Tutorial Overview
| Property | Value |
|---|---|
| Difficulty | Advanced |
| Time | 30-45 minutes |
| Prerequisites | Understanding of NEB, ASE, catalysis |
| Goal | Find transition states using CatTsunami tools |
FAIR chemistry models can be used to enumerate and study reaction pathways via transition state search tools built into ASE or in packages like Sella via the ASE interface.
Since the NEB calculations here can be a bit time consuming, we’ll use a small number of steps during the documentation testing, and otherwise use a reasonable guess.
import os
# Use a small number of steps here to keep the docs fast during CI, but otherwise do quite reasonable settings.
fast_docs = os.environ.get("FAST_DOCS", "false").lower() == "true"
if fast_docs:
optimization_steps = 20
else:
optimization_steps = 300Need to install fairchem-core or get UMA access or getting permissions/401 errors?
Install the necessary packages using pip, uv etc
! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunamiGet access to any necessary huggingface gated models
Get and login to your Huggingface account
Request access to https://
huggingface .co /facebook /UMA Create a Huggingface token at https://
huggingface .co /settings /tokens/ with the permission “Permissions: Read access to contents of all public gated repos you can access” Add the token as an environment variable using
huggingface-cli loginor by setting the HF_TOKEN environment variable.
# Login using the huggingface-cli utility
! huggingface-cli login
# alternatively,
import os
os.environ['HF_TOKEN'] = 'MY_TOKEN'Do enumerations in an AdsorbML style¶
from __future__ import annotations
import matplotlib.pyplot as plt
from ase.io import read
from ase.mep import DyNEB
from ase.optimize import BFGS
from fairchem.applications.cattsunami.core import Reaction
from fairchem.applications.cattsunami.core.autoframe import AutoFrameDissociation
from fairchem.applications.cattsunami.databases import DISSOCIATION_REACTION_DB_PATH
from fairchem.core import FAIRChemCalculator, pretrained_mlip
from fairchem.data.oc.core import Adsorbate, AdsorbateSlabConfig, Bulk, Slab
from fairchem.data.oc.databases.pkls import ADSORBATE_PKL_PATH, BULK_PKL_PATH
from x3dase.x3d import X3D
# Instantiate the reaction class for the reaction of interest
reaction = Reaction(
reaction_str_from_db="*CH -> *C + *H",
reaction_db_path=DISSOCIATION_REACTION_DB_PATH,
adsorbate_db_path=ADSORBATE_PKL_PATH,
)/home/runner/work/_tool/Python/3.12.13/x64/lib/python3.12/site-packages/fairchem/applications/cattsunami/core/reaction.py:29: UserWarning: Loading data from a pickle file. Pickle files can execute arbitrary code and should only be loaded from trusted sources. Consider migrating to a safer format such as Parquet, CSV, or JSON.
reaction_db = safe_pickle_load(reaction_db_path)
/home/runner/work/_tool/Python/3.12.13/x64/lib/python3.12/site-packages/fairchem/applications/cattsunami/core/reaction.py:30: UserWarning: Loading data from a pickle file. Pickle files can execute arbitrary code and should only be loaded from trusted sources. Consider migrating to a safer format such as Parquet, CSV, or JSON.
adsorbate_db = safe_pickle_load(adsorbate_db_path)
# Instantiate our adsorbate class for the reactant and product
reactant = Adsorbate(
adsorbate_id_from_db=reaction.reactant1_idx, adsorbate_db_path=ADSORBATE_PKL_PATH
)
product1 = Adsorbate(
adsorbate_id_from_db=reaction.product1_idx, adsorbate_db_path=ADSORBATE_PKL_PATH
)
product2 = Adsorbate(
adsorbate_id_from_db=reaction.product2_idx, adsorbate_db_path=ADSORBATE_PKL_PATH
)/home/runner/work/_tool/Python/3.12.13/x64/lib/python3.12/site-packages/fairchem/data/oc/core/adsorbate.py:79: UserWarning: Loading data from a pickle file. Pickle files can execute arbitrary code and should only be loaded from trusted sources. Consider migrating to a safer format such as Parquet, CSV, or JSON.
adsorbate_db = safe_pickle_load(fp)
# Grab the bulk and cut the slab we are interested in
bulk = Bulk(bulk_src_id_from_db="mp-33", bulk_db_path=BULK_PKL_PATH)
slab = Slab.from_bulk_get_specific_millers(bulk=bulk, specific_millers=(0, 0, 1))/home/runner/work/_tool/Python/3.12.13/x64/lib/python3.12/site-packages/fairchem/data/oc/core/bulk.py:66: UserWarning: Loading data from a pickle file. Pickle files can execute arbitrary code and should only be loaded from trusted sources. Consider migrating to a safer format such as Parquet, CSV, or JSON.
bulk_db = safe_pickle_load(fp)
# Perform site enumeration
# For AdsorbML num_sites = 100, but we use 5 here for brevity. This should be increased for practical use.
reactant_configs = AdsorbateSlabConfig(
slab=slab[0],
adsorbate=reactant,
mode="random_site_heuristic_placement",
num_sites=10,
).atoms_list
product1_configs = AdsorbateSlabConfig(
slab=slab[0],
adsorbate=product1,
mode="random_site_heuristic_placement",
num_sites=10,
).atoms_list
product2_configs = AdsorbateSlabConfig(
slab=slab[0],
adsorbate=product2,
mode="random_site_heuristic_placement",
num_sites=10,
).atoms_list# Instantiate the calculator
predictor = pretrained_mlip.get_predict_unit("uma-s-1p2")
calc = FAIRChemCalculator(predictor, task_name="oc20")WARNING:root:device was not explicitly set, using device='cuda'.
# Relax the reactant systems
reactant_energies = []
for config in reactant_configs:
config.calc = calc
config.pbc = True
opt = BFGS(config)
opt.run(fmax=0.05, steps=optimization_steps)
reactant_energies.append(config.get_potential_energy()) Step Time Energy fmax
BFGS: 0 13:59:01 -302.377159 4.033550
BFGS: 1 13:59:01 -302.756927 2.864879
BFGS: 2 13:59:02 -303.571709 3.179405
BFGS: 3 13:59:02 -303.718813 2.643171
BFGS: 4 13:59:03 -303.866537 4.060524
BFGS: 5 13:59:03 -303.979866 1.089437
BFGS: 6 13:59:04 -304.017050 0.657097
BFGS: 7 13:59:04 -304.117465 1.465145
BFGS: 8 13:59:04 -304.196723 1.268684
BFGS: 9 13:59:05 -304.263028 0.887219
BFGS: 10 13:59:05 -304.327376 0.828753
BFGS: 11 13:59:06 -304.406162 1.487010
BFGS: 12 13:59:06 -304.461403 1.586093
BFGS: 13 13:59:07 -304.516674 0.976915
BFGS: 14 13:59:07 -304.542116 0.595823
BFGS: 15 13:59:08 -304.562422 0.671416
BFGS: 16 13:59:08 -304.583519 0.453953
BFGS: 17 13:59:09 -304.595983 0.476704
BFGS: 18 13:59:09 -304.603303 0.308666
BFGS: 19 13:59:10 -304.614500 0.381227
BFGS: 20 13:59:10 -304.624236 0.424500
BFGS: 21 13:59:11 -304.641605 0.531150
BFGS: 22 13:59:11 -304.654330 0.363756
BFGS: 23 13:59:12 -304.661525 0.185212
BFGS: 24 13:59:12 -304.665937 0.195353
BFGS: 25 13:59:12 -304.670987 0.282192
BFGS: 26 13:59:13 -304.675729 0.232773
BFGS: 27 13:59:13 -304.678290 0.127289
BFGS: 28 13:59:13 -304.679406 0.094754
BFGS: 29 13:59:13 -304.680132 0.079986
BFGS: 30 13:59:14 -304.680681 0.079977
BFGS: 31 13:59:14 -304.681140 0.058162
BFGS: 32 13:59:15 -304.681417 0.041743
Step Time Energy fmax
BFGS: 0 13:59:15 -301.234961 4.153289
BFGS: 1 13:59:15 -301.624001 3.505340
BFGS: 2 13:59:16 -302.624814 3.196998
BFGS: 3 13:59:16 -302.698811 3.744120
BFGS: 4 13:59:16 -302.934623 2.335901
BFGS: 5 13:59:17 -303.089741 1.935133
BFGS: 6 13:59:17 -303.138828 1.409362
BFGS: 7 13:59:17 -303.367464 1.873934
BFGS: 8 13:59:18 -303.481249 2.174307
BFGS: 9 13:59:18 -303.650812 1.754901
BFGS: 10 13:59:19 -303.787293 1.695290
BFGS: 11 13:59:19 -303.956344 1.391820
BFGS: 12 13:59:20 -303.988760 1.014979
BFGS: 13 13:59:20 -304.021863 0.666821
BFGS: 14 13:59:21 -304.059997 1.021572
BFGS: 15 13:59:21 -304.091329 0.934143
BFGS: 16 13:59:22 -304.130336 0.626260
BFGS: 17 13:59:22 -304.144017 0.378411
BFGS: 18 13:59:22 -304.153976 0.258484
BFGS: 19 13:59:23 -304.161946 0.355943
BFGS: 20 13:59:23 -304.175041 0.466732
BFGS: 21 13:59:24 -304.191950 0.436940
BFGS: 22 13:59:24 -304.208632 0.389680
BFGS: 23 13:59:24 -304.226619 0.595761
BFGS: 24 13:59:25 -304.260507 1.152890
BFGS: 25 13:59:25 -304.263469 1.572360
BFGS: 26 13:59:25 -304.317610 1.087632
BFGS: 27 13:59:26 -304.362857 0.908574
BFGS: 28 13:59:26 -304.459694 0.533623
BFGS: 29 13:59:27 -304.476613 0.488870
BFGS: 30 13:59:27 -304.503000 0.509797
BFGS: 31 13:59:28 -304.567943 0.676123
BFGS: 32 13:59:28 -304.595340 0.531812
BFGS: 33 13:59:29 -304.613421 0.380507
BFGS: 34 13:59:29 -304.626551 0.323684
BFGS: 35 13:59:30 -304.640717 0.374729
BFGS: 36 13:59:30 -304.655861 0.415353
BFGS: 37 13:59:31 -304.666042 0.279133
BFGS: 38 13:59:31 -304.670280 0.137630
BFGS: 39 13:59:31 -304.672406 0.131263
BFGS: 40 13:59:32 -304.674706 0.125674
BFGS: 41 13:59:32 -304.677472 0.107429
BFGS: 42 13:59:32 -304.679683 0.079859
BFGS: 43 13:59:33 -304.680708 0.051170
BFGS: 44 13:59:33 -304.681070 0.040008
Step Time Energy fmax
BFGS: 0 13:59:34 -301.108356 4.022362
BFGS: 1 13:59:34 -301.510561 3.145961
BFGS: 2 13:59:34 -302.635560 3.572207
BFGS: 3 13:59:35 -302.726497 4.637135
BFGS: 4 13:59:35 -303.024540 2.250006
BFGS: 5 13:59:35 -303.095459 2.479889
BFGS: 6 13:59:36 -303.144164 0.530808
BFGS: 7 13:59:36 -303.157385 0.487606
BFGS: 8 13:59:37 -303.244938 0.618485
BFGS: 9 13:59:37 -303.261471 0.500246
BFGS: 10 13:59:38 -303.290167 0.528977
BFGS: 11 13:59:38 -303.334630 0.981805
BFGS: 12 13:59:39 -303.395017 1.509315
BFGS: 13 13:59:39 -303.474272 1.849652
BFGS: 14 13:59:39 -303.587659 1.945861
BFGS: 15 13:59:40 -303.699833 1.487412
BFGS: 16 13:59:40 -303.834216 1.874408
BFGS: 17 13:59:41 -304.025872 1.360255
BFGS: 18 13:59:41 -304.088343 0.855784
BFGS: 19 13:59:42 -304.131032 0.764442
BFGS: 20 13:59:42 -304.158706 0.499805
BFGS: 21 13:59:43 -304.178575 1.085581
BFGS: 22 13:59:43 -304.197391 0.742782
BFGS: 23 13:59:43 -304.219788 0.493589
BFGS: 24 13:59:44 -304.231102 0.535119
BFGS: 25 13:59:44 -304.252862 0.451928
BFGS: 26 13:59:44 -304.265419 0.424073
BFGS: 27 13:59:45 -304.282083 0.495992
BFGS: 28 13:59:45 -304.299140 0.493698
BFGS: 29 13:59:46 -304.314062 0.440256
BFGS: 30 13:59:46 -304.322737 0.258065
BFGS: 31 13:59:47 -304.327532 0.240623
BFGS: 32 13:59:47 -304.333346 0.307671
BFGS: 33 13:59:47 -304.339723 0.279573
BFGS: 34 13:59:48 -304.343042 0.174950
BFGS: 35 13:59:48 -304.345153 0.109347
BFGS: 36 13:59:49 -304.347405 0.130556
BFGS: 37 13:59:49 -304.349312 0.145748
BFGS: 38 13:59:50 -304.350427 0.097600
BFGS: 39 13:59:50 -304.350863 0.050839
BFGS: 40 13:59:50 -304.351097 0.043547
Step Time Energy fmax
BFGS: 0 13:59:51 -302.200580 4.144550
BFGS: 1 13:59:51 -302.576236 3.164374
BFGS: 2 13:59:52 -303.462064 3.197712
BFGS: 3 13:59:52 -303.648696 2.987702
BFGS: 4 13:59:53 -303.951418 2.162474
BFGS: 5 13:59:53 -304.152493 2.796384
BFGS: 6 13:59:53 -304.266789 1.729081
BFGS: 7 13:59:54 -304.471648 0.954381
BFGS: 8 13:59:54 -304.510875 0.884396
BFGS: 9 13:59:54 -304.572038 0.681734
BFGS: 10 13:59:55 -304.632830 0.578828
BFGS: 11 13:59:55 -304.652150 0.391184
BFGS: 12 13:59:56 -304.658356 0.172744
BFGS: 13 13:59:56 -304.661374 0.166694
BFGS: 14 13:59:56 -304.665605 0.220109
BFGS: 15 13:59:57 -304.668839 0.185174
BFGS: 16 13:59:57 -304.670489 0.104752
BFGS: 17 13:59:58 -304.671398 0.098702
BFGS: 18 13:59:58 -304.672578 0.106845
BFGS: 19 13:59:58 -304.674412 0.161124
BFGS: 20 13:59:59 -304.676676 0.149115
BFGS: 21 13:59:59 -304.678312 0.104217
BFGS: 22 14:00:00 -304.679122 0.102470
BFGS: 23 14:00:00 -304.679691 0.105964
BFGS: 24 14:00:01 -304.680301 0.090557
BFGS: 25 14:00:01 -304.680822 0.076416
BFGS: 26 14:00:02 -304.681116 0.048391
Step Time Energy fmax
BFGS: 0 14:00:02 -300.588009 4.050703
BFGS: 1 14:00:03 -301.083041 4.150738
BFGS: 2 14:00:03 -302.522304 3.690680
BFGS: 3 14:00:03 -302.285862 9.131151
BFGS: 4 14:00:04 -302.776051 3.353359
BFGS: 5 14:00:04 -302.923028 2.759339
BFGS: 6 14:00:05 -303.061731 3.019167
BFGS: 7 14:00:05 -303.128026 0.769904
BFGS: 8 14:00:05 -303.137520 0.388967
BFGS: 9 14:00:06 -303.144248 0.264123
BFGS: 10 14:00:06 -303.150978 0.323637
BFGS: 11 14:00:07 -303.159862 0.355393
BFGS: 12 14:00:07 -303.163250 0.246330
BFGS: 13 14:00:07 -303.164558 0.156896
BFGS: 14 14:00:08 -303.166738 0.155445
BFGS: 15 14:00:08 -303.169877 0.260355
BFGS: 16 14:00:08 -303.173634 0.284772
BFGS: 17 14:00:09 -303.176196 0.187246
BFGS: 18 14:00:09 -303.177172 0.074904
BFGS: 19 14:00:10 -303.177557 0.068956
BFGS: 20 14:00:10 -303.178091 0.093443
BFGS: 21 14:00:11 -303.178754 0.105433
BFGS: 22 14:00:11 -303.179186 0.066835
BFGS: 23 14:00:11 -303.179306 0.029773
Step Time Energy fmax
BFGS: 0 14:00:12 -302.360786 3.903381
BFGS: 1 14:00:12 -302.722037 2.872397
BFGS: 2 14:00:13 -303.585064 3.207592
BFGS: 3 14:00:13 -303.751812 2.815319
BFGS: 4 14:00:13 -304.044700 1.947191
BFGS: 5 14:00:14 -304.112414 1.058097
BFGS: 6 14:00:14 -304.205415 0.718187
BFGS: 7 14:00:14 -304.269683 0.899059
BFGS: 8 14:00:15 -304.291458 0.609925
BFGS: 9 14:00:15 -304.317292 0.551835
BFGS: 10 14:00:16 -304.330874 0.367982
BFGS: 11 14:00:16 -304.340807 0.232465
BFGS: 12 14:00:17 -304.342692 0.135063
BFGS: 13 14:00:17 -304.343590 0.117166
BFGS: 14 14:00:18 -304.345299 0.157834
BFGS: 15 14:00:18 -304.346579 0.154457
BFGS: 16 14:00:18 -304.347436 0.098981
BFGS: 17 14:00:19 -304.347982 0.075627
BFGS: 18 14:00:19 -304.348796 0.114476
BFGS: 19 14:00:20 -304.350110 0.167116
BFGS: 20 14:00:20 -304.351488 0.147643
BFGS: 21 14:00:21 -304.352134 0.069440
BFGS: 22 14:00:21 -304.352347 0.047761
Step Time Energy fmax
BFGS: 0 14:00:22 -302.292288 3.984271
BFGS: 1 14:00:22 -302.660593 2.971129
BFGS: 2 14:00:22 -303.500531 3.179662
BFGS: 3 14:00:23 -303.647265 2.742486
BFGS: 4 14:00:23 -303.859979 3.361878
BFGS: 5 14:00:23 -303.950635 1.061091
BFGS: 6 14:00:24 -303.992644 0.834751
BFGS: 7 14:00:24 -304.102170 0.719269
BFGS: 8 14:00:25 -304.120576 0.629102
BFGS: 9 14:00:25 -304.177457 0.519537
BFGS: 10 14:00:26 -304.190033 0.331666
BFGS: 11 14:00:26 -304.198446 0.419965
BFGS: 12 14:00:27 -304.207676 0.445189
BFGS: 13 14:00:27 -304.223753 0.424979
BFGS: 14 14:00:27 -304.236368 0.403348
BFGS: 15 14:00:28 -304.249242 0.427993
BFGS: 16 14:00:28 -304.262928 0.349187
BFGS: 17 14:00:29 -304.276674 0.456061
BFGS: 18 14:00:29 -304.291273 0.416679
BFGS: 19 14:00:30 -304.303464 0.281788
BFGS: 20 14:00:30 -304.309774 0.284131
BFGS: 21 14:00:31 -304.313775 0.280472
BFGS: 22 14:00:31 -304.319575 0.303991
BFGS: 23 14:00:32 -304.326307 0.313341
BFGS: 24 14:00:32 -304.333093 0.190153
BFGS: 25 14:00:32 -304.338126 0.185204
BFGS: 26 14:00:33 -304.341006 0.229661
BFGS: 27 14:00:33 -304.345065 0.238818
BFGS: 28 14:00:34 -304.348194 0.169967
BFGS: 29 14:00:34 -304.350004 0.082388
BFGS: 30 14:00:35 -304.350668 0.066018
BFGS: 31 14:00:35 -304.351195 0.067113
BFGS: 32 14:00:36 -304.351826 0.064528
BFGS: 33 14:00:36 -304.352194 0.038174
Step Time Energy fmax
BFGS: 0 14:00:36 -301.079174 3.919259
BFGS: 1 14:00:37 -301.478515 3.318498
BFGS: 2 14:00:37 -302.668653 3.360050
BFGS: 3 14:00:37 -302.506526 7.960793
BFGS: 4 14:00:38 -302.973479 2.676533
BFGS: 5 14:00:38 -303.100592 1.701849
BFGS: 6 14:00:39 -303.176555 1.609111
BFGS: 7 14:00:39 -303.198044 0.724344
BFGS: 8 14:00:40 -303.227973 0.886123
BFGS: 9 14:00:40 -303.296452 1.508415
BFGS: 10 14:00:40 -303.393172 2.467433
BFGS: 11 14:00:41 -303.504547 2.695596
BFGS: 12 14:00:41 -303.661257 2.177674
BFGS: 13 14:00:41 -303.957034 1.125878
BFGS: 14 14:00:42 -304.034271 1.853438
BFGS: 15 14:00:42 -304.093156 0.998005
BFGS: 16 14:00:42 -304.130123 0.302797
BFGS: 17 14:00:43 -304.136651 0.291018
BFGS: 18 14:00:43 -304.146485 0.374249
BFGS: 19 14:00:43 -304.155926 0.394974
BFGS: 20 14:00:44 -304.163497 0.309337
BFGS: 21 14:00:44 -304.168413 0.334774
BFGS: 22 14:00:44 -304.173433 0.385771
BFGS: 23 14:00:45 -304.181002 0.342163
BFGS: 24 14:00:45 -304.191010 0.303602
BFGS: 25 14:00:45 -304.203701 0.531919
BFGS: 26 14:00:46 -304.223203 0.913376
BFGS: 27 14:00:46 -304.260628 1.395023
BFGS: 28 14:00:47 -304.290777 1.618025
BFGS: 29 14:00:47 -304.347283 1.158592
BFGS: 30 14:00:48 -304.460705 0.918565
BFGS: 31 14:00:48 -304.509281 1.086128
BFGS: 32 14:00:48 -304.483449 1.243168
BFGS: 33 14:00:49 -304.561382 0.475376
BFGS: 34 14:00:49 -304.578682 0.339565
BFGS: 35 14:00:50 -304.607839 0.423313
BFGS: 36 14:00:50 -304.616364 0.402539
BFGS: 37 14:00:51 -304.634170 0.265353
BFGS: 38 14:00:51 -304.640836 0.266989
BFGS: 39 14:00:51 -304.646225 0.271589
BFGS: 40 14:00:52 -304.652420 0.314947
BFGS: 41 14:00:52 -304.660461 0.281462
BFGS: 42 14:00:53 -304.667277 0.179920
BFGS: 43 14:00:53 -304.670665 0.126650
BFGS: 44 14:00:53 -304.672361 0.111615
BFGS: 45 14:00:54 -304.673817 0.119186
BFGS: 46 14:00:54 -304.675860 0.152832
BFGS: 47 14:00:54 -304.677969 0.124188
BFGS: 48 14:00:55 -304.679111 0.059609
BFGS: 49 14:00:55 -304.679575 0.060234
BFGS: 50 14:00:56 -304.679968 0.056796
BFGS: 51 14:00:56 -304.680463 0.072581
BFGS: 52 14:00:56 -304.681033 0.062673
BFGS: 53 14:00:57 -304.681415 0.033173
Step Time Energy fmax
BFGS: 0 14:00:57 -300.717714 4.092144
BFGS: 1 14:00:58 -301.181782 3.813433
BFGS: 2 14:00:58 -302.530721 3.673945
BFGS: 3 14:00:59 -302.470485 7.436620
BFGS: 4 14:00:59 -302.873743 2.943570
BFGS: 5 14:00:59 -303.068371 1.257836
BFGS: 6 14:01:00 -303.113483 1.357823
BFGS: 7 14:01:00 -303.128182 0.573424
BFGS: 8 14:01:01 -303.137440 0.485481
BFGS: 9 14:01:01 -303.147971 0.639179
BFGS: 10 14:01:02 -303.160331 0.510614
BFGS: 11 14:01:02 -303.165047 0.263421
BFGS: 12 14:01:02 -303.166807 0.152858
BFGS: 13 14:01:03 -303.168427 0.322994
BFGS: 14 14:01:03 -303.171973 0.532489
BFGS: 15 14:01:04 -303.176211 0.561481
BFGS: 16 14:01:04 -303.179495 0.346406
BFGS: 17 14:01:04 -303.180880 0.099126
BFGS: 18 14:01:05 -303.181531 0.118544
BFGS: 19 14:01:05 -303.182342 0.180753
BFGS: 20 14:01:06 -303.183459 0.224718
BFGS: 21 14:01:06 -303.184226 0.140329
BFGS: 22 14:01:06 -303.184463 0.035222
Step Time Energy fmax
BFGS: 0 14:01:07 -300.712407 4.103009
BFGS: 1 14:01:07 -301.163324 3.638933
BFGS: 2 14:01:08 -302.478952 3.590279
BFGS: 3 14:01:08 -302.298798 8.747290
BFGS: 4 14:01:08 -302.793543 3.023935
BFGS: 5 14:01:09 -302.968633 2.016601
BFGS: 6 14:01:09 -303.073345 2.233528
BFGS: 7 14:01:10 -303.109579 0.698955
BFGS: 8 14:01:10 -303.122465 0.524464
BFGS: 9 14:01:10 -303.152330 0.731103
BFGS: 10 14:01:11 -303.164452 0.513853
BFGS: 11 14:01:11 -303.169458 0.179557
BFGS: 12 14:01:12 -303.170539 0.135732
BFGS: 13 14:01:12 -303.172555 0.323295
BFGS: 14 14:01:12 -303.175123 0.405649
BFGS: 15 14:01:13 -303.177346 0.303786
BFGS: 16 14:01:13 -303.178461 0.121402
BFGS: 17 14:01:13 -303.179064 0.126315
BFGS: 18 14:01:13 -303.179798 0.189026
BFGS: 19 14:01:13 -303.180927 0.210298
BFGS: 20 14:01:14 -303.181900 0.156434
BFGS: 21 14:01:14 -303.182323 0.054150
BFGS: 22 14:01:15 -303.182480 0.039208
# Relax the product systems
product1_energies = []
for config in product1_configs:
config.calc = calc
config.pbc = True
opt = BFGS(config)
opt.run(fmax=0.05, steps=optimization_steps)
product1_energies.append(config.get_potential_energy()) Step Time Energy fmax
BFGS: 0 14:01:15 -296.564720 4.377050
BFGS: 1 14:01:16 -297.023780 4.590570
BFGS: 2 14:01:16 -298.389224 3.420470
BFGS: 3 14:01:16 -298.188989 8.415218
BFGS: 4 14:01:17 -298.700958 1.957340
BFGS: 5 14:01:17 -298.787615 1.477880
BFGS: 6 14:01:18 -298.983812 2.462784
BFGS: 7 14:01:18 -299.260875 3.032857
BFGS: 8 14:01:19 -299.460499 2.479972
BFGS: 9 14:01:19 -299.568138 1.828913
BFGS: 10 14:01:20 -299.855125 1.192726
BFGS: 11 14:01:20 -299.944839 1.252651
BFGS: 12 14:01:20 -300.024870 1.329978
BFGS: 13 14:01:21 -300.108247 1.481150
BFGS: 14 14:01:21 -300.220651 1.423333
BFGS: 15 14:01:22 -300.310562 1.286746
BFGS: 16 14:01:22 -300.443110 1.191166
BFGS: 17 14:01:22 -300.479064 0.875088
BFGS: 18 14:01:23 -300.511505 0.401954
BFGS: 19 14:01:23 -300.521653 0.455752
BFGS: 20 14:01:23 -300.547434 0.399687
BFGS: 21 14:01:24 -300.560828 0.291322
BFGS: 22 14:01:24 -300.567801 0.163866
BFGS: 23 14:01:25 -300.570068 0.126775
BFGS: 24 14:01:25 -300.571679 0.114080
BFGS: 25 14:01:25 -300.573837 0.122857
BFGS: 26 14:01:26 -300.575987 0.114054
BFGS: 27 14:01:26 -300.577357 0.067258
BFGS: 28 14:01:26 -300.577834 0.038912
Step Time Energy fmax
BFGS: 0 14:01:27 -296.297053 4.375437
BFGS: 1 14:01:27 -296.786920 4.627318
BFGS: 2 14:01:28 -298.268033 3.114205
BFGS: 3 14:01:28 -297.477632 12.364161
BFGS: 4 14:01:28 -298.477672 1.849973
BFGS: 5 14:01:29 -298.543774 1.096853
BFGS: 6 14:01:29 -298.594486 1.079286
BFGS: 7 14:01:30 -298.612976 0.982389
BFGS: 8 14:01:30 -298.713225 1.426256
BFGS: 9 14:01:30 -298.757570 1.366048
BFGS: 10 14:01:31 -299.185753 1.810813
BFGS: 11 14:01:31 -299.643467 1.599888
BFGS: 12 14:01:31 -299.731712 2.556261
BFGS: 13 14:01:32 -299.803430 0.862949
BFGS: 14 14:01:32 -299.828974 0.621066
BFGS: 15 14:01:33 -299.882672 1.090988
BFGS: 16 14:01:33 -299.932239 0.994319
BFGS: 17 14:01:33 -300.019009 1.094605
BFGS: 18 14:01:34 -300.051232 1.156775
BFGS: 19 14:01:34 -300.220269 1.543712
BFGS: 20 14:01:35 -300.313531 1.296386
BFGS: 21 14:01:35 -300.289719 1.516856
BFGS: 22 14:01:35 -300.369787 1.229984
BFGS: 23 14:01:36 -300.401425 0.999755
BFGS: 24 14:01:36 -300.439100 0.858037
BFGS: 25 14:01:37 -300.537604 0.413785
BFGS: 26 14:01:37 -300.548167 0.437431
BFGS: 27 14:01:37 -300.557592 0.366890
BFGS: 28 14:01:38 -300.564377 0.239134
BFGS: 29 14:01:38 -300.570076 0.123929
BFGS: 30 14:01:39 -300.572664 0.095667
BFGS: 31 14:01:39 -300.573841 0.106282
BFGS: 32 14:01:39 -300.574977 0.105488
BFGS: 33 14:01:40 -300.576269 0.093347
BFGS: 34 14:01:40 -300.577187 0.076660
BFGS: 35 14:01:40 -300.577673 0.044145
Step Time Energy fmax
BFGS: 0 14:01:41 -297.538037 4.748966
BFGS: 1 14:01:41 -298.008593 4.833548
BFGS: 2 14:01:42 -299.213921 3.838393
BFGS: 3 14:01:42 -299.690894 2.985768
BFGS: 4 14:01:42 -299.832834 1.946833
BFGS: 5 14:01:43 -300.222724 1.452174
BFGS: 6 14:01:43 -300.315337 1.340579
BFGS: 7 14:01:44 -300.405242 1.191480
BFGS: 8 14:01:44 -300.498124 0.853191
BFGS: 9 14:01:44 -300.540806 0.446336
BFGS: 10 14:01:45 -300.553042 0.378412
BFGS: 11 14:01:45 -300.561138 0.284645
BFGS: 12 14:01:46 -300.567200 0.175101
BFGS: 13 14:01:46 -300.571239 0.102372
BFGS: 14 14:01:46 -300.573224 0.094533
BFGS: 15 14:01:46 -300.574092 0.107371
BFGS: 16 14:01:47 -300.574855 0.104842
BFGS: 17 14:01:47 -300.575959 0.087233
BFGS: 18 14:01:47 -300.576946 0.067797
BFGS: 19 14:01:48 -300.577518 0.055304
BFGS: 20 14:01:48 -300.577823 0.053185
BFGS: 21 14:01:48 -300.578062 0.047850
Step Time Energy fmax
BFGS: 0 14:01:49 -296.226817 4.393550
BFGS: 1 14:01:49 -296.731589 4.661774
BFGS: 2 14:01:49 -298.254230 3.028926
BFGS: 3 14:01:50 -297.259227 13.744837
BFGS: 4 14:01:50 -298.443805 1.821117
BFGS: 5 14:01:50 -298.506454 1.044834
BFGS: 6 14:01:51 -298.548001 0.847151
BFGS: 7 14:01:51 -298.557867 0.659920
BFGS: 8 14:01:51 -298.591096 0.562201
BFGS: 9 14:01:52 -298.598010 0.606033
BFGS: 10 14:01:52 -298.673676 1.180327
BFGS: 11 14:01:53 -298.749310 1.925980
BFGS: 12 14:01:53 -298.830608 2.542646
BFGS: 13 14:01:53 -298.911362 2.797943
BFGS: 14 14:01:54 -298.981807 3.053153
BFGS: 15 14:01:54 -299.182102 2.850680
BFGS: 16 14:01:55 -299.788071 1.586838
BFGS: 17 14:01:55 -299.793470 1.216736
BFGS: 18 14:01:55 -299.893902 0.826830
BFGS: 19 14:01:56 -299.938986 0.753697
BFGS: 20 14:01:56 -299.977330 0.614677
BFGS: 21 14:01:56 -300.018660 0.240491
BFGS: 22 14:01:57 -300.024580 0.220353
BFGS: 23 14:01:57 -300.027345 0.180846
BFGS: 24 14:01:58 -300.033084 0.158239
BFGS: 25 14:01:58 -300.035811 0.148056
BFGS: 26 14:01:59 -300.038056 0.146564
BFGS: 27 14:01:59 -300.039856 0.128967
BFGS: 28 14:01:59 -300.041528 0.083342
BFGS: 29 14:02:00 -300.042481 0.056705
BFGS: 30 14:02:00 -300.042868 0.050408
BFGS: 31 14:02:00 -300.043090 0.052222
BFGS: 32 14:02:01 -300.043361 0.049146
Step Time Energy fmax
BFGS: 0 14:02:01 -296.709276 4.369783
BFGS: 1 14:02:01 -297.162683 4.562746
BFGS: 2 14:02:02 -298.491368 3.455247
BFGS: 3 14:02:02 -298.420849 7.444706
BFGS: 4 14:02:03 -298.837738 1.955587
BFGS: 5 14:02:03 -298.932614 1.615199
BFGS: 6 14:02:03 -299.250151 2.581663
BFGS: 7 14:02:04 -299.469783 2.736687
BFGS: 8 14:02:04 -299.576376 1.743612
BFGS: 9 14:02:05 -299.721467 0.809354
BFGS: 10 14:02:05 -299.762164 0.874496
BFGS: 11 14:02:05 -299.804966 0.796226
BFGS: 12 14:02:06 -299.830910 0.585119
BFGS: 13 14:02:06 -299.846597 0.391619
BFGS: 14 14:02:07 -299.855309 0.380043
BFGS: 15 14:02:07 -299.865361 0.335269
BFGS: 16 14:02:08 -299.873162 0.241211
BFGS: 17 14:02:08 -299.875817 0.183261
BFGS: 18 14:02:09 -299.877336 0.178382
BFGS: 19 14:02:09 -299.880779 0.253564
BFGS: 20 14:02:09 -299.886259 0.423072
BFGS: 21 14:02:10 -299.893945 0.517894
BFGS: 22 14:02:10 -299.903218 0.412958
BFGS: 23 14:02:10 -299.918485 0.470385
BFGS: 24 14:02:11 -299.937418 0.535593
BFGS: 25 14:02:11 -299.959761 0.911535
BFGS: 26 14:02:12 -299.976383 0.906774
BFGS: 27 14:02:12 -300.005209 0.557145
BFGS: 28 14:02:12 -300.021915 0.284319
BFGS: 29 14:02:13 -300.028834 0.240112
BFGS: 30 14:02:13 -300.033955 0.204740
BFGS: 31 14:02:13 -300.037830 0.149725
BFGS: 32 14:02:14 -300.041146 0.089254
BFGS: 33 14:02:14 -300.042219 0.045952
Step Time Energy fmax
BFGS: 0 14:02:14 -296.785263 4.432215
BFGS: 1 14:02:15 -297.230000 4.622149
BFGS: 2 14:02:15 -298.522918 3.682288
BFGS: 3 14:02:15 -298.682056 5.950413
BFGS: 4 14:02:16 -298.961235 2.010443
BFGS: 5 14:02:16 -299.079033 1.886476
BFGS: 6 14:02:16 -299.545235 2.147128
BFGS: 7 14:02:17 -299.898762 1.781771
BFGS: 8 14:02:17 -299.982000 1.959626
BFGS: 9 14:02:18 -300.108319 1.277232
BFGS: 10 14:02:18 -300.309040 1.250538
BFGS: 11 14:02:19 -300.491321 0.918680
BFGS: 12 14:02:19 -300.512924 0.622154
BFGS: 13 14:02:20 -300.543108 0.388871
BFGS: 14 14:02:20 -300.549043 0.329308
BFGS: 15 14:02:20 -300.562207 0.298027
BFGS: 16 14:02:21 -300.568482 0.180538
BFGS: 17 14:02:21 -300.570500 0.128315
BFGS: 18 14:02:22 -300.572046 0.152875
BFGS: 19 14:02:22 -300.573476 0.178968
BFGS: 20 14:02:22 -300.575162 0.178403
BFGS: 21 14:02:23 -300.576724 0.134246
BFGS: 22 14:02:23 -300.577674 0.065433
BFGS: 23 14:02:24 -300.578032 0.028781
Step Time Energy fmax
BFGS: 0 14:02:24 -296.889527 4.335835
BFGS: 1 14:02:24 -297.331089 4.510095
BFGS: 2 14:02:25 -298.608665 3.431265
BFGS: 3 14:02:25 -298.613917 6.693679
BFGS: 4 14:02:25 -298.965721 1.901071
BFGS: 5 14:02:26 -299.059535 1.623493
BFGS: 6 14:02:26 -299.395852 2.048542
BFGS: 7 14:02:26 -299.661112 2.049873
BFGS: 8 14:02:27 -299.761846 1.234946
BFGS: 9 14:02:27 -299.858132 0.948374
BFGS: 10 14:02:28 -299.961346 0.606332
BFGS: 11 14:02:28 -299.988788 0.656257
BFGS: 12 14:02:29 -300.008551 0.557298
BFGS: 13 14:02:29 -300.019985 0.328557
BFGS: 14 14:02:29 -300.026190 0.177262
BFGS: 15 14:02:30 -300.030802 0.241143
BFGS: 16 14:02:30 -300.035902 0.267166
BFGS: 17 14:02:31 -300.039616 0.213168
BFGS: 18 14:02:31 -300.041153 0.137845
BFGS: 19 14:02:32 -300.041778 0.084843
BFGS: 20 14:02:32 -300.042270 0.091930
BFGS: 21 14:02:33 -300.042874 0.101269
BFGS: 22 14:02:33 -300.043419 0.074416
BFGS: 23 14:02:34 -300.043649 0.031951
Step Time Energy fmax
BFGS: 0 14:02:34 -297.040424 4.407629
BFGS: 1 14:02:34 -297.494352 4.557538
BFGS: 2 14:02:35 -298.738569 3.595055
BFGS: 3 14:02:35 -299.023239 4.617481
BFGS: 4 14:02:36 -299.222529 1.772696
BFGS: 5 14:02:36 -299.349781 1.693234
BFGS: 6 14:02:36 -299.694679 0.754467
BFGS: 7 14:02:36 -299.731738 1.224513
BFGS: 8 14:02:37 -299.772815 0.613248
BFGS: 9 14:02:37 -299.807123 0.615001
BFGS: 10 14:02:37 -299.838349 0.504559
BFGS: 11 14:02:38 -299.862966 0.344626
BFGS: 12 14:02:38 -299.874207 0.221804
BFGS: 13 14:02:39 -299.878715 0.248075
BFGS: 14 14:02:39 -299.882281 0.253763
BFGS: 15 14:02:39 -299.886518 0.254669
BFGS: 16 14:02:40 -299.890511 0.286635
BFGS: 17 14:02:40 -299.896454 0.345874
BFGS: 18 14:02:41 -299.905458 0.396648
BFGS: 19 14:02:41 -299.919813 0.411499
BFGS: 20 14:02:41 -299.941674 0.421416
BFGS: 21 14:02:42 -299.969762 0.393572
BFGS: 22 14:02:42 -299.988617 0.627642
BFGS: 23 14:02:42 -300.002530 0.608798
BFGS: 24 14:02:43 -300.020436 0.321734
BFGS: 25 14:02:43 -300.029789 0.215588
BFGS: 26 14:02:43 -300.034793 0.183885
BFGS: 27 14:02:44 -300.037711 0.182570
BFGS: 28 14:02:44 -300.040201 0.159319
BFGS: 29 14:02:44 -300.042191 0.097085
BFGS: 30 14:02:44 -300.043073 0.044717
Step Time Energy fmax
BFGS: 0 14:02:45 -296.559782 4.375878
BFGS: 1 14:02:45 -297.019000 4.590173
BFGS: 2 14:02:46 -298.385919 3.415229
BFGS: 3 14:02:46 -298.176476 8.476731
BFGS: 4 14:02:46 -298.695178 1.955516
BFGS: 5 14:02:47 -298.781282 1.468066
BFGS: 6 14:02:47 -298.970734 2.428457
BFGS: 7 14:02:47 -299.234947 3.011084
BFGS: 8 14:02:48 -299.449130 2.509700
BFGS: 9 14:02:48 -299.544620 1.797784
BFGS: 10 14:02:48 -299.752688 1.231405
BFGS: 11 14:02:49 -299.943626 1.220897
BFGS: 12 14:02:50 -300.013936 1.272390
BFGS: 13 14:02:50 -300.101748 1.419674
BFGS: 14 14:02:51 -300.203716 1.506987
BFGS: 15 14:02:51 -300.292326 1.157670
BFGS: 16 14:02:51 -300.400223 1.141854
BFGS: 17 14:02:52 -300.473475 0.869668
BFGS: 18 14:02:52 -300.507013 0.498421
BFGS: 19 14:02:53 -300.521631 0.393313
BFGS: 20 14:02:53 -300.534764 0.503179
BFGS: 21 14:02:54 -300.547624 0.447697
BFGS: 22 14:02:54 -300.561777 0.334328
BFGS: 23 14:02:54 -300.568970 0.180797
BFGS: 24 14:02:55 -300.571378 0.102371
BFGS: 25 14:02:55 -300.572746 0.097570
BFGS: 26 14:02:55 -300.574269 0.111598
BFGS: 27 14:02:56 -300.575774 0.111467
BFGS: 28 14:02:56 -300.577156 0.072552
BFGS: 29 14:02:57 -300.577912 0.038075
Step Time Energy fmax
BFGS: 0 14:02:57 -297.377774 4.363009
BFGS: 1 14:02:57 -297.822292 4.465985
BFGS: 2 14:02:57 -299.033325 3.311642
BFGS: 3 14:02:58 -299.202410 4.802170
BFGS: 4 14:02:58 -299.436951 1.579214
BFGS: 5 14:02:59 -299.543601 1.466295
BFGS: 6 14:02:59 -299.840986 1.073441
BFGS: 7 14:03:00 -299.885086 1.060130
BFGS: 8 14:03:00 -299.950389 0.761883
BFGS: 9 14:03:00 -299.990133 0.770311
BFGS: 10 14:03:01 -300.019736 0.473709
BFGS: 11 14:03:01 -300.029899 0.237913
BFGS: 12 14:03:03 -300.032854 0.245258
BFGS: 13 14:03:03 -300.036207 0.192047
BFGS: 14 14:03:04 -300.038534 0.161955
BFGS: 15 14:03:04 -300.039738 0.143961
BFGS: 16 14:03:04 -300.040426 0.118158
BFGS: 17 14:03:05 -300.041248 0.108477
BFGS: 18 14:03:05 -300.042381 0.109959
BFGS: 19 14:03:05 -300.043246 0.080258
BFGS: 20 14:03:06 -300.043580 0.041838
product2_energies = []
for config in product2_configs:
config.calc = calc
config.pbc = True
opt = BFGS(config)
opt.run(fmax=0.05, steps=optimization_steps)
product2_energies.append(config.get_potential_energy()) Step Time Energy fmax
BFGS: 0 14:03:06 -295.210438 1.454616
BFGS: 1 14:03:07 -295.300062 1.318673
BFGS: 2 14:03:07 -295.504626 1.800332
BFGS: 3 14:03:07 -295.556186 0.545756
BFGS: 4 14:03:08 -295.568002 0.562283
BFGS: 5 14:03:08 -295.597600 0.298647
BFGS: 6 14:03:09 -295.603204 0.313868
BFGS: 7 14:03:10 -295.610689 0.357865
BFGS: 8 14:03:10 -295.618682 0.349344
BFGS: 9 14:03:11 -295.627939 0.389248
BFGS: 10 14:03:11 -295.635068 0.334897
BFGS: 11 14:03:11 -295.640643 0.461730
BFGS: 12 14:03:12 -295.654152 0.731454
BFGS: 13 14:03:12 -295.698340 1.196041
BFGS: 14 14:03:12 -295.701237 1.271006
BFGS: 15 14:03:13 -295.717168 1.231565
BFGS: 16 14:03:13 -295.721451 1.226727
BFGS: 17 14:03:13 -295.726392 1.186046
BFGS: 18 14:03:14 -295.730995 1.151661
BFGS: 19 14:03:14 -295.801344 0.530441
BFGS: 20 14:03:15 -295.813903 0.374802
BFGS: 21 14:03:15 -295.826022 0.309885
BFGS: 22 14:03:15 -295.835345 0.219276
BFGS: 23 14:03:16 -295.842890 0.112803
BFGS: 24 14:03:16 -295.845629 0.083230
BFGS: 25 14:03:17 -295.846519 0.079058
BFGS: 26 14:03:17 -295.846991 0.083093
BFGS: 27 14:03:17 -295.847601 0.085596
BFGS: 28 14:03:17 -295.848359 0.086529
BFGS: 29 14:03:18 -295.849055 0.087561
BFGS: 30 14:03:18 -295.849660 0.099257
BFGS: 31 14:03:19 -295.850492 0.123047
BFGS: 32 14:03:19 -295.852247 0.200492
BFGS: 33 14:03:19 -295.856744 0.349183
BFGS: 34 14:03:20 -295.865420 0.571662
BFGS: 35 14:03:20 -295.867372 0.671086
BFGS: 36 14:03:20 -295.880081 0.498073
BFGS: 37 14:03:21 -295.895180 0.334518
BFGS: 38 14:03:21 -295.916824 0.222511
BFGS: 39 14:03:22 -295.922733 0.234280
BFGS: 40 14:03:22 -295.925914 0.189164
BFGS: 41 14:03:22 -295.929116 0.125219
BFGS: 42 14:03:22 -295.930742 0.109189
BFGS: 43 14:03:23 -295.931670 0.061935
BFGS: 44 14:03:23 -295.932100 0.050282
BFGS: 45 14:03:24 -295.932453 0.039912
Step Time Energy fmax
BFGS: 0 14:03:24 -295.361122 1.198061
BFGS: 1 14:03:25 -295.432633 1.097990
BFGS: 2 14:03:25 -295.649583 1.170725
BFGS: 3 14:03:25 -295.674774 0.597854
BFGS: 4 14:03:26 -295.686887 0.470709
BFGS: 5 14:03:26 -295.728040 0.570684
BFGS: 6 14:03:27 -295.736598 0.548629
BFGS: 7 14:03:27 -295.789012 0.605983
BFGS: 8 14:03:27 -295.806729 0.382232
BFGS: 9 14:03:28 -295.819747 0.348149
BFGS: 10 14:03:28 -295.824357 0.299748
BFGS: 11 14:03:29 -295.831267 0.193215
BFGS: 12 14:03:29 -295.836070 0.111606
BFGS: 13 14:03:29 -295.838355 0.146381
BFGS: 14 14:03:30 -295.839053 0.127281
BFGS: 15 14:03:30 -295.839561 0.099729
BFGS: 16 14:03:30 -295.840389 0.049537
Step Time Energy fmax
BFGS: 0 14:03:31 -295.380502 1.172019
BFGS: 1 14:03:31 -295.449170 1.075564
BFGS: 2 14:03:31 -295.661958 1.097451
BFGS: 3 14:03:31 -295.684561 0.589652
BFGS: 4 14:03:32 -295.696733 0.470712
BFGS: 5 14:03:32 -295.736397 0.581104
BFGS: 6 14:03:33 -295.745588 0.558330
BFGS: 7 14:03:33 -295.790343 0.571168
BFGS: 8 14:03:33 -295.820205 0.547794
BFGS: 9 14:03:34 -295.845769 0.520939
BFGS: 10 14:03:34 -295.857421 0.464803
BFGS: 11 14:03:34 -295.867060 0.376483
BFGS: 12 14:03:35 -295.879584 0.272426
BFGS: 13 14:03:35 -295.890486 0.228271
BFGS: 14 14:03:35 -295.895780 0.271084
BFGS: 15 14:03:36 -295.898970 0.249888
BFGS: 16 14:03:36 -295.903837 0.213409
BFGS: 17 14:03:37 -295.911022 0.202132
BFGS: 18 14:03:37 -295.917912 0.153938
BFGS: 19 14:03:37 -295.921785 0.156065
BFGS: 20 14:03:38 -295.923828 0.129906
BFGS: 21 14:03:38 -295.925281 0.107186
BFGS: 22 14:03:39 -295.927692 0.098094
BFGS: 23 14:03:39 -295.929827 0.083000
BFGS: 24 14:03:40 -295.931030 0.066423
BFGS: 25 14:03:40 -295.931509 0.051050
BFGS: 26 14:03:40 -295.931815 0.043290
Step Time Energy fmax
BFGS: 0 14:03:41 -295.090978 1.742677
BFGS: 1 14:03:41 -295.204496 1.570499
BFGS: 2 14:03:42 -295.387668 2.487677
BFGS: 3 14:03:42 -295.477448 0.462086
BFGS: 4 14:03:42 -295.494016 0.620670
BFGS: 5 14:03:43 -295.520671 0.685140
BFGS: 6 14:03:43 -295.535290 0.457648
BFGS: 7 14:03:44 -295.543605 0.259132
BFGS: 8 14:03:44 -295.548188 0.312975
BFGS: 9 14:03:44 -295.554810 0.298519
BFGS: 10 14:03:45 -295.558772 0.182571
BFGS: 11 14:03:45 -295.560130 0.059607
BFGS: 12 14:03:46 -295.560292 0.014996
Step Time Energy fmax
BFGS: 0 14:03:46 -295.487417 0.976197
BFGS: 1 14:03:46 -295.548439 0.905702
BFGS: 2 14:03:47 -295.759372 0.768400
BFGS: 3 14:03:47 -295.775412 0.470948
BFGS: 4 14:03:48 -295.785134 0.457320
BFGS: 5 14:03:48 -295.816036 0.451032
BFGS: 6 14:03:49 -295.823213 0.383064
BFGS: 7 14:03:49 -295.833106 0.343184
BFGS: 8 14:03:50 -295.839611 0.216838
BFGS: 9 14:03:50 -295.843885 0.128322
BFGS: 10 14:03:50 -295.845276 0.126951
BFGS: 11 14:03:51 -295.846087 0.115981
BFGS: 12 14:03:51 -295.847206 0.100312
BFGS: 13 14:03:52 -295.848451 0.090495
BFGS: 14 14:03:52 -295.849360 0.091574
BFGS: 15 14:03:52 -295.849935 0.096107
BFGS: 16 14:03:53 -295.850633 0.103313
BFGS: 17 14:03:53 -295.852065 0.119925
BFGS: 18 14:03:53 -295.854909 0.158024
BFGS: 19 14:03:54 -295.859271 0.227259
BFGS: 20 14:03:54 -295.864850 0.305696
BFGS: 21 14:03:55 -295.873313 0.401934
BFGS: 22 14:03:55 -295.884122 0.465518
BFGS: 23 14:03:56 -295.898662 0.399641
BFGS: 24 14:03:56 -295.919651 0.358596
BFGS: 25 14:03:56 -295.938294 0.264344
BFGS: 26 14:03:57 -295.948980 0.232548
BFGS: 27 14:03:57 -295.954417 0.170431
BFGS: 28 14:03:58 -295.957455 0.134381
BFGS: 29 14:03:58 -295.960264 0.118657
BFGS: 30 14:03:58 -295.964276 0.113762
BFGS: 31 14:03:59 -295.965853 0.081712
BFGS: 32 14:03:59 -295.966388 0.057915
BFGS: 33 14:04:00 -295.966633 0.043173
Step Time Energy fmax
BFGS: 0 14:04:00 -295.192462 1.489281
BFGS: 1 14:04:01 -295.284983 1.349141
BFGS: 2 14:04:01 -295.486657 1.900510
BFGS: 3 14:04:01 -295.543502 0.531059
BFGS: 4 14:04:01 -295.555788 0.571628
BFGS: 5 14:04:02 -295.583847 0.387505
BFGS: 6 14:04:02 -295.590508 0.275609
BFGS: 7 14:04:02 -295.596505 0.327397
BFGS: 8 14:04:03 -295.602958 0.334298
BFGS: 9 14:04:03 -295.610340 0.330420
BFGS: 10 14:04:04 -295.615706 0.245230
BFGS: 11 14:04:04 -295.618931 0.317646
BFGS: 12 14:04:04 -295.623241 0.433830
BFGS: 13 14:04:05 -295.643427 0.817265
BFGS: 14 14:04:05 -295.687939 1.239885
BFGS: 15 14:04:06 -295.711035 1.225173
BFGS: 16 14:04:06 -295.723696 1.201890
BFGS: 17 14:04:06 -295.738058 1.123491
BFGS: 18 14:04:07 -295.784025 0.706098
BFGS: 19 14:04:07 -295.795401 0.587076
BFGS: 20 14:04:07 -295.803162 0.512757
BFGS: 21 14:04:08 -295.810662 0.444354
BFGS: 22 14:04:08 -295.823752 0.318147
BFGS: 23 14:04:09 -295.837102 0.186876
BFGS: 24 14:04:09 -295.844721 0.176434
BFGS: 25 14:04:09 -295.847298 0.151199
BFGS: 26 14:04:10 -295.848920 0.113156
BFGS: 27 14:04:10 -295.850898 0.105615
BFGS: 28 14:04:11 -295.852711 0.110358
BFGS: 29 14:04:11 -295.853874 0.121195
BFGS: 30 14:04:12 -295.854608 0.132770
BFGS: 31 14:04:12 -295.855552 0.148232
BFGS: 32 14:04:12 -295.857564 0.177726
BFGS: 33 14:04:13 -295.862167 0.234659
BFGS: 34 14:04:13 -295.871339 0.314362
BFGS: 35 14:04:14 -295.878384 0.358607
BFGS: 36 14:04:14 -295.891094 0.281139
BFGS: 37 14:04:14 -295.908816 0.227599
BFGS: 38 14:04:14 -295.915657 0.172921
BFGS: 39 14:04:15 -295.925752 0.142906
BFGS: 40 14:04:15 -295.929222 0.105195
BFGS: 41 14:04:16 -295.930581 0.100090
BFGS: 42 14:04:16 -295.931583 0.074049
BFGS: 43 14:04:16 -295.932186 0.042178
Step Time Energy fmax
BFGS: 0 14:04:17 -295.700589 0.695409
BFGS: 1 14:04:17 -295.747425 0.619814
BFGS: 2 14:04:18 -295.916973 0.377914
BFGS: 3 14:04:18 -295.927023 0.378836
BFGS: 4 14:04:18 -295.929782 0.363107
BFGS: 5 14:04:19 -295.955533 0.179030
BFGS: 6 14:04:19 -295.956699 0.170147
BFGS: 7 14:04:20 -295.961816 0.120411
BFGS: 8 14:04:20 -295.963028 0.099194
BFGS: 9 14:04:21 -295.963808 0.094250
BFGS: 10 14:04:21 -295.964463 0.081803
BFGS: 11 14:04:21 -295.965344 0.062574
BFGS: 12 14:04:22 -295.966016 0.055740
BFGS: 13 14:04:22 -295.966417 0.058693
BFGS: 14 14:04:23 -295.966669 0.050296
BFGS: 15 14:04:23 -295.966915 0.030904
Step Time Energy fmax
BFGS: 0 14:04:23 -295.090082 1.746213
BFGS: 1 14:04:24 -295.203826 1.573163
BFGS: 2 14:04:24 -295.387285 2.487241
BFGS: 3 14:04:25 -295.476874 0.462595
BFGS: 4 14:04:25 -295.493454 0.621244
BFGS: 5 14:04:25 -295.520245 0.685941
BFGS: 6 14:04:26 -295.534932 0.458608
BFGS: 7 14:04:26 -295.543291 0.260243
BFGS: 8 14:04:26 -295.547901 0.314058
BFGS: 9 14:04:27 -295.554597 0.299269
BFGS: 10 14:04:27 -295.558581 0.182728
BFGS: 11 14:04:28 -295.559939 0.059351
BFGS: 12 14:04:28 -295.560099 0.015431
Step Time Energy fmax
BFGS: 0 14:04:28 -295.122392 1.645155
BFGS: 1 14:04:29 -295.228530 1.486292
BFGS: 2 14:04:29 -295.417144 2.323545
BFGS: 3 14:04:30 -295.497921 0.477797
BFGS: 4 14:04:30 -295.513090 0.605032
BFGS: 5 14:04:31 -295.538369 0.617041
BFGS: 6 14:04:31 -295.550154 0.372236
BFGS: 7 14:04:31 -295.556627 0.255153
BFGS: 8 14:04:32 -295.560886 0.299365
BFGS: 9 14:04:32 -295.566281 0.273421
BFGS: 10 14:04:33 -295.569739 0.174051
BFGS: 11 14:04:33 -295.570955 0.074437
BFGS: 12 14:04:34 -295.571193 0.075960
BFGS: 13 14:04:34 -295.571403 0.085643
BFGS: 14 14:04:35 -295.571869 0.103893
BFGS: 15 14:04:35 -295.572834 0.127443
BFGS: 16 14:04:35 -295.574619 0.144143
BFGS: 17 14:04:35 -295.577304 0.173706
BFGS: 18 14:04:36 -295.582005 0.316893
BFGS: 19 14:04:36 -295.594667 0.623721
BFGS: 20 14:04:37 -295.654763 0.687664
BFGS: 21 14:04:37 -295.724986 0.664293
BFGS: 22 14:04:37 -295.741317 0.842660
BFGS: 23 14:04:38 -295.774244 0.600594
BFGS: 24 14:04:38 -295.801607 0.565163
BFGS: 25 14:04:38 -295.878894 0.302051
BFGS: 26 14:04:39 -295.887505 0.233144
BFGS: 27 14:04:39 -295.892802 0.262412
BFGS: 28 14:04:40 -295.900078 0.314101
BFGS: 29 14:04:40 -295.910018 0.351482
BFGS: 30 14:04:40 -295.916506 0.333517
BFGS: 31 14:04:41 -295.922338 0.291381
BFGS: 32 14:04:41 -295.929565 0.296082
BFGS: 33 14:04:41 -295.939103 0.341128
BFGS: 34 14:04:42 -295.948317 0.284410
BFGS: 35 14:04:42 -295.954458 0.174676
BFGS: 36 14:04:42 -295.958374 0.115918
BFGS: 37 14:04:43 -295.961077 0.112948
BFGS: 38 14:04:43 -295.963039 0.105346
BFGS: 39 14:04:44 -295.964383 0.083791
BFGS: 40 14:04:44 -295.965381 0.071496
BFGS: 41 14:04:44 -295.966119 0.041871
Step Time Energy fmax
BFGS: 0 14:04:45 -295.535554 0.895502
BFGS: 1 14:04:45 -295.592238 0.838137
BFGS: 2 14:04:45 -295.797561 0.607977
BFGS: 3 14:04:46 -295.811728 0.443074
BFGS: 4 14:04:46 -295.819752 0.450221
BFGS: 5 14:04:47 -295.852001 0.405863
BFGS: 6 14:04:47 -295.858679 0.370231
BFGS: 7 14:04:47 -295.867784 0.341911
BFGS: 8 14:04:48 -295.874001 0.207310
BFGS: 9 14:04:48 -295.878714 0.243312
BFGS: 10 14:04:49 -295.881317 0.253356
BFGS: 11 14:04:49 -295.884282 0.253492
BFGS: 12 14:04:49 -295.889701 0.257084
BFGS: 13 14:04:50 -295.898518 0.282550
BFGS: 14 14:04:50 -295.908705 0.360524
BFGS: 15 14:04:50 -295.918785 0.462506
BFGS: 16 14:04:51 -295.931161 0.421589
BFGS: 17 14:04:51 -295.942239 0.292509
BFGS: 18 14:04:52 -295.954857 0.157049
BFGS: 19 14:04:52 -295.959895 0.110924
BFGS: 20 14:04:52 -295.961606 0.130901
BFGS: 21 14:04:53 -295.962560 0.092800
BFGS: 22 14:04:53 -295.963644 0.082491
BFGS: 23 14:04:54 -295.965695 0.062193
BFGS: 24 14:04:54 -295.966115 0.050535
BFGS: 25 14:04:54 -295.966345 0.040121
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 14:04:55 -303.897737 0.400945
BFGS: 1 14:04:55 -303.904496 0.301350
BFGS: 2 14:04:56 -303.918697 0.182117
BFGS: 3 14:04:56 -303.921659 0.157526
BFGS: 4 14:04:57 -303.924077 0.114973
BFGS: 5 14:04:57 -303.925523 0.108738
BFGS: 6 14:04:57 -303.926721 0.087044
BFGS: 7 14:04:58 -303.927448 0.076810
BFGS: 8 14:04:58 -303.927813 0.058375
BFGS: 9 14:04:58 -303.928023 0.040625
Step Time Energy fmax
BFGS: 0 14:04:59 -303.896002 0.375434
BFGS: 1 14:04:59 -303.903028 0.285242
BFGS: 2 14:05:00 -303.918306 0.179801
BFGS: 3 14:05:00 -303.921416 0.151779
BFGS: 4 14:05:00 -303.923900 0.111890
BFGS: 5 14:05:01 -303.925319 0.106784
BFGS: 6 14:05:01 -303.926521 0.086707
BFGS: 7 14:05:02 -303.927288 0.081397
BFGS: 8 14:05:02 -303.927695 0.063014
BFGS: 9 14:05:02 -303.927933 0.042004
/home/runner/work/_tool/Python/3.12.13/x64/lib/python3.12/site-packages/fairchem/applications/cattsunami/core/autoframe.py:1551: UserWarning: torch.range is deprecated and will be removed in a future release because its behavior is inconsistent with Python's range builtin. Instead, use torch.arange, which produces values in [start, end).
alpha = torch.range(0, num_frames - 1, device=device) / (num_frames - 1)
Run NEBs¶
## This will run all NEBs enumerated - to just run one, run the code cell below.
# On GPU, each NEB takes an average of ~1 minute so this could take around a half hour on GPU
# But much longer on CPU
# Remember that not all NEBs will converge -- the k, nframes would be adjusted to achieve convergence
fmax = 0.05 # [eV / ang**2]
delta_fmax_climb = 0.4
converged_idxs = []
for idx, frame_set in enumerate(frame_sets):
neb = DyNEB(frame_set, k=1)
for image in frame_set:
image.calc = FAIRChemCalculator(predictor, task_name="oc20")
optimizer = BFGS(
neb,
trajectory=f"ch_dissoc_on_Ru_{idx}.traj",
)
conv = optimizer.run(fmax=fmax + delta_fmax_climb, steps=optimization_steps)
if conv:
neb.climb = True
conv = optimizer.run(fmax=fmax, steps=optimization_steps)
if conv:
converged_idxs.append(idx)
print(converged_idxs)This cell will run a shorter calculations for just a single one of the enumerated transition state pathways. You can adapt this code to run transition state searches via nudged elastic band (NEB) calculations for any reaction.
# If you run the above cell -- dont run this one
fmax = 0.05 # [eV / ang**2]
delta_fmax_climb = 0.4
images = frame_sets[0]
neb = DyNEB(images, k=1)
for image in images:
image.calc = FAIRChemCalculator(predictor, task_name="oc20")
optimizer = BFGS(
neb,
trajectory="ch_dissoc_on_Ru_0.traj",
)
conv = optimizer.run(fmax=fmax + delta_fmax_climb, steps=optimization_steps)
if conv:
neb.climb = True
conv = optimizer.run(fmax=fmax, steps=optimization_steps)/home/runner/work/_tool/Python/3.12.13/x64/lib/python3.12/site-packages/ase/mep/neb.py:329: UserWarning: The default method has changed from 'aseneb' to 'improvedtangent'. The 'aseneb' method is an unpublished, custom implementation that is not recommended as it frequently results in very poor bands. Please explicitly set method='improvedtangent' to silence this warning, or set method='aseneb' if you strictly require the old behavior (results may vary). See: https://gitlab.com/ase/ase/-/merge_requests/3952
warnings.warn(
Step Time Energy fmax
BFGS: 0 14:05:22 -301.629004 3.045871
BFGS: 1 14:05:25 -301.904076 2.486102
BFGS: 2 14:05:28 -302.347482 5.677942
BFGS: 3 14:05:31 -302.554419 2.049548
BFGS: 4 14:05:34 -303.045259 2.401325
BFGS: 5 14:05:40 -303.132283 1.753209
BFGS: 6 14:05:43 -303.301897 1.384698
BFGS: 7 14:05:46 -303.416877 1.332622
BFGS: 8 14:05:50 -303.494720 1.858450
BFGS: 9 14:05:53 -303.501178 1.158701
BFGS: 10 14:05:56 -303.536727 1.537008
BFGS: 11 14:05:59 -303.572954 1.453617
BFGS: 12 14:06:03 -303.589300 0.916835
BFGS: 13 14:06:07 -303.600087 0.561668
BFGS: 14 14:06:11 -303.620020 0.632089
BFGS: 15 14:06:15 -303.650837 0.709823
BFGS: 16 14:06:18 -303.678918 0.885464
BFGS: 17 14:06:21 -303.696915 0.661258
BFGS: 18 14:06:24 -303.710539 0.607180
BFGS: 19 14:06:31 -303.721722 0.633464
BFGS: 20 14:06:34 -303.725171 0.499792
BFGS: 21 14:06:38 -303.723123 0.364566
BFGS: 22 14:06:43 -303.716211 0.516817
BFGS: 23 14:06:47 -303.711979 0.487472
BFGS: 24 14:06:50 -303.704643 0.433855
BFGS: 25 14:06:54 -303.697557 0.401130
BFGS: 26 14:06:57 -303.691914 0.389196
BFGS: 27 14:07:01 -303.691403 0.444877
BFGS: 28 14:07:05 -303.697430 0.364556
BFGS: 29 14:07:12 -303.712743 0.385259
BFGS: 30 14:07:15 -303.742808 0.448405
BFGS: 31 14:07:18 -303.782304 0.530862
BFGS: 32 14:07:22 -303.809245 0.563839
BFGS: 33 14:07:26 -303.810271 0.655647
BFGS: 34 14:07:30 -303.801990 0.682605
BFGS: 35 14:07:33 -303.796295 0.564351
BFGS: 36 14:07:39 -303.788555 0.479526
BFGS: 37 14:07:42 -303.776215 0.387606
BFGS: 38 14:07:45 -303.760148 0.409106
BFGS: 39 14:07:48 -303.744943 0.370245
BFGS: 40 14:07:51 -303.736881 0.358255
BFGS: 41 14:07:55 -303.737921 0.313648
BFGS: 42 14:07:58 -303.743051 0.286456
BFGS: 43 14:08:01 -303.749816 0.290932
BFGS: 44 14:08:04 -303.753797 0.245453
BFGS: 45 14:08:08 -303.754899 0.209739
BFGS: 46 14:08:10 -303.752567 0.237133
BFGS: 47 14:08:16 -303.744120 0.375466
BFGS: 48 14:08:22 -303.731204 0.607935
BFGS: 49 14:08:26 -303.716332 0.919238
BFGS: 50 14:08:33 -303.731737 0.713683
BFGS: 51 14:08:38 -303.735481 0.686329
BFGS: 52 14:08:41 -303.740630 0.790610
BFGS: 53 14:08:44 -303.738924 0.785031
BFGS: 54 14:08:47 -303.730997 0.847174
BFGS: 55 14:08:52 -303.726112 0.946078
BFGS: 56 14:08:56 -303.726627 0.987987
BFGS: 57 14:08:59 -303.731411 0.868493
BFGS: 58 14:09:05 -303.741209 0.675792
BFGS: 59 14:09:08 -303.746466 0.705431
BFGS: 60 14:09:12 -303.749827 0.699218
BFGS: 61 14:09:15 -303.751642 0.652081
BFGS: 62 14:09:18 -303.753342 0.679820
BFGS: 63 14:09:23 -303.753060 0.741758
BFGS: 64 14:09:26 -303.748093 0.935440
BFGS: 65 14:09:29 -303.753046 0.675137
BFGS: 66 14:09:33 -303.752035 0.627970
BFGS: 67 14:09:38 -303.748014 0.488444
BFGS: 68 14:09:42 -303.748083 0.479564
BFGS: 69 14:09:49 -303.749846 0.411014
BFGS: 70 14:09:54 -303.753284 0.383194
BFGS: 71 14:09:57 -303.755600 0.402441
BFGS: 72 14:10:01 -303.757559 0.460009
BFGS: 73 14:10:07 -303.757690 0.410529
BFGS: 74 14:10:10 -303.759038 0.354052
BFGS: 75 14:10:16 -303.760471 0.340213
BFGS: 76 14:10:20 -303.758387 0.401725
BFGS: 77 14:10:27 -303.758758 0.391936
BFGS: 78 14:10:29 -303.760903 0.314864
BFGS: 79 14:10:32 -303.761341 0.350241
BFGS: 80 14:10:36 -303.761691 0.312130
BFGS: 81 14:10:42 -303.762172 0.344047
BFGS: 82 14:10:46 -303.760905 0.461349
BFGS: 83 14:10:49 -303.761897 0.356853
BFGS: 84 14:10:51 -303.762270 0.245247
BFGS: 85 14:10:55 -303.762738 0.217346
BFGS: 86 14:10:58 -303.763119 0.253238
BFGS: 87 14:11:01 -303.763024 0.227711
BFGS: 88 14:11:08 -303.762928 0.249241
BFGS: 89 14:11:15 -303.763037 0.266476
BFGS: 90 14:11:18 -303.763040 0.240247
BFGS: 91 14:11:21 -303.762770 0.224733
BFGS: 92 14:11:24 -303.762510 0.212428
BFGS: 93 14:11:27 -303.762408 0.221716
BFGS: 94 14:11:31 -303.762288 0.231860
BFGS: 95 14:11:33 -303.762079 0.239611
BFGS: 96 14:11:36 -303.761772 0.245687
BFGS: 97 14:11:40 -303.761508 0.243694
BFGS: 98 14:11:43 -303.761476 0.234158
BFGS: 99 14:11:46 -303.761609 0.227296
BFGS: 100 14:11:49 -303.761803 0.232450
BFGS: 101 14:11:52 -303.761957 0.237303
BFGS: 102 14:11:57 -303.761902 0.237381
BFGS: 103 14:12:02 -303.761639 0.224472
BFGS: 104 14:12:06 -303.761317 0.231029
BFGS: 105 14:12:09 -303.761068 0.244642
BFGS: 106 14:12:12 -303.760876 0.257740
BFGS: 107 14:12:16 -303.760833 0.268619
BFGS: 108 14:12:20 -303.760896 0.276195
BFGS: 109 14:12:25 -303.760953 0.276219
BFGS: 110 14:12:30 -303.761001 0.264178
BFGS: 111 14:12:33 -303.760984 0.243427
BFGS: 112 14:12:37 -303.761452 0.306368
BFGS: 113 14:12:39 -303.763759 0.359530
BFGS: 114 14:12:42 -303.764326 0.253568
BFGS: 115 14:12:45 -303.763778 0.172573
BFGS: 116 14:12:48 -303.762992 0.165677
BFGS: 117 14:12:53 -303.762835 0.156090
BFGS: 118 14:12:59 -303.762816 0.163255
BFGS: 119 14:13:06 -303.762827 0.195028
BFGS: 120 14:13:08 -303.763145 0.198161
BFGS: 121 14:13:11 -303.763878 0.166211
BFGS: 122 14:13:14 -303.764108 0.171489
BFGS: 123 14:13:18 -303.762827 0.234811
BFGS: 124 14:13:22 -303.761400 0.534306
BFGS: 125 14:13:25 -303.758271 0.827157
BFGS: 126 14:13:27 -303.751136 1.115178
BFGS: 127 14:13:30 -303.742034 1.274638
BFGS: 128 14:13:33 -303.704298 1.663448
BFGS: 129 14:13:36 -303.603647 2.183312
BFGS: 130 14:13:39 -303.676063 1.219953
BFGS: 131 14:13:42 -303.757710 0.961554
BFGS: 132 14:13:50 -303.778742 0.977214
BFGS: 133 14:13:55 -303.788490 0.685883
BFGS: 134 14:13:58 -303.790831 0.576022
BFGS: 135 14:14:02 -303.788593 0.500035
BFGS: 136 14:14:05 -303.787610 0.424679
BFGS: 137 14:14:08 -303.781490 0.500565
BFGS: 138 14:14:11 -303.774581 0.538386
BFGS: 139 14:14:14 -303.767433 0.576147
BFGS: 140 14:14:17 -303.758369 0.763523
BFGS: 141 14:14:20 -303.742477 1.130289
BFGS: 142 14:14:23 -303.714958 1.837874
BFGS: 143 14:14:26 -303.733517 1.401415
BFGS: 144 14:14:29 -303.769511 0.740895
BFGS: 145 14:14:32 -303.784996 0.413002
BFGS: 146 14:14:34 -303.780557 0.437288
BFGS: 147 14:14:37 -303.755231 0.776499
BFGS: 148 14:14:40 -303.736894 1.173003
BFGS: 149 14:14:44 -303.709281 1.808967
BFGS: 150 14:14:48 -303.736427 1.263893
BFGS: 151 14:14:50 -303.742356 1.146755
BFGS: 152 14:14:53 -303.745078 0.996266
BFGS: 153 14:15:00 -303.739900 1.010619
BFGS: 154 14:15:03 -303.731427 1.124003
BFGS: 155 14:15:06 -303.739804 1.075985
BFGS: 156 14:15:14 -303.750539 0.969925
BFGS: 157 14:15:16 -303.760898 1.153430
BFGS: 158 14:15:19 -303.749440 1.096813
BFGS: 159 14:15:22 -303.655775 1.158398
BFGS: 160 14:15:28 -303.660142 1.252433
BFGS: 161 14:15:32 -303.714443 1.085764
BFGS: 162 14:15:35 -303.746440 0.773778
BFGS: 163 14:15:38 -303.760552 0.567029
BFGS: 164 14:15:44 -303.761803 0.735389
BFGS: 165 14:15:47 -303.757783 0.905968
BFGS: 166 14:15:53 -303.728037 1.082823
BFGS: 167 14:15:57 -303.639298 0.948081
BFGS: 168 14:16:00 -303.677718 1.099126
BFGS: 169 14:16:03 -303.740510 0.723294
BFGS: 170 14:16:08 -303.756846 0.492272
BFGS: 171 14:16:14 -303.761272 0.667469
BFGS: 172 14:16:17 -303.705824 1.017166
BFGS: 173 14:16:19 -303.661834 1.143460
BFGS: 174 14:16:20 -303.664968 1.178953
BFGS: 175 14:16:26 -303.669304 1.150933
BFGS: 176 14:16:29 -303.691017 0.961689
BFGS: 177 14:16:34 -303.664862 1.023152
BFGS: 178 14:16:36 -303.597692 1.100072
BFGS: 179 14:16:38 -303.600133 1.051019
BFGS: 180 14:16:43 -303.624701 0.972186
BFGS: 181 14:16:48 -303.621123 0.966152
BFGS: 182 14:16:51 -303.602480 1.703470
BFGS: 183 14:16:53 -303.530997 1.730660
BFGS: 184 14:16:56 -303.336662 2.051806
BFGS: 185 14:16:58 -303.462865 2.010312
BFGS: 186 14:17:05 -303.575037 1.132450
BFGS: 187 14:17:06 -303.655455 0.971270
BFGS: 188 14:17:10 -303.663128 0.966334
BFGS: 189 14:17:13 -303.624334 0.906470
BFGS: 190 14:17:19 -303.620245 0.835885
BFGS: 191 14:17:25 -303.614527 0.879314
BFGS: 192 14:17:28 -303.616352 0.836642
BFGS: 193 14:17:32 -303.576018 0.866879
BFGS: 194 14:17:35 -303.546218 0.956988
BFGS: 195 14:17:42 -303.574807 0.932187
BFGS: 196 14:17:44 -303.586333 0.883707
BFGS: 197 14:17:46 -303.570452 0.874972
BFGS: 198 14:17:51 -303.542320 0.958319
BFGS: 199 14:17:52 -303.536159 0.968854
BFGS: 200 14:17:55 -303.530609 0.822269
BFGS: 201 14:17:57 -303.556017 0.807473
BFGS: 202 14:18:02 -303.702929 1.220597
BFGS: 203 14:18:05 -303.796492 1.460971
BFGS: 204 14:18:09 -303.808600 1.229590
BFGS: 205 14:18:12 -303.809491 1.149758
BFGS: 206 14:18:14 -303.833988 1.088604
BFGS: 207 14:18:19 -303.860567 1.197791
BFGS: 208 14:18:22 -303.877643 1.190294
BFGS: 209 14:18:24 -303.881050 1.123627
BFGS: 210 14:18:29 -303.878011 1.057936
BFGS: 211 14:18:31 -303.879581 1.061545
BFGS: 212 14:18:38 -303.879597 1.113924
BFGS: 213 14:18:43 -303.878746 0.973614
BFGS: 214 14:18:49 -303.881703 0.942614
BFGS: 215 14:18:51 -303.886444 1.028989
BFGS: 216 14:18:56 -303.887583 1.060458
BFGS: 217 14:18:59 -303.886041 1.080721
BFGS: 218 14:19:03 -303.880275 1.072832
BFGS: 219 14:19:10 -303.859796 1.001974
BFGS: 220 14:19:15 -303.845067 0.954798
BFGS: 221 14:19:18 -303.834988 1.025899
BFGS: 222 14:19:21 -303.814066 1.130676
BFGS: 223 14:19:27 -303.821460 1.021733
BFGS: 224 14:19:32 -303.821746 0.868855
BFGS: 225 14:19:41 -303.803923 0.843978
BFGS: 226 14:19:44 -303.783020 1.011230
BFGS: 227 14:19:51 -303.781875 1.001915
BFGS: 228 14:19:58 -303.798233 0.765526
BFGS: 229 14:20:03 -303.818380 0.795570
BFGS: 230 14:20:08 -303.825300 0.629722
BFGS: 231 14:20:12 -303.813251 0.575227
BFGS: 232 14:20:15 -303.817138 0.672121
BFGS: 233 14:20:23 -303.826763 0.727859
BFGS: 234 14:20:29 -303.829246 0.703491
BFGS: 235 14:20:37 -303.833800 0.595342
BFGS: 236 14:20:42 -303.837108 0.598620
BFGS: 237 14:20:48 -303.841144 0.701797
BFGS: 238 14:20:51 -303.839890 0.718419
BFGS: 239 14:20:57 -303.831340 0.723425
BFGS: 240 14:21:01 -303.823745 0.785640
BFGS: 241 14:21:05 -303.807110 0.959007
BFGS: 242 14:21:08 -303.715950 1.210768
BFGS: 243 14:21:13 -303.746858 0.954278
BFGS: 244 14:21:18 -303.737049 0.919205
BFGS: 245 14:21:25 -303.692395 0.819374
BFGS: 246 14:21:30 -303.631745 0.724859
BFGS: 247 14:21:33 -303.609852 0.829213
BFGS: 248 14:21:36 -303.648161 1.005810
BFGS: 249 14:21:39 -303.723561 0.978374
BFGS: 250 14:21:46 -303.733732 1.311105
BFGS: 251 14:21:49 -303.743260 1.224107
BFGS: 252 14:21:54 -303.761941 1.148790
BFGS: 253 14:22:01 -303.781230 1.075917
BFGS: 254 14:22:09 -303.783719 0.948180
BFGS: 255 14:22:12 -303.786190 0.648131
BFGS: 256 14:22:18 -303.790399 0.652142
BFGS: 257 14:22:21 -303.807644 0.793859
BFGS: 258 14:22:26 -303.833590 0.801535
BFGS: 259 14:22:34 -303.845395 0.733377
BFGS: 260 14:22:36 -303.824686 0.711106
BFGS: 261 14:22:38 -303.814128 0.668998
BFGS: 262 14:22:39 -303.811141 0.693022
BFGS: 263 14:22:40 -303.808216 0.718637
BFGS: 264 14:22:42 -303.809231 0.743748
BFGS: 265 14:22:44 -303.817642 0.733846
BFGS: 266 14:22:46 -303.817620 0.802076
BFGS: 267 14:22:48 -303.790646 0.893945
BFGS: 268 14:22:50 -303.759858 0.911751
BFGS: 269 14:22:55 -303.733784 1.079585
BFGS: 270 14:22:57 -303.708596 1.176865
BFGS: 271 14:22:59 -303.685604 1.235646
BFGS: 272 14:23:02 -303.664919 1.301651
BFGS: 273 14:23:04 -303.647296 1.416859
BFGS: 274 14:23:06 -303.635947 1.541362
BFGS: 275 14:23:07 -303.691232 1.654980
BFGS: 276 14:23:09 -303.724930 1.264805
BFGS: 277 14:23:13 -303.739855 1.054115
BFGS: 278 14:23:14 -303.740890 1.366300
BFGS: 279 14:23:17 -303.749340 1.466050
BFGS: 280 14:23:19 -303.762819 1.437208
BFGS: 281 14:23:20 -303.778416 1.386941
BFGS: 282 14:23:22 -303.792031 1.238116
BFGS: 283 14:23:24 -303.801651 1.178622
BFGS: 284 14:23:26 -303.808116 1.397381
BFGS: 285 14:23:28 -303.813223 1.596094
BFGS: 286 14:23:29 -303.814219 1.746941
BFGS: 287 14:23:32 -303.814501 1.989731
BFGS: 288 14:23:33 -303.704086 2.288313
BFGS: 289 14:23:35 -303.658847 2.118442
BFGS: 290 14:23:37 -303.601991 2.110868
BFGS: 291 14:23:39 -303.538678 2.141328
BFGS: 292 14:23:41 -303.469320 1.771803
BFGS: 293 14:23:43 -303.411271 1.667282
BFGS: 294 14:23:44 -303.358089 1.713929
BFGS: 295 14:23:46 -303.234454 2.307950
BFGS: 296 14:23:48 -302.904628 4.161295
BFGS: 297 14:23:50 -302.037487 8.429719
BFGS: 298 14:23:51 -300.841657 13.902523
BFGS: 299 14:23:53 -298.888118 22.532569
BFGS: 300 14:23:54 -299.091008 19.088626
BFGS: 301 14:23:56 -300.943561 7.075626
BFGS: 302 14:23:57 -301.700013 4.464671
BFGS: 303 14:24:01 -302.219723 3.424135
BFGS: 304 14:24:02 -302.856666 2.422493
BFGS: 305 14:24:04 -303.327912 2.147227
BFGS: 306 14:24:06 -303.564525 1.873954
BFGS: 307 14:24:07 -303.659676 1.556354
BFGS: 308 14:24:11 -303.730940 1.489944
BFGS: 309 14:24:13 -303.681961 2.547533
BFGS: 310 14:24:15 -303.450792 3.767719
BFGS: 311 14:24:16 -303.602902 2.474463
BFGS: 312 14:24:18 -303.548425 3.010274
BFGS: 313 14:24:20 -303.537989 2.418257
BFGS: 314 14:24:22 -303.591058 2.558903
BFGS: 315 14:24:24 -303.763759 2.548667
BFGS: 316 14:24:26 -303.823217 2.317126
BFGS: 317 14:24:30 -303.864148 2.305378
BFGS: 318 14:24:33 -303.906723 2.172495
BFGS: 319 14:24:34 -303.944271 2.130969
BFGS: 320 14:24:38 -303.936637 1.911194
BFGS: 321 14:24:39 -303.881220 1.770505
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_9624/3247994494.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")