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,
)Warp 1.18.0 initialized:
CUDA Toolkit 13.4, Driver 13.1
Devices:
"cpu" : "x86_64"
"cuda:0" : "Tesla T4" (16 GiB, sm_75, mempool enabled)
Kernel cache:
/home/runner/.cache/warp/1.18.0
/home/runner/work/_tool/Python/3.12.15/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/3.12.15/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/3.12.15/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/3.12.15/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-1p2p1")
calc = FAIRChemCalculator(predictor, task_name="oc20")WARNING:root:device was not explicitly set, using device='cuda'.
# Relax the reactant systems
reactant_energies = []
for config in reactant_configs:
config.calc = calc
config.pbc = True
opt = BFGS(config)
opt.run(fmax=0.05, steps=optimization_steps)
reactant_energies.append(config.get_potential_energy())WARNING:root:Model is being compiled this might take a while for the first time
W1007 02:59:33.490000 9537 site-packages/torch/_logging/_internal.py:1345] [0/0] Profiler record function <class 'torch.autograd.profiler.record_function'> will be ignored
Step Time Energy fmax
BFGS: 0 03:00:18 -301.819195 4.109245
BFGS: 1 03:00:19 -302.204768 2.984100
BFGS: 2 03:00:19 -303.144773 3.440136
BFGS: 3 03:00:19 -303.324700 3.184730
BFGS: 4 03:00:19 -303.698051 2.075691
BFGS: 5 03:00:19 -303.814792 2.380466
BFGS: 6 03:00:19 -303.927945 1.997151
BFGS: 7 03:00:20 -304.056838 1.414661
BFGS: 8 03:00:20 -304.100217 0.710727
BFGS: 9 03:00:20 -304.130503 0.662909
BFGS: 10 03:00:20 -304.238913 0.520408
BFGS: 11 03:00:20 -304.252345 0.415068
BFGS: 12 03:00:21 -304.260168 0.370811
BFGS: 13 03:00:21 -304.280435 0.715137
BFGS: 14 03:00:21 -304.288821 0.608156
BFGS: 15 03:00:21 -304.299808 0.190691
BFGS: 16 03:00:21 -304.303490 0.179402
BFGS: 17 03:00:21 -304.309772 0.316418
BFGS: 18 03:00:22 -304.315176 0.337795
BFGS: 19 03:00:22 -304.319521 0.210034
BFGS: 20 03:00:22 -304.321800 0.163781
BFGS: 21 03:00:22 -304.323512 0.159969
BFGS: 22 03:00:22 -304.326096 0.202633
BFGS: 23 03:00:22 -304.328977 0.208574
BFGS: 24 03:00:22 -304.331032 0.117719
BFGS: 25 03:00:23 -304.332180 0.121868
BFGS: 26 03:00:23 -304.333080 0.139576
BFGS: 27 03:00:23 -304.334017 0.118135
BFGS: 28 03:00:23 -304.334670 0.074858
BFGS: 29 03:00:23 -304.334903 0.031858
Step Time Energy fmax
BFGS: 0 03:00:23 -302.217711 3.992112
BFGS: 1 03:00:24 -302.596360 3.301158
BFGS: 2 03:00:24 -303.552914 2.939825
BFGS: 3 03:00:24 -303.747928 3.031068
BFGS: 4 03:00:24 -303.967006 1.699529
BFGS: 5 03:00:24 -304.121606 1.554034
BFGS: 6 03:00:24 -304.173940 1.058475
BFGS: 7 03:00:24 -304.266356 0.599511
BFGS: 8 03:00:25 -304.278277 0.570755
BFGS: 9 03:00:25 -304.312657 0.385841
BFGS: 10 03:00:25 -304.320294 0.299062
BFGS: 11 03:00:25 -304.323797 0.151424
BFGS: 12 03:00:25 -304.325459 0.124171
BFGS: 13 03:00:26 -304.327519 0.148127
BFGS: 14 03:00:26 -304.328584 0.103944
BFGS: 15 03:00:26 -304.329201 0.092777
BFGS: 16 03:00:26 -304.329813 0.098547
BFGS: 17 03:00:26 -304.330838 0.119752
BFGS: 18 03:00:27 -304.332094 0.129829
BFGS: 19 03:00:27 -304.333128 0.092711
BFGS: 20 03:00:27 -304.333716 0.084259
BFGS: 21 03:00:27 -304.334133 0.079866
BFGS: 22 03:00:27 -304.334572 0.096440
BFGS: 23 03:00:27 -304.334938 0.077769
BFGS: 24 03:00:27 -304.335106 0.035360
Step Time Energy fmax
BFGS: 0 03:00:28 -301.470097 4.178938
BFGS: 1 03:00:28 -301.867420 3.163062
BFGS: 2 03:00:28 -302.862332 3.435804
BFGS: 3 03:00:28 -303.012788 3.355432
BFGS: 4 03:00:29 -303.316733 2.012181
BFGS: 5 03:00:29 -303.466407 3.759541
BFGS: 6 03:00:29 -303.592309 1.970692
BFGS: 7 03:00:29 -303.792289 0.953485
BFGS: 8 03:00:29 -303.870340 2.361717
BFGS: 9 03:00:29 -303.952648 1.017796
BFGS: 10 03:00:29 -303.983776 0.803140
BFGS: 11 03:00:29 -304.064231 0.897444
BFGS: 12 03:00:29 -304.089344 0.825471
BFGS: 13 03:00:29 -304.142201 0.290154
BFGS: 14 03:00:29 -304.148223 0.257640
BFGS: 15 03:00:29 -304.171435 0.369221
BFGS: 16 03:00:29 -304.176079 0.343265
BFGS: 17 03:00:30 -304.185519 0.386689
BFGS: 18 03:00:30 -304.207420 0.687153
BFGS: 19 03:00:30 -304.262649 1.120903
BFGS: 20 03:00:30 -304.176616 1.784006
BFGS: 21 03:00:30 -304.340039 1.362759
BFGS: 22 03:00:30 -304.379332 1.086615
BFGS: 23 03:00:30 -304.444744 0.498995
BFGS: 24 03:00:30 -304.460851 0.473567
BFGS: 25 03:00:31 -304.511395 0.554092
BFGS: 26 03:00:31 -304.532189 0.398676
BFGS: 27 03:00:31 -304.553572 0.540508
BFGS: 28 03:00:31 -304.570688 0.520158
BFGS: 29 03:00:31 -304.592496 0.649951
BFGS: 30 03:00:31 -304.611553 0.565926
BFGS: 31 03:00:31 -304.625778 0.273090
BFGS: 32 03:00:32 -304.632703 0.242772
BFGS: 33 03:00:32 -304.638366 0.263025
BFGS: 34 03:00:32 -304.646714 0.378506
BFGS: 35 03:00:32 -304.654288 0.304067
BFGS: 36 03:00:32 -304.657957 0.125213
BFGS: 37 03:00:32 -304.659109 0.089201
BFGS: 38 03:00:32 -304.660094 0.109018
BFGS: 39 03:00:32 -304.661306 0.139573
BFGS: 40 03:00:32 -304.662450 0.108473
BFGS: 41 03:00:32 -304.663092 0.044731
Step Time Energy fmax
BFGS: 0 03:00:32 -301.838798 4.053158
BFGS: 1 03:00:32 -302.221885 3.333111
BFGS: 2 03:00:33 -303.228475 3.139428
BFGS: 3 03:00:33 -303.400633 4.312278
BFGS: 4 03:00:33 -303.687766 2.211314
BFGS: 5 03:00:33 -303.925859 1.910727
BFGS: 6 03:00:33 -303.984476 1.089139
BFGS: 7 03:00:33 -304.069242 0.885651
BFGS: 8 03:00:33 -304.100231 0.803228
BFGS: 9 03:00:33 -304.141760 0.644051
BFGS: 10 03:00:33 -304.170061 0.532687
BFGS: 11 03:00:33 -304.198764 0.607299
BFGS: 12 03:00:33 -304.213287 0.427665
BFGS: 13 03:00:34 -304.223132 0.433022
BFGS: 14 03:00:34 -304.236731 0.592814
BFGS: 15 03:00:34 -304.253413 0.699220
BFGS: 16 03:00:34 -304.264488 0.495669
BFGS: 17 03:00:34 -304.273640 0.304386
BFGS: 18 03:00:34 -304.282202 0.423094
BFGS: 19 03:00:35 -304.292861 0.417025
BFGS: 20 03:00:35 -304.301727 0.295376
BFGS: 21 03:00:35 -304.307050 0.261074
BFGS: 22 03:00:35 -304.310440 0.228735
BFGS: 23 03:00:35 -304.313268 0.225971
BFGS: 24 03:00:35 -304.318396 0.257563
BFGS: 25 03:00:35 -304.323562 0.228954
BFGS: 26 03:00:36 -304.327118 0.178948
BFGS: 27 03:00:36 -304.328898 0.115937
BFGS: 28 03:00:36 -304.330443 0.131418
BFGS: 29 03:00:36 -304.332275 0.142445
BFGS: 30 03:00:36 -304.333678 0.119944
BFGS: 31 03:00:37 -304.334277 0.077230
BFGS: 32 03:00:37 -304.334540 0.051487
BFGS: 33 03:00:37 -304.334764 0.036776
Step Time Energy fmax
BFGS: 0 03:00:37 -300.963495 3.985429
BFGS: 1 03:00:37 -301.374324 3.459941
BFGS: 2 03:00:37 -302.602397 3.357463
BFGS: 3 03:00:38 -302.090909 11.405861
BFGS: 4 03:00:38 -302.904155 2.728748
BFGS: 5 03:00:38 -303.029879 1.978127
BFGS: 6 03:00:38 -303.139899 1.344256
BFGS: 7 03:00:38 -303.160703 0.544473
BFGS: 8 03:00:39 -303.180785 0.599484
BFGS: 9 03:00:39 -303.229525 0.970235
BFGS: 10 03:00:39 -303.258073 1.006646
BFGS: 11 03:00:39 -303.304109 0.734625
BFGS: 12 03:00:39 -303.393135 1.110942
BFGS: 13 03:00:40 -303.511287 1.655712
BFGS: 14 03:00:40 -303.566980 2.537242
BFGS: 15 03:00:40 -303.707249 2.565658
BFGS: 16 03:00:40 -303.794019 1.906736
BFGS: 17 03:00:41 -303.955709 1.075565
BFGS: 18 03:00:41 -303.988263 1.053140
BFGS: 19 03:00:41 -304.030120 0.677248
BFGS: 20 03:00:41 -304.065613 0.464280
BFGS: 21 03:00:41 -304.083141 0.561336
BFGS: 22 03:00:41 -304.106233 0.644940
BFGS: 23 03:00:42 -304.126103 0.643014
BFGS: 24 03:00:42 -304.144074 0.539627
BFGS: 25 03:00:42 -304.161266 0.375163
BFGS: 26 03:00:42 -304.179858 0.420493
BFGS: 27 03:00:42 -304.201892 0.581080
BFGS: 28 03:00:42 -304.221294 0.541633
BFGS: 29 03:00:42 -304.233536 0.295738
BFGS: 30 03:00:42 -304.241473 0.285601
BFGS: 31 03:00:43 -304.252090 0.311202
BFGS: 32 03:00:43 -304.261723 0.578950
BFGS: 33 03:00:43 -304.265958 0.354300
BFGS: 34 03:00:43 -304.279562 0.314275
BFGS: 35 03:00:43 -304.289858 0.278346
BFGS: 36 03:00:43 -304.298235 0.301317
BFGS: 37 03:00:43 -304.304536 0.394495
BFGS: 38 03:00:43 -304.316207 0.414454
BFGS: 39 03:00:44 -304.321806 0.258760
BFGS: 40 03:00:44 -304.325161 0.131433
BFGS: 41 03:00:44 -304.327345 0.130793
BFGS: 42 03:00:44 -304.330371 0.216626
BFGS: 43 03:00:44 -304.332118 0.159776
BFGS: 44 03:00:44 -304.332806 0.080348
BFGS: 45 03:00:44 -304.333221 0.053949
BFGS: 46 03:00:44 -304.333711 0.082510
BFGS: 47 03:00:45 -304.334233 0.104445
BFGS: 48 03:00:45 -304.334648 0.071994
BFGS: 49 03:00:45 -304.334834 0.028376
Step Time Energy fmax
BFGS: 0 03:00:45 -301.011244 4.119029
BFGS: 1 03:00:45 -301.420666 3.152574
BFGS: 2 03:00:45 -302.535073 3.558362
BFGS: 3 03:00:46 -302.603109 5.128041
BFGS: 4 03:00:46 -302.920066 2.313018
BFGS: 5 03:00:46 -303.024935 2.301998
BFGS: 6 03:00:46 -303.064690 0.601952
BFGS: 7 03:00:46 -303.085341 0.507773
BFGS: 8 03:00:47 -303.164428 0.948641
BFGS: 9 03:00:47 -303.178101 0.437627
BFGS: 10 03:00:47 -303.188727 0.274886
BFGS: 11 03:00:47 -303.194798 0.421135
BFGS: 12 03:00:47 -303.203722 0.471928
BFGS: 13 03:00:47 -303.208303 0.376942
BFGS: 14 03:00:47 -303.211366 0.291427
BFGS: 15 03:00:47 -303.214898 0.337193
BFGS: 16 03:00:48 -303.225135 0.662170
BFGS: 17 03:00:48 -303.304517 1.894222
BFGS: 18 03:00:48 -303.542782 2.097653
BFGS: 19 03:00:48 -303.853986 2.060892
BFGS: 20 03:00:48 -303.893220 3.303950
BFGS: 21 03:00:48 -304.094410 1.503742
BFGS: 22 03:00:48 -304.257283 1.613528
BFGS: 23 03:00:49 -304.395572 0.854407
BFGS: 24 03:00:49 -304.434377 0.834054
BFGS: 25 03:00:49 -304.484569 0.740390
BFGS: 26 03:00:49 -304.514450 0.517820
BFGS: 27 03:00:49 -304.544024 0.513754
BFGS: 28 03:00:49 -304.557499 0.421863
BFGS: 29 03:00:50 -304.582241 0.459136
BFGS: 30 03:00:50 -304.601943 0.364698
BFGS: 31 03:00:50 -304.616421 0.269865
BFGS: 32 03:00:50 -304.623062 0.256551
BFGS: 33 03:00:50 -304.629183 0.249240
BFGS: 34 03:00:51 -304.638112 0.233609
BFGS: 35 03:00:51 -304.645316 0.263912
BFGS: 36 03:00:51 -304.648770 0.247598
BFGS: 37 03:00:51 -304.651147 0.196715
BFGS: 38 03:00:52 -304.653978 0.152755
BFGS: 39 03:00:52 -304.656970 0.169042
BFGS: 40 03:00:52 -304.659622 0.134050
BFGS: 41 03:00:52 -304.661219 0.085902
BFGS: 42 03:00:52 -304.661925 0.076536
BFGS: 43 03:00:52 -304.662499 0.062773
BFGS: 44 03:00:53 -304.663187 0.046889
Step Time Energy fmax
BFGS: 0 03:00:53 -301.038213 3.994321
BFGS: 1 03:00:53 -301.445306 3.192121
BFGS: 2 03:00:53 -302.619685 3.571723
BFGS: 3 03:00:53 -302.637012 5.980525
BFGS: 4 03:00:53 -302.978023 2.482137
BFGS: 5 03:00:53 -303.109526 1.202870
BFGS: 6 03:00:54 -303.128201 0.761092
BFGS: 7 03:00:54 -303.157313 0.961282
BFGS: 8 03:00:54 -303.177587 1.096071
BFGS: 9 03:00:54 -303.222983 0.835404
BFGS: 10 03:00:54 -303.240961 0.527588
BFGS: 11 03:00:54 -303.283255 0.734325
BFGS: 12 03:00:54 -303.337837 1.295768
BFGS: 13 03:00:55 -303.420445 1.976840
BFGS: 14 03:00:55 -303.539550 2.289683
BFGS: 15 03:00:55 -303.655312 1.733267
BFGS: 16 03:00:55 -303.747085 1.994152
BFGS: 17 03:00:55 -303.946127 2.030288
BFGS: 18 03:00:55 -304.223904 1.413057
BFGS: 19 03:00:56 -304.358947 2.296489
BFGS: 20 03:00:56 -304.439767 0.818340
BFGS: 21 03:00:56 -304.480331 0.761821
BFGS: 22 03:00:56 -304.542177 0.450956
BFGS: 23 03:00:56 -304.559557 0.395244
BFGS: 24 03:00:57 -304.579259 0.356967
BFGS: 25 03:00:57 -304.586603 0.332147
BFGS: 26 03:00:57 -304.603359 0.298047
BFGS: 27 03:00:57 -304.612472 0.318917
BFGS: 28 03:00:58 -304.619727 0.311194
BFGS: 29 03:00:58 -304.625759 0.269078
BFGS: 30 03:00:58 -304.634466 0.259327
BFGS: 31 03:00:58 -304.643591 0.259663
BFGS: 32 03:00:58 -304.649448 0.190870
BFGS: 33 03:00:58 -304.652704 0.180480
BFGS: 34 03:00:58 -304.655659 0.210013
BFGS: 35 03:00:59 -304.658737 0.165175
BFGS: 36 03:00:59 -304.660848 0.098690
BFGS: 37 03:00:59 -304.661815 0.059580
BFGS: 38 03:00:59 -304.662283 0.065794
BFGS: 39 03:00:59 -304.662744 0.066852
BFGS: 40 03:00:59 -304.663302 0.053989
BFGS: 41 03:01:00 -304.663699 0.034996
Step Time Energy fmax
BFGS: 0 03:01:00 -302.191525 4.136089
BFGS: 1 03:01:00 -302.582323 2.987241
BFGS: 2 03:01:00 -303.472708 3.261636
BFGS: 3 03:01:01 -303.638016 2.900256
BFGS: 4 03:01:01 -303.918260 1.315577
BFGS: 5 03:01:01 -303.967195 0.923888
BFGS: 6 03:01:02 -304.058280 0.719423
BFGS: 7 03:01:02 -304.157964 1.054453
BFGS: 8 03:01:02 -304.224098 0.940653
BFGS: 9 03:01:02 -304.312919 1.098935
BFGS: 10 03:01:03 -304.415077 0.959401
BFGS: 11 03:01:03 -304.478147 0.851262
BFGS: 12 03:01:03 -304.523039 0.839056
BFGS: 13 03:01:03 -304.553964 0.636649
BFGS: 14 03:01:04 -304.571293 0.452983
BFGS: 15 03:01:04 -304.583024 0.297905
BFGS: 16 03:01:04 -304.593055 0.287916
BFGS: 17 03:01:04 -304.600706 0.272254
BFGS: 18 03:01:04 -304.607380 0.272087
BFGS: 19 03:01:04 -304.618483 0.272082
BFGS: 20 03:01:05 -304.628731 0.253388
BFGS: 21 03:01:05 -304.637243 0.231767
BFGS: 22 03:01:05 -304.643703 0.219233
BFGS: 23 03:01:05 -304.649957 0.205450
BFGS: 24 03:01:05 -304.655516 0.134959
BFGS: 25 03:01:06 -304.658867 0.095785
BFGS: 26 03:01:06 -304.660296 0.093237
BFGS: 27 03:01:06 -304.661277 0.112920
BFGS: 28 03:01:06 -304.662355 0.102677
BFGS: 29 03:01:06 -304.663228 0.059628
BFGS: 30 03:01:07 -304.663654 0.027569
Step Time Energy fmax
BFGS: 0 03:01:07 -301.055213 4.170700
BFGS: 1 03:01:07 -301.450221 3.614855
BFGS: 2 03:01:07 -302.510341 3.198578
BFGS: 3 03:01:07 -302.412653 6.710808
BFGS: 4 03:01:07 -302.809280 2.525256
BFGS: 5 03:01:08 -302.939834 1.530482
BFGS: 6 03:01:08 -303.041147 1.712875
BFGS: 7 03:01:08 -303.080933 0.888285
BFGS: 8 03:01:08 -303.170622 1.393094
BFGS: 9 03:01:08 -303.207307 1.075068
BFGS: 10 03:01:08 -303.246699 0.661731
BFGS: 11 03:01:08 -303.267815 0.581252
BFGS: 12 03:01:08 -303.312882 1.212848
BFGS: 13 03:01:08 -303.372530 1.631475
BFGS: 14 03:01:08 -303.441684 2.028097
BFGS: 15 03:01:09 -303.519666 2.022672
BFGS: 16 03:01:09 -303.690661 2.198693
BFGS: 17 03:01:09 -303.831718 2.464544
BFGS: 18 03:01:09 -303.943471 1.377594
BFGS: 19 03:01:09 -304.034848 0.710663
BFGS: 20 03:01:09 -304.057798 0.620486
BFGS: 21 03:01:10 -304.072139 0.636469
BFGS: 22 03:01:10 -304.092674 0.553830
BFGS: 23 03:01:10 -304.112692 0.498356
BFGS: 24 03:01:10 -304.126283 0.281564
BFGS: 25 03:01:10 -304.132380 0.244287
BFGS: 26 03:01:10 -304.137720 0.237771
BFGS: 27 03:01:10 -304.143771 0.262862
BFGS: 28 03:01:10 -304.150453 0.201647
BFGS: 29 03:01:11 -304.155525 0.178297
BFGS: 30 03:01:11 -304.158479 0.168427
BFGS: 31 03:01:11 -304.160539 0.150474
BFGS: 32 03:01:11 -304.162955 0.167434
BFGS: 33 03:01:11 -304.165773 0.151520
BFGS: 34 03:01:11 -304.168456 0.152355
BFGS: 35 03:01:11 -304.171027 0.178669
BFGS: 36 03:01:11 -304.174338 0.233035
BFGS: 37 03:01:11 -304.180653 0.322246
BFGS: 38 03:01:11 -304.194334 0.580374
BFGS: 39 03:01:12 -304.210244 0.533619
BFGS: 40 03:01:12 -304.246327 0.609416
BFGS: 41 03:01:12 -304.229243 0.640406
BFGS: 42 03:01:12 -304.278386 0.472417
BFGS: 43 03:01:12 -304.287018 0.379336
BFGS: 44 03:01:12 -304.297551 0.281288
BFGS: 45 03:01:12 -304.305764 0.269013
BFGS: 46 03:01:12 -304.316276 0.219610
BFGS: 47 03:01:13 -304.321573 0.209028
BFGS: 48 03:01:13 -304.324536 0.160070
BFGS: 49 03:01:13 -304.327155 0.116350
BFGS: 50 03:01:13 -304.329993 0.100625
BFGS: 51 03:01:14 -304.332586 0.104588
BFGS: 52 03:01:14 -304.334233 0.070642
BFGS: 53 03:01:14 -304.334818 0.031537
Step Time Energy fmax
BFGS: 0 03:01:14 -301.989198 4.228397
BFGS: 1 03:01:14 -302.398195 3.576136
BFGS: 2 03:01:15 -303.368893 2.910844
BFGS: 3 03:01:15 -303.522030 2.747851
BFGS: 4 03:01:15 -303.740137 1.711174
BFGS: 5 03:01:15 -303.879643 1.934907
BFGS: 6 03:01:15 -303.930059 1.004606
BFGS: 7 03:01:16 -304.001632 0.626546
BFGS: 8 03:01:16 -304.029110 0.779176
BFGS: 9 03:01:16 -304.065313 0.756266
BFGS: 10 03:01:16 -304.107682 0.693476
BFGS: 11 03:01:16 -304.134571 0.366359
BFGS: 12 03:01:17 -304.142999 0.272175
BFGS: 13 03:01:17 -304.148988 0.298203
BFGS: 14 03:01:17 -304.158290 0.259589
BFGS: 15 03:01:17 -304.163974 0.193822
BFGS: 16 03:01:18 -304.167353 0.177124
BFGS: 17 03:01:18 -304.170691 0.187314
BFGS: 18 03:01:18 -304.175962 0.322568
BFGS: 19 03:01:18 -304.185214 0.443770
BFGS: 20 03:01:19 -304.199129 0.462607
BFGS: 21 03:01:19 -304.214482 0.539214
BFGS: 22 03:01:19 -304.235895 0.474384
BFGS: 23 03:01:19 -304.250087 0.472842
BFGS: 24 03:01:20 -304.259604 0.533923
BFGS: 25 03:01:20 -304.274065 0.398237
BFGS: 26 03:01:20 -304.289650 0.350919
BFGS: 27 03:01:21 -304.295537 0.277550
BFGS: 28 03:01:21 -304.302325 0.228238
BFGS: 29 03:01:21 -304.309919 0.315401
BFGS: 30 03:01:21 -304.317629 0.277755
BFGS: 31 03:01:22 -304.322478 0.158318
BFGS: 32 03:01:22 -304.325104 0.151851
BFGS: 33 03:01:22 -304.327412 0.136957
BFGS: 34 03:01:22 -304.330041 0.178002
BFGS: 35 03:01:22 -304.332561 0.156385
BFGS: 36 03:01:22 -304.333808 0.070192
BFGS: 37 03:01:22 -304.334161 0.041886
# Relax the product systems
product1_energies = []
for config in product1_configs:
config.calc = calc
config.pbc = True
opt = BFGS(config)
opt.run(fmax=0.05, steps=optimization_steps)
product1_energies.append(config.get_potential_energy())WARNING:root:The UMA fast path (merge_mole + compile) is only available for fixed composition, task, charge, and spin. This is optimized for MD applications. Falling back to a less optimized version for subsequent evaluations. Reason: 'Compositions differ from merged model'.
Use inference_settings='batch' for heterogeneous batched evaluations.
Step Time Energy fmax
BFGS: 0 03:01:29 -297.084711 4.462347
BFGS: 1 03:01:29 -297.540058 4.575047
BFGS: 2 03:01:29 -298.787541 3.495628
BFGS: 3 03:01:30 -298.932809 5.558545
BFGS: 4 03:01:30 -299.203589 1.859782
BFGS: 5 03:01:30 -299.316341 1.744871
BFGS: 6 03:01:30 -299.706356 1.345279
BFGS: 7 03:01:31 -299.850791 1.475389
BFGS: 8 03:01:31 -299.898689 0.845442
BFGS: 9 03:01:32 -299.971926 0.757845
BFGS: 10 03:01:32 -300.013322 0.660258
BFGS: 11 03:01:32 -300.031352 0.540814
BFGS: 12 03:01:33 -300.042684 0.267610
BFGS: 13 03:01:33 -300.046555 0.255338
BFGS: 14 03:01:33 -300.048635 0.203937
BFGS: 15 03:01:34 -300.050702 0.127567
BFGS: 16 03:01:34 -300.051870 0.115314
BFGS: 17 03:01:35 -300.052344 0.093244
BFGS: 18 03:01:35 -300.052739 0.071524
BFGS: 19 03:01:35 -300.053271 0.083958
BFGS: 20 03:01:36 -300.053774 0.066870
BFGS: 21 03:01:36 -300.054074 0.042795
Step Time Energy fmax
BFGS: 0 03:01:36 -296.858122 4.448718
BFGS: 1 03:01:36 -297.317494 4.594838
BFGS: 2 03:01:36 -298.639440 3.369729
BFGS: 3 03:01:37 -298.513269 7.417799
BFGS: 4 03:01:37 -298.960155 2.009442
BFGS: 5 03:01:38 -299.094033 1.727672
BFGS: 6 03:01:38 -299.459718 1.821140
BFGS: 7 03:01:38 -299.679288 1.495335
BFGS: 8 03:01:38 -299.765576 1.104497
BFGS: 9 03:01:39 -299.836697 0.882883
BFGS: 10 03:01:39 -299.933561 0.794562
BFGS: 11 03:01:39 -299.964358 0.556849
BFGS: 12 03:01:40 -299.982245 0.390896
BFGS: 13 03:01:40 -300.005414 0.258766
BFGS: 14 03:01:40 -300.014816 0.342178
BFGS: 15 03:01:41 -300.022547 0.355200
BFGS: 16 03:01:41 -300.029236 0.270265
BFGS: 17 03:01:41 -300.036120 0.244425
BFGS: 18 03:01:41 -300.042355 0.283792
BFGS: 19 03:01:42 -300.047477 0.240580
BFGS: 20 03:01:42 -300.050533 0.156528
BFGS: 21 03:01:42 -300.052144 0.077721
BFGS: 22 03:01:43 -300.052959 0.058092
BFGS: 23 03:01:43 -300.053400 0.076374
BFGS: 24 03:01:43 -300.053754 0.074879
BFGS: 25 03:01:44 -300.054053 0.046630
Step Time Energy fmax
BFGS: 0 03:01:44 -297.309461 4.666599
BFGS: 1 03:01:44 -297.785569 4.747690
BFGS: 2 03:01:45 -299.027273 3.749933
BFGS: 3 03:01:45 -299.427545 3.614018
BFGS: 4 03:01:45 -299.577215 1.566133
BFGS: 5 03:01:45 -299.732755 1.382151
BFGS: 6 03:01:46 -299.916634 1.195669
BFGS: 7 03:01:46 -299.962476 1.229283
BFGS: 8 03:01:46 -300.224098 1.323426
BFGS: 9 03:01:47 -300.347431 1.740715
BFGS: 10 03:01:47 -300.410179 1.349851
BFGS: 11 03:01:47 -300.497864 0.988658
BFGS: 12 03:01:47 -300.528749 0.781611
BFGS: 13 03:01:48 -300.546436 0.538924
BFGS: 14 03:01:48 -300.561821 0.351538
BFGS: 15 03:01:49 -300.572339 0.394613
BFGS: 16 03:01:49 -300.583265 0.376741
BFGS: 17 03:01:49 -300.591652 0.246223
BFGS: 18 03:01:49 -300.596271 0.164185
BFGS: 19 03:01:50 -300.598019 0.104939
BFGS: 20 03:01:50 -300.599252 0.122685
BFGS: 21 03:01:50 -300.600986 0.131867
BFGS: 22 03:01:51 -300.602618 0.110495
BFGS: 23 03:01:51 -300.603509 0.064284
BFGS: 24 03:01:51 -300.603751 0.038160
Step Time Energy fmax
BFGS: 0 03:01:51 -297.477216 4.479276
BFGS: 1 03:01:52 -297.934149 4.526189
BFGS: 2 03:01:52 -299.115563 3.293253
BFGS: 3 03:01:52 -299.322315 4.225158
BFGS: 4 03:01:53 -299.519506 1.411134
BFGS: 5 03:01:53 -299.621760 1.336415
BFGS: 6 03:01:53 -299.895160 0.947875
BFGS: 7 03:01:53 -299.930042 0.831563
BFGS: 8 03:01:54 -299.993933 0.713379
BFGS: 9 03:01:54 -300.020529 0.562126
BFGS: 10 03:01:54 -300.035963 0.267888
BFGS: 11 03:01:55 -300.039045 0.186670
BFGS: 12 03:01:55 -300.043035 0.184391
BFGS: 13 03:01:55 -300.046512 0.187160
BFGS: 14 03:01:56 -300.048531 0.163032
BFGS: 15 03:01:56 -300.049742 0.132903
BFGS: 16 03:01:56 -300.051050 0.133078
BFGS: 17 03:01:57 -300.052580 0.152453
BFGS: 18 03:01:57 -300.053732 0.104190
BFGS: 19 03:01:57 -300.054201 0.032380
Step Time Energy fmax
BFGS: 0 03:01:58 -295.961421 4.360468
BFGS: 1 03:01:58 -296.509241 4.677279
BFGS: 2 03:01:58 -298.209935 2.837207
BFGS: 3 03:01:58 -296.408826 19.584997
BFGS: 4 03:01:59 -298.362516 1.770370
BFGS: 5 03:01:59 -298.420041 1.016265
BFGS: 6 03:01:59 -298.456243 0.517465
BFGS: 7 03:02:00 -298.460270 0.269735
BFGS: 8 03:02:00 -298.466811 0.065258
BFGS: 9 03:02:00 -298.468172 0.074368
BFGS: 10 03:02:00 -298.468332 0.027121
Step Time Energy fmax
BFGS: 0 03:02:01 -296.228110 4.370615
BFGS: 1 03:02:01 -296.718367 4.610711
BFGS: 2 03:02:02 -298.214827 3.217436
BFGS: 3 03:02:02 -297.451322 12.275275
BFGS: 4 03:02:02 -298.436719 1.899871
BFGS: 5 03:02:02 -298.504322 1.100928
BFGS: 6 03:02:03 -298.552037 1.021402
BFGS: 7 03:02:03 -298.569340 0.953796
BFGS: 8 03:02:04 -298.666828 1.399601
BFGS: 9 03:02:04 -298.708480 1.282961
BFGS: 10 03:02:04 -299.120631 1.830914
BFGS: 11 03:02:05 -299.558671 2.308799
BFGS: 12 03:02:05 -299.937054 1.109195
BFGS: 13 03:02:05 -300.038558 1.361572
BFGS: 14 03:02:06 -300.077176 1.783684
BFGS: 15 03:02:06 -300.240802 1.516183
BFGS: 16 03:02:07 -300.466484 1.261905
BFGS: 17 03:02:07 -300.501950 0.733621
BFGS: 18 03:02:07 -300.522018 0.559643
BFGS: 19 03:02:08 -300.542225 0.521377
BFGS: 20 03:02:08 -300.569783 0.386157
BFGS: 21 03:02:08 -300.577075 0.321842
BFGS: 22 03:02:09 -300.585331 0.279043
BFGS: 23 03:02:09 -300.591911 0.193321
BFGS: 24 03:02:09 -300.596246 0.163161
BFGS: 25 03:02:10 -300.598467 0.125541
BFGS: 26 03:02:10 -300.599885 0.088061
BFGS: 27 03:02:10 -300.601294 0.077124
BFGS: 28 03:02:11 -300.602654 0.065530
BFGS: 29 03:02:11 -300.603458 0.062412
BFGS: 30 03:02:11 -300.603746 0.039963
Step Time Energy fmax
BFGS: 0 03:02:12 -296.904823 4.543624
BFGS: 1 03:02:12 -297.377041 4.677538
BFGS: 2 03:02:12 -298.689329 3.689458
BFGS: 3 03:02:12 -298.896867 5.660660
BFGS: 4 03:02:12 -299.169648 2.010892
BFGS: 5 03:02:12 -299.303540 1.873998
BFGS: 6 03:02:13 -299.622709 1.258325
BFGS: 7 03:02:13 -299.648505 1.071359
BFGS: 8 03:02:13 -299.699064 1.166554
BFGS: 9 03:02:14 -299.731302 1.411424
BFGS: 10 03:02:14 -299.787999 1.689159
BFGS: 11 03:02:14 -299.858733 1.780432
BFGS: 12 03:02:14 -299.986287 2.189742
BFGS: 13 03:02:14 -300.100377 1.946713
BFGS: 14 03:02:15 -300.172364 2.071351
BFGS: 15 03:02:15 -300.289957 1.389866
BFGS: 16 03:02:15 -300.407856 1.592181
BFGS: 17 03:02:15 -300.449401 0.964198
BFGS: 18 03:02:16 -300.479328 0.651566
BFGS: 19 03:02:16 -300.513346 0.844024
BFGS: 20 03:02:16 -300.537579 0.721326
BFGS: 21 03:02:17 -300.564543 0.408720
BFGS: 22 03:02:17 -300.575980 0.333024
BFGS: 23 03:02:17 -300.582296 0.299980
BFGS: 24 03:02:17 -300.586508 0.248828
BFGS: 25 03:02:17 -300.591023 0.228568
BFGS: 26 03:02:18 -300.594989 0.170621
BFGS: 27 03:02:18 -300.597239 0.108681
BFGS: 28 03:02:18 -300.598201 0.095586
BFGS: 29 03:02:19 -300.598880 0.097011
BFGS: 30 03:02:19 -300.599683 0.092736
BFGS: 31 03:02:19 -300.600678 0.071251
BFGS: 32 03:02:20 -300.601521 0.078933
BFGS: 33 03:02:20 -300.601963 0.072097
BFGS: 34 03:02:20 -300.602211 0.065354
BFGS: 35 03:02:21 -300.602525 0.059467
BFGS: 36 03:02:21 -300.603006 0.045626
Step Time Energy fmax
BFGS: 0 03:02:21 -297.305072 4.509285
BFGS: 1 03:02:21 -297.772043 4.583569
BFGS: 2 03:02:22 -299.001348 3.418356
BFGS: 3 03:02:22 -299.220930 4.481493
BFGS: 4 03:02:22 -299.428592 1.471649
BFGS: 5 03:02:23 -299.526347 1.289839
BFGS: 6 03:02:23 -299.744262 1.448245
BFGS: 7 03:02:23 -299.778652 0.793196
BFGS: 8 03:02:23 -299.827763 0.885687
BFGS: 9 03:02:24 -299.882180 0.941363
BFGS: 10 03:02:24 -299.913061 0.761663
BFGS: 11 03:02:24 -299.937712 0.516085
BFGS: 12 03:02:24 -299.950068 0.512460
BFGS: 13 03:02:24 -299.958109 0.555031
BFGS: 14 03:02:25 -299.976010 0.589630
BFGS: 15 03:02:25 -299.991234 0.460939
BFGS: 16 03:02:25 -300.004353 0.375653
BFGS: 17 03:02:25 -300.017674 0.407182
BFGS: 18 03:02:26 -300.032185 0.337601
BFGS: 19 03:02:26 -300.041780 0.259003
BFGS: 20 03:02:26 -300.045530 0.225245
BFGS: 21 03:02:26 -300.048516 0.136455
BFGS: 22 03:02:27 -300.051153 0.162191
BFGS: 23 03:02:27 -300.052539 0.126112
BFGS: 24 03:02:27 -300.053661 0.079604
BFGS: 25 03:02:27 -300.054139 0.038354
Step Time Energy fmax
BFGS: 0 03:02:27 -297.180558 4.663071
BFGS: 1 03:02:27 -297.638046 4.777720
BFGS: 2 03:02:28 -298.876374 4.009334
BFGS: 3 03:02:28 -299.368922 3.661056
BFGS: 4 03:02:28 -299.551841 2.078063
BFGS: 5 03:02:28 -300.068521 1.806228
BFGS: 6 03:02:28 -300.166228 1.968449
BFGS: 7 03:02:29 -300.260099 1.442323
BFGS: 8 03:02:29 -300.453589 1.174191
BFGS: 9 03:02:29 -300.528360 1.033489
BFGS: 10 03:02:30 -300.550388 0.487811
BFGS: 11 03:02:30 -300.562856 0.391876
BFGS: 12 03:02:30 -300.592428 0.224825
BFGS: 13 03:02:31 -300.596396 0.195100
BFGS: 14 03:02:31 -300.598847 0.106896
BFGS: 15 03:02:31 -300.599741 0.087539
BFGS: 16 03:02:32 -300.600740 0.087048
BFGS: 17 03:02:32 -300.601439 0.092440
BFGS: 18 03:02:32 -300.602309 0.101228
BFGS: 19 03:02:33 -300.603037 0.079882
BFGS: 20 03:02:33 -300.603419 0.044762
Step Time Energy fmax
BFGS: 0 03:02:33 -296.128013 4.359428
BFGS: 1 03:02:33 -296.633674 4.622423
BFGS: 2 03:02:34 -298.194731 3.093366
BFGS: 3 03:02:34 -297.122300 14.451662
BFGS: 4 03:02:35 -298.389036 1.865805
BFGS: 5 03:02:35 -298.452949 1.045819
BFGS: 6 03:02:35 -298.491491 0.743463
BFGS: 7 03:02:36 -298.499271 0.562003
BFGS: 8 03:02:36 -298.523913 0.450559
BFGS: 9 03:02:36 -298.528814 0.502203
BFGS: 10 03:02:36 -298.549632 0.721717
BFGS: 11 03:02:37 -298.607924 1.489871
BFGS: 12 03:02:37 -298.665528 2.411038
BFGS: 13 03:02:37 -298.712626 3.088732
BFGS: 14 03:02:37 -298.831931 3.318623
BFGS: 15 03:02:38 -299.015387 3.586828
BFGS: 16 03:02:38 -299.343287 3.804519
BFGS: 17 03:02:38 -300.181091 2.234052
BFGS: 18 03:02:38 -300.443478 1.010206
BFGS: 19 03:02:39 -300.488904 0.857878
BFGS: 20 03:02:39 -300.577009 0.478829
BFGS: 21 03:02:39 -300.582082 0.308963
BFGS: 22 03:02:39 -300.589090 0.235227
BFGS: 23 03:02:40 -300.594589 0.193752
BFGS: 24 03:02:40 -300.597418 0.149017
BFGS: 25 03:02:40 -300.598509 0.120679
BFGS: 26 03:02:40 -300.599573 0.141839
BFGS: 27 03:02:41 -300.601045 0.133229
BFGS: 28 03:02:41 -300.602394 0.077945
BFGS: 29 03:02:41 -300.603072 0.045239
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 03:02:41 -295.109691 1.638525
BFGS: 1 03:02:42 -295.215762 1.477748
BFGS: 2 03:02:42 -295.414082 2.160563
BFGS: 3 03:02:42 -295.484608 0.514508
BFGS: 4 03:02:43 -295.498684 0.615410
BFGS: 5 03:02:43 -295.527260 0.551141
BFGS: 6 03:02:43 -295.537036 0.285803
BFGS: 7 03:02:44 -295.542941 0.285798
BFGS: 8 03:02:44 -295.548116 0.312042
BFGS: 9 03:02:44 -295.553479 0.244727
BFGS: 10 03:02:45 -295.556367 0.133249
BFGS: 11 03:02:45 -295.556982 0.056236
BFGS: 12 03:02:45 -295.557099 0.059467
BFGS: 13 03:02:46 -295.557275 0.067124
BFGS: 14 03:02:46 -295.557601 0.077050
BFGS: 15 03:02:46 -295.558143 0.082354
BFGS: 16 03:02:46 -295.558793 0.076841
BFGS: 17 03:02:47 -295.559508 0.075198
BFGS: 18 03:02:47 -295.560680 0.146153
BFGS: 19 03:02:47 -295.564181 0.354469
BFGS: 20 03:02:47 -295.574159 0.757451
BFGS: 21 03:02:48 -295.612457 0.994700
BFGS: 22 03:02:48 -295.672800 1.027723
BFGS: 23 03:02:48 -295.693666 1.021306
BFGS: 24 03:02:49 -295.715536 0.890819
BFGS: 25 03:02:49 -295.742343 0.782739
BFGS: 26 03:02:49 -295.800334 0.471359
BFGS: 27 03:02:49 -295.814438 0.289177
BFGS: 28 03:02:50 -295.824728 0.311683
BFGS: 29 03:02:50 -295.828448 0.282283
BFGS: 30 03:02:50 -295.831692 0.182782
BFGS: 31 03:02:51 -295.834289 0.112366
BFGS: 32 03:02:51 -295.836077 0.110220
BFGS: 33 03:02:51 -295.836981 0.111425
BFGS: 34 03:02:52 -295.837722 0.114393
BFGS: 35 03:02:52 -295.838885 0.123207
BFGS: 36 03:02:52 -295.840984 0.137961
BFGS: 37 03:02:53 -295.843927 0.160816
BFGS: 38 03:02:53 -295.847311 0.184498
BFGS: 39 03:02:53 -295.851626 0.234538
BFGS: 40 03:02:54 -295.859088 0.308868
BFGS: 41 03:02:54 -295.870210 0.373190
BFGS: 42 03:02:54 -295.889339 0.371727
BFGS: 43 03:02:55 -295.904862 0.332733
BFGS: 44 03:02:55 -295.909871 0.187686
BFGS: 45 03:02:55 -295.914511 0.181474
BFGS: 46 03:02:56 -295.916853 0.133976
BFGS: 47 03:02:56 -295.921680 0.060060
BFGS: 48 03:02:56 -295.922294 0.056496
BFGS: 49 03:02:57 -295.922635 0.040570
Step Time Energy fmax
BFGS: 0 03:02:57 -295.520199 0.922659
BFGS: 1 03:02:57 -295.577500 0.865046
BFGS: 2 03:02:57 -295.778790 0.621786
BFGS: 3 03:02:58 -295.791387 0.490005
BFGS: 4 03:02:58 -295.805264 0.519903
BFGS: 5 03:02:58 -295.836169 0.541397
BFGS: 6 03:02:58 -295.852713 0.486496
BFGS: 7 03:02:59 -295.870161 0.578194
BFGS: 8 03:02:59 -295.886319 0.457118
BFGS: 9 03:02:59 -295.899953 0.248343
BFGS: 10 03:03:00 -295.907164 0.265568
BFGS: 11 03:03:00 -295.910564 0.239480
BFGS: 12 03:03:00 -295.912917 0.199851
BFGS: 13 03:03:01 -295.916073 0.137052
BFGS: 14 03:03:01 -295.918678 0.109372
BFGS: 15 03:03:01 -295.920005 0.120103
BFGS: 16 03:03:01 -295.920691 0.106952
BFGS: 17 03:03:02 -295.921465 0.077062
BFGS: 18 03:03:02 -295.922367 0.044056
Step Time Energy fmax
BFGS: 0 03:03:02 -295.161088 1.510744
BFGS: 1 03:03:03 -295.256937 1.368049
BFGS: 2 03:03:03 -295.461636 1.910937
BFGS: 3 03:03:03 -295.518568 0.545949
BFGS: 4 03:03:03 -295.530835 0.588331
BFGS: 5 03:03:04 -295.559816 0.374550
BFGS: 6 03:03:04 -295.565752 0.261361
BFGS: 7 03:03:04 -295.571626 0.314366
BFGS: 8 03:03:04 -295.577148 0.302301
BFGS: 9 03:03:05 -295.582551 0.240404
BFGS: 10 03:03:05 -295.585137 0.166251
BFGS: 11 03:03:05 -295.586145 0.193201
BFGS: 12 03:03:05 -295.587728 0.247074
BFGS: 13 03:03:06 -295.592621 0.381538
BFGS: 14 03:03:06 -295.624297 0.746831
BFGS: 15 03:03:06 -295.701546 0.768022
BFGS: 16 03:03:07 -295.803540 0.640317
BFGS: 17 03:03:07 -295.874740 0.434611
BFGS: 18 03:03:07 -295.890246 0.503855
BFGS: 19 03:03:07 -295.910284 0.366388
BFGS: 20 03:03:08 -295.946181 0.262204
BFGS: 21 03:03:08 -295.950043 0.235118
BFGS: 22 03:03:09 -295.952700 0.182353
BFGS: 23 03:03:09 -295.954707 0.118428
BFGS: 24 03:03:09 -295.956975 0.073156
BFGS: 25 03:03:09 -295.957963 0.061501
BFGS: 26 03:03:09 -295.958325 0.052392
BFGS: 27 03:03:10 -295.958590 0.048078
Step Time Energy fmax
BFGS: 0 03:03:10 -295.130064 1.584769
BFGS: 1 03:03:10 -295.231950 1.431258
BFGS: 2 03:03:10 -295.432697 2.054503
BFGS: 3 03:03:11 -295.497403 0.526155
BFGS: 4 03:03:11 -295.510635 0.603246
BFGS: 5 03:03:11 -295.539160 0.485326
BFGS: 6 03:03:11 -295.547174 0.233686
BFGS: 7 03:03:12 -295.552696 0.293374
BFGS: 8 03:03:12 -295.557841 0.305397
BFGS: 9 03:03:12 -295.562950 0.227340
BFGS: 10 03:03:13 -295.565538 0.118702
BFGS: 11 03:03:13 -295.566131 0.097069
BFGS: 12 03:03:13 -295.566412 0.107945
BFGS: 13 03:03:14 -295.567155 0.137129
BFGS: 14 03:03:14 -295.568708 0.180510
BFGS: 15 03:03:14 -295.572673 0.242152
BFGS: 16 03:03:15 -295.587209 0.336351
BFGS: 17 03:03:15 -295.593596 0.597230
BFGS: 18 03:03:15 -295.609888 0.618908
BFGS: 19 03:03:16 -295.649337 0.400870
BFGS: 20 03:03:16 -295.668256 0.564339
BFGS: 21 03:03:16 -295.685896 0.707696
BFGS: 22 03:03:16 -295.714030 0.810728
BFGS: 23 03:03:17 -295.740041 0.683211
BFGS: 24 03:03:17 -295.760996 0.606435
BFGS: 25 03:03:17 -295.778341 0.561023
BFGS: 26 03:03:17 -295.787696 0.450192
BFGS: 27 03:03:18 -295.799357 0.371831
BFGS: 28 03:03:18 -295.811212 0.261505
BFGS: 29 03:03:18 -295.820414 0.256808
BFGS: 30 03:03:19 -295.823626 0.221974
BFGS: 31 03:03:19 -295.825652 0.187273
BFGS: 32 03:03:19 -295.827634 0.097932
BFGS: 33 03:03:20 -295.828982 0.080855
BFGS: 34 03:03:20 -295.829498 0.078465
BFGS: 35 03:03:20 -295.829848 0.064110
BFGS: 36 03:03:21 -295.830283 0.061805
BFGS: 37 03:03:21 -295.830699 0.066854
BFGS: 38 03:03:21 -295.830999 0.073651
BFGS: 39 03:03:22 -295.831283 0.079081
BFGS: 40 03:03:22 -295.831834 0.088285
BFGS: 41 03:03:23 -295.833321 0.112307
BFGS: 42 03:03:23 -295.838076 0.223936
BFGS: 43 03:03:23 -295.845419 0.445710
BFGS: 44 03:03:23 -295.850231 0.619208
BFGS: 45 03:03:24 -295.869800 0.536705
BFGS: 46 03:03:24 -295.912938 0.372534
BFGS: 47 03:03:24 -295.917635 0.319083
BFGS: 48 03:03:24 -295.935574 0.229193
BFGS: 49 03:03:25 -295.942883 0.196660
BFGS: 50 03:03:25 -295.949005 0.144319
BFGS: 51 03:03:25 -295.956388 0.082301
BFGS: 52 03:03:26 -295.957091 0.074467
BFGS: 53 03:03:26 -295.957784 0.062402
BFGS: 54 03:03:27 -295.958619 0.049147
Step Time Energy fmax
BFGS: 0 03:03:27 -295.433885 1.080011
BFGS: 1 03:03:27 -295.497709 1.000655
BFGS: 2 03:03:28 -295.708260 0.866997
BFGS: 3 03:03:28 -295.724479 0.554264
BFGS: 4 03:03:28 -295.739773 0.527700
BFGS: 5 03:03:28 -295.773705 0.612594
BFGS: 6 03:03:28 -295.789295 0.583367
BFGS: 7 03:03:29 -295.813181 0.613915
BFGS: 8 03:03:29 -295.841594 0.570605
BFGS: 9 03:03:29 -295.870086 0.399859
BFGS: 10 03:03:29 -295.886573 0.425390
BFGS: 11 03:03:29 -295.895360 0.366552
BFGS: 12 03:03:29 -295.900514 0.300881
BFGS: 13 03:03:30 -295.908156 0.194722
BFGS: 14 03:03:30 -295.913998 0.174717
BFGS: 15 03:03:30 -295.916691 0.189424
BFGS: 16 03:03:30 -295.918028 0.167294
BFGS: 17 03:03:31 -295.919531 0.119547
BFGS: 18 03:03:31 -295.921290 0.061164
BFGS: 19 03:03:31 -295.922571 0.054258
BFGS: 20 03:03:31 -295.923021 0.032395
Step Time Energy fmax
BFGS: 0 03:03:32 -295.512312 0.858242
BFGS: 1 03:03:32 -295.570142 0.797913
BFGS: 2 03:03:32 -295.767601 0.591323
BFGS: 3 03:03:33 -295.778885 0.393658
BFGS: 4 03:03:33 -295.786960 0.399986
BFGS: 5 03:03:33 -295.806285 0.392934
BFGS: 6 03:03:34 -295.812405 0.326102
BFGS: 7 03:03:34 -295.818139 0.268735
BFGS: 8 03:03:34 -295.822154 0.176508
BFGS: 9 03:03:34 -295.824820 0.102642
BFGS: 10 03:03:35 -295.825808 0.101545
BFGS: 11 03:03:35 -295.826245 0.079942
BFGS: 12 03:03:35 -295.826712 0.058130
BFGS: 13 03:03:36 -295.827201 0.044600
Step Time Energy fmax
BFGS: 0 03:03:36 -295.491550 0.994219
BFGS: 1 03:03:36 -295.550471 0.932391
BFGS: 2 03:03:36 -295.763744 0.690870
BFGS: 3 03:03:37 -295.777605 0.507013
BFGS: 4 03:03:37 -295.791520 0.537480
BFGS: 5 03:03:37 -295.826307 0.563083
BFGS: 6 03:03:38 -295.843778 0.563858
BFGS: 7 03:03:38 -295.862199 0.646524
BFGS: 8 03:03:38 -295.880556 0.482634
BFGS: 9 03:03:39 -295.893915 0.350032
BFGS: 10 03:03:39 -295.902767 0.370724
BFGS: 11 03:03:39 -295.908243 0.353801
BFGS: 12 03:03:39 -295.914672 0.320545
BFGS: 13 03:03:39 -295.923819 0.281986
BFGS: 14 03:03:40 -295.932958 0.254628
BFGS: 15 03:03:40 -295.939174 0.262478
BFGS: 16 03:03:40 -295.943766 0.229718
BFGS: 17 03:03:41 -295.948339 0.170560
BFGS: 18 03:03:41 -295.953178 0.105206
BFGS: 19 03:03:41 -295.956013 0.083242
BFGS: 20 03:03:42 -295.957049 0.077427
BFGS: 21 03:03:42 -295.957515 0.065863
BFGS: 22 03:03:42 -295.958002 0.059173
BFGS: 23 03:03:43 -295.958615 0.049776
Step Time Energy fmax
BFGS: 0 03:03:43 -295.125776 1.593960
BFGS: 1 03:03:43 -295.228435 1.439628
BFGS: 2 03:03:43 -295.429065 2.083441
BFGS: 3 03:03:44 -295.495227 0.525882
BFGS: 4 03:03:44 -295.508720 0.608220
BFGS: 5 03:03:44 -295.537301 0.501739
BFGS: 6 03:03:44 -295.545728 0.245243
BFGS: 7 03:03:45 -295.551352 0.292216
BFGS: 8 03:03:45 -295.556512 0.307465
BFGS: 9 03:03:45 -295.561674 0.229868
BFGS: 10 03:03:46 -295.564337 0.122323
BFGS: 11 03:03:46 -295.564940 0.092910
BFGS: 12 03:03:46 -295.565189 0.102355
BFGS: 13 03:03:47 -295.565823 0.127748
BFGS: 14 03:03:47 -295.567125 0.165614
BFGS: 15 03:03:47 -295.570241 0.221489
BFGS: 16 03:03:47 -295.578755 0.273525
BFGS: 17 03:03:48 -295.592580 0.478848
BFGS: 18 03:03:48 -295.596865 0.713089
BFGS: 19 03:03:48 -295.621353 0.461050
BFGS: 20 03:03:49 -295.646740 0.508004
BFGS: 21 03:03:49 -295.716369 0.854231
BFGS: 22 03:03:49 -295.762877 0.920427
BFGS: 23 03:03:49 -295.789352 0.682118
BFGS: 24 03:03:50 -295.799535 0.693418
BFGS: 25 03:03:50 -295.807189 0.696995
BFGS: 26 03:03:50 -295.815613 0.693117
BFGS: 27 03:03:50 -295.825125 0.680279
BFGS: 28 03:03:50 -295.832181 0.665595
BFGS: 29 03:03:50 -295.837892 0.652444
BFGS: 30 03:03:50 -295.844399 0.640338
BFGS: 31 03:03:51 -295.854377 0.621266
BFGS: 32 03:03:51 -295.867812 0.581236
BFGS: 33 03:03:51 -295.880679 0.523055
BFGS: 34 03:03:51 -295.891773 0.488710
BFGS: 35 03:03:51 -295.900095 0.473965
BFGS: 36 03:03:51 -295.908457 0.437486
BFGS: 37 03:03:52 -295.920315 0.429791
BFGS: 38 03:03:52 -295.928167 0.352152
BFGS: 39 03:03:52 -295.932375 0.352481
BFGS: 40 03:03:52 -295.934820 0.328852
BFGS: 41 03:03:52 -295.937595 0.335622
BFGS: 42 03:03:53 -295.941192 0.307542
BFGS: 43 03:03:53 -295.945065 0.271230
BFGS: 44 03:03:53 -295.946762 0.244484
BFGS: 45 03:03:53 -295.947959 0.222751
BFGS: 46 03:03:54 -295.949701 0.189259
BFGS: 47 03:03:54 -295.952351 0.146670
BFGS: 48 03:03:54 -295.955122 0.097603
BFGS: 49 03:03:54 -295.956892 0.073004
BFGS: 50 03:03:54 -295.957742 0.066685
BFGS: 51 03:03:55 -295.958289 0.055561
BFGS: 52 03:03:55 -295.958847 0.039415
Step Time Energy fmax
BFGS: 0 03:03:55 -295.300847 1.270964
BFGS: 1 03:03:55 -295.377609 1.161559
BFGS: 2 03:03:56 -295.594307 1.270723
BFGS: 3 03:03:56 -295.621830 0.605960
BFGS: 4 03:03:56 -295.633252 0.471331
BFGS: 5 03:03:56 -295.669292 0.515064
BFGS: 6 03:03:56 -295.675482 0.490934
BFGS: 7 03:03:57 -295.739612 0.570583
BFGS: 8 03:03:57 -295.752892 0.669347
BFGS: 9 03:03:57 -295.767065 0.633658
BFGS: 10 03:03:57 -295.797176 0.376428
BFGS: 11 03:03:58 -295.812498 0.209233
BFGS: 12 03:03:58 -295.819730 0.273204
BFGS: 13 03:03:58 -295.821924 0.234314
BFGS: 14 03:03:58 -295.823670 0.176450
BFGS: 15 03:03:59 -295.827184 0.103255
BFGS: 16 03:03:59 -295.828775 0.079942
BFGS: 17 03:03:59 -295.829536 0.062160
BFGS: 18 03:03:59 -295.829839 0.060662
BFGS: 19 03:03:59 -295.830178 0.065379
BFGS: 20 03:04:00 -295.830636 0.073105
BFGS: 21 03:04:00 -295.831138 0.077569
BFGS: 22 03:04:00 -295.831549 0.077057
BFGS: 23 03:04:00 -295.831974 0.078042
BFGS: 24 03:04:00 -295.832760 0.089033
BFGS: 25 03:04:00 -295.834937 0.173446
BFGS: 26 03:04:01 -295.842118 0.388344
BFGS: 27 03:04:01 -295.848377 0.529874
BFGS: 28 03:04:01 -295.863285 0.549028
BFGS: 29 03:04:01 -295.894008 0.383378
BFGS: 30 03:04:02 -295.911485 0.366357
BFGS: 31 03:04:02 -295.901494 0.357576
BFGS: 32 03:04:02 -295.931619 0.206530
BFGS: 33 03:04:02 -295.935287 0.257217
BFGS: 34 03:04:03 -295.944502 0.158868
BFGS: 35 03:04:03 -295.951243 0.145416
BFGS: 36 03:04:03 -295.956745 0.089412
BFGS: 37 03:04:04 -295.957882 0.070072
BFGS: 38 03:04:04 -295.958451 0.060276
BFGS: 39 03:04:04 -295.958878 0.046571
Step Time Energy fmax
BFGS: 0 03:04:04 -295.318074 1.252315
BFGS: 1 03:04:04 -295.391670 1.149827
BFGS: 2 03:04:04 -295.609444 1.238086
BFGS: 3 03:04:04 -295.636122 0.601106
BFGS: 4 03:04:04 -295.647397 0.463247
BFGS: 5 03:04:05 -295.683990 0.524947
BFGS: 6 03:04:05 -295.690799 0.505781
BFGS: 7 03:04:05 -295.762740 0.611742
BFGS: 8 03:04:06 -295.794607 0.896041
BFGS: 9 03:04:06 -295.816906 0.910917
BFGS: 10 03:04:06 -295.884402 0.630065
BFGS: 11 03:04:06 -295.906560 0.419803
BFGS: 12 03:04:06 -295.928278 0.317531
BFGS: 13 03:04:07 -295.936430 0.279662
BFGS: 14 03:04:07 -295.939953 0.284045
BFGS: 15 03:04:07 -295.948737 0.221857
BFGS: 16 03:04:07 -295.953714 0.120431
BFGS: 17 03:04:07 -295.956034 0.084383
BFGS: 18 03:04:07 -295.956738 0.068782
BFGS: 19 03:04:08 -295.957370 0.062712
BFGS: 20 03:04:08 -295.958104 0.054198
BFGS: 21 03:04:08 -295.958718 0.043557
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 03:04:08 -303.664075 0.916124
BFGS: 1 03:04:09 -303.684845 0.732701
BFGS: 2 03:04:09 -303.752636 0.642481
BFGS: 3 03:04:09 -303.777512 0.708016
BFGS: 4 03:04:09 -303.808082 0.671120
BFGS: 5 03:04:10 -303.840865 0.533116
BFGS: 6 03:04:10 -303.866813 0.379674
BFGS: 7 03:04:10 -303.871253 0.258476
BFGS: 8 03:04:10 -303.878279 0.166286
BFGS: 9 03:04:10 -303.882198 0.125875
BFGS: 10 03:04:10 -303.883911 0.171411
BFGS: 11 03:04:10 -303.885333 0.160621
BFGS: 12 03:04:10 -303.887137 0.143319
BFGS: 13 03:04:11 -303.888927 0.126769
BFGS: 14 03:04:11 -303.890219 0.123293
BFGS: 15 03:04:11 -303.891120 0.120531
BFGS: 16 03:04:11 -303.892346 0.111354
BFGS: 17 03:04:11 -303.894838 0.153320
BFGS: 18 03:04:11 -303.899637 0.231535
BFGS: 19 03:04:12 -303.906876 0.336115
BFGS: 20 03:04:12 -303.913791 0.348940
BFGS: 21 03:04:12 -303.924740 0.411110
BFGS: 22 03:04:12 -303.928271 0.504508
BFGS: 23 03:04:13 -303.939435 0.409206
BFGS: 24 03:04:13 -303.968827 0.289839
BFGS: 25 03:04:13 -303.988720 0.306947
BFGS: 26 03:04:13 -304.003971 0.413384
BFGS: 27 03:04:13 -304.014304 0.418835
BFGS: 28 03:04:13 -304.043060 0.377921
BFGS: 29 03:04:13 -304.061376 0.372529
BFGS: 30 03:04:14 -304.087508 0.462110
BFGS: 31 03:04:14 -304.105144 0.474200
BFGS: 32 03:04:14 -304.131370 0.474675
BFGS: 33 03:04:15 -304.160789 0.567304
BFGS: 34 03:04:15 -304.197989 0.641704
BFGS: 35 03:04:15 -304.237384 0.677746
BFGS: 36 03:04:15 -304.285566 0.718172
BFGS: 37 03:04:16 -304.316787 0.670062
BFGS: 38 03:04:16 -304.329894 0.521515
BFGS: 39 03:04:16 -304.379843 0.590802
BFGS: 40 03:04:17 -304.395353 0.382154
BFGS: 41 03:04:17 -304.411372 0.253847
BFGS: 42 03:04:17 -304.419234 0.175009
BFGS: 43 03:04:17 -304.423980 0.123408
BFGS: 44 03:04:18 -304.426707 0.102962
BFGS: 45 03:04:18 -304.428360 0.105871
BFGS: 46 03:04:18 -304.429356 0.107462
BFGS: 47 03:04:18 -304.430293 0.110744
BFGS: 48 03:04:19 -304.431625 0.118619
BFGS: 49 03:04:19 -304.433457 0.131719
BFGS: 50 03:04:19 -304.435745 0.147608
BFGS: 51 03:04:19 -304.438751 0.171810
BFGS: 52 03:04:20 -304.443668 0.231537
BFGS: 53 03:04:20 -304.452369 0.364585
BFGS: 54 03:04:20 -304.465324 0.522972
BFGS: 55 03:04:20 -304.483984 0.602625
BFGS: 56 03:04:21 -304.504568 0.325036
BFGS: 57 03:04:21 -304.509983 0.202350
BFGS: 58 03:04:21 -304.516615 0.163868
BFGS: 59 03:04:22 -304.520036 0.131753
BFGS: 60 03:04:22 -304.522629 0.132547
BFGS: 61 03:04:22 -304.524033 0.128212
BFGS: 62 03:04:23 -304.525752 0.095577
BFGS: 63 03:04:23 -304.526888 0.057369
BFGS: 64 03:04:23 -304.527547 0.044952
Step Time Energy fmax
BFGS: 0 03:04:23 -303.649270 0.891083
BFGS: 1 03:04:24 -303.669157 0.707897
BFGS: 2 03:04:24 -303.731368 0.654382
BFGS: 3 03:04:24 -303.759470 0.743286
BFGS: 4 03:04:24 -303.791469 0.736119
BFGS: 5 03:04:25 -303.826478 0.546117
BFGS: 6 03:04:25 -303.864239 0.423471
BFGS: 7 03:04:25 -303.869268 0.294635
BFGS: 8 03:04:25 -303.878000 0.172238
BFGS: 9 03:04:26 -303.882278 0.116507
BFGS: 10 03:04:26 -303.884082 0.163908
BFGS: 11 03:04:26 -303.885647 0.157311
BFGS: 12 03:04:26 -303.887472 0.147570
BFGS: 13 03:04:26 -303.889292 0.130693
BFGS: 14 03:04:27 -303.890688 0.131265
BFGS: 15 03:04:27 -303.891746 0.133371
BFGS: 16 03:04:27 -303.893271 0.130684
BFGS: 17 03:04:28 -303.896275 0.183541
BFGS: 18 03:04:28 -303.902429 0.367846
BFGS: 19 03:04:28 -303.910124 0.633565
BFGS: 20 03:04:28 -303.920027 0.546744
BFGS: 21 03:04:28 -303.937268 0.400375
BFGS: 22 03:04:28 -303.939421 0.668583
BFGS: 23 03:04:29 -303.951794 0.549765
BFGS: 24 03:04:29 -303.965139 0.471432
BFGS: 25 03:04:29 -303.982175 0.416404
BFGS: 26 03:04:29 -304.009648 0.335077
BFGS: 27 03:04:29 -304.021118 0.364929
BFGS: 28 03:04:29 -304.030694 0.476801
BFGS: 29 03:04:30 -304.050140 0.397329
BFGS: 30 03:04:30 -304.080462 0.345445
BFGS: 31 03:04:30 -304.111322 0.380197
BFGS: 32 03:04:30 -304.139378 0.448000
BFGS: 33 03:04:30 -304.167045 0.637035
BFGS: 34 03:04:31 -304.195330 0.832393
BFGS: 35 03:04:31 -304.235401 1.084106
BFGS: 36 03:04:31 -304.260532 0.999464
BFGS: 37 03:04:31 -304.370828 0.548280
BFGS: 38 03:04:31 -304.405844 0.357403
BFGS: 39 03:04:31 -304.420128 0.294475
BFGS: 40 03:04:32 -304.428520 0.280959
BFGS: 41 03:04:32 -304.435787 0.211203
BFGS: 42 03:04:32 -304.445584 0.206962
BFGS: 43 03:04:32 -304.453872 0.188063
BFGS: 44 03:04:32 -304.457572 0.195916
BFGS: 45 03:04:33 -304.460021 0.203489
BFGS: 46 03:04:33 -304.463763 0.220131
BFGS: 47 03:04:33 -304.469911 0.249248
BFGS: 48 03:04:33 -304.480845 0.369366
BFGS: 49 03:04:34 -304.493475 0.409479
BFGS: 50 03:04:34 -304.507198 0.290181
BFGS: 51 03:04:34 -304.515282 0.187339
BFGS: 52 03:04:35 -304.519259 0.140110
BFGS: 53 03:04:35 -304.522203 0.117467
BFGS: 54 03:04:35 -304.523795 0.124910
BFGS: 55 03:04:35 -304.525229 0.106646
BFGS: 56 03:04:35 -304.526353 0.072042
BFGS: 57 03:04:36 -304.527117 0.044892
Step Time Energy fmax
BFGS: 0 03:04:36 -304.417637 0.343105
BFGS: 1 03:04:36 -304.422669 0.265171
BFGS: 2 03:04:36 -304.437296 0.171245
BFGS: 3 03:04:36 -304.440180 0.171236
BFGS: 4 03:04:37 -304.442551 0.120633
BFGS: 5 03:04:37 -304.443682 0.104838
BFGS: 6 03:04:37 -304.444523 0.080083
BFGS: 7 03:04:37 -304.445113 0.071779
BFGS: 8 03:04:37 -304.445551 0.065847
BFGS: 9 03:04:38 -304.445905 0.050825
BFGS: 10 03:04:38 -304.446197 0.054663
BFGS: 11 03:04:38 -304.446429 0.042075
Step Time Energy fmax
BFGS: 0 03:04:38 -304.413887 0.405110
BFGS: 1 03:04:39 -304.419653 0.305144
BFGS: 2 03:04:39 -304.433815 0.178738
BFGS: 3 03:04:39 -304.436695 0.164293
BFGS: 4 03:04:39 -304.439359 0.137978
BFGS: 5 03:04:40 -304.440830 0.124678
BFGS: 6 03:04:40 -304.441956 0.097349
BFGS: 7 03:04:40 -304.442730 0.071872
BFGS: 8 03:04:41 -304.443230 0.056405
BFGS: 9 03:04:41 -304.443582 0.051459
BFGS: 10 03:04:41 -304.443880 0.051229
BFGS: 11 03:04:41 -304.444144 0.043996
Step Time Energy fmax
BFGS: 0 03:04:41 -301.669618 1.435292
BFGS: 1 03:04:42 -301.715743 0.796725
BFGS: 2 03:04:42 -301.760551 0.844619
BFGS: 3 03:04:42 -301.837929 1.339536
BFGS: 4 03:04:43 -301.939868 1.627306
BFGS: 5 03:04:43 -302.004009 1.279796
BFGS: 6 03:04:43 -302.047369 0.943790
BFGS: 7 03:04:43 -302.102005 0.838652
BFGS: 8 03:04:43 -302.152306 0.471537
BFGS: 9 03:04:43 -302.169588 0.451528
BFGS: 10 03:04:43 -302.179114 0.356117
BFGS: 11 03:04:44 -302.188991 0.303599
BFGS: 12 03:04:44 -302.198952 0.356969
BFGS: 13 03:04:44 -302.207991 0.363681
BFGS: 14 03:04:44 -302.219306 0.391572
BFGS: 15 03:04:44 -302.238197 0.404016
BFGS: 16 03:04:44 -302.273502 0.633345
BFGS: 17 03:04:45 -302.316905 1.162551
BFGS: 18 03:04:45 -302.370247 1.825574
BFGS: 19 03:04:45 -302.427508 2.534807
BFGS: 20 03:04:45 -302.493906 3.002644
BFGS: 21 03:04:45 -302.567377 3.213955
BFGS: 22 03:04:46 -302.635231 2.543018
BFGS: 23 03:04:46 -302.796843 2.296146
BFGS: 24 03:04:46 -303.152107 2.145206
BFGS: 25 03:04:47 -303.554750 2.017931
BFGS: 26 03:04:47 -303.795415 1.513283
BFGS: 27 03:04:47 -303.900994 1.830947
BFGS: 28 03:04:47 -303.959433 1.034498
BFGS: 29 03:04:48 -304.006460 1.214027
BFGS: 30 03:04:48 -304.055516 1.083528
BFGS: 31 03:04:48 -304.093461 0.852271
BFGS: 32 03:04:48 -304.125608 0.527190
BFGS: 33 03:04:48 -304.157638 0.576982
BFGS: 34 03:04:49 -304.220934 0.700462
BFGS: 35 03:04:49 -304.282522 0.890645
BFGS: 36 03:04:49 -304.336060 0.964130
BFGS: 37 03:04:49 -304.383403 1.031203
BFGS: 38 03:04:50 -304.435365 0.700358
BFGS: 39 03:04:50 -304.490319 0.379824
BFGS: 40 03:04:50 -304.507574 0.294317
BFGS: 41 03:04:50 -304.518060 0.229764
BFGS: 42 03:04:51 -304.522060 0.187284
BFGS: 43 03:04:51 -304.524390 0.149010
BFGS: 44 03:04:51 -304.526560 0.094699
BFGS: 45 03:04:51 -304.528339 0.087309
BFGS: 46 03:04:52 -304.529363 0.071160
BFGS: 47 03:04:52 -304.529931 0.050737
BFGS: 48 03:04:52 -304.530303 0.043545
Step Time Energy fmax
BFGS: 0 03:04:52 -301.962585 1.024902
BFGS: 1 03:04:52 -301.992849 0.809289
BFGS: 2 03:04:53 -302.070479 0.942404
BFGS: 3 03:04:53 -302.131512 1.022373
BFGS: 4 03:04:53 -302.173875 0.760871
BFGS: 5 03:04:53 -302.191121 0.597436
BFGS: 6 03:04:53 -302.214535 0.533696
BFGS: 7 03:04:54 -302.243213 0.400353
BFGS: 8 03:04:54 -302.262153 0.402721
BFGS: 9 03:04:54 -302.271861 0.348050
BFGS: 10 03:04:54 -302.284247 0.393454
BFGS: 11 03:04:54 -302.304577 0.544651
BFGS: 12 03:04:55 -302.343729 1.052623
BFGS: 13 03:04:55 -302.406790 1.934616
BFGS: 14 03:04:55 -302.469426 2.954454
BFGS: 15 03:04:55 -302.522172 3.747116
BFGS: 16 03:04:56 -302.497638 3.238283
BFGS: 17 03:04:56 -302.578104 3.559691
BFGS: 18 03:04:56 -302.579024 4.127140
BFGS: 19 03:04:57 -302.654391 3.956395
BFGS: 20 03:04:57 -302.720637 3.002717
BFGS: 21 03:04:57 -302.819401 3.314567
BFGS: 22 03:04:57 -303.020661 3.218096
BFGS: 23 03:04:58 -303.177881 2.787337
BFGS: 24 03:04:58 -303.264508 3.064122
BFGS: 25 03:04:58 -303.325797 2.505230
BFGS: 26 03:04:58 -303.374637 2.198741
BFGS: 27 03:04:59 -303.404024 2.049924
BFGS: 28 03:04:59 -303.442982 2.143422
BFGS: 29 03:04:59 -303.473240 2.235519
BFGS: 30 03:04:59 -303.497507 2.404894
BFGS: 31 03:05:00 -303.518426 2.366645
BFGS: 32 03:05:00 -303.542276 2.226760
BFGS: 33 03:05:00 -303.557708 1.986182
BFGS: 34 03:05:00 -303.574923 1.772463
BFGS: 35 03:05:01 -303.595297 1.607729
BFGS: 36 03:05:01 -303.612569 1.530508
BFGS: 37 03:05:01 -303.629316 1.460008
BFGS: 38 03:05:02 -303.650658 1.364643
BFGS: 39 03:05:02 -303.673699 1.143902
BFGS: 40 03:05:02 -303.707028 0.884512
BFGS: 41 03:05:02 -303.723207 0.867012
BFGS: 42 03:05:03 -303.736216 1.045976
BFGS: 43 03:05:03 -303.741990 1.172830
BFGS: 44 03:05:03 -303.749406 1.291912
BFGS: 45 03:05:03 -303.755490 1.290667
BFGS: 46 03:05:04 -303.758955 1.228420
BFGS: 47 03:05:04 -303.760241 1.193445
BFGS: 48 03:05:04 -303.761933 1.148632
BFGS: 49 03:05:04 -303.763725 1.125050
BFGS: 50 03:05:04 -303.765460 1.139099
BFGS: 51 03:05:04 -303.766659 1.186880
BFGS: 52 03:05:04 -303.767684 1.246550
BFGS: 53 03:05:05 -303.768898 1.312376
BFGS: 54 03:05:05 -303.770479 1.372827
BFGS: 55 03:05:05 -303.772245 1.400179
BFGS: 56 03:05:05 -303.773832 1.381949
BFGS: 57 03:05:05 -303.775026 1.340462
BFGS: 58 03:05:06 -303.775941 1.308032
BFGS: 59 03:05:06 -303.776757 1.302211
BFGS: 60 03:05:06 -303.777568 1.330166
BFGS: 61 03:05:06 -303.778311 1.384513
BFGS: 62 03:05:06 -303.778843 1.433698
BFGS: 63 03:05:06 -303.779196 1.459925
BFGS: 64 03:05:07 -303.779491 1.470481
BFGS: 65 03:05:07 -303.779840 1.473604
BFGS: 66 03:05:07 -303.780282 1.474713
BFGS: 67 03:05:07 -303.780686 1.478221
BFGS: 68 03:05:07 -303.780958 1.487435
BFGS: 69 03:05:07 -303.781160 1.500509
BFGS: 70 03:05:08 -303.781385 1.518216
BFGS: 71 03:05:08 -303.781644 1.536712
BFGS: 72 03:05:08 -303.781862 1.545423
BFGS: 73 03:05:08 -303.781995 1.540536
BFGS: 74 03:05:08 -303.782072 1.531139
BFGS: 75 03:05:09 -303.782130 1.522874
BFGS: 76 03:05:09 -303.782190 1.518548
BFGS: 77 03:05:09 -303.782257 1.520999
BFGS: 78 03:05:09 -303.782312 1.530384
BFGS: 79 03:05:10 -303.782344 1.539812
BFGS: 80 03:05:10 -303.782364 1.546745
BFGS: 81 03:05:10 -303.782379 1.550912
BFGS: 82 03:05:10 -303.782394 1.553636
BFGS: 83 03:05:11 -303.782415 1.554101
BFGS: 84 03:05:11 -303.782429 1.553599
BFGS: 85 03:05:11 -303.782437 1.552087
BFGS: 86 03:05:11 -303.782441 1.552193
BFGS: 87 03:05:11 -303.782447 1.552060
BFGS: 88 03:05:12 -303.782450 1.553496
BFGS: 89 03:05:12 -303.782455 1.554137
BFGS: 90 03:05:12 -303.782458 1.555571
BFGS: 91 03:05:12 -303.782460 1.555204
BFGS: 92 03:05:13 -303.782460 1.555587
BFGS: 93 03:05:13 -303.782458 1.555323
BFGS: 94 03:05:13 -303.782460 1.555573
BFGS: 95 03:05:13 -303.782462 1.555643
BFGS: 96 03:05:13 -303.782460 1.556069
BFGS: 97 03:05:14 -303.782462 1.556153
BFGS: 98 03:05:14 -303.782463 1.556438
BFGS: 99 03:05:14 -303.782462 1.556598
BFGS: 100 03:05:14 -303.782463 1.556802
BFGS: 101 03:05:14 -303.782462 1.556818
BFGS: 102 03:05:14 -303.782462 1.556754
BFGS: 103 03:05:15 -303.782461 1.556705
BFGS: 104 03:05:15 -303.782464 1.556643
BFGS: 105 03:05:15 -303.782461 1.556676
BFGS: 106 03:05:15 -303.782462 1.556590
BFGS: 107 03:05:16 -303.782462 1.556670
BFGS: 108 03:05:16 -303.782464 1.556690
BFGS: 109 03:05:16 -303.782466 1.556693
BFGS: 110 03:05:16 -303.782461 1.556771
BFGS: 111 03:05:17 -303.782462 1.556667
BFGS: 112 03:05:17 -303.782462 1.556652
BFGS: 113 03:05:17 -303.782464 1.556622
BFGS: 114 03:05:17 -303.782461 1.556641
BFGS: 115 03:05:18 -303.782463 1.556594
BFGS: 116 03:05:18 -303.782462 1.556606
BFGS: 117 03:05:18 -303.782464 1.556682
BFGS: 118 03:05:18 -303.782463 1.556662
BFGS: 119 03:05:18 -303.782464 1.556628
BFGS: 120 03:05:18 -303.782463 1.556645
BFGS: 121 03:05:19 -303.782464 1.556663
BFGS: 122 03:05:19 -303.782465 1.556684
BFGS: 123 03:05:19 -303.782461 1.556696
BFGS: 124 03:05:20 -303.782463 1.556664
BFGS: 125 03:05:20 -303.782464 1.556663
BFGS: 126 03:05:20 -303.782461 1.556693
BFGS: 127 03:05:20 -303.782461 1.556678
BFGS: 128 03:05:21 -303.782464 1.556652
BFGS: 129 03:05:21 -303.782463 1.556663
BFGS: 130 03:05:21 -303.782461 1.556683
BFGS: 131 03:05:22 -303.782460 1.556666
BFGS: 132 03:05:22 -303.782461 1.556642
BFGS: 133 03:05:22 -303.782463 1.556631
BFGS: 134 03:05:22 -303.782459 1.556680
BFGS: 135 03:05:22 -303.782465 1.556635
BFGS: 136 03:05:23 -303.782462 1.556650
BFGS: 137 03:05:23 -303.782460 1.556667
BFGS: 138 03:05:23 -303.782464 1.556651
BFGS: 139 03:05:23 -303.782461 1.556678
BFGS: 140 03:05:24 -303.782465 1.556649
BFGS: 141 03:05:24 -303.782464 1.556652
BFGS: 142 03:05:24 -303.782460 1.556679
BFGS: 143 03:05:25 -303.782460 1.556682
BFGS: 144 03:05:25 -303.782464 1.556650
BFGS: 145 03:05:25 -303.782461 1.556666
BFGS: 146 03:05:25 -303.782462 1.556684
BFGS: 147 03:05:26 -303.782463 1.556652
BFGS: 148 03:05:26 -303.782462 1.556663
BFGS: 149 03:05:26 -303.782458 1.556676
BFGS: 150 03:05:26 -303.782462 1.556651
BFGS: 151 03:05:26 -303.782466 1.556652
BFGS: 152 03:05:27 -303.782462 1.556679
BFGS: 153 03:05:27 -303.782462 1.556667
BFGS: 154 03:05:27 -303.782462 1.556651
BFGS: 155 03:05:28 -303.782463 1.556653
BFGS: 156 03:05:28 -303.782463 1.556652
BFGS: 157 03:05:28 -303.782462 1.556666
BFGS: 158 03:05:28 -303.782459 1.556676
BFGS: 159 03:05:28 -303.782464 1.556648
BFGS: 160 03:05:28 -303.782462 1.556665
BFGS: 161 03:05:29 -303.782461 1.556675
BFGS: 162 03:05:29 -303.782463 1.556652
BFGS: 163 03:05:29 -303.782464 1.556642
BFGS: 164 03:05:30 -303.782461 1.556679
BFGS: 165 03:05:30 -303.782460 1.556677
BFGS: 166 03:05:30 -303.782463 1.556639
BFGS: 167 03:05:30 -303.782463 1.556639
BFGS: 168 03:05:31 -303.782461 1.556680
BFGS: 169 03:05:31 -303.782461 1.556678
BFGS: 170 03:05:31 -303.782464 1.556632
BFGS: 171 03:05:31 -303.782463 1.556637
BFGS: 172 03:05:31 -303.782462 1.556687
BFGS: 173 03:05:32 -303.782462 1.556681
BFGS: 174 03:05:32 -303.782463 1.556632
BFGS: 175 03:05:32 -303.782463 1.556640
BFGS: 176 03:05:33 -303.782462 1.556681
BFGS: 177 03:05:33 -303.782464 1.556654
BFGS: 178 03:05:33 -303.782464 1.556640
BFGS: 179 03:05:33 -303.782464 1.556656
BFGS: 180 03:05:34 -303.782462 1.556679
BFGS: 181 03:05:34 -303.782461 1.556678
BFGS: 182 03:05:34 -303.782462 1.556637
BFGS: 183 03:05:34 -303.782463 1.556637
BFGS: 184 03:05:34 -303.782464 1.556678
BFGS: 185 03:05:35 -303.782462 1.556679
BFGS: 186 03:05:35 -303.782459 1.556635
BFGS: 187 03:05:35 -303.782462 1.556640
BFGS: 188 03:05:36 -303.782463 1.556679
BFGS: 189 03:05:36 -303.782464 1.556677
BFGS: 190 03:05:36 -303.782462 1.556586
BFGS: 191 03:05:36 -303.782463 1.556640
BFGS: 192 03:05:36 -303.782464 1.556678
BFGS: 193 03:05:36 -303.782463 1.556652
BFGS: 194 03:05:37 -303.782462 1.556652
BFGS: 195 03:05:37 -303.782461 1.556678
BFGS: 196 03:05:37 -303.782460 1.556665
BFGS: 197 03:05:37 -303.782460 1.556677
BFGS: 198 03:05:38 -303.782463 1.556649
BFGS: 199 03:05:38 -303.782464 1.556649
BFGS: 200 03:05:38 -303.782462 1.556669
Step Time Energy fmax
BFGS: 0 03:05:38 -301.810339 1.242369
BFGS: 1 03:05:39 -301.855843 0.914633
BFGS: 2 03:05:39 -301.932264 0.958463
BFGS: 3 03:05:39 -302.012234 1.216578
BFGS: 4 03:05:39 -302.079194 1.038616
BFGS: 5 03:05:39 -302.108948 0.813171
BFGS: 6 03:05:39 -302.142625 0.724116
BFGS: 7 03:05:40 -302.184063 0.535886
BFGS: 8 03:05:40 -302.206465 0.424090
BFGS: 9 03:05:40 -302.215837 0.370818
BFGS: 10 03:05:40 -302.224258 0.279632
BFGS: 11 03:05:40 -302.231956 0.293972
BFGS: 12 03:05:40 -302.241279 0.314349
BFGS: 13 03:05:41 -302.250287 0.375890
BFGS: 14 03:05:41 -302.263943 0.489366
BFGS: 15 03:05:41 -302.291853 0.635811
BFGS: 16 03:05:41 -302.330385 1.243254
BFGS: 17 03:05:41 -302.374419 1.943018
BFGS: 18 03:05:41 -302.427816 2.500629
BFGS: 19 03:05:42 -302.503011 2.776624
BFGS: 20 03:05:42 -302.617529 2.721743
BFGS: 21 03:05:42 -302.772081 2.053126
BFGS: 22 03:05:42 -302.980397 1.828296
BFGS: 23 03:05:43 -303.065176 1.786822
BFGS: 24 03:05:43 -303.397777 1.530358
BFGS: 25 03:05:43 -303.552682 1.939105
BFGS: 26 03:05:43 -303.657062 1.216824
BFGS: 27 03:05:43 -303.711188 0.772086
BFGS: 28 03:05:43 -303.753450 0.477200
BFGS: 29 03:05:44 -303.811685 0.503506
BFGS: 30 03:05:44 -303.853889 0.608127
BFGS: 31 03:05:44 -303.875097 0.593037
BFGS: 32 03:05:44 -303.930439 0.395053
BFGS: 33 03:05:45 -303.943809 0.326026
BFGS: 34 03:05:45 -303.957710 0.211268
BFGS: 35 03:05:45 -303.961220 0.195405
BFGS: 36 03:05:45 -303.965125 0.156761
BFGS: 37 03:05:46 -303.967596 0.095459
BFGS: 38 03:05:46 -303.968908 0.125325
BFGS: 39 03:05:46 -303.969853 0.139443
BFGS: 40 03:05:46 -303.971296 0.115160
BFGS: 41 03:05:46 -303.972457 0.086515
BFGS: 42 03:05:46 -303.972985 0.045537
Step Time Energy fmax
BFGS: 0 03:05:47 -302.018175 0.483151
BFGS: 1 03:05:47 -302.028607 0.460300
BFGS: 2 03:05:47 -302.073741 0.452564
BFGS: 3 03:05:47 -302.084550 0.473060
BFGS: 4 03:05:48 -302.150182 0.708217
BFGS: 5 03:05:48 -302.206104 0.644860
BFGS: 6 03:05:48 -302.240554 0.476439
BFGS: 7 03:05:48 -302.276853 0.398684
BFGS: 8 03:05:48 -302.298483 0.386974
BFGS: 9 03:05:49 -302.316166 0.317602
BFGS: 10 03:05:49 -302.329368 0.194421
BFGS: 11 03:05:49 -302.335686 0.184832
BFGS: 12 03:05:49 -302.339104 0.199269
BFGS: 13 03:05:50 -302.342223 0.172231
BFGS: 14 03:05:50 -302.346355 0.170273
BFGS: 15 03:05:50 -302.350835 0.126362
BFGS: 16 03:05:50 -302.353737 0.157049
BFGS: 17 03:05:50 -302.355131 0.112960
BFGS: 18 03:05:51 -302.356106 0.095671
BFGS: 19 03:05:51 -302.357599 0.104797
BFGS: 20 03:05:51 -302.358874 0.091124
BFGS: 21 03:05:51 -302.359597 0.068608
BFGS: 22 03:05:52 -302.359933 0.064103
BFGS: 23 03:05:52 -302.360309 0.072264
BFGS: 24 03:05:52 -302.361210 0.098827
BFGS: 25 03:05:52 -302.364344 0.157865
BFGS: 26 03:05:52 -302.379023 0.606012
BFGS: 27 03:05:53 -302.433090 1.337985
BFGS: 28 03:05:53 -302.609681 2.106144
BFGS: 29 03:05:53 -302.980136 2.656682
BFGS: 30 03:05:53 -303.483310 2.583533
BFGS: 31 03:05:53 -303.808404 1.341228
BFGS: 32 03:05:53 -304.127054 1.526701
BFGS: 33 03:05:53 -304.289390 1.215929
BFGS: 34 03:05:54 -304.344896 0.682923
BFGS: 35 03:05:54 -304.373130 0.451477
BFGS: 36 03:05:54 -304.400834 0.447730
BFGS: 37 03:05:54 -304.429484 0.443072
BFGS: 38 03:05:55 -304.442191 0.312993
BFGS: 39 03:05:55 -304.452523 0.298214
BFGS: 40 03:05:55 -304.461586 0.232922
BFGS: 41 03:05:55 -304.468756 0.180862
BFGS: 42 03:05:56 -304.473445 0.194992
BFGS: 43 03:05:56 -304.477076 0.157980
BFGS: 44 03:05:56 -304.480022 0.123059
BFGS: 45 03:05:56 -304.482400 0.083669
BFGS: 46 03:05:57 -304.483760 0.058546
BFGS: 47 03:05:57 -304.484249 0.042651
/home/runner/work/_tool/Python/3.12.15/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/3.12.15/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 03:07:03 -302.183059 3.648895
BFGS: 1 03:07:06 -302.325413 2.704891
BFGS: 2 03:07:13 -302.682151 7.849939
BFGS: 3 03:07:15 -302.752181 2.117143
BFGS: 4 03:07:17 -302.984094 1.899132
BFGS: 5 03:07:19 -303.218022 1.779767
BFGS: 6 03:07:21 -303.417902 1.959389
BFGS: 7 03:07:23 -303.492044 1.496069
BFGS: 8 03:07:30 -303.550690 1.041338
BFGS: 9 03:07:37 -303.610288 1.346264
BFGS: 10 03:07:42 -303.638024 0.758110
BFGS: 11 03:07:48 -303.658550 0.847050
BFGS: 12 03:07:53 -303.684235 0.821722
BFGS: 13 03:07:55 -303.697407 0.730437
BFGS: 14 03:08:03 -303.703327 0.584516
BFGS: 15 03:08:04 -303.708075 0.629170
BFGS: 16 03:08:06 -303.714500 0.738538
BFGS: 17 03:08:12 -303.720067 0.771970
BFGS: 18 03:08:18 -303.723955 0.657322
BFGS: 19 03:08:19 -303.729386 0.510066
BFGS: 20 03:08:21 -303.736412 0.413368
BFGS: 21 03:08:22 -303.744418 0.440057
BFGS: 22 03:08:24 -303.751807 0.549884
BFGS: 23 03:08:26 -303.756020 0.439980
BFGS: 24 03:08:32 -303.759150 0.275993
BFGS: 25 03:08:38 -303.763013 0.292709
BFGS: 26 03:08:43 -303.768254 0.348029
BFGS: 27 03:08:45 -303.774106 0.380480
BFGS: 28 03:08:47 -303.780521 0.307652
BFGS: 29 03:08:48 -303.787236 0.292193
BFGS: 30 03:08:51 -303.794859 0.314518
BFGS: 31 03:08:52 -303.803219 0.335342
BFGS: 32 03:08:55 -303.812597 0.365001
BFGS: 33 03:09:01 -303.820028 0.454118
BFGS: 34 03:09:03 -303.825968 0.459006
BFGS: 35 03:09:06 -303.828728 0.440062
BFGS: 36 03:09:09 -303.828501 0.523213
BFGS: 37 03:09:11 -303.816143 0.554983
BFGS: 38 03:09:13 -303.804687 0.657020
BFGS: 39 03:09:15 -303.801234 0.618439
BFGS: 40 03:09:17 -303.791465 0.551779
BFGS: 41 03:09:19 -303.777497 0.537411
BFGS: 42 03:09:22 -303.745351 0.434771
BFGS: 43 03:09:25 -303.719783 0.445622
BFGS: 44 03:09:27 -303.704911 0.508327
BFGS: 45 03:09:32 -303.693777 0.427952
BFGS: 46 03:09:35 -303.696711 0.454245
BFGS: 47 03:09:41 -303.705683 0.315315
BFGS: 48 03:09:43 -303.715809 0.324944
BFGS: 49 03:09:45 -303.736107 0.435012
BFGS: 50 03:09:48 -303.747797 0.424750
BFGS: 51 03:09:53 -303.751966 0.384490
BFGS: 52 03:09:55 -303.744994 0.352890
BFGS: 53 03:09:57 -303.726115 0.495322
BFGS: 54 03:10:01 -303.703950 0.586915
BFGS: 55 03:10:08 -303.695449 0.414451
BFGS: 56 03:10:10 -303.695233 0.489965
BFGS: 57 03:10:12 -303.715838 0.495115
BFGS: 58 03:10:19 -303.741395 0.522149
BFGS: 59 03:10:21 -303.766953 0.346026
BFGS: 60 03:10:23 -303.774161 0.331365
BFGS: 61 03:10:25 -303.788672 0.364409
BFGS: 62 03:10:30 -303.794155 0.466284
BFGS: 63 03:10:31 -303.781937 0.603223
BFGS: 64 03:10:33 -303.740230 0.821823
BFGS: 65 03:10:36 -303.681300 0.920957
BFGS: 66 03:10:38 -303.752348 0.950940
BFGS: 67 03:10:39 -303.803509 1.350408
BFGS: 68 03:10:41 -303.774824 1.400473
BFGS: 69 03:10:43 -303.730813 1.107960
BFGS: 70 03:10:45 -303.755125 0.547662
BFGS: 71 03:10:47 -303.793184 0.380054
BFGS: 72 03:10:50 -303.779262 0.596971
BFGS: 73 03:10:52 -303.715005 0.988284
BFGS: 74 03:10:53 -303.722988 0.844131
BFGS: 75 03:10:55 -303.807596 0.964335
BFGS: 76 03:11:00 -303.800664 0.972996
BFGS: 77 03:11:02 -303.785332 0.369146
BFGS: 78 03:11:08 -303.798968 0.338632
BFGS: 79 03:11:09 -303.788617 0.429006
BFGS: 80 03:11:14 -303.800879 0.274954
BFGS: 81 03:11:16 -303.793602 0.516530
BFGS: 82 03:11:19 -303.804326 0.240902
BFGS: 83 03:11:20 -303.804540 0.201591
BFGS: 84 03:11:22 -303.803060 0.218636
BFGS: 85 03:11:23 -303.800683 0.197597
BFGS: 86 03:11:25 -303.800788 0.161399
BFGS: 87 03:11:28 -303.800066 0.151540
BFGS: 88 03:11:33 -303.799333 0.140228
BFGS: 89 03:11:38 -303.797104 0.252189
BFGS: 90 03:11:41 -303.796348 0.270061
BFGS: 91 03:11:42 -303.800979 0.141374
BFGS: 92 03:11:46 -303.802625 0.109524
BFGS: 93 03:11:49 -303.799169 0.230636
BFGS: 94 03:11:50 -303.800121 0.165372
BFGS: 95 03:11:55 -303.798285 0.453126
BFGS: 96 03:11:57 -303.801901 0.123583
BFGS: 97 03:11:58 -303.802731 0.077109
BFGS: 98 03:12:01 -303.802731 0.071489
BFGS: 99 03:12:03 -303.802731 0.148085
BFGS: 100 03:12:06 -303.802731 0.062292
BFGS: 101 03:12:10 -303.802731 0.055684
BFGS: 102 03:12:11 -303.802731 0.032278
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_9537/3247994494.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")