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 DeprecationWarning: The symbol `warp.vec` will soon be removed from the public API. Use `warp.types.vector` instead.
/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 18:55:30 -301.616453 4.179877
BFGS: 1 18:55:31 -302.005821 3.096934
BFGS: 2 18:55:31 -302.955560 3.438912
BFGS: 3 18:55:31 -303.118048 3.229347
BFGS: 4 18:55:32 -303.458299 2.028994
BFGS: 5 18:55:32 -303.586323 3.126801
BFGS: 6 18:55:32 -303.694733 2.123912
BFGS: 7 18:55:33 -303.908245 1.421415
BFGS: 8 18:55:33 -303.950673 0.723580
BFGS: 9 18:55:34 -303.979808 0.606841
BFGS: 10 18:55:34 -304.090505 0.753267
BFGS: 11 18:55:34 -304.110033 0.554766
BFGS: 12 18:55:35 -304.128937 0.302023
BFGS: 13 18:55:35 -304.134401 0.261400
BFGS: 14 18:55:36 -304.149407 0.176033
BFGS: 15 18:55:36 -304.151145 0.152947
BFGS: 16 18:55:36 -304.153331 0.145034
BFGS: 17 18:55:37 -304.156400 0.159218
BFGS: 18 18:55:37 -304.159998 0.147597
BFGS: 19 18:55:38 -304.162000 0.102205
BFGS: 20 18:55:38 -304.162876 0.083407
BFGS: 21 18:55:39 -304.163597 0.070391
BFGS: 22 18:55:39 -304.164568 0.074633
BFGS: 23 18:55:40 -304.165448 0.076711
BFGS: 24 18:55:40 -304.165906 0.051226
BFGS: 25 18:55:40 -304.166104 0.045685
Step Time Energy fmax
BFGS: 0 18:55:41 -301.122943 4.047329
BFGS: 1 18:55:41 -301.520329 3.157751
BFGS: 2 18:55:42 -302.625493 3.500530
BFGS: 3 18:55:42 -302.682316 5.161881
BFGS: 4 18:55:42 -302.983176 2.474296
BFGS: 5 18:55:43 -303.120108 1.787535
BFGS: 6 18:55:43 -303.145831 0.730420
BFGS: 7 18:55:44 -303.177842 0.917380
BFGS: 8 18:55:44 -303.220591 1.266184
BFGS: 9 18:55:45 -303.269529 1.071373
BFGS: 10 18:55:45 -303.299173 0.655718
BFGS: 11 18:55:46 -303.337196 0.778636
BFGS: 12 18:55:46 -303.402064 1.675841
BFGS: 13 18:55:47 -303.505013 2.569993
BFGS: 14 18:55:47 -303.621059 2.716421
BFGS: 15 18:55:47 -303.785672 1.442631
BFGS: 16 18:55:48 -303.874225 1.324476
BFGS: 17 18:55:48 -303.937186 2.329223
BFGS: 18 18:55:49 -304.053281 1.206076
BFGS: 19 18:55:49 -304.084293 0.867298
BFGS: 20 18:55:49 -304.136642 0.474264
BFGS: 21 18:55:50 -304.151373 0.477868
BFGS: 22 18:55:50 -304.166886 0.624559
BFGS: 23 18:55:51 -304.181107 0.603703
BFGS: 24 18:55:51 -304.201009 0.422597
BFGS: 25 18:55:52 -304.220147 0.428378
BFGS: 26 18:55:52 -304.236461 0.503878
BFGS: 27 18:55:53 -304.251450 0.575182
BFGS: 28 18:55:53 -304.273700 0.432804
BFGS: 29 18:55:54 -304.286804 0.308782
BFGS: 30 18:55:54 -304.294711 0.303701
BFGS: 31 18:55:54 -304.300398 0.339708
BFGS: 32 18:55:55 -304.305655 0.315872
BFGS: 33 18:55:55 -304.319276 0.293366
BFGS: 34 18:55:55 -304.327995 0.255055
BFGS: 35 18:55:56 -304.334093 0.189772
BFGS: 36 18:55:56 -304.337747 0.193800
BFGS: 37 18:55:57 -304.341283 0.180784
BFGS: 38 18:55:57 -304.345049 0.138968
BFGS: 39 18:55:58 -304.347836 0.085274
BFGS: 40 18:55:58 -304.349184 0.079864
BFGS: 41 18:55:59 -304.349755 0.054570
BFGS: 42 18:55:59 -304.350218 0.058438
BFGS: 43 18:56:00 -304.350881 0.061741
BFGS: 44 18:56:00 -304.351477 0.050032
BFGS: 45 18:56:00 -304.351798 0.039103
Step Time Energy fmax
BFGS: 0 18:56:01 -300.791037 4.106643
BFGS: 1 18:56:01 -301.234796 3.566831
BFGS: 2 18:56:01 -302.512053 3.615194
BFGS: 3 18:56:02 -302.478794 7.033852
BFGS: 4 18:56:02 -302.867228 2.807630
BFGS: 5 18:56:03 -303.058723 0.920787
BFGS: 6 18:56:03 -303.097058 1.242882
BFGS: 7 18:56:03 -303.116842 0.577813
BFGS: 8 18:56:04 -303.134144 0.765880
BFGS: 9 18:56:04 -303.156589 0.798056
BFGS: 10 18:56:05 -303.168316 0.413271
BFGS: 11 18:56:05 -303.171541 0.151615
BFGS: 12 18:56:06 -303.172946 0.207851
BFGS: 13 18:56:06 -303.175454 0.404767
BFGS: 14 18:56:06 -303.178954 0.490073
BFGS: 15 18:56:07 -303.181997 0.361409
BFGS: 16 18:56:07 -303.183583 0.149419
BFGS: 17 18:56:08 -303.184545 0.139197
BFGS: 18 18:56:08 -303.185761 0.219797
BFGS: 19 18:56:08 -303.187528 0.282863
BFGS: 20 18:56:09 -303.188982 0.201857
BFGS: 21 18:56:09 -303.189587 0.071786
BFGS: 22 18:56:10 -303.189864 0.061262
BFGS: 23 18:56:10 -303.190179 0.122331
BFGS: 24 18:56:10 -303.190697 0.175489
BFGS: 25 18:56:11 -303.191337 0.160714
BFGS: 26 18:56:11 -303.191842 0.075197
BFGS: 27 18:56:12 -303.192175 0.066561
BFGS: 28 18:56:12 -303.192588 0.132897
BFGS: 29 18:56:12 -303.193613 0.278531
BFGS: 30 18:56:13 -303.198963 0.619808
BFGS: 31 18:56:13 -303.252552 0.483521
BFGS: 32 18:56:13 -303.406951 0.869775
BFGS: 33 18:56:14 -303.699949 1.060869
BFGS: 34 18:56:14 -303.926439 1.077482
BFGS: 35 18:56:15 -303.987048 1.456962
BFGS: 36 18:56:15 -304.036333 0.595006
BFGS: 37 18:56:16 -304.074195 0.713750
BFGS: 38 18:56:16 -304.116072 0.545265
BFGS: 39 18:56:17 -304.156823 0.320047
BFGS: 40 18:56:17 -304.164402 0.347514
BFGS: 41 18:56:17 -304.171635 0.205236
BFGS: 42 18:56:18 -304.180188 0.336778
BFGS: 43 18:56:18 -304.187288 0.300968
BFGS: 44 18:56:18 -304.192803 0.238185
BFGS: 45 18:56:19 -304.197245 0.313712
BFGS: 46 18:56:19 -304.202938 0.450604
BFGS: 47 18:56:20 -304.212726 0.582196
BFGS: 48 18:56:20 -304.238492 0.753013
BFGS: 49 18:56:20 -304.253392 0.946056
BFGS: 50 18:56:21 -304.287580 0.776815
BFGS: 51 18:56:21 -304.327314 0.784291
BFGS: 52 18:56:22 -304.403526 0.713980
BFGS: 53 18:56:22 -304.457619 1.039160
BFGS: 54 18:56:23 -304.482886 0.893012
BFGS: 55 18:56:23 -304.531457 0.614129
BFGS: 56 18:56:23 -304.570696 0.523421
BFGS: 57 18:56:24 -304.612109 0.342372
BFGS: 58 18:56:24 -304.620540 0.339407
BFGS: 59 18:56:25 -304.632772 0.303387
BFGS: 60 18:56:25 -304.645005 0.248471
BFGS: 61 18:56:26 -304.654464 0.223741
BFGS: 62 18:56:26 -304.659787 0.210971
BFGS: 63 18:56:27 -304.664582 0.188732
BFGS: 64 18:56:27 -304.670351 0.143932
BFGS: 65 18:56:28 -304.675684 0.117114
BFGS: 66 18:56:28 -304.678700 0.121949
BFGS: 67 18:56:29 -304.679742 0.104676
BFGS: 68 18:56:29 -304.680195 0.075960
BFGS: 69 18:56:29 -304.680693 0.042714
Step Time Energy fmax
BFGS: 0 18:56:30 -301.771386 4.071089
BFGS: 1 18:56:30 -302.155997 3.154509
BFGS: 2 18:56:31 -303.155593 3.327178
BFGS: 3 18:56:31 -303.338330 3.761203
BFGS: 4 18:56:32 -303.625536 2.270710
BFGS: 5 18:56:32 -303.835192 2.547952
BFGS: 6 18:56:33 -303.917217 1.097817
BFGS: 7 18:56:33 -303.988502 0.632620
BFGS: 8 18:56:34 -304.067612 1.139159
BFGS: 9 18:56:34 -304.107567 1.077486
BFGS: 10 18:56:35 -304.197053 0.905344
BFGS: 11 18:56:35 -304.264234 1.115403
BFGS: 12 18:56:36 -304.326545 1.062745
BFGS: 13 18:56:36 -304.358996 0.978849
BFGS: 14 18:56:36 -304.417999 1.424464
BFGS: 15 18:56:37 -304.471835 1.699540
BFGS: 16 18:56:37 -304.515585 1.068270
BFGS: 17 18:56:38 -304.548646 0.526242
BFGS: 18 18:56:38 -304.561990 0.390384
BFGS: 19 18:56:39 -304.575581 0.528237
BFGS: 20 18:56:39 -304.594938 0.659305
BFGS: 21 18:56:39 -304.612563 0.447388
BFGS: 22 18:56:40 -304.623003 0.323983
BFGS: 23 18:56:40 -304.630873 0.328336
BFGS: 24 18:56:41 -304.641398 0.414208
BFGS: 25 18:56:41 -304.654490 0.454754
BFGS: 26 18:56:41 -304.665071 0.315287
BFGS: 27 18:56:42 -304.670095 0.155838
BFGS: 28 18:56:42 -304.672516 0.139654
BFGS: 29 18:56:43 -304.675204 0.148113
BFGS: 30 18:56:43 -304.677941 0.122252
BFGS: 31 18:56:44 -304.679617 0.107265
BFGS: 32 18:56:44 -304.680311 0.068289
BFGS: 33 18:56:44 -304.680677 0.049831
Step Time Energy fmax
BFGS: 0 18:56:45 -301.919544 4.090588
BFGS: 1 18:56:45 -302.308337 3.175247
BFGS: 2 18:56:46 -303.295578 3.268195
BFGS: 3 18:56:46 -303.476852 3.297451
BFGS: 4 18:56:47 -303.728753 2.089531
BFGS: 5 18:56:47 -303.876505 1.980782
BFGS: 6 18:56:47 -303.928204 0.943111
BFGS: 7 18:56:48 -303.987937 0.624994
BFGS: 8 18:56:48 -304.057032 1.088474
BFGS: 9 18:56:49 -304.092107 1.000241
BFGS: 10 18:56:49 -304.141601 0.607878
BFGS: 11 18:56:49 -304.174192 0.575996
BFGS: 12 18:56:50 -304.191909 0.409780
BFGS: 13 18:56:50 -304.203170 0.355196
BFGS: 14 18:56:51 -304.213785 0.394955
BFGS: 15 18:56:51 -304.226105 0.483735
BFGS: 16 18:56:51 -304.242744 0.571812
BFGS: 17 18:56:52 -304.270112 0.786164
BFGS: 18 18:56:52 -304.249033 1.908239
BFGS: 19 18:56:53 -304.325103 0.887192
BFGS: 20 18:56:53 -304.362962 0.868905
BFGS: 21 18:56:53 -304.443996 1.073740
BFGS: 22 18:56:54 -304.495477 0.514379
BFGS: 23 18:56:54 -304.516904 0.395745
BFGS: 24 18:56:55 -304.541763 0.446513
BFGS: 25 18:56:55 -304.560120 0.461277
BFGS: 26 18:56:56 -304.590279 0.443124
BFGS: 27 18:56:56 -304.610071 0.383926
BFGS: 28 18:56:56 -304.626092 0.384228
BFGS: 29 18:56:57 -304.638737 0.365219
BFGS: 30 18:56:57 -304.653363 0.301085
BFGS: 31 18:56:58 -304.664075 0.210779
BFGS: 32 18:56:58 -304.669309 0.146655
BFGS: 33 18:56:59 -304.671867 0.142088
BFGS: 34 18:56:59 -304.674216 0.146207
BFGS: 35 18:56:59 -304.676913 0.155275
BFGS: 36 18:57:00 -304.679264 0.115220
BFGS: 37 18:57:00 -304.680428 0.054479
BFGS: 38 18:57:01 -304.680818 0.052660
BFGS: 39 18:57:01 -304.681023 0.044093
Step Time Energy fmax
BFGS: 0 18:57:02 -301.908225 4.152627
BFGS: 1 18:57:02 -302.303087 3.345824
BFGS: 2 18:57:03 -303.247367 3.127502
BFGS: 3 18:57:03 -303.400049 2.906571
BFGS: 4 18:57:03 -303.657469 1.884938
BFGS: 5 18:57:04 -303.788500 2.326136
BFGS: 6 18:57:04 -303.854072 1.372659
BFGS: 7 18:57:05 -303.957494 0.780666
BFGS: 8 18:57:05 -303.983127 0.749065
BFGS: 9 18:57:05 -304.047984 0.859471
BFGS: 10 18:57:06 -304.094200 0.823432
BFGS: 11 18:57:06 -304.122431 0.419054
BFGS: 12 18:57:06 -304.131965 0.279813
BFGS: 13 18:57:07 -304.140309 0.327789
BFGS: 14 18:57:07 -304.152328 0.287469
BFGS: 15 18:57:08 -304.157708 0.177938
BFGS: 16 18:57:08 -304.160068 0.141889
BFGS: 17 18:57:09 -304.162660 0.192689
BFGS: 18 18:57:09 -304.166201 0.266470
BFGS: 19 18:57:09 -304.170525 0.254233
BFGS: 20 18:57:10 -304.174331 0.196630
BFGS: 21 18:57:10 -304.177313 0.143167
BFGS: 22 18:57:11 -304.179867 0.197901
BFGS: 23 18:57:11 -304.182927 0.243114
BFGS: 24 18:57:12 -304.186390 0.187052
BFGS: 25 18:57:12 -304.189316 0.208997
BFGS: 26 18:57:12 -304.192946 0.232643
BFGS: 27 18:57:13 -304.200036 0.321322
BFGS: 28 18:57:13 -304.214196 0.626054
BFGS: 29 18:57:14 -304.228576 0.723085
BFGS: 30 18:57:14 -304.255990 0.768209
BFGS: 31 18:57:15 -304.279321 0.752266
BFGS: 32 18:57:15 -304.296855 0.626944
BFGS: 33 18:57:16 -304.315808 0.395275
BFGS: 34 18:57:16 -304.327114 0.205003
BFGS: 35 18:57:17 -304.334962 0.153142
BFGS: 36 18:57:17 -304.339154 0.138355
BFGS: 37 18:57:17 -304.341179 0.137019
BFGS: 38 18:57:18 -304.343618 0.120694
BFGS: 39 18:57:18 -304.346681 0.107126
BFGS: 40 18:57:19 -304.349399 0.081923
BFGS: 41 18:57:19 -304.350753 0.111223
BFGS: 42 18:57:20 -304.351402 0.105973
BFGS: 43 18:57:20 -304.351975 0.078961
BFGS: 44 18:57:20 -304.352478 0.038541
Step Time Energy fmax
BFGS: 0 18:57:21 -300.828352 4.018534
BFGS: 1 18:57:21 -301.268358 3.616815
BFGS: 2 18:57:22 -302.572300 3.614463
BFGS: 3 18:57:22 -302.519806 7.127039
BFGS: 4 18:57:22 -302.905697 2.838321
BFGS: 5 18:57:23 -303.078943 1.161861
BFGS: 6 18:57:23 -303.116361 1.213002
BFGS: 7 18:57:24 -303.128957 0.534545
BFGS: 8 18:57:24 -303.139230 0.567630
BFGS: 9 18:57:24 -303.151522 0.724950
BFGS: 10 18:57:24 -303.166248 0.583840
BFGS: 11 18:57:25 -303.172444 0.304297
BFGS: 12 18:57:25 -303.175616 0.222054
BFGS: 13 18:57:26 -303.179343 0.476212
BFGS: 14 18:57:26 -303.185900 0.704663
BFGS: 15 18:57:27 -303.193626 0.689038
BFGS: 16 18:57:27 -303.199358 0.414389
BFGS: 17 18:57:28 -303.202460 0.197054
BFGS: 18 18:57:28 -303.205005 0.293313
BFGS: 19 18:57:28 -303.208964 0.491110
BFGS: 20 18:57:29 -303.215489 0.612681
BFGS: 21 18:57:29 -303.225019 0.572051
BFGS: 22 18:57:30 -303.249537 0.879983
BFGS: 23 18:57:30 -303.231969 1.883316
BFGS: 24 18:57:31 -303.267856 1.178409
BFGS: 25 18:57:31 -303.283967 1.280830
BFGS: 26 18:57:32 -303.388094 2.491398
BFGS: 27 18:57:32 -303.453152 3.420892
BFGS: 28 18:57:33 -303.556100 3.906682
BFGS: 29 18:57:33 -303.571449 3.030397
BFGS: 30 18:57:33 -303.584734 2.899054
BFGS: 31 18:57:34 -303.600346 3.012764
BFGS: 32 18:57:34 -303.628009 2.918441
BFGS: 33 18:57:35 -303.639346 2.832821
BFGS: 34 18:57:35 -303.645651 2.726729
BFGS: 35 18:57:36 -303.654083 2.659989
BFGS: 36 18:57:36 -303.662585 2.519133
BFGS: 37 18:57:37 -303.669365 2.511243
BFGS: 38 18:57:37 -303.673032 2.414866
BFGS: 39 18:57:37 -303.675225 2.530814
BFGS: 40 18:57:38 -303.677469 2.475678
BFGS: 41 18:57:38 -303.680637 2.474849
BFGS: 42 18:57:39 -303.683151 2.412906
BFGS: 43 18:57:39 -303.685172 2.369441
BFGS: 44 18:57:39 -303.687630 2.310271
BFGS: 45 18:57:40 -303.690940 2.242311
BFGS: 46 18:57:40 -303.694952 2.170376
BFGS: 47 18:57:41 -303.699520 2.098837
BFGS: 48 18:57:41 -303.706241 1.977631
BFGS: 49 18:57:42 -303.742889 1.431167
BFGS: 50 18:57:42 -303.311984 8.406006
BFGS: 51 18:57:42 -303.840269 2.521185
BFGS: 52 18:57:43 -303.899757 1.435444
BFGS: 53 18:57:43 -303.962589 1.297797
BFGS: 54 18:57:44 -304.012663 1.171102
BFGS: 55 18:57:44 -304.025334 1.184853
BFGS: 56 18:57:45 -304.035201 1.321475
BFGS: 57 18:57:45 -304.047253 1.364127
BFGS: 58 18:57:45 -304.060169 1.567291
BFGS: 59 18:57:46 -304.071378 1.465551
BFGS: 60 18:57:46 -304.078130 1.539920
BFGS: 61 18:57:47 -304.083134 1.521952
BFGS: 62 18:57:47 -304.089638 1.547278
BFGS: 63 18:57:47 -304.097143 1.605888
BFGS: 64 18:57:48 -304.103430 1.687381
BFGS: 65 18:57:48 -304.106944 1.741372
BFGS: 66 18:57:49 -304.109141 1.754118
BFGS: 67 18:57:49 -304.111479 1.740023
BFGS: 68 18:57:50 -304.113825 1.711567
BFGS: 69 18:57:50 -304.115719 1.695407
BFGS: 70 18:57:51 -304.117238 1.703795
BFGS: 71 18:57:51 -304.118750 1.731865
BFGS: 72 18:57:51 -304.120432 1.769252
BFGS: 73 18:57:51 -304.122031 1.794582
BFGS: 74 18:57:52 -304.123129 1.791331
BFGS: 75 18:57:52 -304.123724 1.768908
BFGS: 76 18:57:52 -304.124135 1.740151
BFGS: 77 18:57:53 -304.124537 1.710732
BFGS: 78 18:57:53 -304.124918 1.692128
BFGS: 79 18:57:54 -304.125212 1.693279
BFGS: 80 18:57:54 -304.125395 1.707854
BFGS: 81 18:57:54 -304.125505 1.722237
BFGS: 82 18:57:55 -304.125603 1.731268
BFGS: 83 18:57:55 -304.125723 1.730929
BFGS: 84 18:57:55 -304.125843 1.716944
BFGS: 85 18:57:56 -304.125933 1.694742
BFGS: 86 18:57:56 -304.125996 1.675408
BFGS: 87 18:57:57 -304.126060 1.660444
BFGS: 88 18:57:57 -304.126136 1.650445
BFGS: 89 18:57:58 -304.126206 1.650221
BFGS: 90 18:57:58 -304.126249 1.657853
BFGS: 91 18:57:59 -304.126271 1.664542
BFGS: 92 18:57:59 -304.126288 1.668747
BFGS: 93 18:58:00 -304.126298 1.669948
BFGS: 94 18:58:00 -304.126319 1.666894
BFGS: 95 18:58:00 -304.126325 1.661865
BFGS: 96 18:58:01 -304.126331 1.657971
BFGS: 97 18:58:01 -304.126333 1.655460
BFGS: 98 18:58:02 -304.126339 1.654167
BFGS: 99 18:58:02 -304.126344 1.654553
BFGS: 100 18:58:03 -304.126344 1.656172
BFGS: 101 18:58:03 -304.126345 1.657703
BFGS: 102 18:58:04 -304.126348 1.658843
BFGS: 103 18:58:04 -304.126345 1.659686
BFGS: 104 18:58:05 -304.126346 1.660039
BFGS: 105 18:58:05 -304.126345 1.659714
BFGS: 106 18:58:05 -304.126351 1.659028
BFGS: 107 18:58:06 -304.126349 1.658494
BFGS: 108 18:58:06 -304.126348 1.658008
BFGS: 109 18:58:07 -304.126350 1.657696
BFGS: 110 18:58:07 -304.126346 1.657525
BFGS: 111 18:58:08 -304.126346 1.657556
BFGS: 112 18:58:08 -304.126349 1.657711
BFGS: 113 18:58:08 -304.126350 1.657887
BFGS: 114 18:58:09 -304.126349 1.658067
BFGS: 115 18:58:09 -304.126345 1.658152
BFGS: 116 18:58:10 -304.126350 1.658114
BFGS: 117 18:58:10 -304.126348 1.658083
BFGS: 118 18:58:11 -304.126347 1.657981
BFGS: 119 18:58:11 -304.126348 1.657870
BFGS: 120 18:58:12 -304.126348 1.657800
BFGS: 121 18:58:12 -304.126350 1.657827
BFGS: 122 18:58:12 -304.126349 1.657837
BFGS: 123 18:58:13 -304.126348 1.657907
BFGS: 124 18:58:13 -304.126348 1.657961
BFGS: 125 18:58:13 -304.126347 1.657968
BFGS: 126 18:58:14 -304.126348 1.657971
BFGS: 127 18:58:14 -304.126348 1.658005
BFGS: 128 18:58:15 -304.126348 1.657980
BFGS: 129 18:58:15 -304.126349 1.657968
BFGS: 130 18:58:15 -304.126348 1.657998
BFGS: 131 18:58:16 -304.126349 1.657959
BFGS: 132 18:58:16 -304.126349 1.657970
BFGS: 133 18:58:17 -304.126348 1.658025
BFGS: 134 18:58:17 -304.126348 1.657985
BFGS: 135 18:58:18 -304.126349 1.657961
BFGS: 136 18:58:18 -304.126350 1.657962
BFGS: 137 18:58:18 -304.126351 1.657964
BFGS: 138 18:58:19 -304.126349 1.657995
BFGS: 139 18:58:19 -304.126350 1.658002
BFGS: 140 18:58:20 -304.126347 1.657985
BFGS: 141 18:58:20 -304.126348 1.657972
BFGS: 142 18:58:21 -304.126351 1.657952
BFGS: 143 18:58:21 -304.126351 1.657970
BFGS: 144 18:58:22 -304.126348 1.657992
BFGS: 145 18:58:22 -304.126347 1.657976
BFGS: 146 18:58:22 -304.126351 1.657965
BFGS: 147 18:58:23 -304.126349 1.657966
BFGS: 148 18:58:23 -304.126349 1.658006
BFGS: 149 18:58:24 -304.126348 1.658015
BFGS: 150 18:58:24 -304.126349 1.657944
BFGS: 151 18:58:24 -304.126352 1.657954
BFGS: 152 18:58:25 -304.126347 1.658019
BFGS: 153 18:58:25 -304.126347 1.657997
BFGS: 154 18:58:26 -304.126350 1.657960
BFGS: 155 18:58:26 -304.126349 1.657966
BFGS: 156 18:58:27 -304.126348 1.658026
BFGS: 157 18:58:27 -304.126350 1.657990
BFGS: 158 18:58:27 -304.126349 1.657985
BFGS: 159 18:58:28 -304.126350 1.657963
BFGS: 160 18:58:28 -304.126348 1.657999
BFGS: 161 18:58:29 -304.126346 1.657993
BFGS: 162 18:58:29 -304.126350 1.657922
BFGS: 163 18:58:30 -304.126351 1.657959
BFGS: 164 18:58:30 -304.126349 1.657992
BFGS: 165 18:58:30 -304.126349 1.657971
BFGS: 166 18:58:31 -304.126351 1.657963
BFGS: 167 18:58:31 -304.126350 1.657971
BFGS: 168 18:58:32 -304.126349 1.657990
BFGS: 169 18:58:32 -304.126349 1.657993
BFGS: 170 18:58:33 -304.126348 1.657987
BFGS: 171 18:58:33 -304.126351 1.657962
BFGS: 172 18:58:34 -304.126348 1.658009
BFGS: 173 18:58:34 -304.126351 1.657971
BFGS: 174 18:58:34 -304.126350 1.658003
BFGS: 175 18:58:35 -304.126350 1.657955
BFGS: 176 18:58:35 -304.126349 1.658004
BFGS: 177 18:58:36 -304.126348 1.658006
BFGS: 178 18:58:36 -304.126352 1.657957
BFGS: 179 18:58:37 -304.126351 1.657961
BFGS: 180 18:58:37 -304.126349 1.657996
BFGS: 181 18:58:37 -304.126349 1.657986
BFGS: 182 18:58:38 -304.126351 1.657969
BFGS: 183 18:58:38 -304.126348 1.658011
BFGS: 184 18:58:39 -304.126349 1.657984
BFGS: 185 18:58:39 -304.126348 1.658003
BFGS: 186 18:58:39 -304.126347 1.657992
BFGS: 187 18:58:40 -304.126347 1.657997
BFGS: 188 18:58:40 -304.126352 1.657964
BFGS: 189 18:58:41 -304.126350 1.657965
BFGS: 190 18:58:41 -304.126349 1.657976
BFGS: 191 18:58:42 -304.126352 1.657961
BFGS: 192 18:58:42 -304.126348 1.658002
BFGS: 193 18:58:43 -304.126346 1.658007
BFGS: 194 18:58:43 -304.126348 1.658002
BFGS: 195 18:58:43 -304.126352 1.657956
BFGS: 196 18:58:44 -304.126349 1.658006
BFGS: 197 18:58:44 -304.126346 1.657995
BFGS: 198 18:58:44 -304.126349 1.657991
BFGS: 199 18:58:45 -304.126348 1.657959
BFGS: 200 18:58:45 -304.126351 1.657960
BFGS: 201 18:58:46 -304.126350 1.657988
BFGS: 202 18:58:46 -304.126352 1.657964
BFGS: 203 18:58:47 -304.126353 1.657958
BFGS: 204 18:58:47 -304.126350 1.657976
BFGS: 205 18:58:48 -304.126349 1.657971
BFGS: 206 18:58:48 -304.126350 1.657916
BFGS: 207 18:58:49 -304.126346 1.657985
BFGS: 208 18:58:49 -304.126351 1.657961
BFGS: 209 18:58:50 -304.126348 1.657976
BFGS: 210 18:58:50 -304.126351 1.657971
BFGS: 211 18:58:51 -304.126349 1.657960
BFGS: 212 18:58:51 -304.126350 1.657958
BFGS: 213 18:58:52 -304.126348 1.657989
BFGS: 214 18:58:52 -304.126351 1.657961
BFGS: 215 18:58:53 -304.126347 1.658001
BFGS: 216 18:58:53 -304.126349 1.657971
BFGS: 217 18:58:53 -304.126349 1.657997
BFGS: 218 18:58:54 -304.126350 1.657962
BFGS: 219 18:58:54 -304.126350 1.657949
BFGS: 220 18:58:55 -304.126353 1.657962
BFGS: 221 18:58:55 -304.126349 1.657999
BFGS: 222 18:58:56 -304.126348 1.658002
BFGS: 223 18:58:56 -304.126348 1.657955
BFGS: 224 18:58:56 -304.126351 1.657961
BFGS: 225 18:58:57 -304.126350 1.657965
BFGS: 226 18:58:57 -304.126349 1.657982
BFGS: 227 18:58:57 -304.126346 1.657971
BFGS: 228 18:58:58 -304.126348 1.657959
BFGS: 229 18:58:58 -304.126348 1.657988
BFGS: 230 18:58:59 -304.126346 1.658002
BFGS: 231 18:58:59 -304.126349 1.657942
BFGS: 232 18:59:00 -304.126346 1.657972
BFGS: 233 18:59:00 -304.126349 1.657974
BFGS: 234 18:59:01 -304.126350 1.657960
BFGS: 235 18:59:01 -304.126352 1.657955
BFGS: 236 18:59:01 -304.126347 1.657985
BFGS: 237 18:59:02 -304.126349 1.657991
BFGS: 238 18:59:02 -304.126352 1.657953
BFGS: 239 18:59:02 -304.126350 1.657964
BFGS: 240 18:59:03 -304.126349 1.657994
BFGS: 241 18:59:03 -304.126350 1.657961
BFGS: 242 18:59:03 -304.126351 1.657959
BFGS: 243 18:59:04 -304.126349 1.657991
BFGS: 244 18:59:04 -304.126347 1.657965
BFGS: 245 18:59:05 -304.126350 1.657957
BFGS: 246 18:59:05 -304.126348 1.657999
BFGS: 247 18:59:06 -304.126349 1.657997
BFGS: 248 18:59:06 -304.126351 1.657959
BFGS: 249 18:59:06 -304.126349 1.657960
BFGS: 250 18:59:07 -304.126346 1.658007
BFGS: 251 18:59:07 -304.126349 1.657994
BFGS: 252 18:59:08 -304.126347 1.657991
BFGS: 253 18:59:08 -304.126350 1.657964
BFGS: 254 18:59:09 -304.126347 1.658009
BFGS: 255 18:59:09 -304.126348 1.657998
BFGS: 256 18:59:09 -304.126348 1.657995
BFGS: 257 18:59:10 -304.126349 1.658001
BFGS: 258 18:59:10 -304.126349 1.657975
BFGS: 259 18:59:11 -304.126345 1.657990
BFGS: 260 18:59:11 -304.126347 1.657960
BFGS: 261 18:59:11 -304.126350 1.657962
BFGS: 262 18:59:12 -304.126351 1.657936
BFGS: 263 18:59:12 -304.126352 1.657959
BFGS: 264 18:59:13 -304.126346 1.658004
BFGS: 265 18:59:13 -304.126352 1.657961
BFGS: 266 18:59:13 -304.126351 1.657953
BFGS: 267 18:59:14 -304.126348 1.657999
BFGS: 268 18:59:14 -304.126348 1.657959
BFGS: 269 18:59:15 -304.126349 1.658001
BFGS: 270 18:59:15 -304.126349 1.657973
BFGS: 271 18:59:15 -304.126348 1.657999
BFGS: 272 18:59:16 -304.126349 1.657954
BFGS: 273 18:59:16 -304.126347 1.658003
BFGS: 274 18:59:16 -304.126346 1.658010
BFGS: 275 18:59:17 -304.126347 1.658002
BFGS: 276 18:59:17 -304.126347 1.658001
BFGS: 277 18:59:17 -304.126347 1.658000
BFGS: 278 18:59:17 -304.126352 1.657930
BFGS: 279 18:59:18 -304.126351 1.657952
BFGS: 280 18:59:18 -304.126349 1.657957
BFGS: 281 18:59:18 -304.126349 1.657964
BFGS: 282 18:59:19 -304.126351 1.657959
BFGS: 283 18:59:19 -304.126350 1.657959
BFGS: 284 18:59:20 -304.126346 1.657974
BFGS: 285 18:59:20 -304.126347 1.657996
BFGS: 286 18:59:20 -304.126349 1.657961
BFGS: 287 18:59:21 -304.126351 1.657960
BFGS: 288 18:59:21 -304.126346 1.657999
BFGS: 289 18:59:22 -304.126350 1.657965
BFGS: 290 18:59:22 -304.126349 1.657954
BFGS: 291 18:59:22 -304.126352 1.657954
BFGS: 292 18:59:23 -304.126347 1.657996
BFGS: 293 18:59:23 -304.126349 1.657992
BFGS: 294 18:59:24 -304.126351 1.657956
BFGS: 295 18:59:24 -304.126348 1.657957
BFGS: 296 18:59:24 -304.126352 1.657954
BFGS: 297 18:59:25 -304.126349 1.657995
BFGS: 298 18:59:25 -304.126350 1.657955
BFGS: 299 18:59:26 -304.126349 1.657956
BFGS: 300 18:59:26 -304.126347 1.657962
Step Time Energy fmax
BFGS: 0 18:59:27 -300.581667 3.987877
BFGS: 1 18:59:27 -301.053980 3.953728
BFGS: 2 18:59:27 -302.438052 3.649576
BFGS: 3 18:59:28 -302.115517 9.238752
BFGS: 4 18:59:28 -302.587941 3.626464
BFGS: 5 18:59:29 -302.660230 3.490577
BFGS: 6 18:59:29 -302.921672 1.310146
BFGS: 7 18:59:30 -302.964659 1.812600
BFGS: 8 18:59:30 -303.015034 1.721056
BFGS: 9 18:59:30 -303.138765 0.563477
BFGS: 10 18:59:31 -303.153920 0.325835
BFGS: 11 18:59:31 -303.157538 0.262130
BFGS: 12 18:59:31 -303.167381 0.364574
BFGS: 13 18:59:32 -303.172075 0.264705
BFGS: 14 18:59:32 -303.173924 0.156130
BFGS: 15 18:59:33 -303.175052 0.123422
BFGS: 16 18:59:33 -303.176193 0.129129
BFGS: 17 18:59:34 -303.177772 0.112192
BFGS: 18 18:59:34 -303.179417 0.076067
BFGS: 19 18:59:34 -303.180332 0.089853
BFGS: 20 18:59:35 -303.180704 0.099623
BFGS: 21 18:59:35 -303.181007 0.090021
BFGS: 22 18:59:36 -303.181429 0.062079
BFGS: 23 18:59:36 -303.181920 0.031882
Step Time Energy fmax
BFGS: 0 18:59:36 -302.116386 4.132447
BFGS: 1 18:59:37 -302.506859 3.010176
BFGS: 2 18:59:37 -303.401544 3.284843
BFGS: 3 18:59:37 -303.565036 2.926900
BFGS: 4 18:59:38 -303.855411 1.437387
BFGS: 5 18:59:38 -303.907721 1.032056
BFGS: 6 18:59:39 -303.993074 0.703210
BFGS: 7 18:59:39 -304.077793 0.950816
BFGS: 8 18:59:39 -304.120755 0.789155
BFGS: 9 18:59:40 -304.195253 0.953866
BFGS: 10 18:59:40 -304.286271 0.807116
BFGS: 11 18:59:41 -304.337074 0.994518
BFGS: 12 18:59:41 -304.372675 1.145941
BFGS: 13 18:59:41 -304.458069 1.165584
BFGS: 14 18:59:42 -304.498050 0.734581
BFGS: 15 18:59:42 -304.528931 0.457647
BFGS: 16 18:59:42 -304.551160 0.350015
BFGS: 17 18:59:43 -304.561000 0.392049
BFGS: 18 18:59:43 -304.582835 0.354679
BFGS: 19 18:59:44 -304.601988 0.356238
BFGS: 20 18:59:44 -304.616531 0.341281
BFGS: 21 18:59:44 -304.626838 0.333370
BFGS: 22 18:59:45 -304.637825 0.319505
BFGS: 23 18:59:45 -304.650547 0.277465
BFGS: 24 18:59:46 -304.662572 0.196294
BFGS: 25 18:59:46 -304.670106 0.154869
BFGS: 26 18:59:46 -304.673172 0.175157
BFGS: 27 18:59:47 -304.675415 0.187046
BFGS: 28 18:59:47 -304.678155 0.150920
BFGS: 29 18:59:48 -304.679846 0.072820
BFGS: 30 18:59:48 -304.680518 0.043970
Step Time Energy fmax
BFGS: 0 18:59:48 -301.207512 4.104782
BFGS: 1 18:59:49 -301.607209 3.106281
BFGS: 2 18:59:49 -302.663214 3.521837
BFGS: 3 18:59:50 -302.785171 3.722446
BFGS: 4 18:59:50 -303.071233 2.011547
BFGS: 5 18:59:51 -303.134421 2.439228
BFGS: 6 18:59:51 -303.189351 0.748540
BFGS: 7 18:59:52 -303.218632 0.694435
BFGS: 8 18:59:52 -303.481936 1.085826
BFGS: 9 18:59:52 -303.590889 1.752288
BFGS: 10 18:59:53 -303.705372 1.614344
BFGS: 11 18:59:53 -303.936497 1.326998
BFGS: 12 18:59:53 -303.993862 1.534770
BFGS: 13 18:59:54 -304.070592 0.930654
BFGS: 14 18:59:54 -304.105828 0.565410
BFGS: 15 18:59:55 -304.117239 0.335871
BFGS: 16 18:59:55 -304.125773 0.287984
BFGS: 17 18:59:55 -304.136426 0.236208
BFGS: 18 18:59:56 -304.143774 0.199815
BFGS: 19 18:59:56 -304.147615 0.187110
BFGS: 20 18:59:57 -304.150080 0.174497
BFGS: 21 18:59:57 -304.152889 0.156399
BFGS: 22 18:59:58 -304.156851 0.222500
BFGS: 23 18:59:58 -304.160823 0.205785
BFGS: 24 18:59:59 -304.163225 0.096558
BFGS: 25 18:59:59 -304.164454 0.096578
BFGS: 26 19:00:00 -304.165697 0.101884
BFGS: 27 19:00:00 -304.167265 0.109369
BFGS: 28 19:00:00 -304.168524 0.076215
BFGS: 29 19:00:01 -304.169167 0.060464
BFGS: 30 19:00:01 -304.169566 0.067866
BFGS: 31 19:00:01 -304.170141 0.087113
BFGS: 32 19:00:02 -304.171234 0.107801
BFGS: 33 19:00:02 -304.173101 0.122736
BFGS: 34 19:00:03 -304.175609 0.141573
BFGS: 35 19:00:03 -304.178496 0.183015
BFGS: 36 19:00:04 -304.183702 0.282697
BFGS: 37 19:00:04 -304.203108 0.662385
BFGS: 38 19:00:04 -304.219217 1.161616
BFGS: 39 19:00:05 -304.231773 1.308485
BFGS: 40 19:00:05 -304.239114 1.121914
BFGS: 41 19:00:05 -304.245589 1.047728
BFGS: 42 19:00:06 -304.246445 0.899923
BFGS: 43 19:00:06 -304.249041 1.018244
BFGS: 44 19:00:07 -304.251332 1.145791
BFGS: 45 19:00:07 -304.253972 1.264891
BFGS: 46 19:00:07 -304.256914 1.336301
BFGS: 47 19:00:08 -304.258725 1.300478
BFGS: 48 19:00:08 -304.260263 1.225433
BFGS: 49 19:00:08 -304.262106 1.144017
BFGS: 50 19:00:09 -304.264479 1.083953
BFGS: 51 19:00:09 -304.266566 1.094912
BFGS: 52 19:00:09 -304.267840 1.169525
BFGS: 53 19:00:10 -304.268589 1.247706
BFGS: 54 19:00:10 -304.269313 1.316994
BFGS: 55 19:00:10 -304.270035 1.352347
BFGS: 56 19:00:11 -304.270662 1.339251
BFGS: 57 19:00:11 -304.271104 1.295284
BFGS: 58 19:00:12 -304.271368 1.253242
BFGS: 59 19:00:12 -304.271536 1.229587
BFGS: 60 19:00:13 -304.271674 1.221421
BFGS: 61 19:00:13 -304.271821 1.225833
BFGS: 62 19:00:14 -304.271979 1.239443
BFGS: 63 19:00:14 -304.272096 1.252016
BFGS: 64 19:00:15 -304.272175 1.256484
BFGS: 65 19:00:15 -304.272231 1.254968
BFGS: 66 19:00:15 -304.272304 1.250119
BFGS: 67 19:00:16 -304.272385 1.244009
BFGS: 68 19:00:16 -304.272448 1.241210
BFGS: 69 19:00:16 -304.272481 1.243259
BFGS: 70 19:00:17 -304.272501 1.246925
BFGS: 71 19:00:17 -304.272523 1.251212
BFGS: 72 19:00:18 -304.272553 1.253966
BFGS: 73 19:00:18 -304.272571 1.253004
BFGS: 74 19:00:18 -304.272584 1.249683
BFGS: 75 19:00:19 -304.272593 1.246504
BFGS: 76 19:00:19 -304.272597 1.243729
BFGS: 77 19:00:20 -304.272604 1.242026
BFGS: 78 19:00:20 -304.272611 1.242724
BFGS: 79 19:00:20 -304.272616 1.245292
BFGS: 80 19:00:21 -304.272618 1.247689
BFGS: 81 19:00:21 -304.272616 1.249613
BFGS: 82 19:00:22 -304.272621 1.251121
BFGS: 83 19:00:22 -304.272624 1.251854
BFGS: 84 19:00:22 -304.272625 1.251146
BFGS: 85 19:00:22 -304.272626 1.249833
BFGS: 86 19:00:23 -304.272626 1.248876
BFGS: 87 19:00:23 -304.272626 1.247907
BFGS: 88 19:00:24 -304.272626 1.247622
BFGS: 89 19:00:24 -304.272625 1.247943
BFGS: 90 19:00:25 -304.272627 1.248766
BFGS: 91 19:00:25 -304.272627 1.249447
BFGS: 92 19:00:26 -304.272629 1.249849
BFGS: 93 19:00:26 -304.272628 1.250154
BFGS: 94 19:00:26 -304.272627 1.250171
BFGS: 95 19:00:27 -304.272629 1.249845
BFGS: 96 19:00:27 -304.272627 1.249564
BFGS: 97 19:00:28 -304.272628 1.249292
BFGS: 98 19:00:28 -304.272627 1.249023
BFGS: 99 19:00:28 -304.272627 1.248945
BFGS: 100 19:00:29 -304.272627 1.249020
BFGS: 101 19:00:29 -304.272628 1.249242
BFGS: 102 19:00:30 -304.272627 1.249342
BFGS: 103 19:00:30 -304.272627 1.249421
BFGS: 104 19:00:31 -304.272628 1.249479
BFGS: 105 19:00:31 -304.272628 1.249469
BFGS: 106 19:00:32 -304.272628 1.249498
BFGS: 107 19:00:32 -304.272625 1.249398
BFGS: 108 19:00:32 -304.272626 1.249350
BFGS: 109 19:00:33 -304.272625 1.249344
BFGS: 110 19:00:33 -304.272629 1.249275
BFGS: 111 19:00:33 -304.272627 1.249351
BFGS: 112 19:00:34 -304.272626 1.249308
BFGS: 113 19:00:34 -304.272629 1.249272
BFGS: 114 19:00:35 -304.272631 1.249321
BFGS: 115 19:00:35 -304.272627 1.249332
BFGS: 116 19:00:36 -304.272626 1.249436
BFGS: 117 19:00:36 -304.272628 1.249353
BFGS: 118 19:00:36 -304.272627 1.249403
BFGS: 119 19:00:37 -304.272628 1.249329
BFGS: 120 19:00:37 -304.272628 1.249348
BFGS: 121 19:00:37 -304.272628 1.249380
BFGS: 122 19:00:38 -304.272627 1.249341
BFGS: 123 19:00:39 -304.272627 1.249395
BFGS: 124 19:00:39 -304.272628 1.249337
BFGS: 125 19:00:39 -304.272628 1.249383
BFGS: 126 19:00:40 -304.272627 1.249342
BFGS: 127 19:00:40 -304.272627 1.249344
BFGS: 128 19:00:41 -304.272629 1.249345
BFGS: 129 19:00:41 -304.272629 1.249387
BFGS: 130 19:00:41 -304.272628 1.249348
BFGS: 131 19:00:42 -304.272628 1.249346
BFGS: 132 19:00:42 -304.272628 1.249346
BFGS: 133 19:00:43 -304.272627 1.249342
BFGS: 134 19:00:43 -304.272628 1.249342
BFGS: 135 19:00:43 -304.272630 1.249349
BFGS: 136 19:00:44 -304.272628 1.249349
BFGS: 137 19:00:44 -304.272627 1.249341
BFGS: 138 19:00:45 -304.272627 1.249343
BFGS: 139 19:00:45 -304.272628 1.249409
BFGS: 140 19:00:46 -304.272627 1.249347
BFGS: 141 19:00:46 -304.272630 1.249345
BFGS: 142 19:00:46 -304.272627 1.249339
BFGS: 143 19:00:47 -304.272628 1.249419
BFGS: 144 19:00:47 -304.272627 1.249348
BFGS: 145 19:00:47 -304.272626 1.249341
BFGS: 146 19:00:48 -304.272630 1.249349
BFGS: 147 19:00:48 -304.272628 1.249347
BFGS: 148 19:00:49 -304.272629 1.249344
BFGS: 149 19:00:49 -304.272627 1.249341
BFGS: 150 19:00:50 -304.272628 1.249347
BFGS: 151 19:00:50 -304.272628 1.249347
BFGS: 152 19:00:50 -304.272626 1.249348
BFGS: 153 19:00:51 -304.272627 1.249342
BFGS: 154 19:00:51 -304.272628 1.249354
BFGS: 155 19:00:51 -304.272628 1.249349
BFGS: 156 19:00:52 -304.272628 1.249385
BFGS: 157 19:00:52 -304.272626 1.249343
BFGS: 158 19:00:52 -304.272628 1.249350
BFGS: 159 19:00:53 -304.272626 1.249353
BFGS: 160 19:00:53 -304.272627 1.249343
BFGS: 161 19:00:53 -304.272627 1.249350
BFGS: 162 19:00:54 -304.272630 1.249344
BFGS: 163 19:00:54 -304.272626 1.249346
BFGS: 164 19:00:54 -304.272628 1.249344
BFGS: 165 19:00:55 -304.272628 1.249342
BFGS: 166 19:00:55 -304.272628 1.249350
BFGS: 167 19:00:56 -304.272626 1.249348
BFGS: 168 19:00:56 -304.272627 1.249350
BFGS: 169 19:00:56 -304.272626 1.249342
BFGS: 170 19:00:57 -304.272628 1.249351
BFGS: 171 19:00:57 -304.272629 1.249346
BFGS: 172 19:00:58 -304.272626 1.249353
BFGS: 173 19:00:58 -304.272627 1.249344
BFGS: 174 19:00:58 -304.272630 1.249343
BFGS: 175 19:00:59 -304.272628 1.249355
BFGS: 176 19:00:59 -304.272627 1.249339
BFGS: 177 19:00:59 -304.272630 1.249341
BFGS: 178 19:01:00 -304.272627 1.249349
BFGS: 179 19:01:00 -304.272628 1.249340
BFGS: 180 19:01:01 -304.272628 1.249381
BFGS: 181 19:01:01 -304.272627 1.249346
BFGS: 182 19:01:02 -304.272627 1.249347
BFGS: 183 19:01:02 -304.272628 1.249350
BFGS: 184 19:01:02 -304.272628 1.249324
BFGS: 185 19:01:03 -304.272627 1.249350
BFGS: 186 19:01:03 -304.272627 1.249346
BFGS: 187 19:01:04 -304.272627 1.249343
BFGS: 188 19:01:04 -304.272628 1.249347
BFGS: 189 19:01:04 -304.272627 1.249342
BFGS: 190 19:01:05 -304.272627 1.249347
BFGS: 191 19:01:05 -304.272627 1.249395
BFGS: 192 19:01:06 -304.272627 1.249342
BFGS: 193 19:01:06 -304.272627 1.249339
BFGS: 194 19:01:06 -304.272630 1.249347
BFGS: 195 19:01:07 -304.272628 1.249346
BFGS: 196 19:01:07 -304.272628 1.249391
BFGS: 197 19:01:08 -304.272627 1.249342
BFGS: 198 19:01:08 -304.272628 1.249382
BFGS: 199 19:01:09 -304.272629 1.249347
BFGS: 200 19:01:09 -304.272626 1.249385
BFGS: 201 19:01:09 -304.272628 1.249349
BFGS: 202 19:01:10 -304.272627 1.249353
BFGS: 203 19:01:10 -304.272629 1.249338
BFGS: 204 19:01:11 -304.272627 1.249349
BFGS: 205 19:01:11 -304.272627 1.249355
BFGS: 206 19:01:11 -304.272630 1.249378
BFGS: 207 19:01:12 -304.272627 1.249382
BFGS: 208 19:01:12 -304.272628 1.249339
BFGS: 209 19:01:12 -304.272625 1.249356
BFGS: 210 19:01:13 -304.272627 1.249346
BFGS: 211 19:01:13 -304.272629 1.249348
BFGS: 212 19:01:14 -304.272627 1.249346
BFGS: 213 19:01:14 -304.272627 1.249348
BFGS: 214 19:01:14 -304.272629 1.249383
BFGS: 215 19:01:15 -304.272628 1.249348
BFGS: 216 19:01:16 -304.272628 1.249340
BFGS: 217 19:01:16 -304.272628 1.249341
BFGS: 218 19:01:16 -304.272628 1.249383
BFGS: 219 19:01:17 -304.272628 1.249346
BFGS: 220 19:01:17 -304.272627 1.249345
BFGS: 221 19:01:18 -304.272628 1.249339
BFGS: 222 19:01:18 -304.272627 1.249346
BFGS: 223 19:01:18 -304.272628 1.249346
BFGS: 224 19:01:19 -304.272628 1.249346
BFGS: 225 19:01:19 -304.272627 1.249347
BFGS: 226 19:01:20 -304.272629 1.249386
BFGS: 227 19:01:20 -304.272626 1.249347
BFGS: 228 19:01:21 -304.272626 1.249346
BFGS: 229 19:01:21 -304.272627 1.249340
BFGS: 230 19:01:21 -304.272626 1.249347
BFGS: 231 19:01:22 -304.272627 1.249347
BFGS: 232 19:01:22 -304.272627 1.249340
BFGS: 233 19:01:23 -304.272626 1.249351
BFGS: 234 19:01:23 -304.272629 1.249346
BFGS: 235 19:01:23 -304.272628 1.249338
BFGS: 236 19:01:24 -304.272626 1.249387
BFGS: 237 19:01:24 -304.272626 1.249349
BFGS: 238 19:01:25 -304.272627 1.249346
BFGS: 239 19:01:25 -304.272628 1.249342
BFGS: 240 19:01:26 -304.272627 1.249340
BFGS: 241 19:01:26 -304.272627 1.249379
BFGS: 242 19:01:27 -304.272627 1.249343
BFGS: 243 19:01:27 -304.272627 1.249345
BFGS: 244 19:01:27 -304.272627 1.249385
BFGS: 245 19:01:28 -304.272628 1.249339
BFGS: 246 19:01:28 -304.272628 1.249341
BFGS: 247 19:01:28 -304.272626 1.249344
BFGS: 248 19:01:29 -304.272628 1.249384
BFGS: 249 19:01:29 -304.272628 1.249339
BFGS: 250 19:01:30 -304.272629 1.249344
BFGS: 251 19:01:30 -304.272627 1.249345
BFGS: 252 19:01:30 -304.272628 1.249377
BFGS: 253 19:01:31 -304.272626 1.249337
BFGS: 254 19:01:31 -304.272628 1.249344
BFGS: 255 19:01:32 -304.272627 1.249344
BFGS: 256 19:01:32 -304.272626 1.249347
BFGS: 257 19:01:33 -304.272626 1.249340
BFGS: 258 19:01:33 -304.272626 1.249396
BFGS: 259 19:01:33 -304.272626 1.249349
BFGS: 260 19:01:34 -304.272627 1.249338
BFGS: 261 19:01:34 -304.272626 1.249346
BFGS: 262 19:01:35 -304.272629 1.249345
BFGS: 263 19:01:35 -304.272629 1.249337
BFGS: 264 19:01:36 -304.272626 1.249337
BFGS: 265 19:01:36 -304.272629 1.249345
BFGS: 266 19:01:37 -304.272627 1.249344
BFGS: 267 19:01:37 -304.272627 1.249340
BFGS: 268 19:01:38 -304.272626 1.249346
BFGS: 269 19:01:38 -304.272627 1.249345
BFGS: 270 19:01:38 -304.272627 1.249339
BFGS: 271 19:01:39 -304.272625 1.249351
BFGS: 272 19:01:39 -304.272628 1.249386
BFGS: 273 19:01:40 -304.272628 1.249351
BFGS: 274 19:01:40 -304.272626 1.249337
BFGS: 275 19:01:41 -304.272627 1.249337
BFGS: 276 19:01:41 -304.272627 1.249337
BFGS: 277 19:01:41 -304.272627 1.249354
BFGS: 278 19:01:42 -304.272627 1.249352
BFGS: 279 19:01:42 -304.272626 1.249337
BFGS: 280 19:01:43 -304.272629 1.249340
BFGS: 281 19:01:43 -304.272629 1.249345
BFGS: 282 19:01:44 -304.272627 1.249345
BFGS: 283 19:01:44 -304.272626 1.249344
BFGS: 284 19:01:44 -304.272625 1.249336
BFGS: 285 19:01:45 -304.272627 1.249345
BFGS: 286 19:01:45 -304.272627 1.249344
BFGS: 287 19:01:46 -304.272629 1.249339
BFGS: 288 19:01:46 -304.272628 1.249337
BFGS: 289 19:01:46 -304.272626 1.249351
BFGS: 290 19:01:47 -304.272629 1.249344
BFGS: 291 19:01:47 -304.272627 1.249338
BFGS: 292 19:01:48 -304.272627 1.249339
BFGS: 293 19:01:48 -304.272628 1.249353
BFGS: 294 19:01:48 -304.272626 1.249352
BFGS: 295 19:01:49 -304.272627 1.249336
BFGS: 296 19:01:49 -304.272626 1.249338
BFGS: 297 19:01:50 -304.272627 1.249352
BFGS: 298 19:01:50 -304.272628 1.249344
BFGS: 299 19:01:50 -304.272628 1.249338
BFGS: 300 19:01:51 -304.272628 1.249339
# 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 19:01:51 -297.051245 4.501759
BFGS: 1 19:01:52 -297.513075 4.648221
BFGS: 2 19:01:52 -298.739219 3.832569
BFGS: 3 19:01:52 -299.207486 3.304779
BFGS: 4 19:01:53 -299.353816 1.699250
BFGS: 5 19:01:53 -299.626736 1.551134
BFGS: 6 19:01:53 -299.723698 1.915609
BFGS: 7 19:01:54 -299.798884 0.863281
BFGS: 8 19:01:54 -299.825882 0.770655
BFGS: 9 19:01:54 -299.954181 0.683590
BFGS: 10 19:01:55 -299.997565 0.941438
BFGS: 11 19:01:55 -300.075181 1.465887
BFGS: 12 19:01:56 -300.145774 1.619680
BFGS: 13 19:01:56 -300.238561 1.390674
BFGS: 14 19:01:57 -300.369385 0.831791
BFGS: 15 19:01:57 -300.415688 1.062226
BFGS: 16 19:01:57 -300.466082 0.709018
BFGS: 17 19:01:58 -300.493910 0.609953
BFGS: 18 19:01:58 -300.535332 0.369393
BFGS: 19 19:01:59 -300.546469 0.303810
BFGS: 20 19:01:59 -300.557734 0.257491
BFGS: 21 19:02:00 -300.564443 0.216591
BFGS: 22 19:02:00 -300.568261 0.165339
BFGS: 23 19:02:00 -300.570622 0.153864
BFGS: 24 19:02:01 -300.572910 0.138505
BFGS: 25 19:02:01 -300.575220 0.120470
BFGS: 26 19:02:02 -300.576892 0.083660
BFGS: 27 19:02:02 -300.577585 0.045630
Step Time Energy fmax
BFGS: 0 19:02:02 -296.440346 4.364491
BFGS: 1 19:02:03 -296.911708 4.590331
BFGS: 2 19:02:03 -298.325622 3.235202
BFGS: 3 19:02:04 -297.815846 10.442001
BFGS: 4 19:02:04 -298.570033 1.891954
BFGS: 5 19:02:05 -298.642550 1.230462
BFGS: 6 19:02:05 -298.722870 1.509627
BFGS: 7 19:02:06 -298.775952 1.631867
BFGS: 8 19:02:06 -299.000239 1.682949
BFGS: 9 19:02:07 -299.164466 1.782071
BFGS: 10 19:02:07 -299.237785 1.669564
BFGS: 11 19:02:07 -299.379827 1.363786
BFGS: 12 19:02:08 -299.789757 0.596985
BFGS: 13 19:02:08 -299.810991 0.553345
BFGS: 14 19:02:09 -299.826938 0.552704
BFGS: 15 19:02:09 -299.847247 0.419441
BFGS: 16 19:02:10 -299.862794 0.228560
BFGS: 17 19:02:10 -299.870107 0.173941
BFGS: 18 19:02:10 -299.872958 0.178923
BFGS: 19 19:02:11 -299.875613 0.184961
BFGS: 20 19:02:11 -299.880499 0.208871
BFGS: 21 19:02:11 -299.886319 0.238650
BFGS: 22 19:02:12 -299.891751 0.284484
BFGS: 23 19:02:12 -299.897822 0.304688
BFGS: 24 19:02:13 -299.908107 0.345152
BFGS: 25 19:02:13 -299.926087 0.531480
BFGS: 26 19:02:13 -299.952849 0.503491
BFGS: 27 19:02:13 -299.979897 0.593128
BFGS: 28 19:02:14 -299.982501 0.573439
BFGS: 29 19:02:14 -300.006709 0.323497
BFGS: 30 19:02:15 -300.015903 0.274977
BFGS: 31 19:02:15 -300.027989 0.258564
BFGS: 32 19:02:15 -300.037890 0.119121
BFGS: 33 19:02:16 -300.040113 0.099236
BFGS: 34 19:02:16 -300.040914 0.091612
BFGS: 35 19:02:16 -300.041967 0.064492
BFGS: 36 19:02:17 -300.042649 0.059510
BFGS: 37 19:02:17 -300.043066 0.045830
Step Time Energy fmax
BFGS: 0 19:02:17 -295.982123 4.457717
BFGS: 1 19:02:18 -296.554855 4.801744
BFGS: 2 19:02:18 -298.262092 2.719205
BFGS: 3 19:02:19 -296.367516 20.141729
BFGS: 4 19:02:19 -298.402532 1.705234
BFGS: 5 19:02:20 -298.457159 1.003965
BFGS: 6 19:02:20 -298.492961 0.545906
BFGS: 7 19:02:20 -298.496951 0.272421
BFGS: 8 19:02:21 -298.502547 0.086956
BFGS: 9 19:02:21 -298.504186 0.080385
BFGS: 10 19:02:22 -298.504412 0.028066
Step Time Energy fmax
BFGS: 0 19:02:22 -296.531772 4.347498
BFGS: 1 19:02:23 -296.992989 4.563845
BFGS: 2 19:02:23 -298.371146 3.265919
BFGS: 3 19:02:23 -297.959732 9.724576
BFGS: 4 19:02:24 -298.627983 1.899943
BFGS: 5 19:02:24 -298.702522 1.287232
BFGS: 6 19:02:25 -298.799227 1.659401
BFGS: 7 19:02:25 -298.871441 1.811607
BFGS: 8 19:02:25 -299.099165 1.757451
BFGS: 9 19:02:26 -299.286953 1.746050
BFGS: 10 19:02:26 -299.398919 1.492411
BFGS: 11 19:02:26 -299.509114 1.365507
BFGS: 12 19:02:27 -299.938044 0.901879
BFGS: 13 19:02:27 -299.954756 0.625565
BFGS: 14 19:02:28 -299.976575 0.473299
BFGS: 15 19:02:28 -300.013688 0.375525
BFGS: 16 19:02:29 -300.019228 0.360442
BFGS: 17 19:02:29 -300.029419 0.293314
BFGS: 18 19:02:29 -300.034044 0.201812
BFGS: 19 19:02:30 -300.036924 0.210317
BFGS: 20 19:02:30 -300.038801 0.151486
BFGS: 21 19:02:30 -300.040344 0.116966
BFGS: 22 19:02:31 -300.041690 0.093206
BFGS: 23 19:02:31 -300.042594 0.089138
BFGS: 24 19:02:31 -300.043021 0.071081
BFGS: 25 19:02:32 -300.043289 0.050415
BFGS: 26 19:02:32 -300.043511 0.036049
Step Time Energy fmax
BFGS: 0 19:02:32 -297.189010 4.447122
BFGS: 1 19:02:32 -297.649888 4.573548
BFGS: 2 19:02:33 -298.922575 3.465889
BFGS: 3 19:02:33 -299.095434 5.131637
BFGS: 4 19:02:34 -299.346871 1.612361
BFGS: 5 19:02:34 -299.443004 1.366286
BFGS: 6 19:02:35 -299.611275 2.031952
BFGS: 7 19:02:35 -299.665509 0.753120
BFGS: 8 19:02:35 -299.689241 0.744347
BFGS: 9 19:02:36 -299.788769 1.013042
BFGS: 10 19:02:36 -299.823139 0.839238
BFGS: 11 19:02:36 -299.862227 0.341386
BFGS: 12 19:02:37 -299.868385 0.283422
BFGS: 13 19:02:37 -299.874786 0.274650
BFGS: 14 19:02:38 -299.879738 0.266845
BFGS: 15 19:02:38 -299.882929 0.242859
BFGS: 16 19:02:38 -299.885251 0.239357
BFGS: 17 19:02:39 -299.889742 0.294945
BFGS: 18 19:02:39 -299.898463 0.475011
BFGS: 19 19:02:40 -299.911090 0.648756
BFGS: 20 19:02:40 -299.925921 0.601735
BFGS: 21 19:02:41 -299.958720 0.474443
BFGS: 22 19:02:41 -299.972121 0.731778
BFGS: 23 19:02:42 -300.001178 0.643184
BFGS: 24 19:02:42 -300.020892 0.483103
BFGS: 25 19:02:42 -300.032710 0.253422
BFGS: 26 19:02:43 -300.035263 0.199701
BFGS: 27 19:02:43 -300.038265 0.160473
BFGS: 28 19:02:44 -300.041274 0.131065
BFGS: 29 19:02:44 -300.042969 0.081895
BFGS: 30 19:02:44 -300.043390 0.028922
Step Time Energy fmax
BFGS: 0 19:02:45 -296.106412 4.420437
BFGS: 1 19:02:45 -296.638962 4.719497
BFGS: 2 19:02:45 -298.243225 2.902293
BFGS: 3 19:02:46 -296.887361 16.436081
BFGS: 4 19:02:46 -298.409456 1.779545
BFGS: 5 19:02:46 -298.468717 1.008100
BFGS: 6 19:02:47 -298.505270 0.639319
BFGS: 7 19:02:47 -298.510678 0.393925
BFGS: 8 19:02:48 -298.520669 0.216090
BFGS: 9 19:02:48 -298.522691 0.230930
BFGS: 10 19:02:49 -298.523886 0.200078
BFGS: 11 19:02:49 -298.526110 0.183655
BFGS: 12 19:02:49 -298.533475 0.314086
BFGS: 13 19:02:50 -298.565872 0.727446
BFGS: 14 19:02:50 -298.587328 1.443631
BFGS: 15 19:02:51 -298.632719 1.294377
BFGS: 16 19:02:51 -298.744608 1.090462
BFGS: 17 19:02:52 -298.835930 1.316127
BFGS: 18 19:02:52 -298.991495 1.725751
BFGS: 19 19:02:53 -299.121338 1.922984
BFGS: 20 19:02:53 -299.137043 1.754781
BFGS: 21 19:02:53 -299.251227 1.607996
BFGS: 22 19:02:54 -299.407526 1.472683
BFGS: 23 19:02:54 -299.740247 1.317675
BFGS: 24 19:02:55 -299.831029 0.905336
BFGS: 25 19:02:55 -299.846112 0.555260
BFGS: 26 19:02:56 -299.858608 0.151513
BFGS: 27 19:02:56 -299.861025 0.215565
BFGS: 28 19:02:56 -299.865272 0.252833
BFGS: 29 19:02:57 -299.867693 0.191552
BFGS: 30 19:02:57 -299.869093 0.099854
BFGS: 31 19:02:57 -299.869667 0.083388
BFGS: 32 19:02:58 -299.870346 0.105026
BFGS: 33 19:02:58 -299.871488 0.144388
BFGS: 34 19:02:58 -299.872996 0.173909
BFGS: 35 19:02:59 -299.874547 0.183415
BFGS: 36 19:02:59 -299.876557 0.196373
BFGS: 37 19:03:00 -299.880734 0.261247
BFGS: 38 19:03:00 -299.888238 0.556272
BFGS: 39 19:03:00 -299.902179 0.615497
BFGS: 40 19:03:01 -299.944877 0.557818
BFGS: 41 19:03:01 -299.911964 0.639613
BFGS: 42 19:03:02 -299.978129 0.262159
BFGS: 43 19:03:02 -299.986158 0.755867
BFGS: 44 19:03:02 -300.002449 0.417886
BFGS: 45 19:03:03 -300.019796 0.291509
BFGS: 46 19:03:03 -300.034965 0.192416
BFGS: 47 19:03:04 -300.038143 0.111549
BFGS: 48 19:03:04 -300.039785 0.095728
BFGS: 49 19:03:04 -300.041045 0.089877
BFGS: 50 19:03:05 -300.042021 0.078516
BFGS: 51 19:03:05 -300.042964 0.061742
BFGS: 52 19:03:06 -300.043430 0.032096
Step Time Energy fmax
BFGS: 0 19:03:06 -296.973785 4.352325
BFGS: 1 19:03:06 -297.417224 4.513221
BFGS: 2 19:03:07 -298.679545 3.472929
BFGS: 3 19:03:07 -298.784957 5.959136
BFGS: 4 19:03:08 -299.076169 1.876073
BFGS: 5 19:03:08 -299.180137 1.698668
BFGS: 6 19:03:09 -299.560217 1.570362
BFGS: 7 19:03:09 -299.721084 1.539207
BFGS: 8 19:03:09 -299.788424 0.909638
BFGS: 9 19:03:10 -299.882998 0.752000
BFGS: 10 19:03:10 -299.917017 0.815454
BFGS: 11 19:03:11 -299.965345 0.746591
BFGS: 12 19:03:11 -299.985895 0.371133
BFGS: 13 19:03:12 -299.995227 0.295759
BFGS: 14 19:03:12 -300.001281 0.340028
BFGS: 15 19:03:12 -300.012406 0.352970
BFGS: 16 19:03:13 -300.021344 0.263360
BFGS: 17 19:03:13 -300.026869 0.161780
BFGS: 18 19:03:14 -300.031689 0.213136
BFGS: 19 19:03:14 -300.036206 0.241691
BFGS: 20 19:03:14 -300.040134 0.197690
BFGS: 21 19:03:15 -300.042389 0.107156
BFGS: 22 19:03:15 -300.043049 0.043734
Step Time Energy fmax
BFGS: 0 19:03:15 -297.142967 4.389296
BFGS: 1 19:03:16 -297.592254 4.527531
BFGS: 2 19:03:16 -298.865739 3.414644
BFGS: 3 19:03:17 -298.929405 5.972880
BFGS: 4 19:03:17 -299.250741 1.832959
BFGS: 5 19:03:18 -299.349818 1.591855
BFGS: 6 19:03:18 -299.563880 1.856598
BFGS: 7 19:03:18 -299.605388 0.909445
BFGS: 8 19:03:19 -299.634925 0.957965
BFGS: 9 19:03:19 -299.689293 1.307582
BFGS: 10 19:03:20 -299.733727 1.406568
BFGS: 11 19:03:20 -299.787185 1.244084
BFGS: 12 19:03:20 -299.826368 0.970050
BFGS: 13 19:03:21 -299.891219 1.113655
BFGS: 14 19:03:21 -299.911660 1.010927
BFGS: 15 19:03:21 -299.975550 0.822161
BFGS: 16 19:03:22 -299.997677 0.356245
BFGS: 17 19:03:22 -300.000982 0.396854
BFGS: 18 19:03:22 -300.004453 0.371183
BFGS: 19 19:03:23 -300.009193 0.411304
BFGS: 20 19:03:23 -300.011435 0.380209
BFGS: 21 19:03:24 -300.012701 0.326607
BFGS: 22 19:03:24 -300.013405 0.287175
BFGS: 23 19:03:25 -300.014200 0.250729
BFGS: 24 19:03:25 -300.015079 0.246216
BFGS: 25 19:03:25 -300.015885 0.231559
BFGS: 26 19:03:26 -300.016325 0.251868
BFGS: 27 19:03:26 -300.016602 0.271857
BFGS: 28 19:03:26 -300.016910 0.289366
BFGS: 29 19:03:27 -300.017333 0.300032
BFGS: 30 19:03:27 -300.017780 0.292661
BFGS: 31 19:03:28 -300.018053 0.271077
BFGS: 32 19:03:28 -300.018181 0.253559
BFGS: 33 19:03:28 -300.018286 0.241590
BFGS: 34 19:03:29 -300.018434 0.232555
BFGS: 35 19:03:29 -300.018606 0.231425
BFGS: 36 19:03:30 -300.018734 0.239952
BFGS: 37 19:03:30 -300.018802 0.250180
BFGS: 38 19:03:30 -300.018852 0.257917
BFGS: 39 19:03:31 -300.018920 0.264197
BFGS: 40 19:03:31 -300.019001 0.265663
BFGS: 41 19:03:32 -300.019065 0.260075
BFGS: 42 19:03:32 -300.019101 0.252764
BFGS: 43 19:03:32 -300.019122 0.247693
BFGS: 44 19:03:33 -300.019150 0.244268
BFGS: 45 19:03:33 -300.019183 0.243890
BFGS: 46 19:03:33 -300.019211 0.247682
BFGS: 47 19:03:34 -300.019221 0.252362
BFGS: 48 19:03:34 -300.019227 0.255500
BFGS: 49 19:03:34 -300.019236 0.257960
BFGS: 50 19:03:35 -300.019246 0.259207
BFGS: 51 19:03:35 -300.019255 0.258295
BFGS: 52 19:03:36 -300.019260 0.255749
BFGS: 53 19:03:36 -300.019264 0.253606
BFGS: 54 19:03:36 -300.019264 0.252086
BFGS: 55 19:03:37 -300.019270 0.250904
BFGS: 56 19:03:37 -300.019274 0.250741
BFGS: 57 19:03:38 -300.019278 0.252051
BFGS: 58 19:03:38 -300.019278 0.253640
BFGS: 59 19:03:38 -300.019280 0.254767
BFGS: 60 19:03:39 -300.019279 0.255782
BFGS: 61 19:03:39 -300.019282 0.256411
BFGS: 62 19:03:40 -300.019283 0.256333
BFGS: 63 19:03:40 -300.019284 0.255668
BFGS: 64 19:03:40 -300.019285 0.255034
BFGS: 65 19:03:41 -300.019287 0.254548
BFGS: 66 19:03:41 -300.019287 0.254198
BFGS: 67 19:03:42 -300.019286 0.254240
BFGS: 68 19:03:42 -300.019288 0.254738
BFGS: 69 19:03:43 -300.019287 0.255289
BFGS: 70 19:03:43 -300.019288 0.255687
BFGS: 71 19:03:43 -300.019288 0.255989
BFGS: 72 19:03:44 -300.019287 0.255953
BFGS: 73 19:03:44 -300.019288 0.255602
BFGS: 74 19:03:45 -300.019288 0.255280
BFGS: 75 19:03:45 -300.019288 0.255080
BFGS: 76 19:03:45 -300.019290 0.254919
BFGS: 77 19:03:46 -300.019289 0.254871
BFGS: 78 19:03:46 -300.019288 0.254981
BFGS: 79 19:03:46 -300.019290 0.255196
BFGS: 80 19:03:47 -300.019289 0.255357
BFGS: 81 19:03:47 -300.019288 0.255448
BFGS: 82 19:03:48 -300.019290 0.255543
BFGS: 83 19:03:48 -300.019289 0.255561
BFGS: 84 19:03:49 -300.019288 0.255534
BFGS: 85 19:03:49 -300.019289 0.255481
BFGS: 86 19:03:49 -300.019289 0.255428
BFGS: 87 19:03:50 -300.019289 0.255390
BFGS: 88 19:03:50 -300.019287 0.255404
BFGS: 89 19:03:50 -300.019287 0.255383
BFGS: 90 19:03:51 -300.019289 0.255396
BFGS: 91 19:03:51 -300.019288 0.255418
BFGS: 92 19:03:52 -300.019286 0.255442
BFGS: 93 19:03:52 -300.019288 0.255451
BFGS: 94 19:03:52 -300.019288 0.255473
BFGS: 95 19:03:52 -300.019289 0.255465
BFGS: 96 19:03:53 -300.019288 0.255443
BFGS: 97 19:03:53 -300.019288 0.255409
BFGS: 98 19:03:53 -300.019289 0.255416
BFGS: 99 19:03:54 -300.019287 0.255412
BFGS: 100 19:03:54 -300.019288 0.255416
BFGS: 101 19:03:55 -300.019287 0.255405
BFGS: 102 19:03:55 -300.019289 0.255413
BFGS: 103 19:03:55 -300.019288 0.255409
BFGS: 104 19:03:56 -300.019289 0.255415
BFGS: 105 19:03:56 -300.019290 0.255408
BFGS: 106 19:03:57 -300.019288 0.255414
BFGS: 107 19:03:57 -300.019289 0.255414
BFGS: 108 19:03:57 -300.019289 0.255415
BFGS: 109 19:03:58 -300.019290 0.255414
BFGS: 110 19:03:58 -300.019288 0.255411
BFGS: 111 19:03:59 -300.019289 0.255411
BFGS: 112 19:03:59 -300.019289 0.255419
BFGS: 113 19:04:00 -300.019287 0.255413
BFGS: 114 19:04:00 -300.019290 0.255414
BFGS: 115 19:04:00 -300.019289 0.255412
BFGS: 116 19:04:01 -300.019288 0.255412
BFGS: 117 19:04:01 -300.019288 0.255416
BFGS: 118 19:04:02 -300.019291 0.255416
BFGS: 119 19:04:02 -300.019288 0.255418
BFGS: 120 19:04:03 -300.019288 0.255413
BFGS: 121 19:04:03 -300.019289 0.255411
BFGS: 122 19:04:03 -300.019289 0.255416
BFGS: 123 19:04:04 -300.019289 0.255415
BFGS: 124 19:04:04 -300.019287 0.255409
BFGS: 125 19:04:05 -300.019288 0.255413
BFGS: 126 19:04:05 -300.019290 0.255422
BFGS: 127 19:04:05 -300.019289 0.255417
BFGS: 128 19:04:06 -300.019287 0.255412
BFGS: 129 19:04:06 -300.019289 0.255411
BFGS: 130 19:04:06 -300.019289 0.255417
BFGS: 131 19:04:07 -300.019289 0.255415
BFGS: 132 19:04:07 -300.019288 0.255416
BFGS: 133 19:04:08 -300.019287 0.255416
BFGS: 134 19:04:08 -300.019289 0.255399
BFGS: 135 19:04:08 -300.019288 0.255412
BFGS: 136 19:04:09 -300.019289 0.255417
BFGS: 137 19:04:09 -300.019288 0.255413
BFGS: 138 19:04:10 -300.019288 0.255402
BFGS: 139 19:04:10 -300.019289 0.255410
BFGS: 140 19:04:10 -300.019289 0.255413
BFGS: 141 19:04:11 -300.019290 0.255417
BFGS: 142 19:04:11 -300.019288 0.255401
BFGS: 143 19:04:12 -300.019287 0.255417
BFGS: 144 19:04:12 -300.019289 0.255411
BFGS: 145 19:04:13 -300.019289 0.255415
BFGS: 146 19:04:13 -300.019289 0.255399
BFGS: 147 19:04:14 -300.019287 0.255413
BFGS: 148 19:04:14 -300.019289 0.255409
BFGS: 149 19:04:14 -300.019287 0.255409
BFGS: 150 19:04:15 -300.019288 0.255405
BFGS: 151 19:04:15 -300.019289 0.255421
BFGS: 152 19:04:16 -300.019289 0.255407
BFGS: 153 19:04:16 -300.019289 0.255406
BFGS: 154 19:04:16 -300.019288 0.255424
BFGS: 155 19:04:17 -300.019288 0.255403
BFGS: 156 19:04:17 -300.019290 0.255405
BFGS: 157 19:04:18 -300.019289 0.255411
BFGS: 158 19:04:18 -300.019289 0.255405
BFGS: 159 19:04:18 -300.019289 0.255415
BFGS: 160 19:04:19 -300.019287 0.255412
BFGS: 161 19:04:19 -300.019288 0.255410
BFGS: 162 19:04:20 -300.019288 0.255416
BFGS: 163 19:04:20 -300.019289 0.255416
BFGS: 164 19:04:20 -300.019290 0.255420
BFGS: 165 19:04:21 -300.019288 0.255411
BFGS: 166 19:04:21 -300.019288 0.255411
BFGS: 167 19:04:21 -300.019288 0.255411
BFGS: 168 19:04:22 -300.019287 0.255416
BFGS: 169 19:04:22 -300.019288 0.255417
BFGS: 170 19:04:23 -300.019288 0.255418
BFGS: 171 19:04:23 -300.019289 0.255409
BFGS: 172 19:04:23 -300.019288 0.255413
BFGS: 173 19:04:24 -300.019288 0.255412
BFGS: 174 19:04:24 -300.019288 0.255420
BFGS: 175 19:04:25 -300.019289 0.255417
BFGS: 176 19:04:25 -300.019289 0.255414
BFGS: 177 19:04:25 -300.019288 0.255414
BFGS: 178 19:04:26 -300.019289 0.255415
BFGS: 179 19:04:26 -300.019288 0.255413
BFGS: 180 19:04:27 -300.019288 0.255408
BFGS: 181 19:04:27 -300.019288 0.255416
BFGS: 182 19:04:28 -300.019288 0.255406
BFGS: 183 19:04:28 -300.019289 0.255406
BFGS: 184 19:04:28 -300.019290 0.255420
BFGS: 185 19:04:29 -300.019289 0.255421
BFGS: 186 19:04:29 -300.019289 0.255387
BFGS: 187 19:04:29 -300.019288 0.255406
BFGS: 188 19:04:30 -300.019289 0.255424
BFGS: 189 19:04:30 -300.019289 0.255419
BFGS: 190 19:04:31 -300.019288 0.255407
BFGS: 191 19:04:31 -300.019289 0.255409
BFGS: 192 19:04:31 -300.019289 0.255415
BFGS: 193 19:04:32 -300.019288 0.255415
BFGS: 194 19:04:32 -300.019289 0.255409
BFGS: 195 19:04:33 -300.019287 0.255410
BFGS: 196 19:04:33 -300.019289 0.255410
BFGS: 197 19:04:34 -300.019289 0.255417
BFGS: 198 19:04:34 -300.019289 0.255406
BFGS: 199 19:04:34 -300.019288 0.255410
BFGS: 200 19:04:35 -300.019289 0.255420
BFGS: 201 19:04:35 -300.019289 0.255416
BFGS: 202 19:04:36 -300.019288 0.255404
BFGS: 203 19:04:36 -300.019288 0.255409
BFGS: 204 19:04:37 -300.019287 0.255436
BFGS: 205 19:04:37 -300.019288 0.255417
BFGS: 206 19:04:37 -300.019289 0.255408
BFGS: 207 19:04:38 -300.019287 0.255416
BFGS: 208 19:04:38 -300.019289 0.255414
BFGS: 209 19:04:39 -300.019289 0.255410
BFGS: 210 19:04:39 -300.019289 0.255401
BFGS: 211 19:04:40 -300.019288 0.255417
BFGS: 212 19:04:40 -300.019287 0.255408
BFGS: 213 19:04:40 -300.019288 0.255415
BFGS: 214 19:04:40 -300.019290 0.255420
BFGS: 215 19:04:41 -300.019288 0.255408
BFGS: 216 19:04:41 -300.019288 0.255411
BFGS: 217 19:04:42 -300.019289 0.255412
BFGS: 218 19:04:42 -300.019289 0.255414
BFGS: 219 19:04:43 -300.019288 0.255400
BFGS: 220 19:04:43 -300.019289 0.255416
BFGS: 221 19:04:44 -300.019289 0.255415
BFGS: 222 19:04:44 -300.019289 0.255413
BFGS: 223 19:04:45 -300.019288 0.255409
BFGS: 224 19:04:45 -300.019288 0.255410
BFGS: 225 19:04:46 -300.019289 0.255417
BFGS: 226 19:04:46 -300.019289 0.255413
BFGS: 227 19:04:47 -300.019288 0.255405
BFGS: 228 19:04:47 -300.019287 0.255409
BFGS: 229 19:04:47 -300.019289 0.255403
BFGS: 230 19:04:48 -300.019289 0.255413
BFGS: 231 19:04:48 -300.019287 0.255405
BFGS: 232 19:04:48 -300.019287 0.255412
BFGS: 233 19:04:49 -300.019289 0.255417
BFGS: 234 19:04:49 -300.019288 0.255412
BFGS: 235 19:04:50 -300.019286 0.255405
BFGS: 236 19:04:50 -300.019288 0.255412
BFGS: 237 19:04:50 -300.019289 0.255415
BFGS: 238 19:04:51 -300.019287 0.255419
BFGS: 239 19:04:51 -300.019288 0.255411
BFGS: 240 19:04:52 -300.019288 0.255415
BFGS: 241 19:04:52 -300.019288 0.255417
BFGS: 242 19:04:53 -300.019289 0.255416
BFGS: 243 19:04:53 -300.019288 0.255397
BFGS: 244 19:04:53 -300.019288 0.255411
BFGS: 245 19:04:54 -300.019288 0.255400
BFGS: 246 19:04:54 -300.019288 0.255419
BFGS: 247 19:04:54 -300.019288 0.255410
BFGS: 248 19:04:55 -300.019288 0.255412
BFGS: 249 19:04:55 -300.019288 0.255437
BFGS: 250 19:04:56 -300.019288 0.255414
BFGS: 251 19:04:56 -300.019288 0.255414
BFGS: 252 19:04:57 -300.019289 0.255420
BFGS: 253 19:04:57 -300.019288 0.255417
BFGS: 254 19:04:57 -300.019289 0.255372
BFGS: 255 19:04:58 -300.019288 0.255410
BFGS: 256 19:04:58 -300.019288 0.255415
BFGS: 257 19:04:59 -300.019289 0.255415
BFGS: 258 19:04:59 -300.019290 0.255319
BFGS: 259 19:05:00 -300.019288 0.255410
BFGS: 260 19:05:00 -300.019288 0.255416
BFGS: 261 19:05:00 -300.019289 0.255415
BFGS: 262 19:05:01 -300.019289 0.255400
BFGS: 263 19:05:01 -300.019288 0.255410
BFGS: 264 19:05:02 -300.019288 0.255414
BFGS: 265 19:05:02 -300.019289 0.255417
BFGS: 266 19:05:02 -300.019289 0.255359
BFGS: 267 19:05:03 -300.019290 0.255412
BFGS: 268 19:05:03 -300.019289 0.255416
BFGS: 269 19:05:03 -300.019287 0.255413
BFGS: 270 19:05:04 -300.019288 0.255354
BFGS: 271 19:05:04 -300.019288 0.255412
BFGS: 272 19:05:05 -300.019288 0.255417
BFGS: 273 19:05:05 -300.019288 0.255417
BFGS: 274 19:05:05 -300.019287 0.255397
BFGS: 275 19:05:06 -300.019288 0.255411
BFGS: 276 19:05:06 -300.019288 0.255413
BFGS: 277 19:05:07 -300.019289 0.255415
BFGS: 278 19:05:07 -300.019289 0.255337
BFGS: 279 19:05:08 -300.019288 0.255416
BFGS: 280 19:05:08 -300.019289 0.255420
BFGS: 281 19:05:08 -300.019288 0.255415
BFGS: 282 19:05:09 -300.019287 0.255413
BFGS: 283 19:05:09 -300.019288 0.255404
BFGS: 284 19:05:10 -300.019289 0.255410
BFGS: 285 19:05:10 -300.019288 0.255414
BFGS: 286 19:05:10 -300.019289 0.255411
BFGS: 287 19:05:11 -300.019288 0.255396
BFGS: 288 19:05:11 -300.019290 0.255399
BFGS: 289 19:05:11 -300.019288 0.255417
BFGS: 290 19:05:12 -300.019288 0.255410
BFGS: 291 19:05:12 -300.019288 0.255401
BFGS: 292 19:05:12 -300.019287 0.255410
BFGS: 293 19:05:13 -300.019289 0.255409
BFGS: 294 19:05:13 -300.019288 0.255417
BFGS: 295 19:05:13 -300.019288 0.255415
BFGS: 296 19:05:14 -300.019287 0.255413
BFGS: 297 19:05:14 -300.019287 0.255414
BFGS: 298 19:05:15 -300.019288 0.255415
BFGS: 299 19:05:15 -300.019289 0.255414
BFGS: 300 19:05:16 -300.019289 0.255398
Step Time Energy fmax
BFGS: 0 19:05:16 -296.208029 4.382769
BFGS: 1 19:05:16 -296.713433 4.656009
BFGS: 2 19:05:17 -298.246727 3.010051
BFGS: 3 19:05:17 -297.208396 14.053452
BFGS: 4 19:05:18 -298.433651 1.815163
BFGS: 5 19:05:18 -298.496106 1.036638
BFGS: 6 19:05:19 -298.537041 0.841471
BFGS: 7 19:05:19 -298.546241 0.648076
BFGS: 8 19:05:19 -298.576430 0.544173
BFGS: 9 19:05:20 -298.582982 0.604971
BFGS: 10 19:05:20 -298.646034 1.352958
BFGS: 11 19:05:20 -298.720675 2.290404
BFGS: 12 19:05:21 -298.783998 3.027867
BFGS: 13 19:05:21 -298.867317 3.286544
BFGS: 14 19:05:21 -299.038787 3.787625
BFGS: 15 19:05:22 -299.584346 3.486369
BFGS: 16 19:05:22 -300.108225 2.014922
BFGS: 17 19:05:23 -300.292277 1.350364
BFGS: 18 19:05:23 -300.394829 1.308663
BFGS: 19 19:05:23 -300.535779 0.531063
BFGS: 20 19:05:24 -300.544624 0.329459
BFGS: 21 19:05:24 -300.553997 0.238194
BFGS: 22 19:05:25 -300.561461 0.233125
BFGS: 23 19:05:25 -300.566526 0.236196
BFGS: 24 19:05:26 -300.569504 0.177105
BFGS: 25 19:05:26 -300.571646 0.149699
BFGS: 26 19:05:26 -300.573356 0.134866
BFGS: 27 19:05:27 -300.574966 0.113690
BFGS: 28 19:05:27 -300.576233 0.101053
BFGS: 29 19:05:28 -300.576850 0.077638
BFGS: 30 19:05:28 -300.577292 0.063180
BFGS: 31 19:05:29 -300.577785 0.055087
BFGS: 32 19:05:29 -300.578180 0.047241
Step Time Energy fmax
BFGS: 0 19:05:29 -297.391614 4.359174
BFGS: 1 19:05:30 -297.835145 4.458277
BFGS: 2 19:05:30 -299.042181 3.308461
BFGS: 3 19:05:31 -299.216006 4.773004
BFGS: 4 19:05:31 -299.448182 1.594543
BFGS: 5 19:05:31 -299.558334 1.496865
BFGS: 6 19:05:32 -299.864797 0.933017
BFGS: 7 19:05:32 -299.908397 1.007796
BFGS: 8 19:05:33 -299.957568 0.621469
BFGS: 9 19:05:33 -300.000572 0.710180
BFGS: 10 19:05:33 -300.024146 0.505081
BFGS: 11 19:05:34 -300.036388 0.206183
BFGS: 12 19:05:34 -300.038505 0.177360
BFGS: 13 19:05:34 -300.040123 0.154908
BFGS: 14 19:05:35 -300.041356 0.102071
BFGS: 15 19:05:35 -300.041922 0.092474
BFGS: 16 19:05:36 -300.042249 0.078299
BFGS: 17 19:05:36 -300.042564 0.070390
BFGS: 18 19:05:37 -300.043046 0.074824
BFGS: 19 19:05:37 -300.043456 0.054035
BFGS: 20 19:05:38 -300.043637 0.032324
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 19:05:38 -295.302095 1.292261
BFGS: 1 19:05:38 -295.379571 1.178412
BFGS: 2 19:05:39 -295.593784 1.381139
BFGS: 3 19:05:39 -295.626380 0.594312
BFGS: 4 19:05:40 -295.637655 0.500013
BFGS: 5 19:05:40 -295.675166 0.493009
BFGS: 6 19:05:40 -295.681303 0.485568
BFGS: 7 19:05:41 -295.747669 0.585549
BFGS: 8 19:05:41 -295.764173 0.608150
BFGS: 9 19:05:41 -295.777805 0.638010
BFGS: 10 19:05:42 -295.807899 0.516628
BFGS: 11 19:05:42 -295.826364 0.280949
BFGS: 12 19:05:43 -295.831759 0.204961
BFGS: 13 19:05:43 -295.834328 0.216567
BFGS: 14 19:05:43 -295.835683 0.207763
BFGS: 15 19:05:44 -295.838430 0.180499
BFGS: 16 19:05:44 -295.840047 0.125684
BFGS: 17 19:05:45 -295.840881 0.049787
Step Time Energy fmax
BFGS: 0 19:05:45 -295.714768 0.694538
BFGS: 1 19:05:46 -295.761186 0.619863
BFGS: 2 19:05:46 -295.924398 0.355086
BFGS: 3 19:05:46 -295.933574 0.341925
BFGS: 4 19:05:47 -295.935692 0.326069
BFGS: 5 19:05:47 -295.954150 0.188717
BFGS: 6 19:05:47 -295.955761 0.177476
BFGS: 7 19:05:48 -295.961637 0.126934
BFGS: 8 19:05:48 -295.962670 0.107594
BFGS: 9 19:05:49 -295.963580 0.094676
BFGS: 10 19:05:49 -295.964335 0.084039
BFGS: 11 19:05:49 -295.965339 0.062030
BFGS: 12 19:05:50 -295.965993 0.053888
BFGS: 13 19:05:50 -295.966322 0.050556
BFGS: 14 19:05:50 -295.966536 0.042843
Step Time Energy fmax
BFGS: 0 19:05:51 -295.257810 1.372652
BFGS: 1 19:05:51 -295.340055 1.249057
BFGS: 2 19:05:51 -295.550721 1.601901
BFGS: 3 19:05:52 -295.592973 0.572502
BFGS: 4 19:05:52 -295.604050 0.539097
BFGS: 5 19:05:52 -295.636211 0.375860
BFGS: 6 19:05:52 -295.640990 0.391105
BFGS: 7 19:05:53 -295.661914 0.458084
BFGS: 8 19:05:53 -295.675191 0.551815
BFGS: 9 19:05:53 -295.695715 0.576604
BFGS: 10 19:05:54 -295.713352 0.822520
BFGS: 11 19:05:54 -295.759416 1.198759
BFGS: 12 19:05:55 -295.782661 1.217692
BFGS: 13 19:05:55 -295.829975 1.126821
BFGS: 14 19:05:55 -295.891407 0.774846
BFGS: 15 19:05:56 -295.922690 0.453637
BFGS: 16 19:05:56 -295.937230 0.291860
BFGS: 17 19:05:57 -295.943933 0.323710
BFGS: 18 19:05:57 -295.948878 0.333449
BFGS: 19 19:05:58 -295.955007 0.285618
BFGS: 20 19:05:58 -295.959802 0.170763
BFGS: 21 19:05:58 -295.962321 0.100625
BFGS: 22 19:05:59 -295.963513 0.085737
BFGS: 23 19:05:59 -295.964159 0.077234
BFGS: 24 19:06:00 -295.964888 0.069817
BFGS: 25 19:06:00 -295.965796 0.064175
BFGS: 26 19:06:01 -295.966362 0.038490
Step Time Energy fmax
BFGS: 0 19:06:01 -295.195778 1.480954
BFGS: 1 19:06:01 -295.287808 1.342306
BFGS: 2 19:06:02 -295.490477 1.892848
BFGS: 3 19:06:02 -295.546977 0.535154
BFGS: 4 19:06:02 -295.559248 0.572138
BFGS: 5 19:06:03 -295.587478 0.376858
BFGS: 6 19:06:03 -295.594036 0.282602
BFGS: 7 19:06:04 -295.600239 0.333405
BFGS: 8 19:06:04 -295.606968 0.339668
BFGS: 9 19:06:05 -295.614681 0.346102
BFGS: 10 19:06:05 -295.620511 0.263949
BFGS: 11 19:06:06 -295.624203 0.347712
BFGS: 12 19:06:06 -295.629581 0.485915
BFGS: 13 19:06:06 -295.657689 0.960142
BFGS: 14 19:06:07 -295.691971 1.414400
BFGS: 15 19:06:07 -295.745138 1.016618
BFGS: 16 19:06:08 -295.755483 0.949838
BFGS: 17 19:06:08 -295.818738 0.334196
BFGS: 18 19:06:08 -295.828680 0.300232
BFGS: 19 19:06:09 -295.834922 0.284285
BFGS: 20 19:06:09 -295.838453 0.254037
BFGS: 21 19:06:09 -295.846070 0.137268
BFGS: 22 19:06:10 -295.847748 0.091732
BFGS: 23 19:06:10 -295.848842 0.095034
BFGS: 24 19:06:10 -295.849530 0.098246
BFGS: 25 19:06:11 -295.850575 0.102402
BFGS: 26 19:06:11 -295.851888 0.105882
BFGS: 27 19:06:11 -295.853213 0.111901
BFGS: 28 19:06:12 -295.854291 0.122329
BFGS: 29 19:06:12 -295.855566 0.137669
BFGS: 30 19:06:12 -295.858142 0.168908
BFGS: 31 19:06:13 -295.864961 0.309444
BFGS: 32 19:06:13 -295.877779 0.506970
BFGS: 33 19:06:13 -295.882475 0.568529
BFGS: 34 19:06:14 -295.901986 0.357353
BFGS: 35 19:06:14 -295.921818 0.277270
BFGS: 36 19:06:15 -295.938617 0.213772
BFGS: 37 19:06:15 -295.946958 0.249257
BFGS: 38 19:06:15 -295.956883 0.221953
BFGS: 39 19:06:16 -295.962322 0.125689
BFGS: 40 19:06:16 -295.964465 0.092453
BFGS: 41 19:06:17 -295.965290 0.080486
BFGS: 42 19:06:17 -295.965939 0.064087
BFGS: 43 19:06:17 -295.966594 0.043434
Step Time Energy fmax
BFGS: 0 19:06:18 -295.092928 1.735652
BFGS: 1 19:06:18 -295.205983 1.563931
BFGS: 2 19:06:18 -295.390118 2.470990
BFGS: 3 19:06:19 -295.478782 0.463811
BFGS: 4 19:06:19 -295.495228 0.619578
BFGS: 5 19:06:19 -295.521837 0.679852
BFGS: 6 19:06:20 -295.536210 0.449822
BFGS: 7 19:06:20 -295.544326 0.258958
BFGS: 8 19:06:20 -295.548877 0.311984
BFGS: 9 19:06:21 -295.555377 0.296082
BFGS: 10 19:06:21 -295.559277 0.181087
BFGS: 11 19:06:21 -295.560602 0.058559
BFGS: 12 19:06:22 -295.560763 0.016055
Step Time Energy fmax
BFGS: 0 19:06:22 -295.424185 1.101960
BFGS: 1 19:06:22 -295.488525 1.016704
BFGS: 2 19:06:23 -295.699091 0.963289
BFGS: 3 19:06:23 -295.718362 0.563628
BFGS: 4 19:06:24 -295.731150 0.499772
BFGS: 5 19:06:24 -295.771006 0.605043
BFGS: 6 19:06:24 -295.783230 0.582192
BFGS: 7 19:06:25 -295.814299 0.613046
BFGS: 8 19:06:25 -295.848244 0.609708
BFGS: 9 19:06:26 -295.879532 0.439152
BFGS: 10 19:06:26 -295.896350 0.442020
BFGS: 11 19:06:26 -295.904369 0.369233
BFGS: 12 19:06:27 -295.910926 0.284047
BFGS: 13 19:06:27 -295.918801 0.175765
BFGS: 14 19:06:28 -295.923914 0.177905
BFGS: 15 19:06:28 -295.925971 0.183445
BFGS: 16 19:06:28 -295.927195 0.161406
BFGS: 17 19:06:28 -295.928912 0.110664
BFGS: 18 19:06:29 -295.930884 0.068448
BFGS: 19 19:06:29 -295.932238 0.055286
BFGS: 20 19:06:29 -295.932685 0.032148
Step Time Energy fmax
BFGS: 0 19:06:29 -295.339331 1.236347
BFGS: 1 19:06:29 -295.412846 1.130134
BFGS: 2 19:06:30 -295.627973 1.239785
BFGS: 3 19:06:30 -295.655124 0.602110
BFGS: 4 19:06:30 -295.666897 0.466152
BFGS: 5 19:06:30 -295.706391 0.544241
BFGS: 6 19:06:30 -295.713796 0.527836
BFGS: 7 19:06:31 -295.777788 0.560961
BFGS: 8 19:06:31 -295.795759 0.511520
BFGS: 9 19:06:31 -295.807299 0.505192
BFGS: 10 19:06:32 -295.818278 0.415826
BFGS: 11 19:06:32 -295.832948 0.243613
BFGS: 12 19:06:32 -295.840627 0.159446
BFGS: 13 19:06:33 -295.843372 0.193214
BFGS: 14 19:06:33 -295.844626 0.177052
BFGS: 15 19:06:33 -295.846366 0.130716
BFGS: 16 19:06:34 -295.848587 0.102016
BFGS: 17 19:06:34 -295.850443 0.100606
BFGS: 18 19:06:35 -295.851330 0.106306
BFGS: 19 19:06:35 -295.851898 0.107817
BFGS: 20 19:06:35 -295.852752 0.116032
BFGS: 21 19:06:36 -295.854566 0.133966
BFGS: 22 19:06:36 -295.857940 0.169886
BFGS: 23 19:06:36 -295.862857 0.222073
BFGS: 24 19:06:37 -295.869269 0.260130
BFGS: 25 19:06:37 -295.878131 0.329135
BFGS: 26 19:06:37 -295.892303 0.305895
BFGS: 27 19:06:38 -295.909231 0.196576
BFGS: 28 19:06:38 -295.917441 0.208124
BFGS: 29 19:06:39 -295.924081 0.145454
BFGS: 30 19:06:39 -295.926268 0.107288
BFGS: 31 19:06:39 -295.928120 0.081886
BFGS: 32 19:06:40 -295.930082 0.056247
BFGS: 33 19:06:40 -295.931736 0.055396
BFGS: 34 19:06:40 -295.932328 0.046366
Step Time Energy fmax
BFGS: 0 19:06:40 -295.494476 1.017825
BFGS: 1 19:06:41 -295.553390 0.952137
BFGS: 2 19:06:41 -295.769392 0.754413
BFGS: 3 19:06:41 -295.786257 0.523076
BFGS: 4 19:06:42 -295.798637 0.545401
BFGS: 5 19:06:42 -295.845765 0.592845
BFGS: 6 19:06:42 -295.862498 0.638035
BFGS: 7 19:06:43 -295.889552 0.740506
BFGS: 8 19:06:43 -295.913370 0.558450
BFGS: 9 19:06:43 -295.931441 0.344610
BFGS: 10 19:06:43 -295.939943 0.333098
BFGS: 11 19:06:44 -295.944559 0.297342
BFGS: 12 19:06:44 -295.949227 0.243772
BFGS: 13 19:06:44 -295.954660 0.178889
BFGS: 14 19:06:45 -295.958541 0.157444
BFGS: 15 19:06:45 -295.960488 0.157626
BFGS: 16 19:06:45 -295.961896 0.130466
BFGS: 17 19:06:46 -295.963621 0.082663
BFGS: 18 19:06:46 -295.965327 0.060775
BFGS: 19 19:06:47 -295.966255 0.045139
Step Time Energy fmax
BFGS: 0 19:06:47 -295.266325 1.358224
BFGS: 1 19:06:47 -295.347694 1.234807
BFGS: 2 19:06:48 -295.557277 1.523633
BFGS: 3 19:06:48 -295.595516 0.579178
BFGS: 4 19:06:48 -295.606536 0.526412
BFGS: 5 19:06:49 -295.640232 0.411676
BFGS: 6 19:06:49 -295.644907 0.413896
BFGS: 7 19:06:49 -295.680229 0.576191
BFGS: 8 19:06:50 -295.693762 0.503255
BFGS: 9 19:06:50 -295.716616 0.762741
BFGS: 10 19:06:50 -295.743332 0.995303
BFGS: 11 19:06:51 -295.760959 1.000504
BFGS: 12 19:06:51 -295.806358 0.828380
BFGS: 13 19:06:51 -295.840932 0.538968
BFGS: 14 19:06:52 -295.863269 0.276489
BFGS: 15 19:06:52 -295.869494 0.359977
BFGS: 16 19:06:53 -295.876597 0.407156
BFGS: 17 19:06:53 -295.885143 0.366343
BFGS: 18 19:06:53 -295.893605 0.253387
BFGS: 19 19:06:54 -295.899746 0.242023
BFGS: 20 19:06:54 -295.904042 0.219723
BFGS: 21 19:06:54 -295.907020 0.207431
BFGS: 22 19:06:55 -295.911564 0.254529
BFGS: 23 19:06:55 -295.918340 0.239126
BFGS: 24 19:06:55 -295.923140 0.140524
BFGS: 25 19:06:56 -295.925874 0.119182
BFGS: 26 19:06:56 -295.927502 0.092354
BFGS: 27 19:06:56 -295.928716 0.090775
BFGS: 28 19:06:57 -295.930260 0.076019
BFGS: 29 19:06:57 -295.931562 0.047435
Step Time Energy fmax
BFGS: 0 19:06:57 -295.189073 1.494491
BFGS: 1 19:06:58 -295.281995 1.354908
BFGS: 2 19:06:58 -295.482663 1.953778
BFGS: 3 19:06:58 -295.542734 0.525848
BFGS: 4 19:06:59 -295.555272 0.576715
BFGS: 5 19:06:59 -295.582202 0.424931
BFGS: 6 19:06:59 -295.589502 0.258716
BFGS: 7 19:07:00 -295.595231 0.313916
BFGS: 8 19:07:00 -295.601212 0.329764
BFGS: 9 19:07:01 -295.608066 0.317801
BFGS: 10 19:07:01 -295.613239 0.233006
BFGS: 11 19:07:01 -295.616216 0.290002
BFGS: 12 19:07:02 -295.619431 0.382284
BFGS: 13 19:07:02 -295.632209 0.673035
BFGS: 14 19:07:02 -295.678465 1.152624
BFGS: 15 19:07:03 -295.770631 1.128075
BFGS: 16 19:07:03 -295.851758 0.842018
BFGS: 17 19:07:03 -295.859960 0.847128
BFGS: 18 19:07:04 -295.890177 0.677510
BFGS: 19 19:07:04 -295.911520 0.549554
BFGS: 20 19:07:04 -295.936059 0.324789
BFGS: 21 19:07:05 -295.942392 0.285364
BFGS: 22 19:07:05 -295.948388 0.277142
BFGS: 23 19:07:06 -295.953759 0.218529
BFGS: 24 19:07:06 -295.959525 0.136309
BFGS: 25 19:07:06 -295.963054 0.111196
BFGS: 26 19:07:07 -295.964399 0.090743
BFGS: 27 19:07:07 -295.965089 0.065169
BFGS: 28 19:07:07 -295.965821 0.051101
BFGS: 29 19:07:08 -295.966450 0.040986
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 19:07:08 -303.900865 0.391989
BFGS: 1 19:07:09 -303.907570 0.294139
BFGS: 2 19:07:09 -303.921350 0.165974
BFGS: 3 19:07:09 -303.923989 0.140968
BFGS: 4 19:07:09 -303.926127 0.111482
BFGS: 5 19:07:10 -303.927674 0.112435
BFGS: 6 19:07:10 -303.929003 0.092992
BFGS: 7 19:07:10 -303.929775 0.072526
BFGS: 8 19:07:11 -303.930137 0.056927
BFGS: 9 19:07:11 -303.930339 0.037435
Step Time Energy fmax
BFGS: 0 19:07:11 -303.906711 0.320315
BFGS: 1 19:07:12 -303.911583 0.246047
BFGS: 2 19:07:12 -303.922928 0.158124
BFGS: 3 19:07:13 -303.925185 0.133857
BFGS: 4 19:07:13 -303.926957 0.092339
BFGS: 5 19:07:13 -303.928105 0.086704
BFGS: 6 19:07:14 -303.929128 0.070167
BFGS: 7 19:07:14 -303.929763 0.076201
BFGS: 8 19:07:14 -303.930110 0.057882
BFGS: 9 19:07:15 -303.930318 0.041029
Step Time Energy fmax
BFGS: 0 19:07:15 -303.904740 0.284455
BFGS: 1 19:07:16 -303.909435 0.232693
BFGS: 2 19:07:16 -303.921313 0.165359
BFGS: 3 19:07:16 -303.923585 0.138736
BFGS: 4 19:07:17 -303.925345 0.089862
BFGS: 5 19:07:17 -303.926356 0.083637
BFGS: 6 19:07:18 -303.927206 0.069146
BFGS: 7 19:07:18 -303.927729 0.071016
BFGS: 8 19:07:18 -303.928017 0.051588
BFGS: 9 19:07:18 -303.928184 0.035309
Step Time Energy fmax
BFGS: 0 19:07:19 -303.103551 1.053262
BFGS: 1 19:07:19 -303.135903 0.791989
BFGS: 2 19:07:19 -303.200648 0.674381
BFGS: 3 19:07:20 -303.230802 0.663736
BFGS: 4 19:07:20 -303.268426 0.760918
BFGS: 5 19:07:20 -303.299119 0.656904
BFGS: 6 19:07:20 -303.346338 0.576108
BFGS: 7 19:07:21 -303.363562 0.384578
BFGS: 8 19:07:21 -303.368395 0.261635
BFGS: 9 19:07:21 -303.377672 0.175441
BFGS: 10 19:07:22 -303.381269 0.163864
BFGS: 11 19:07:22 -303.383782 0.205787
BFGS: 12 19:07:23 -303.386356 0.180642
BFGS: 13 19:07:23 -303.389130 0.164804
BFGS: 14 19:07:23 -303.391825 0.173363
BFGS: 15 19:07:24 -303.394057 0.165269
BFGS: 16 19:07:24 -303.396245 0.173398
BFGS: 17 19:07:24 -303.399944 0.182393
BFGS: 18 19:07:25 -303.405677 0.255653
BFGS: 19 19:07:25 -303.412435 0.350435
BFGS: 20 19:07:25 -303.419625 0.318238
BFGS: 21 19:07:26 -303.429453 0.377766
BFGS: 22 19:07:26 -303.442275 0.499636
BFGS: 23 19:07:27 -303.468282 0.836675
BFGS: 24 19:07:27 -303.503144 0.897310
BFGS: 25 19:07:27 -303.540292 0.657880
BFGS: 26 19:07:27 -303.566521 0.772881
BFGS: 27 19:07:28 -303.613407 0.718421
BFGS: 28 19:07:28 -303.658794 0.672595
BFGS: 29 19:07:28 -303.736495 0.754581
BFGS: 30 19:07:28 -303.793797 0.938596
BFGS: 31 19:07:29 -303.832201 0.789592
BFGS: 32 19:07:29 -303.870701 0.562297
BFGS: 33 19:07:29 -303.882133 0.661829
BFGS: 34 19:07:30 -303.899966 0.451331
BFGS: 35 19:07:30 -303.914942 0.235078
BFGS: 36 19:07:31 -303.919811 0.174909
BFGS: 37 19:07:31 -303.922733 0.137082
BFGS: 38 19:07:31 -303.924647 0.105201
BFGS: 39 19:07:32 -303.926273 0.063578
BFGS: 40 19:07:32 -303.927187 0.059070
BFGS: 41 19:07:32 -303.927606 0.048185
Step Time Energy fmax
BFGS: 0 19:07:33 -303.901898 0.321751
BFGS: 1 19:07:33 -303.907733 0.249408
BFGS: 2 19:07:34 -303.921420 0.161687
BFGS: 3 19:07:34 -303.924012 0.138001
BFGS: 4 19:07:34 -303.926172 0.109964
BFGS: 5 19:07:35 -303.927619 0.104177
BFGS: 6 19:07:35 -303.928834 0.081424
BFGS: 7 19:07:35 -303.929551 0.074311
BFGS: 8 19:07:36 -303.929923 0.059888
BFGS: 9 19:07:36 -303.930164 0.043299
Step Time Energy fmax
BFGS: 0 19:07:36 -303.897942 0.365377
BFGS: 1 19:07:37 -303.904650 0.275940
BFGS: 2 19:07:37 -303.918582 0.171540
BFGS: 3 19:07:37 -303.921271 0.144123
BFGS: 4 19:07:38 -303.923539 0.112701
BFGS: 5 19:07:38 -303.925131 0.115252
BFGS: 6 19:07:39 -303.926491 0.095496
BFGS: 7 19:07:39 -303.927284 0.076004
BFGS: 8 19:07:39 -303.927658 0.058162
BFGS: 9 19:07:40 -303.927872 0.041092
Step Time Energy fmax
BFGS: 0 19:07:40 -303.901358 0.328437
BFGS: 1 19:07:40 -303.906789 0.257946
BFGS: 2 19:07:41 -303.920107 0.168280
BFGS: 3 19:07:41 -303.922664 0.144938
BFGS: 4 19:07:41 -303.924824 0.109073
BFGS: 5 19:07:42 -303.926142 0.096984
BFGS: 6 19:07:42 -303.927174 0.073458
BFGS: 7 19:07:43 -303.927726 0.066134
BFGS: 8 19:07:43 -303.927999 0.049920
Step Time Energy fmax
BFGS: 0 19:07:43 -303.904035 0.303027
BFGS: 1 19:07:44 -303.909098 0.247582
BFGS: 2 19:07:44 -303.921455 0.163733
BFGS: 3 19:07:44 -303.923861 0.137552
BFGS: 4 19:07:45 -303.926064 0.104596
BFGS: 5 19:07:45 -303.927513 0.109883
BFGS: 6 19:07:46 -303.928755 0.092243
BFGS: 7 19:07:46 -303.929545 0.081558
BFGS: 8 19:07:46 -303.929961 0.063415
BFGS: 9 19:07:47 -303.930194 0.041780
/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 19:08:56 -301.882157 4.154644
BFGS: 1 19:09:00 -302.179034 3.364641
BFGS: 2 19:09:02 -302.771319 5.171553
BFGS: 3 19:09:05 -302.877755 1.548565
BFGS: 4 19:09:10 -303.025680 0.933134
BFGS: 5 19:09:13 -303.043233 0.790328
BFGS: 6 19:09:15 -303.050676 0.653693
BFGS: 7 19:09:20 -303.068114 0.809231
BFGS: 8 19:09:23 -303.088998 0.800315
BFGS: 9 19:09:27 -303.117061 0.767790
BFGS: 10 19:09:30 -303.153200 0.693961
BFGS: 11 19:09:33 -303.215494 0.932898
BFGS: 12 19:09:39 -303.266033 1.168013
BFGS: 13 19:09:42 -303.269016 1.233438
BFGS: 14 19:09:47 -303.279463 1.063641
BFGS: 15 19:09:50 -303.291242 0.808215
BFGS: 16 19:09:53 -303.308775 1.319820
BFGS: 17 19:09:57 -303.305158 0.923728
BFGS: 18 19:10:00 -303.322603 1.083069
BFGS: 19 19:10:03 -303.363162 1.113293
BFGS: 20 19:10:06 -303.402016 1.129657
BFGS: 21 19:10:10 -303.454744 1.188311
BFGS: 22 19:10:12 -303.476832 1.121805
BFGS: 23 19:10:15 -303.540224 1.318928
BFGS: 24 19:10:18 -303.583500 1.170887
BFGS: 25 19:10:21 -303.617333 0.847559
BFGS: 26 19:10:24 -303.644853 0.605362
BFGS: 27 19:10:27 -303.672837 0.495417
BFGS: 28 19:10:29 -303.682662 0.659565
BFGS: 29 19:10:32 -303.694361 0.539770
BFGS: 30 19:10:35 -303.713706 0.375991
BFGS: 31 19:10:39 -303.705495 0.538105
BFGS: 32 19:10:43 -303.695002 0.539426
BFGS: 33 19:10:47 -303.679706 0.515221
BFGS: 34 19:10:50 -303.671003 0.431294
BFGS: 35 19:10:53 -303.659710 0.351882
BFGS: 36 19:10:56 -303.650508 0.333318
BFGS: 37 19:10:59 -303.645321 0.258613
BFGS: 38 19:11:02 -303.646111 0.240981
BFGS: 39 19:11:05 -303.647795 0.307916
BFGS: 40 19:11:08 -303.647975 0.308744
BFGS: 41 19:11:11 -303.648126 0.244666
BFGS: 42 19:11:14 -303.650307 0.295700
BFGS: 43 19:11:16 -303.653515 0.357957
BFGS: 44 19:11:21 -303.654097 0.262591
BFGS: 45 19:11:23 -303.652646 0.287215
BFGS: 46 19:11:26 -303.651520 0.294358
BFGS: 47 19:11:28 -303.651149 0.281021
BFGS: 48 19:11:29 -303.651529 0.266151
BFGS: 49 19:11:32 -303.652245 0.249950
BFGS: 50 19:11:35 -303.653098 0.254391
BFGS: 51 19:11:38 -303.654520 0.252485
BFGS: 52 19:11:42 -303.656994 0.322540
BFGS: 53 19:11:45 -303.660279 0.367272
BFGS: 54 19:11:47 -303.663394 0.371791
BFGS: 55 19:11:51 -303.664765 0.347769
BFGS: 56 19:11:55 -303.666026 0.417480
BFGS: 57 19:11:57 -303.669825 0.362984
BFGS: 58 19:12:02 -303.680781 0.415003
BFGS: 59 19:12:04 -303.696932 0.775571
BFGS: 60 19:12:08 -303.698359 0.739188
BFGS: 61 19:12:11 -303.690493 0.608998
BFGS: 62 19:12:13 -303.699381 0.309385
BFGS: 63 19:12:16 -303.710802 0.638329
BFGS: 64 19:12:18 -303.713893 0.848163
BFGS: 65 19:12:21 -303.704419 1.324711
BFGS: 66 19:12:24 -303.715747 0.606951
BFGS: 67 19:12:26 -303.713488 0.219986
BFGS: 68 19:12:32 -303.715113 0.259900
BFGS: 69 19:12:35 -303.717902 0.338291
BFGS: 70 19:12:38 -303.718915 0.346468
BFGS: 71 19:12:42 -303.715752 0.425784
BFGS: 72 19:12:45 -303.713888 0.567285
BFGS: 73 19:12:47 -303.708962 0.707664
BFGS: 74 19:12:51 -303.713810 0.457016
BFGS: 75 19:12:54 -303.712264 0.419073
BFGS: 76 19:12:56 -303.713609 0.345946
BFGS: 77 19:13:00 -303.712985 0.403394
BFGS: 78 19:13:03 -303.707081 0.515710
BFGS: 79 19:13:05 -303.689399 0.742180
BFGS: 80 19:13:09 -303.705995 0.505012
BFGS: 81 19:13:12 -303.709231 0.439827
BFGS: 82 19:13:15 -303.711646 0.336510
BFGS: 83 19:13:17 -303.713341 0.381534
BFGS: 84 19:13:21 -303.717029 0.334393
BFGS: 85 19:13:24 -303.720271 0.299095
BFGS: 86 19:13:26 -303.721420 0.243194
BFGS: 87 19:13:30 -303.720900 0.213800
BFGS: 88 19:13:33 -303.720532 0.188075
BFGS: 89 19:13:35 -303.720676 0.134597
BFGS: 90 19:13:37 -303.720676 0.134597
BFGS: 91 19:13:39 -303.720676 0.162843
BFGS: 92 19:13:40 -303.720676 0.218648
BFGS: 93 19:13:42 -303.720676 0.306696
BFGS: 94 19:13:44 -303.720676 0.461121
BFGS: 95 19:13:47 -303.720676 0.540570
BFGS: 96 19:13:50 -303.720676 0.559488
BFGS: 97 19:13:57 -303.720676 0.344750
BFGS: 98 19:14:02 -303.720676 0.560372
BFGS: 99 19:14:06 -303.720676 0.628754
BFGS: 100 19:14:11 -303.720676 0.595884
BFGS: 101 19:14:15 -303.720676 0.467899
BFGS: 102 19:14:19 -303.720676 0.367706
BFGS: 103 19:14:24 -303.720676 0.441166
BFGS: 104 19:14:28 -303.720676 0.278804
BFGS: 105 19:14:31 -303.720676 0.464435
BFGS: 106 19:14:36 -303.720676 0.474245
BFGS: 107 19:14:42 -303.720676 0.529717
BFGS: 108 19:14:49 -303.720676 0.433454
BFGS: 109 19:14:52 -303.720676 0.370102
BFGS: 110 19:14:55 -303.720676 0.394258
BFGS: 111 19:14:58 -303.720676 0.226115
BFGS: 112 19:15:05 -303.720676 0.178037
BFGS: 113 19:15:10 -303.720676 0.180830
BFGS: 114 19:15:12 -303.720676 0.377103
BFGS: 115 19:15:16 -303.720676 0.345318
BFGS: 116 19:15:19 -303.720676 0.420558
BFGS: 117 19:15:23 -303.720676 0.229732
BFGS: 118 19:15:27 -303.720676 0.174856
BFGS: 119 19:15:32 -303.720676 0.613150
BFGS: 120 19:15:38 -303.720676 0.378411
BFGS: 121 19:15:44 -303.720676 0.325377
BFGS: 122 19:15:52 -303.720676 0.561169
BFGS: 123 19:15:57 -303.720676 0.498466
BFGS: 124 19:16:02 -303.720676 0.387207
BFGS: 125 19:16:07 -303.720676 0.428933
BFGS: 126 19:16:13 -303.720099 0.626495
BFGS: 127 19:16:17 -303.719877 0.898723
BFGS: 128 19:16:21 -303.719862 0.518141
BFGS: 129 19:16:25 -303.719675 0.519069
BFGS: 130 19:16:28 -303.720038 0.891244
BFGS: 131 19:16:32 -303.720824 0.751651
BFGS: 132 19:16:37 -303.720824 0.443304
BFGS: 133 19:16:40 -303.720824 0.451731
BFGS: 134 19:16:43 -303.720824 0.777720
BFGS: 135 19:16:46 -303.720824 0.601295
BFGS: 136 19:16:53 -303.720824 0.378254
BFGS: 137 19:16:59 -303.720824 0.587090
BFGS: 138 19:17:03 -303.720824 0.801094
BFGS: 139 19:17:06 -303.720824 0.540341
BFGS: 140 19:17:09 -303.720824 0.371016
BFGS: 141 19:17:10 -303.720824 0.709927
BFGS: 142 19:17:11 -303.720824 0.519714
BFGS: 143 19:17:16 -303.720824 0.448546
BFGS: 144 19:17:17 -303.720824 0.480647
BFGS: 145 19:17:18 -303.720824 0.275597
BFGS: 146 19:17:19 -303.720824 0.366297
BFGS: 147 19:17:20 -303.720824 0.403988
BFGS: 148 19:17:22 -303.720824 0.307939
BFGS: 149 19:17:23 -303.720824 0.406008
BFGS: 150 19:17:24 -303.720824 0.624171
BFGS: 151 19:17:25 -303.720824 0.624417
BFGS: 152 19:17:27 -303.720824 0.710959
BFGS: 153 19:17:28 -303.720824 0.570238
BFGS: 154 19:17:29 -303.720824 0.683000
BFGS: 155 19:17:30 -303.720824 0.445665
BFGS: 156 19:17:31 -303.720824 0.465364
BFGS: 157 19:17:33 -303.720824 0.508814
BFGS: 158 19:17:35 -303.720824 0.507362
BFGS: 159 19:17:36 -303.720824 0.510617
BFGS: 160 19:17:38 -303.720824 0.418761
BFGS: 161 19:17:39 -303.720824 0.492796
BFGS: 162 19:17:42 -303.720824 0.581243
BFGS: 163 19:17:43 -303.720824 0.829223
BFGS: 164 19:17:44 -303.720824 0.575304
BFGS: 165 19:17:51 -303.720824 0.329500
BFGS: 166 19:17:52 -303.720824 0.175078
BFGS: 167 19:17:55 -303.720824 0.183259
BFGS: 168 19:17:56 -303.720824 0.431143
BFGS: 169 19:18:00 -303.720824 0.577959
BFGS: 170 19:18:01 -303.720824 0.284477
BFGS: 171 19:18:05 -303.720824 0.383707
BFGS: 172 19:18:06 -303.720824 0.196617
BFGS: 173 19:18:08 -303.720824 0.456847
BFGS: 174 19:18:12 -303.720824 0.435562
BFGS: 175 19:18:15 -303.720824 0.212080
BFGS: 176 19:18:16 -303.720824 0.253326
BFGS: 177 19:18:17 -303.720824 0.243684
BFGS: 178 19:18:20 -303.720824 0.175065
BFGS: 179 19:18:22 -303.720824 0.192988
BFGS: 180 19:18:24 -303.720824 0.270768
BFGS: 181 19:18:25 -303.720824 0.654055
BFGS: 182 19:18:25 -303.720824 0.269125
BFGS: 183 19:18:26 -303.720824 0.242194
BFGS: 184 19:18:28 -303.720824 0.251444
BFGS: 185 19:18:28 -303.720824 0.259307
BFGS: 186 19:18:29 -303.720824 0.274762
BFGS: 187 19:18:30 -303.720824 0.299326
BFGS: 188 19:18:30 -303.720824 0.401632
BFGS: 189 19:18:31 -303.720824 0.371491
BFGS: 190 19:18:32 -303.720824 0.313597
BFGS: 191 19:18:33 -303.720824 0.667473
BFGS: 192 19:18:34 -303.720824 0.736681
BFGS: 193 19:18:35 -303.720824 0.732188
BFGS: 194 19:18:35 -303.720824 0.653779
BFGS: 195 19:18:37 -303.720824 0.629885
BFGS: 196 19:18:38 -303.720824 0.518337
BFGS: 197 19:18:40 -303.720824 0.495937
BFGS: 198 19:18:41 -303.720824 0.442153
BFGS: 199 19:18:42 -303.720824 0.438606
BFGS: 200 19:18:43 -303.720824 0.407335
BFGS: 201 19:18:48 -303.720824 0.431667
BFGS: 202 19:18:49 -303.720824 0.637200
BFGS: 203 19:18:50 -303.720824 0.380901
BFGS: 204 19:18:51 -303.720824 0.338529
BFGS: 205 19:18:52 -303.720824 0.311724
BFGS: 206 19:18:52 -303.720824 0.294059
BFGS: 207 19:18:54 -303.720824 0.266300
BFGS: 208 19:18:54 -303.720824 0.245408
BFGS: 209 19:18:55 -303.720824 0.242885
BFGS: 210 19:18:56 -303.720824 0.262771
BFGS: 211 19:18:57 -303.720824 0.285074
BFGS: 212 19:18:58 -303.720824 0.244634
BFGS: 213 19:18:59 -303.720824 0.430779
BFGS: 214 19:19:00 -303.720824 0.633120
BFGS: 215 19:19:03 -303.720824 0.250641
BFGS: 216 19:19:05 -303.720824 0.350473
BFGS: 217 19:19:06 -303.720824 0.431487
BFGS: 218 19:19:07 -303.720824 0.308568
BFGS: 219 19:19:08 -303.720824 0.273607
BFGS: 220 19:19:09 -303.720824 0.346200
BFGS: 221 19:19:10 -303.720824 0.349140
BFGS: 222 19:19:15 -303.720824 0.235169
BFGS: 223 19:19:19 -303.720824 0.221037
BFGS: 224 19:19:20 -303.720824 0.376945
BFGS: 225 19:19:21 -303.720824 0.374296
BFGS: 226 19:19:21 -303.720824 0.273274
BFGS: 227 19:19:22 -303.720824 0.220279
BFGS: 228 19:19:23 -303.720824 0.349952
BFGS: 229 19:19:23 -303.720824 0.286391
BFGS: 230 19:19:24 -303.720824 0.378796
BFGS: 231 19:19:26 -303.720824 0.448958
BFGS: 232 19:19:27 -303.720824 0.477062
BFGS: 233 19:19:28 -303.720824 0.229885
BFGS: 234 19:19:32 -303.720824 0.258448
BFGS: 235 19:19:33 -303.720824 0.265410
BFGS: 236 19:19:34 -303.720824 0.226959
BFGS: 237 19:19:34 -303.720824 0.219724
BFGS: 238 19:19:37 -303.720824 0.178561
BFGS: 239 19:19:39 -303.720824 0.272458
BFGS: 240 19:19:40 -303.720824 0.420556
BFGS: 241 19:19:40 -303.720824 0.199033
BFGS: 242 19:19:41 -303.720824 0.211891
BFGS: 243 19:19:42 -303.720824 0.313520
BFGS: 244 19:19:42 -303.720824 0.887207
BFGS: 245 19:19:43 -303.720824 0.400739
BFGS: 246 19:19:44 -303.720824 0.372453
BFGS: 247 19:19:45 -303.720824 0.478193
BFGS: 248 19:19:45 -303.720824 0.180158
BFGS: 249 19:19:46 -303.720824 0.138835
BFGS: 250 19:19:52 -303.720824 0.135047
BFGS: 251 19:19:53 -303.720824 0.146469
BFGS: 252 19:19:54 -303.720824 0.419840
BFGS: 253 19:19:54 -303.720824 0.349746
BFGS: 254 19:19:55 -303.720824 0.351628
BFGS: 255 19:19:59 -303.720824 0.423754
BFGS: 256 19:20:00 -303.720824 0.340787
BFGS: 257 19:20:01 -303.720824 0.337882
BFGS: 258 19:20:05 -303.720824 0.355073
BFGS: 259 19:20:08 -303.720824 0.416170
BFGS: 260 19:20:08 -303.720824 0.666490
BFGS: 261 19:20:09 -303.720824 0.725103
BFGS: 262 19:20:10 -303.720824 0.375447
BFGS: 263 19:20:11 -303.720824 0.252330
BFGS: 264 19:20:12 -303.720824 0.154171
BFGS: 265 19:20:14 -303.720824 0.141342
BFGS: 266 19:20:15 -303.720824 0.145203
BFGS: 267 19:20:17 -303.720824 0.183368
BFGS: 268 19:20:18 -303.720824 0.200832
BFGS: 269 19:20:20 -303.720824 0.152113
BFGS: 270 19:20:22 -303.720824 0.128364
BFGS: 271 19:20:23 -303.720824 0.117455
BFGS: 272 19:20:24 -303.720824 0.067773
BFGS: 273 19:20:25 -303.720824 0.052540
BFGS: 274 19:20:26 -303.720824 0.032600
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_9842/3247994494.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")