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 05:22:53 -301.635040 4.087651
BFGS: 1 05:22:53 -302.021198 3.274333
BFGS: 2 05:22:54 -303.047805 3.309308
BFGS: 3 05:22:54 -303.206566 4.520027
BFGS: 4 05:22:54 -303.512302 2.447057
BFGS: 5 05:22:54 -303.809769 2.531893
BFGS: 6 05:22:54 -303.907363 1.788966
BFGS: 7 05:22:54 -304.014433 1.927070
BFGS: 8 05:22:54 -304.086867 0.907380
BFGS: 9 05:22:54 -304.157983 0.852462
BFGS: 10 05:22:54 -304.284973 1.069737
BFGS: 11 05:22:54 -304.366516 1.288283
BFGS: 12 05:22:54 -304.485678 1.044118
BFGS: 13 05:22:55 -304.559406 0.804207
BFGS: 14 05:22:55 -304.582454 0.670535
BFGS: 15 05:22:55 -304.600295 0.611461
BFGS: 16 05:22:55 -304.622914 0.406910
BFGS: 17 05:22:55 -304.631514 0.330986
BFGS: 18 05:22:55 -304.637070 0.306028
BFGS: 19 05:22:55 -304.642211 0.261748
BFGS: 20 05:22:55 -304.650994 0.385578
BFGS: 21 05:22:55 -304.662769 0.371529
BFGS: 22 05:22:55 -304.672492 0.236181
BFGS: 23 05:22:55 -304.677605 0.188264
BFGS: 24 05:22:55 -304.681243 0.217069
BFGS: 25 05:22:56 -304.684906 0.191263
BFGS: 26 05:22:56 -304.688037 0.137704
BFGS: 27 05:22:56 -304.689830 0.097668
BFGS: 28 05:22:56 -304.690666 0.063581
BFGS: 29 05:22:56 -304.691096 0.068203
BFGS: 30 05:22:56 -304.691419 0.062836
BFGS: 31 05:22:56 -304.691753 0.048656
Step Time Energy fmax
BFGS: 0 05:22:56 -302.496020 3.991482
BFGS: 1 05:22:56 -302.854682 2.847279
BFGS: 2 05:22:57 -303.694731 3.216690
BFGS: 3 05:22:57 -303.864716 2.850189
BFGS: 4 05:22:57 -304.162454 1.396218
BFGS: 5 05:22:57 -304.235990 1.459039
BFGS: 6 05:22:57 -304.501778 1.679082
BFGS: 7 05:22:57 -304.575263 0.975456
BFGS: 8 05:22:57 -304.607555 0.801686
BFGS: 9 05:22:57 -304.658517 0.619432
BFGS: 10 05:22:57 -304.669885 0.454149
BFGS: 11 05:22:57 -304.680541 0.147892
BFGS: 12 05:22:57 -304.682032 0.102222
BFGS: 13 05:22:57 -304.682887 0.098620
BFGS: 14 05:22:58 -304.684111 0.090297
BFGS: 15 05:22:58 -304.685476 0.084301
BFGS: 16 05:22:58 -304.686518 0.082973
BFGS: 17 05:22:58 -304.687287 0.092936
BFGS: 18 05:22:58 -304.688219 0.091652
BFGS: 19 05:22:58 -304.689366 0.069252
BFGS: 20 05:22:58 -304.690258 0.045094
Step Time Energy fmax
BFGS: 0 05:22:58 -300.966413 4.051584
BFGS: 1 05:22:58 -301.362065 3.358859
BFGS: 2 05:22:58 -302.498297 3.478137
BFGS: 3 05:22:58 -302.372715 7.644518
BFGS: 4 05:22:59 -302.821959 2.805690
BFGS: 5 05:22:59 -302.976479 1.688318
BFGS: 6 05:22:59 -303.068482 1.831718
BFGS: 7 05:22:59 -303.099503 0.807123
BFGS: 8 05:22:59 -303.139129 0.952783
BFGS: 9 05:22:59 -303.176112 1.132298
BFGS: 10 05:22:59 -303.202233 0.835536
BFGS: 11 05:22:59 -303.215939 0.382050
BFGS: 12 05:22:59 -303.220864 0.267901
BFGS: 13 05:22:59 -303.225209 0.432451
BFGS: 14 05:22:59 -303.232149 0.477122
BFGS: 15 05:22:59 -303.237697 0.397420
BFGS: 16 05:23:00 -303.242360 0.345545
BFGS: 17 05:23:00 -303.247977 0.406427
BFGS: 18 05:23:00 -303.266308 0.821398
BFGS: 19 05:23:00 -303.352743 1.952587
BFGS: 20 05:23:00 -303.534507 2.355590
BFGS: 21 05:23:00 -303.506221 3.383739
BFGS: 22 05:23:00 -303.660468 2.143462
BFGS: 23 05:23:00 -303.721126 1.959246
BFGS: 24 05:23:00 -304.026809 1.115661
BFGS: 25 05:23:00 -304.083217 1.259814
BFGS: 26 05:23:00 -304.152468 1.259334
BFGS: 27 05:23:01 -304.208261 0.945041
BFGS: 28 05:23:01 -304.247082 0.703237
BFGS: 29 05:23:01 -304.269593 0.385663
BFGS: 30 05:23:01 -304.278416 0.346546
BFGS: 31 05:23:01 -304.290264 0.342967
BFGS: 32 05:23:01 -304.303713 0.378454
BFGS: 33 05:23:01 -304.315390 0.383518
BFGS: 34 05:23:01 -304.323703 0.324811
BFGS: 35 05:23:01 -304.329079 0.259884
BFGS: 36 05:23:01 -304.334238 0.204241
BFGS: 37 05:23:01 -304.338826 0.212027
BFGS: 38 05:23:01 -304.342448 0.221971
BFGS: 39 05:23:02 -304.346008 0.205021
BFGS: 40 05:23:02 -304.349246 0.157900
BFGS: 41 05:23:02 -304.352128 0.104634
BFGS: 42 05:23:02 -304.353826 0.095157
BFGS: 43 05:23:02 -304.354527 0.097688
BFGS: 44 05:23:02 -304.354810 0.086612
BFGS: 45 05:23:02 -304.355095 0.082715
BFGS: 46 05:23:02 -304.355514 0.089734
BFGS: 47 05:23:02 -304.355946 0.083030
BFGS: 48 05:23:02 -304.356207 0.065332
BFGS: 49 05:23:02 -304.356301 0.060508
BFGS: 50 05:23:03 -304.356360 0.066904
BFGS: 51 05:23:03 -304.356434 0.069815
BFGS: 52 05:23:03 -304.356513 0.065371
BFGS: 53 05:23:03 -304.356571 0.054567
BFGS: 54 05:23:03 -304.356603 0.044782
Step Time Energy fmax
BFGS: 0 05:23:03 -302.701422 3.680643
BFGS: 1 05:23:03 -303.042716 2.603767
BFGS: 2 05:23:03 -303.760042 3.043500
BFGS: 3 05:23:03 -303.890406 2.335871
BFGS: 4 05:23:03 -304.050322 2.418870
BFGS: 5 05:23:03 -304.101787 1.048656
BFGS: 6 05:23:03 -304.164776 0.674564
BFGS: 7 05:23:04 -304.222969 0.706097
BFGS: 8 05:23:04 -304.253078 0.514180
BFGS: 9 05:23:04 -304.269776 0.401124
BFGS: 10 05:23:04 -304.285375 0.371057
BFGS: 11 05:23:04 -304.299782 0.381523
BFGS: 12 05:23:04 -304.307746 0.265809
BFGS: 13 05:23:04 -304.311313 0.221781
BFGS: 14 05:23:04 -304.318357 0.301420
BFGS: 15 05:23:04 -304.326197 0.389441
BFGS: 16 05:23:04 -304.333384 0.312099
BFGS: 17 05:23:04 -304.337519 0.206057
BFGS: 18 05:23:05 -304.339663 0.180996
BFGS: 19 05:23:05 -304.341889 0.194228
BFGS: 20 05:23:05 -304.345526 0.257793
BFGS: 21 05:23:05 -304.349883 0.222919
BFGS: 22 05:23:05 -304.352631 0.109830
BFGS: 23 05:23:05 -304.353710 0.082811
BFGS: 24 05:23:05 -304.354408 0.077144
BFGS: 25 05:23:05 -304.355114 0.097607
BFGS: 26 05:23:05 -304.356067 0.107671
BFGS: 27 05:23:05 -304.356784 0.075575
BFGS: 28 05:23:05 -304.357056 0.024021
Step Time Energy fmax
BFGS: 0 05:23:05 -300.822320 3.973430
BFGS: 1 05:23:06 -301.248801 3.532779
BFGS: 2 05:23:06 -302.551487 3.606015
BFGS: 3 05:23:06 -302.332344 8.864014
BFGS: 4 05:23:06 -302.849924 3.053590
BFGS: 5 05:23:06 -303.003662 2.158342
BFGS: 6 05:23:06 -303.103040 2.103892
BFGS: 7 05:23:06 -303.133365 0.488360
BFGS: 8 05:23:06 -303.141372 0.344524
BFGS: 9 05:23:06 -303.165161 0.710940
BFGS: 10 05:23:06 -303.177618 0.605950
BFGS: 11 05:23:06 -303.184255 0.285150
BFGS: 12 05:23:07 -303.186460 0.212571
BFGS: 13 05:23:07 -303.191810 0.433628
BFGS: 14 05:23:07 -303.198345 0.552662
BFGS: 15 05:23:07 -303.206783 0.520489
BFGS: 16 05:23:07 -303.212995 0.334934
BFGS: 17 05:23:07 -303.216581 0.207107
BFGS: 18 05:23:07 -303.219416 0.271756
BFGS: 19 05:23:07 -303.224770 0.436962
BFGS: 20 05:23:07 -303.241247 0.797013
BFGS: 21 05:23:07 -303.286278 1.701411
BFGS: 22 05:23:07 -303.371134 1.652985
BFGS: 23 05:23:07 -303.497274 1.956989
BFGS: 24 05:23:08 -303.561119 2.766082
BFGS: 25 05:23:08 -303.758135 1.555789
BFGS: 26 05:23:08 -303.841861 0.840101
BFGS: 27 05:23:08 -303.900538 0.724173
BFGS: 28 05:23:08 -303.984131 0.931949
BFGS: 29 05:23:08 -304.031293 0.753434
BFGS: 30 05:23:08 -304.067349 0.678874
BFGS: 31 05:23:08 -304.127741 0.857518
BFGS: 32 05:23:08 -304.205465 1.302306
BFGS: 33 05:23:08 -304.286713 0.945121
BFGS: 34 05:23:08 -304.355343 1.097866
BFGS: 35 05:23:09 -304.408462 1.524291
BFGS: 36 05:23:09 -304.446473 0.669600
BFGS: 37 05:23:09 -304.473062 0.566623
BFGS: 38 05:23:09 -304.492071 0.733718
BFGS: 39 05:23:09 -304.522089 0.932159
BFGS: 40 05:23:09 -304.559041 0.937230
BFGS: 41 05:23:09 -304.600173 0.615249
BFGS: 42 05:23:09 -304.633962 0.433199
BFGS: 43 05:23:09 -304.653676 0.540792
BFGS: 44 05:23:09 -304.667389 0.510841
BFGS: 45 05:23:09 -304.677975 0.366260
BFGS: 46 05:23:09 -304.682838 0.222465
BFGS: 47 05:23:10 -304.684667 0.148123
BFGS: 48 05:23:10 -304.685447 0.114376
BFGS: 49 05:23:10 -304.686244 0.094972
BFGS: 50 05:23:10 -304.687259 0.075728
BFGS: 51 05:23:10 -304.688423 0.080722
BFGS: 52 05:23:10 -304.689599 0.084643
BFGS: 53 05:23:10 -304.690572 0.074874
BFGS: 54 05:23:10 -304.691092 0.064214
BFGS: 55 05:23:10 -304.691310 0.055904
BFGS: 56 05:23:10 -304.691460 0.043125
Step Time Energy fmax
BFGS: 0 05:23:10 -301.196298 4.094991
BFGS: 1 05:23:11 -301.578721 3.310567
BFGS: 2 05:23:11 -302.600677 3.400988
BFGS: 3 05:23:11 -302.674715 4.606100
BFGS: 4 05:23:11 -302.956190 2.468921
BFGS: 5 05:23:11 -303.117427 1.994242
BFGS: 6 05:23:11 -303.161001 1.217086
BFGS: 7 05:23:11 -303.296796 1.797467
BFGS: 8 05:23:11 -303.408616 2.038638
BFGS: 9 05:23:11 -303.552110 2.205143
BFGS: 10 05:23:11 -303.676271 1.665797
BFGS: 11 05:23:11 -303.910977 1.532288
BFGS: 12 05:23:11 -303.931802 2.934059
BFGS: 13 05:23:12 -304.028031 0.947120
BFGS: 14 05:23:12 -304.055564 0.642939
BFGS: 15 05:23:12 -304.073379 0.658948
BFGS: 16 05:23:12 -304.113288 0.523111
BFGS: 17 05:23:12 -304.129749 0.433388
BFGS: 18 05:23:12 -304.146220 0.326965
BFGS: 19 05:23:12 -304.154600 0.235091
BFGS: 20 05:23:12 -304.162054 0.305711
BFGS: 21 05:23:12 -304.168655 0.335332
BFGS: 22 05:23:12 -304.178006 0.422084
BFGS: 23 05:23:12 -304.189591 0.377365
BFGS: 24 05:23:13 -304.202218 0.292491
BFGS: 25 05:23:13 -304.218520 0.452942
BFGS: 26 05:23:13 -304.256000 1.033515
BFGS: 27 05:23:13 -304.193369 1.805933
BFGS: 28 05:23:13 -304.293396 1.017826
BFGS: 29 05:23:13 -304.327764 0.661171
BFGS: 30 05:23:13 -304.365785 0.548232
BFGS: 31 05:23:13 -304.399734 1.278867
BFGS: 32 05:23:13 -304.457192 0.665436
BFGS: 33 05:23:13 -304.475489 0.621389
BFGS: 34 05:23:13 -304.561507 0.620031
BFGS: 35 05:23:13 -304.595750 0.598494
BFGS: 36 05:23:14 -304.641695 0.408686
BFGS: 37 05:23:14 -304.653538 0.304775
BFGS: 38 05:23:14 -304.663967 0.240283
BFGS: 39 05:23:14 -304.671341 0.246307
BFGS: 40 05:23:14 -304.679432 0.229740
BFGS: 41 05:23:14 -304.684560 0.168363
BFGS: 42 05:23:14 -304.687053 0.100713
BFGS: 43 05:23:14 -304.688476 0.082748
BFGS: 44 05:23:14 -304.689501 0.075675
BFGS: 45 05:23:14 -304.690224 0.064317
BFGS: 46 05:23:14 -304.690814 0.068849
BFGS: 47 05:23:15 -304.691372 0.060659
BFGS: 48 05:23:15 -304.691838 0.041845
Step Time Energy fmax
BFGS: 0 05:23:15 -300.979733 4.073054
BFGS: 1 05:23:15 -301.377030 3.368691
BFGS: 2 05:23:15 -302.518894 3.478708
BFGS: 3 05:23:15 -302.370046 7.854965
BFGS: 4 05:23:15 -302.837967 2.847675
BFGS: 5 05:23:15 -302.988636 1.825168
BFGS: 6 05:23:15 -303.085345 1.888755
BFGS: 7 05:23:15 -303.115437 0.730292
BFGS: 8 05:23:15 -303.144215 0.802236
BFGS: 9 05:23:15 -303.185573 1.047907
BFGS: 10 05:23:16 -303.210486 0.877782
BFGS: 11 05:23:16 -303.227933 0.431015
BFGS: 12 05:23:16 -303.234338 0.330296
BFGS: 13 05:23:16 -303.240395 0.542972
BFGS: 14 05:23:16 -303.251307 0.670771
BFGS: 15 05:23:16 -303.262317 0.627580
BFGS: 16 05:23:16 -303.274067 0.609681
BFGS: 17 05:23:16 -303.294912 0.859292
BFGS: 18 05:23:16 -303.390522 2.219012
BFGS: 19 05:23:16 -303.699893 2.332823
BFGS: 20 05:23:16 -303.757935 2.387197
BFGS: 21 05:23:17 -303.899377 1.059324
BFGS: 22 05:23:17 -303.967465 0.793534
BFGS: 23 05:23:17 -304.076040 0.828906
BFGS: 24 05:23:17 -304.103203 0.597537
BFGS: 25 05:23:17 -304.133857 0.495138
BFGS: 26 05:23:17 -304.146372 0.376045
BFGS: 27 05:23:17 -304.159741 0.471805
BFGS: 28 05:23:17 -304.172377 0.424344
BFGS: 29 05:23:17 -304.181509 0.274851
BFGS: 30 05:23:17 -304.188257 0.287971
BFGS: 31 05:23:17 -304.202898 0.634341
BFGS: 32 05:23:17 -304.241231 1.612245
BFGS: 33 05:23:18 -304.265765 1.809613
BFGS: 34 05:23:18 -304.317528 1.168893
BFGS: 35 05:23:18 -304.386454 0.612765
BFGS: 36 05:23:18 -304.422307 0.485165
BFGS: 37 05:23:18 -304.462604 0.604139
BFGS: 38 05:23:18 -304.492784 1.005857
BFGS: 39 05:23:18 -304.527849 0.872682
BFGS: 40 05:23:18 -304.571836 0.683597
BFGS: 41 05:23:18 -304.606714 0.500645
BFGS: 42 05:23:18 -304.624818 0.546586
BFGS: 43 05:23:18 -304.657229 0.393159
BFGS: 44 05:23:18 -304.670778 0.216178
BFGS: 45 05:23:19 -304.675960 0.152266
BFGS: 46 05:23:19 -304.678874 0.137857
BFGS: 47 05:23:19 -304.682547 0.146678
BFGS: 48 05:23:19 -304.686084 0.147223
BFGS: 49 05:23:19 -304.688867 0.119080
BFGS: 50 05:23:19 -304.690110 0.082883
BFGS: 51 05:23:19 -304.690584 0.054623
BFGS: 52 05:23:19 -304.690869 0.037725
Step Time Energy fmax
BFGS: 0 05:23:19 -301.715461 4.059034
BFGS: 1 05:23:19 -302.087750 3.161958
BFGS: 2 05:23:19 -303.052609 3.347101
BFGS: 3 05:23:20 -303.234941 3.653985
BFGS: 4 05:23:20 -303.534917 2.278067
BFGS: 5 05:23:20 -303.863803 3.416773
BFGS: 6 05:23:20 -304.023067 2.264851
BFGS: 7 05:23:20 -304.235130 1.699569
BFGS: 8 05:23:20 -304.327619 1.079821
BFGS: 9 05:23:20 -304.396211 1.154499
BFGS: 10 05:23:20 -304.558286 0.955702
BFGS: 11 05:23:20 -304.612768 0.613995
BFGS: 12 05:23:20 -304.640724 0.471880
BFGS: 13 05:23:20 -304.647621 0.468898
BFGS: 14 05:23:20 -304.663475 0.336115
BFGS: 15 05:23:21 -304.668686 0.323435
BFGS: 16 05:23:21 -304.672406 0.170676
BFGS: 17 05:23:21 -304.673856 0.146617
BFGS: 18 05:23:21 -304.675801 0.178816
BFGS: 19 05:23:21 -304.679108 0.315915
BFGS: 20 05:23:21 -304.683448 0.333452
BFGS: 21 05:23:21 -304.686535 0.188106
BFGS: 22 05:23:21 -304.687695 0.082069
BFGS: 23 05:23:21 -304.688366 0.097116
BFGS: 24 05:23:21 -304.689157 0.157297
BFGS: 25 05:23:21 -304.690287 0.191949
BFGS: 26 05:23:22 -304.691275 0.148146
BFGS: 27 05:23:22 -304.691742 0.056228
BFGS: 28 05:23:22 -304.691890 0.044385
Step Time Energy fmax
BFGS: 0 05:23:22 -301.209756 4.098430
BFGS: 1 05:23:22 -301.596510 3.091290
BFGS: 2 05:23:22 -302.619947 3.561289
BFGS: 3 05:23:22 -302.742085 3.656199
BFGS: 4 05:23:22 -303.030185 2.109179
BFGS: 5 05:23:22 -303.097092 2.584542
BFGS: 6 05:23:22 -303.159352 0.776403
BFGS: 7 05:23:22 -303.190619 0.715463
BFGS: 8 05:23:22 -303.448960 0.976394
BFGS: 9 05:23:23 -303.547218 1.521091
BFGS: 10 05:23:23 -303.664360 1.779269
BFGS: 11 05:23:23 -303.885850 1.323772
BFGS: 12 05:23:23 -303.993628 1.523519
BFGS: 13 05:23:23 -304.079453 0.895035
BFGS: 14 05:23:23 -304.122330 0.437171
BFGS: 15 05:23:23 -304.136565 0.608925
BFGS: 16 05:23:23 -304.165139 0.487232
BFGS: 17 05:23:23 -304.192275 0.598602
BFGS: 18 05:23:24 -304.208685 0.591924
BFGS: 19 05:23:24 -304.223654 0.480016
BFGS: 20 05:23:24 -304.244330 0.545277
BFGS: 21 05:23:24 -304.298829 1.201685
BFGS: 22 05:23:24 -304.323455 1.920328
BFGS: 23 05:23:24 -304.388800 1.453123
BFGS: 24 05:23:24 -304.450057 1.031937
BFGS: 25 05:23:24 -304.506370 0.509874
BFGS: 26 05:23:24 -304.527193 0.502819
BFGS: 27 05:23:24 -304.561286 0.594496
BFGS: 28 05:23:24 -304.583520 0.357552
BFGS: 29 05:23:24 -304.596895 0.372840
BFGS: 30 05:23:25 -304.611079 0.411055
BFGS: 31 05:23:25 -304.630869 0.414072
BFGS: 32 05:23:25 -304.650338 0.369303
BFGS: 33 05:23:25 -304.663306 0.244435
BFGS: 34 05:23:25 -304.669251 0.207480
BFGS: 35 05:23:25 -304.673449 0.201068
BFGS: 36 05:23:25 -304.678161 0.169627
BFGS: 37 05:23:25 -304.683283 0.152003
BFGS: 38 05:23:25 -304.687794 0.109633
BFGS: 39 05:23:25 -304.689906 0.059487
BFGS: 40 05:23:25 -304.690528 0.065565
BFGS: 41 05:23:26 -304.690805 0.057905
BFGS: 42 05:23:26 -304.691123 0.044393
Step Time Energy fmax
BFGS: 0 05:23:26 -301.224272 4.078201
BFGS: 1 05:23:26 -301.611888 3.091297
BFGS: 2 05:23:26 -302.655116 3.582792
BFGS: 3 05:23:26 -302.766621 4.086275
BFGS: 4 05:23:26 -303.053117 2.296914
BFGS: 5 05:23:26 -303.135789 2.812814
BFGS: 6 05:23:26 -303.199568 0.762841
BFGS: 7 05:23:26 -303.229341 0.741861
BFGS: 8 05:23:26 -303.491224 0.859721
BFGS: 9 05:23:26 -303.578977 1.604637
BFGS: 10 05:23:27 -303.678143 1.480785
BFGS: 11 05:23:27 -303.930217 1.702746
BFGS: 12 05:23:27 -304.043320 1.610551
BFGS: 13 05:23:27 -304.119329 1.083255
BFGS: 14 05:23:27 -304.168299 0.550460
BFGS: 15 05:23:27 -304.178277 0.744961
BFGS: 16 05:23:27 -304.197779 0.497092
BFGS: 17 05:23:27 -304.218613 0.476179
BFGS: 18 05:23:27 -304.239484 0.452808
BFGS: 19 05:23:27 -304.250538 0.294910
BFGS: 20 05:23:27 -304.260952 0.334371
BFGS: 21 05:23:28 -304.273798 0.543721
BFGS: 22 05:23:28 -304.290216 0.613027
BFGS: 23 05:23:28 -304.306165 0.373407
BFGS: 24 05:23:28 -304.314797 0.270052
BFGS: 25 05:23:28 -304.321130 0.254653
BFGS: 26 05:23:28 -304.328863 0.424625
BFGS: 27 05:23:28 -304.336821 0.404592
BFGS: 28 05:23:28 -304.342750 0.230716
BFGS: 29 05:23:28 -304.345407 0.146516
BFGS: 30 05:23:28 -304.346796 0.139890
BFGS: 31 05:23:28 -304.348895 0.164812
BFGS: 32 05:23:28 -304.351436 0.202161
BFGS: 33 05:23:29 -304.353805 0.141418
BFGS: 34 05:23:29 -304.354964 0.048575
# 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 05:23:29 -296.211344 4.386212
BFGS: 1 05:23:29 -296.704910 4.687673
BFGS: 2 05:23:29 -298.230510 3.256709
BFGS: 3 05:23:29 -297.477825 12.206785
BFGS: 4 05:23:29 -298.455217 1.895670
BFGS: 5 05:23:29 -298.522689 1.093723
BFGS: 6 05:23:29 -298.569612 1.010625
BFGS: 7 05:23:29 -298.585340 0.895652
BFGS: 8 05:23:29 -298.669662 1.099923
BFGS: 9 05:23:30 -298.698926 1.169235
BFGS: 10 05:23:30 -299.084253 1.720333
BFGS: 11 05:23:30 -299.408830 2.157631
BFGS: 12 05:23:30 -299.702317 1.496566
BFGS: 13 05:23:30 -299.652010 2.996495
BFGS: 14 05:23:30 -299.790797 0.937758
BFGS: 15 05:23:30 -299.814217 0.687168
BFGS: 16 05:23:30 -299.866861 0.851893
BFGS: 17 05:23:30 -299.884324 0.647399
BFGS: 18 05:23:30 -299.898821 0.346429
BFGS: 19 05:23:30 -299.904599 0.273838
BFGS: 20 05:23:30 -299.910346 0.157032
BFGS: 21 05:23:31 -299.912590 0.179261
BFGS: 22 05:23:31 -299.915368 0.220875
BFGS: 23 05:23:31 -299.919697 0.283848
BFGS: 24 05:23:31 -299.926316 0.376574
BFGS: 25 05:23:31 -299.933755 0.460636
BFGS: 26 05:23:31 -299.949638 0.672433
BFGS: 27 05:23:31 -300.014529 1.405902
BFGS: 28 05:23:31 -300.188857 1.406373
BFGS: 29 05:23:31 -300.301424 0.942580
BFGS: 30 05:23:31 -300.461746 1.131326
BFGS: 31 05:23:31 -300.502038 0.837512
BFGS: 32 05:23:32 -300.548843 0.551168
BFGS: 33 05:23:32 -300.570374 0.430086
BFGS: 34 05:23:32 -300.596933 0.367683
BFGS: 35 05:23:32 -300.609410 0.323194
BFGS: 36 05:23:32 -300.615267 0.240965
BFGS: 37 05:23:32 -300.618707 0.175993
BFGS: 38 05:23:32 -300.621028 0.111580
BFGS: 39 05:23:32 -300.622372 0.064846
BFGS: 40 05:23:32 -300.623140 0.086581
BFGS: 41 05:23:32 -300.623713 0.085794
BFGS: 42 05:23:32 -300.624209 0.076133
BFGS: 43 05:23:32 -300.624595 0.046258
Step Time Energy fmax
BFGS: 0 05:23:33 -295.956101 4.352749
BFGS: 1 05:23:33 -296.497414 4.745050
BFGS: 2 05:23:33 -298.214257 2.975831
BFGS: 3 05:23:33 -296.590026 18.367777
BFGS: 4 05:23:33 -298.380065 1.845402
BFGS: 5 05:23:33 -298.441181 1.043782
BFGS: 6 05:23:33 -298.476304 0.534709
BFGS: 7 05:23:33 -298.480169 0.237911
BFGS: 8 05:23:33 -298.484096 0.081964
BFGS: 9 05:23:33 -298.485830 0.104258
BFGS: 10 05:23:33 -298.486243 0.066007
BFGS: 11 05:23:33 -298.486338 0.043001
Step Time Energy fmax
BFGS: 0 05:23:34 -296.157513 4.381445
BFGS: 1 05:23:34 -296.658440 4.700967
BFGS: 2 05:23:34 -298.218259 3.217364
BFGS: 3 05:23:34 -297.334235 13.127014
BFGS: 4 05:23:34 -298.431265 1.890599
BFGS: 5 05:23:34 -298.497387 1.068129
BFGS: 6 05:23:34 -298.539225 0.881324
BFGS: 7 05:23:34 -298.549935 0.714035
BFGS: 8 05:23:34 -298.595374 0.695466
BFGS: 9 05:23:34 -298.608692 0.844247
BFGS: 10 05:23:34 -298.678837 1.559275
BFGS: 11 05:23:35 -298.767362 2.460844
BFGS: 12 05:23:35 -298.848227 3.016772
BFGS: 13 05:23:35 -298.925945 3.328079
BFGS: 14 05:23:35 -299.135074 3.133792
BFGS: 15 05:23:35 -299.801306 1.154459
BFGS: 16 05:23:35 -299.824106 0.983300
BFGS: 17 05:23:35 -299.850949 1.072571
BFGS: 18 05:23:35 -299.884649 0.578587
BFGS: 19 05:23:35 -299.898754 0.414592
BFGS: 20 05:23:35 -299.910954 0.239395
BFGS: 21 05:23:35 -299.919740 0.276587
BFGS: 22 05:23:35 -299.928354 0.328725
BFGS: 23 05:23:36 -299.935764 0.387442
BFGS: 24 05:23:36 -299.946206 0.479476
BFGS: 25 05:23:36 -299.982177 0.838172
BFGS: 26 05:23:36 -300.045764 1.252574
BFGS: 27 05:23:36 -300.059170 1.224541
BFGS: 28 05:23:36 -300.190104 1.225761
BFGS: 29 05:23:36 -300.340434 0.980379
BFGS: 30 05:23:36 -300.432127 0.730931
BFGS: 31 05:23:36 -300.489555 0.565880
BFGS: 32 05:23:36 -300.552870 0.447134
BFGS: 33 05:23:36 -300.581228 0.435664
BFGS: 34 05:23:37 -300.596963 0.394600
BFGS: 35 05:23:37 -300.606041 0.297633
BFGS: 36 05:23:37 -300.612767 0.218477
BFGS: 37 05:23:37 -300.619501 0.125266
BFGS: 38 05:23:37 -300.622324 0.062833
BFGS: 39 05:23:37 -300.623214 0.050715
BFGS: 40 05:23:37 -300.623517 0.044582
Step Time Energy fmax
BFGS: 0 05:23:37 -296.065145 4.358581
BFGS: 1 05:23:37 -296.579711 4.709768
BFGS: 2 05:23:37 -298.205004 3.116025
BFGS: 3 05:23:37 -297.024454 15.234103
BFGS: 4 05:23:37 -298.395329 1.878085
BFGS: 5 05:23:38 -298.459188 1.047007
BFGS: 6 05:23:38 -298.495645 0.687182
BFGS: 7 05:23:38 -298.501343 0.442230
BFGS: 8 05:23:38 -298.512388 0.287309
BFGS: 9 05:23:38 -298.515820 0.332641
BFGS: 10 05:23:38 -298.519383 0.335689
BFGS: 11 05:23:38 -298.525195 0.349144
BFGS: 12 05:23:38 -298.546583 0.570460
BFGS: 13 05:23:38 -298.601464 1.184519
BFGS: 14 05:23:38 -298.843627 3.941925
BFGS: 15 05:23:38 -299.231590 5.140784
BFGS: 16 05:23:39 -299.836350 3.394034
BFGS: 17 05:23:39 -300.004105 3.274367
BFGS: 18 05:23:39 -300.188695 1.532792
BFGS: 19 05:23:39 -300.307018 1.255219
BFGS: 20 05:23:39 -300.419462 1.528580
BFGS: 21 05:23:39 -300.470397 1.554083
BFGS: 22 05:23:39 -300.522468 1.066948
BFGS: 23 05:23:39 -300.570891 0.625903
BFGS: 24 05:23:39 -300.579398 0.595976
BFGS: 25 05:23:39 -300.610624 0.242144
BFGS: 26 05:23:39 -300.614925 0.192906
BFGS: 27 05:23:39 -300.618213 0.130598
BFGS: 28 05:23:40 -300.619539 0.114562
BFGS: 29 05:23:40 -300.621181 0.098278
BFGS: 30 05:23:40 -300.622908 0.109512
BFGS: 31 05:23:40 -300.624109 0.078356
BFGS: 32 05:23:40 -300.624445 0.042118
Step Time Energy fmax
BFGS: 0 05:23:40 -296.256760 4.386266
BFGS: 1 05:23:40 -296.742514 4.675910
BFGS: 2 05:23:40 -298.240960 3.306180
BFGS: 3 05:23:40 -297.614056 11.364346
BFGS: 4 05:23:40 -298.480797 1.908995
BFGS: 5 05:23:40 -298.550629 1.129247
BFGS: 6 05:23:41 -298.605405 1.191406
BFGS: 7 05:23:41 -298.629838 1.159224
BFGS: 8 05:23:41 -298.790152 1.391189
BFGS: 9 05:23:41 -298.874950 2.106730
BFGS: 10 05:23:41 -299.013792 2.661372
BFGS: 11 05:23:41 -299.179880 2.869785
BFGS: 12 05:23:41 -299.432739 2.798361
BFGS: 13 05:23:41 -300.017534 1.393353
BFGS: 14 05:23:41 -300.133622 1.218957
BFGS: 15 05:23:41 -300.197759 1.247252
BFGS: 16 05:23:41 -300.391787 1.542899
BFGS: 17 05:23:41 -300.477690 1.119804
BFGS: 18 05:23:42 -300.544121 0.566893
BFGS: 19 05:23:42 -300.553583 0.480899
BFGS: 20 05:23:42 -300.574275 0.513262
BFGS: 21 05:23:42 -300.601711 0.439149
BFGS: 22 05:23:42 -300.612754 0.278729
BFGS: 23 05:23:42 -300.616156 0.162964
BFGS: 24 05:23:42 -300.617945 0.137270
BFGS: 25 05:23:42 -300.620458 0.119221
BFGS: 26 05:23:42 -300.622592 0.126102
BFGS: 27 05:23:42 -300.623869 0.091512
BFGS: 28 05:23:42 -300.624285 0.050855
BFGS: 29 05:23:42 -300.624472 0.040365
Step Time Energy fmax
BFGS: 0 05:23:43 -296.456461 4.434383
BFGS: 1 05:23:43 -296.924394 4.680404
BFGS: 2 05:23:43 -298.323713 3.494244
BFGS: 3 05:23:43 -298.125132 8.417154
BFGS: 4 05:23:43 -298.636853 1.940887
BFGS: 5 05:23:43 -298.718384 1.372536
BFGS: 6 05:23:43 -298.859361 2.149115
BFGS: 7 05:23:43 -299.037267 2.710597
BFGS: 8 05:23:43 -299.307750 2.800409
BFGS: 9 05:23:43 -299.498972 2.379752
BFGS: 10 05:23:43 -299.567330 1.863266
BFGS: 11 05:23:44 -299.709253 1.773763
BFGS: 12 05:23:44 -300.385987 1.590580
BFGS: 13 05:23:44 -300.455753 1.159234
BFGS: 14 05:23:44 -300.490331 1.096513
BFGS: 15 05:23:44 -300.558192 0.861691
BFGS: 16 05:23:44 -300.590415 0.579709
BFGS: 17 05:23:44 -300.602746 0.368825
BFGS: 18 05:23:44 -300.608063 0.220530
BFGS: 19 05:23:44 -300.612284 0.230360
BFGS: 20 05:23:44 -300.618103 0.191606
BFGS: 21 05:23:44 -300.620741 0.154026
BFGS: 22 05:23:44 -300.622196 0.120584
BFGS: 23 05:23:45 -300.623028 0.090767
BFGS: 24 05:23:45 -300.623687 0.059290
BFGS: 25 05:23:45 -300.624158 0.037163
Step Time Energy fmax
BFGS: 0 05:23:45 -296.280652 4.409681
BFGS: 1 05:23:45 -296.769014 4.690812
BFGS: 2 05:23:45 -298.256233 3.316022
BFGS: 3 05:23:45 -297.667824 11.072046
BFGS: 4 05:23:45 -298.500085 1.903476
BFGS: 5 05:23:45 -298.570205 1.148704
BFGS: 6 05:23:45 -298.629058 1.230372
BFGS: 7 05:23:45 -298.657838 1.226224
BFGS: 8 05:23:46 -298.825908 1.318582
BFGS: 9 05:23:46 -298.923249 2.061510
BFGS: 10 05:23:46 -299.059556 2.355532
BFGS: 11 05:23:46 -299.205747 2.323098
BFGS: 12 05:23:46 -299.581196 1.568798
BFGS: 13 05:23:46 -299.831238 1.145277
BFGS: 14 05:23:46 -299.838343 0.607678
BFGS: 15 05:23:46 -299.857531 0.494612
BFGS: 16 05:23:46 -299.877566 0.636342
BFGS: 17 05:23:46 -299.894856 0.461631
BFGS: 18 05:23:46 -299.907582 0.234771
BFGS: 19 05:23:46 -299.910423 0.157960
BFGS: 20 05:23:47 -299.912928 0.155340
BFGS: 21 05:23:47 -299.915541 0.218185
BFGS: 22 05:23:47 -299.918516 0.268048
BFGS: 23 05:23:47 -299.921489 0.278588
BFGS: 24 05:23:47 -299.924890 0.276967
BFGS: 25 05:23:47 -299.929929 0.299937
BFGS: 26 05:23:47 -299.936777 0.383435
BFGS: 27 05:23:47 -299.948058 0.603416
BFGS: 28 05:23:47 -299.964790 0.773944
BFGS: 29 05:23:47 -299.987613 0.674926
BFGS: 30 05:23:47 -300.021387 0.582126
BFGS: 31 05:23:48 -300.027883 0.560429
BFGS: 32 05:23:48 -300.051383 0.246635
BFGS: 33 05:23:48 -300.058621 0.283128
BFGS: 34 05:23:48 -300.067466 0.256065
BFGS: 35 05:23:48 -300.073508 0.165144
BFGS: 36 05:23:48 -300.076526 0.131057
BFGS: 37 05:23:48 -300.078057 0.081939
BFGS: 38 05:23:48 -300.078918 0.070877
BFGS: 39 05:23:48 -300.079495 0.057242
BFGS: 40 05:23:48 -300.079868 0.041557
Step Time Energy fmax
BFGS: 0 05:23:48 -297.197981 4.620150
BFGS: 1 05:23:48 -297.687115 4.753477
BFGS: 2 05:23:49 -298.972653 3.568540
BFGS: 3 05:23:49 -299.218008 4.607468
BFGS: 4 05:23:49 -299.428924 1.501951
BFGS: 5 05:23:49 -299.529330 1.312894
BFGS: 6 05:23:49 -299.702635 1.531538
BFGS: 7 05:23:49 -299.736968 0.782037
BFGS: 8 05:23:49 -299.771188 0.860954
BFGS: 9 05:23:49 -299.849045 0.971580
BFGS: 10 05:23:49 -299.876760 0.736987
BFGS: 11 05:23:49 -299.898068 0.395365
BFGS: 12 05:23:49 -299.904740 0.188041
BFGS: 13 05:23:50 -299.907067 0.150831
BFGS: 14 05:23:50 -299.909906 0.102715
BFGS: 15 05:23:50 -299.910657 0.058959
BFGS: 16 05:23:50 -299.910866 0.040701
Step Time Energy fmax
BFGS: 0 05:23:50 -296.038472 4.357008
BFGS: 1 05:23:50 -296.558694 4.717738
BFGS: 2 05:23:50 -298.204743 3.086948
BFGS: 3 05:23:50 -296.930396 15.919056
BFGS: 4 05:23:50 -298.389181 1.873118
BFGS: 5 05:23:50 -298.452456 1.045762
BFGS: 6 05:23:50 -298.488249 0.642628
BFGS: 7 05:23:50 -298.493273 0.381156
BFGS: 8 05:23:51 -298.501212 0.212467
BFGS: 9 05:23:51 -298.503737 0.247714
BFGS: 10 05:23:51 -298.505436 0.226107
BFGS: 11 05:23:51 -298.507541 0.206534
BFGS: 12 05:23:51 -298.513703 0.258502
BFGS: 13 05:23:51 -298.541721 0.685241
BFGS: 14 05:23:51 -298.578112 1.347078
BFGS: 15 05:23:51 -297.643884 11.140620
BFGS: 16 05:23:51 -298.595609 1.427770
BFGS: 17 05:23:51 -298.612580 1.544463
BFGS: 18 05:23:51 -298.723937 2.122559
BFGS: 19 05:23:51 -298.838696 2.446016
BFGS: 20 05:23:52 -298.837601 2.818954
BFGS: 21 05:23:52 -298.889977 2.457662
BFGS: 22 05:23:52 -298.912481 2.413259
BFGS: 23 05:23:52 -299.015539 2.505380
BFGS: 24 05:23:52 -299.085424 2.732441
BFGS: 25 05:23:52 -299.185874 3.493006
BFGS: 26 05:23:52 -299.260905 3.870347
BFGS: 27 05:23:52 -299.463405 3.549067
BFGS: 28 05:23:52 -299.707859 2.408406
BFGS: 29 05:23:52 -299.803612 2.436113
BFGS: 30 05:23:52 -299.831190 2.283387
BFGS: 31 05:23:53 -299.958555 1.858248
BFGS: 32 05:23:53 -300.073346 1.567535
BFGS: 33 05:23:53 -300.102444 1.573329
BFGS: 34 05:23:53 -300.152633 1.459460
BFGS: 35 05:23:53 -300.205488 1.374868
BFGS: 36 05:23:53 -300.259134 1.453741
BFGS: 37 05:23:53 -300.310143 1.396047
BFGS: 38 05:23:53 -300.352415 1.159252
BFGS: 39 05:23:53 -300.385479 1.123974
BFGS: 40 05:23:53 -300.446775 0.883763
BFGS: 41 05:23:53 -300.486156 0.939395
BFGS: 42 05:23:53 -300.527601 0.850835
BFGS: 43 05:23:54 -300.562937 0.597785
BFGS: 44 05:23:54 -300.590526 0.366278
BFGS: 45 05:23:54 -300.602972 0.313051
BFGS: 46 05:23:54 -300.610558 0.331010
BFGS: 47 05:23:54 -300.616327 0.233282
BFGS: 48 05:23:54 -300.619981 0.118849
BFGS: 49 05:23:54 -300.622019 0.087146
BFGS: 50 05:23:54 -300.623131 0.060850
BFGS: 51 05:23:54 -300.623810 0.058047
BFGS: 52 05:23:54 -300.624191 0.046751
Step Time Energy fmax
BFGS: 0 05:23:54 -297.364563 4.533166
BFGS: 1 05:23:55 -297.838280 4.627143
BFGS: 2 05:23:55 -299.065877 3.379189
BFGS: 3 05:23:55 -299.271309 4.534525
BFGS: 4 05:23:55 -299.484978 1.507410
BFGS: 5 05:23:55 -299.590541 1.377777
BFGS: 6 05:23:55 -299.849479 1.226967
BFGS: 7 05:23:55 -299.886867 0.955204
BFGS: 8 05:23:55 -299.991533 0.930962
BFGS: 9 05:23:55 -300.023152 0.696608
BFGS: 10 05:23:55 -300.049516 0.313900
BFGS: 11 05:23:55 -300.052789 0.206657
BFGS: 12 05:23:55 -300.059745 0.246620
BFGS: 13 05:23:56 -300.064185 0.256000
BFGS: 14 05:23:56 -300.068762 0.202097
BFGS: 15 05:23:56 -300.070994 0.146495
BFGS: 16 05:23:56 -300.073230 0.151994
BFGS: 17 05:23:56 -300.076302 0.149879
BFGS: 18 05:23:56 -300.078767 0.108179
BFGS: 19 05:23:56 -300.080052 0.072025
BFGS: 20 05:23:56 -300.080366 0.031035
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 05:23:56 -295.546981 0.766024
BFGS: 1 05:23:56 -295.604365 0.711359
BFGS: 2 05:23:56 -295.794616 0.564455
BFGS: 3 05:23:57 -295.810232 0.326927
BFGS: 4 05:23:57 -295.814565 0.323069
BFGS: 5 05:23:57 -295.832653 0.253017
BFGS: 6 05:23:57 -295.834609 0.218190
BFGS: 7 05:23:57 -295.839490 0.156446
BFGS: 8 05:23:57 -295.840652 0.084629
BFGS: 9 05:23:57 -295.841056 0.063661
BFGS: 10 05:23:57 -295.841272 0.062555
BFGS: 11 05:23:57 -295.841650 0.056515
BFGS: 12 05:23:57 -295.841963 0.051598
BFGS: 13 05:23:57 -295.842163 0.046702
Step Time Energy fmax
BFGS: 0 05:23:57 -295.548495 0.758851
BFGS: 1 05:23:58 -295.605521 0.704847
BFGS: 2 05:23:58 -295.794861 0.550333
BFGS: 3 05:23:58 -295.810038 0.323769
BFGS: 4 05:23:58 -295.814318 0.320035
BFGS: 5 05:23:58 -295.832236 0.250025
BFGS: 6 05:23:58 -295.834127 0.215418
BFGS: 7 05:23:58 -295.839001 0.146210
BFGS: 8 05:23:58 -295.840045 0.076700
BFGS: 9 05:23:58 -295.840423 0.071691
BFGS: 10 05:23:58 -295.840647 0.067951
BFGS: 11 05:23:58 -295.841008 0.047408
Step Time Energy fmax
BFGS: 0 05:23:59 -295.273147 1.355761
BFGS: 1 05:23:59 -295.356383 1.235035
BFGS: 2 05:23:59 -295.558585 1.691937
BFGS: 3 05:23:59 -295.610010 0.544400
BFGS: 4 05:23:59 -295.620931 0.538458
BFGS: 5 05:23:59 -295.650349 0.344519
BFGS: 6 05:23:59 -295.656034 0.374417
BFGS: 7 05:23:59 -295.668432 0.418888
BFGS: 8 05:23:59 -295.680293 0.506696
BFGS: 9 05:23:59 -295.698907 0.561043
BFGS: 10 05:23:59 -295.716833 0.640843
BFGS: 11 05:23:59 -295.745180 1.011852
BFGS: 12 05:24:00 -295.782043 1.247479
BFGS: 13 05:24:00 -295.821694 1.152227
BFGS: 14 05:24:00 -295.884146 0.864173
BFGS: 15 05:24:00 -295.918918 0.555554
BFGS: 16 05:24:00 -295.941495 0.297259
BFGS: 17 05:24:00 -295.946498 0.311801
BFGS: 18 05:24:00 -295.952753 0.331562
BFGS: 19 05:24:00 -295.958566 0.260400
BFGS: 20 05:24:00 -295.962682 0.145926
BFGS: 21 05:24:00 -295.964873 0.085545
BFGS: 22 05:24:00 -295.965943 0.067296
BFGS: 23 05:24:00 -295.966363 0.060243
BFGS: 24 05:24:01 -295.966752 0.056425
BFGS: 25 05:24:01 -295.967320 0.048428
Step Time Energy fmax
BFGS: 0 05:24:01 -295.372442 1.173840
BFGS: 1 05:24:01 -295.444691 1.076585
BFGS: 2 05:24:01 -295.656135 1.213044
BFGS: 3 05:24:01 -295.686380 0.567674
BFGS: 4 05:24:01 -295.696829 0.461008
BFGS: 5 05:24:01 -295.737487 0.535272
BFGS: 6 05:24:01 -295.745111 0.518608
BFGS: 7 05:24:01 -295.809656 0.432013
BFGS: 8 05:24:01 -295.815961 0.358564
BFGS: 9 05:24:02 -295.822147 0.334874
BFGS: 10 05:24:02 -295.831447 0.237165
BFGS: 11 05:24:02 -295.836320 0.142028
BFGS: 12 05:24:02 -295.838167 0.146192
BFGS: 13 05:24:02 -295.838960 0.135022
BFGS: 14 05:24:02 -295.839781 0.119023
BFGS: 15 05:24:02 -295.840806 0.098571
BFGS: 16 05:24:02 -295.841779 0.065880
BFGS: 17 05:24:02 -295.842220 0.046907
Step Time Energy fmax
BFGS: 0 05:24:02 -295.512208 0.939590
BFGS: 1 05:24:02 -295.572647 0.877054
BFGS: 2 05:24:02 -295.777480 0.759631
BFGS: 3 05:24:03 -295.797441 0.460325
BFGS: 4 05:24:03 -295.805584 0.466449
BFGS: 5 05:24:03 -295.844853 0.423231
BFGS: 6 05:24:03 -295.850835 0.384527
BFGS: 7 05:24:03 -295.872996 0.278424
BFGS: 8 05:24:03 -295.875896 0.228447
BFGS: 9 05:24:03 -295.877956 0.221762
BFGS: 10 05:24:03 -295.883965 0.214552
BFGS: 11 05:24:03 -295.889528 0.229138
BFGS: 12 05:24:03 -295.896011 0.275798
BFGS: 13 05:24:03 -295.902116 0.326278
BFGS: 14 05:24:04 -295.911932 0.381745
BFGS: 15 05:24:04 -295.925669 0.381055
BFGS: 16 05:24:04 -295.941891 0.287922
BFGS: 17 05:24:04 -295.955522 0.177936
BFGS: 18 05:24:04 -295.958625 0.144631
BFGS: 19 05:24:04 -295.960483 0.134094
BFGS: 20 05:24:04 -295.962108 0.123462
BFGS: 21 05:24:04 -295.966016 0.078985
BFGS: 22 05:24:04 -295.966935 0.055084
BFGS: 23 05:24:04 -295.967236 0.041883
Step Time Energy fmax
BFGS: 0 05:24:04 -295.716960 0.723064
BFGS: 1 05:24:04 -295.766715 0.645422
BFGS: 2 05:24:05 -295.923054 0.275047
BFGS: 3 05:24:05 -295.929612 0.217411
BFGS: 4 05:24:05 -295.930642 0.193721
BFGS: 5 05:24:05 -295.933542 0.093094
BFGS: 6 05:24:05 -295.934247 0.070908
BFGS: 7 05:24:05 -295.934812 0.065205
BFGS: 8 05:24:05 -295.935273 0.052992
BFGS: 9 05:24:05 -295.935955 0.039099
Step Time Energy fmax
BFGS: 0 05:24:05 -295.104836 1.750561
BFGS: 1 05:24:05 -295.221707 1.576540
BFGS: 2 05:24:05 -295.386199 2.737657
BFGS: 3 05:24:06 -295.501481 0.470149
BFGS: 4 05:24:06 -295.519924 0.602942
BFGS: 5 05:24:06 -295.539307 0.665675
BFGS: 6 05:24:06 -295.556991 0.474361
BFGS: 7 05:24:06 -295.564329 0.196746
BFGS: 8 05:24:06 -295.568865 0.273777
BFGS: 9 05:24:06 -295.574315 0.296383
BFGS: 10 05:24:06 -295.578198 0.222524
BFGS: 11 05:24:06 -295.580379 0.099631
BFGS: 12 05:24:06 -295.580723 0.020717
Step Time Energy fmax
BFGS: 0 05:24:06 -295.103218 1.756681
BFGS: 1 05:24:06 -295.220560 1.581868
BFGS: 2 05:24:07 -295.384577 2.749128
BFGS: 3 05:24:07 -295.500581 0.474427
BFGS: 4 05:24:07 -295.519136 0.603231
BFGS: 5 05:24:07 -295.538462 0.667738
BFGS: 6 05:24:07 -295.556396 0.478102
BFGS: 7 05:24:07 -295.563838 0.195573
BFGS: 8 05:24:07 -295.568383 0.272641
BFGS: 9 05:24:07 -295.573917 0.296820
BFGS: 10 05:24:07 -295.577803 0.224289
BFGS: 11 05:24:07 -295.580023 0.101113
BFGS: 12 05:24:07 -295.580375 0.021652
Step Time Energy fmax
BFGS: 0 05:24:08 -295.348184 1.222772
BFGS: 1 05:24:08 -295.421735 1.118584
BFGS: 2 05:24:08 -295.628681 1.292305
BFGS: 3 05:24:08 -295.661687 0.567757
BFGS: 4 05:24:08 -295.671892 0.478642
BFGS: 5 05:24:08 -295.709632 0.511116
BFGS: 6 05:24:08 -295.716342 0.501112
BFGS: 7 05:24:08 -295.792248 0.512414
BFGS: 8 05:24:08 -295.814517 0.679623
BFGS: 9 05:24:08 -295.828558 0.660339
BFGS: 10 05:24:08 -295.854493 0.581148
BFGS: 11 05:24:08 -295.893687 0.338631
BFGS: 12 05:24:09 -295.900234 0.312527
BFGS: 13 05:24:09 -295.905223 0.337844
BFGS: 14 05:24:09 -295.912131 0.348467
BFGS: 15 05:24:09 -295.919767 0.299925
BFGS: 16 05:24:09 -295.925646 0.175572
BFGS: 17 05:24:09 -295.929052 0.129268
BFGS: 18 05:24:09 -295.930796 0.091333
BFGS: 19 05:24:09 -295.931740 0.098154
BFGS: 20 05:24:09 -295.932982 0.113196
BFGS: 21 05:24:09 -295.934460 0.092434
BFGS: 22 05:24:09 -295.935357 0.045816
Step Time Energy fmax
BFGS: 0 05:24:09 -295.358818 1.196988
BFGS: 1 05:24:10 -295.432492 1.096394
BFGS: 2 05:24:10 -295.643882 1.264813
BFGS: 3 05:24:10 -295.675945 0.571106
BFGS: 4 05:24:10 -295.686400 0.472452
BFGS: 5 05:24:10 -295.726155 0.526738
BFGS: 6 05:24:10 -295.733482 0.513509
BFGS: 7 05:24:10 -295.801045 0.456240
BFGS: 8 05:24:10 -295.808608 0.408450
BFGS: 9 05:24:10 -295.815269 0.395428
BFGS: 10 05:24:10 -295.827995 0.275296
BFGS: 11 05:24:10 -295.834791 0.140445
BFGS: 12 05:24:11 -295.836362 0.146435
BFGS: 13 05:24:11 -295.837187 0.148179
BFGS: 14 05:24:11 -295.838176 0.138056
BFGS: 15 05:24:11 -295.839350 0.108308
BFGS: 16 05:24:11 -295.840115 0.061166
BFGS: 17 05:24:11 -295.840361 0.023590
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 05:24:11 -304.117359 0.662563
BFGS: 1 05:24:11 -304.135649 0.612771
BFGS: 2 05:24:11 -304.194991 0.545392
BFGS: 3 05:24:11 -304.207236 0.532932
BFGS: 4 05:24:11 -304.237799 0.517959
BFGS: 5 05:24:12 -304.265037 0.438802
BFGS: 6 05:24:12 -304.288499 0.442832
BFGS: 7 05:24:12 -304.308565 0.499274
BFGS: 8 05:24:12 -304.335388 0.561828
BFGS: 9 05:24:12 -304.368752 0.677681
BFGS: 10 05:24:12 -304.394984 0.580182
BFGS: 11 05:24:12 -304.416635 0.365530
BFGS: 12 05:24:12 -304.425079 0.363420
BFGS: 13 05:24:12 -304.434084 0.264683
BFGS: 14 05:24:12 -304.440971 0.202061
BFGS: 15 05:24:12 -304.446372 0.153742
BFGS: 16 05:24:12 -304.450232 0.122532
BFGS: 17 05:24:13 -304.452203 0.102386
BFGS: 18 05:24:13 -304.453448 0.105106
BFGS: 19 05:24:13 -304.454410 0.083104
BFGS: 20 05:24:13 -304.454942 0.062066
BFGS: 21 05:24:13 -304.455272 0.049463
Step Time Energy fmax
BFGS: 0 05:24:13 -304.396862 0.389198
BFGS: 1 05:24:13 -304.401069 0.327650
BFGS: 2 05:24:13 -304.410889 0.145017
BFGS: 3 05:24:13 -304.413161 0.170232
BFGS: 4 05:24:13 -304.415143 0.194036
BFGS: 5 05:24:13 -304.416927 0.166013
BFGS: 6 05:24:14 -304.418517 0.101412
BFGS: 7 05:24:14 -304.419543 0.087479
BFGS: 8 05:24:14 -304.420155 0.091621
BFGS: 9 05:24:14 -304.420691 0.099259
BFGS: 10 05:24:14 -304.421574 0.108113
BFGS: 11 05:24:14 -304.422979 0.137306
BFGS: 12 05:24:14 -304.424862 0.202286
BFGS: 13 05:24:14 -304.427110 0.232278
BFGS: 14 05:24:14 -304.429837 0.200444
BFGS: 15 05:24:14 -304.432967 0.246560
BFGS: 16 05:24:14 -304.438241 0.300439
BFGS: 17 05:24:15 -304.447814 0.532701
BFGS: 18 05:24:15 -304.463610 0.942195
BFGS: 19 05:24:15 -304.482569 1.115865
BFGS: 20 05:24:15 -304.507514 0.691416
BFGS: 21 05:24:15 -304.521503 0.397549
BFGS: 22 05:24:15 -304.528577 0.266299
BFGS: 23 05:24:15 -304.532752 0.155655
BFGS: 24 05:24:15 -304.535588 0.087193
BFGS: 25 05:24:15 -304.536542 0.104831
BFGS: 26 05:24:15 -304.537415 0.106507
BFGS: 27 05:24:15 -304.538423 0.084325
BFGS: 28 05:24:15 -304.539263 0.054488
BFGS: 29 05:24:16 -304.539732 0.035682
Step Time Energy fmax
BFGS: 0 05:24:16 -303.794915 1.016548
BFGS: 1 05:24:16 -303.819606 0.567089
BFGS: 2 05:24:16 -303.835772 0.346836
BFGS: 3 05:24:16 -303.841662 0.381377
BFGS: 4 05:24:16 -303.863018 0.693551
BFGS: 5 05:24:16 -303.949421 1.434685
BFGS: 6 05:24:16 -303.882618 1.961510
BFGS: 7 05:24:16 -303.994784 1.302574
BFGS: 8 05:24:16 -304.027257 1.207979
BFGS: 9 05:24:17 -304.182989 1.461006
BFGS: 10 05:24:17 -304.229508 0.628185
BFGS: 11 05:24:17 -304.264166 0.636938
BFGS: 12 05:24:17 -304.339628 0.745480
BFGS: 13 05:24:17 -304.398677 1.242958
BFGS: 14 05:24:17 -304.471631 1.312759
BFGS: 15 05:24:17 -304.526551 0.844073
BFGS: 16 05:24:17 -304.557758 0.734335
BFGS: 17 05:24:17 -304.584849 0.807421
BFGS: 18 05:24:17 -304.602282 0.506209
BFGS: 19 05:24:17 -304.619126 0.530475
BFGS: 20 05:24:17 -304.647802 0.437126
BFGS: 21 05:24:18 -304.658788 0.405614
BFGS: 22 05:24:18 -304.666267 0.411388
BFGS: 23 05:24:18 -304.675232 0.286936
BFGS: 24 05:24:18 -304.681270 0.351289
BFGS: 25 05:24:18 -304.685030 0.184387
BFGS: 26 05:24:18 -304.687154 0.150302
BFGS: 27 05:24:18 -304.688931 0.103814
BFGS: 28 05:24:18 -304.689807 0.072738
BFGS: 29 05:24:18 -304.690639 0.056495
BFGS: 30 05:24:18 -304.691251 0.058859
BFGS: 31 05:24:18 -304.691640 0.063612
BFGS: 32 05:24:18 -304.691883 0.051584
BFGS: 33 05:24:19 -304.692034 0.032806
Step Time Energy fmax
BFGS: 0 05:24:19 -301.812163 1.293439
BFGS: 1 05:24:19 -301.858886 0.896397
BFGS: 2 05:24:19 -301.924082 0.870881
BFGS: 3 05:24:19 -301.994963 1.133784
BFGS: 4 05:24:19 -302.068552 1.013734
BFGS: 5 05:24:19 -302.106608 0.819685
BFGS: 6 05:24:19 -302.139200 0.734754
BFGS: 7 05:24:19 -302.185205 0.443864
BFGS: 8 05:24:19 -302.208899 0.430089
BFGS: 9 05:24:20 -302.222366 0.366301
BFGS: 10 05:24:20 -302.231171 0.301024
BFGS: 11 05:24:20 -302.242146 0.312122
BFGS: 12 05:24:20 -302.254045 0.347371
BFGS: 13 05:24:20 -302.264173 0.450213
BFGS: 14 05:24:20 -302.280214 0.521695
BFGS: 15 05:24:20 -302.320769 0.855834
BFGS: 16 05:24:20 -302.368993 1.560305
BFGS: 17 05:24:20 -302.422205 2.334859
BFGS: 18 05:24:20 -302.480429 2.949028
BFGS: 19 05:24:20 -302.545544 3.216933
BFGS: 20 05:24:20 -302.653424 2.915947
BFGS: 21 05:24:21 -302.855100 1.943062
BFGS: 22 05:24:21 -303.156845 1.569968
BFGS: 23 05:24:21 -303.286388 1.567375
BFGS: 24 05:24:21 -303.452688 1.578459
BFGS: 25 05:24:21 -303.636076 1.223416
BFGS: 26 05:24:21 -303.707489 0.957923
BFGS: 27 05:24:21 -303.748398 0.804682
BFGS: 28 05:24:21 -303.808756 0.728761
BFGS: 29 05:24:21 -303.850944 0.589432
BFGS: 30 05:24:21 -303.884134 0.590538
BFGS: 31 05:24:21 -303.920356 0.658927
BFGS: 32 05:24:21 -303.943022 0.526828
BFGS: 33 05:24:22 -303.961378 0.206761
BFGS: 34 05:24:22 -303.967020 0.214693
BFGS: 35 05:24:22 -303.973875 0.183946
BFGS: 36 05:24:22 -303.978038 0.155494
BFGS: 37 05:24:22 -303.981211 0.132903
BFGS: 38 05:24:22 -303.982793 0.128127
BFGS: 39 05:24:22 -303.984112 0.134486
BFGS: 40 05:24:22 -303.985700 0.108385
BFGS: 41 05:24:22 -303.987408 0.084935
BFGS: 42 05:24:22 -303.988589 0.058979
BFGS: 43 05:24:22 -303.989140 0.051422
BFGS: 44 05:24:23 -303.989418 0.054624
BFGS: 45 05:24:23 -303.989675 0.045926
Step Time Energy fmax
BFGS: 0 05:24:23 -302.025779 0.521476
BFGS: 1 05:24:23 -302.036639 0.496966
BFGS: 2 05:24:23 -302.081118 0.475899
BFGS: 3 05:24:23 -302.092245 0.496904
BFGS: 4 05:24:23 -302.157553 0.721929
BFGS: 5 05:24:23 -302.223499 0.715501
BFGS: 6 05:24:23 -302.266589 0.611718
BFGS: 7 05:24:23 -302.310688 0.435697
BFGS: 8 05:24:23 -302.333281 0.304419
BFGS: 9 05:24:24 -302.342558 0.248925
BFGS: 10 05:24:24 -302.350915 0.155036
BFGS: 11 05:24:24 -302.354951 0.138049
BFGS: 12 05:24:24 -302.356898 0.117096
BFGS: 13 05:24:24 -302.358084 0.121985
BFGS: 14 05:24:24 -302.359263 0.097774
BFGS: 15 05:24:24 -302.360944 0.088476
BFGS: 16 05:24:24 -302.363039 0.076729
BFGS: 17 05:24:24 -302.364359 0.061913
BFGS: 18 05:24:24 -302.364970 0.068572
BFGS: 19 05:24:24 -302.365525 0.068595
BFGS: 20 05:24:24 -302.366554 0.072948
BFGS: 21 05:24:25 -302.368100 0.081034
BFGS: 22 05:24:25 -302.369810 0.099299
BFGS: 23 05:24:25 -302.371379 0.131722
BFGS: 24 05:24:25 -302.375017 0.238445
BFGS: 25 05:24:25 -302.381421 0.769676
BFGS: 26 05:24:25 -302.397941 1.594123
BFGS: 27 05:24:25 -302.449006 2.125653
BFGS: 28 05:24:25 -302.464365 3.088773
BFGS: 29 05:24:25 -302.281358 3.851033
BFGS: 30 05:24:25 -302.610517 3.059004
BFGS: 31 05:24:25 -302.676937 3.020904
BFGS: 32 05:24:26 -302.859842 3.178793
BFGS: 33 05:24:26 -302.941015 3.129721
BFGS: 34 05:24:26 -303.088178 2.713969
BFGS: 35 05:24:26 -303.129756 2.937770
BFGS: 36 05:24:26 -303.210049 2.950263
BFGS: 37 05:24:26 -303.319846 2.768243
BFGS: 38 05:24:26 -303.357796 2.210644
BFGS: 39 05:24:26 -303.383197 2.147099
BFGS: 40 05:24:26 -303.406900 2.120990
BFGS: 41 05:24:26 -303.442429 2.173395
BFGS: 42 05:24:26 -303.468924 2.293238
BFGS: 43 05:24:26 -303.488380 2.431340
BFGS: 44 05:24:27 -303.503404 2.527683
BFGS: 45 05:24:27 -303.524680 2.625788
BFGS: 46 05:24:27 -303.548155 2.680039
BFGS: 47 05:24:27 -303.571262 2.651968
BFGS: 48 05:24:27 -303.595638 2.522552
BFGS: 49 05:24:27 -303.628248 2.249275
BFGS: 50 05:24:27 -303.667463 1.816188
BFGS: 51 05:24:27 -303.718728 1.460641
BFGS: 52 05:24:27 -303.809161 1.411779
BFGS: 53 05:24:27 -303.886767 1.200579
BFGS: 54 05:24:27 -303.912740 1.418232
BFGS: 55 05:24:28 -304.034666 1.013513
BFGS: 56 05:24:28 -304.091253 0.692285
BFGS: 57 05:24:28 -304.130213 0.645007
BFGS: 58 05:24:28 -304.148605 0.439504
BFGS: 59 05:24:28 -304.161390 0.133835
BFGS: 60 05:24:28 -304.165128 0.089469
BFGS: 61 05:24:28 -304.167178 0.075406
BFGS: 62 05:24:28 -304.168110 0.063322
BFGS: 63 05:24:28 -304.168708 0.058645
BFGS: 64 05:24:28 -304.169117 0.055003
BFGS: 65 05:24:28 -304.169420 0.046198
Step Time Energy fmax
BFGS: 0 05:24:29 -301.812432 1.480086
BFGS: 1 05:24:29 -301.868239 1.067467
BFGS: 2 05:24:29 -301.928764 0.761597
BFGS: 3 05:24:29 -301.984295 0.942707
BFGS: 4 05:24:29 -302.037601 0.903442
BFGS: 5 05:24:29 -302.071864 0.824076
BFGS: 6 05:24:29 -302.101726 0.677415
BFGS: 7 05:24:29 -302.152578 0.673447
BFGS: 8 05:24:29 -302.195960 0.758494
BFGS: 9 05:24:29 -302.224583 0.673351
BFGS: 10 05:24:29 -302.249815 0.706123
BFGS: 11 05:24:29 -302.359513 1.247600
BFGS: 12 05:24:30 -302.423104 5.319909
BFGS: 13 05:24:30 -302.911974 3.451373
BFGS: 14 05:24:30 -303.075698 2.959833
BFGS: 15 05:24:30 -303.250138 1.278284
BFGS: 16 05:24:30 -303.321780 1.023363
BFGS: 17 05:24:30 -303.429522 1.156017
BFGS: 18 05:24:30 -303.576816 1.160781
BFGS: 19 05:24:30 -303.621590 0.738460
BFGS: 20 05:24:30 -303.639477 0.360404
BFGS: 21 05:24:30 -303.652481 0.374643
BFGS: 22 05:24:30 -303.668337 0.348090
BFGS: 23 05:24:31 -303.682143 0.318750
BFGS: 24 05:24:31 -303.688025 0.139723
BFGS: 25 05:24:31 -303.689206 0.083212
BFGS: 26 05:24:31 -303.689778 0.097694
BFGS: 27 05:24:31 -303.690767 0.117235
BFGS: 28 05:24:31 -303.692080 0.131087
BFGS: 29 05:24:31 -303.693440 0.137598
BFGS: 30 05:24:31 -303.694561 0.161870
BFGS: 31 05:24:31 -303.696156 0.207880
BFGS: 32 05:24:31 -303.700271 0.326492
BFGS: 33 05:24:31 -303.713913 0.735361
BFGS: 34 05:24:31 -303.717780 0.934359
BFGS: 35 05:24:32 -303.745373 0.847980
BFGS: 36 05:24:32 -303.785480 0.662780
BFGS: 37 05:24:32 -303.847001 0.566585
BFGS: 38 05:24:32 -303.859726 0.361207
BFGS: 39 05:24:32 -303.870382 0.226958
BFGS: 40 05:24:32 -303.877341 0.206939
BFGS: 41 05:24:32 -303.884905 0.181581
BFGS: 42 05:24:32 -303.894473 0.097301
BFGS: 43 05:24:32 -303.897748 0.057602
BFGS: 44 05:24:32 -303.898520 0.055301
BFGS: 45 05:24:32 -303.898961 0.055375
BFGS: 46 05:24:32 -303.899772 0.057571
BFGS: 47 05:24:33 -303.900463 0.052930
BFGS: 48 05:24:33 -303.900979 0.039987
Step Time Energy fmax
BFGS: 0 05:24:33 -301.815499 0.673072
BFGS: 1 05:24:33 -301.826332 0.441885
BFGS: 2 05:24:33 -301.842099 0.346031
BFGS: 3 05:24:33 -301.847217 0.375720
BFGS: 4 05:24:33 -301.875113 0.716537
BFGS: 5 05:24:33 -301.894052 0.745991
BFGS: 6 05:24:34 -301.910790 0.698339
BFGS: 7 05:24:34 -301.930157 0.691598
BFGS: 8 05:24:34 -301.950475 0.671199
BFGS: 9 05:24:34 -301.970286 0.540555
BFGS: 10 05:24:34 -301.985945 0.299098
BFGS: 11 05:24:34 -301.993067 0.201306
BFGS: 12 05:24:34 -301.998088 0.236413
BFGS: 13 05:24:34 -302.004744 0.255810
BFGS: 14 05:24:34 -302.017251 0.693547
BFGS: 15 05:24:34 -302.029148 1.492881
BFGS: 16 05:24:34 -302.048960 2.320071
BFGS: 17 05:24:34 -302.078995 3.108451
BFGS: 18 05:24:35 -302.111453 3.626456
BFGS: 19 05:24:35 -302.180778 3.452426
BFGS: 20 05:24:35 -302.408332 2.336531
BFGS: 21 05:24:35 -302.729655 2.003505
BFGS: 22 05:24:35 -303.119820 1.758633
BFGS: 23 05:24:35 -303.102825 2.322794
BFGS: 24 05:24:35 -303.343454 1.055956
BFGS: 25 05:24:35 -303.437934 1.135642
BFGS: 26 05:24:35 -303.604913 0.647649
BFGS: 27 05:24:35 -303.624180 0.567439
BFGS: 28 05:24:35 -303.655392 0.440802
BFGS: 29 05:24:36 -303.665723 0.422155
BFGS: 30 05:24:36 -303.682136 0.521278
BFGS: 31 05:24:36 -303.696788 0.444737
BFGS: 32 05:24:36 -303.709400 0.412329
BFGS: 33 05:24:36 -303.719106 0.477279
BFGS: 34 05:24:36 -303.733350 0.659993
BFGS: 35 05:24:36 -303.774034 1.169316
BFGS: 36 05:24:36 -303.836157 1.576417
BFGS: 37 05:24:36 -303.804174 1.565357
BFGS: 38 05:24:36 -303.927299 1.569530
BFGS: 39 05:24:36 -304.004112 1.506695
BFGS: 40 05:24:36 -304.274294 0.799558
BFGS: 41 05:24:37 -304.317750 0.768321
BFGS: 42 05:24:37 -304.377923 0.471371
BFGS: 43 05:24:37 -304.402078 0.270757
BFGS: 44 05:24:37 -304.415617 0.232738
BFGS: 45 05:24:37 -304.422111 0.273459
BFGS: 46 05:24:37 -304.427628 0.276684
BFGS: 47 05:24:37 -304.432620 0.219426
BFGS: 48 05:24:37 -304.436894 0.147510
BFGS: 49 05:24:37 -304.439965 0.157020
BFGS: 50 05:24:37 -304.441984 0.162282
BFGS: 51 05:24:37 -304.443602 0.165261
BFGS: 52 05:24:37 -304.445610 0.170705
BFGS: 53 05:24:38 -304.449324 0.186058
BFGS: 54 05:24:38 -304.456688 0.256047
BFGS: 55 05:24:38 -304.466843 0.463623
BFGS: 56 05:24:38 -304.477521 0.428584
BFGS: 57 05:24:38 -304.495301 0.345499
BFGS: 58 05:24:38 -304.507436 0.342660
BFGS: 59 05:24:38 -304.522174 0.257623
BFGS: 60 05:24:38 -304.531484 0.169356
BFGS: 61 05:24:38 -304.534866 0.116687
BFGS: 62 05:24:38 -304.536295 0.070957
BFGS: 63 05:24:38 -304.536818 0.062444
BFGS: 64 05:24:39 -304.537472 0.073911
BFGS: 65 05:24:39 -304.538258 0.078516
BFGS: 66 05:24:39 -304.539093 0.060737
BFGS: 67 05:24:39 -304.539632 0.033563
/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 05:24:55 -302.745281 3.480172
BFGS: 1 05:24:56 -302.920212 3.012091
BFGS: 2 05:24:57 -303.376127 7.886105
BFGS: 3 05:24:58 -303.405467 1.877355
BFGS: 4 05:24:59 -303.536106 1.620791
BFGS: 5 05:24:59 -303.684422 0.953508
BFGS: 6 05:25:00 -303.707787 0.805746
BFGS: 7 05:25:01 -303.763457 0.691500
BFGS: 8 05:25:02 -303.780584 0.655667
BFGS: 9 05:25:02 -303.800350 0.494749
BFGS: 10 05:25:03 -303.805103 0.404538
BFGS: 11 05:25:04 -303.809154 0.445593
BFGS: 12 05:25:05 -303.810391 0.417664
BFGS: 13 05:25:05 -303.809523 0.406362
BFGS: 14 05:25:06 -303.807692 0.376567
BFGS: 15 05:25:07 -303.804106 0.346668
BFGS: 16 05:25:08 -303.801486 0.365717
BFGS: 17 05:25:08 -303.800412 0.442032
BFGS: 18 05:25:09 -303.801822 0.490110
BFGS: 19 05:25:10 -303.807598 0.559858
BFGS: 20 05:25:11 -303.818588 0.743028
BFGS: 21 05:25:12 -303.827410 0.890378
BFGS: 22 05:25:12 -303.832298 0.719121
BFGS: 23 05:25:13 -303.836267 0.475353
BFGS: 24 05:25:14 -303.839827 0.478606
BFGS: 25 05:25:15 -303.841533 0.467688
BFGS: 26 05:25:15 -303.839702 0.440838
BFGS: 27 05:25:16 -303.834175 0.380550
BFGS: 28 05:25:17 -303.829016 0.422619
BFGS: 29 05:25:18 -303.827814 0.441640
BFGS: 30 05:25:18 -303.829135 0.423357
BFGS: 31 05:25:19 -303.830377 0.339706
BFGS: 32 05:25:20 -303.833190 0.362771
BFGS: 33 05:25:21 -303.838625 0.399205
BFGS: 34 05:25:22 -303.841870 0.319661
BFGS: 35 05:25:22 -303.841994 0.323184
BFGS: 36 05:25:23 -303.839729 0.259872
BFGS: 37 05:25:24 -303.839131 0.287363
BFGS: 38 05:25:25 -303.839854 0.330744
BFGS: 39 05:25:25 -303.837911 0.273784
BFGS: 40 05:25:26 -303.837087 0.223808
BFGS: 41 05:25:27 -303.833401 0.244278
BFGS: 42 05:25:28 -303.831289 0.273386
BFGS: 43 05:25:28 -303.828891 0.246083
BFGS: 44 05:25:29 -303.829533 0.257846
BFGS: 45 05:25:30 -303.832371 0.204332
BFGS: 46 05:25:31 -303.835128 0.186122
BFGS: 47 05:25:31 -303.836908 0.222618
BFGS: 48 05:25:32 -303.838098 0.278229
BFGS: 49 05:25:33 -303.839776 0.265162
BFGS: 50 05:25:34 -303.841138 0.253592
BFGS: 51 05:25:34 -303.841560 0.249461
BFGS: 52 05:25:35 -303.839724 0.321557
BFGS: 53 05:25:36 -303.836969 0.465336
BFGS: 54 05:25:37 -303.833821 0.541288
BFGS: 55 05:25:37 -303.832991 0.490125
BFGS: 56 05:25:38 -303.833456 0.503968
BFGS: 57 05:25:39 -303.834321 0.504660
BFGS: 58 05:25:40 -303.835596 0.503594
BFGS: 59 05:25:41 -303.835932 0.504688
BFGS: 60 05:25:41 -303.836349 0.495207
BFGS: 61 05:25:42 -303.836334 0.487253
BFGS: 62 05:25:43 -303.835352 0.522689
BFGS: 63 05:25:44 -303.835093 0.536614
BFGS: 64 05:25:44 -303.837157 0.405306
BFGS: 65 05:25:45 -303.838788 0.406566
BFGS: 66 05:25:46 -303.838471 0.661175
BFGS: 67 05:25:47 -303.836785 1.274999
BFGS: 68 05:25:47 -303.837074 1.320519
BFGS: 69 05:25:48 -303.838367 0.491326
BFGS: 70 05:25:49 -303.836911 0.435214
BFGS: 71 05:25:50 -303.839733 0.387326
BFGS: 72 05:25:51 -303.840329 0.315416
BFGS: 73 05:25:51 -303.839274 0.333141
BFGS: 74 05:25:52 -303.837591 0.569524
BFGS: 75 05:25:53 -303.834603 1.094246
BFGS: 76 05:25:53 -303.832588 1.709109
BFGS: 77 05:25:54 -303.831634 2.215629
BFGS: 78 05:25:55 -303.831995 2.437467
BFGS: 79 05:25:56 -303.826557 2.120237
BFGS: 80 05:25:56 -303.819134 1.681298
BFGS: 81 05:25:57 -303.821912 0.887848
BFGS: 82 05:25:58 -303.837692 1.037556
BFGS: 83 05:25:59 -303.843631 0.749449
BFGS: 84 05:25:59 -303.838245 0.611096
BFGS: 85 05:26:00 -303.836799 0.316756
BFGS: 86 05:26:01 -303.839293 0.257921
BFGS: 87 05:26:01 -303.839663 0.241503
BFGS: 88 05:26:02 -303.839336 0.316551
BFGS: 89 05:26:03 -303.839654 0.335452
BFGS: 90 05:26:04 -303.839650 0.343983
BFGS: 91 05:26:05 -303.837917 0.449500
BFGS: 92 05:26:05 -303.833919 0.721946
BFGS: 93 05:26:06 -303.821818 1.309067
BFGS: 94 05:26:07 -303.807168 1.547473
BFGS: 95 05:26:07 -303.801292 1.825526
BFGS: 96 05:26:08 -303.803643 1.748557
BFGS: 97 05:26:09 -303.812269 1.473548
BFGS: 98 05:26:10 -303.831721 0.783651
BFGS: 99 05:26:10 -303.833381 0.567600
BFGS: 100 05:26:11 -303.832172 0.516161
BFGS: 101 05:26:12 -303.838619 0.463873
BFGS: 102 05:26:13 -303.839893 0.357841
BFGS: 103 05:26:14 -303.838504 0.300365
BFGS: 104 05:26:14 -303.838171 0.368631
BFGS: 105 05:26:15 -303.838425 0.460399
BFGS: 106 05:26:16 -303.838663 0.732417
BFGS: 107 05:26:17 -303.835384 1.225568
BFGS: 108 05:26:17 -303.827327 1.313624
BFGS: 109 05:26:18 -303.827376 0.772343
BFGS: 110 05:26:19 -303.838604 0.904745
BFGS: 111 05:26:20 -303.839228 0.696714
BFGS: 112 05:26:20 -303.837347 0.453100
BFGS: 113 05:26:21 -303.837487 0.328290
BFGS: 114 05:26:22 -303.837774 0.701533
BFGS: 115 05:26:23 -303.838278 0.534391
BFGS: 116 05:26:24 -303.835965 0.444797
BFGS: 117 05:26:24 -303.839869 0.312446
BFGS: 118 05:26:25 -303.840219 0.250901
BFGS: 119 05:26:26 -303.840834 0.200206
BFGS: 120 05:26:27 -303.839646 0.382494
BFGS: 121 05:26:27 -303.839832 0.365043
BFGS: 122 05:26:28 -303.838484 0.358513
BFGS: 123 05:26:29 -303.839959 0.255957
BFGS: 124 05:26:29 -303.839686 0.413686
BFGS: 125 05:26:30 -303.841079 0.168325
BFGS: 126 05:26:30 -303.841079 0.397474
BFGS: 127 05:26:31 -303.841079 1.287608
BFGS: 128 05:26:31 -303.841079 0.591939
BFGS: 129 05:26:32 -303.841079 0.694324
BFGS: 130 05:26:32 -303.841079 0.867190
BFGS: 131 05:26:33 -303.841079 0.846576
BFGS: 132 05:26:33 -303.841079 0.397387
BFGS: 133 05:26:34 -303.841079 0.580966
BFGS: 134 05:26:35 -303.841079 0.777627
BFGS: 135 05:26:35 -303.841079 0.819441
BFGS: 136 05:26:36 -303.841079 0.860075
BFGS: 137 05:26:36 -303.841079 0.792770
BFGS: 138 05:26:37 -303.841079 0.588368
BFGS: 139 05:26:38 -303.841079 0.430518
BFGS: 140 05:26:38 -303.841079 0.313064
BFGS: 141 05:26:39 -303.841079 0.331198
BFGS: 142 05:26:40 -303.841079 0.469762
BFGS: 143 05:26:40 -303.841079 0.987010
BFGS: 144 05:26:41 -303.841079 0.656986
BFGS: 145 05:26:41 -303.841079 0.590480
BFGS: 146 05:26:42 -303.841079 0.565271
BFGS: 147 05:26:43 -303.841079 0.543783
BFGS: 148 05:26:43 -303.841079 0.496308
BFGS: 149 05:26:44 -303.841079 0.435287
BFGS: 150 05:26:45 -303.841079 0.410687
BFGS: 151 05:26:45 -303.841079 0.389793
BFGS: 152 05:26:46 -303.841079 0.362254
BFGS: 153 05:26:47 -303.841079 0.272926
BFGS: 154 05:26:47 -303.841079 0.165624
BFGS: 155 05:26:48 -303.841079 0.116734
BFGS: 156 05:26:48 -303.841079 0.086337
BFGS: 157 05:26:49 -303.841079 0.102202
BFGS: 158 05:26:50 -303.841079 0.085403
BFGS: 159 05:26:50 -303.841079 0.062077
BFGS: 160 05:26:51 -303.841079 0.115833
BFGS: 161 05:26:51 -303.841079 0.280459
BFGS: 162 05:26:51 -303.841079 0.432214
BFGS: 163 05:26:52 -303.841079 0.294573
BFGS: 164 05:26:52 -303.841079 0.213109
BFGS: 165 05:26:52 -303.841079 0.543564
BFGS: 166 05:26:53 -303.841079 0.895596
BFGS: 167 05:26:53 -303.841079 0.836697
BFGS: 168 05:26:54 -303.841079 0.447997
BFGS: 169 05:26:54 -303.841079 0.289811
BFGS: 170 05:26:54 -303.841079 0.398646
BFGS: 171 05:26:55 -303.841079 0.629300
BFGS: 172 05:26:55 -303.841079 0.523958
BFGS: 173 05:26:55 -303.841079 0.278067
BFGS: 174 05:26:56 -303.841079 0.130883
BFGS: 175 05:26:56 -303.841079 0.343743
BFGS: 176 05:26:56 -303.841079 0.799529
BFGS: 177 05:26:57 -303.841079 0.367549
BFGS: 178 05:26:57 -303.841079 0.376630
BFGS: 179 05:26:57 -303.841079 0.484809
BFGS: 180 05:26:58 -303.841079 0.480804
BFGS: 181 05:26:58 -303.841079 0.436061
BFGS: 182 05:26:58 -303.841079 0.396822
BFGS: 183 05:26:59 -303.841079 0.325970
BFGS: 184 05:26:59 -303.841079 0.269478
BFGS: 185 05:27:00 -303.841079 0.154601
BFGS: 186 05:27:00 -303.841079 0.118555
BFGS: 187 05:27:00 -303.841079 0.106522
BFGS: 188 05:27:01 -303.841079 0.161052
BFGS: 189 05:27:01 -303.841079 0.252046
BFGS: 190 05:27:01 -303.841079 0.364068
BFGS: 191 05:27:02 -303.841079 0.843217
BFGS: 192 05:27:02 -303.841079 0.501391
BFGS: 193 05:27:02 -303.841079 0.463129
BFGS: 194 05:27:03 -303.841079 0.198916
BFGS: 195 05:27:03 -303.841079 0.160997
BFGS: 196 05:27:03 -303.841079 0.426089
BFGS: 197 05:27:04 -303.841079 0.670730
BFGS: 198 05:27:04 -303.841079 0.735836
BFGS: 199 05:27:04 -303.841079 0.679399
BFGS: 200 05:27:05 -303.841079 0.623201
BFGS: 201 05:27:05 -303.841079 0.344591
BFGS: 202 05:27:06 -303.841079 0.259952
BFGS: 203 05:27:06 -303.841079 0.328284
BFGS: 204 05:27:06 -303.841079 0.355848
BFGS: 205 05:27:07 -303.841079 0.246057
BFGS: 206 05:27:07 -303.841079 0.378428
BFGS: 207 05:27:07 -303.841079 0.739580
BFGS: 208 05:27:08 -303.841079 0.419962
BFGS: 209 05:27:08 -303.841079 0.366884
BFGS: 210 05:27:08 -303.841079 0.443304
BFGS: 211 05:27:09 -303.841079 0.328910
BFGS: 212 05:27:09 -303.841079 0.294035
BFGS: 213 05:27:09 -303.841079 0.420781
BFGS: 214 05:27:10 -303.841079 0.518458
BFGS: 215 05:27:10 -303.841079 0.642243
BFGS: 216 05:27:11 -303.841079 0.772574
BFGS: 217 05:27:11 -303.841079 0.298912
BFGS: 218 05:27:11 -303.841079 0.312422
BFGS: 219 05:27:12 -303.841079 0.201878
BFGS: 220 05:27:12 -303.841079 0.149585
BFGS: 221 05:27:12 -303.841079 0.496477
BFGS: 222 05:27:13 -303.841079 0.904166
BFGS: 223 05:27:13 -303.841079 0.830329
BFGS: 224 05:27:13 -303.841079 0.543921
BFGS: 225 05:27:14 -303.841079 0.871223
BFGS: 226 05:27:14 -303.841079 0.847809
BFGS: 227 05:27:14 -303.841079 0.710270
BFGS: 228 05:27:15 -303.841079 0.518183
BFGS: 229 05:27:15 -303.841079 0.682047
BFGS: 230 05:27:15 -303.841079 0.621118
BFGS: 231 05:27:16 -303.841079 0.615204
BFGS: 232 05:27:16 -303.841079 0.274871
BFGS: 233 05:27:17 -303.841079 0.151009
BFGS: 234 05:27:17 -303.841079 0.147794
BFGS: 235 05:27:17 -303.841079 0.125787
BFGS: 236 05:27:18 -303.841079 0.407620
BFGS: 237 05:27:18 -303.841079 1.133162
BFGS: 238 05:27:18 -303.841079 0.376411
BFGS: 239 05:27:19 -303.841079 0.410398
BFGS: 240 05:27:19 -303.841079 0.481295
BFGS: 241 05:27:19 -303.841079 0.592263
BFGS: 242 05:27:20 -303.841079 1.051508
BFGS: 243 05:27:20 -303.841079 1.231732
BFGS: 244 05:27:20 -303.841079 0.450850
BFGS: 245 05:27:21 -303.841079 0.303487
BFGS: 246 05:27:21 -303.841079 0.423260
BFGS: 247 05:27:22 -303.841079 0.335768
BFGS: 248 05:27:22 -303.841079 0.221885
BFGS: 249 05:27:22 -303.841079 0.182526
BFGS: 250 05:27:23 -303.841079 0.435979
BFGS: 251 05:27:23 -303.841079 0.574645
BFGS: 252 05:27:23 -303.841079 0.616807
BFGS: 253 05:27:24 -303.841079 0.490104
BFGS: 254 05:27:24 -303.841079 0.278458
BFGS: 255 05:27:24 -303.841079 0.234373
BFGS: 256 05:27:25 -303.841079 0.227007
BFGS: 257 05:27:25 -303.841079 0.222099
BFGS: 258 05:27:25 -303.841079 0.226970
BFGS: 259 05:27:26 -303.841079 0.242556
BFGS: 260 05:27:26 -303.841079 0.243596
BFGS: 261 05:27:27 -303.841079 0.207043
BFGS: 262 05:27:27 -303.841079 0.168744
BFGS: 263 05:27:27 -303.841079 0.168149
BFGS: 264 05:27:28 -303.841079 0.187756
BFGS: 265 05:27:28 -303.841079 0.202420
BFGS: 266 05:27:28 -303.841079 0.234042
BFGS: 267 05:27:29 -303.841079 0.239968
BFGS: 268 05:27:29 -303.841079 0.216764
BFGS: 269 05:27:29 -303.841079 0.182581
BFGS: 270 05:27:30 -303.841079 0.144433
BFGS: 271 05:27:30 -303.841079 0.144816
BFGS: 272 05:27:30 -303.841079 0.157831
BFGS: 273 05:27:31 -303.841079 0.151803
BFGS: 274 05:27:31 -303.841079 0.335863
BFGS: 275 05:27:32 -303.841079 1.001561
BFGS: 276 05:27:32 -303.841079 0.516937
BFGS: 277 05:27:32 -303.841079 0.579794
BFGS: 278 05:27:33 -303.841079 1.362372
BFGS: 279 05:27:33 -303.841079 1.191670
BFGS: 280 05:27:33 -303.841079 0.453954
BFGS: 281 05:27:34 -303.841079 0.374202
BFGS: 282 05:27:34 -303.841079 0.449474
BFGS: 283 05:27:35 -303.841079 0.410964
BFGS: 284 05:27:35 -303.841079 0.335508
BFGS: 285 05:27:35 -303.841079 0.321364
BFGS: 286 05:27:36 -303.841079 0.307191
BFGS: 287 05:27:36 -303.841079 0.277047
BFGS: 288 05:27:36 -303.841079 0.207242
BFGS: 289 05:27:37 -303.841079 0.224215
BFGS: 290 05:27:37 -303.841079 0.250942
BFGS: 291 05:27:37 -303.841079 0.271785
BFGS: 292 05:27:38 -303.841079 0.275229
BFGS: 293 05:27:38 -303.841079 0.257589
BFGS: 294 05:27:38 -303.841079 0.217792
BFGS: 295 05:27:39 -303.841079 0.198048
BFGS: 296 05:27:39 -303.841079 0.219520
BFGS: 297 05:27:40 -303.841079 0.891554
BFGS: 298 05:27:40 -303.841079 0.428251
BFGS: 299 05:27:40 -303.841079 0.686256
BFGS: 300 05:27:41 -303.841079 0.517813
BFGS: 301 05:27:41 -303.841079 0.348671
BFGS: 302 05:27:41 -303.841079 0.412590
BFGS: 303 05:27:42 -303.841079 0.293865
BFGS: 304 05:27:42 -303.841079 0.194121
BFGS: 305 05:27:42 -303.841079 0.224250
BFGS: 306 05:27:43 -303.841079 0.246096
BFGS: 307 05:27:43 -303.841079 0.223529
BFGS: 308 05:27:43 -303.841079 0.452556
BFGS: 309 05:27:44 -303.841079 0.368725
BFGS: 310 05:27:44 -303.841079 0.190534
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_7872/3247994494.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")