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)!
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/3.12.11/x64/lib/python3.12/site-packages/torchtnt/utils/version.py:12: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
# 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-1")
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=200)
reactant_energies.append(config.get_potential_energy())
Step Time Energy fmax
BFGS: 0 14:56:28 -300.729987 3.975307
BFGS: 1 14:56:28 -301.178684 3.811137
BFGS: 2 14:56:28 -302.531348 3.730178
BFGS: 3 14:56:28 -302.322989 9.024432
BFGS: 4 14:56:28 -302.838586 3.132934
BFGS: 5 14:56:28 -303.003752 2.166920
BFGS: 6 14:56:28 -303.099672 2.123594
BFGS: 7 14:56:29 -303.129174 0.436022
BFGS: 8 14:56:29 -303.135154 0.328405
BFGS: 9 14:56:29 -303.148429 0.575332
BFGS: 10 14:56:29 -303.158216 0.594109
BFGS: 11 14:56:29 -303.166051 0.339206
BFGS: 12 14:56:29 -303.167870 0.177952
BFGS: 13 14:56:29 -303.170333 0.256269
BFGS: 14 14:56:29 -303.173955 0.336264
BFGS: 15 14:56:29 -303.179184 0.345611
BFGS: 16 14:56:29 -303.183999 0.305077
BFGS: 17 14:56:30 -303.186609 0.160365
BFGS: 18 14:56:30 -303.187405 0.118588
BFGS: 19 14:56:30 -303.187919 0.135855
BFGS: 20 14:56:30 -303.188895 0.161642
BFGS: 21 14:56:30 -303.189747 0.128428
BFGS: 22 14:56:30 -303.190137 0.055457
BFGS: 23 14:56:30 -303.190258 0.040976
Step Time Energy fmax
BFGS: 0 14:56:30 -301.130795 4.016484
BFGS: 1 14:56:30 -301.531429 3.120505
BFGS: 2 14:56:30 -302.655829 3.601029
BFGS: 3 14:56:31 -302.738604 4.843439
BFGS: 4 14:56:31 -303.035242 2.424658
BFGS: 5 14:56:31 -303.154626 2.197711
BFGS: 6 14:56:31 -303.188865 0.704545
BFGS: 7 14:56:31 -303.217536 0.767846
BFGS: 8 14:56:31 -303.398549 1.937336
BFGS: 9 14:56:31 -303.507524 2.277606
BFGS: 10 14:56:31 -303.648690 1.941904
BFGS: 11 14:56:31 -303.811539 1.842857
BFGS: 12 14:56:32 -303.989560 2.075281
BFGS: 13 14:56:32 -304.093652 1.031585
BFGS: 14 14:56:32 -304.122899 0.493614
BFGS: 15 14:56:32 -304.129909 0.370607
BFGS: 16 14:56:32 -304.143153 0.345572
BFGS: 17 14:56:32 -304.153599 0.304924
BFGS: 18 14:56:32 -304.157940 0.197380
BFGS: 19 14:56:32 -304.160096 0.181171
BFGS: 20 14:56:32 -304.162875 0.215677
BFGS: 21 14:56:33 -304.166697 0.229154
BFGS: 22 14:56:33 -304.170561 0.193192
BFGS: 23 14:56:33 -304.173466 0.223078
BFGS: 24 14:56:33 -304.175639 0.175349
BFGS: 25 14:56:33 -304.177340 0.102339
BFGS: 26 14:56:33 -304.178856 0.104127
BFGS: 27 14:56:33 -304.180349 0.161712
BFGS: 28 14:56:33 -304.181936 0.183782
BFGS: 29 14:56:33 -304.183507 0.144580
BFGS: 30 14:56:33 -304.184794 0.089360
BFGS: 31 14:56:34 -304.185932 0.109729
BFGS: 32 14:56:34 -304.187467 0.191770
BFGS: 33 14:56:34 -304.190592 0.305785
BFGS: 34 14:56:34 -304.198355 0.491286
BFGS: 35 14:56:34 -304.209947 0.951986
BFGS: 36 14:56:34 -304.223941 0.656616
BFGS: 37 14:56:34 -304.257105 0.414509
BFGS: 38 14:56:34 -304.231440 1.267710
BFGS: 39 14:56:34 -304.286853 0.698504
BFGS: 40 14:56:35 -304.297538 0.416031
BFGS: 41 14:56:35 -304.310630 0.297100
BFGS: 42 14:56:35 -304.318346 0.320558
BFGS: 43 14:56:35 -304.329559 0.240637
BFGS: 44 14:56:35 -304.332911 0.228194
BFGS: 45 14:56:35 -304.336909 0.187229
BFGS: 46 14:56:35 -304.343415 0.119050
BFGS: 47 14:56:35 -304.348865 0.127610
BFGS: 48 14:56:35 -304.351589 0.093148
BFGS: 49 14:56:35 -304.352650 0.069437
BFGS: 50 14:56:36 -304.353083 0.059783
BFGS: 51 14:56:36 -304.353430 0.048695
Step Time Energy fmax
BFGS: 0 14:56:36 -302.889353 3.559203
BFGS: 1 14:56:36 -303.226438 2.709630
BFGS: 2 14:56:36 -303.939129 2.656917
BFGS: 3 14:56:36 -304.052743 1.890856
BFGS: 4 14:56:36 -304.173245 1.904689
BFGS: 5 14:56:36 -304.213641 0.871004
BFGS: 6 14:56:36 -304.269309 0.574197
BFGS: 7 14:56:36 -304.292157 0.613855
BFGS: 8 14:56:37 -304.304249 0.416655
BFGS: 9 14:56:37 -304.315453 0.272419
BFGS: 10 14:56:37 -304.323813 0.248438
BFGS: 11 14:56:37 -304.330887 0.274373
BFGS: 12 14:56:37 -304.334789 0.203868
BFGS: 13 14:56:37 -304.336147 0.157079
BFGS: 14 14:56:37 -304.338109 0.152456
BFGS: 15 14:56:37 -304.342151 0.234992
BFGS: 16 14:56:37 -304.346543 0.271553
BFGS: 17 14:56:38 -304.349644 0.185799
BFGS: 18 14:56:38 -304.351050 0.075784
BFGS: 19 14:56:38 -304.351778 0.062930
BFGS: 20 14:56:38 -304.352585 0.106814
BFGS: 21 14:56:38 -304.353595 0.114951
BFGS: 22 14:56:38 -304.354181 0.067208
BFGS: 23 14:56:38 -304.354330 0.022605
Step Time Energy fmax
BFGS: 0 14:56:38 -302.203618 4.122120
BFGS: 1 14:56:38 -302.599690 2.960327
BFGS: 2 14:56:38 -303.474889 3.269895
BFGS: 3 14:56:39 -303.633052 2.810588
BFGS: 4 14:56:39 -303.812164 3.937332
BFGS: 5 14:56:39 -303.926103 0.868230
BFGS: 6 14:56:39 -303.959805 0.699531
BFGS: 7 14:56:39 -304.071893 0.891588
BFGS: 8 14:56:39 -304.107966 0.608604
BFGS: 9 14:56:39 -304.134605 0.517823
BFGS: 10 14:56:39 -304.157433 0.406208
BFGS: 11 14:56:39 -304.171162 0.340338
BFGS: 12 14:56:39 -304.177546 0.168111
BFGS: 13 14:56:40 -304.179814 0.137679
BFGS: 14 14:56:40 -304.181226 0.149682
BFGS: 15 14:56:40 -304.183053 0.144514
BFGS: 16 14:56:40 -304.184802 0.150181
BFGS: 17 14:56:40 -304.186937 0.195643
BFGS: 18 14:56:40 -304.190234 0.261371
BFGS: 19 14:56:40 -304.195186 0.311226
BFGS: 20 14:56:40 -304.202671 0.345440
BFGS: 21 14:56:40 -304.235433 0.819021
BFGS: 22 14:56:41 -304.235035 1.626795
BFGS: 23 14:56:41 -304.275805 1.107382
BFGS: 24 14:56:41 -304.291120 1.196085
BFGS: 25 14:56:41 -304.319392 1.736753
BFGS: 26 14:56:41 -304.333065 1.551641
BFGS: 27 14:56:41 -304.351086 1.454249
BFGS: 28 14:56:41 -304.420275 1.622318
BFGS: 29 14:56:41 -304.461461 1.578217
BFGS: 30 14:56:41 -304.492205 1.320446
BFGS: 31 14:56:41 -304.509346 1.298911
BFGS: 32 14:56:42 -304.535003 1.351155
BFGS: 33 14:56:42 -304.550411 1.337959
BFGS: 34 14:56:42 -304.575226 1.272627
BFGS: 35 14:56:42 -304.584882 1.193381
BFGS: 36 14:56:42 -304.592537 1.158826
BFGS: 37 14:56:42 -304.600492 1.120120
BFGS: 38 14:56:42 -304.609581 1.010728
BFGS: 39 14:56:42 -304.614548 0.919596
BFGS: 40 14:56:42 -304.617149 0.872213
BFGS: 41 14:56:43 -304.619246 0.853264
BFGS: 42 14:56:43 -304.621076 0.844751
BFGS: 43 14:56:43 -304.623169 0.829570
BFGS: 44 14:56:43 -304.624898 0.803144
BFGS: 45 14:56:43 -304.625963 0.783758
BFGS: 46 14:56:43 -304.626705 0.778776
BFGS: 47 14:56:43 -304.627424 0.778639
BFGS: 48 14:56:43 -304.628200 0.777026
BFGS: 49 14:56:43 -304.628966 0.775827
BFGS: 50 14:56:43 -304.629582 0.773943
BFGS: 51 14:56:44 -304.630040 0.773956
BFGS: 52 14:56:44 -304.630566 0.769267
BFGS: 53 14:56:44 -304.631424 0.756408
BFGS: 54 14:56:44 -304.632571 0.740025
BFGS: 55 14:56:44 -304.633560 0.722131
BFGS: 56 14:56:44 -304.634086 0.701035
BFGS: 57 14:56:44 -304.634429 0.704028
BFGS: 58 14:56:44 -304.634826 0.705664
BFGS: 59 14:56:44 -304.635261 0.712126
BFGS: 60 14:56:44 -304.635588 0.711480
BFGS: 61 14:56:45 -304.635753 0.713993
BFGS: 62 14:56:45 -304.635852 0.710597
BFGS: 63 14:56:45 -304.635970 0.708047
BFGS: 64 14:56:45 -304.636109 0.703237
BFGS: 65 14:56:45 -304.636218 0.700742
BFGS: 66 14:56:45 -304.636281 0.700007
BFGS: 67 14:56:45 -304.636321 0.700309
BFGS: 68 14:56:45 -304.636372 0.700353
BFGS: 69 14:56:45 -304.636427 0.699848
BFGS: 70 14:56:46 -304.636469 0.698503
BFGS: 71 14:56:46 -304.636493 0.697344
BFGS: 72 14:56:46 -304.636502 0.696652
BFGS: 73 14:56:46 -304.636515 0.696283
BFGS: 74 14:56:46 -304.636531 0.696481
BFGS: 75 14:56:46 -304.636543 0.697306
BFGS: 76 14:56:46 -304.636551 0.698164
BFGS: 77 14:56:46 -304.636553 0.698733
BFGS: 78 14:56:46 -304.636557 0.698931
BFGS: 79 14:56:46 -304.636557 0.699074
BFGS: 80 14:56:47 -304.636560 0.698914
BFGS: 81 14:56:47 -304.636562 0.698598
BFGS: 82 14:56:47 -304.636561 0.698344
BFGS: 83 14:56:47 -304.636563 0.698135
BFGS: 84 14:56:47 -304.636564 0.698076
BFGS: 85 14:56:47 -304.636564 0.698027
BFGS: 86 14:56:47 -304.636567 0.698235
BFGS: 87 14:56:47 -304.636568 0.698338
BFGS: 88 14:56:47 -304.636568 0.698521
BFGS: 89 14:56:47 -304.636567 0.698612
BFGS: 90 14:56:48 -304.636567 0.698721
BFGS: 91 14:56:48 -304.636565 0.698820
BFGS: 92 14:56:48 -304.636567 0.698827
BFGS: 93 14:56:48 -304.636565 0.698791
BFGS: 94 14:56:48 -304.636567 0.698788
BFGS: 95 14:56:48 -304.636568 0.698720
BFGS: 96 14:56:48 -304.636568 0.698709
BFGS: 97 14:56:48 -304.636566 0.698702
BFGS: 98 14:56:48 -304.636568 0.698727
BFGS: 99 14:56:49 -304.636569 0.698743
BFGS: 100 14:56:49 -304.636569 0.698739
BFGS: 101 14:56:49 -304.636568 0.698737
BFGS: 102 14:56:49 -304.636567 0.698786
BFGS: 103 14:56:49 -304.636569 0.698761
BFGS: 104 14:56:49 -304.636569 0.698716
BFGS: 105 14:56:49 -304.636567 0.698718
BFGS: 106 14:56:49 -304.636569 0.698741
BFGS: 107 14:56:49 -304.636569 0.698718
BFGS: 108 14:56:49 -304.636569 0.698759
BFGS: 109 14:56:50 -304.636569 0.698757
BFGS: 110 14:56:50 -304.636567 0.698773
BFGS: 111 14:56:50 -304.636567 0.698751
BFGS: 112 14:56:50 -304.636569 0.698726
BFGS: 113 14:56:50 -304.636569 0.698738
BFGS: 114 14:56:50 -304.636569 0.698754
BFGS: 115 14:56:50 -304.636567 0.698744
BFGS: 116 14:56:50 -304.636569 0.698717
BFGS: 117 14:56:50 -304.636566 0.698726
BFGS: 118 14:56:50 -304.636567 0.698735
BFGS: 119 14:56:51 -304.636568 0.698752
BFGS: 120 14:56:51 -304.636569 0.698733
BFGS: 121 14:56:51 -304.636565 0.698729
BFGS: 122 14:56:51 -304.636567 0.698751
BFGS: 123 14:56:51 -304.636568 0.698745
BFGS: 124 14:56:51 -304.636567 0.698734
BFGS: 125 14:56:51 -304.636567 0.698731
BFGS: 126 14:56:51 -304.636569 0.698763
BFGS: 127 14:56:51 -304.636569 0.698747
BFGS: 128 14:56:52 -304.636569 0.698757
BFGS: 129 14:56:52 -304.636569 0.698735
BFGS: 130 14:56:52 -304.636569 0.698731
BFGS: 131 14:56:52 -304.636569 0.698750
BFGS: 132 14:56:52 -304.636568 0.698746
BFGS: 133 14:56:52 -304.636569 0.698738
BFGS: 134 14:56:52 -304.636569 0.698748
BFGS: 135 14:56:52 -304.636568 0.698743
BFGS: 136 14:56:52 -304.636569 0.698739
BFGS: 137 14:56:52 -304.636568 0.698746
BFGS: 138 14:56:53 -304.636569 0.698738
BFGS: 139 14:56:53 -304.636567 0.698736
BFGS: 140 14:56:53 -304.636567 0.698735
BFGS: 141 14:56:53 -304.636569 0.698736
BFGS: 142 14:56:53 -304.636567 0.698742
BFGS: 143 14:56:53 -304.636567 0.698751
BFGS: 144 14:56:53 -304.636568 0.698733
BFGS: 145 14:56:53 -304.636569 0.698753
BFGS: 146 14:56:53 -304.636568 0.698740
BFGS: 147 14:56:53 -304.636566 0.698732
BFGS: 148 14:56:54 -304.636568 0.698744
BFGS: 149 14:56:54 -304.636569 0.698744
BFGS: 150 14:56:54 -304.636569 0.698744
BFGS: 151 14:56:54 -304.636567 0.698753
BFGS: 152 14:56:54 -304.636567 0.698733
BFGS: 153 14:56:54 -304.636567 0.698743
BFGS: 154 14:56:54 -304.636567 0.698734
BFGS: 155 14:56:54 -304.636567 0.698733
BFGS: 156 14:56:54 -304.636567 0.698740
BFGS: 157 14:56:55 -304.636567 0.698730
BFGS: 158 14:56:55 -304.636569 0.698741
BFGS: 159 14:56:55 -304.636567 0.698746
BFGS: 160 14:56:55 -304.636567 0.698749
BFGS: 161 14:56:55 -304.636567 0.698734
BFGS: 162 14:56:55 -304.636569 0.698744
BFGS: 163 14:56:55 -304.636567 0.698732
BFGS: 164 14:56:55 -304.636570 0.698726
BFGS: 165 14:56:55 -304.636567 0.698733
BFGS: 166 14:56:55 -304.636569 0.698751
BFGS: 167 14:56:56 -304.636567 0.698735
BFGS: 168 14:56:56 -304.636568 0.698750
BFGS: 169 14:56:56 -304.636569 0.698723
BFGS: 170 14:56:56 -304.636569 0.698745
BFGS: 171 14:56:56 -304.636568 0.698731
BFGS: 172 14:56:56 -304.636569 0.698750
BFGS: 173 14:56:56 -304.636569 0.698731
BFGS: 174 14:56:56 -304.636569 0.698742
BFGS: 175 14:56:57 -304.636570 0.698728
BFGS: 176 14:56:57 -304.636567 0.698732
BFGS: 177 14:56:57 -304.636567 0.698732
BFGS: 178 14:56:57 -304.636567 0.698731
BFGS: 179 14:56:57 -304.636569 0.698747
BFGS: 180 14:56:57 -304.636568 0.698758
BFGS: 181 14:56:57 -304.636567 0.698751
BFGS: 182 14:56:57 -304.636569 0.698740
BFGS: 183 14:56:57 -304.636567 0.698744
BFGS: 184 14:56:58 -304.636567 0.698732
BFGS: 185 14:56:58 -304.636569 0.698748
BFGS: 186 14:56:58 -304.636569 0.698747
BFGS: 187 14:56:58 -304.636566 0.698733
BFGS: 188 14:56:58 -304.636570 0.698740
BFGS: 189 14:56:58 -304.636569 0.698745
BFGS: 190 14:56:58 -304.636567 0.698751
BFGS: 191 14:56:58 -304.636568 0.698744
BFGS: 192 14:56:58 -304.636570 0.698740
BFGS: 193 14:56:58 -304.636569 0.698746
BFGS: 194 14:56:59 -304.636567 0.698751
BFGS: 195 14:56:59 -304.636569 0.698744
BFGS: 196 14:56:59 -304.636569 0.698740
BFGS: 197 14:56:59 -304.636569 0.698745
BFGS: 198 14:56:59 -304.636569 0.698750
BFGS: 199 14:56:59 -304.636569 0.698743
BFGS: 200 14:56:59 -304.636568 0.698743
Step Time Energy fmax
BFGS: 0 14:56:59 -301.339383 4.154280
BFGS: 1 14:56:59 -301.736998 3.423238
BFGS: 2 14:56:59 -302.783606 3.330447
BFGS: 3 14:57:00 -302.878681 4.781281
BFGS: 4 14:57:00 -303.177169 2.473105
BFGS: 5 14:57:00 -303.405635 2.143679
BFGS: 6 14:57:00 -303.505635 2.368234
BFGS: 7 14:57:00 -303.812668 1.396425
BFGS: 8 14:57:00 -303.798742 2.075079
BFGS: 9 14:57:00 -303.936722 0.961609
BFGS: 10 14:57:00 -303.986818 0.789220
BFGS: 11 14:57:00 -304.083658 0.569179
BFGS: 12 14:57:01 -304.102277 0.491328
BFGS: 13 14:57:01 -304.128217 0.402929
BFGS: 14 14:57:01 -304.143193 0.375549
BFGS: 15 14:57:01 -304.152672 0.294615
BFGS: 16 14:57:01 -304.159026 0.269531
BFGS: 17 14:57:01 -304.163681 0.164109
BFGS: 18 14:57:01 -304.165550 0.148018
BFGS: 19 14:57:01 -304.167167 0.144220
BFGS: 20 14:57:01 -304.169532 0.219752
BFGS: 21 14:57:01 -304.172547 0.255073
BFGS: 22 14:57:02 -304.175171 0.187508
BFGS: 23 14:57:02 -304.176736 0.101964
BFGS: 24 14:57:02 -304.177675 0.103603
BFGS: 25 14:57:02 -304.178740 0.120246
BFGS: 26 14:57:02 -304.180755 0.167859
BFGS: 27 14:57:02 -304.182928 0.155998
BFGS: 28 14:57:02 -304.184393 0.108233
BFGS: 29 14:57:02 -304.185462 0.111025
BFGS: 30 14:57:02 -304.186925 0.126436
BFGS: 31 14:57:02 -304.190068 0.234607
BFGS: 32 14:57:03 -304.197751 0.414096
BFGS: 33 14:57:03 -304.210705 0.632108
BFGS: 34 14:57:03 -304.226255 0.531581
BFGS: 35 14:57:03 -304.230808 0.707227
BFGS: 36 14:57:03 -304.233835 1.069159
BFGS: 37 14:57:03 -304.289741 0.431095
BFGS: 38 14:57:03 -304.303257 0.270768
BFGS: 39 14:57:03 -304.313779 0.269434
BFGS: 40 14:57:03 -304.323617 0.225520
BFGS: 41 14:57:04 -304.332636 0.193855
BFGS: 42 14:57:04 -304.335623 0.170050
BFGS: 43 14:57:04 -304.338614 0.144762
BFGS: 44 14:57:04 -304.342478 0.155606
BFGS: 45 14:57:04 -304.347235 0.156635
BFGS: 46 14:57:04 -304.350881 0.112699
BFGS: 47 14:57:04 -304.352662 0.062669
BFGS: 48 14:57:04 -304.353343 0.056698
BFGS: 49 14:57:04 -304.353648 0.042520
Step Time Energy fmax
BFGS: 0 14:57:04 -301.375461 4.109099
BFGS: 1 14:57:05 -301.763329 3.106690
BFGS: 2 14:57:05 -302.762129 3.509149
BFGS: 3 14:57:05 -302.910099 3.337728
BFGS: 4 14:57:05 -303.211165 1.932880
BFGS: 5 14:57:05 -303.328752 3.148805
BFGS: 6 14:57:05 -303.421598 1.786269
BFGS: 7 14:57:05 -303.620712 1.104479
BFGS: 8 14:57:05 -303.889808 2.188857
BFGS: 9 14:57:05 -303.951268 2.031340
BFGS: 10 14:57:06 -304.077384 0.817418
BFGS: 11 14:57:06 -304.110166 1.040858
BFGS: 12 14:57:06 -304.150824 1.116143
BFGS: 13 14:57:06 -304.213115 0.558242
BFGS: 14 14:57:06 -304.227609 0.459391
BFGS: 15 14:57:06 -304.262852 0.741663
BFGS: 16 14:57:06 -304.302349 1.074750
BFGS: 17 14:57:06 -304.349072 1.224046
BFGS: 18 14:57:06 -304.395987 1.015741
BFGS: 19 14:57:06 -304.480257 0.690906
BFGS: 20 14:57:07 -304.531033 0.548250
BFGS: 21 14:57:07 -304.535913 1.125164
BFGS: 22 14:57:07 -304.572065 0.418574
BFGS: 23 14:57:07 -304.580939 0.425738
BFGS: 24 14:57:07 -304.604025 0.487032
BFGS: 25 14:57:07 -304.623723 0.660207
BFGS: 26 14:57:07 -304.644565 0.500888
BFGS: 27 14:57:07 -304.654372 0.306874
BFGS: 28 14:57:07 -304.660799 0.282971
BFGS: 29 14:57:07 -304.668085 0.346993
BFGS: 30 14:57:08 -304.676992 0.373285
BFGS: 31 14:57:08 -304.684744 0.209401
BFGS: 32 14:57:08 -304.687752 0.105678
BFGS: 33 14:57:08 -304.688873 0.084030
BFGS: 34 14:57:08 -304.689996 0.081927
BFGS: 35 14:57:08 -304.691414 0.111737
BFGS: 36 14:57:08 -304.692850 0.099318
BFGS: 37 14:57:08 -304.693705 0.050947
BFGS: 38 14:57:08 -304.694059 0.025034
Step Time Energy fmax
BFGS: 0 14:57:09 -300.766543 3.934827
BFGS: 1 14:57:09 -301.208542 3.760237
BFGS: 2 14:57:09 -302.559868 3.689113
BFGS: 3 14:57:09 -302.392154 8.449686
BFGS: 4 14:57:09 -302.858311 3.090431
BFGS: 5 14:57:09 -303.018263 2.091984
BFGS: 6 14:57:09 -303.105816 1.952463
BFGS: 7 14:57:09 -303.130070 0.404176
BFGS: 8 14:57:09 -303.135575 0.281867
BFGS: 9 14:57:09 -303.146938 0.598696
BFGS: 10 14:57:10 -303.157467 0.679517
BFGS: 11 14:57:10 -303.168598 0.464750
BFGS: 12 14:57:10 -303.171848 0.245321
BFGS: 13 14:57:10 -303.175733 0.299089
BFGS: 14 14:57:10 -303.181356 0.424526
BFGS: 15 14:57:10 -303.188897 0.450445
BFGS: 16 14:57:10 -303.195880 0.365868
BFGS: 17 14:57:10 -303.199808 0.172999
BFGS: 18 14:57:10 -303.201253 0.127183
BFGS: 19 14:57:11 -303.202461 0.160188
BFGS: 20 14:57:11 -303.204921 0.270508
BFGS: 21 14:57:11 -303.208511 0.317702
BFGS: 22 14:57:11 -303.212092 0.246652
BFGS: 23 14:57:11 -303.216348 0.231084
BFGS: 24 14:57:11 -303.244820 0.841941
BFGS: 25 14:57:11 -303.280909 1.817372
BFGS: 26 14:57:11 -303.514936 2.920664
BFGS: 27 14:57:11 -303.821021 0.868922
BFGS: 28 14:57:11 -303.789626 2.493583
BFGS: 29 14:57:12 -303.908565 1.003817
BFGS: 30 14:57:12 -303.952376 0.987832
BFGS: 31 14:57:12 -304.187577 1.699081
BFGS: 32 14:57:12 -304.254097 1.450687
BFGS: 33 14:57:12 -304.420948 0.735683
BFGS: 34 14:57:12 -304.449852 0.721310
BFGS: 35 14:57:12 -304.510298 0.592616
BFGS: 36 14:57:12 -304.547935 0.488336
BFGS: 37 14:57:12 -304.569098 0.472166
BFGS: 38 14:57:12 -304.587035 0.471047
BFGS: 39 14:57:13 -304.611946 0.545838
BFGS: 40 14:57:13 -304.639452 0.482454
BFGS: 41 14:57:13 -304.660213 0.413129
BFGS: 42 14:57:13 -304.671344 0.294822
BFGS: 43 14:57:13 -304.677575 0.197301
BFGS: 44 14:57:13 -304.682679 0.172557
BFGS: 45 14:57:13 -304.686394 0.139557
BFGS: 46 14:57:13 -304.688621 0.131620
BFGS: 47 14:57:13 -304.689736 0.113968
BFGS: 48 14:57:14 -304.690373 0.089897
BFGS: 49 14:57:14 -304.690909 0.065318
BFGS: 50 14:57:14 -304.691387 0.063654
BFGS: 51 14:57:14 -304.691819 0.079623
BFGS: 52 14:57:14 -304.692303 0.092591
BFGS: 53 14:57:14 -304.692834 0.093164
BFGS: 54 14:57:14 -304.693309 0.062978
BFGS: 55 14:57:14 -304.693647 0.037777
Step Time Energy fmax
BFGS: 0 14:57:14 -300.933484 4.054908
BFGS: 1 14:57:14 -301.344125 3.266325
BFGS: 2 14:57:15 -302.519982 3.679683
BFGS: 3 14:57:15 -302.562440 5.757724
BFGS: 4 14:57:15 -302.904256 2.597440
BFGS: 5 14:57:15 -303.056898 1.944935
BFGS: 6 14:57:15 -303.085083 0.749869
BFGS: 7 14:57:15 -303.109600 0.658731
BFGS: 8 14:57:15 -303.143985 1.060232
BFGS: 9 14:57:15 -303.175150 0.840385
BFGS: 10 14:57:15 -303.189325 0.294968
BFGS: 11 14:57:16 -303.191809 0.176146
BFGS: 12 14:57:16 -303.194035 0.306574
BFGS: 13 14:57:16 -303.197976 0.462351
BFGS: 14 14:57:16 -303.202328 0.448381
BFGS: 15 14:57:16 -303.205559 0.296696
BFGS: 16 14:57:16 -303.207396 0.200296
BFGS: 17 14:57:16 -303.211192 0.365894
BFGS: 18 14:57:16 -303.217216 0.635255
BFGS: 19 14:57:16 -303.247054 1.228865
BFGS: 20 14:57:16 -303.348329 1.090884
BFGS: 21 14:57:17 -303.286268 3.462213
BFGS: 22 14:57:17 -303.688109 2.745386
BFGS: 23 14:57:17 -303.891393 1.341326
BFGS: 24 14:57:17 -303.944262 1.248984
BFGS: 25 14:57:17 -303.994009 0.982783
BFGS: 26 14:57:17 -304.023838 0.596427
BFGS: 27 14:57:17 -304.049441 0.426945
BFGS: 28 14:57:17 -304.090435 0.606475
BFGS: 29 14:57:17 -304.098800 0.652545
BFGS: 30 14:57:17 -304.131732 0.451487
BFGS: 31 14:57:18 -304.141610 0.272074
BFGS: 32 14:57:18 -304.148991 0.286584
BFGS: 33 14:57:18 -304.157849 0.318127
BFGS: 34 14:57:18 -304.170081 0.210124
BFGS: 35 14:57:18 -304.176360 0.153012
BFGS: 36 14:57:18 -304.179219 0.192200
BFGS: 37 14:57:18 -304.182133 0.282988
BFGS: 38 14:57:18 -304.186361 0.343979
BFGS: 39 14:57:18 -304.192072 0.312579
BFGS: 40 14:57:19 -304.197844 0.229440
BFGS: 41 14:57:19 -304.203747 0.271812
BFGS: 42 14:57:19 -304.212090 0.560169
BFGS: 43 14:57:19 -304.231193 0.944437
BFGS: 44 14:57:19 -304.259668 1.204598
BFGS: 45 14:57:19 -304.276110 1.146193
BFGS: 46 14:57:19 -304.288775 1.505976
BFGS: 47 14:57:19 -304.307029 1.509235
BFGS: 48 14:57:19 -304.363032 1.421340
BFGS: 49 14:57:19 -304.425300 0.899398
BFGS: 50 14:57:20 -304.461875 1.221674
BFGS: 51 14:57:20 -304.521417 0.641866
BFGS: 52 14:57:20 -304.554170 0.659285
BFGS: 53 14:57:20 -304.633490 0.625791
BFGS: 54 14:57:20 -304.654683 0.386841
BFGS: 55 14:57:20 -304.668584 0.308254
BFGS: 56 14:57:20 -304.674302 0.259572
BFGS: 57 14:57:20 -304.679700 0.224927
BFGS: 58 14:57:20 -304.683888 0.186197
BFGS: 59 14:57:21 -304.687551 0.153130
BFGS: 60 14:57:21 -304.689965 0.123420
BFGS: 61 14:57:21 -304.691272 0.080713
BFGS: 62 14:57:21 -304.691919 0.083998
BFGS: 63 14:57:21 -304.692288 0.078674
BFGS: 64 14:57:21 -304.692661 0.064611
BFGS: 65 14:57:21 -304.693078 0.064822
BFGS: 66 14:57:21 -304.693489 0.060152
BFGS: 67 14:57:21 -304.693776 0.052701
BFGS: 68 14:57:21 -304.693927 0.047218
Step Time Energy fmax
BFGS: 0 14:57:22 -300.676051 4.020761
BFGS: 1 14:57:22 -301.128136 3.797906
BFGS: 2 14:57:22 -302.500295 3.745046
BFGS: 3 14:57:22 -302.371047 8.230850
BFGS: 4 14:57:22 -302.818580 3.133850
BFGS: 5 14:57:22 -303.006820 1.963244
BFGS: 6 14:57:22 -303.098048 2.023197
BFGS: 7 14:57:22 -303.125343 0.657764
BFGS: 8 14:57:22 -303.135342 0.419222
BFGS: 9 14:57:22 -303.148839 0.634470
BFGS: 10 14:57:23 -303.161698 0.589613
BFGS: 11 14:57:23 -303.167800 0.291498
BFGS: 12 14:57:23 -303.169182 0.149514
BFGS: 13 14:57:23 -303.170494 0.254016
BFGS: 14 14:57:23 -303.172790 0.399696
BFGS: 15 14:57:23 -303.175799 0.433983
BFGS: 16 14:57:23 -303.178390 0.292095
BFGS: 17 14:57:23 -303.179708 0.110464
BFGS: 18 14:57:23 -303.180246 0.139995
BFGS: 19 14:57:24 -303.180870 0.179820
BFGS: 20 14:57:24 -303.181865 0.188353
BFGS: 21 14:57:24 -303.182627 0.118906
BFGS: 22 14:57:24 -303.182877 0.039544
Step Time Energy fmax
BFGS: 0 14:57:24 -300.881868 3.989520
BFGS: 1 14:57:24 -301.301759 3.446752
BFGS: 2 14:57:24 -302.555570 3.661070
BFGS: 3 14:57:24 -302.492601 7.185074
BFGS: 4 14:57:24 -302.891185 2.866604
BFGS: 5 14:57:24 -303.060889 1.333759
BFGS: 6 14:57:25 -303.110225 1.428441
BFGS: 7 14:57:25 -303.127264 0.664855
BFGS: 8 14:57:25 -303.144206 0.730588
BFGS: 9 14:57:25 -303.161283 0.847175
BFGS: 10 14:57:25 -303.181983 0.597527
BFGS: 11 14:57:25 -303.189453 0.281872
BFGS: 12 14:57:25 -303.192899 0.257921
BFGS: 13 14:57:25 -303.196868 0.510927
BFGS: 14 14:57:25 -303.204978 0.791256
BFGS: 15 14:57:25 -303.216011 0.851380
BFGS: 16 14:57:26 -303.226768 0.617231
BFGS: 17 14:57:26 -303.234224 0.413631
BFGS: 18 14:57:26 -303.247365 0.804132
BFGS: 19 14:57:26 -303.295395 2.442118
BFGS: 20 14:57:26 -303.303139 3.721417
BFGS: 21 14:57:26 -303.344804 3.349769
BFGS: 22 14:57:26 -303.391685 3.308021
BFGS: 23 14:57:26 -303.574444 3.138645
BFGS: 24 14:57:26 -303.718327 2.796880
BFGS: 25 14:57:27 -303.833651 1.247538
BFGS: 26 14:57:27 -303.906500 1.066263
BFGS: 27 14:57:27 -303.985355 1.240165
BFGS: 28 14:57:27 -304.079844 0.900695
BFGS: 29 14:57:27 -304.142354 0.518071
BFGS: 30 14:57:27 -304.153821 0.472618
BFGS: 31 14:57:27 -304.197805 0.394748
BFGS: 32 14:57:27 -304.222244 0.452476
BFGS: 33 14:57:27 -304.248084 0.509775
BFGS: 34 14:57:27 -304.266357 0.437394
BFGS: 35 14:57:28 -304.284469 0.380015
BFGS: 36 14:57:28 -304.301846 0.358248
BFGS: 37 14:57:28 -304.317145 0.314232
BFGS: 38 14:57:28 -304.326985 0.260573
BFGS: 39 14:57:28 -304.333451 0.240869
BFGS: 40 14:57:28 -304.338124 0.186982
BFGS: 41 14:57:28 -304.341411 0.147644
BFGS: 42 14:57:28 -304.344340 0.140352
BFGS: 43 14:57:28 -304.347473 0.141640
BFGS: 44 14:57:28 -304.350110 0.128869
BFGS: 45 14:57:29 -304.351585 0.097249
BFGS: 46 14:57:29 -304.352179 0.062178
BFGS: 47 14:57:29 -304.352548 0.038075
# 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=200)
product1_energies.append(config.get_potential_energy())
Step Time Energy fmax
BFGS: 0 14:57:29 -296.263446 4.403864
BFGS: 1 14:57:29 -296.746897 4.680793
BFGS: 2 14:57:29 -298.234274 3.346214
BFGS: 3 14:57:29 -297.636285 11.203980
BFGS: 4 14:57:29 -298.478903 1.934431
BFGS: 5 14:57:29 -298.550101 1.143371
BFGS: 6 14:57:30 -298.607194 1.239468
BFGS: 7 14:57:30 -298.633809 1.218440
BFGS: 8 14:57:30 -298.804715 1.391747
BFGS: 9 14:57:30 -298.892071 2.183495
BFGS: 10 14:57:30 -299.049952 2.762264
BFGS: 11 14:57:30 -299.236541 3.067420
BFGS: 12 14:57:30 -299.475109 3.394370
BFGS: 13 14:57:30 -300.006883 2.594593
BFGS: 14 14:57:30 -300.420127 1.214195
BFGS: 15 14:57:30 -300.470956 1.266305
BFGS: 16 14:57:31 -300.519940 0.878565
BFGS: 17 14:57:31 -300.580701 0.607060
BFGS: 18 14:57:31 -300.588163 0.345968
BFGS: 19 14:57:31 -300.596867 0.289703
BFGS: 20 14:57:31 -300.608725 0.317575
BFGS: 21 14:57:31 -300.616331 0.215734
BFGS: 22 14:57:31 -300.619326 0.129297
BFGS: 23 14:57:31 -300.620401 0.094389
BFGS: 24 14:57:31 -300.621617 0.097656
BFGS: 25 14:57:31 -300.622993 0.108894
BFGS: 26 14:57:32 -300.624159 0.074859
BFGS: 27 14:57:32 -300.624627 0.037892
Step Time Energy fmax
BFGS: 0 14:57:32 -296.098858 4.390932
BFGS: 1 14:57:32 -296.607697 4.709877
BFGS: 2 14:57:32 -298.197828 3.195516
BFGS: 3 14:57:32 -297.147783 14.357820
BFGS: 4 14:57:32 -298.398361 1.912260
BFGS: 5 14:57:32 -298.463789 1.065913
BFGS: 6 14:57:32 -298.502259 0.767164
BFGS: 7 14:57:33 -298.509610 0.549472
BFGS: 8 14:57:33 -298.530007 0.431412
BFGS: 9 14:57:33 -298.536761 0.522119
BFGS: 10 14:57:33 -298.546873 0.622427
BFGS: 11 14:57:33 -298.568706 0.786938
BFGS: 12 14:57:33 -298.644495 1.492064
BFGS: 13 14:57:33 -298.370638 5.438472
BFGS: 14 14:57:33 -298.877418 1.473249
BFGS: 15 14:57:33 -299.147370 2.393551
BFGS: 16 14:57:33 -299.377085 2.855627
BFGS: 17 14:57:34 -299.475929 3.285108
BFGS: 18 14:57:34 -299.574211 3.012196
BFGS: 19 14:57:34 -299.741833 2.717503
BFGS: 20 14:57:34 -299.822556 2.466995
BFGS: 21 14:57:34 -299.934157 2.149402
BFGS: 22 14:57:34 -300.123903 1.927082
BFGS: 23 14:57:34 -300.290729 1.185895
BFGS: 24 14:57:34 -300.414776 1.032592
BFGS: 25 14:57:34 -300.497033 0.784511
BFGS: 26 14:57:34 -300.529037 0.713185
BFGS: 27 14:57:35 -300.584167 0.610018
BFGS: 28 14:57:35 -300.595442 0.486868
BFGS: 29 14:57:35 -300.604243 0.351983
BFGS: 30 14:57:35 -300.611136 0.222236
BFGS: 31 14:57:35 -300.615935 0.200334
BFGS: 32 14:57:35 -300.620143 0.123630
BFGS: 33 14:57:35 -300.621657 0.121119
BFGS: 34 14:57:35 -300.622407 0.117401
BFGS: 35 14:57:35 -300.623022 0.099415
BFGS: 36 14:57:36 -300.623778 0.062792
BFGS: 37 14:57:36 -300.624416 0.056511
BFGS: 38 14:57:36 -300.624738 0.042880
Step Time Energy fmax
BFGS: 0 14:57:36 -297.653094 4.924202
BFGS: 1 14:57:36 -298.150919 4.976437
BFGS: 2 14:57:36 -299.347709 3.709201
BFGS: 3 14:57:36 -299.784466 2.826000
BFGS: 4 14:57:36 -299.925604 1.797827
BFGS: 5 14:57:36 -300.278556 1.481476
BFGS: 6 14:57:36 -300.388244 1.248079
BFGS: 7 14:57:37 -300.457416 1.146892
BFGS: 8 14:57:37 -300.546242 0.829953
BFGS: 9 14:57:37 -300.586035 0.558377
BFGS: 10 14:57:37 -300.601519 0.403859
BFGS: 11 14:57:37 -300.610434 0.251604
BFGS: 12 14:57:37 -300.614608 0.156316
BFGS: 13 14:57:37 -300.617507 0.128488
BFGS: 14 14:57:37 -300.619886 0.125435
BFGS: 15 14:57:37 -300.620814 0.112958
BFGS: 16 14:57:37 -300.621893 0.119139
BFGS: 17 14:57:38 -300.623069 0.115045
BFGS: 18 14:57:38 -300.624032 0.085618
BFGS: 19 14:57:38 -300.624517 0.054770
BFGS: 20 14:57:38 -300.624764 0.039560
Step Time Energy fmax
BFGS: 0 14:57:38 -296.011962 4.392594
BFGS: 1 14:57:38 -296.539863 4.735369
BFGS: 2 14:57:38 -298.195790 3.103703
BFGS: 3 14:57:38 -296.840919 16.591502
BFGS: 4 14:57:38 -298.376616 1.894651
BFGS: 5 14:57:39 -298.439847 1.058281
BFGS: 6 14:57:39 -298.475578 0.612558
BFGS: 7 14:57:39 -298.480257 0.343750
BFGS: 8 14:57:39 -298.486944 0.176839
BFGS: 9 14:57:39 -298.489323 0.213175
BFGS: 10 14:57:39 -298.490607 0.186075
BFGS: 11 14:57:39 -298.491731 0.161751
BFGS: 12 14:57:39 -298.494431 0.175519
BFGS: 13 14:57:39 -298.502477 0.324776
BFGS: 14 14:57:39 -298.529168 0.834310
BFGS: 15 14:57:40 -298.550967 1.359489
BFGS: 16 14:57:40 -298.556378 2.049580
BFGS: 17 14:57:40 -298.573393 1.786446
BFGS: 18 14:57:40 -298.627960 2.103621
BFGS: 19 14:57:40 -298.675831 2.691550
BFGS: 20 14:57:40 -298.697453 3.069930
BFGS: 21 14:57:40 -298.746301 2.871767
BFGS: 22 14:57:40 -298.838751 2.745811
BFGS: 23 14:57:40 -298.916438 2.656807
BFGS: 24 14:57:40 -298.932594 2.466226
BFGS: 25 14:57:41 -298.959865 2.597496
BFGS: 26 14:57:41 -299.010225 2.950678
BFGS: 27 14:57:41 -299.026926 2.913696
BFGS: 28 14:57:41 -299.043510 2.746633
BFGS: 29 14:57:41 -299.058228 2.486067
BFGS: 30 14:57:41 -299.069800 2.217210
BFGS: 31 14:57:41 -299.078025 2.023942
BFGS: 32 14:57:41 -299.086214 1.890561
BFGS: 33 14:57:41 -299.094391 1.842501
BFGS: 34 14:57:42 -299.102870 1.874783
BFGS: 35 14:57:42 -299.116400 1.964603
BFGS: 36 14:57:42 -299.141988 2.103749
BFGS: 37 14:57:42 -299.182333 2.241529
BFGS: 38 14:57:42 -299.254132 2.258211
BFGS: 39 14:57:42 -299.396432 2.067553
BFGS: 40 14:57:42 -299.530318 1.872618
BFGS: 41 14:57:42 -299.640452 1.669267
BFGS: 42 14:57:42 -299.757260 1.554861
BFGS: 43 14:57:42 -299.800410 1.369292
BFGS: 44 14:57:43 -299.825221 1.478394
BFGS: 45 14:57:43 -299.878135 1.745812
BFGS: 46 14:57:43 -299.892938 1.778034
BFGS: 47 14:57:43 -299.952215 1.807627
BFGS: 48 14:57:43 -299.987369 1.751860
BFGS: 49 14:57:43 -300.057044 1.656012
BFGS: 50 14:57:43 -300.124040 1.821955
BFGS: 51 14:57:43 -300.195042 1.760430
BFGS: 52 14:57:43 -300.253278 1.530358
BFGS: 53 14:57:44 -300.325171 1.183279
BFGS: 54 14:57:44 -300.412420 0.929684
BFGS: 55 14:57:44 -300.475597 1.017245
BFGS: 56 14:57:44 -300.514453 0.983536
BFGS: 57 14:57:44 -300.545021 0.828417
BFGS: 58 14:57:44 -300.569318 0.674853
BFGS: 59 14:57:44 -300.584341 0.659108
BFGS: 60 14:57:44 -300.591668 0.549830
BFGS: 61 14:57:44 -300.594301 0.442002
BFGS: 62 14:57:44 -300.596096 0.386104
BFGS: 63 14:57:45 -300.599058 0.320123
BFGS: 64 14:57:45 -300.600582 0.310375
BFGS: 65 14:57:45 -300.601262 0.326923
BFGS: 66 14:57:45 -300.601563 0.343284
BFGS: 67 14:57:45 -300.601796 0.354413
BFGS: 68 14:57:45 -300.602016 0.359268
BFGS: 69 14:57:45 -300.602184 0.356799
BFGS: 70 14:57:45 -300.602290 0.350887
BFGS: 71 14:57:45 -300.602362 0.344796
BFGS: 72 14:57:45 -300.602422 0.339321
BFGS: 73 14:57:46 -300.602478 0.335542
BFGS: 74 14:57:46 -300.602532 0.334153
BFGS: 75 14:57:46 -300.602586 0.335305
BFGS: 76 14:57:46 -300.602628 0.338574
BFGS: 77 14:57:46 -300.602658 0.342169
BFGS: 78 14:57:46 -300.602676 0.344692
BFGS: 79 14:57:46 -300.602691 0.346325
BFGS: 80 14:57:46 -300.602712 0.347471
BFGS: 81 14:57:46 -300.602727 0.347821
BFGS: 82 14:57:47 -300.602742 0.347267
BFGS: 83 14:57:47 -300.602749 0.346550
BFGS: 84 14:57:47 -300.602752 0.345965
BFGS: 85 14:57:47 -300.602757 0.345690
BFGS: 86 14:57:47 -300.602762 0.345801
BFGS: 87 14:57:47 -300.602767 0.346354
BFGS: 88 14:57:47 -300.602767 0.346914
BFGS: 89 14:57:47 -300.602769 0.347217
BFGS: 90 14:57:47 -300.602770 0.347283
BFGS: 91 14:57:47 -300.602773 0.347033
BFGS: 92 14:57:48 -300.602773 0.346456
BFGS: 93 14:57:48 -300.602775 0.345989
BFGS: 94 14:57:48 -300.602775 0.345747
BFGS: 95 14:57:48 -300.602774 0.345727
BFGS: 96 14:57:48 -300.602775 0.345834
BFGS: 97 14:57:48 -300.602775 0.346190
BFGS: 98 14:57:48 -300.602776 0.346515
BFGS: 99 14:57:48 -300.602776 0.346757
BFGS: 100 14:57:48 -300.602775 0.346827
BFGS: 101 14:57:48 -300.602777 0.346807
BFGS: 102 14:57:49 -300.602777 0.346729
BFGS: 103 14:57:49 -300.602775 0.346550
BFGS: 104 14:57:49 -300.602778 0.346366
BFGS: 105 14:57:49 -300.602778 0.346308
BFGS: 106 14:57:49 -300.602777 0.346300
BFGS: 107 14:57:49 -300.602775 0.346337
BFGS: 108 14:57:49 -300.602777 0.346306
BFGS: 109 14:57:49 -300.602778 0.346382
BFGS: 110 14:57:49 -300.602775 0.346468
BFGS: 111 14:57:50 -300.602776 0.346436
BFGS: 112 14:57:50 -300.602777 0.346475
BFGS: 113 14:57:50 -300.602777 0.346439
BFGS: 114 14:57:50 -300.602778 0.346446
BFGS: 115 14:57:50 -300.602776 0.346377
BFGS: 116 14:57:50 -300.602777 0.346412
BFGS: 117 14:57:50 -300.602778 0.346412
BFGS: 118 14:57:50 -300.602777 0.346407
BFGS: 119 14:57:50 -300.602778 0.346438
BFGS: 120 14:57:50 -300.602776 0.346468
BFGS: 121 14:57:51 -300.602778 0.346429
BFGS: 122 14:57:51 -300.602777 0.346465
BFGS: 123 14:57:51 -300.602778 0.346468
BFGS: 124 14:57:51 -300.602777 0.346433
BFGS: 125 14:57:51 -300.602778 0.346433
BFGS: 126 14:57:51 -300.602778 0.346435
BFGS: 127 14:57:51 -300.602778 0.346435
BFGS: 128 14:57:51 -300.602776 0.346474
BFGS: 129 14:57:51 -300.602778 0.346473
BFGS: 130 14:57:51 -300.602777 0.346436
BFGS: 131 14:57:52 -300.602778 0.346437
BFGS: 132 14:57:52 -300.602778 0.346440
BFGS: 133 14:57:52 -300.602777 0.346443
BFGS: 134 14:57:52 -300.602778 0.346440
BFGS: 135 14:57:52 -300.602778 0.346442
BFGS: 136 14:57:52 -300.602777 0.346442
BFGS: 137 14:57:52 -300.602778 0.346444
BFGS: 138 14:57:52 -300.602778 0.346442
BFGS: 139 14:57:52 -300.602780 0.346445
BFGS: 140 14:57:53 -300.602777 0.346445
BFGS: 141 14:57:53 -300.602778 0.346446
BFGS: 142 14:57:53 -300.602779 0.346447
BFGS: 143 14:57:53 -300.602777 0.346446
BFGS: 144 14:57:53 -300.602777 0.346448
BFGS: 145 14:57:53 -300.602778 0.346444
BFGS: 146 14:57:53 -300.602778 0.346445
BFGS: 147 14:57:53 -300.602776 0.346444
BFGS: 148 14:57:53 -300.602777 0.346443
BFGS: 149 14:57:53 -300.602778 0.346443
BFGS: 150 14:57:54 -300.602778 0.346478
BFGS: 151 14:57:54 -300.602777 0.346444
BFGS: 152 14:57:54 -300.602775 0.346444
BFGS: 153 14:57:54 -300.602778 0.346445
BFGS: 154 14:57:54 -300.602778 0.346446
BFGS: 155 14:57:54 -300.602779 0.346445
BFGS: 156 14:57:54 -300.602775 0.346441
BFGS: 157 14:57:54 -300.602778 0.346447
BFGS: 158 14:57:54 -300.602778 0.346444
BFGS: 159 14:57:54 -300.602776 0.346483
BFGS: 160 14:57:55 -300.602778 0.346445
BFGS: 161 14:57:55 -300.602778 0.346444
BFGS: 162 14:57:55 -300.602780 0.346449
BFGS: 163 14:57:55 -300.602777 0.346444
BFGS: 164 14:57:55 -300.602777 0.346441
BFGS: 165 14:57:55 -300.602778 0.346445
BFGS: 166 14:57:55 -300.602778 0.346444
BFGS: 167 14:57:55 -300.602778 0.346445
BFGS: 168 14:57:55 -300.602776 0.346447
BFGS: 169 14:57:56 -300.602778 0.346445
BFGS: 170 14:57:56 -300.602778 0.346446
BFGS: 171 14:57:56 -300.602776 0.346443
BFGS: 172 14:57:56 -300.602778 0.346445
BFGS: 173 14:57:56 -300.602776 0.346448
BFGS: 174 14:57:56 -300.602777 0.346443
BFGS: 175 14:57:56 -300.602775 0.346446
BFGS: 176 14:57:56 -300.602778 0.346447
BFGS: 177 14:57:56 -300.602778 0.346443
BFGS: 178 14:57:56 -300.602776 0.346447
BFGS: 179 14:57:57 -300.602778 0.346447
BFGS: 180 14:57:57 -300.602780 0.346441
BFGS: 181 14:57:57 -300.602777 0.346451
BFGS: 182 14:57:57 -300.602775 0.346443
BFGS: 183 14:57:57 -300.602778 0.346445
BFGS: 184 14:57:57 -300.602778 0.346446
BFGS: 185 14:57:57 -300.602778 0.346445
BFGS: 186 14:57:57 -300.602778 0.346443
BFGS: 187 14:57:57 -300.602778 0.346448
BFGS: 188 14:57:57 -300.602778 0.346437
BFGS: 189 14:57:58 -300.602775 0.346443
BFGS: 190 14:57:58 -300.602778 0.346445
BFGS: 191 14:57:58 -300.602776 0.346444
BFGS: 192 14:57:58 -300.602777 0.346441
BFGS: 193 14:57:58 -300.602778 0.346441
BFGS: 194 14:57:58 -300.602778 0.346447
BFGS: 195 14:57:58 -300.602778 0.346448
BFGS: 196 14:57:58 -300.602778 0.346442
BFGS: 197 14:57:58 -300.602779 0.346445
BFGS: 198 14:57:59 -300.602777 0.346448
BFGS: 199 14:57:59 -300.602776 0.346447
BFGS: 200 14:57:59 -300.602777 0.346442
Step Time Energy fmax
BFGS: 0 14:57:59 -296.959401 4.511147
BFGS: 1 14:57:59 -297.423145 4.649578
BFGS: 2 14:57:59 -298.722794 3.505118
BFGS: 3 14:57:59 -298.750816 6.428765
BFGS: 4 14:57:59 -299.104788 2.031241
BFGS: 5 14:57:59 -299.237810 1.824245
BFGS: 6 14:57:59 -299.651942 1.447807
BFGS: 7 14:58:00 -299.864185 0.977993
BFGS: 8 14:58:00 -299.900660 0.936880
BFGS: 9 14:58:00 -299.998879 0.862634
BFGS: 10 14:58:00 -300.020968 0.781243
BFGS: 11 14:58:00 -300.043951 0.332904
BFGS: 12 14:58:00 -300.048380 0.199461
BFGS: 13 14:58:00 -300.051677 0.213042
BFGS: 14 14:58:00 -300.056436 0.280250
BFGS: 15 14:58:00 -300.061824 0.275303
BFGS: 16 14:58:01 -300.065046 0.207321
BFGS: 17 14:58:01 -300.066448 0.147007
BFGS: 18 14:58:01 -300.067842 0.130406
BFGS: 19 14:58:01 -300.069726 0.151460
BFGS: 20 14:58:01 -300.071389 0.143089
BFGS: 21 14:58:01 -300.072319 0.089577
BFGS: 22 14:58:01 -300.072684 0.030855
Step Time Energy fmax
BFGS: 0 14:58:01 -296.455605 4.445281
BFGS: 1 14:58:01 -296.929217 4.677061
BFGS: 2 14:58:01 -298.333266 3.495836
BFGS: 3 14:58:02 -298.108364 8.665780
BFGS: 4 14:58:02 -298.644030 1.974740
BFGS: 5 14:58:02 -298.728036 1.425871
BFGS: 6 14:58:02 -298.880837 2.173111
BFGS: 7 14:58:02 -299.075520 2.740446
BFGS: 8 14:58:02 -299.325298 2.584220
BFGS: 9 14:58:02 -299.384312 1.820852
BFGS: 10 14:58:02 -299.483338 1.722870
BFGS: 11 14:58:02 -299.597932 1.398330
BFGS: 12 14:58:02 -299.811171 1.054945
BFGS: 13 14:58:03 -299.872569 0.797846
BFGS: 14 14:58:03 -299.890846 0.566429
BFGS: 15 14:58:03 -299.905494 0.270492
BFGS: 16 14:58:03 -299.913975 0.327270
BFGS: 17 14:58:03 -299.922588 0.421986
BFGS: 18 14:58:03 -299.938290 0.533328
BFGS: 19 14:58:03 -299.952428 0.596326
BFGS: 20 14:58:03 -299.968286 0.654898
BFGS: 21 14:58:03 -300.012873 1.111217
BFGS: 22 14:58:04 -300.080917 1.830567
BFGS: 23 14:58:04 -300.087283 2.376067
BFGS: 24 14:58:04 -300.212877 1.967352
BFGS: 25 14:58:04 -300.325182 1.463252
BFGS: 26 14:58:04 -300.519655 0.822998
BFGS: 27 14:58:04 -300.535842 0.657548
BFGS: 28 14:58:04 -300.580142 0.371056
BFGS: 29 14:58:04 -300.597738 0.313033
BFGS: 30 14:58:04 -300.606449 0.296429
BFGS: 31 14:58:04 -300.612714 0.223754
BFGS: 32 14:58:05 -300.616927 0.149393
BFGS: 33 14:58:05 -300.620127 0.112923
BFGS: 34 14:58:05 -300.622382 0.076187
BFGS: 35 14:58:05 -300.623542 0.070605
BFGS: 36 14:58:05 -300.624091 0.056316
BFGS: 37 14:58:05 -300.624337 0.044513
Step Time Energy fmax
BFGS: 0 14:58:05 -296.858179 4.511640
BFGS: 1 14:58:05 -297.324902 4.672678
BFGS: 2 14:58:05 -298.614809 3.637818
BFGS: 3 14:58:05 -298.801748 5.563844
BFGS: 4 14:58:06 -299.059427 1.929369
BFGS: 5 14:58:06 -299.176300 1.808830
BFGS: 6 14:58:06 -299.591185 1.513042
BFGS: 7 14:58:06 -299.728801 1.656403
BFGS: 8 14:58:06 -299.786303 0.757712
BFGS: 9 14:58:06 -299.835613 0.638362
BFGS: 10 14:58:06 -299.903279 0.770664
BFGS: 11 14:58:06 -299.930401 0.728860
BFGS: 12 14:58:06 -299.963565 0.424700
BFGS: 13 14:58:07 -299.973753 0.409816
BFGS: 14 14:58:07 -299.982857 0.449950
BFGS: 15 14:58:07 -299.995218 0.451865
BFGS: 16 14:58:07 -300.005889 0.352819
BFGS: 17 14:58:07 -300.013274 0.277180
BFGS: 18 14:58:07 -300.024004 0.377440
BFGS: 19 14:58:07 -300.037078 0.525722
BFGS: 20 14:58:07 -300.051359 0.508802
BFGS: 21 14:58:08 -300.062000 0.330252
BFGS: 22 14:58:08 -300.066818 0.119365
BFGS: 23 14:58:08 -300.068303 0.102802
BFGS: 24 14:58:08 -300.069079 0.092177
BFGS: 25 14:58:08 -300.070637 0.066775
BFGS: 26 14:58:08 -300.071293 0.058265
BFGS: 27 14:58:08 -300.072275 0.037425
Step Time Energy fmax
BFGS: 0 14:58:08 -297.650988 4.542725
BFGS: 1 14:58:08 -298.123920 4.568849
BFGS: 2 14:58:08 -299.282010 3.050596
BFGS: 3 14:58:09 -299.440061 3.843849
BFGS: 4 14:58:09 -299.635536 1.263779
BFGS: 5 14:58:09 -299.721150 1.117193
BFGS: 6 14:58:09 -299.969641 0.697585
BFGS: 7 14:58:09 -299.993215 0.633907
BFGS: 8 14:58:09 -300.048911 0.405565
BFGS: 9 14:58:09 -300.058312 0.229746
BFGS: 10 14:58:09 -300.063058 0.150049
BFGS: 11 14:58:09 -300.064940 0.136781
BFGS: 12 14:58:10 -300.067160 0.119795
BFGS: 13 14:58:10 -300.068359 0.102846
BFGS: 14 14:58:10 -300.069048 0.097639
BFGS: 15 14:58:10 -300.069639 0.098133
BFGS: 16 14:58:10 -300.070461 0.099209
BFGS: 17 14:58:10 -300.071505 0.099077
BFGS: 18 14:58:10 -300.072375 0.064233
BFGS: 19 14:58:10 -300.072827 0.025638
Step Time Energy fmax
BFGS: 0 14:58:10 -295.948924 4.393768
BFGS: 1 14:58:10 -296.493449 4.750829
BFGS: 2 14:58:11 -298.201881 3.012385
BFGS: 3 14:58:11 -296.569160 18.521242
BFGS: 4 14:58:11 -298.368301 1.867957
BFGS: 5 14:58:11 -298.429769 1.050644
BFGS: 6 14:58:11 -298.464703 0.523087
BFGS: 7 14:58:11 -298.468465 0.229421
BFGS: 8 14:58:11 -298.472223 0.088508
BFGS: 9 14:58:11 -298.474016 0.101718
BFGS: 10 14:58:11 -298.474493 0.063720
BFGS: 11 14:58:12 -298.474591 0.039067
Step Time Energy fmax
BFGS: 0 14:58:12 -296.993506 4.539346
BFGS: 1 14:58:12 -297.463421 4.686054
BFGS: 2 14:58:12 -298.784531 3.473856
BFGS: 3 14:58:12 -298.809581 6.373285
BFGS: 4 14:58:12 -299.187375 1.930951
BFGS: 5 14:58:12 -299.331148 1.739309
BFGS: 6 14:58:12 -299.716023 1.029791
BFGS: 7 14:58:12 -299.784244 1.440336
BFGS: 8 14:58:12 -299.823692 0.622185
BFGS: 9 14:58:13 -299.852389 0.529488
BFGS: 10 14:58:13 -299.940735 0.679889
BFGS: 11 14:58:13 -299.954272 0.512566
BFGS: 12 14:58:13 -299.967878 0.358340
BFGS: 13 14:58:13 -299.972593 0.388907
BFGS: 14 14:58:13 -299.999238 0.495012
BFGS: 15 14:58:13 -300.010123 0.403640
BFGS: 16 14:58:13 -300.017082 0.333993
BFGS: 17 14:58:13 -300.034938 0.392053
BFGS: 18 14:58:13 -300.047666 0.445235
BFGS: 19 14:58:14 -300.058256 0.371065
BFGS: 20 14:58:14 -300.064276 0.184148
BFGS: 21 14:58:14 -300.066049 0.147438
BFGS: 22 14:58:14 -300.068250 0.105642
BFGS: 23 14:58:14 -300.069714 0.104291
BFGS: 24 14:58:14 -300.071395 0.097214
BFGS: 25 14:58:14 -300.072232 0.064700
BFGS: 26 14:58:14 -300.072530 0.035768
product2_energies = []
for config in product2_configs:
config.calc = calc
config.pbc = True
opt = BFGS(config)
opt.run(fmax=0.05, steps=200)
product2_energies.append(config.get_potential_energy())
Step Time Energy fmax
BFGS: 0 14:58:14 -295.110806 1.712510
BFGS: 1 14:58:15 -295.222834 1.539362
BFGS: 2 14:58:15 -295.395338 2.547773
BFGS: 3 14:58:15 -295.495395 0.430115
BFGS: 4 14:58:15 -295.512256 0.598949
BFGS: 5 14:58:15 -295.532842 0.645673
BFGS: 6 14:58:15 -295.549267 0.435562
BFGS: 7 14:58:15 -295.555652 0.203853
BFGS: 8 14:58:15 -295.559916 0.275197
BFGS: 9 14:58:15 -295.565011 0.289616
BFGS: 10 14:58:15 -295.568736 0.208448
BFGS: 11 14:58:16 -295.570639 0.088090
BFGS: 12 14:58:16 -295.570933 0.030466
Step Time Energy fmax
BFGS: 0 14:58:16 -295.577765 0.743440
BFGS: 1 14:58:16 -295.629894 0.662603
BFGS: 2 14:58:16 -295.807866 0.406097
BFGS: 3 14:58:16 -295.819716 0.270067
BFGS: 4 14:58:16 -295.822682 0.267098
BFGS: 5 14:58:16 -295.835678 0.217380
BFGS: 6 14:58:16 -295.837093 0.189608
BFGS: 7 14:58:16 -295.840604 0.130211
BFGS: 8 14:58:17 -295.841677 0.072225
BFGS: 9 14:58:17 -295.842151 0.082840
BFGS: 10 14:58:17 -295.842505 0.089138
BFGS: 11 14:58:17 -295.843199 0.096409
BFGS: 12 14:58:17 -295.844082 0.101926
BFGS: 13 14:58:17 -295.845029 0.108413
BFGS: 14 14:58:17 -295.845991 0.125154
BFGS: 15 14:58:17 -295.847587 0.200216
BFGS: 16 14:58:17 -295.851911 0.365898
BFGS: 17 14:58:18 -295.859416 0.697304
BFGS: 18 14:58:18 -295.869688 0.631260
BFGS: 19 14:58:18 -295.911670 0.314286
BFGS: 20 14:58:18 -295.888430 0.422336
BFGS: 21 14:58:18 -295.915830 0.178358
BFGS: 22 14:58:18 -295.916426 0.305907
BFGS: 23 14:58:18 -295.921252 0.165972
BFGS: 24 14:58:18 -295.923614 0.130378
BFGS: 25 14:58:18 -295.929925 0.077600
BFGS: 26 14:58:18 -295.930662 0.064681
BFGS: 27 14:58:19 -295.931049 0.057891
BFGS: 28 14:58:19 -295.931614 0.054261
BFGS: 29 14:58:19 -295.932256 0.041855
Step Time Energy fmax
BFGS: 0 14:58:19 -295.402081 1.132536
BFGS: 1 14:58:19 -295.469762 1.043253
BFGS: 2 14:58:19 -295.681029 1.122711
BFGS: 3 14:58:19 -295.707277 0.566681
BFGS: 4 14:58:19 -295.718461 0.482896
BFGS: 5 14:58:19 -295.761756 0.565150
BFGS: 6 14:58:20 -295.770563 0.539728
BFGS: 7 14:58:20 -295.827671 0.462315
BFGS: 8 14:58:20 -295.835970 0.309302
BFGS: 9 14:58:20 -295.840994 0.297786
BFGS: 10 14:58:20 -295.845608 0.246320
BFGS: 11 14:58:20 -295.851591 0.180173
BFGS: 12 14:58:20 -295.855222 0.151864
BFGS: 13 14:58:20 -295.856851 0.156233
BFGS: 14 14:58:20 -295.858308 0.155581
BFGS: 15 14:58:20 -295.860868 0.166525
BFGS: 16 14:58:21 -295.865232 0.192366
BFGS: 17 14:58:21 -295.870643 0.238608
BFGS: 18 14:58:21 -295.875431 0.282626
BFGS: 19 14:58:21 -295.880675 0.323253
BFGS: 20 14:58:21 -295.889652 0.372481
BFGS: 21 14:58:21 -295.904934 0.358965
BFGS: 22 14:58:21 -295.922065 0.334158
BFGS: 23 14:58:21 -295.953177 0.234890
BFGS: 24 14:58:21 -295.950958 0.210826
BFGS: 25 14:58:21 -295.959779 0.116010
BFGS: 26 14:58:22 -295.961418 0.102998
BFGS: 27 14:58:22 -295.963673 0.074804
BFGS: 28 14:58:22 -295.965653 0.078077
BFGS: 29 14:58:22 -295.966558 0.064921
BFGS: 30 14:58:22 -295.967036 0.042051
Step Time Energy fmax
BFGS: 0 14:58:22 -295.675997 0.720398
BFGS: 1 14:58:22 -295.722523 0.642329
BFGS: 2 14:58:22 -295.884237 0.331075
BFGS: 3 14:58:22 -295.894591 0.333430
BFGS: 4 14:58:23 -295.896782 0.322412
BFGS: 5 14:58:23 -295.917862 0.167855
BFGS: 6 14:58:23 -295.920350 0.156525
BFGS: 7 14:58:23 -295.922976 0.150537
BFGS: 8 14:58:23 -295.924919 0.144024
BFGS: 9 14:58:23 -295.927664 0.127046
BFGS: 10 14:58:23 -295.929328 0.106077
BFGS: 11 14:58:23 -295.930087 0.087704
BFGS: 12 14:58:23 -295.930454 0.076436
BFGS: 13 14:58:23 -295.930998 0.060297
BFGS: 14 14:58:24 -295.931808 0.044717
Step Time Energy fmax
BFGS: 0 14:58:24 -295.479399 1.021501
BFGS: 1 14:58:24 -295.540290 0.951161
BFGS: 2 14:58:24 -295.748886 0.882236
BFGS: 3 14:58:24 -295.769935 0.497183
BFGS: 4 14:58:24 -295.780404 0.506704
BFGS: 5 14:58:24 -295.825584 0.534298
BFGS: 6 14:58:24 -295.834960 0.486004
BFGS: 7 14:58:24 -295.868269 0.405944
BFGS: 8 14:58:24 -295.877907 0.276271
BFGS: 9 14:58:25 -295.884078 0.287703
BFGS: 10 14:58:25 -295.887564 0.280559
BFGS: 11 14:58:25 -295.893780 0.275032
BFGS: 12 14:58:25 -295.901838 0.291622
BFGS: 13 14:58:25 -295.909868 0.322551
BFGS: 14 14:58:25 -295.916747 0.335807
BFGS: 15 14:58:25 -295.925694 0.328605
BFGS: 16 14:58:25 -295.938020 0.278529
BFGS: 17 14:58:25 -295.950807 0.216285
BFGS: 18 14:58:26 -295.958242 0.143875
BFGS: 19 14:58:26 -295.960654 0.126426
BFGS: 20 14:58:26 -295.961992 0.109299
BFGS: 21 14:58:26 -295.963369 0.094044
BFGS: 22 14:58:26 -295.965607 0.063642
BFGS: 23 14:58:26 -295.966672 0.049718
Step Time Energy fmax
BFGS: 0 14:58:26 -295.211702 1.454497
BFGS: 1 14:58:26 -295.301784 1.316170
BFGS: 2 14:58:26 -295.495790 1.904124
BFGS: 3 14:58:26 -295.556422 0.514891
BFGS: 4 14:58:27 -295.568389 0.561539
BFGS: 5 14:58:27 -295.594744 0.397844
BFGS: 6 14:58:27 -295.601899 0.283688
BFGS: 7 14:58:27 -295.607631 0.335795
BFGS: 8 14:58:27 -295.614935 0.353270
BFGS: 9 14:58:27 -295.622815 0.360370
BFGS: 10 14:58:27 -295.629867 0.279496
BFGS: 11 14:58:27 -295.634444 0.376375
BFGS: 12 14:58:27 -295.641306 0.549761
BFGS: 13 14:58:28 -295.676750 1.113343
BFGS: 14 14:58:28 -295.698078 1.406574
BFGS: 15 14:58:28 -295.710221 1.272219
BFGS: 16 14:58:28 -295.718002 1.225937
BFGS: 17 14:58:28 -295.722585 1.253648
BFGS: 18 14:58:28 -295.730820 1.296799
BFGS: 19 14:58:28 -295.738156 1.267785
BFGS: 20 14:58:28 -295.744815 1.178303
BFGS: 21 14:58:28 -295.747045 1.120117
BFGS: 22 14:58:28 -295.748298 1.089722
BFGS: 23 14:58:29 -295.749669 1.095810
BFGS: 24 14:58:29 -295.751508 1.105904
BFGS: 25 14:58:29 -295.753097 1.122603
BFGS: 26 14:58:29 -295.754018 1.158163
BFGS: 27 14:58:29 -295.754682 1.182686
BFGS: 28 14:58:29 -295.755524 1.203016
BFGS: 29 14:58:29 -295.756659 1.214482
BFGS: 30 14:58:29 -295.757834 1.208334
BFGS: 31 14:58:29 -295.758659 1.189611
BFGS: 32 14:58:30 -295.759267 1.171834
BFGS: 33 14:58:30 -295.760111 1.154491
BFGS: 34 14:58:30 -295.761869 1.131678
BFGS: 35 14:58:30 -295.765608 1.092024
BFGS: 36 14:58:30 -295.772362 0.990477
BFGS: 37 14:58:30 -295.781436 0.843837
BFGS: 38 14:58:30 -295.800826 0.783578
BFGS: 39 14:58:30 -295.833702 0.820148
BFGS: 40 14:58:30 -295.887849 0.580226
BFGS: 41 14:58:30 -295.892754 0.641268
BFGS: 42 14:58:31 -295.941642 0.336710
BFGS: 43 14:58:31 -295.950589 0.214913
BFGS: 44 14:58:31 -295.955860 0.215724
BFGS: 45 14:58:31 -295.958897 0.186701
BFGS: 46 14:58:31 -295.964068 0.111392
BFGS: 47 14:58:31 -295.965741 0.071703
BFGS: 48 14:58:31 -295.966343 0.049515
Step Time Energy fmax
BFGS: 0 14:58:31 -295.149339 1.593779
BFGS: 1 14:58:31 -295.251245 1.436884
BFGS: 2 14:58:31 -295.433435 2.273049
BFGS: 3 14:58:32 -295.516029 0.452347
BFGS: 4 14:58:32 -295.530571 0.585068
BFGS: 5 14:58:32 -295.552505 0.579878
BFGS: 6 14:58:32 -295.564523 0.342939
BFGS: 7 14:58:32 -295.569683 0.238734
BFGS: 8 14:58:32 -295.574273 0.298580
BFGS: 9 14:58:32 -295.578827 0.281131
BFGS: 10 14:58:32 -295.582617 0.186337
BFGS: 11 14:58:32 -295.584127 0.102761
BFGS: 12 14:58:33 -295.584539 0.110858
BFGS: 13 14:58:33 -295.585027 0.133873
BFGS: 14 14:58:33 -295.586194 0.181506
BFGS: 15 14:58:33 -295.589295 0.268196
BFGS: 16 14:58:33 -295.602956 0.415070
BFGS: 17 14:58:33 -295.615883 0.554691
BFGS: 18 14:58:33 -295.636034 0.353392
BFGS: 19 14:58:33 -295.688696 0.459084
BFGS: 20 14:58:33 -295.774978 0.501114
BFGS: 21 14:58:33 -295.553410 1.126283
BFGS: 22 14:58:34 -295.764188 1.183783
BFGS: 23 14:58:34 -295.785510 0.369832
BFGS: 24 14:58:34 -295.820714 0.200377
BFGS: 25 14:58:34 -295.826439 0.259691
BFGS: 26 14:58:34 -295.830168 0.269298
BFGS: 27 14:58:34 -295.833795 0.195682
BFGS: 28 14:58:34 -295.837344 0.096998
BFGS: 29 14:58:34 -295.838526 0.069118
BFGS: 30 14:58:34 -295.839206 0.061424
BFGS: 31 14:58:34 -295.839680 0.064343
BFGS: 32 14:58:35 -295.840174 0.071735
BFGS: 33 14:58:35 -295.840662 0.076389
BFGS: 34 14:58:35 -295.841144 0.078262
BFGS: 35 14:58:35 -295.841627 0.079189
BFGS: 36 14:58:35 -295.842090 0.083039
BFGS: 37 14:58:35 -295.842578 0.093427
BFGS: 38 14:58:35 -295.843418 0.117964
BFGS: 39 14:58:35 -295.845258 0.174473
BFGS: 40 14:58:35 -295.849113 0.286645
BFGS: 41 14:58:36 -295.856400 0.425132
BFGS: 42 14:58:36 -295.865392 0.449536
BFGS: 43 14:58:36 -295.883325 0.439849
BFGS: 44 14:58:36 -295.902113 0.431905
BFGS: 45 14:58:36 -295.907493 0.281598
BFGS: 46 14:58:36 -295.920726 0.167590
BFGS: 47 14:58:36 -295.928564 0.135177
BFGS: 48 14:58:36 -295.931295 0.064455
BFGS: 49 14:58:36 -295.932076 0.059503
BFGS: 50 14:58:36 -295.932435 0.055371
BFGS: 51 14:58:37 -295.932751 0.043692
Step Time Energy fmax
BFGS: 0 14:58:37 -295.118151 1.685701
BFGS: 1 14:58:37 -295.227950 1.516426
BFGS: 2 14:58:37 -295.402445 2.492459
BFGS: 3 14:58:37 -295.499014 0.415258
BFGS: 4 14:58:37 -295.515385 0.596389
BFGS: 5 14:58:37 -295.536168 0.634639
BFGS: 6 14:58:37 -295.551596 0.418746
BFGS: 7 14:58:37 -295.557658 0.209315
BFGS: 8 14:58:38 -295.561948 0.280031
BFGS: 9 14:58:38 -295.566793 0.287665
BFGS: 10 14:58:38 -295.570507 0.200266
BFGS: 11 14:58:38 -295.572269 0.082236
BFGS: 12 14:58:38 -295.572543 0.040180
Step Time Energy fmax
BFGS: 0 14:58:38 -295.136522 1.630753
BFGS: 1 14:58:38 -295.241744 1.469340
BFGS: 2 14:58:38 -295.420128 2.384734
BFGS: 3 14:58:38 -295.509664 0.435926
BFGS: 4 14:58:38 -295.525153 0.591246
BFGS: 5 14:58:39 -295.546501 0.608332
BFGS: 6 14:58:39 -295.559998 0.380232
BFGS: 7 14:58:39 -295.565505 0.223691
BFGS: 8 14:58:39 -295.569940 0.289946
BFGS: 9 14:58:39 -295.574485 0.283650
BFGS: 10 14:58:39 -295.578232 0.187841
BFGS: 11 14:58:39 -295.579814 0.086361
BFGS: 12 14:58:39 -295.580135 0.082218
BFGS: 13 14:58:39 -295.580361 0.093201
BFGS: 14 14:58:39 -295.580856 0.116380
BFGS: 15 14:58:40 -295.581974 0.154451
BFGS: 16 14:58:40 -295.584608 0.205972
BFGS: 17 14:58:40 -295.590748 0.251046
BFGS: 18 14:58:40 -295.604245 0.464935
BFGS: 19 14:58:40 -295.472651 2.352640
BFGS: 20 14:58:40 -295.680490 0.600805
BFGS: 21 14:58:40 -295.778606 0.530847
BFGS: 22 14:58:40 -295.855625 0.474911
BFGS: 23 14:58:40 -295.887804 0.772509
BFGS: 24 14:58:41 -295.917419 0.406691
BFGS: 25 14:58:41 -295.930355 0.305129
BFGS: 26 14:58:41 -295.945277 0.299956
BFGS: 27 14:58:41 -295.952806 0.210367
BFGS: 28 14:58:41 -295.958227 0.174771
BFGS: 29 14:58:41 -295.960622 0.149417
BFGS: 30 14:58:41 -295.962246 0.120311
BFGS: 31 14:58:41 -295.963329 0.099003
BFGS: 32 14:58:41 -295.964636 0.090350
BFGS: 33 14:58:41 -295.966033 0.062998
BFGS: 34 14:58:42 -295.966869 0.043079
Step Time Energy fmax
BFGS: 0 14:58:42 -295.240499 1.404578
BFGS: 1 14:58:42 -295.326043 1.275223
BFGS: 2 14:58:42 -295.523221 1.802405
BFGS: 3 14:58:42 -295.578315 0.532060
BFGS: 4 14:58:42 -295.589850 0.552438
BFGS: 5 14:58:42 -295.617968 0.309608
BFGS: 6 14:58:42 -295.624122 0.328025
BFGS: 7 14:58:42 -295.631676 0.375578
BFGS: 8 14:58:43 -295.640894 0.380950
BFGS: 9 14:58:43 -295.652457 0.466630
BFGS: 10 14:58:43 -295.663841 0.419484
BFGS: 11 14:58:43 -295.674707 0.625086
BFGS: 12 14:58:43 -295.704614 1.084362
BFGS: 13 14:58:43 -295.746477 1.423802
BFGS: 14 14:58:43 -295.754650 1.415359
BFGS: 15 14:58:43 -295.796539 1.347427
BFGS: 16 14:58:43 -295.834201 1.161571
BFGS: 17 14:58:43 -295.898248 0.655496
BFGS: 18 14:58:44 -295.923882 0.407297
BFGS: 19 14:58:44 -295.937792 0.345371
BFGS: 20 14:58:44 -295.944167 0.348356
BFGS: 21 14:58:44 -295.951864 0.316593
BFGS: 22 14:58:44 -295.958760 0.218679
BFGS: 23 14:58:44 -295.962709 0.112999
BFGS: 24 14:58:44 -295.964407 0.079678
BFGS: 25 14:58:44 -295.965131 0.070587
BFGS: 26 14:58:44 -295.965603 0.064874
BFGS: 27 14:58:45 -295.966204 0.056815
BFGS: 28 14:58:45 -295.966840 0.043207
Enumerate NEBs#
af = AutoFrameDissociation(
reaction=reaction,
reactant_system=reactant_configs[reactant_energies.index(min(reactant_energies))],
product1_systems=product1_configs,
product1_energies=product1_energies,
product2_systems=product2_configs,
product2_energies=product2_energies,
r_product1_max=2, # r1 in the above fig
r_product2_max=3, # r3 in the above fig
r_product2_min=1, # r2 in the above fig
)
import random
nframes = 10
random.seed(
42
) # set the seed to make the random generation deterministic for the tutorial!
frame_sets, mapping_idxs = af.get_neb_frames(
calc,
n_frames=nframes,
n_pdt1_sites=4, # = 5 in the above fig (step 1)
n_pdt2_sites=4, # = 5 in the above fig (step 2)
)
Step Time Energy fmax
BFGS: 0 14:58:45 -303.710669 0.937795
BFGS: 1 14:58:45 -303.733560 0.714294
BFGS: 2 14:58:45 -303.788630 0.618940
BFGS: 3 14:58:45 -303.818504 0.749359
BFGS: 4 14:58:45 -303.845886 0.805889
BFGS: 5 14:58:45 -303.871457 0.572342
BFGS: 6 14:58:45 -303.909149 0.284898
BFGS: 7 14:58:45 -303.913289 0.255070
BFGS: 8 14:58:46 -303.919632 0.150940
BFGS: 9 14:58:46 -303.922240 0.129996
BFGS: 10 14:58:46 -303.923822 0.111770
BFGS: 11 14:58:46 -303.925029 0.146952
BFGS: 12 14:58:46 -303.926293 0.147022
BFGS: 13 14:58:46 -303.927413 0.104757
BFGS: 14 14:58:46 -303.928319 0.114142
BFGS: 15 14:58:46 -303.928906 0.084038
BFGS: 16 14:58:46 -303.929332 0.088050
BFGS: 17 14:58:47 -303.929787 0.079657
BFGS: 18 14:58:47 -303.930430 0.121550
BFGS: 19 14:58:47 -303.931277 0.144316
BFGS: 20 14:58:47 -303.931980 0.106565
BFGS: 21 14:58:47 -303.932296 0.046374
Step Time Energy fmax
BFGS: 0 14:58:47 -303.709636 0.954965
BFGS: 1 14:58:47 -303.734097 0.719071
BFGS: 2 14:58:47 -303.788195 0.626666
BFGS: 3 14:58:47 -303.817300 0.674437
BFGS: 4 14:58:48 -303.846396 0.739635
BFGS: 5 14:58:48 -303.870971 0.525964
BFGS: 6 14:58:48 -303.909129 0.308595
BFGS: 7 14:58:48 -303.913109 0.282125
BFGS: 8 14:58:48 -303.919736 0.147894
BFGS: 9 14:58:48 -303.922714 0.115872
BFGS: 10 14:58:48 -303.924261 0.115699
BFGS: 11 14:58:48 -303.925333 0.150086
BFGS: 12 14:58:49 -303.926680 0.149438
BFGS: 13 14:58:49 -303.927965 0.104027
BFGS: 14 14:58:49 -303.928947 0.110765
BFGS: 15 14:58:49 -303.929578 0.098768
BFGS: 16 14:58:49 -303.930149 0.107845
BFGS: 17 14:58:49 -303.930932 0.104894
BFGS: 18 14:58:49 -303.932124 0.167672
BFGS: 19 14:58:49 -303.933903 0.218388
BFGS: 20 14:58:49 -303.936007 0.198824
BFGS: 21 14:58:49 -303.938163 0.204044
BFGS: 22 14:58:50 -303.940132 0.289716
BFGS: 23 14:58:50 -303.942772 0.300922
BFGS: 24 14:58:50 -303.954312 0.537107
BFGS: 25 14:58:50 -303.971620 0.523852
BFGS: 26 14:58:50 -303.984015 0.416366
BFGS: 27 14:58:50 -303.914654 1.025783
BFGS: 28 14:58:50 -304.007071 0.395282
BFGS: 29 14:58:50 -304.014708 0.283393
BFGS: 30 14:58:50 -304.043529 0.297410
BFGS: 31 14:58:51 -304.065001 0.457332
BFGS: 32 14:58:51 -304.086618 0.694091
BFGS: 33 14:58:51 -304.114347 0.847512
BFGS: 34 14:58:51 -304.147072 0.977539
BFGS: 35 14:58:51 -304.185539 1.074934
BFGS: 36 14:58:51 -304.232337 1.089328
BFGS: 37 14:58:51 -304.297853 1.078071
BFGS: 38 14:58:51 -304.385114 1.033867
BFGS: 39 14:58:51 -304.432731 0.913730
BFGS: 40 14:58:51 -304.453066 0.529586
BFGS: 41 14:58:52 -304.492047 0.357872
BFGS: 42 14:58:52 -304.511393 0.274525
BFGS: 43 14:58:52 -304.521040 0.184366
BFGS: 44 14:58:52 -304.525712 0.102692
BFGS: 45 14:58:52 -304.528110 0.067729
BFGS: 46 14:58:52 -304.529205 0.057279
BFGS: 47 14:58:52 -304.529907 0.063066
BFGS: 48 14:58:52 -304.530793 0.063094
BFGS: 49 14:58:52 -304.531428 0.046308
Step Time Energy fmax
BFGS: 0 14:58:53 -304.426781 0.304751
BFGS: 1 14:58:53 -304.431694 0.244953
BFGS: 2 14:58:53 -304.444028 0.141420
BFGS: 3 14:58:53 -304.446910 0.105280
BFGS: 4 14:58:53 -304.448473 0.086192
BFGS: 5 14:58:53 -304.449240 0.089263
BFGS: 6 14:58:53 -304.450007 0.077135
BFGS: 7 14:58:53 -304.450656 0.054785
BFGS: 8 14:58:53 -304.451114 0.071619
BFGS: 9 14:58:53 -304.451412 0.061043
BFGS: 10 14:58:54 -304.451666 0.046230
Step Time Energy fmax
BFGS: 0 14:58:54 -303.784393 0.596121
BFGS: 1 14:58:54 -303.794938 0.468928
BFGS: 2 14:58:54 -303.814056 0.500670
BFGS: 3 14:58:54 -303.824199 0.646285
BFGS: 4 14:58:54 -303.844849 0.740868
BFGS: 5 14:58:54 -303.860682 0.596849
BFGS: 6 14:58:54 -303.881601 0.431534
BFGS: 7 14:58:55 -303.898388 0.475353
BFGS: 8 14:58:55 -303.914171 0.663314
BFGS: 9 14:58:55 -303.944365 0.788348
BFGS: 10 14:58:55 -303.968231 0.706691
BFGS: 11 14:58:55 -303.985644 0.534854
BFGS: 12 14:58:55 -304.006623 0.537852
BFGS: 13 14:58:55 -304.029796 0.628375
BFGS: 14 14:58:55 -304.062801 0.703825
BFGS: 15 14:58:55 -304.115620 0.929232
BFGS: 16 14:58:55 -304.171371 1.104376
BFGS: 17 14:58:56 -304.225218 1.245928
BFGS: 18 14:58:56 -304.277356 1.261925
BFGS: 19 14:58:56 -304.345732 0.759965
BFGS: 20 14:58:56 -304.391492 0.482869
BFGS: 21 14:58:56 -304.407891 0.508885
BFGS: 22 14:58:56 -304.428827 0.328411
BFGS: 23 14:58:56 -304.442847 0.249107
BFGS: 24 14:58:56 -304.451654 0.247298
BFGS: 25 14:58:56 -304.456205 0.262352
BFGS: 26 14:58:56 -304.459300 0.267674
BFGS: 27 14:58:57 -304.464975 0.284516
BFGS: 28 14:58:57 -304.474056 0.414323
BFGS: 29 14:58:57 -304.489181 0.603865
BFGS: 30 14:58:57 -304.503932 0.466469
BFGS: 31 14:58:57 -304.517957 0.194025
BFGS: 32 14:58:57 -304.521491 0.163586
BFGS: 33 14:58:57 -304.524353 0.163619
BFGS: 34 14:58:57 -304.527361 0.156396
BFGS: 35 14:58:57 -304.530862 0.103795
BFGS: 36 14:58:58 -304.532392 0.052181
BFGS: 37 14:58:58 -304.532778 0.035032
/home/runner/work/fairchem/fairchem/src/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=200)
if conv:
neb.climb = True
conv = optimizer.run(fmax=fmax, steps=300)
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=200)
if conv:
neb.climb = True
conv = optimizer.run(fmax=fmax, steps=300)
Step Time Energy fmax
BFGS: 0 14:59:09 -303.002111 3.751470
BFGS: 1 14:59:10 -303.126503 2.891745
BFGS: 2 14:59:11 -303.328548 11.080772
BFGS: 3 14:59:12 -303.296182 2.006473
BFGS: 4 14:59:13 -303.354251 1.689564
BFGS: 5 14:59:14 -303.491278 2.648975
BFGS: 6 14:59:15 -303.523468 1.037700
BFGS: 7 14:59:15 -303.590640 0.924142
BFGS: 8 14:59:16 -303.615012 0.949683
BFGS: 9 14:59:17 -303.652719 0.605449
BFGS: 10 14:59:18 -303.670092 0.647384
BFGS: 11 14:59:19 -303.683516 0.473615
BFGS: 12 14:59:20 -303.684167 0.430197
BFGS: 13 14:59:21 -303.675842 0.392761
BFGS: 14 14:59:22 -303.677787 0.363459
BFGS: 15 14:59:23 -303.676105 0.307857
BFGS: 16 14:59:24 -303.671477 0.251260
BFGS: 17 14:59:24 -303.667274 0.193869
BFGS: 18 14:59:25 -303.665168 0.148419
BFGS: 19 14:59:26 -303.663694 0.140008
BFGS: 20 14:59:27 -303.663037 0.116143
BFGS: 21 14:59:28 -303.662858 0.118798
BFGS: 22 14:59:28 -303.662970 0.107991
BFGS: 23 14:59:29 -303.663380 0.098335
BFGS: 24 14:59:30 -303.663852 0.087243
BFGS: 25 14:59:31 -303.664052 0.085558
BFGS: 26 14:59:31 -303.664053 0.108719
BFGS: 27 14:59:32 -303.663485 0.099666
BFGS: 28 14:59:33 -303.662811 0.070335
BFGS: 29 14:59:33 -303.663074 0.063643
BFGS: 30 14:59:33 -303.663074 0.065123
BFGS: 31 14:59:34 -303.663074 0.059047
BFGS: 32 14:59:34 -303.663074 0.048976
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_10193/3247994494.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")