Transition State Search (NEBs)#
FAIR chemistry models can be used to enumerate and study reaction pathways via transition state search tools built into ASE or in packages like Sella via the ASE interface.
The first section of this tutorial walks through how to use the CatTsunami tools to automatically enumerate a number of hypothetical initial/final configurations for various types of reactions on a heterogeneous catalyst surface. If you already have a NEB you’re looking to optimize, you can jump straight to the last section (Run NEBs)!
Since the NEB calculations here can be a bit time consuming, we’ll use a small number of steps during the documentation testing, and otherwise use a reasonable guess.
import os
# Use a small number of steps here to keep the docs fast during CI, but otherwise do quite reasonable settings.
fast_docs = os.environ.get("FAST_DOCS", "false").lower() == "true"
if fast_docs:
optimization_steps = 20
else:
optimization_steps = 300
Need to install fairchem-core or get UMA access or getting permissions/401 errors?
Install the necessary packages using pip, uv etc
Get access to any necessary huggingface gated models
Get and login to your Huggingface account
Request access to https://huggingface.co/facebook/UMA
Create a Huggingface token at https://huggingface.co/settings/tokens/ with the permission “Permissions: Read access to contents of all public gated repos you can access”
Add the token as an environment variable using
huggingface-cli loginor by setting the HF_TOKEN environment variable.
Do enumerations in an AdsorbML style#
from __future__ import annotations
import matplotlib.pyplot as plt
from ase.io import read
from ase.mep import DyNEB
from ase.optimize import BFGS
from fairchem.applications.cattsunami.core import Reaction
from fairchem.applications.cattsunami.core.autoframe import AutoFrameDissociation
from fairchem.applications.cattsunami.databases import DISSOCIATION_REACTION_DB_PATH
from fairchem.core import FAIRChemCalculator, pretrained_mlip
from fairchem.data.oc.core import Adsorbate, AdsorbateSlabConfig, Bulk, Slab
from fairchem.data.oc.databases.pkls import ADSORBATE_PKL_PATH, BULK_PKL_PATH
from x3dase.x3d import X3D
# Instantiate the reaction class for the reaction of interest
reaction = Reaction(
reaction_str_from_db="*CH -> *C + *H",
reaction_db_path=DISSOCIATION_REACTION_DB_PATH,
adsorbate_db_path=ADSORBATE_PKL_PATH,
)
# Instantiate our adsorbate class for the reactant and product
reactant = Adsorbate(
adsorbate_id_from_db=reaction.reactant1_idx, adsorbate_db_path=ADSORBATE_PKL_PATH
)
product1 = Adsorbate(
adsorbate_id_from_db=reaction.product1_idx, adsorbate_db_path=ADSORBATE_PKL_PATH
)
product2 = Adsorbate(
adsorbate_id_from_db=reaction.product2_idx, adsorbate_db_path=ADSORBATE_PKL_PATH
)
# Grab the bulk and cut the slab we are interested in
bulk = Bulk(bulk_src_id_from_db="mp-33", bulk_db_path=BULK_PKL_PATH)
slab = Slab.from_bulk_get_specific_millers(bulk=bulk, specific_millers=(0, 0, 1))
# Perform site enumeration
# For AdsorbML num_sites = 100, but we use 5 here for brevity. This should be increased for practical use.
reactant_configs = AdsorbateSlabConfig(
slab=slab[0],
adsorbate=reactant,
mode="random_site_heuristic_placement",
num_sites=10,
).atoms_list
product1_configs = AdsorbateSlabConfig(
slab=slab[0],
adsorbate=product1,
mode="random_site_heuristic_placement",
num_sites=10,
).atoms_list
product2_configs = AdsorbateSlabConfig(
slab=slab[0],
adsorbate=product2,
mode="random_site_heuristic_placement",
num_sites=10,
).atoms_list
# Instantiate the calculator
predictor = pretrained_mlip.get_predict_unit("uma-s-1p1")
calc = FAIRChemCalculator(predictor, task_name="oc20")
WARNING:root:device was not explicitly set, using device='cuda'.
# Relax the reactant systems
reactant_energies = []
for config in reactant_configs:
config.calc = calc
config.pbc = True
opt = BFGS(config)
opt.run(fmax=0.05, steps=optimization_steps)
reactant_energies.append(config.get_potential_energy())
Step Time Energy fmax
BFGS: 0 17:35:10 -302.200892 4.175940
BFGS: 1 17:35:10 -302.577503 3.397333
BFGS: 2 17:35:10 -303.468994 2.980258
BFGS: 3 17:35:10 -303.633559 2.819043
BFGS: 4 17:35:10 -303.852443 1.827604
BFGS: 5 17:35:11 -304.028002 2.267210
BFGS: 6 17:35:11 -304.100093 1.318172
BFGS: 7 17:35:11 -304.241600 0.848792
BFGS: 8 17:35:11 -304.288077 1.015600
BFGS: 9 17:35:11 -304.363265 0.960483
BFGS: 10 17:35:11 -304.440851 0.870203
BFGS: 11 17:35:11 -304.491719 0.981628
BFGS: 12 17:35:11 -304.526390 1.024227
BFGS: 13 17:35:11 -304.575664 0.752652
BFGS: 14 17:35:11 -304.605152 0.578557
BFGS: 15 17:35:11 -304.619120 0.470870
BFGS: 16 17:35:12 -304.631542 0.384981
BFGS: 17 17:35:12 -304.639531 0.427509
BFGS: 18 17:35:12 -304.650686 0.450874
BFGS: 19 17:35:12 -304.662159 0.285516
BFGS: 20 17:35:12 -304.668047 0.194390
Step Time Energy fmax
BFGS: 0 17:35:12 -300.670284 3.976907
BFGS: 1 17:35:12 -301.135848 3.974111
BFGS: 2 17:35:12 -302.540216 3.690204
BFGS: 3 17:35:12 -302.246352 9.712445
BFGS: 4 17:35:12 -302.809558 3.291132
BFGS: 5 17:35:13 -302.958286 2.649224
BFGS: 6 17:35:13 -303.083281 2.837852
BFGS: 7 17:35:13 -303.140541 0.683343
BFGS: 8 17:35:13 -303.147871 0.327119
BFGS: 9 17:35:13 -303.152880 0.268696
BFGS: 10 17:35:13 -303.158657 0.341415
BFGS: 11 17:35:13 -303.167864 0.382583
BFGS: 12 17:35:13 -303.172669 0.275016
BFGS: 13 17:35:13 -303.174561 0.179294
BFGS: 14 17:35:13 -303.178136 0.202048
BFGS: 15 17:35:13 -303.182159 0.306348
BFGS: 16 17:35:14 -303.187087 0.306362
BFGS: 17 17:35:14 -303.190091 0.170701
BFGS: 18 17:35:14 -303.191030 0.065889
BFGS: 19 17:35:14 -303.191301 0.056020
BFGS: 20 17:35:14 -303.191695 0.071404
Step Time Energy fmax
BFGS: 0 17:35:14 -300.642350 4.030977
BFGS: 1 17:35:14 -301.095286 3.772559
BFGS: 2 17:35:14 -302.472920 3.669120
BFGS: 3 17:35:14 -302.156099 10.031545
BFGS: 4 17:35:14 -302.749632 3.282861
BFGS: 5 17:35:14 -302.906644 2.654715
BFGS: 6 17:35:15 -303.060982 2.963211
BFGS: 7 17:35:15 -303.127248 0.604351
BFGS: 8 17:35:15 -303.138615 0.508588
BFGS: 9 17:35:15 -303.158271 0.412763
BFGS: 10 17:35:15 -303.170918 0.413799
BFGS: 11 17:35:15 -303.177457 0.244886
BFGS: 12 17:35:15 -303.178669 0.162065
BFGS: 13 17:35:15 -303.180290 0.165669
BFGS: 14 17:35:15 -303.181859 0.208538
BFGS: 15 17:35:15 -303.184236 0.199640
BFGS: 16 17:35:16 -303.185996 0.108295
BFGS: 17 17:35:16 -303.186845 0.108675
BFGS: 18 17:35:16 -303.187319 0.133052
BFGS: 19 17:35:16 -303.188045 0.142581
BFGS: 20 17:35:16 -303.188940 0.111963
Step Time Energy fmax
BFGS: 0 17:35:16 -302.083781 4.078391
BFGS: 1 17:35:16 -302.458846 2.891434
BFGS: 2 17:35:16 -303.364341 3.386244
BFGS: 3 17:35:16 -303.545918 3.101952
BFGS: 4 17:35:16 -303.873605 1.720166
BFGS: 5 17:35:16 -303.952412 1.632444
BFGS: 6 17:35:17 -304.024775 1.648534
BFGS: 7 17:35:17 -304.191849 0.950014
BFGS: 8 17:35:17 -304.238111 0.921382
BFGS: 9 17:35:17 -304.389680 0.976215
BFGS: 10 17:35:17 -304.461922 1.057281
BFGS: 11 17:35:17 -304.516063 1.171226
BFGS: 12 17:35:17 -304.550213 0.985444
BFGS: 13 17:35:17 -304.612675 0.567253
BFGS: 14 17:35:17 -304.620363 0.453543
BFGS: 15 17:35:17 -304.627825 0.276298
BFGS: 16 17:35:17 -304.637345 0.286517
BFGS: 17 17:35:18 -304.645408 0.344159
BFGS: 18 17:35:18 -304.656387 0.348683
BFGS: 19 17:35:18 -304.663178 0.274844
BFGS: 20 17:35:18 -304.667521 0.225847
Step Time Energy fmax
BFGS: 0 17:35:18 -300.964954 3.904233
BFGS: 1 17:35:18 -301.372290 3.341049
BFGS: 2 17:35:18 -302.619583 3.518683
BFGS: 3 17:35:18 -302.417299 8.514359
BFGS: 4 17:35:18 -302.922584 2.868352
BFGS: 5 17:35:18 -303.059547 1.912612
BFGS: 6 17:35:18 -303.140682 1.686857
BFGS: 7 17:35:19 -303.160910 0.516306
BFGS: 8 17:35:19 -303.172206 0.515793
BFGS: 9 17:35:19 -303.207620 0.961909
BFGS: 10 17:35:19 -303.238021 0.950294
BFGS: 11 17:35:19 -303.261236 0.640133
BFGS: 12 17:35:19 -303.297341 0.744500
BFGS: 13 17:35:19 -303.366918 1.793704
BFGS: 14 17:35:19 -303.442478 2.613605
BFGS: 15 17:35:19 -303.591885 3.014492
BFGS: 16 17:35:19 -303.620688 2.083064
BFGS: 17 17:35:19 -303.793063 1.554804
BFGS: 18 17:35:20 -303.893337 1.414014
BFGS: 19 17:35:20 -303.975048 0.882078
BFGS: 20 17:35:20 -304.027605 0.861781
Step Time Energy fmax
BFGS: 0 17:35:20 -301.964669 4.081961
BFGS: 1 17:35:20 -302.337966 2.972460
BFGS: 2 17:35:20 -303.237351 3.393514
BFGS: 3 17:35:20 -303.406903 3.119359
BFGS: 4 17:35:20 -303.770870 2.022768
BFGS: 5 17:35:20 -303.855544 1.770035
BFGS: 6 17:35:20 -303.985300 1.588646
BFGS: 7 17:35:21 -304.054180 0.813804
BFGS: 8 17:35:21 -304.081738 0.756493
BFGS: 9 17:35:21 -304.156259 0.791888
BFGS: 10 17:35:21 -304.184661 0.603598
BFGS: 11 17:35:21 -304.196332 0.384006
BFGS: 12 17:35:21 -304.204427 0.390875
BFGS: 13 17:35:21 -304.216269 0.605217
BFGS: 14 17:35:21 -304.234578 0.677047
BFGS: 15 17:35:21 -304.245922 0.440843
BFGS: 16 17:35:21 -304.255747 0.361408
BFGS: 17 17:35:21 -304.272181 0.633054
BFGS: 18 17:35:22 -304.285528 0.749253
BFGS: 19 17:35:22 -304.303151 0.587804
BFGS: 20 17:35:22 -304.312462 0.267319
Step Time Energy fmax
BFGS: 0 17:35:22 -301.698564 4.134722
BFGS: 1 17:35:22 -302.084520 3.462567
BFGS: 2 17:35:22 -303.054933 3.100693
BFGS: 3 17:35:22 -303.179997 3.024791
BFGS: 4 17:35:22 -303.416847 2.176643
BFGS: 5 17:35:22 -303.625282 3.337961
BFGS: 6 17:35:22 -303.725985 1.647630
BFGS: 7 17:35:22 -303.858560 0.799164
BFGS: 8 17:35:23 -303.906944 0.966336
BFGS: 9 17:35:23 -303.943918 0.910579
BFGS: 10 17:35:23 -304.028653 0.985954
BFGS: 11 17:35:23 -304.067386 0.872202
BFGS: 12 17:35:23 -304.108719 0.416538
BFGS: 13 17:35:23 -304.121510 0.366012
BFGS: 14 17:35:23 -304.137941 0.530312
BFGS: 15 17:35:23 -304.152393 0.524075
BFGS: 16 17:35:23 -304.159738 0.316194
BFGS: 17 17:35:23 -304.163556 0.171384
BFGS: 18 17:35:23 -304.168839 0.289893
BFGS: 19 17:35:24 -304.176851 0.441711
BFGS: 20 17:35:24 -304.186274 0.522243
Step Time Energy fmax
BFGS: 0 17:35:24 -301.447917 4.130641
BFGS: 1 17:35:24 -301.829225 3.517734
BFGS: 2 17:35:24 -302.813450 3.121973
BFGS: 3 17:35:24 -302.903050 3.543979
BFGS: 4 17:35:24 -303.148841 2.372288
BFGS: 5 17:35:24 -303.371490 2.346380
BFGS: 6 17:35:24 -303.472708 2.360409
BFGS: 7 17:35:24 -303.776688 0.913247
BFGS: 8 17:35:24 -303.832476 0.823800
BFGS: 9 17:35:25 -303.944235 0.950887
BFGS: 10 17:35:25 -303.977131 0.855604
BFGS: 11 17:35:25 -304.032880 0.691553
BFGS: 12 17:35:25 -304.067165 0.655310
BFGS: 13 17:35:25 -304.095935 0.534522
BFGS: 14 17:35:25 -304.116789 0.596653
BFGS: 15 17:35:25 -304.139234 0.345100
BFGS: 16 17:35:25 -304.146911 0.238085
BFGS: 17 17:35:25 -304.151866 0.199158
BFGS: 18 17:35:25 -304.158455 0.344775
BFGS: 19 17:35:26 -304.167654 0.436753
BFGS: 20 17:35:26 -304.176821 0.371739
Step Time Energy fmax
BFGS: 0 17:35:26 -301.285086 4.141883
BFGS: 1 17:35:26 -301.670560 3.291813
BFGS: 2 17:35:26 -302.695539 3.431600
BFGS: 3 17:35:26 -302.774666 4.671262
BFGS: 4 17:35:26 -303.063474 2.557376
BFGS: 5 17:35:26 -303.248511 1.998468
BFGS: 6 17:35:26 -303.304645 1.636275
BFGS: 7 17:35:26 -303.598025 1.875561
BFGS: 8 17:35:27 -303.780198 2.050112
BFGS: 9 17:35:27 -303.861765 1.497142
BFGS: 10 17:35:27 -304.040576 0.955810
BFGS: 11 17:35:27 -304.072567 0.934921
BFGS: 12 17:35:27 -304.100520 0.682158
BFGS: 13 17:35:27 -304.131192 0.500707
BFGS: 14 17:35:27 -304.144020 0.473914
BFGS: 15 17:35:27 -304.157956 0.409200
BFGS: 16 17:35:27 -304.175407 0.430827
BFGS: 17 17:35:28 -304.189021 0.276575
BFGS: 18 17:35:28 -304.198471 0.297329
BFGS: 19 17:35:28 -304.210801 0.429624
BFGS: 20 17:35:28 -304.236527 0.852400
Step Time Energy fmax
BFGS: 0 17:35:28 -300.981558 4.032426
BFGS: 1 17:35:28 -301.365026 3.484472
BFGS: 2 17:35:28 -302.464331 3.313683
BFGS: 3 17:35:28 -302.289625 7.785514
BFGS: 4 17:35:28 -302.761341 2.740574
BFGS: 5 17:35:28 -302.898999 1.872154
BFGS: 6 17:35:28 -303.020450 1.915501
BFGS: 7 17:35:29 -303.059969 0.786249
BFGS: 8 17:35:29 -303.113685 0.973791
BFGS: 9 17:35:29 -303.168177 1.447053
BFGS: 10 17:35:29 -303.195961 0.999588
BFGS: 11 17:35:29 -303.220084 0.331739
BFGS: 12 17:35:29 -303.225392 0.215636
BFGS: 13 17:35:29 -303.230660 0.277894
BFGS: 14 17:35:29 -303.235594 0.296222
BFGS: 15 17:35:29 -303.240447 0.311863
BFGS: 16 17:35:29 -303.244929 0.339853
BFGS: 17 17:35:29 -303.250883 0.402509
BFGS: 18 17:35:30 -303.272714 0.713480
BFGS: 19 17:35:30 -303.373472 1.705173
BFGS: 20 17:35:30 -303.557619 2.274874
# 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 17:35:30 -297.105501 4.542213
BFGS: 1 17:35:30 -297.580023 4.683217
BFGS: 2 17:35:30 -298.865478 3.549758
BFGS: 3 17:35:30 -299.041777 5.370274
BFGS: 4 17:35:30 -299.304318 1.823620
BFGS: 5 17:35:30 -299.418891 1.648852
BFGS: 6 17:35:30 -299.671743 1.597673
BFGS: 7 17:35:30 -299.704727 0.949659
BFGS: 8 17:35:31 -299.756049 1.104594
BFGS: 9 17:35:31 -299.819645 1.370220
BFGS: 10 17:35:31 -299.880335 1.312297
BFGS: 11 17:35:31 -299.937532 0.908570
BFGS: 12 17:35:31 -299.974706 0.640867
BFGS: 13 17:35:31 -299.989490 0.583125
BFGS: 14 17:35:31 -300.011871 0.485592
BFGS: 15 17:35:31 -300.036597 0.455487
BFGS: 16 17:35:31 -300.049659 0.324400
BFGS: 17 17:35:31 -300.054117 0.262328
BFGS: 18 17:35:32 -300.058632 0.242303
BFGS: 19 17:35:32 -300.065475 0.240810
BFGS: 20 17:35:32 -300.071169 0.161832
Step Time Energy fmax
BFGS: 0 17:35:32 -297.008796 4.505387
BFGS: 1 17:35:32 -297.475962 4.654163
BFGS: 2 17:35:32 -298.782596 3.465737
BFGS: 3 17:35:32 -298.798807 6.398206
BFGS: 4 17:35:32 -299.160251 1.992197
BFGS: 5 17:35:32 -299.292124 1.782799
BFGS: 6 17:35:32 -299.691113 1.194517
BFGS: 7 17:35:32 -299.820850 1.756967
BFGS: 8 17:35:33 -299.869631 0.767452
BFGS: 9 17:35:33 -299.915088 0.677214
BFGS: 10 17:35:33 -300.000187 0.839005
BFGS: 11 17:35:33 -300.021598 0.684849
BFGS: 12 17:35:33 -300.041075 0.235187
BFGS: 13 17:35:33 -300.044567 0.235191
BFGS: 14 17:35:33 -300.050377 0.305918
BFGS: 15 17:35:33 -300.060093 0.339549
BFGS: 16 17:35:33 -300.068433 0.270440
BFGS: 17 17:35:33 -300.071622 0.178632
BFGS: 18 17:35:33 -300.073125 0.123423
BFGS: 19 17:35:34 -300.075673 0.138174
BFGS: 20 17:35:34 -300.077780 0.145238
Step Time Energy fmax
BFGS: 0 17:35:34 -296.551938 4.455297
BFGS: 1 17:35:34 -297.020329 4.684224
BFGS: 2 17:35:34 -298.395630 3.586998
BFGS: 3 17:35:34 -298.348875 7.420330
BFGS: 4 17:35:34 -298.757224 1.983667
BFGS: 5 17:35:34 -298.850928 1.603036
BFGS: 6 17:35:34 -299.163603 2.779935
BFGS: 7 17:35:34 -299.437746 2.930745
BFGS: 8 17:35:34 -299.517523 2.056604
BFGS: 9 17:35:35 -299.670842 1.656211
BFGS: 10 17:35:35 -299.808042 1.033548
BFGS: 11 17:35:35 -299.932987 1.037398
BFGS: 12 17:35:35 -299.990346 1.078738
BFGS: 13 17:35:35 -300.036580 1.229025
BFGS: 14 17:35:35 -300.146145 1.612452
BFGS: 15 17:35:35 -300.227730 1.517370
BFGS: 16 17:35:35 -300.342948 1.475810
BFGS: 17 17:35:35 -300.456343 1.181240
BFGS: 18 17:35:35 -300.504008 0.811438
BFGS: 19 17:35:36 -300.536894 0.633086
BFGS: 20 17:35:36 -300.561222 0.647380
Step Time Energy fmax
BFGS: 0 17:35:36 -296.102102 4.368147
BFGS: 1 17:35:36 -296.611223 4.708052
BFGS: 2 17:35:36 -298.209760 3.156590
BFGS: 3 17:35:36 -297.149686 14.337531
BFGS: 4 17:35:36 -298.408017 1.881364
BFGS: 5 17:35:36 -298.472479 1.051148
BFGS: 6 17:35:36 -298.510402 0.748281
BFGS: 7 17:35:36 -298.517440 0.527343
BFGS: 8 17:35:36 -298.535544 0.396548
BFGS: 9 17:35:37 -298.540814 0.460298
BFGS: 10 17:35:37 -298.549055 0.518438
BFGS: 11 17:35:37 -298.566593 0.624896
BFGS: 12 17:35:37 -298.629447 1.151895
BFGS: 13 17:35:37 -298.674111 1.968653
BFGS: 14 17:35:37 -298.750078 1.834771
BFGS: 15 17:35:37 -299.038649 2.009468
BFGS: 16 17:35:37 -299.426034 1.551767
BFGS: 17 17:35:37 -299.552414 1.298557
BFGS: 18 17:35:37 -299.643414 1.239989
BFGS: 19 17:35:37 -299.751010 1.004355
BFGS: 20 17:35:38 -299.910450 0.815285
Step Time Energy fmax
BFGS: 0 17:35:38 -296.497717 4.446427
BFGS: 1 17:35:38 -296.963887 4.685438
BFGS: 2 17:35:38 -298.347999 3.537731
BFGS: 3 17:35:38 -298.224420 7.907537
BFGS: 4 17:35:38 -298.681182 1.952608
BFGS: 5 17:35:38 -298.766697 1.454343
BFGS: 6 17:35:38 -298.956987 2.434821
BFGS: 7 17:35:38 -299.246420 2.994581
BFGS: 8 17:35:38 -299.504092 2.734715
BFGS: 9 17:35:38 -299.602614 1.857418
BFGS: 10 17:35:39 -299.712763 1.805521
BFGS: 11 17:35:39 -300.185240 1.698526
BFGS: 12 17:35:39 -300.459605 1.116247
BFGS: 13 17:35:39 -300.507886 0.924032
BFGS: 14 17:35:39 -300.551694 0.469272
BFGS: 15 17:35:39 -300.573535 0.541985
BFGS: 16 17:35:39 -300.589488 0.501628
BFGS: 17 17:35:39 -300.602508 0.376223
BFGS: 18 17:35:39 -300.609602 0.238457
BFGS: 19 17:35:39 -300.615111 0.158636
BFGS: 20 17:35:40 -300.617633 0.183985
Step Time Energy fmax
BFGS: 0 17:35:40 -295.926169 4.352866
BFGS: 1 17:35:40 -296.476677 4.756594
BFGS: 2 17:35:40 -298.220896 2.922875
BFGS: 3 17:35:40 -296.442699 19.394516
BFGS: 4 17:35:40 -298.379554 1.826358
BFGS: 5 17:35:40 -298.439628 1.045344
BFGS: 6 17:35:40 -298.474703 0.540207
BFGS: 7 17:35:40 -298.478322 0.219148
BFGS: 8 17:35:40 -298.481641 0.086039
BFGS: 9 17:35:40 -298.483371 0.076426
BFGS: 10 17:35:41 -298.483746 0.037043
Step Time Energy fmax
BFGS: 0 17:35:41 -297.284756 4.784444
BFGS: 1 17:35:41 -297.763082 4.928422
BFGS: 2 17:35:41 -299.025000 3.992941
BFGS: 3 17:35:41 -299.476532 3.890126
BFGS: 4 17:35:41 -299.650129 2.119190
BFGS: 5 17:35:41 -299.939487 1.880631
BFGS: 6 17:35:41 -300.033031 1.510592
BFGS: 7 17:35:41 -300.067365 1.466582
BFGS: 8 17:35:41 -300.177267 1.365472
BFGS: 9 17:35:41 -300.186663 1.272031
BFGS: 10 17:35:42 -300.195519 1.236795
BFGS: 11 17:35:42 -300.217574 1.053711
BFGS: 12 17:35:42 -300.224824 1.103504
BFGS: 13 17:35:42 -300.235151 1.054502
BFGS: 14 17:35:42 -300.242049 1.143599
BFGS: 15 17:35:42 -300.251164 1.276447
BFGS: 16 17:35:42 -300.257450 1.319798
BFGS: 17 17:35:42 -300.262821 1.267585
BFGS: 18 17:35:42 -300.265785 1.160277
BFGS: 19 17:35:42 -300.267880 1.059638
BFGS: 20 17:35:42 -300.269993 0.988319
Step Time Energy fmax
BFGS: 0 17:35:43 -297.793938 4.517099
BFGS: 1 17:35:43 -298.270081 4.497119
BFGS: 2 17:35:43 -299.390639 2.763687
BFGS: 3 17:35:43 -299.452086 3.769332
BFGS: 4 17:35:43 -299.683437 1.154304
BFGS: 5 17:35:43 -299.758191 0.997258
BFGS: 6 17:35:43 -300.005036 0.625449
BFGS: 7 17:35:43 -300.024180 0.497621
BFGS: 8 17:35:43 -300.062238 0.268743
BFGS: 9 17:35:43 -300.071359 0.158021
BFGS: 10 17:35:44 -300.075227 0.112160
BFGS: 11 17:35:44 -300.076349 0.082492
BFGS: 12 17:35:44 -300.077019 0.073157
BFGS: 13 17:35:44 -300.077730 0.073857
BFGS: 14 17:35:44 -300.078370 0.079559
BFGS: 15 17:35:44 -300.078850 0.084631
BFGS: 16 17:35:44 -300.079268 0.082284
BFGS: 17 17:35:44 -300.079751 0.068222
BFGS: 18 17:35:44 -300.080230 0.042997
Step Time Energy fmax
BFGS: 0 17:35:44 -296.786226 4.493097
BFGS: 1 17:35:44 -297.256160 4.684445
BFGS: 2 17:35:45 -298.578484 3.643708
BFGS: 3 17:35:45 -298.723971 5.999361
BFGS: 4 17:35:45 -299.015034 1.978823
BFGS: 5 17:35:45 -299.132557 1.838225
BFGS: 6 17:35:45 -299.547973 1.545265
BFGS: 7 17:35:45 -299.650598 2.013781
BFGS: 8 17:35:45 -299.726286 0.936955
BFGS: 9 17:35:45 -299.768572 0.680712
BFGS: 10 17:35:45 -299.852300 0.758866
BFGS: 11 17:35:45 -299.873115 0.723282
BFGS: 12 17:35:45 -299.902094 0.369149
BFGS: 13 17:35:46 -299.909463 0.211234
BFGS: 14 17:35:46 -299.913784 0.196975
BFGS: 15 17:35:46 -299.919285 0.266456
BFGS: 16 17:35:46 -299.924639 0.277910
BFGS: 17 17:35:46 -299.927407 0.245430
BFGS: 18 17:35:46 -299.929857 0.240823
BFGS: 19 17:35:46 -299.935614 0.364058
BFGS: 20 17:35:46 -299.946538 0.701237
Step Time Energy fmax
BFGS: 0 17:35:46 -297.285907 4.647336
BFGS: 1 17:35:46 -297.780408 4.759162
BFGS: 2 17:35:46 -299.048754 3.478817
BFGS: 3 17:35:47 -299.283484 4.285325
BFGS: 4 17:35:47 -299.483498 1.304948
BFGS: 5 17:35:47 -299.573607 1.148704
BFGS: 6 17:35:47 -299.752143 1.046903
BFGS: 7 17:35:47 -299.775856 0.747766
BFGS: 8 17:35:47 -299.852687 0.787406
BFGS: 9 17:35:47 -299.877431 0.628138
BFGS: 10 17:35:47 -299.895263 0.427430
BFGS: 11 17:35:47 -299.904254 0.246289
BFGS: 12 17:35:47 -299.908213 0.164214
BFGS: 13 17:35:48 -299.910085 0.115208
BFGS: 14 17:35:48 -299.911006 0.070945
BFGS: 15 17:35:48 -299.911308 0.070815
BFGS: 16 17:35:48 -299.911950 0.099257
BFGS: 17 17:35:48 -299.912803 0.133069
BFGS: 18 17:35:48 -299.913765 0.151370
BFGS: 19 17:35:48 -299.914754 0.166466
BFGS: 20 17:35:48 -299.916553 0.230903
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 17:35:48 -295.486720 0.964653
BFGS: 1 17:35:48 -295.549352 0.896355
BFGS: 2 17:35:48 -295.756552 0.830728
BFGS: 3 17:35:49 -295.777218 0.457673
BFGS: 4 17:35:49 -295.785582 0.454704
BFGS: 5 17:35:49 -295.822414 0.427530
BFGS: 6 17:35:49 -295.827977 0.379901
BFGS: 7 17:35:49 -295.847812 0.185282
BFGS: 8 17:35:49 -295.850341 0.157231
BFGS: 9 17:35:49 -295.851551 0.154378
BFGS: 10 17:35:49 -295.853827 0.143687
BFGS: 11 17:35:49 -295.856011 0.136260
BFGS: 12 17:35:49 -295.858099 0.140749
BFGS: 13 17:35:49 -295.859469 0.150671
BFGS: 14 17:35:50 -295.861066 0.162818
BFGS: 15 17:35:50 -295.864099 0.186724
BFGS: 16 17:35:50 -295.870749 0.246723
BFGS: 17 17:35:50 -295.882594 0.353451
BFGS: 18 17:35:50 -295.895231 0.497853
BFGS: 19 17:35:50 -295.909085 0.448805
BFGS: 20 17:35:50 -295.922987 0.355780
Step Time Energy fmax
BFGS: 0 17:35:50 -295.530495 0.950905
BFGS: 1 17:35:50 -295.589003 0.893383
BFGS: 2 17:35:50 -295.794887 0.714741
BFGS: 3 17:35:50 -295.814825 0.512194
BFGS: 4 17:35:51 -295.824235 0.522395
BFGS: 5 17:35:51 -295.876306 0.538300
BFGS: 6 17:35:51 -295.886639 0.542460
BFGS: 7 17:35:51 -295.923817 0.378352
BFGS: 8 17:35:51 -295.932006 0.324760
BFGS: 9 17:35:51 -295.937883 0.308412
BFGS: 10 17:35:51 -295.943158 0.284860
BFGS: 11 17:35:51 -295.948688 0.251097
BFGS: 12 17:35:51 -295.955101 0.195046
BFGS: 13 17:35:51 -295.959103 0.174331
BFGS: 14 17:35:52 -295.961446 0.148861
BFGS: 15 17:35:52 -295.963043 0.128441
BFGS: 16 17:35:52 -295.964955 0.091199
BFGS: 17 17:35:52 -295.966747 0.051713
BFGS: 18 17:35:52 -295.967531 0.035884
Step Time Energy fmax
BFGS: 0 17:35:52 -295.286870 1.328832
BFGS: 1 17:35:52 -295.368478 1.211264
BFGS: 2 17:35:52 -295.573917 1.602464
BFGS: 3 17:35:52 -295.620511 0.555334
BFGS: 4 17:35:52 -295.631190 0.528449
BFGS: 5 17:35:52 -295.662625 0.389501
BFGS: 6 17:35:53 -295.668029 0.409438
BFGS: 7 17:35:53 -295.689570 0.493030
BFGS: 8 17:35:53 -295.705058 0.611199
BFGS: 9 17:35:53 -295.731755 0.593324
BFGS: 10 17:35:53 -295.752308 0.822747
BFGS: 11 17:35:53 -295.782404 1.029899
BFGS: 12 17:35:53 -295.817111 0.913746
BFGS: 13 17:35:53 -295.864614 0.536994
BFGS: 14 17:35:53 -295.876791 0.293546
BFGS: 15 17:35:53 -295.885013 0.299317
BFGS: 16 17:35:53 -295.889756 0.305423
BFGS: 17 17:35:54 -295.896729 0.299933
BFGS: 18 17:35:54 -295.906032 0.308872
BFGS: 19 17:35:54 -295.913668 0.325403
BFGS: 20 17:35:54 -295.919423 0.315947
Step Time Energy fmax
BFGS: 0 17:35:54 -295.370062 1.178991
BFGS: 1 17:35:54 -295.442769 1.081621
BFGS: 2 17:35:54 -295.655554 1.227169
BFGS: 3 17:35:54 -295.686186 0.568798
BFGS: 4 17:35:54 -295.696689 0.462832
BFGS: 5 17:35:54 -295.737206 0.534913
BFGS: 6 17:35:54 -295.744867 0.519818
BFGS: 7 17:35:55 -295.811169 0.451490
BFGS: 8 17:35:55 -295.817957 0.375604
BFGS: 9 17:35:55 -295.824286 0.355167
BFGS: 10 17:35:55 -295.834341 0.256760
BFGS: 11 17:35:55 -295.839806 0.143763
BFGS: 12 17:35:55 -295.841661 0.145819
BFGS: 13 17:35:55 -295.842542 0.138942
BFGS: 14 17:35:55 -295.843539 0.128439
BFGS: 15 17:35:55 -295.844979 0.109940
BFGS: 16 17:35:55 -295.846269 0.084681
BFGS: 17 17:35:56 -295.846948 0.089646
BFGS: 18 17:35:56 -295.847310 0.090371
BFGS: 19 17:35:56 -295.847775 0.092255
BFGS: 20 17:35:56 -295.848822 0.115328
Step Time Energy fmax
BFGS: 0 17:35:56 -295.596784 0.746254
BFGS: 1 17:35:56 -295.649940 0.678979
BFGS: 2 17:35:56 -295.832351 0.420478
BFGS: 3 17:35:56 -295.847733 0.409513
BFGS: 4 17:35:56 -295.852695 0.405058
BFGS: 5 17:35:56 -295.885396 0.326068
BFGS: 6 17:35:56 -295.889283 0.310379
BFGS: 7 17:35:57 -295.906923 0.272168
BFGS: 8 17:35:57 -295.908743 0.271974
BFGS: 9 17:35:57 -295.919009 0.243042
BFGS: 10 17:35:57 -295.922681 0.186222
BFGS: 11 17:35:57 -295.925396 0.175233
BFGS: 12 17:35:57 -295.927478 0.208247
BFGS: 13 17:35:57 -295.930242 0.199792
BFGS: 14 17:35:57 -295.933072 0.142531
BFGS: 15 17:35:57 -295.934947 0.098150
BFGS: 16 17:35:57 -295.935744 0.048025
Step Time Energy fmax
BFGS: 0 17:35:57 -295.293595 1.314462
BFGS: 1 17:35:58 -295.373454 1.197048
BFGS: 2 17:35:58 -295.578103 1.510162
BFGS: 3 17:35:58 -295.619986 0.557989
BFGS: 4 17:35:58 -295.630226 0.516830
BFGS: 5 17:35:58 -295.662208 0.409494
BFGS: 6 17:35:58 -295.667236 0.419484
BFGS: 7 17:35:58 -295.698413 0.576525
BFGS: 8 17:35:58 -295.714785 0.585116
BFGS: 9 17:35:58 -295.743599 0.760677
BFGS: 10 17:35:58 -295.769486 0.988365
BFGS: 11 17:35:58 -295.799106 0.991460
BFGS: 12 17:35:59 -295.840138 0.896134
BFGS: 13 17:35:59 -295.886231 0.531017
BFGS: 14 17:35:59 -295.904641 0.321177
BFGS: 15 17:35:59 -295.912133 0.394903
BFGS: 16 17:35:59 -295.917976 0.410281
BFGS: 17 17:35:59 -295.924461 0.344652
BFGS: 18 17:35:59 -295.929897 0.208635
BFGS: 19 17:35:59 -295.932838 0.087606
BFGS: 20 17:35:59 -295.934322 0.070830
Step Time Energy fmax
BFGS: 0 17:35:59 -295.250651 1.384325
BFGS: 1 17:36:00 -295.337152 1.256950
BFGS: 2 17:36:00 -295.539540 1.726741
BFGS: 3 17:36:00 -295.592004 0.540332
BFGS: 4 17:36:00 -295.603061 0.543792
BFGS: 5 17:36:00 -295.631756 0.318773
BFGS: 6 17:36:00 -295.637312 0.353147
BFGS: 7 17:36:00 -295.647051 0.396530
BFGS: 8 17:36:00 -295.657119 0.426534
BFGS: 9 17:36:00 -295.670995 0.474107
BFGS: 10 17:36:00 -295.683043 0.492598
BFGS: 11 17:36:00 -295.696346 0.719800
BFGS: 12 17:36:01 -295.727606 1.110650
BFGS: 13 17:36:01 -295.755409 0.986867
BFGS: 14 17:36:01 -295.804893 0.397353
BFGS: 15 17:36:01 -295.793246 0.751413
BFGS: 16 17:36:01 -295.824384 0.221840
BFGS: 17 17:36:01 -295.827688 0.227411
BFGS: 18 17:36:01 -295.832340 0.249381
BFGS: 19 17:36:01 -295.834846 0.230173
BFGS: 20 17:36:01 -295.838105 0.149800
Step Time Energy fmax
BFGS: 0 17:36:01 -295.592782 0.754594
BFGS: 1 17:36:01 -295.645881 0.670221
BFGS: 2 17:36:02 -295.825585 0.395883
BFGS: 3 17:36:02 -295.839831 0.352820
BFGS: 4 17:36:02 -295.843726 0.347137
BFGS: 5 17:36:02 -295.866304 0.267332
BFGS: 6 17:36:02 -295.869009 0.243074
BFGS: 7 17:36:02 -295.879686 0.209086
BFGS: 8 17:36:02 -295.882180 0.247319
BFGS: 9 17:36:02 -295.885768 0.298655
BFGS: 10 17:36:02 -295.890595 0.339589
BFGS: 11 17:36:02 -295.898406 0.351778
BFGS: 12 17:36:02 -295.905049 0.288744
BFGS: 13 17:36:03 -295.913368 0.308511
BFGS: 14 17:36:03 -295.917873 0.333916
BFGS: 15 17:36:03 -295.924273 0.306479
BFGS: 16 17:36:03 -295.930048 0.197196
BFGS: 17 17:36:03 -295.933228 0.130616
BFGS: 18 17:36:03 -295.934589 0.064045
BFGS: 19 17:36:03 -295.935080 0.069919
BFGS: 20 17:36:03 -295.935477 0.063223
Step Time Energy fmax
BFGS: 0 17:36:03 -295.495223 0.979634
BFGS: 1 17:36:03 -295.556896 0.913072
BFGS: 2 17:36:04 -295.764728 0.819285
BFGS: 3 17:36:04 -295.785606 0.474255
BFGS: 4 17:36:04 -295.794624 0.484451
BFGS: 5 17:36:04 -295.837013 0.473342
BFGS: 6 17:36:04 -295.844415 0.426177
BFGS: 7 17:36:04 -295.871249 0.318119
BFGS: 8 17:36:04 -295.876960 0.246579
BFGS: 9 17:36:04 -295.879486 0.243993
BFGS: 10 17:36:04 -295.884759 0.239818
BFGS: 11 17:36:04 -295.889611 0.247739
BFGS: 12 17:36:04 -295.897039 0.284515
BFGS: 13 17:36:05 -295.902971 0.316020
BFGS: 14 17:36:05 -295.910164 0.337358
BFGS: 15 17:36:05 -295.921107 0.340615
BFGS: 16 17:36:05 -295.936361 0.276267
BFGS: 17 17:36:05 -295.950258 0.234048
BFGS: 18 17:36:05 -295.957458 0.156133
BFGS: 19 17:36:05 -295.959825 0.140202
BFGS: 20 17:36:05 -295.961619 0.115947
Step Time Energy fmax
BFGS: 0 17:36:05 -295.475304 1.013917
BFGS: 1 17:36:05 -295.537200 0.942117
BFGS: 2 17:36:05 -295.741866 0.857598
BFGS: 3 17:36:06 -295.762825 0.493046
BFGS: 4 17:36:06 -295.773159 0.503590
BFGS: 5 17:36:06 -295.819862 0.572433
BFGS: 6 17:36:06 -295.830827 0.533414
BFGS: 7 17:36:06 -295.875992 0.548772
BFGS: 8 17:36:06 -295.893653 0.349419
BFGS: 9 17:36:06 -295.908277 0.332545
BFGS: 10 17:36:06 -295.912293 0.308822
BFGS: 11 17:36:06 -295.918617 0.241956
BFGS: 12 17:36:06 -295.924243 0.173534
BFGS: 13 17:36:06 -295.927993 0.148038
BFGS: 14 17:36:07 -295.929585 0.145131
BFGS: 15 17:36:07 -295.930823 0.121856
BFGS: 16 17:36:07 -295.932463 0.085876
BFGS: 17 17:36:07 -295.934476 0.068853
BFGS: 18 17:36:07 -295.935783 0.054361
BFGS: 19 17:36:07 -295.936165 0.030635
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 17:36:07 -303.942248 0.221424
BFGS: 1 17:36:07 -303.945481 0.197102
BFGS: 2 17:36:07 -303.955775 0.133363
BFGS: 3 17:36:07 -303.958465 0.112658
BFGS: 4 17:36:08 -303.960055 0.104583
BFGS: 5 17:36:08 -303.960797 0.084232
BFGS: 6 17:36:08 -303.961595 0.059057
BFGS: 7 17:36:08 -303.962354 0.063708
BFGS: 8 17:36:08 -303.962944 0.091686
BFGS: 9 17:36:08 -303.963341 0.085044
BFGS: 10 17:36:08 -303.963711 0.055379
BFGS: 11 17:36:08 -303.964054 0.065724
BFGS: 12 17:36:08 -303.964302 0.048879
Step Time Energy fmax
BFGS: 0 17:36:08 -303.180078 0.976244
BFGS: 1 17:36:09 -303.208898 0.752800
BFGS: 2 17:36:09 -303.278441 0.699080
BFGS: 3 17:36:09 -303.311997 0.684720
BFGS: 4 17:36:09 -303.343556 0.739717
BFGS: 5 17:36:09 -303.372889 0.559756
BFGS: 6 17:36:09 -303.416795 0.420701
BFGS: 7 17:36:09 -303.421299 0.298189
BFGS: 8 17:36:09 -303.428189 0.154560
BFGS: 9 17:36:09 -303.431931 0.174346
BFGS: 10 17:36:09 -303.434184 0.157152
BFGS: 11 17:36:10 -303.436107 0.180020
BFGS: 12 17:36:10 -303.438080 0.144754
BFGS: 13 17:36:10 -303.439571 0.124349
BFGS: 14 17:36:10 -303.440857 0.120739
BFGS: 15 17:36:10 -303.441659 0.080831
BFGS: 16 17:36:10 -303.442340 0.077928
BFGS: 17 17:36:10 -303.443133 0.077346
BFGS: 18 17:36:10 -303.443943 0.113953
BFGS: 19 17:36:10 -303.444626 0.102695
BFGS: 20 17:36:10 -303.445028 0.055098
BFGS: 21 17:36:10 -303.445235 0.053470
BFGS: 22 17:36:11 -303.445435 0.053930
BFGS: 23 17:36:11 -303.445766 0.075084
BFGS: 24 17:36:11 -303.446251 0.081821
BFGS: 25 17:36:11 -303.446822 0.080229
BFGS: 26 17:36:11 -303.447404 0.100611
BFGS: 27 17:36:11 -303.448309 0.133264
BFGS: 28 17:36:11 -303.451054 0.263438
BFGS: 29 17:36:11 -303.454849 0.626857
BFGS: 30 17:36:11 -303.464987 0.705500
BFGS: 31 17:36:11 -303.495925 0.945955
BFGS: 32 17:36:11 -303.552833 1.215243
BFGS: 33 17:36:12 -303.620513 1.250394
BFGS: 34 17:36:12 -303.649223 1.226457
BFGS: 35 17:36:12 -303.717500 0.980428
BFGS: 36 17:36:12 -303.768135 0.808937
BFGS: 37 17:36:12 -303.842453 0.593778
BFGS: 38 17:36:12 -303.877894 0.492940
BFGS: 39 17:36:12 -303.902933 0.498266
BFGS: 40 17:36:12 -303.918597 0.363460
BFGS: 41 17:36:12 -303.940457 0.224598
BFGS: 42 17:36:12 -303.949928 0.188675
BFGS: 43 17:36:12 -303.954310 0.136739
BFGS: 44 17:36:13 -303.956761 0.100064
BFGS: 45 17:36:13 -303.958233 0.113643
BFGS: 46 17:36:13 -303.960188 0.120604
BFGS: 47 17:36:13 -303.962255 0.099550
BFGS: 48 17:36:13 -303.963757 0.061649
BFGS: 49 17:36:13 -303.964341 0.037499
Step Time Energy fmax
BFGS: 0 17:36:13 -303.172121 1.000271
BFGS: 1 17:36:13 -303.200977 0.774822
BFGS: 2 17:36:13 -303.269817 0.682496
BFGS: 3 17:36:13 -303.305385 0.751587
BFGS: 4 17:36:14 -303.338543 0.824252
BFGS: 5 17:36:14 -303.367534 0.633143
BFGS: 6 17:36:14 -303.416376 0.387991
BFGS: 7 17:36:14 -303.420533 0.293130
BFGS: 8 17:36:14 -303.430361 0.186565
BFGS: 9 17:36:14 -303.432630 0.200083
BFGS: 10 17:36:14 -303.435209 0.182638
BFGS: 11 17:36:14 -303.437412 0.205396
BFGS: 12 17:36:14 -303.439385 0.147794
BFGS: 13 17:36:14 -303.440721 0.138302
BFGS: 14 17:36:15 -303.441958 0.112763
BFGS: 15 17:36:15 -303.442820 0.097269
BFGS: 16 17:36:15 -303.443664 0.094271
BFGS: 17 17:36:15 -303.444682 0.119853
BFGS: 18 17:36:15 -303.445797 0.142956
BFGS: 19 17:36:15 -303.446743 0.103417
BFGS: 20 17:36:15 -303.447342 0.086478
BFGS: 21 17:36:15 -303.447837 0.094388
BFGS: 22 17:36:15 -303.448748 0.132441
BFGS: 23 17:36:15 -303.450940 0.237985
BFGS: 24 17:36:15 -303.455774 0.441206
BFGS: 25 17:36:16 -303.461833 0.500283
BFGS: 26 17:36:16 -303.475654 0.574658
BFGS: 27 17:36:16 -303.497600 0.648412
BFGS: 28 17:36:16 -303.530401 0.871262
BFGS: 29 17:36:16 -303.596978 1.315220
BFGS: 30 17:36:16 -303.650682 1.279594
BFGS: 31 17:36:16 -303.744197 0.930824
BFGS: 32 17:36:16 -303.807287 0.901885
BFGS: 33 17:36:16 -303.841320 0.746116
BFGS: 34 17:36:16 -303.870593 0.873142
BFGS: 35 17:36:16 -303.909659 0.639116
BFGS: 36 17:36:17 -303.927623 0.454905
BFGS: 37 17:36:17 -303.937744 0.373985
BFGS: 38 17:36:17 -303.944993 0.304247
BFGS: 39 17:36:17 -303.954938 0.151682
BFGS: 40 17:36:17 -303.958974 0.099429
BFGS: 41 17:36:17 -303.961117 0.106603
BFGS: 42 17:36:17 -303.962022 0.094510
BFGS: 43 17:36:17 -303.962664 0.077529
BFGS: 44 17:36:17 -303.963350 0.059621
BFGS: 45 17:36:17 -303.964139 0.053134
BFGS: 46 17:36:17 -303.964763 0.040785
Step Time Energy fmax
BFGS: 0 17:36:18 -303.883160 0.681892
BFGS: 1 17:36:18 -303.894699 0.616562
BFGS: 2 17:36:18 -303.936928 0.368839
BFGS: 3 17:36:18 -303.946278 0.300415
BFGS: 4 17:36:18 -303.952110 0.224768
BFGS: 5 17:36:18 -303.955198 0.164946
BFGS: 6 17:36:18 -303.958574 0.103138
BFGS: 7 17:36:18 -303.960959 0.098249
BFGS: 8 17:36:18 -303.962180 0.093639
BFGS: 9 17:36:18 -303.962737 0.081852
BFGS: 10 17:36:19 -303.963289 0.061629
BFGS: 11 17:36:19 -303.963828 0.065642
BFGS: 12 17:36:19 -303.964211 0.054935
BFGS: 13 17:36:19 -303.964416 0.033736
Step Time Energy fmax
BFGS: 0 17:36:19 -303.732174 0.674791
BFGS: 1 17:36:19 -303.747690 0.441761
BFGS: 2 17:36:19 -303.775807 0.462238
BFGS: 3 17:36:19 -303.786633 0.473690
BFGS: 4 17:36:19 -303.801372 0.514649
BFGS: 5 17:36:20 -303.818266 0.645055
BFGS: 6 17:36:20 -303.851020 1.026926
BFGS: 7 17:36:20 -303.901984 1.473669
BFGS: 8 17:36:20 -304.000209 1.983232
BFGS: 9 17:36:20 -304.135982 1.637154
BFGS: 10 17:36:20 -304.254563 1.288958
BFGS: 11 17:36:20 -304.343543 1.041933
BFGS: 12 17:36:20 -304.362166 1.570677
BFGS: 13 17:36:20 -304.438937 0.750200
BFGS: 14 17:36:20 -304.462745 0.496977
BFGS: 15 17:36:20 -304.493747 0.364540
BFGS: 16 17:36:21 -304.508404 0.346210
BFGS: 17 17:36:21 -304.518726 0.351801
BFGS: 18 17:36:21 -304.527573 0.252158
BFGS: 19 17:36:21 -304.532365 0.118745
BFGS: 20 17:36:21 -304.534781 0.124283
BFGS: 21 17:36:21 -304.536010 0.105450
BFGS: 22 17:36:21 -304.536499 0.066059
BFGS: 23 17:36:21 -304.536905 0.063533
BFGS: 24 17:36:21 -304.537572 0.057817
BFGS: 25 17:36:21 -304.538455 0.080136
BFGS: 26 17:36:21 -304.539163 0.076225
BFGS: 27 17:36:22 -304.539483 0.049377
Step Time Energy fmax
BFGS: 0 17:36:22 -303.703844 0.661838
BFGS: 1 17:36:22 -303.718615 0.420660
BFGS: 2 17:36:22 -303.743023 0.314186
BFGS: 3 17:36:22 -303.748713 0.273611
BFGS: 4 17:36:22 -303.753673 0.221863
BFGS: 5 17:36:22 -303.757281 0.230965
BFGS: 6 17:36:22 -303.762996 0.314479
BFGS: 7 17:36:22 -303.770134 0.415899
BFGS: 8 17:36:22 -303.779907 0.491584
BFGS: 9 17:36:23 -303.794959 0.630302
BFGS: 10 17:36:23 -303.842650 1.018167
BFGS: 11 17:36:23 -303.890557 1.370656
BFGS: 12 17:36:23 -303.926756 1.687543
BFGS: 13 17:36:23 -304.027216 1.623214
BFGS: 14 17:36:23 -304.175348 1.121113
BFGS: 15 17:36:23 -304.308894 0.955030
BFGS: 16 17:36:23 -304.350438 0.730204
BFGS: 17 17:36:23 -304.403168 0.605944
BFGS: 18 17:36:23 -304.425658 0.360877
BFGS: 19 17:36:23 -304.435145 0.266979
BFGS: 20 17:36:24 -304.441226 0.258931
BFGS: 21 17:36:24 -304.445511 0.204144
BFGS: 22 17:36:24 -304.448479 0.143473
BFGS: 23 17:36:24 -304.450133 0.117162
BFGS: 24 17:36:24 -304.451193 0.074269
BFGS: 25 17:36:24 -304.452157 0.066227
BFGS: 26 17:36:24 -304.452883 0.071637
BFGS: 27 17:36:24 -304.453278 0.060728
BFGS: 28 17:36:24 -304.453568 0.052117
BFGS: 29 17:36:24 -304.453982 0.048432
Step Time Energy fmax
BFGS: 0 17:36:25 -303.355364 1.106404
BFGS: 1 17:36:25 -303.388883 0.980370
BFGS: 2 17:36:25 -303.560850 1.211230
BFGS: 3 17:36:25 -303.618762 1.410959
BFGS: 4 17:36:25 -303.717341 1.508628
BFGS: 5 17:36:25 -303.858766 1.553853
BFGS: 6 17:36:25 -304.005891 1.375236
BFGS: 7 17:36:25 -304.149637 1.615664
BFGS: 8 17:36:25 -304.247676 1.316244
BFGS: 9 17:36:25 -304.330916 0.578520
BFGS: 10 17:36:26 -304.354023 0.649728
BFGS: 11 17:36:26 -304.380291 0.655116
BFGS: 12 17:36:26 -304.400963 0.605010
BFGS: 13 17:36:26 -304.429291 0.370673
BFGS: 14 17:36:26 -304.440984 0.168578
BFGS: 15 17:36:26 -304.444879 0.120448
BFGS: 16 17:36:26 -304.446789 0.146600
BFGS: 17 17:36:26 -304.448921 0.173193
BFGS: 18 17:36:26 -304.451071 0.152591
BFGS: 19 17:36:26 -304.452684 0.098203
BFGS: 20 17:36:26 -304.453617 0.062164
BFGS: 21 17:36:27 -304.454362 0.068118
BFGS: 22 17:36:27 -304.454946 0.063507
BFGS: 23 17:36:27 -304.455350 0.049070
Step Time Energy fmax
BFGS: 0 17:36:27 -303.363230 0.838673
BFGS: 1 17:36:27 -303.389455 0.826068
BFGS: 2 17:36:27 -303.520919 0.747004
BFGS: 3 17:36:27 -303.539054 0.658069
BFGS: 4 17:36:27 -303.599358 0.556825
BFGS: 5 17:36:27 -303.613482 0.596006
BFGS: 6 17:36:27 -303.668473 0.596777
BFGS: 7 17:36:28 -303.691821 0.607878
BFGS: 8 17:36:28 -303.740590 0.800701
BFGS: 9 17:36:28 -303.790940 0.789106
BFGS: 10 17:36:28 -303.839242 0.801402
BFGS: 11 17:36:28 -303.909856 0.528357
BFGS: 12 17:36:28 -303.927922 0.311213
BFGS: 13 17:36:28 -303.934208 0.650142
BFGS: 14 17:36:28 -303.944602 0.288090
BFGS: 15 17:36:28 -303.950021 0.196715
BFGS: 16 17:36:28 -303.959351 0.100756
BFGS: 17 17:36:28 -303.961569 0.085473
BFGS: 18 17:36:29 -303.962376 0.079025
BFGS: 19 17:36:29 -303.962851 0.066620
BFGS: 20 17:36:29 -303.963500 0.051803
BFGS: 21 17:36:29 -303.964214 0.059339
BFGS: 22 17:36:29 -303.964821 0.053048
BFGS: 23 17:36:29 -303.965127 0.036376
Step Time Energy fmax
BFGS: 0 17:36:29 -303.686113 1.259794
BFGS: 1 17:36:29 -303.723146 0.773711
BFGS: 2 17:36:29 -303.770583 0.820263
BFGS: 3 17:36:29 -303.789058 0.804235
BFGS: 4 17:36:30 -303.837153 0.534271
BFGS: 5 17:36:30 -303.852676 0.500752
BFGS: 6 17:36:30 -303.873587 0.546392
BFGS: 7 17:36:30 -303.895624 0.512530
BFGS: 8 17:36:30 -303.912991 0.428544
BFGS: 9 17:36:30 -303.930744 0.380478
BFGS: 10 17:36:30 -303.945148 0.289302
BFGS: 11 17:36:30 -303.953268 0.232755
BFGS: 12 17:36:30 -303.957028 0.180165
BFGS: 13 17:36:30 -303.958956 0.118368
BFGS: 14 17:36:31 -303.960286 0.098108
BFGS: 15 17:36:31 -303.961613 0.096302
BFGS: 16 17:36:31 -303.962933 0.082354
BFGS: 17 17:36:31 -303.963835 0.068907
BFGS: 18 17:36:31 -303.964313 0.057141
BFGS: 19 17:36:31 -303.964624 0.060119
BFGS: 20 17:36:31 -303.964872 0.044585
Step Time Energy fmax
BFGS: 0 17:36:31 -303.144380 0.883037
BFGS: 1 17:36:31 -303.178443 0.868890
BFGS: 2 17:36:31 -303.326373 0.743333
BFGS: 3 17:36:32 -303.350614 0.543219
BFGS: 4 17:36:32 -303.370310 0.343464
BFGS: 5 17:36:32 -303.378646 0.303521
BFGS: 6 17:36:32 -303.390740 0.348362
BFGS: 7 17:36:32 -303.398663 0.263752
BFGS: 8 17:36:32 -303.403354 0.154625
BFGS: 9 17:36:32 -303.405356 0.112946
BFGS: 10 17:36:32 -303.407372 0.136576
BFGS: 11 17:36:32 -303.409671 0.215911
BFGS: 12 17:36:33 -303.412235 0.220779
BFGS: 13 17:36:33 -303.414252 0.144669
BFGS: 14 17:36:33 -303.415643 0.124643
BFGS: 15 17:36:33 -303.417000 0.117247
BFGS: 16 17:36:33 -303.418484 0.139174
BFGS: 17 17:36:33 -303.420429 0.175506
BFGS: 18 17:36:33 -303.423708 0.218774
BFGS: 19 17:36:33 -303.429249 0.330068
BFGS: 20 17:36:33 -303.436316 0.404609
BFGS: 21 17:36:33 -303.448001 0.471915
BFGS: 22 17:36:33 -303.476471 0.922005
BFGS: 23 17:36:34 -303.503761 0.904028
BFGS: 24 17:36:34 -303.545091 0.888781
BFGS: 25 17:36:34 -303.609136 0.690267
BFGS: 26 17:36:34 -303.655043 0.607452
BFGS: 27 17:36:34 -303.711648 0.767864
BFGS: 28 17:36:34 -303.762863 1.068628
BFGS: 29 17:36:34 -303.832480 1.078325
BFGS: 30 17:36:34 -303.877788 0.638715
BFGS: 31 17:36:34 -303.901355 0.457480
BFGS: 32 17:36:34 -303.913563 0.433693
BFGS: 33 17:36:35 -303.928505 0.442601
BFGS: 34 17:36:35 -303.940759 0.372763
BFGS: 35 17:36:35 -303.948509 0.218280
BFGS: 36 17:36:35 -303.952152 0.206456
BFGS: 37 17:36:35 -303.954992 0.173026
BFGS: 38 17:36:35 -303.957017 0.144014
BFGS: 39 17:36:35 -303.959783 0.140012
BFGS: 40 17:36:35 -303.962155 0.092810
BFGS: 41 17:36:35 -303.963272 0.042912
Step Time Energy fmax
BFGS: 0 17:36:35 -303.696823 1.314109
BFGS: 1 17:36:36 -303.749336 0.781153
BFGS: 2 17:36:36 -303.811797 0.898142
BFGS: 3 17:36:36 -303.833963 0.809410
BFGS: 4 17:36:36 -303.873964 0.535044
BFGS: 5 17:36:36 -303.890990 0.497859
BFGS: 6 17:36:36 -303.911664 0.543036
BFGS: 7 17:36:36 -303.932766 0.500693
BFGS: 8 17:36:36 -303.950513 0.337274
BFGS: 9 17:36:36 -303.962997 0.341360
BFGS: 10 17:36:36 -303.971305 0.263045
BFGS: 11 17:36:36 -303.978648 0.216944
BFGS: 12 17:36:37 -303.983767 0.151396
BFGS: 13 17:36:37 -303.985931 0.092237
BFGS: 14 17:36:37 -303.986932 0.081427
BFGS: 15 17:36:37 -303.987921 0.074200
BFGS: 16 17:36:37 -303.989030 0.083869
BFGS: 17 17:36:37 -303.989990 0.071580
BFGS: 18 17:36:37 -303.990436 0.048425
Step Time Energy fmax
BFGS: 0 17:36:37 -302.665074 2.447076
BFGS: 1 17:36:37 -302.772406 1.679751
BFGS: 2 17:36:37 -302.905789 0.926071
BFGS: 3 17:36:38 -303.010443 1.063037
BFGS: 4 17:36:38 -303.121761 1.628207
BFGS: 5 17:36:38 -303.179182 1.154404
BFGS: 6 17:36:38 -303.365996 0.924594
BFGS: 7 17:36:38 -303.382542 0.635790
BFGS: 8 17:36:38 -303.415674 0.251587
BFGS: 9 17:36:38 -303.424013 0.227367
BFGS: 10 17:36:38 -303.428277 0.234644
BFGS: 11 17:36:38 -303.434244 0.180446
BFGS: 12 17:36:38 -303.439642 0.157135
BFGS: 13 17:36:38 -303.442407 0.123804
BFGS: 14 17:36:39 -303.443514 0.098718
BFGS: 15 17:36:39 -303.444136 0.070955
BFGS: 16 17:36:39 -303.444708 0.076960
BFGS: 17 17:36:39 -303.445331 0.084565
BFGS: 18 17:36:39 -303.446067 0.093223
BFGS: 19 17:36:39 -303.447006 0.102865
BFGS: 20 17:36:39 -303.448116 0.109117
BFGS: 21 17:36:39 -303.449387 0.135297
BFGS: 22 17:36:39 -303.451239 0.187428
BFGS: 23 17:36:39 -303.455120 0.264712
BFGS: 24 17:36:39 -303.463282 0.576300
BFGS: 25 17:36:40 -303.477488 0.778819
BFGS: 26 17:36:40 -303.512557 0.943314
BFGS: 27 17:36:40 -303.554193 0.683634
BFGS: 28 17:36:40 -303.580799 0.730036
BFGS: 29 17:36:40 -303.602188 0.552154
BFGS: 30 17:36:40 -303.631090 0.601575
BFGS: 31 17:36:40 -303.689869 0.736059
BFGS: 32 17:36:40 -303.756015 0.818999
BFGS: 33 17:36:40 -303.826600 0.800964
BFGS: 34 17:36:40 -303.883404 0.772304
BFGS: 35 17:36:41 -303.934780 0.386947
BFGS: 36 17:36:41 -303.945448 0.233426
BFGS: 37 17:36:41 -303.954147 0.150406
BFGS: 38 17:36:41 -303.958775 0.126255
BFGS: 39 17:36:41 -303.960419 0.089402
BFGS: 40 17:36:41 -303.961055 0.064643
BFGS: 41 17:36:41 -303.961797 0.059571
BFGS: 42 17:36:41 -303.962786 0.065413
BFGS: 43 17:36:41 -303.963708 0.052807
BFGS: 44 17:36:41 -303.964184 0.035553
Step Time Energy fmax
BFGS: 0 17:36:42 -301.887113 1.146215
BFGS: 1 17:36:42 -301.916551 0.778293
BFGS: 2 17:36:42 -301.974268 0.925482
BFGS: 3 17:36:42 -302.041050 1.229800
BFGS: 4 17:36:42 -302.109736 1.105007
BFGS: 5 17:36:42 -302.141612 0.777371
BFGS: 6 17:36:42 -302.170196 0.615005
BFGS: 7 17:36:42 -302.204354 0.530990
BFGS: 8 17:36:42 -302.225285 0.402565
BFGS: 9 17:36:42 -302.235597 0.355053
BFGS: 10 17:36:42 -302.244553 0.321287
BFGS: 11 17:36:43 -302.258085 0.434500
BFGS: 12 17:36:43 -302.273138 0.535802
BFGS: 13 17:36:43 -302.286637 0.551445
BFGS: 14 17:36:43 -302.313888 0.650957
BFGS: 15 17:36:43 -302.363686 1.139777
BFGS: 16 17:36:43 -302.402784 2.066790
BFGS: 17 17:36:43 -302.538642 2.070785
BFGS: 18 17:36:43 -302.628370 2.545374
BFGS: 19 17:36:43 -302.730026 2.644050
BFGS: 20 17:36:43 -302.854266 2.348110
BFGS: 21 17:36:43 -302.888146 2.672037
BFGS: 22 17:36:44 -302.954409 2.330696
BFGS: 23 17:36:44 -303.111447 1.920223
BFGS: 24 17:36:44 -303.212166 1.622652
BFGS: 25 17:36:44 -303.270450 1.902201
BFGS: 26 17:36:44 -303.355162 2.456842
BFGS: 27 17:36:44 -303.484583 2.910960
BFGS: 28 17:36:44 -303.667046 2.920895
BFGS: 29 17:36:44 -303.818242 2.636089
BFGS: 30 17:36:44 -303.993809 2.090875
BFGS: 31 17:36:44 -304.142308 1.388454
BFGS: 32 17:36:45 -304.255771 1.353479
BFGS: 33 17:36:45 -304.337800 1.118528
BFGS: 34 17:36:45 -304.395318 0.793657
BFGS: 35 17:36:45 -304.417727 0.594438
BFGS: 36 17:36:45 -304.431253 0.583493
BFGS: 37 17:36:45 -304.440244 0.621612
BFGS: 38 17:36:45 -304.447931 0.619535
BFGS: 39 17:36:45 -304.454770 0.557005
BFGS: 40 17:36:45 -304.457493 0.490256
BFGS: 41 17:36:45 -304.459722 0.418403
BFGS: 42 17:36:45 -304.462031 0.346661
BFGS: 43 17:36:46 -304.463714 0.316154
BFGS: 44 17:36:46 -304.464625 0.323666
BFGS: 45 17:36:46 -304.465250 0.340533
BFGS: 46 17:36:46 -304.466005 0.357064
BFGS: 47 17:36:46 -304.466850 0.361740
BFGS: 48 17:36:46 -304.467491 0.348012
BFGS: 49 17:36:46 -304.467891 0.327939
BFGS: 50 17:36:46 -304.468270 0.308704
BFGS: 51 17:36:46 -304.468845 0.289476
BFGS: 52 17:36:46 -304.469646 0.279589
BFGS: 53 17:36:46 -304.470422 0.289514
BFGS: 54 17:36:47 -304.470915 0.311570
BFGS: 55 17:36:47 -304.471243 0.331022
BFGS: 56 17:36:47 -304.471642 0.348085
BFGS: 57 17:36:47 -304.472186 0.358186
BFGS: 58 17:36:47 -304.472723 0.350931
BFGS: 59 17:36:47 -304.473069 0.329653
BFGS: 60 17:36:47 -304.473253 0.310127
BFGS: 61 17:36:47 -304.473387 0.297659
BFGS: 62 17:36:47 -304.473505 0.292750
BFGS: 63 17:36:47 -304.473582 0.296469
BFGS: 64 17:36:47 -304.473625 0.302673
BFGS: 65 17:36:48 -304.473659 0.308277
BFGS: 66 17:36:48 -304.473695 0.312695
BFGS: 67 17:36:48 -304.473742 0.313889
BFGS: 68 17:36:48 -304.473780 0.309944
BFGS: 69 17:36:48 -304.473802 0.304137
BFGS: 70 17:36:48 -304.473814 0.299148
BFGS: 71 17:36:48 -304.473833 0.294053
BFGS: 72 17:36:48 -304.473854 0.289694
BFGS: 73 17:36:48 -304.473875 0.288533
BFGS: 74 17:36:48 -304.473886 0.290517
BFGS: 75 17:36:49 -304.473891 0.292941
BFGS: 76 17:36:49 -304.473899 0.295091
BFGS: 77 17:36:49 -304.473907 0.296371
BFGS: 78 17:36:49 -304.473913 0.295671
BFGS: 79 17:36:49 -304.473919 0.293533
BFGS: 80 17:36:49 -304.473921 0.291758
BFGS: 81 17:36:49 -304.473923 0.290338
BFGS: 82 17:36:49 -304.473924 0.289095
BFGS: 83 17:36:49 -304.473927 0.288570
BFGS: 84 17:36:49 -304.473929 0.289233
BFGS: 85 17:36:49 -304.473929 0.290267
BFGS: 86 17:36:50 -304.473929 0.290926
BFGS: 87 17:36:50 -304.473931 0.291414
BFGS: 88 17:36:50 -304.473930 0.291644
BFGS: 89 17:36:50 -304.473931 0.291384
BFGS: 90 17:36:50 -304.473934 0.290702
BFGS: 91 17:36:50 -304.473933 0.290065
BFGS: 92 17:36:50 -304.473932 0.289744
BFGS: 93 17:36:50 -304.473933 0.289495
BFGS: 94 17:36:50 -304.473934 0.289471
BFGS: 95 17:36:50 -304.473935 0.289850
BFGS: 96 17:36:50 -304.473934 0.290365
BFGS: 97 17:36:51 -304.473934 0.290655
BFGS: 98 17:36:51 -304.473934 0.290795
BFGS: 99 17:36:51 -304.473934 0.290855
BFGS: 100 17:36:51 -304.473932 0.290801
BFGS: 101 17:36:51 -304.473934 0.290583
BFGS: 102 17:36:51 -304.473936 0.290410
BFGS: 103 17:36:51 -304.473934 0.290301
BFGS: 104 17:36:51 -304.473935 0.290260
BFGS: 105 17:36:51 -304.473932 0.290265
BFGS: 106 17:36:51 -304.473936 0.290293
BFGS: 107 17:36:51 -304.473937 0.290401
BFGS: 108 17:36:52 -304.473934 0.290462
BFGS: 109 17:36:52 -304.473935 0.290477
BFGS: 110 17:36:52 -304.473936 0.290520
BFGS: 111 17:36:52 -304.473936 0.290508
BFGS: 112 17:36:52 -304.473934 0.290468
BFGS: 113 17:36:52 -304.473935 0.290463
BFGS: 114 17:36:52 -304.473936 0.290430
BFGS: 115 17:36:52 -304.473936 0.290426
BFGS: 116 17:36:52 -304.473934 0.290403
BFGS: 117 17:36:52 -304.473933 0.290416
BFGS: 118 17:36:53 -304.473936 0.290455
BFGS: 119 17:36:53 -304.473937 0.290429
BFGS: 120 17:36:53 -304.473934 0.290455
BFGS: 121 17:36:53 -304.473937 0.290449
BFGS: 122 17:36:53 -304.473933 0.290433
BFGS: 123 17:36:53 -304.473937 0.290431
BFGS: 124 17:36:53 -304.473934 0.290429
BFGS: 125 17:36:53 -304.473934 0.290418
BFGS: 126 17:36:53 -304.473933 0.290436
BFGS: 127 17:36:53 -304.473934 0.290456
BFGS: 128 17:36:53 -304.473934 0.290450
BFGS: 129 17:36:54 -304.473934 0.290418
BFGS: 130 17:36:54 -304.473935 0.290434
BFGS: 131 17:36:54 -304.473936 0.290440
BFGS: 132 17:36:54 -304.473934 0.290460
BFGS: 133 17:36:54 -304.473934 0.290443
BFGS: 134 17:36:54 -304.473934 0.290432
BFGS: 135 17:36:54 -304.473934 0.290443
BFGS: 136 17:36:54 -304.473934 0.290440
BFGS: 137 17:36:54 -304.473934 0.290436
BFGS: 138 17:36:54 -304.473935 0.290440
BFGS: 139 17:36:54 -304.473934 0.290455
BFGS: 140 17:36:55 -304.473935 0.290455
BFGS: 141 17:36:55 -304.473933 0.290438
BFGS: 142 17:36:55 -304.473934 0.290440
BFGS: 143 17:36:55 -304.473934 0.290458
BFGS: 144 17:36:55 -304.473934 0.290436
BFGS: 145 17:36:55 -304.473932 0.290434
BFGS: 146 17:36:55 -304.473934 0.290453
BFGS: 147 17:36:55 -304.473935 0.290459
BFGS: 148 17:36:55 -304.473935 0.290449
BFGS: 149 17:36:55 -304.473934 0.290443
BFGS: 150 17:36:55 -304.473934 0.290455
BFGS: 151 17:36:56 -304.473933 0.290448
BFGS: 152 17:36:56 -304.473934 0.290451
BFGS: 153 17:36:56 -304.473933 0.290443
BFGS: 154 17:36:56 -304.473934 0.290447
BFGS: 155 17:36:56 -304.473933 0.290449
BFGS: 156 17:36:56 -304.473934 0.290458
BFGS: 157 17:36:56 -304.473934 0.290447
BFGS: 158 17:36:56 -304.473934 0.290444
BFGS: 159 17:36:56 -304.473935 0.290451
BFGS: 160 17:36:56 -304.473934 0.290439
BFGS: 161 17:36:57 -304.473935 0.290445
BFGS: 162 17:36:57 -304.473934 0.290447
BFGS: 163 17:36:57 -304.473934 0.290438
BFGS: 164 17:36:57 -304.473935 0.290440
BFGS: 165 17:36:57 -304.473935 0.290448
BFGS: 166 17:36:57 -304.473935 0.290450
BFGS: 167 17:36:57 -304.473934 0.290451
BFGS: 168 17:36:57 -304.473934 0.290458
BFGS: 169 17:36:57 -304.473934 0.290439
BFGS: 170 17:36:57 -304.473935 0.290446
BFGS: 171 17:36:57 -304.473934 0.290445
BFGS: 172 17:36:58 -304.473934 0.290447
BFGS: 173 17:36:58 -304.473933 0.290444
BFGS: 174 17:36:58 -304.473934 0.290447
BFGS: 175 17:36:58 -304.473934 0.290450
BFGS: 176 17:36:58 -304.473934 0.290445
BFGS: 177 17:36:58 -304.473935 0.290444
BFGS: 178 17:36:58 -304.473935 0.290446
BFGS: 179 17:36:58 -304.473935 0.290446
BFGS: 180 17:36:58 -304.473932 0.290448
BFGS: 181 17:36:58 -304.473934 0.290432
BFGS: 182 17:36:58 -304.473935 0.290444
BFGS: 183 17:36:59 -304.473934 0.290447
BFGS: 184 17:36:59 -304.473934 0.290448
BFGS: 185 17:36:59 -304.473934 0.290434
BFGS: 186 17:36:59 -304.473934 0.290446
BFGS: 187 17:36:59 -304.473935 0.290445
BFGS: 188 17:36:59 -304.473934 0.290454
BFGS: 189 17:36:59 -304.473935 0.290445
BFGS: 190 17:36:59 -304.473934 0.290448
BFGS: 191 17:36:59 -304.473936 0.290452
BFGS: 192 17:36:59 -304.473934 0.290451
BFGS: 193 17:37:00 -304.473935 0.290443
BFGS: 194 17:37:00 -304.473934 0.290446
BFGS: 195 17:37:00 -304.473934 0.290448
BFGS: 196 17:37:00 -304.473934 0.290447
BFGS: 197 17:37:00 -304.473935 0.290444
BFGS: 198 17:37:00 -304.473935 0.290450
BFGS: 199 17:37:00 -304.473934 0.290436
BFGS: 200 17:37:00 -304.473934 0.290447
Step Time Energy fmax
BFGS: 0 17:37:00 -302.003571 0.909525
BFGS: 1 17:37:00 -302.031953 0.739233
BFGS: 2 17:37:00 -302.110154 0.818588
BFGS: 3 17:37:01 -302.156100 0.822525
BFGS: 4 17:37:01 -302.189705 0.687794
BFGS: 5 17:37:01 -302.209464 0.610327
BFGS: 6 17:37:01 -302.242499 0.446496
BFGS: 7 17:37:01 -302.261787 0.287812
BFGS: 8 17:37:01 -302.272841 0.302837
BFGS: 9 17:37:01 -302.280595 0.290066
BFGS: 10 17:37:01 -302.288821 0.313642
BFGS: 11 17:37:01 -302.300908 0.361413
BFGS: 12 17:37:01 -302.313230 0.408156
BFGS: 13 17:37:01 -302.328499 0.533661
BFGS: 14 17:37:02 -302.372290 1.001158
BFGS: 15 17:37:02 -302.420339 1.820901
BFGS: 16 17:37:02 -302.465623 2.685973
BFGS: 17 17:37:02 -302.506843 3.270413
BFGS: 18 17:37:02 -302.559769 3.364949
BFGS: 19 17:37:02 -302.671970 3.049418
BFGS: 20 17:37:02 -302.900534 1.980360
BFGS: 21 17:37:02 -303.285464 1.594652
BFGS: 22 17:37:02 -303.421553 1.518617
BFGS: 23 17:37:02 -303.561495 1.761363
BFGS: 24 17:37:02 -303.657702 1.449375
BFGS: 25 17:37:03 -303.712479 1.065627
BFGS: 26 17:37:03 -303.807686 0.761319
BFGS: 27 17:37:03 -303.849128 0.758996
BFGS: 28 17:37:03 -303.906731 0.869980
BFGS: 29 17:37:03 -303.929840 0.821685
BFGS: 30 17:37:03 -303.952097 0.632617
BFGS: 31 17:37:03 -303.966346 0.388850
BFGS: 32 17:37:03 -303.975360 0.184378
BFGS: 33 17:37:03 -303.978955 0.117313
BFGS: 34 17:37:03 -303.980626 0.118966
BFGS: 35 17:37:04 -303.981996 0.104095
BFGS: 36 17:37:04 -303.984017 0.087799
BFGS: 37 17:37:04 -303.986128 0.091776
BFGS: 38 17:37:04 -303.987467 0.096707
BFGS: 39 17:37:04 -303.988028 0.097701
BFGS: 40 17:37:04 -303.988594 0.083587
BFGS: 41 17:37:04 -303.989391 0.059882
BFGS: 42 17:37:04 -303.990121 0.039190
Step Time Energy fmax
BFGS: 0 17:37:04 -301.806301 1.311285
BFGS: 1 17:37:04 -301.851579 0.846408
BFGS: 2 17:37:05 -301.920648 0.929893
BFGS: 3 17:37:05 -301.993027 1.170992
BFGS: 4 17:37:05 -302.069178 1.023067
BFGS: 5 17:37:05 -302.108420 0.816894
BFGS: 6 17:37:05 -302.145319 0.723446
BFGS: 7 17:37:05 -302.187044 0.424107
BFGS: 8 17:37:05 -302.205777 0.387260
BFGS: 9 17:37:05 -302.218128 0.350850
BFGS: 10 17:37:05 -302.226065 0.289631
BFGS: 11 17:37:05 -302.234702 0.283559
BFGS: 12 17:37:05 -302.244193 0.278373
BFGS: 13 17:37:06 -302.250897 0.304306
BFGS: 14 17:37:06 -302.259311 0.356437
BFGS: 15 17:37:06 -302.278409 0.404712
BFGS: 16 17:37:06 -302.315294 0.716738
BFGS: 17 17:37:06 -302.357456 1.370997
BFGS: 18 17:37:06 -302.408484 2.062227
BFGS: 19 17:37:06 -302.465751 2.716359
BFGS: 20 17:37:06 -302.528667 3.111507
BFGS: 21 17:37:06 -302.608984 3.192310
BFGS: 22 17:37:06 -302.689371 2.852702
BFGS: 23 17:37:06 -302.742250 1.950131
BFGS: 24 17:37:07 -302.855382 1.729347
BFGS: 25 17:37:07 -303.045850 1.582015
BFGS: 26 17:37:07 -303.134589 1.590025
BFGS: 27 17:37:07 -303.344971 1.197698
BFGS: 28 17:37:07 -303.503423 1.054646
BFGS: 29 17:37:07 -303.534606 0.823858
BFGS: 30 17:37:07 -303.584496 0.694176
BFGS: 31 17:37:07 -303.634183 0.560810
BFGS: 32 17:37:07 -303.658486 0.524950
BFGS: 33 17:37:07 -303.678106 0.533407
BFGS: 34 17:37:07 -303.738589 0.462838
BFGS: 35 17:37:08 -303.786415 0.602820
BFGS: 36 17:37:08 -303.823231 0.639141
BFGS: 37 17:37:08 -303.856437 0.670422
BFGS: 38 17:37:08 -303.881290 0.848842
BFGS: 39 17:37:08 -303.922421 0.733239
BFGS: 40 17:37:08 -303.967426 0.261953
BFGS: 41 17:37:08 -303.976396 0.202316
BFGS: 42 17:37:08 -303.980617 0.175487
BFGS: 43 17:37:08 -303.983500 0.139792
BFGS: 44 17:37:08 -303.986727 0.088682
BFGS: 45 17:37:09 -303.988025 0.078946
BFGS: 46 17:37:09 -303.988883 0.089172
BFGS: 47 17:37:09 -303.989802 0.079115
BFGS: 48 17:37:09 -303.990483 0.050381
BFGS: 49 17:37:09 -303.990743 0.026785
Step Time Energy fmax
BFGS: 0 17:37:09 -301.962906 1.014709
BFGS: 1 17:37:09 -301.998484 0.843847
BFGS: 2 17:37:09 -302.077352 0.821426
BFGS: 3 17:37:09 -302.127719 0.854391
BFGS: 4 17:37:09 -302.167023 0.738434
BFGS: 5 17:37:10 -302.189877 0.676160
BFGS: 6 17:37:10 -302.223516 0.517558
BFGS: 7 17:37:10 -302.246120 0.297080
BFGS: 8 17:37:10 -302.259352 0.317040
BFGS: 9 17:37:10 -302.268103 0.282469
BFGS: 10 17:37:10 -302.275323 0.283787
BFGS: 11 17:37:10 -302.286136 0.297321
BFGS: 12 17:37:10 -302.297211 0.354147
BFGS: 13 17:37:10 -302.307652 0.454759
BFGS: 14 17:37:10 -302.329380 0.550388
BFGS: 15 17:37:10 -302.374489 1.163432
BFGS: 16 17:37:11 -302.419611 2.043053
BFGS: 17 17:37:11 -302.464831 2.797993
BFGS: 18 17:37:11 -302.508675 3.244224
BFGS: 19 17:37:11 -302.578038 3.190495
BFGS: 20 17:37:11 -302.713224 2.582637
BFGS: 21 17:37:11 -302.997057 1.821085
BFGS: 22 17:37:11 -303.240214 1.382423
BFGS: 23 17:37:11 -303.461596 1.454338
BFGS: 24 17:37:11 -303.565783 1.385479
BFGS: 25 17:37:11 -303.667319 1.202859
BFGS: 26 17:37:11 -303.730488 1.122464
BFGS: 27 17:37:12 -303.819192 0.870102
BFGS: 28 17:37:12 -303.865869 0.791915
BFGS: 29 17:37:12 -303.911044 0.620394
BFGS: 30 17:37:12 -303.937136 0.608845
BFGS: 31 17:37:12 -303.962299 0.424439
BFGS: 32 17:37:12 -303.975026 0.283199
BFGS: 33 17:37:12 -303.981112 0.117506
BFGS: 34 17:37:12 -303.982633 0.120543
BFGS: 35 17:37:12 -303.983849 0.131679
BFGS: 36 17:37:12 -303.985695 0.116453
BFGS: 37 17:37:12 -303.987307 0.073024
BFGS: 38 17:37:13 -303.988166 0.066265
BFGS: 39 17:37:13 -303.988565 0.084939
BFGS: 40 17:37:13 -303.989028 0.089984
BFGS: 41 17:37:13 -303.989675 0.079171
BFGS: 42 17:37:13 -303.990267 0.052920
BFGS: 43 17:37:13 -303.990570 0.034097
/home/runner/work/fairchem/fairchem/src/fairchem/applications/cattsunami/core/autoframe.py:1551: UserWarning: torch.range is deprecated and will be removed in a future release because its behavior is inconsistent with Python's range builtin. Instead, use torch.arange, which produces values in [start, end).
alpha = torch.range(0, num_frames - 1, device=device) / (num_frames - 1)
Run NEBs#
## This will run all NEBs enumerated - to just run one, run the code cell below.
# On GPU, each NEB takes an average of ~1 minute so this could take around a half hour on GPU
# But much longer on CPU
# Remember that not all NEBs will converge -- the k, nframes would be adjusted to achieve convergence
fmax = 0.05 # [eV / ang**2]
delta_fmax_climb = 0.4
converged_idxs = []
for idx, frame_set in enumerate(frame_sets):
neb = DyNEB(frame_set, k=1)
for image in frame_set:
image.calc = FAIRChemCalculator(predictor, task_name="oc20")
optimizer = BFGS(
neb,
trajectory=f"ch_dissoc_on_Ru_{idx}.traj",
)
conv = optimizer.run(fmax=fmax + delta_fmax_climb, steps=optimization_steps)
if conv:
neb.climb = True
conv = optimizer.run(fmax=fmax, steps=optimization_steps)
if conv:
converged_idxs.append(idx)
print(converged_idxs)
This cell will run a shorter calculations for just a single one of the enumerated transition state pathways. You can adapt this code to run transition state searches via nudged elastic band (NEB) calculations for any reaction.
# If you run the above cell -- dont run this one
fmax = 0.05 # [eV / ang**2]
delta_fmax_climb = 0.4
images = frame_sets[0]
neb = DyNEB(images, k=1)
for image in images:
image.calc = FAIRChemCalculator(predictor, task_name="oc20")
optimizer = BFGS(
neb,
trajectory="ch_dissoc_on_Ru_0.traj",
)
conv = optimizer.run(fmax=fmax + delta_fmax_climb, steps=optimization_steps)
if conv:
neb.climb = True
conv = optimizer.run(fmax=fmax, steps=optimization_steps)
Step Time Energy fmax
BFGS: 0 17:37:54 -301.647183 2.957993
BFGS: 1 17:37:55 -301.936049 2.581749
BFGS: 2 17:37:56 -302.418110 6.176684
BFGS: 3 17:37:57 -302.634029 2.087945
BFGS: 4 17:37:57 -303.111527 1.972367
BFGS: 5 17:37:58 -303.177416 1.697970
BFGS: 6 17:37:59 -303.311123 1.341916
BFGS: 7 17:38:00 -303.416268 1.233124
BFGS: 8 17:38:01 -303.543946 1.985293
BFGS: 9 17:38:02 -303.547132 1.470583
BFGS: 10 17:38:02 -303.579330 1.111178
BFGS: 11 17:38:03 -303.626226 1.119084
BFGS: 12 17:38:04 -303.641251 0.935141
BFGS: 13 17:38:05 -303.662779 0.672142
BFGS: 14 17:38:06 -303.683991 0.705294
BFGS: 15 17:38:06 -303.710452 0.698287
BFGS: 16 17:38:07 -303.727089 0.731216
BFGS: 17 17:38:08 -303.739683 0.639775
BFGS: 18 17:38:09 -303.746371 0.735735
BFGS: 19 17:38:10 -303.746205 0.712337
BFGS: 20 17:38:11 -303.739634 0.660651
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_9718/3247994494.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")