08 -304.689244 0.129144
BFGS: 218 21:22:08 -304.689244 0.129137
BFGS: 219 21:22:08 -304.689244 0.129233
BFGS: 220 21:22:08 -304.689246 0.129189
BFGS: 221 21:22:08 -304.689244 0.129140
BFGS: 222 21:22:08 -304.689244 0.129133
BFGS: 223 21:22:08 -304.689246 0.129177
BFGS: 224 21:22:08 -304.689246 0.129182
BFGS: 225 21:22:08 -304.689246 0.129055
BFGS: 226 21:22:08 -304.689244 0.129139
BFGS: 227 21:22:08 -304.689245 0.129184
BFGS: 228 21:22:09 -304.689246 0.129141
BFGS: 229 21:22:09 -304.689244 0.129181
BFGS: 230 21:22:09 -304.689244 0.129187
BFGS: 231 21:22:09 -304.689246 0.129144
BFGS: 232 21:22:09 -304.689244 0.129139
BFGS: 233 21:22:09 -304.689246 0.129243
BFGS: 234 21:22:09 -304.689245 0.129186
BFGS: 235 21:22:09 -304.689244 0.129139
BFGS: 236 21:22:09 -304.689246 0.129129
BFGS: 237 21:22:09 -304.689244 0.129353
BFGS: 238 21:22:09 -304.689244 0.129187
BFGS: 239 21:22:09 -304.689244 0.129136
BFGS: 240 21:22:10 -304.689244 0.129135
BFGS: 241 21:22:10 -304.689245 0.129395
BFGS: 242 21:22:10 -304.689245 0.129192
BFGS: 243 21:22:10 -304.689246 0.129130
BFGS: 244 21:22:10 -304.689246 0.129131
BFGS: 245 21:22:10 -304.689246 0.129242
BFGS: 246 21:22:10 -304.689247 0.129191
BFGS: 247 21:22:10 -304.689245 0.129130
BFGS: 248 21:22:10 -304.689246 0.129136
BFGS: 249 21:22:10 -304.689246 0.129292
BFGS: 250 21:22:10 -304.689246 0.129185
BFGS: 251 21:22:10 -304.689245 0.129132
BFGS: 252 21:22:11 -304.689246 0.129131
BFGS: 253 21:22:11 -304.689246 0.129236
BFGS: 254 21:22:11 -304.689247 0.129185
BFGS: 255 21:22:11 -304.689244 0.129134
BFGS: 256 21:22:11 -304.689246 0.129138
BFGS: 257 21:22:11 -304.689245 0.129410
BFGS: 258 21:22:11 -304.689246 0.129191
BFGS: 259 21:22:11 -304.689246 0.129200
BFGS: 260 21:22:11 -304.689244 0.129073
BFGS: 261 21:22:11 -304.689245 0.129127
BFGS: 262 21:22:11 -304.689246 0.129186
BFGS: 263 21:22:11 -304.689244 0.129200
BFGS: 264 21:22:12 -304.689245 0.127945
BFGS: 265 21:22:12 -304.689245 0.129133
BFGS: 266 21:22:12 -304.689246 0.129143
BFGS: 267 21:22:12 -304.689246 0.129239
BFGS: 268 21:22:12 -304.689247 0.129184
BFGS: 269 21:22:12 -304.689246 0.129133
BFGS: 270 21:22:12 -304.689244 0.129138
BFGS: 271 21:22:12 -304.689244 0.129362
BFGS: 272 21:22:12 -304.689246 0.129192
BFGS: 273 21:22:12 -304.689246 0.129199
BFGS: 274 21:22:12 -304.689246 0.129147
BFGS: 275 21:22:12 -304.689245 0.129207
BFGS: 276 21:22:13 -304.689246 0.129080
BFGS: 277 21:22:13 -304.689247 0.129126
BFGS: 278 21:22:13 -304.689246 0.129132
BFGS: 279 21:22:13 -304.689246 0.129260
BFGS: 280 21:22:13 -304.689244 0.129209
BFGS: 281 21:22:13 -304.689244 0.129132
BFGS: 282 21:22:13 -304.689246 0.129134
BFGS: 283 21:22:13 -304.689246 0.129433
BFGS: 284 21:22:13 -304.689244 0.129144
BFGS: 285 21:22:14 -304.689245 0.129194
BFGS: 286 21:22:14 -304.689246 0.129141
BFGS: 287 21:22:14 -304.689246 0.129136
BFGS: 288 21:22:14 -304.689246 0.129185
BFGS: 289 21:22:14 -304.689246 0.129180
BFGS: 290 21:22:14 -304.689244 0.128881
BFGS: 291 21:22:14 -304.689245 0.129141
BFGS: 292 21:22:14 -304.689245 0.129184
BFGS: 293 21:22:14 -304.689245 0.129210
BFGS: 294 21:22:14 -304.689246 0.129077
BFGS: 295 21:22:14 -304.689245 0.129132
BFGS: 296 21:22:14 -304.689246 0.129186
BFGS: 297 21:22:15 -304.689246 0.129142
BFGS: 298 21:22:15 -304.689244 0.129185
BFGS: 299 21:22:15 -304.689246 0.129130
BFGS: 300 21:22:15 -304.689245 0.129137
Step Time Energy fmax
BFGS: 0 21:22:15 -302.448596 4.046439
BFGS: 1 21:22:15 -302.812276 3.048961
BFGS: 2 21:22:15 -303.652134 3.095557
BFGS: 3 21:22:15 -303.812085 2.748342
BFGS: 4 21:22:15 -304.068007 1.341089
BFGS: 5 21:22:15 -304.139372 1.500039
BFGS: 6 21:22:15 -304.263133 2.044030
BFGS: 7 21:22:15 -304.429885 1.496937
BFGS: 8 21:22:16 -304.477698 1.062379
BFGS: 9 21:22:16 -304.565680 1.048636
BFGS: 10 21:22:16 -304.600266 1.092402
BFGS: 11 21:22:16 -304.628337 0.605364
BFGS: 12 21:22:16 -304.640928 0.262519
BFGS: 13 21:22:16 -304.646350 0.279484
BFGS: 14 21:22:16 -304.655414 0.304426
BFGS: 15 21:22:16 -304.662916 0.239742
BFGS: 16 21:22:16 -304.668285 0.192168
BFGS: 17 21:22:16 -304.671713 0.188823
BFGS: 18 21:22:16 -304.675144 0.193072
BFGS: 19 21:22:16 -304.678727 0.175477
BFGS: 20 21:22:17 -304.681695 0.132420
BFGS: 21 21:22:17 -304.683875 0.128810
BFGS: 22 21:22:17 -304.685793 0.127072
BFGS: 23 21:22:17 -304.687663 0.133936
BFGS: 24 21:22:17 -304.689373 0.097904
BFGS: 25 21:22:17 -304.690436 0.045240
Step Time Energy fmax
BFGS: 0 21:22:17 -301.240680 4.006689
BFGS: 1 21:22:17 -301.622556 2.976833
BFGS: 2 21:22:17 -302.663473 3.604301
BFGS: 3 21:22:17 -302.790363 3.799642
BFGS: 4 21:22:17 -303.085749 1.994693
BFGS: 5 21:22:17 -303.149598 2.341774
BFGS: 6 21:22:18 -303.201659 0.772556
BFGS: 7 21:22:18 -303.233853 0.675583
BFGS: 8 21:22:18 -303.475004 1.343450
BFGS: 9 21:22:18 -303.604747 1.637458
BFGS: 10 21:22:18 -303.772207 1.850318
BFGS: 11 21:22:18 -303.971206 1.519092
BFGS: 12 21:22:18 -304.104464 1.816920
BFGS: 13 21:22:18 -304.223380 1.281458
BFGS: 14 21:22:18 -304.327186 0.901292
BFGS: 15 21:22:18 -304.360313 0.877320
BFGS: 16 21:22:18 -304.432463 0.925989
BFGS: 17 21:22:18 -304.487914 0.765811
BFGS: 18 21:22:19 -304.549666 0.713131
BFGS: 19 21:22:19 -304.590914 0.574165
BFGS: 20 21:22:19 -304.606697 0.366774
BFGS: 21 21:22:19 -304.621639 0.362148
BFGS: 22 21:22:19 -304.633996 0.520239
BFGS: 23 21:22:19 -304.646741 0.472475
BFGS: 24 21:22:19 -304.654613 0.244207
BFGS: 25 21:22:19 -304.658381 0.243042
BFGS: 26 21:22:19 -304.663540 0.307623
BFGS: 27 21:22:19 -304.671208 0.433511
BFGS: 28 21:22:19 -304.679222 0.362546
BFGS: 29 21:22:19 -304.683526 0.161332
BFGS: 30 21:22:20 -304.685168 0.108473
BFGS: 31 21:22:20 -304.686458 0.125117
BFGS: 32 21:22:20 -304.687792 0.159838
BFGS: 33 21:22:20 -304.689446 0.145935
BFGS: 34 21:22:20 -304.690848 0.095471
BFGS: 35 21:22:20 -304.691525 0.047274
# 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 21:22:20 -296.751959 4.478050
BFGS: 1 21:22:20 -297.218683 4.655324
BFGS: 2 21:22:20 -298.532833 3.511352
BFGS: 3 21:22:20 -298.546563 6.754098
BFGS: 4 21:22:20 -298.899859 1.938203
BFGS: 5 21:22:21 -298.994992 1.646349
BFGS: 6 21:22:21 -299.324722 2.088282
BFGS: 7 21:22:21 -299.603233 2.094832
BFGS: 8 21:22:21 -299.753609 1.361123
BFGS: 9 21:22:21 -299.838831 0.999578
BFGS: 10 21:22:21 -300.008911 0.836079
BFGS: 11 21:22:21 -300.025768 0.702822
BFGS: 12 21:22:21 -300.050915 0.314031
BFGS: 13 21:22:21 -300.056285 0.218795
BFGS: 14 21:22:21 -300.061922 0.287027
BFGS: 15 21:22:21 -300.070281 0.287464
BFGS: 16 21:22:21 -300.074919 0.209458
BFGS: 17 21:22:22 -300.076667 0.134673
BFGS: 18 21:22:22 -300.077394 0.088003
BFGS: 19 21:22:22 -300.078180 0.111862
BFGS: 20 21:22:22 -300.079067 0.128282
BFGS: 21 21:22:22 -300.079931 0.109547
BFGS: 22 21:22:22 -300.080449 0.058570
BFGS: 23 21:22:22 -300.080613 0.022116
Step Time Energy fmax
BFGS: 0 21:22:22 -296.446032 4.422057
BFGS: 1 21:22:22 -296.916379 4.666737
BFGS: 2 21:22:22 -298.325025 3.478238
BFGS: 3 21:22:22 -298.096343 8.644281
BFGS: 4 21:22:22 -298.633390 1.950410
BFGS: 5 21:22:23 -298.715298 1.388769
BFGS: 6 21:22:23 -298.857513 2.142159
BFGS: 7 21:22:23 -299.037088 2.716388
BFGS: 8 21:22:23 -299.296731 2.713902
BFGS: 9 21:22:23 -299.420037 1.946073
BFGS: 10 21:22:23 -299.491945 1.854092
BFGS: 11 21:22:23 -300.034577 1.199324
BFGS: 12 21:22:23 -300.131990 1.161905
BFGS: 13 21:22:23 -300.245113 1.333305
BFGS: 14 21:22:23 -300.336598 1.291552
BFGS: 15 21:22:23 -300.437610 1.125769
BFGS: 16 21:22:23 -300.510743 0.908864
BFGS: 17 21:22:24 -300.541440 0.712184
BFGS: 18 21:22:24 -300.570077 0.345129
BFGS: 19 21:22:24 -300.581210 0.486698
BFGS: 20 21:22:24 -300.595705 0.522771
BFGS: 21 21:22:24 -300.610513 0.377750
BFGS: 22 21:22:24 -300.618512 0.169829
BFGS: 23 21:22:24 -300.620824 0.080736
BFGS: 24 21:22:24 -300.621681 0.069613
BFGS: 25 21:22:24 -300.622381 0.081578
BFGS: 26 21:22:24 -300.623068 0.087174
BFGS: 27 21:22:24 -300.623907 0.066952
BFGS: 28 21:22:25 -300.624576 0.033366
Step Time Energy fmax
BFGS: 0 21:22:25 -297.017448 4.583205
BFGS: 1 21:22:25 -297.498118 4.752612
BFGS: 2 21:22:25 -298.770860 3.816429
BFGS: 3 21:22:25 -299.184639 3.878368
BFGS: 4 21:22:25 -299.353235 1.720990
BFGS: 5 21:22:25 -299.558327 1.638113
BFGS: 6 21:22:25 -299.761226 1.232354
BFGS: 7 21:22:25 -299.791146 0.648943
BFGS: 8 21:22:25 -299.819642 0.611074
BFGS: 9 21:22:25 -299.896165 0.509752
BFGS: 10 21:22:25 -299.909269 0.352300
BFGS: 11 21:22:26 -299.926263 0.382483
BFGS: 12 21:22:26 -299.934237 0.454637
BFGS: 13 21:22:26 -299.949172 0.530531
BFGS: 14 21:22:26 -299.959132 0.567420
BFGS: 15 21:22:26 -300.011647 1.186312
BFGS: 16 21:22:26 -300.060536 1.766894
BFGS: 17 21:22:26 -300.137941 1.721704
BFGS: 18 21:22:26 -300.265842 1.660951
BFGS: 19 21:22:26 -300.329906 1.172280
BFGS: 20 21:22:26 -300.461235 0.712161
BFGS: 21 21:22:26 -300.508677 0.895923
BFGS: 22 21:22:26 -300.544049 0.812199
BFGS: 23 21:22:27 -300.582661 0.430522
BFGS: 24 21:22:27 -300.595656 0.381463
BFGS: 25 21:22:27 -300.603845 0.338553
BFGS: 26 21:22:27 -300.613057 0.234626
BFGS: 27 21:22:27 -300.618689 0.159115
BFGS: 28 21:22:27 -300.622295 0.100801
BFGS: 29 21:22:27 -300.623325 0.051895
BFGS: 30 21:22:27 -300.623616 0.049067
Step Time Energy fmax
BFGS: 0 21:22:27 -297.250190 4.552490
BFGS: 1 21:22:27 -297.727027 4.667856
BFGS: 2 21:22:27 -298.981858 3.472253
BFGS: 3 21:22:27 -299.197332 4.747592
BFGS: 4 21:22:28 -299.420469 1.599775
BFGS: 5 21:22:28 -299.531117 1.440499
BFGS: 6 21:22:28 -299.768620 1.513571
BFGS: 7 21:22:28 -299.805063 0.891715
BFGS: 8 21:22:28 -299.873745 1.043789
BFGS: 9 21:22:28 -299.933650 1.073938
BFGS: 10 21:22:28 -299.975294 0.778657
BFGS: 11 21:22:28 -300.001181 0.491516
BFGS: 12 21:22:28 -300.010720 0.406345
BFGS: 13 21:22:28 -300.017599 0.453969
BFGS: 14 21:22:28 -300.030063 0.491275
BFGS: 15 21:22:28 -300.042509 0.388067
BFGS: 16 21:22:29 -300.051099 0.248517
BFGS: 17 21:22:29 -300.058562 0.288020
BFGS: 18 21:22:29 -300.067076 0.238346
BFGS: 19 21:22:29 -300.073160 0.173353
BFGS: 20 21:22:29 -300.076452 0.144268
BFGS: 21 21:22:29 -300.077838 0.096745
BFGS: 22 21:22:29 -300.078629 0.053536
BFGS: 23 21:22:29 -300.079166 0.047453
Step Time Energy fmax
BFGS: 0 21:22:29 -297.227583 4.505389
BFGS: 1 21:22:29 -297.694166 4.622231
BFGS: 2 21:22:29 -298.938008 3.465783
BFGS: 3 21:22:29 -299.133472 4.985581
BFGS: 4 21:22:30 -299.371275 1.758805
BFGS: 5 21:22:30 -299.492445 1.663113
BFGS: 6 21:22:30 -299.835582 0.867359
BFGS: 7 21:22:30 -299.890116 1.591484
BFGS: 8 21:22:30 -299.940295 0.962981
BFGS: 9 21:22:30 -300.017577 0.837245
BFGS: 10 21:22:30 -300.050191 0.613407
BFGS: 11 21:22:30 -300.065835 0.305084
BFGS: 12 21:22:30 -300.071026 0.217691
BFGS: 13 21:22:30 -300.073445 0.227040
BFGS: 14 21:22:30 -300.075577 0.172928
BFGS: 15 21:22:31 -300.076991 0.124359
BFGS: 16 21:22:31 -300.077748 0.101777
BFGS: 17 21:22:31 -300.078123 0.084090
BFGS: 18 21:22:31 -300.078519 0.086077
BFGS: 19 21:22:31 -300.079188 0.096703
BFGS: 20 21:22:31 -300.079974 0.092779
BFGS: 21 21:22:31 -300.080486 0.064159
BFGS: 22 21:22:31 -300.080667 0.024674
Step Time Energy fmax
BFGS: 0 21:22:31 -296.013477 4.355608
BFGS: 1 21:22:31 -296.539685 4.727520
BFGS: 2 21:22:31 -298.206717 3.059587
BFGS: 3 21:22:31 -296.837545 16.600302
BFGS: 4 21:22:32 -298.385762 1.868072
BFGS: 5 21:22:32 -298.448484 1.046345
BFGS: 6 21:22:32 -298.484000 0.607539
BFGS: 7 21:22:32 -298.488598 0.334247
BFGS: 8 21:22:32 -298.494865 0.161054
BFGS: 9 21:22:32 -298.496994 0.194654
BFGS: 10 21:22:32 -298.497989 0.164663
BFGS: 11 21:22:32 -298.498862 0.139444
BFGS: 12 21:22:32 -298.501094 0.159204
BFGS: 13 21:22:32 -298.507727 0.311537
BFGS: 14 21:22:32 -298.533908 0.712652
BFGS: 15 21:22:32 -298.545897 1.234519
BFGS: 16 21:22:33 -298.600850 0.704754
BFGS: 17 21:22:33 -298.640774 0.868556
BFGS: 18 21:22:33 -298.718156 1.318763
BFGS: 19 21:22:33 -298.793419 1.866355
BFGS: 20 21:22:33 -298.858617 2.382457
BFGS: 21 21:22:33 -298.991129 2.551267
BFGS: 22 21:22:33 -299.374224 1.865609
BFGS: 23 21:22:33 -299.773970 0.700875
BFGS: 24 21:22:33 -299.820856 0.588977
BFGS: 25 21:22:33 -299.880142 0.917545
BFGS: 26 21:22:33 -299.908576 0.624331
BFGS: 27 21:22:33 -299.926544 0.399688
BFGS: 28 21:22:34 -299.931906 0.388930
BFGS: 29 21:22:34 -299.944733 0.374328
BFGS: 30 21:22:34 -299.960240 0.438521
BFGS: 31 21:22:34 -299.972635 0.437349
BFGS: 32 21:22:34 -299.981787 0.452996
BFGS: 33 21:22:34 -299.990451 0.494876
BFGS: 34 21:22:34 -300.005351 0.511923
BFGS: 35 21:22:34 -300.027533 0.385836
BFGS: 36 21:22:34 -300.044731 0.349711
BFGS: 37 21:22:34 -300.055717 0.362981
BFGS: 38 21:22:34 -300.064336 0.270578
BFGS: 39 21:22:34 -300.067349 0.220101
BFGS: 40 21:22:35 -300.072527 0.149348
BFGS: 41 21:22:35 -300.074807 0.126476
BFGS: 42 21:22:35 -300.078067 0.112521
BFGS: 43 21:22:35 -300.078889 0.111465
BFGS: 44 21:22:35 -300.079393 0.091483
BFGS: 45 21:22:35 -300.079854 0.062732
BFGS: 46 21:22:35 -300.080154 0.034002
Step Time Energy fmax
BFGS: 0 21:22:35 -295.926916 4.352847
BFGS: 1 21:22:35 -296.477184 4.756491
BFGS: 2 21:22:35 -298.220697 2.924386
BFGS: 3 21:22:35 -296.446780 19.366400
BFGS: 4 21:22:36 -298.379552 1.826942
BFGS: 5 21:22:36 -298.439656 1.043916
BFGS: 6 21:22:36 -298.474738 0.539555
BFGS: 7 21:22:36 -298.478357 0.218961
BFGS: 8 21:22:36 -298.481695 0.085914
BFGS: 9 21:22:36 -298.483421 0.077101
BFGS: 10 21:22:36 -298.483798 0.037595
Step Time Energy fmax
BFGS: 0 21:22:36 -296.110780 4.369124
BFGS: 1 21:22:36 -296.618177 4.704709
BFGS: 2 21:22:36 -298.209937 3.166094
BFGS: 3 21:22:36 -297.180105 14.120380
BFGS: 4 21:22:36 -298.410547 1.883040
BFGS: 5 21:22:37 -298.475271 1.052685
BFGS: 6 21:22:37 -298.513604 0.767640
BFGS: 7 21:22:37 -298.521062 0.553886
BFGS: 8 21:22:37 -298.541901 0.435481
BFGS: 9 21:22:37 -298.548116 0.514200
BFGS: 10 21:22:37 -298.558933 0.610608
BFGS: 11 21:22:37 -298.586028 0.827075
BFGS: 12 21:22:37 -298.657755 1.523209
BFGS: 13 21:22:37 -298.692067 2.446903
BFGS: 14 21:22:37 -298.804461 1.368687
BFGS: 15 21:22:37 -298.910374 1.625215
BFGS: 16 21:22:37 -299.124228 2.375423
BFGS: 17 21:22:38 -299.297524 2.757865
BFGS: 18 21:22:38 -299.418970 3.084338
BFGS: 19 21:22:38 -299.635150 2.493826
BFGS: 20 21:22:38 -299.715167 1.966919
BFGS: 21 21:22:38 -299.778773 1.308871
BFGS: 22 21:22:38 -299.847244 0.490249
BFGS: 23 21:22:38 -299.875227 0.488171
BFGS: 24 21:22:38 -299.889631 0.406352
BFGS: 25 21:22:38 -299.895860 0.263810
BFGS: 26 21:22:38 -299.901657 0.162547
BFGS: 27 21:22:38 -299.908215 0.202057
BFGS: 28 21:22:38 -299.911851 0.194882
BFGS: 29 21:22:39 -299.913540 0.162300
BFGS: 30 21:22:39 -299.914777 0.140176
BFGS: 31 21:22:39 -299.916935 0.156316
BFGS: 32 21:22:39 -299.919504 0.231505
BFGS: 33 21:22:39 -299.922122 0.296447
BFGS: 34 21:22:39 -299.925191 0.325810
BFGS: 35 21:22:39 -299.931825 0.342388
BFGS: 36 21:22:39 -299.942616 0.378192
BFGS: 37 21:22:39 -299.963487 0.449428
BFGS: 38 21:22:40 -300.007674 0.634945
BFGS: 39 21:22:40 -299.956352 0.756916
BFGS: 40 21:22:40 -300.024348 0.377116
BFGS: 41 21:22:40 -300.031689 0.545685
BFGS: 42 21:22:40 -300.043762 0.337661
BFGS: 43 21:22:40 -300.057762 0.208671
BFGS: 44 21:22:40 -300.072858 0.116544
BFGS: 45 21:22:40 -300.076962 0.067002
BFGS: 46 21:22:40 -300.077793 0.080476
BFGS: 47 21:22:40 -300.078335 0.078566
BFGS: 48 21:22:40 -300.079311 0.057692
BFGS: 49 21:22:40 -300.080069 0.038091
Step Time Energy fmax
BFGS: 0 21:22:41 -296.266958 4.383309
BFGS: 1 21:22:41 -296.750274 4.670750
BFGS: 2 21:22:41 -298.241737 3.303793
BFGS: 3 21:22:41 -297.631042 11.237979
BFGS: 4 21:22:41 -298.482643 1.904742
BFGS: 5 21:22:41 -298.552510 1.126652
BFGS: 6 21:22:41 -298.607898 1.214593
BFGS: 7 21:22:41 -298.633068 1.187397
BFGS: 8 21:22:41 -298.795151 1.395030
BFGS: 9 21:22:41 -298.881642 2.133996
BFGS: 10 21:22:41 -299.025448 2.818627
BFGS: 11 21:22:41 -299.199011 3.127016
BFGS: 12 21:22:42 -299.416530 3.667396
BFGS: 13 21:22:42 -299.849946 3.468877
BFGS: 14 21:22:42 -300.472677 1.484861
BFGS: 15 21:22:42 -300.520685 0.969691
BFGS: 16 21:22:42 -300.567852 0.503868
BFGS: 17 21:22:42 -300.588112 0.450702
BFGS: 18 21:22:42 -300.601173 0.305008
BFGS: 19 21:22:42 -300.606581 0.247703
BFGS: 20 21:22:42 -300.611185 0.179753
BFGS: 21 21:22:42 -300.615662 0.132009
BFGS: 22 21:22:42 -300.619144 0.139501
BFGS: 23 21:22:42 -300.620948 0.111161
BFGS: 24 21:22:43 -300.621842 0.073294
BFGS: 25 21:22:43 -300.622948 0.044131
Step Time Energy fmax
BFGS: 0 21:22:43 -296.298534 4.392655
BFGS: 1 21:22:43 -296.780248 4.668293
BFGS: 2 21:22:43 -298.255567 3.339114
BFGS: 3 21:22:43 -297.723512 10.709214
BFGS: 4 21:22:43 -298.507652 1.916084
BFGS: 5 21:22:43 -298.579421 1.173850
BFGS: 6 21:22:43 -298.644119 1.357018
BFGS: 7 21:22:43 -298.680720 1.416515
BFGS: 8 21:22:43 -298.887691 1.491894
BFGS: 9 21:22:44 -299.012717 2.042013
BFGS: 10 21:22:44 -299.148292 2.166555
BFGS: 11 21:22:44 -299.368962 2.280764
BFGS: 12 21:22:44 -299.865064 1.081049
BFGS: 13 21:22:44 -300.019595 0.867168
BFGS: 14 21:22:44 -300.057031 0.951136
BFGS: 15 21:22:44 -300.241264 1.325557
BFGS: 16 21:22:44 -300.272827 1.355860
BFGS: 17 21:22:44 -300.396031 1.028171
BFGS: 18 21:22:44 -300.465976 0.930863
BFGS: 19 21:22:44 -300.513344 0.646314
BFGS: 20 21:22:44 -300.543652 0.518037
BFGS: 21 21:22:45 -300.571107 0.505207
BFGS: 22 21:22:45 -300.590472 0.401447
BFGS: 23 21:22:45 -300.604132 0.347580
BFGS: 24 21:22:45 -300.612324 0.241403
BFGS: 25 21:22:45 -300.616504 0.158020
BFGS: 26 21:22:45 -300.618767 0.150611
BFGS: 27 21:22:45 -300.620610 0.156384
BFGS: 28 21:22:45 -300.622528 0.136354
BFGS: 29 21:22:45 -300.623936 0.083720
BFGS: 30 21:22:45 -300.624436 0.040957
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 21:22:45 -295.370118 1.182254
BFGS: 1 21:22:45 -295.441888 1.083840
BFGS: 2 21:22:46 -295.650501 1.214413
BFGS: 3 21:22:46 -295.680735 0.566129
BFGS: 4 21:22:46 -295.691113 0.460640
BFGS: 5 21:22:46 -295.731157 0.536099
BFGS: 6 21:22:46 -295.738675 0.521398
BFGS: 7 21:22:46 -295.811965 0.448316
BFGS: 8 21:22:46 -295.822290 0.482777
BFGS: 9 21:22:46 -295.830460 0.460346
BFGS: 10 21:22:46 -295.842610 0.386225
BFGS: 11 21:22:46 -295.860805 0.235813
BFGS: 12 21:22:46 -295.865319 0.227432
BFGS: 13 21:22:46 -295.867494 0.232224
BFGS: 14 21:22:47 -295.872273 0.232941
BFGS: 15 21:22:47 -295.879245 0.275899
BFGS: 16 21:22:47 -295.886936 0.293923
BFGS: 17 21:22:47 -295.891752 0.277455
BFGS: 18 21:22:47 -295.896292 0.248665
BFGS: 19 21:22:47 -295.902285 0.289230
BFGS: 20 21:22:47 -295.911829 0.345394
BFGS: 21 21:22:47 -295.921470 0.278562
BFGS: 22 21:22:47 -295.927136 0.141939
BFGS: 23 21:22:47 -295.930302 0.108277
BFGS: 24 21:22:47 -295.931910 0.081698
BFGS: 25 21:22:47 -295.933247 0.073362
BFGS: 26 21:22:48 -295.935068 0.051944
BFGS: 27 21:22:48 -295.935952 0.043130
Step Time Energy fmax
BFGS: 0 21:22:48 -295.247799 1.394083
BFGS: 1 21:22:48 -295.334227 1.265808
BFGS: 2 21:22:48 -295.534198 1.747129
BFGS: 3 21:22:48 -295.588080 0.533977
BFGS: 4 21:22:48 -295.599083 0.545441
BFGS: 5 21:22:48 -295.626897 0.299532
BFGS: 6 21:22:48 -295.632754 0.337906
BFGS: 7 21:22:48 -295.641164 0.384146
BFGS: 8 21:22:48 -295.650333 0.385631
BFGS: 9 21:22:48 -295.662495 0.448157
BFGS: 10 21:22:49 -295.673184 0.429125
BFGS: 11 21:22:49 -295.683743 0.632687
BFGS: 12 21:22:49 -295.714679 1.069119
BFGS: 13 21:22:49 -295.731390 1.198983
BFGS: 14 21:22:49 -295.761648 1.070381
BFGS: 15 21:22:49 -295.801871 0.780266
BFGS: 16 21:22:49 -295.838804 0.370876
BFGS: 17 21:22:49 -295.851194 0.348604
BFGS: 18 21:22:49 -295.857887 0.398456
BFGS: 19 21:22:49 -295.863946 0.404494
BFGS: 20 21:22:49 -295.872379 0.323771
BFGS: 21 21:22:49 -295.879476 0.240284
BFGS: 22 21:22:50 -295.884410 0.235117
BFGS: 23 21:22:50 -295.887805 0.234315
BFGS: 24 21:22:50 -295.891313 0.252611
BFGS: 25 21:22:50 -295.898465 0.331114
BFGS: 26 21:22:50 -295.908303 0.322037
BFGS: 27 21:22:50 -295.916244 0.228030
BFGS: 28 21:22:50 -295.922560 0.156058
BFGS: 29 21:22:50 -295.925473 0.135938
BFGS: 30 21:22:50 -295.928873 0.125696
BFGS: 31 21:22:50 -295.932066 0.092911
BFGS: 32 21:22:50 -295.934424 0.057496
BFGS: 33 21:22:50 -295.935330 0.046147
Step Time Energy fmax
BFGS: 0 21:22:51 -295.292291 1.313210
BFGS: 1 21:22:51 -295.373392 1.196688
BFGS: 2 21:22:51 -295.579843 1.558907
BFGS: 3 21:22:51 -295.624438 0.560610
BFGS: 4 21:22:51 -295.635040 0.523407
BFGS: 5 21:22:51 -295.667846 0.416652
BFGS: 6 21:22:51 -295.673356 0.430490
BFGS: 7 21:22:51 -295.703459 0.597126
BFGS: 8 21:22:51 -295.720748 0.638949
BFGS: 9 21:22:51 -295.748303 0.667099
BFGS: 10 21:22:51 -295.763982 0.770766
BFGS: 11 21:22:52 -295.797307 0.771436
BFGS: 12 21:22:52 -295.819179 0.554900
BFGS: 13 21:22:52 -295.836454 0.288182
BFGS: 14 21:22:52 -295.842382 0.212365
BFGS: 15 21:22:52 -295.844529 0.245926
BFGS: 16 21:22:52 -295.847541 0.250252
BFGS: 17 21:22:52 -295.850842 0.189791
BFGS: 18 21:22:52 -295.853180 0.133680
BFGS: 19 21:22:52 -295.854488 0.128966
BFGS: 20 21:22:52 -295.855286 0.126358
BFGS: 21 21:22:52 -295.856338 0.131140
BFGS: 22 21:22:52 -295.858705 0.185272
BFGS: 23 21:22:53 -295.862754 0.236913
BFGS: 24 21:22:53 -295.867767 0.233417
BFGS: 25 21:22:53 -295.874510 0.274264
BFGS: 26 21:22:53 -295.888747 0.368418
BFGS: 27 21:22:53 -295.901466 0.437617
BFGS: 28 21:22:53 -295.919630 0.354929
BFGS: 29 21:22:53 -295.939912 0.283808
BFGS: 30 21:22:53 -295.955218 0.161090
BFGS: 31 21:22:53 -295.960836 0.114285
BFGS: 32 21:22:53 -295.962374 0.138100
BFGS: 33 21:22:53 -295.963894 0.102297
BFGS: 34 21:22:53 -295.965555 0.076248
BFGS: 35 21:22:54 -295.967520 0.041608
Step Time Energy fmax
BFGS: 0 21:22:54 -295.108607 1.734291
BFGS: 1 21:22:54 -295.224065 1.562863
BFGS: 2 21:22:54 -295.389905 2.703634
BFGS: 3 21:22:54 -295.503009 0.461196
BFGS: 4 21:22:54 -295.521148 0.602152
BFGS: 5 21:22:54 -295.540619 0.661051
BFGS: 6 21:22:54 -295.557742 0.466212
BFGS: 7 21:22:54 -295.564877 0.198611
BFGS: 8 21:22:54 -295.569395 0.275523
BFGS: 9 21:22:54 -295.574641 0.294724
BFGS: 10 21:22:54 -295.578492 0.218024
BFGS: 11 21:22:55 -295.580574 0.095798
BFGS: 12 21:22:55 -295.580894 0.020835
Step Time Energy fmax
BFGS: 0 21:22:55 -295.654574 0.744515
BFGS: 1 21:22:55 -295.703478 0.662313
BFGS: 2 21:22:55 -295.867115 0.308090
BFGS: 3 21:22:55 -295.878856 0.319826
BFGS: 4 21:22:55 -295.880960 0.310619
BFGS: 5 21:22:55 -295.899182 0.213522
BFGS: 6 21:22:55 -295.903613 0.207523
BFGS: 7 21:22:55 -295.907952 0.220660
BFGS: 8 21:22:55 -295.911824 0.235636
BFGS: 9 21:22:55 -295.917832 0.248198
BFGS: 10 21:22:56 -295.922766 0.231007
BFGS: 11 21:22:56 -295.926331 0.188906
BFGS: 12 21:22:56 -295.928000 0.155308
BFGS: 13 21:22:56 -295.929518 0.121009
BFGS: 14 21:22:56 -295.931806 0.091765
BFGS: 15 21:22:56 -295.933912 0.100632
BFGS: 16 21:22:56 -295.935088 0.096695
BFGS: 17 21:22:56 -295.935697 0.078459
BFGS: 18 21:22:56 -295.936127 0.051049
BFGS: 19 21:22:56 -295.936463 0.030663
Step Time Energy fmax
BFGS: 0 21:22:56 -295.217767 1.448767
BFGS: 1 21:22:56 -295.309141 1.313190
BFGS: 2 21:22:57 -295.505130 1.915217
BFGS: 3 21:22:57 -295.568209 0.513135
BFGS: 4 21:22:57 -295.580128 0.560880
BFGS: 5 21:22:57 -295.605442 0.403070
BFGS: 6 21:22:57 -295.612705 0.280154
BFGS: 7 21:22:57 -295.618604 0.334239
BFGS: 8 21:22:57 -295.625436 0.348782
BFGS: 9 21:22:57 -295.633156 0.350552
BFGS: 10 21:22:57 -295.639829 0.269660
BFGS: 11 21:22:57 -295.644165 0.362696
BFGS: 12 21:22:57 -295.650286 0.519521
BFGS: 13 21:22:57 -295.680458 1.022939
BFGS: 14 21:22:58 -295.708429 1.338739
BFGS: 15 21:22:58 -295.714515 1.305821
BFGS: 16 21:22:58 -295.717399 1.287354
BFGS: 17 21:22:58 -295.720445 1.281096
BFGS: 18 21:22:58 -295.724621 1.322125
BFGS: 19 21:22:58 -295.725959 1.295366
BFGS: 20 21:22:58 -295.730372 1.261821
BFGS: 21 21:22:58 -295.731734 1.267683
BFGS: 22 21:22:58 -295.732715 1.281197
BFGS: 23 21:22:58 -295.733734 1.285629
BFGS: 24 21:22:58 -295.736098 1.281828
BFGS: 25 21:22:58 -295.740212 1.250248
BFGS: 26 21:22:59 -295.747001 1.157082
BFGS: 27 21:22:59 -295.756475 0.976501
BFGS: 28 21:22:59 -295.768897 0.757094
BFGS: 29 21:22:59 -295.792521 0.761660
BFGS: 30 21:22:59 -295.835880 0.830059
BFGS: 31 21:22:59 -295.864021 0.712410
BFGS: 32 21:22:59 -295.884414 0.437610
BFGS: 33 21:22:59 -295.900395 0.342682
BFGS: 34 21:22:59 -295.905080 0.326758
BFGS: 35 21:22:59 -295.916845 0.327463
BFGS: 36 21:22:59 -295.920919 0.310872
BFGS: 37 21:22:59 -295.922200 0.296564
BFGS: 38 21:23:00 -295.922785 0.296306
BFGS: 39 21:23:00 -295.923405 0.287938
BFGS: 40 21:23:00 -295.923876 0.271844
BFGS: 41 21:23:00 -295.924112 0.271004
BFGS: 42 21:23:00 -295.924185 0.272567
BFGS: 43 21:23:00 -295.924226 0.273825
BFGS: 44 21:23:00 -295.924276 0.274864
BFGS: 45 21:23:00 -295.924324 0.274997
BFGS: 46 21:23:00 -295.924354 0.274140
BFGS: 47 21:23:00 -295.924363 0.273278
BFGS: 48 21:23:00 -295.924370 0.272704
BFGS: 49 21:23:01 -295.924376 0.272330
BFGS: 50 21:23:01 -295.924380 0.272195
BFGS: 51 21:23:01 -295.924387 0.272425
BFGS: 52 21:23:01 -295.924392 0.272940
BFGS: 53 21:23:01 -295.924394 0.273342
BFGS: 54 21:23:01 -295.924394 0.273568
BFGS: 55 21:23:01 -295.924397 0.273720
BFGS: 56 21:23:01 -295.924397 0.273791
BFGS: 57 21:23:01 -295.924400 0.273743
BFGS: 58 21:23:01 -295.924401 0.273568
BFGS: 59 21:23:01 -295.924400 0.273414
BFGS: 60 21:23:01 -295.924401 0.273339
BFGS: 61 21:23:02 -295.924401 0.273313
BFGS: 62 21:23:02 -295.924403 0.273382
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BFGS: 64 21:23:02 -295.924403 0.273731
BFGS: 65 21:23:02 -295.924403 0.273808
BFGS: 66 21:23:02 -295.924405 0.273851
BFGS: 67 21:23:02 -295.924403 0.273862
BFGS: 68 21:23:02 -295.924404 0.273844
BFGS: 69 21:23:02 -295.924404 0.273803
BFGS: 70 21:23:02 -295.924404 0.273777
BFGS: 71 21:23:02 -295.924403 0.273747
BFGS: 72 21:23:02 -295.924405 0.273740
BFGS: 73 21:23:03 -295.924405 0.273728
BFGS: 74 21:23:03 -295.924405 0.273727
BFGS: 75 21:23:03 -295.924405 0.273736
BFGS: 76 21:23:03 -295.924405 0.273742
BFGS: 77 21:23:03 -295.924405 0.273742
BFGS: 78 21:23:03 -295.924405 0.273742
BFGS: 79 21:23:03 -295.924404 0.273734
BFGS: 80 21:23:03 -295.924405 0.273707
BFGS: 81 21:23:03 -295.924406 0.273701
BFGS: 82 21:23:03 -295.924404 0.273696
BFGS: 83 21:23:03 -295.924404 0.273692
BFGS: 84 21:23:03 -295.924404 0.273689
BFGS: 85 21:23:04 -295.924403 0.273691
BFGS: 86 21:23:04 -295.924405 0.273689
BFGS: 87 21:23:04 -295.924403 0.273694
BFGS: 88 21:23:04 -295.924404 0.273696
BFGS: 89 21:23:04 -295.924403 0.273691
BFGS: 90 21:23:04 -295.924404 0.273694
BFGS: 91 21:23:04 -295.924403 0.273695
BFGS: 92 21:23:04 -295.924404 0.273691
BFGS: 93 21:23:04 -295.924404 0.273694
BFGS: 94 21:23:04 -295.924403 0.273693
BFGS: 95 21:23:04 -295.924404 0.273690
BFGS: 96 21:23:04 -295.924402 0.273691
BFGS: 97 21:23:05 -295.924404 0.273691
BFGS: 98 21:23:05 -295.924403 0.273688
BFGS: 99 21:23:05 -295.924404 0.273688
BFGS: 100 21:23:05 -295.924404 0.273692
BFGS: 101 21:23:05 -295.924404 0.273691
BFGS: 102 21:23:05 -295.924404 0.273695
BFGS: 103 21:23:05 -295.924404 0.273691
BFGS: 104 21:23:05 -295.924404 0.273690
BFGS: 105 21:23:05 -295.924403 0.273690
BFGS: 106 21:23:05 -295.924404 0.273691
BFGS: 107 21:23:05 -295.924403 0.273691
BFGS: 108 21:23:05 -295.924404 0.273688
BFGS: 109 21:23:06 -295.924404 0.273690
BFGS: 110 21:23:06 -295.924403 0.273696
BFGS: 111 21:23:06 -295.924403 0.273691
BFGS: 112 21:23:06 -295.924405 0.273691
BFGS: 113 21:23:06 -295.924404 0.273687
BFGS: 114 21:23:06 -295.924403 0.273688
BFGS: 115 21:23:06 -295.924404 0.273689
BFGS: 116 21:23:06 -295.924404 0.273691
BFGS: 117 21:23:06 -295.924404 0.273692
BFGS: 118 21:23:06 -295.924404 0.273691
BFGS: 119 21:23:06 -295.924404 0.273689
BFGS: 120 21:23:06 -295.924404 0.273690
BFGS: 121 21:23:07 -295.924403 0.273694
BFGS: 122 21:23:07 -295.924403 0.273691
BFGS: 123 21:23:07 -295.924403 0.273689
BFGS: 124 21:23:07 -295.924404 0.273691
BFGS: 125 21:23:07 -295.924404 0.273694
BFGS: 126 21:23:07 -295.924405 0.273692
BFGS: 127 21:23:07 -295.924403 0.273691
BFGS: 128 21:23:07 -295.924403 0.273691
BFGS: 129 21:23:07 -295.924405 0.273686
BFGS: 130 21:23:07 -295.924403 0.273691
BFGS: 131 21:23:07 -295.924403 0.273690
BFGS: 132 21:23:07 -295.924404 0.273692
BFGS: 133 21:23:08 -295.924404 0.273688
BFGS: 134 21:23:08 -295.924403 0.273690
BFGS: 135 21:23:08 -295.924403 0.273687
BFGS: 136 21:23:08 -295.924405 0.273690
BFGS: 137 21:23:08 -295.924404 0.273691
BFGS: 138 21:23:08 -295.924403 0.273691
BFGS: 139 21:23:08 -295.924404 0.273691
BFGS: 140 21:23:08 -295.924404 0.273691
BFGS: 141 21:23:08 -295.924404 0.273690
BFGS: 142 21:23:08 -295.924405 0.273691
BFGS: 143 21:23:08 -295.924404 0.273691
BFGS: 144 21:23:08 -295.924405 0.273692
BFGS: 145 21:23:09 -295.924404 0.273689
BFGS: 146 21:23:09 -295.924405 0.273691
BFGS: 147 21:23:09 -295.924405 0.273690
BFGS: 148 21:23:09 -295.924405 0.273690
BFGS: 149 21:23:09 -295.924405 0.273684
BFGS: 150 21:23:09 -295.924404 0.273691
BFGS: 151 21:23:09 -295.924405 0.273691
BFGS: 152 21:23:09 -295.924405 0.273692
BFGS: 153 21:23:09 -295.924404 0.273691
BFGS: 154 21:23:09 -295.924403 0.273686
BFGS: 155 21:23:09 -295.924403 0.273689
BFGS: 156 21:23:10 -295.924404 0.273695
BFGS: 157 21:23:10 -295.924403 0.273690
BFGS: 158 21:23:10 -295.924404 0.273691
BFGS: 159 21:23:10 -295.924403 0.273689
BFGS: 160 21:23:10 -295.924403 0.273691
BFGS: 161 21:23:10 -295.924404 0.273689
BFGS: 162 21:23:10 -295.924405 0.273691
BFGS: 163 21:23:10 -295.924404 0.273690
BFGS: 164 21:23:10 -295.924405 0.273690
BFGS: 165 21:23:10 -295.924404 0.273690
BFGS: 166 21:23:10 -295.924405 0.273692
BFGS: 167 21:23:10 -295.924403 0.273691
BFGS: 168 21:23:11 -295.924405 0.273687
BFGS: 169 21:23:11 -295.924402 0.273689
BFGS: 170 21:23:11 -295.924403 0.273691
BFGS: 171 21:23:11 -295.924405 0.273691
BFGS: 172 21:23:11 -295.924405 0.273691
BFGS: 173 21:23:11 -295.924404 0.273693
BFGS: 174 21:23:11 -295.924403 0.273691
BFGS: 175 21:23:11 -295.924404 0.273690
BFGS: 176 21:23:11 -295.924404 0.273691
BFGS: 177 21:23:11 -295.924403 0.273690
BFGS: 178 21:23:11 -295.924405 0.273690
BFGS: 179 21:23:11 -295.924405 0.273688
BFGS: 180 21:23:12 -295.924403 0.273691
BFGS: 181 21:23:12 -295.924405 0.273690
BFGS: 182 21:23:12 -295.924404 0.273691
BFGS: 183 21:23:12 -295.924405 0.273692
BFGS: 184 21:23:12 -295.924404 0.273687
BFGS: 185 21:23:12 -295.924404 0.273688
BFGS: 186 21:23:12 -295.924404 0.273690
BFGS: 187 21:23:12 -295.924405 0.273685
BFGS: 188 21:23:12 -295.924405 0.273691
BFGS: 189 21:23:12 -295.924403 0.273689
BFGS: 190 21:23:12 -295.924404 0.273691
BFGS: 191 21:23:12 -295.924403 0.273696
BFGS: 192 21:23:13 -295.924404 0.273691
BFGS: 193 21:23:13 -295.924405 0.273689
BFGS: 194 21:23:13 -295.924405 0.273691
BFGS: 195 21:23:13 -295.924405 0.273695
BFGS: 196 21:23:13 -295.924405 0.273687
BFGS: 197 21:23:13 -295.924405 0.273688
BFGS: 198 21:23:13 -295.924405 0.273690
BFGS: 199 21:23:13 -295.924404 0.273688
BFGS: 200 21:23:13 -295.924403 0.273690
BFGS: 201 21:23:13 -295.924404 0.273691
BFGS: 202 21:23:13 -295.924404 0.273692
BFGS: 203 21:23:13 -295.924405 0.273690
BFGS: 204 21:23:14 -295.924403 0.273688
BFGS: 205 21:23:14 -295.924404 0.273690
BFGS: 206 21:23:14 -295.924403 0.273695
BFGS: 207 21:23:14 -295.924403 0.273690
BFGS: 208 21:23:14 -295.924403 0.273685
BFGS: 209 21:23:14 -295.924404 0.273691
BFGS: 210 21:23:14 -295.924404 0.273691
BFGS: 211 21:23:14 -295.924405 0.273692
BFGS: 212 21:23:14 -295.924404 0.273683
BFGS: 213 21:23:14 -295.924405 0.273689
BFGS: 214 21:23:14 -295.924405 0.273692
BFGS: 215 21:23:14 -295.924405 0.273691
BFGS: 216 21:23:15 -295.924403 0.273691
BFGS: 217 21:23:15 -295.924405 0.273691
BFGS: 218 21:23:15 -295.924405 0.273691
BFGS: 219 21:23:15 -295.924403 0.273689
BFGS: 220 21:23:15 -295.924403 0.273691
BFGS: 221 21:23:15 -295.924403 0.273692
BFGS: 222 21:23:15 -295.924405 0.273691
BFGS: 223 21:23:15 -295.924405 0.273689
BFGS: 224 21:23:15 -295.924405 0.273691
BFGS: 225 21:23:15 -295.924404 0.273691
BFGS: 226 21:23:15 -295.924404 0.273691
BFGS: 227 21:23:15 -295.924405 0.273692
BFGS: 228 21:23:16 -295.924405 0.273691
BFGS: 229 21:23:16 -295.924405 0.273690
BFGS: 230 21:23:16 -295.924403 0.273690
BFGS: 231 21:23:16 -295.924404 0.273692
BFGS: 232 21:23:16 -295.924404 0.273692
BFGS: 233 21:23:16 -295.924402 0.273153
BFGS: 234 21:23:16 -295.924405 0.273695
BFGS: 235 21:23:16 -295.924403 0.273694
BFGS: 236 21:23:16 -295.924404 0.273691
BFGS: 237 21:23:16 -295.924404 0.273691
BFGS: 238 21:23:16 -295.924404 0.273694
BFGS: 239 21:23:16 -295.924404 0.273684
BFGS: 240 21:23:17 -295.924404 0.273687
BFGS: 241 21:23:17 -295.924404 0.273685
BFGS: 242 21:23:17 -295.924405 0.273685
BFGS: 243 21:23:17 -295.924404 0.273685
BFGS: 244 21:23:17 -295.924403 0.273687
BFGS: 245 21:23:17 -295.924404 0.273688
BFGS: 246 21:23:17 -295.924405 0.273691
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BFGS: 248 21:23:17 -295.924404 0.273689
BFGS: 249 21:23:17 -295.924405 0.273690
BFGS: 250 21:23:17 -295.924404 0.273680
BFGS: 251 21:23:17 -295.924403 0.273689
BFGS: 252 21:23:18 -295.924403 0.273684
BFGS: 253 21:23:18 -295.924404 0.273685
BFGS: 254 21:23:18 -295.924404 0.273686
BFGS: 255 21:23:18 -295.924404 0.273686
BFGS: 256 21:23:18 -295.924403 0.273689
BFGS: 257 21:23:18 -295.924404 0.273692
BFGS: 258 21:23:18 -295.924403 0.273688
BFGS: 259 21:23:18 -295.924405 0.273682
BFGS: 260 21:23:18 -295.924405 0.273686
BFGS: 261 21:23:18 -295.924405 0.273693
BFGS: 262 21:23:18 -295.924403 0.273688
BFGS: 263 21:23:18 -295.924405 0.273689
BFGS: 264 21:23:19 -295.924404 0.273689
BFGS: 265 21:23:19 -295.924403 0.273691
BFGS: 266 21:23:19 -295.924404 0.273691
BFGS: 267 21:23:19 -295.924404 0.273690
BFGS: 268 21:23:19 -295.924405 0.273685
BFGS: 269 21:23:19 -295.924405 0.273685
BFGS: 270 21:23:19 -295.924405 0.273689
BFGS: 271 21:23:19 -295.924405 0.273690
BFGS: 272 21:23:19 -295.924404 0.273682
BFGS: 273 21:23:19 -295.924406 0.273688
BFGS: 274 21:23:19 -295.924405 0.273689
BFGS: 275 21:23:20 -295.924405 0.273690
BFGS: 276 21:23:20 -295.924403 0.273693
BFGS: 277 21:23:20 -295.924405 0.273689
BFGS: 278 21:23:20 -295.924403 0.273689
BFGS: 279 21:23:20 -295.924403 0.273689
BFGS: 280 21:23:20 -295.924405 0.273692
BFGS: 281 21:23:20 -295.924404 0.273687
BFGS: 282 21:23:20 -295.924405 0.273689
BFGS: 283 21:23:20 -295.924404 0.273689
BFGS: 284 21:23:20 -295.924404 0.273708
BFGS: 285 21:23:20 -295.924405 0.273689
BFGS: 286 21:23:20 -295.924405 0.273689
BFGS: 287 21:23:21 -295.924405 0.273691
BFGS: 288 21:23:21 -295.924403 0.273690
BFGS: 289 21:23:21 -295.924404 0.273689
BFGS: 290 21:23:21 -295.924405 0.273687
BFGS: 291 21:23:21 -295.924404 0.273691
BFGS: 292 21:23:21 -295.924405 0.273690
BFGS: 293 21:23:21 -295.924405 0.273690
BFGS: 294 21:23:21 -295.924405 0.273690
BFGS: 295 21:23:21 -295.924403 0.273686
BFGS: 296 21:23:21 -295.924405 0.273691
BFGS: 297 21:23:21 -295.924404 0.273687
BFGS: 298 21:23:21 -295.924405 0.273687
BFGS: 299 21:23:22 -295.924403 0.273688
BFGS: 300 21:23:22 -295.924405 0.273689
Step Time Energy fmax
BFGS: 0 21:23:22 -295.628836 0.724779
BFGS: 1 21:23:22 -295.679289 0.644036
BFGS: 2 21:23:22 -295.848894 0.256475
BFGS: 3 21:23:22 -295.859688 0.260788
BFGS: 4 21:23:22 -295.861285 0.252680
BFGS: 5 21:23:22 -295.873039 0.183758
BFGS: 6 21:23:22 -295.875239 0.180769
BFGS: 7 21:23:22 -295.877746 0.193609
BFGS: 8 21:23:22 -295.880709 0.227463
BFGS: 9 21:23:22 -295.887203 0.333200
BFGS: 10 21:23:23 -295.899913 0.529911
BFGS: 11 21:23:23 -295.904770 0.663778
BFGS: 12 21:23:23 -295.917840 0.553255
BFGS: 13 21:23:23 -295.927802 0.487498
BFGS: 14 21:23:23 -295.948704 0.241578
BFGS: 15 21:23:23 -295.954980 0.212288
BFGS: 16 21:23:23 -295.961958 0.201009
BFGS: 17 21:23:23 -295.964346 0.169532
BFGS: 18 21:23:23 -295.966057 0.119864
BFGS: 19 21:23:23 -295.967140 0.067653
BFGS: 20 21:23:23 -295.967835 0.038261
Step Time Energy fmax
BFGS: 0 21:23:23 -295.176215 1.540727
BFGS: 1 21:23:24 -295.275307 1.394931
BFGS: 2 21:23:24 -295.460659 2.226575
BFGS: 3 21:23:24 -295.542620 0.469978
BFGS: 4 21:23:24 -295.556682 0.582915
BFGS: 5 21:23:24 -295.578545 0.550003
BFGS: 6 21:23:24 -295.589113 0.307568
BFGS: 7 21:23:24 -295.594451 0.263375
BFGS: 8 21:23:24 -295.599465 0.312384
BFGS: 9 21:23:24 -295.604451 0.285773
BFGS: 10 21:23:24 -295.608738 0.206725
BFGS: 11 21:23:24 -295.610658 0.165303
BFGS: 12 21:23:24 -295.611613 0.198069
BFGS: 13 21:23:25 -295.613568 0.272558
BFGS: 14 21:23:25 -295.619300 0.439915
BFGS: 15 21:23:25 -295.650287 0.821663
BFGS: 16 21:23:25 -295.726830 0.854444
BFGS: 17 21:23:25 -295.823147 0.673299
BFGS: 18 21:23:25 -295.863609 0.661796
BFGS: 19 21:23:25 -295.881365 0.476673
BFGS: 20 21:23:25 -295.915301 0.397157
BFGS: 21 21:23:25 -295.938221 0.270825
BFGS: 22 21:23:25 -295.945141 0.240838
BFGS: 23 21:23:25 -295.949045 0.229644
BFGS: 24 21:23:25 -295.954133 0.214211
BFGS: 25 21:23:26 -295.960154 0.166368
BFGS: 26 21:23:26 -295.963670 0.112122
BFGS: 27 21:23:26 -295.965092 0.095717
BFGS: 28 21:23:26 -295.965785 0.085449
BFGS: 29 21:23:26 -295.966516 0.071057
BFGS: 30 21:23:26 -295.967251 0.055504
BFGS: 31 21:23:26 -295.967715 0.041743
Step Time Energy fmax
BFGS: 0 21:23:26 -295.535548 0.804271
BFGS: 1 21:23:26 -295.593908 0.746760
BFGS: 2 21:23:26 -295.787099 0.614944
BFGS: 3 21:23:26 -295.803355 0.349121
BFGS: 4 21:23:26 -295.808387 0.347419
BFGS: 5 21:23:27 -295.829278 0.278190
BFGS: 6 21:23:27 -295.831568 0.239692
BFGS: 7 21:23:27 -295.837973 0.154212
BFGS: 8 21:23:27 -295.839031 0.079807
BFGS: 9 21:23:27 -295.839408 0.073263
BFGS: 10 21:23:27 -295.839642 0.067622
BFGS: 11 21:23:27 -295.840026 0.041735
Step Time Energy fmax
BFGS: 0 21:23:27 -295.213286 1.460603
BFGS: 1 21:23:27 -295.305665 1.324274
BFGS: 2 21:23:27 -295.500096 1.971215
BFGS: 3 21:23:27 -295.566550 0.508492
BFGS: 4 21:23:27 -295.578805 0.566192
BFGS: 5 21:23:28 -295.603665 0.433050
BFGS: 6 21:23:28 -295.611561 0.271208
BFGS: 7 21:23:28 -295.617409 0.327650
BFGS: 8 21:23:28 -295.624115 0.348926
BFGS: 9 21:23:28 -295.631510 0.344617
BFGS: 10 21:23:28 -295.638066 0.261055
BFGS: 11 21:23:28 -295.642180 0.339869
BFGS: 12 21:23:28 -295.647296 0.478165
BFGS: 13 21:23:28 -295.668581 0.899509
BFGS: 14 21:23:28 -295.707475 1.321660
BFGS: 15 21:23:28 -295.691929 1.377244
BFGS: 16 21:23:29 -295.727395 1.264089
BFGS: 17 21:23:29 -295.738153 1.196878
BFGS: 18 21:23:29 -295.788539 0.682561
BFGS: 19 21:23:29 -295.819775 0.409020
BFGS: 20 21:23:29 -295.830319 0.304517
BFGS: 21 21:23:29 -295.836721 0.297032
BFGS: 22 21:23:29 -295.840889 0.291168
BFGS: 23 21:23:29 -295.845943 0.231644
BFGS: 24 21:23:29 -295.849413 0.133200
BFGS: 25 21:23:29 -295.851301 0.115820
BFGS: 26 21:23:29 -295.852245 0.113108
BFGS: 27 21:23:29 -295.853076 0.113638
BFGS: 28 21:23:30 -295.854443 0.117758
BFGS: 29 21:23:30 -295.856420 0.124725
BFGS: 30 21:23:30 -295.858440 0.141413
BFGS: 31 21:23:30 -295.860446 0.171814
BFGS: 32 21:23:30 -295.863627 0.223494
BFGS: 33 21:23:30 -295.871478 0.326078
BFGS: 34 21:23:30 -295.887530 0.436447
BFGS: 35 21:23:30 -295.894721 0.405903
BFGS: 36 21:23:30 -295.906645 0.411757
BFGS: 37 21:23:30 -295.925941 0.370429
BFGS: 38 21:23:30 -295.951100 0.227796
BFGS: 39 21:23:30 -295.957005 0.191935
BFGS: 40 21:23:31 -295.960202 0.125243
BFGS: 41 21:23:31 -295.962486 0.101335
BFGS: 42 21:23:31 -295.965697 0.064362
BFGS: 43 21:23:31 -295.967085 0.057715
BFGS: 44 21:23:31 -295.967724 0.048700
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 21:23:31 -303.720119 0.903056
BFGS: 1 21:23:31 -303.741153 0.694968
BFGS: 2 21:23:31 -303.794536 0.581905
BFGS: 3 21:23:31 -303.823522 0.720413
BFGS: 4 21:23:31 -303.850425 0.758330
BFGS: 5 21:23:31 -303.874094 0.530931
BFGS: 6 21:23:32 -303.906562 0.260724
BFGS: 7 21:23:32 -303.910129 0.228880
BFGS: 8 21:23:32 -303.916267 0.154359
BFGS: 9 21:23:32 -303.919319 0.124012
BFGS: 10 21:23:32 -303.921084 0.120261
BFGS: 11 21:23:32 -303.922146 0.150448
BFGS: 12 21:23:32 -303.923302 0.143227
BFGS: 13 21:23:32 -303.924362 0.096068
BFGS: 14 21:23:32 -303.925233 0.108979
BFGS: 15 21:23:32 -303.925813 0.087735
BFGS: 16 21:23:32 -303.926277 0.093464
BFGS: 17 21:23:32 -303.926821 0.086203
BFGS: 18 21:23:33 -303.927549 0.126149
BFGS: 19 21:23:33 -303.928483 0.149186
BFGS: 20 21:23:33 -303.929280 0.110493
BFGS: 21 21:23:33 -303.929697 0.051813
BFGS: 22 21:23:33 -303.929925 0.060401
BFGS: 23 21:23:33 -303.930252 0.090480
BFGS: 24 21:23:33 -303.930878 0.114821
BFGS: 25 21:23:33 -303.931925 0.122633
BFGS: 26 21:23:33 -303.933888 0.133604
BFGS: 27 21:23:33 -303.931782 0.385868
BFGS: 28 21:23:33 -303.936752 0.154834
BFGS: 29 21:23:33 -303.939150 0.166658
BFGS: 30 21:23:34 -303.955317 0.315438
BFGS: 31 21:23:34 -303.965522 0.489273
BFGS: 32 21:23:34 -303.978664 0.517801
BFGS: 33 21:23:34 -304.006028 0.452668
BFGS: 34 21:23:34 -304.011225 0.355566
BFGS: 35 21:23:34 -304.025389 0.294239
BFGS: 36 21:23:34 -304.050552 0.292175
BFGS: 37 21:23:34 -304.078583 0.451977
BFGS: 38 21:23:34 -304.100272 0.549464
BFGS: 39 21:23:34 -304.124408 0.539980
BFGS: 40 21:23:34 -304.156317 0.692574
BFGS: 41 21:23:34 -304.201569 0.814206
BFGS: 42 21:23:35 -304.246326 0.909467
BFGS: 43 21:23:35 -304.297815 0.821117
BFGS: 44 21:23:35 -304.351572 0.716093
BFGS: 45 21:23:35 -304.386213 0.509453
BFGS: 46 21:23:35 -304.396601 0.481070
BFGS: 47 21:23:35 -304.439160 0.344193
BFGS: 48 21:23:35 -304.446133 0.294668
BFGS: 49 21:23:35 -304.460482 0.262175
BFGS: 50 21:23:35 -304.466011 0.279550
BFGS: 51 21:23:35 -304.472450 0.280445
BFGS: 52 21:23:35 -304.480184 0.272250
BFGS: 53 21:23:35 -304.490429 0.319642
BFGS: 54 21:23:36 -304.498771 0.392762
BFGS: 55 21:23:36 -304.509637 0.427515
BFGS: 56 21:23:36 -304.520050 0.281193
BFGS: 57 21:23:36 -304.526024 0.235192
BFGS: 58 21:23:36 -304.529306 0.148813
BFGS: 59 21:23:36 -304.530851 0.071915
BFGS: 60 21:23:36 -304.531475 0.054312
BFGS: 61 21:23:36 -304.531868 0.042082
Step Time Energy fmax
BFGS: 0 21:23:36 -303.711185 0.903152
BFGS: 1 21:23:36 -303.732780 0.685528
BFGS: 2 21:23:36 -303.783584 0.583101
BFGS: 3 21:23:37 -303.813525 0.700026
BFGS: 4 21:23:37 -303.843817 0.804009
BFGS: 5 21:23:37 -303.867333 0.589628
BFGS: 6 21:23:37 -303.905929 0.255762
BFGS: 7 21:23:37 -303.909567 0.243181
BFGS: 8 21:23:37 -303.915894 0.157766
BFGS: 9 21:23:37 -303.919182 0.133624
BFGS: 10 21:23:37 -303.921041 0.115214
BFGS: 11 21:23:37 -303.922146 0.147231
BFGS: 12 21:23:37 -303.923268 0.143866
BFGS: 13 21:23:37 -303.924285 0.099146
BFGS: 14 21:23:37 -303.925132 0.110003
BFGS: 15 21:23:38 -303.925729 0.086160
BFGS: 16 21:23:38 -303.926185 0.092409
BFGS: 17 21:23:38 -303.926691 0.085263
BFGS: 18 21:23:38 -303.927361 0.118898
BFGS: 19 21:23:38 -303.928236 0.142038
BFGS: 20 21:23:38 -303.928977 0.104238
BFGS: 21 21:23:38 -303.929318 0.041955
Step Time Energy fmax
BFGS: 0 21:23:38 -304.435145 0.254742
BFGS: 1 21:23:38 -304.438617 0.198892
BFGS: 2 21:23:38 -304.447857 0.126979
BFGS: 3 21:23:39 -304.450158 0.119005
BFGS: 4 21:23:39 -304.451606 0.090526
BFGS: 5 21:23:39 -304.452352 0.064552
BFGS: 6 21:23:39 -304.453037 0.053678
BFGS: 7 21:23:39 -304.453632 0.057248
BFGS: 8 21:23:39 -304.454078 0.066834
BFGS: 9 21:23:39 -304.454372 0.052516
BFGS: 10 21:23:39 -304.454623 0.046453
Step Time Energy fmax
BFGS: 0 21:23:39 -304.434426 0.335639
BFGS: 1 21:23:39 -304.438516 0.255743
BFGS: 2 21:23:39 -304.448863 0.131943
BFGS: 3 21:23:40 -304.451348 0.102115
BFGS: 4 21:23:40 -304.452709 0.082175
BFGS: 5 21:23:40 -304.453379 0.081029
BFGS: 6 21:23:40 -304.454113 0.073083
BFGS: 7 21:23:40 -304.454801 0.056958
BFGS: 8 21:23:40 -304.455306 0.064523
BFGS: 9 21:23:40 -304.455596 0.050008
BFGS: 10 21:23:40 -304.455791 0.040400
Step Time Energy fmax
BFGS: 0 21:23:40 -303.943749 0.297984
BFGS: 1 21:23:40 -303.947926 0.227197
BFGS: 2 21:23:40 -303.957620 0.129880
BFGS: 3 21:23:41 -303.960006 0.121534
BFGS: 4 21:23:41 -303.961571 0.094194
BFGS: 5 21:23:41 -303.962431 0.081140
BFGS: 6 21:23:41 -303.963238 0.069509
BFGS: 7 21:23:41 -303.963946 0.065226
BFGS: 8 21:23:41 -303.964446 0.074722
BFGS: 9 21:23:41 -303.964720 0.056654
BFGS: 10 21:23:41 -303.964906 0.036736
Step Time Energy fmax
BFGS: 0 21:23:41 -303.943303 0.259091
BFGS: 1 21:23:41 -303.947310 0.202342
BFGS: 2 21:23:41 -303.956877 0.130220
BFGS: 3 21:23:42 -303.959436 0.110711
BFGS: 4 21:23:42 -303.960930 0.081873
BFGS: 5 21:23:42 -303.961670 0.070220
BFGS: 6 21:23:42 -303.962402 0.064117
BFGS: 7 21:23:42 -303.963086 0.065635
BFGS: 8 21:23:42 -303.963614 0.075918
BFGS: 9 21:23:42 -303.963925 0.058099
BFGS: 10 21:23:42 -303.964119 0.035913
Step Time Energy fmax
BFGS: 0 21:23:42 -303.946345 0.279080
BFGS: 1 21:23:42 -303.949534 0.214898
BFGS: 2 21:23:42 -303.957498 0.131977
BFGS: 3 21:23:43 -303.959716 0.122439
BFGS: 4 21:23:43 -303.961139 0.093374
BFGS: 5 21:23:43 -303.961901 0.068714
BFGS: 6 21:23:43 -303.962631 0.061908
BFGS: 7 21:23:43 -303.963263 0.064861
BFGS: 8 21:23:43 -303.963729 0.071208
BFGS: 9 21:23:43 -303.964008 0.052048
BFGS: 10 21:23:43 -303.964180 0.032972
Step Time Energy fmax
BFGS: 0 21:23:43 -303.158112 0.969638
BFGS: 1 21:23:43 -303.187999 0.747877
BFGS: 2 21:23:43 -303.251634 0.697131
BFGS: 3 21:23:44 -303.285954 0.695493
BFGS: 4 21:23:44 -303.324047 0.826126
BFGS: 5 21:23:44 -303.354400 0.680043
BFGS: 6 21:23:44 -303.413555 0.511189
BFGS: 7 21:23:44 -303.418558 0.348402
BFGS: 8 21:23:44 -303.427594 0.160488
BFGS: 9 21:23:44 -303.431868 0.163330
BFGS: 10 21:23:44 -303.433963 0.165773
BFGS: 11 21:23:44 -303.436026 0.180490
BFGS: 12 21:23:44 -303.438332 0.131287
BFGS: 13 21:23:44 -303.440011 0.117380
BFGS: 14 21:23:44 -303.441199 0.104986
BFGS: 15 21:23:45 -303.441921 0.079849
BFGS: 16 21:23:45 -303.442663 0.073552
BFGS: 17 21:23:45 -303.443583 0.091592
BFGS: 18 21:23:45 -303.444506 0.121001
BFGS: 19 21:23:45 -303.445201 0.097012
BFGS: 20 21:23:45 -303.445607 0.063548
BFGS: 21 21:23:45 -303.445882 0.059674
BFGS: 22 21:23:45 -303.446258 0.081150
BFGS: 23 21:23:45 -303.446931 0.111560
BFGS: 24 21:23:45 -303.448029 0.133089
BFGS: 25 21:23:45 -303.449532 0.149109
BFGS: 26 21:23:45 -303.451455 0.203460
BFGS: 27 21:23:46 -303.455311 0.286481
BFGS: 28 21:23:46 -303.464503 0.651504
BFGS: 29 21:23:46 -303.481469 0.992676
BFGS: 30 21:23:46 -303.526841 1.246972
BFGS: 31 21:23:46 -303.559260 1.271104
BFGS: 32 21:23:46 -303.661003 1.133086
BFGS: 33 21:23:46 -303.745257 0.680731
BFGS: 34 21:23:46 -303.777219 0.719547
BFGS: 35 21:23:46 -303.831438 0.853488
BFGS: 36 21:23:46 -303.877883 0.648886
BFGS: 37 21:23:46 -303.907106 0.435154
BFGS: 38 21:23:46 -303.922620 0.397022
BFGS: 39 21:23:47 -303.939964 0.311102
BFGS: 40 21:23:47 -303.950038 0.262697
BFGS: 41 21:23:47 -303.956237 0.123947
BFGS: 42 21:23:47 -303.958093 0.098493
BFGS: 43 21:23:47 -303.959403 0.116790
BFGS: 44 21:23:47 -303.961173 0.130545
BFGS: 45 21:23:47 -303.962958 0.104987
BFGS: 46 21:23:47 -303.964045 0.060001
BFGS: 47 21:23:47 -303.964474 0.035516
/home/runner/work/_tool/Python/3.12.12/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)
Step Time Energy fmax
BFGS: 0 21:24:10 -302.160745 3.685149
BFGS: 1 21:24:10 -302.306582 2.735910
BFGS: 2 21:24:11 -302.676426 7.982418
BFGS: 3 21:24:12 -302.752888 2.060682
BFGS: 4 21:24:13 -303.007597 1.995133
BFGS: 5 21:24:13 -303.249504 1.857582
BFGS: 6 21:24:14 -303.478438 1.892635
BFGS: 7 21:24:15 -303.554785 1.430028
BFGS: 8 21:24:16 -303.605026 1.113787
BFGS: 9 21:24:16 -303.660518 1.370427
BFGS: 10 21:24:17 -303.693628 0.767121
BFGS: 11 21:24:18 -303.714022 0.730811
BFGS: 12 21:24:19 -303.736948 0.818550
BFGS: 13 21:24:20 -303.746827 0.680310
BFGS: 14 21:24:20 -303.750801 0.620379
BFGS: 15 21:24:21 -303.755447 0.670064
BFGS: 16 21:24:22 -303.761409 0.786201
BFGS: 17 21:24:23 -303.763830 0.724061
BFGS: 18 21:24:23 -303.765235 0.577296
BFGS: 19 21:24:24 -303.769797 0.445234
BFGS: 20 21:24:25 -303.777051 0.412020
BFGS: 21 21:24:26 -303.785848 0.402280
BFGS: 22 21:24:26 -303.792896 0.407510
BFGS: 23 21:24:27 -303.797311 0.314561
BFGS: 24 21:24:28 -303.800850 0.286328
BFGS: 25 21:24:28 -303.804681 0.323235
BFGS: 26 21:24:29 -303.809514 0.324791
BFGS: 27 21:24:30 -303.815365 0.342076
BFGS: 28 21:24:30 -303.820826 0.347938
BFGS: 29 21:24:31 -303.825431 0.335345
BFGS: 30 21:24:32 -303.831403 0.334278
BFGS: 31 21:24:33 -303.838642 0.348020
BFGS: 32 21:24:33 -303.844813 0.419313
BFGS: 33 21:24:34 -303.847443 0.469218
BFGS: 34 21:24:35 -303.844809 0.528840
BFGS: 35 21:24:36 -303.837898 0.624256
BFGS: 36 21:24:37 -303.832017 0.562913
BFGS: 37 21:24:37 -303.827997 0.743472
BFGS: 38 21:24:38 -303.820254 0.734211
BFGS: 39 21:24:39 -303.816706 0.852520
BFGS: 40 21:24:40 -303.784434 0.804041
BFGS: 41 21:24:40 -303.784487 0.810321
BFGS: 42 21:24:41 -303.729441 0.802284
BFGS: 43 21:24:42 -303.743256 0.596777
BFGS: 44 21:24:43 -303.746710 0.441171
BFGS: 45 21:24:43 -303.743592 0.464767
BFGS: 46 21:24:44 -303.746579 0.533333
BFGS: 47 21:24:45 -303.760055 0.501981
BFGS: 48 21:24:46 -303.782770 0.458614
BFGS: 49 21:24:47 -303.810602 0.523390
BFGS: 50 21:24:47 -303.824642 0.535767
BFGS: 51 21:24:48 -303.827500 0.531932
BFGS: 52 21:24:49 -303.827453 0.525353
BFGS: 53 21:24:50 -303.825264 0.508761
BFGS: 54 21:24:50 -303.816379 0.475329
BFGS: 55 21:24:51 -303.797121 0.487180
BFGS: 56 21:24:52 -303.775230 0.477230
BFGS: 57 21:24:53 -303.764352 0.547002
BFGS: 58 21:24:53 -303.771214 0.477396
BFGS: 59 21:24:54 -303.781061 0.572353
BFGS: 60 21:24:55 -303.788461 0.424005
BFGS: 61 21:24:56 -303.794905 0.334194
BFGS: 62 21:24:57 -303.806898 0.474383
BFGS: 63 21:24:57 -303.829941 0.584273
BFGS: 64 21:24:58 -303.852678 0.629828
BFGS: 65 21:24:59 -303.840710 0.927114
BFGS: 66 21:25:00 -303.812221 0.716628
BFGS: 67 21:25:00 -303.805078 0.499659
BFGS: 68 21:25:01 -303.814467 0.500580
BFGS: 69 21:25:02 -303.844475 0.468837
BFGS: 70 21:25:03 -303.837777 0.406077
BFGS: 71 21:25:03 -303.817658 0.401694
BFGS: 72 21:25:04 -303.824776 0.561687
BFGS: 73 21:25:05 -303.836984 0.564516
BFGS: 74 21:25:06 -303.850963 0.348359
BFGS: 75 21:25:06 -303.846289 0.285416
BFGS: 76 21:25:07 -303.836335 0.472258
BFGS: 77 21:25:08 -303.838179 0.351838
BFGS: 78 21:25:09 -303.839046 0.446782
BFGS: 79 21:25:10 -303.848762 0.593766
BFGS: 80 21:25:10 -303.853721 0.458470
BFGS: 81 21:25:11 -303.834122 0.632143
BFGS: 82 21:25:12 -303.816579 0.612461
BFGS: 83 21:25:13 -303.834608 0.395643
BFGS: 84 21:25:13 -303.839208 0.364210
BFGS: 85 21:25:14 -303.834399 0.448098
BFGS: 86 21:25:15 -303.839722 0.545160
BFGS: 87 21:25:16 -303.834567 0.592367
BFGS: 88 21:25:16 -303.815670 0.638147
BFGS: 89 21:25:17 -303.795585 0.782466
BFGS: 90 21:25:18 -303.787546 0.894113
BFGS: 91 21:25:19 -303.825516 0.789991
BFGS: 92 21:25:20 -303.848895 0.609544
BFGS: 93 21:25:20 -303.820729 0.635689
BFGS: 94 21:25:21 -303.828020 0.652931
BFGS: 95 21:25:22 -303.845809 0.407587
BFGS: 96 21:25:23 -303.854207 0.438690
BFGS: 97 21:25:23 -303.836762 0.653637
BFGS: 98 21:25:24 -303.798926 0.799623
BFGS: 99 21:25:25 -303.780550 0.824313
BFGS: 100 21:25:26 -303.787967 0.760831
BFGS: 101 21:25:26 -303.815007 0.684232
BFGS: 102 21:25:27 -303.827268 0.543413
BFGS: 103 21:25:28 -303.809333 0.647424
BFGS: 104 21:25:29 -303.817768 0.723384
BFGS: 105 21:25:30 -303.846758 0.606802
BFGS: 106 21:25:30 -303.857502 0.450649
BFGS: 107 21:25:31 -303.844291 0.595306
BFGS: 108 21:25:32 -303.822684 0.664078
BFGS: 109 21:25:33 -303.815012 0.449686
BFGS: 110 21:25:34 -303.834949 0.429169
BFGS: 111 21:25:34 -303.818475 0.594772
BFGS: 112 21:25:35 -303.838708 0.461794
BFGS: 113 21:25:36 -303.851019 0.499322
BFGS: 114 21:25:37 -303.835752 0.602813
BFGS: 115 21:25:37 -303.799216 0.736918
BFGS: 116 21:25:38 -303.786873 0.729376
BFGS: 117 21:25:39 -303.816573 0.672091
BFGS: 118 21:25:40 -303.836844 0.632524
BFGS: 119 21:25:40 -303.820723 0.600522
BFGS: 120 21:25:41 -303.792710 0.795757
BFGS: 121 21:25:42 -303.817392 0.807079
BFGS: 122 21:25:43 -303.847943 0.691321
BFGS: 123 21:25:44 -303.853248 0.431051
BFGS: 124 21:25:44 -303.832827 0.625659
BFGS: 125 21:25:45 -303.804176 0.734084
BFGS: 126 21:25:46 -303.805167 0.606507
BFGS: 127 21:25:47 -303.825685 0.692440
BFGS: 128 21:25:47 -303.834587 0.613730
BFGS: 129 21:25:48 -303.808174 0.663901
BFGS: 130 21:25:49 -303.790780 0.755324
BFGS: 131 21:25:50 -303.822632 0.786516
BFGS: 132 21:25:50 -303.849157 0.784525
BFGS: 133 21:25:51 -303.851756 0.438074
BFGS: 134 21:25:52 -303.827611 0.694098
BFGS: 135 21:25:53 -303.805184 0.715704
BFGS: 136 21:25:54 -303.819481 0.459690
BFGS: 137 21:25:54 -303.829223 0.511323
BFGS: 138 21:25:55 -303.813683 0.505301
BFGS: 139 21:25:56 -303.814274 0.566637
BFGS: 140 21:25:57 -303.839319 0.633521
BFGS: 141 21:25:57 -303.852018 0.534983
BFGS: 142 21:25:58 -303.841636 0.564847
BFGS: 143 21:25:59 -303.816162 0.697905
BFGS: 144 21:26:00 -303.813091 0.556130
BFGS: 145 21:26:00 -303.829578 0.425564
BFGS: 146 21:26:01 -303.822077 0.510967
BFGS: 147 21:26:02 -303.833291 0.418957
BFGS: 148 21:26:03 -303.844316 0.371439
BFGS: 149 21:26:04 -303.833000 0.557128
BFGS: 150 21:26:04 -303.823058 0.577270
BFGS: 151 21:26:05 -303.829043 0.334305
BFGS: 152 21:26:06 -303.835258 0.256798
BFGS: 153 21:26:07 -303.833622 0.449876
BFGS: 154 21:26:07 -303.839655 0.364862
BFGS: 155 21:26:08 -303.822296 0.500055
BFGS: 156 21:26:09 -303.815633 0.562872
BFGS: 157 21:26:10 -303.838280 0.381073
BFGS: 158 21:26:10 -303.835867 0.506866
BFGS: 159 21:26:11 -303.813959 0.674356
BFGS: 160 21:26:12 -303.824382 0.701198
BFGS: 161 21:26:13 -303.851011 0.457844
BFGS: 162 21:26:14 -303.845154 0.582042
BFGS: 163 21:26:14 -303.812909 0.648036
BFGS: 164 21:26:15 -303.823182 0.616913
BFGS: 165 21:26:16 -303.842317 0.596581
BFGS: 166 21:26:17 -303.818400 0.572071
BFGS: 167 21:26:18 -303.806361 0.783335
BFGS: 168 21:26:18 -303.840044 0.538372
BFGS: 169 21:26:19 -303.852210 0.411204
BFGS: 170 21:26:20 -303.825976 0.642140
BFGS: 171 21:26:21 -303.804871 0.692642
BFGS: 172 21:26:21 -303.827835 0.438580
BFGS: 173 21:26:22 -303.835716 0.503542
BFGS: 174 21:26:23 -303.803865 0.728728
BFGS: 175 21:26:24 -303.811715 0.613729
BFGS: 176 21:26:24 -303.840227 0.439261
BFGS: 177 21:26:25 -303.849842 0.397168
BFGS: 178 21:26:26 -303.832736 0.606688
BFGS: 179 21:26:27 -303.811860 0.663697
BFGS: 180 21:26:27 -303.827064 0.472007
BFGS: 181 21:26:28 -303.841107 0.563001
BFGS: 182 21:26:29 -303.810503 0.726972
BFGS: 183 21:26:30 -303.804399 0.766319
BFGS: 184 21:26:31 -303.842836 0.523875
BFGS: 185 21:26:31 -303.857027 0.409539
BFGS: 186 21:26:32 -303.828428 0.682879
BFGS: 187 21:26:33 -303.803452 0.696043
BFGS: 188 21:26:34 -303.827623 0.436211
BFGS: 189 21:26:34 -303.834440 0.470663
BFGS: 190 21:26:35 -303.811536 0.627920
BFGS: 191 21:26:36 -303.819791 0.563792
BFGS: 192 21:26:37 -303.848956 0.491629
BFGS: 193 21:26:37 -303.851814 0.449403
BFGS: 194 21:26:38 -303.828097 0.639392
BFGS: 195 21:26:39 -303.809113 0.609316
BFGS: 196 21:26:40 -303.827482 0.350710
BFGS: 197 21:26:40 -303.830662 0.342779
BFGS: 198 21:26:41 -303.836087 0.242434
BFGS: 199 21:26:42 -303.837410 0.363385
BFGS: 200 21:26:43 -303.828500 0.467285
BFGS: 201 21:26:44 -303.817116 0.617315
BFGS: 202 21:26:44 -303.830104 0.375624
BFGS: 203 21:26:45 -303.836735 0.247048
BFGS: 204 21:26:46 -303.835241 0.193527
BFGS: 205 21:26:47 -303.836198 0.231862
BFGS: 206 21:26:47 -303.845791 0.357838
BFGS: 207 21:26:48 -303.861733 0.473132
BFGS: 208 21:26:49 -303.881842 0.826973
BFGS: 209 21:26:49 -303.861528 0.836680
BFGS: 210 21:26:50 -303.816372 0.788128
BFGS: 211 21:26:51 -303.825170 0.563439
BFGS: 212 21:26:52 -303.839368 0.351153
BFGS: 213 21:26:52 -303.838301 0.337640
BFGS: 214 21:26:53 -303.838284 0.345320
BFGS: 215 21:26:54 -303.842024 0.431240
BFGS: 216 21:26:55 -303.843413 0.462863
BFGS: 217 21:26:55 -303.838768 0.415718
BFGS: 218 21:26:56 -303.837298 0.340018
BFGS: 219 21:26:57 -303.836472 0.377809
BFGS: 220 21:26:58 -303.837131 0.443363
BFGS: 221 21:26:59 -303.839592 0.695177
BFGS: 222 21:26:59 -303.841395 0.778208
BFGS: 223 21:27:00 -303.837345 0.543080
BFGS: 224 21:27:01 -303.839159 0.349832
BFGS: 225 21:27:02 -303.841897 0.344908
BFGS: 226 21:27:02 -303.837881 0.316741
BFGS: 227 21:27:03 -303.839515 0.241919
BFGS: 228 21:27:04 -303.840307 0.791421
BFGS: 229 21:27:04 -303.838994 1.090910
BFGS: 230 21:27:05 -303.834265 0.558306
BFGS: 231 21:27:06 -303.839439 0.840991
BFGS: 232 21:27:07 -303.842000 0.658107
BFGS: 233 21:27:08 -303.837838 0.517022
BFGS: 234 21:27:08 -303.836306 0.321031
BFGS: 235 21:27:09 -303.842576 0.439933
BFGS: 236 21:27:10 -303.840093 0.310717
BFGS: 237 21:27:11 -303.840176 0.448273
BFGS: 238 21:27:11 -303.841630 0.338536
BFGS: 239 21:27:12 -303.840084 0.331003
BFGS: 240 21:27:13 -303.840664 0.294168
BFGS: 241 21:27:14 -303.839492 0.442266
BFGS: 242 21:27:14 -303.832647 1.197489
BFGS: 243 21:27:15 -303.835663 0.713255
BFGS: 244 21:27:16 -303.836023 0.393030
BFGS: 245 21:27:17 -303.839324 0.184038
BFGS: 246 21:27:17 -303.840373 0.149335
BFGS: 247 21:27:18 -303.840934 0.161501
BFGS: 248 21:27:19 -303.837037 0.296421
BFGS: 249 21:27:20 -303.838912 0.265234
BFGS: 250 21:27:20 -303.840410 0.262502
BFGS: 251 21:27:21 -303.829374 0.606335
BFGS: 252 21:27:22 -303.815172 0.970542
BFGS: 253 21:27:23 -303.822408 0.533912
BFGS: 254 21:27:24 -303.842348 0.512991
BFGS: 255 21:27:24 -303.836925 0.278035
BFGS: 256 21:27:25 -303.836213 0.325283
BFGS: 257 21:27:26 -303.845548 0.326414
BFGS: 258 21:27:27 -303.849566 0.335101
BFGS: 259 21:27:27 -303.834425 0.360291
BFGS: 260 21:27:28 -303.828317 0.454124
BFGS: 261 21:27:29 -303.841366 0.361681
BFGS: 262 21:27:30 -303.848816 0.429768
BFGS: 263 21:27:30 -303.832142 0.406935
BFGS: 264 21:27:31 -303.831377 0.454752
BFGS: 265 21:27:32 -303.844061 0.578542
BFGS: 266 21:27:33 -303.852005 0.451537
BFGS: 267 21:27:33 -303.833583 0.384521
BFGS: 268 21:27:34 -303.831605 0.444137
BFGS: 269 21:27:35 -303.841446 0.290680
BFGS: 270 21:27:36 -303.841563 0.354420
BFGS: 271 21:27:36 -303.832939 0.706428
BFGS: 272 21:27:37 -303.819966 1.210384
BFGS: 273 21:27:38 -303.830391 0.915707
BFGS: 274 21:27:39 -303.845139 0.849016
BFGS: 275 21:27:40 -303.847417 0.821959
BFGS: 276 21:27:40 -303.836690 0.400612
BFGS: 277 21:27:41 -303.833422 0.502575
BFGS: 278 21:27:42 -303.847740 0.607950
BFGS: 279 21:27:43 -303.854474 0.680889
BFGS: 280 21:27:43 -303.835153 0.429913
BFGS: 281 21:27:44 -303.838164 0.406675
BFGS: 282 21:27:45 -303.848455 0.422612
BFGS: 283 21:27:46 -303.844353 0.377130
BFGS: 284 21:27:46 -303.833696 0.511971
BFGS: 285 21:27:47 -303.844463 0.451734
BFGS: 286 21:27:48 -303.860306 0.524457
BFGS: 287 21:27:49 -303.843842 0.613385
BFGS: 288 21:27:49 -303.828045 0.589577
BFGS: 289 21:27:50 -303.841252 0.431526
BFGS: 290 21:27:51 -303.839100 0.680093
BFGS: 291 21:27:52 -303.821048 0.785793
BFGS: 292 21:27:53 -303.833693 0.474175
BFGS: 293 21:27:53 -303.843079 0.283370
BFGS: 294 21:27:54 -303.837402 0.398885
BFGS: 295 21:27:55 -303.838820 0.736135
BFGS: 296 21:27:55 -303.844345 0.621046
BFGS: 297 21:27:56 -303.827336 0.435486
BFGS: 298 21:27:57 -303.834726 0.376476
BFGS: 299 21:27:58 -303.836822 0.354410
BFGS: 300 21:27:58 -303.840766 0.156779
BFGS: 301 21:27:59 -303.840766 0.267368
BFGS: 302 21:27:59 -303.840766 1.460457
BFGS: 303 21:28:00 -303.840766 0.291534
BFGS: 304 21:28:00 -303.840766 0.180617
BFGS: 305 21:28:00 -303.840766 0.081766
BFGS: 306 21:28:01 -303.840766 0.149185
BFGS: 307 21:28:01 -303.840766 0.204158
BFGS: 308 21:28:01 -303.840766 0.563687
BFGS: 309 21:28:02 -303.840766 1.670706
BFGS: 310 21:28:02 -303.840766 0.670472
BFGS: 311 21:28:02 -303.840766 0.727449
BFGS: 312 21:28:03 -303.840766 1.001888
BFGS: 313 21:28:03 -303.840766 1.009958
BFGS: 314 21:28:03 -303.840766 0.905608
BFGS: 315 21:28:04 -303.840766 1.052450
BFGS: 316 21:28:04 -303.840766 0.799728
BFGS: 317 21:28:04 -303.840766 0.616707
BFGS: 318 21:28:05 -303.840766 0.659954
BFGS: 319 21:28:05 -303.840766 0.636460
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_7441/3247994494.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")