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,
)# 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 19:12:09 -301.968830 4.145445
BFGS: 1 19:12:09 -302.349069 3.436419
BFGS: 2 19:12:10 -303.274389 3.000982
BFGS: 3 19:12:11 -303.418203 2.866805
BFGS: 4 19:12:11 -303.637839 1.968062
BFGS: 5 19:12:12 -303.823618 2.816208
BFGS: 6 19:12:12 -303.909930 1.341685
BFGS: 7 19:12:12 -304.009446 0.695318
BFGS: 8 19:12:13 -304.062541 0.949296
BFGS: 9 19:12:13 -304.106306 0.910958
BFGS: 10 19:12:14 -304.200853 1.100259
BFGS: 11 19:12:14 -304.265797 0.776604
BFGS: 12 19:12:15 -304.309235 0.955503
BFGS: 13 19:12:15 -304.345117 1.155617
BFGS: 14 19:12:16 -304.438852 1.280921
BFGS: 15 19:12:16 -304.495308 0.987023
BFGS: 16 19:12:17 -304.551919 0.709558
BFGS: 17 19:12:17 -304.566767 0.511027
BFGS: 18 19:12:18 -304.583870 0.530200
BFGS: 19 19:12:18 -304.610381 0.524951
BFGS: 20 19:12:19 -304.629050 0.369089
BFGS: 21 19:12:19 -304.642599 0.285080
BFGS: 22 19:12:20 -304.647526 0.275498
BFGS: 23 19:12:20 -304.656689 0.260780
BFGS: 24 19:12:21 -304.666148 0.248044
BFGS: 25 19:12:21 -304.675292 0.206061
BFGS: 26 19:12:22 -304.679892 0.149043
BFGS: 27 19:12:22 -304.681881 0.132452
BFGS: 28 19:12:23 -304.683411 0.126731
BFGS: 29 19:12:23 -304.685461 0.122642
BFGS: 30 19:12:24 -304.688290 0.088624
BFGS: 31 19:12:24 -304.690293 0.059480
BFGS: 32 19:12:24 -304.691046 0.042421
Step Time Energy fmax
BFGS: 0 19:12:25 -301.051360 4.019958
BFGS: 1 19:12:25 -301.445308 3.070402
BFGS: 2 19:12:26 -302.559116 3.618428
BFGS: 3 19:12:26 -302.632328 5.050128
BFGS: 4 19:12:27 -302.948274 2.433216
BFGS: 5 19:12:27 -303.058191 2.492603
BFGS: 6 19:12:27 -303.101811 0.548283
BFGS: 7 19:12:28 -303.119945 0.485754
BFGS: 8 19:12:28 -303.201385 0.781535
BFGS: 9 19:12:29 -303.214372 0.457005
BFGS: 10 19:12:29 -303.222358 0.283917
BFGS: 11 19:12:30 -303.231438 0.478011
BFGS: 12 19:12:30 -303.241993 0.575967
BFGS: 13 19:12:31 -303.250827 0.536311
BFGS: 14 19:12:31 -303.259265 0.484710
BFGS: 15 19:12:32 -303.268731 0.576502
BFGS: 16 19:12:32 -303.327005 1.605666
BFGS: 17 19:12:33 -303.627068 1.543444
BFGS: 18 19:12:33 -303.990028 1.521255
BFGS: 19 19:12:33 -304.177910 2.063454
BFGS: 20 19:12:34 -304.305395 1.294448
BFGS: 21 19:12:34 -304.472956 1.242608
BFGS: 22 19:12:35 -304.512557 0.948919
BFGS: 23 19:12:35 -304.561970 0.577600
BFGS: 24 19:12:36 -304.583840 0.542400
BFGS: 25 19:12:36 -304.596681 0.492078
BFGS: 26 19:12:36 -304.614329 0.346866
BFGS: 27 19:12:37 -304.627313 0.349037
BFGS: 28 19:12:37 -304.639426 0.333764
BFGS: 29 19:12:37 -304.651899 0.292147
BFGS: 30 19:12:38 -304.660932 0.236259
BFGS: 31 19:12:38 -304.666778 0.255848
BFGS: 32 19:12:39 -304.672085 0.229240
BFGS: 33 19:12:39 -304.677166 0.227253
BFGS: 34 19:12:40 -304.681408 0.184435
BFGS: 35 19:12:40 -304.684702 0.150112
BFGS: 36 19:12:40 -304.686960 0.109299
BFGS: 37 19:12:40 -304.688474 0.105779
BFGS: 38 19:12:41 -304.689646 0.082036
BFGS: 39 19:12:41 -304.690411 0.078098
BFGS: 40 19:12:41 -304.690946 0.081941
BFGS: 41 19:12:42 -304.691451 0.060008
BFGS: 42 19:12:42 -304.691867 0.041570
Step Time Energy fmax
BFGS: 0 19:12:43 -302.652176 3.685920
BFGS: 1 19:12:43 -302.995955 2.580280
BFGS: 2 19:12:44 -303.794261 3.143214
BFGS: 3 19:12:44 -303.934368 2.542970
BFGS: 4 19:12:44 -304.109391 2.861543
BFGS: 5 19:12:45 -304.190156 0.712718
BFGS: 6 19:12:45 -304.228734 0.656825
BFGS: 7 19:12:46 -304.315799 0.611697
BFGS: 8 19:12:46 -304.327960 0.418473
BFGS: 9 19:12:47 -304.334749 0.362969
BFGS: 10 19:12:47 -304.347809 0.197241
BFGS: 11 19:12:48 -304.351249 0.131629
BFGS: 12 19:12:48 -304.352141 0.074968
BFGS: 13 19:12:48 -304.352487 0.067438
BFGS: 14 19:12:49 -304.353610 0.100499
BFGS: 15 19:12:49 -304.354173 0.092549
BFGS: 16 19:12:49 -304.354534 0.061323
BFGS: 17 19:12:50 -304.354752 0.056393
BFGS: 18 19:12:50 -304.355153 0.080337
BFGS: 19 19:12:51 -304.355773 0.105934
BFGS: 20 19:12:51 -304.356447 0.087679
BFGS: 21 19:12:52 -304.356816 0.036086
Step Time Energy fmax
BFGS: 0 19:12:52 -301.018798 4.066848
BFGS: 1 19:12:52 -301.417699 3.111917
BFGS: 2 19:12:53 -302.544040 3.658152
BFGS: 3 19:12:53 -302.605688 5.312218
BFGS: 4 19:12:54 -302.932673 2.556612
BFGS: 5 19:12:54 -303.063367 2.385231
BFGS: 6 19:12:54 -303.101411 0.600149
BFGS: 7 19:12:55 -303.119910 0.501058
BFGS: 8 19:12:55 -303.184607 1.016508
BFGS: 9 19:12:56 -303.205536 0.665940
BFGS: 10 19:12:56 -303.214878 0.227717
BFGS: 11 19:12:57 -303.218555 0.252603
BFGS: 12 19:12:57 -303.226768 0.456803
BFGS: 13 19:12:57 -303.233281 0.479528
BFGS: 14 19:12:58 -303.239723 0.410794
BFGS: 15 19:12:58 -303.244262 0.375849
BFGS: 16 19:12:59 -303.257421 0.646168
BFGS: 17 19:12:59 -303.336603 1.944685
BFGS: 18 19:13:00 -303.558887 2.094670
BFGS: 19 19:13:00 -303.722771 2.269861
BFGS: 20 19:13:00 -303.879306 2.324913
BFGS: 21 19:13:01 -303.894886 3.209108
BFGS: 22 19:13:01 -304.039775 0.897509
BFGS: 23 19:13:02 -304.087002 0.865132
BFGS: 24 19:13:03 -304.128818 0.914890
BFGS: 25 19:13:03 -304.168662 0.677927
BFGS: 26 19:13:04 -304.197904 0.473173
BFGS: 27 19:13:04 -304.223617 0.501917
BFGS: 28 19:13:04 -304.244999 0.471575
BFGS: 29 19:13:05 -304.262117 0.407091
BFGS: 30 19:13:05 -304.288529 0.347601
BFGS: 31 19:13:06 -304.309634 0.381529
BFGS: 32 19:13:06 -304.322387 0.407296
BFGS: 33 19:13:07 -304.329905 0.359727
BFGS: 34 19:13:07 -304.335225 0.274475
BFGS: 35 19:13:08 -304.339626 0.262239
BFGS: 36 19:13:08 -304.345901 0.250439
BFGS: 37 19:13:08 -304.350276 0.163488
BFGS: 38 19:13:09 -304.352381 0.093865
BFGS: 39 19:13:09 -304.353929 0.096338
BFGS: 40 19:13:10 -304.354910 0.090370
BFGS: 41 19:13:10 -304.355529 0.064101
BFGS: 42 19:13:10 -304.356090 0.034645
Step Time Energy fmax
BFGS: 0 19:13:11 -301.342227 4.137706
BFGS: 1 19:13:11 -301.727282 3.406317
BFGS: 2 19:13:12 -302.726925 3.309780
BFGS: 3 19:13:12 -302.822169 3.964034
BFGS: 4 19:13:13 -303.081618 2.414932
BFGS: 5 19:13:13 -303.259111 2.424896
BFGS: 6 19:13:14 -303.323362 1.664790
BFGS: 7 19:13:14 -303.614527 1.609418
BFGS: 8 19:13:15 -303.763290 2.336710
BFGS: 9 19:13:15 -303.857686 1.731630
BFGS: 10 19:13:15 -304.082412 1.162730
BFGS: 11 19:13:16 -304.117361 0.761401
BFGS: 12 19:13:16 -304.159176 0.413862
BFGS: 13 19:13:17 -304.186160 0.836702
BFGS: 14 19:13:17 -304.213196 0.813431
BFGS: 15 19:13:18 -304.246014 0.519496
BFGS: 16 19:13:18 -304.256099 0.334211
BFGS: 17 19:13:19 -304.271821 0.438493
BFGS: 18 19:13:19 -304.285669 0.533600
BFGS: 19 19:13:19 -304.302443 0.493594
BFGS: 20 19:13:20 -304.314891 0.363147
BFGS: 21 19:13:20 -304.322780 0.244053
BFGS: 22 19:13:21 -304.330239 0.227266
BFGS: 23 19:13:21 -304.334976 0.216217
BFGS: 24 19:13:22 -304.339362 0.230175
BFGS: 25 19:13:22 -304.343999 0.210310
BFGS: 26 19:13:23 -304.347767 0.136246
BFGS: 27 19:13:23 -304.350129 0.105057
BFGS: 28 19:13:24 -304.351503 0.104250
BFGS: 29 19:13:24 -304.352367 0.091757
BFGS: 30 19:13:24 -304.353225 0.084054
BFGS: 31 19:13:25 -304.354357 0.071428
BFGS: 32 19:13:25 -304.355374 0.061801
BFGS: 33 19:13:26 -304.355907 0.055104
BFGS: 34 19:13:26 -304.356069 0.038623
Step Time Energy fmax
BFGS: 0 19:13:27 -302.506344 3.804068
BFGS: 1 19:13:27 -302.864985 2.790408
BFGS: 2 19:13:27 -303.731873 3.132013
BFGS: 3 19:13:28 -303.889924 2.648826
BFGS: 4 19:13:28 -304.109627 2.337794
BFGS: 5 19:13:29 -304.175899 0.802288
BFGS: 6 19:13:29 -304.234846 0.589341
BFGS: 7 19:13:30 -304.310469 0.843369
BFGS: 8 19:13:30 -304.326979 0.539432
BFGS: 9 19:13:31 -304.339695 0.365603
BFGS: 10 19:13:31 -304.345705 0.270500
BFGS: 11 19:13:31 -304.352992 0.206224
BFGS: 12 19:13:32 -304.355948 0.094869
BFGS: 13 19:13:32 -304.356306 0.047767
Step Time Energy fmax
BFGS: 0 19:13:33 -302.496092 3.859835
BFGS: 1 19:13:33 -302.854114 2.868019
BFGS: 2 19:13:34 -303.647955 3.063371
BFGS: 3 19:13:34 -303.780955 2.486971
BFGS: 4 19:13:35 -303.952174 2.987856
BFGS: 5 19:13:35 -304.025687 0.980425
BFGS: 6 19:13:36 -304.062613 0.554912
BFGS: 7 19:13:36 -304.146285 0.472334
BFGS: 8 19:13:37 -304.165504 0.494845
BFGS: 9 19:13:37 -304.185239 0.456348
BFGS: 10 19:13:38 -304.203309 0.288335
BFGS: 11 19:13:38 -304.213397 0.343863
BFGS: 12 19:13:38 -304.220365 0.350630
BFGS: 13 19:13:39 -304.225911 0.326401
BFGS: 14 19:13:39 -304.235094 0.299894
BFGS: 15 19:13:40 -304.250170 0.397594
BFGS: 16 19:13:40 -304.265946 0.516516
BFGS: 17 19:13:41 -304.278690 0.380637
BFGS: 18 19:13:42 -304.291968 0.305242
BFGS: 19 19:13:42 -304.304298 0.246282
BFGS: 20 19:13:42 -304.313475 0.245546
BFGS: 21 19:13:43 -304.319257 0.245484
BFGS: 22 19:13:43 -304.323518 0.240561
BFGS: 23 19:13:43 -304.327888 0.238689
BFGS: 24 19:13:44 -304.333927 0.209904
BFGS: 25 19:13:44 -304.341445 0.170180
BFGS: 26 19:13:45 -304.345086 0.145463
BFGS: 27 19:13:45 -304.347555 0.157350
BFGS: 28 19:13:45 -304.350186 0.150588
BFGS: 29 19:13:46 -304.352619 0.117192
BFGS: 30 19:13:47 -304.354574 0.067031
BFGS: 31 19:13:47 -304.355535 0.039133
Step Time Energy fmax
BFGS: 0 19:13:47 -302.112993 4.150519
BFGS: 1 19:13:48 -302.493707 3.288792
BFGS: 2 19:13:48 -303.436140 3.126684
BFGS: 3 19:13:49 -303.648313 3.100097
BFGS: 4 19:13:49 -303.911268 2.166884
BFGS: 5 19:13:50 -304.197301 2.671515
BFGS: 6 19:13:50 -304.308418 1.556898
BFGS: 7 19:13:51 -304.506510 1.095846
BFGS: 8 19:13:51 -304.545408 1.074847
BFGS: 9 19:13:51 -304.610927 0.692084
BFGS: 10 19:13:52 -304.652584 0.710229
BFGS: 11 19:13:53 -304.672920 0.515962
BFGS: 12 19:13:53 -304.679834 0.282809
BFGS: 13 19:13:53 -304.682819 0.161960
BFGS: 14 19:13:54 -304.685098 0.147557
BFGS: 15 19:13:54 -304.687009 0.120444
BFGS: 16 19:13:54 -304.687920 0.088736
BFGS: 17 19:13:54 -304.688412 0.087125
BFGS: 18 19:13:55 -304.688930 0.074012
BFGS: 19 19:13:55 -304.689610 0.096083
BFGS: 20 19:13:55 -304.690271 0.083675
BFGS: 21 19:13:56 -304.690619 0.049048
Step Time Energy fmax
BFGS: 0 19:13:56 -302.624175 3.966205
BFGS: 1 19:13:56 -302.977666 2.833655
BFGS: 2 19:13:57 -303.783606 3.142204
BFGS: 3 19:13:58 -303.942740 2.735898
BFGS: 4 19:13:58 -304.237074 1.987587
BFGS: 5 19:13:58 -304.312232 1.153448
BFGS: 6 19:13:58 -304.515921 1.038597
BFGS: 7 19:13:59 -304.577065 1.016607
BFGS: 8 19:13:59 -304.612497 0.751300
BFGS: 9 19:14:00 -304.658983 0.595799
BFGS: 10 19:14:00 -304.675163 0.409426
BFGS: 11 19:14:01 -304.682420 0.119670
BFGS: 12 19:14:01 -304.683960 0.106441
BFGS: 13 19:14:02 -304.684751 0.112845
BFGS: 14 19:14:02 -304.685871 0.098937
BFGS: 15 19:14:03 -304.687067 0.077599
BFGS: 16 19:14:03 -304.687969 0.072268
BFGS: 17 19:14:03 -304.688472 0.077671
BFGS: 18 19:14:03 -304.688892 0.069898
BFGS: 19 19:14:04 -304.689531 0.067956
BFGS: 20 19:14:04 -304.690343 0.075031
BFGS: 21 19:14:05 -304.691017 0.057776
BFGS: 22 19:14:05 -304.691370 0.062054
BFGS: 23 19:14:05 -304.691592 0.056725
BFGS: 24 19:14:06 -304.691851 0.038068
Step Time Energy fmax
BFGS: 0 19:14:06 -301.957694 4.085010
BFGS: 1 19:14:07 -302.332540 3.209301
BFGS: 2 19:14:07 -303.295688 3.248586
BFGS: 3 19:14:08 -303.520452 3.616094
BFGS: 4 19:14:08 -303.818586 2.340404
BFGS: 5 19:14:08 -304.185107 2.219984
BFGS: 6 19:14:09 -304.295854 1.539841
BFGS: 7 19:14:09 -304.502608 0.994972
BFGS: 8 19:14:10 -304.536318 0.868297
BFGS: 9 19:14:10 -304.598149 0.735075
BFGS: 10 19:14:10 -304.662095 0.817892
BFGS: 11 19:14:11 -304.680435 0.396339
BFGS: 12 19:14:11 -304.684167 0.143003
BFGS: 13 19:14:11 -304.685761 0.151220
BFGS: 14 19:14:12 -304.687844 0.148197
BFGS: 15 19:14:12 -304.689693 0.136744
BFGS: 16 19:14:13 -304.690603 0.066879
BFGS: 17 19:14:13 -304.690887 0.043497
# 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 19:14:13 -296.982174 4.619709
BFGS: 1 19:14:14 -297.456339 4.802502
BFGS: 2 19:14:14 -298.745064 3.893683
BFGS: 3 19:14:14 -299.149753 4.224645
BFGS: 4 19:14:15 -299.339843 1.893244
BFGS: 5 19:14:15 -299.568558 1.904727
BFGS: 6 19:14:15 -299.857592 0.973981
BFGS: 7 19:14:16 -299.893227 0.942235
BFGS: 8 19:14:16 -300.144559 1.082927
BFGS: 9 19:14:17 -300.249184 1.356726
BFGS: 10 19:14:17 -300.305959 1.342300
BFGS: 11 19:14:18 -300.405520 2.026199
BFGS: 12 19:14:18 -300.471167 1.111354
BFGS: 13 19:14:19 -300.524112 0.835434
BFGS: 14 19:14:19 -300.548415 0.680760
BFGS: 15 19:14:20 -300.565216 0.626894
BFGS: 16 19:14:20 -300.593143 0.413412
BFGS: 17 19:14:21 -300.602425 0.387953
BFGS: 18 19:14:21 -300.613634 0.241276
BFGS: 19 19:14:22 -300.618421 0.125553
BFGS: 20 19:14:22 -300.620112 0.105100
BFGS: 21 19:14:22 -300.621083 0.115781
BFGS: 22 19:14:23 -300.622581 0.116358
BFGS: 23 19:14:24 -300.623890 0.090985
BFGS: 24 19:14:24 -300.624415 0.035572
Step Time Energy fmax
BFGS: 0 19:14:24 -297.021350 4.643933
BFGS: 1 19:14:25 -297.493147 4.822023
BFGS: 2 19:14:25 -298.769446 3.944522
BFGS: 3 19:14:26 -299.210983 3.992524
BFGS: 4 19:14:26 -299.397486 1.942473
BFGS: 5 19:14:27 -299.710941 1.977212
BFGS: 6 19:14:27 -299.963805 1.254526
BFGS: 7 19:14:28 -300.012944 1.230890
BFGS: 8 19:14:29 -300.344757 1.374540
BFGS: 9 19:14:29 -300.436629 1.522947
BFGS: 10 19:14:29 -300.490504 1.005629
BFGS: 11 19:14:30 -300.538089 0.760958
BFGS: 12 19:14:31 -300.563603 0.582567
BFGS: 13 19:14:31 -300.584383 0.502048
BFGS: 14 19:14:31 -300.597513 0.465388
BFGS: 15 19:14:32 -300.604455 0.361354
BFGS: 16 19:14:32 -300.611861 0.196166
BFGS: 17 19:14:33 -300.616652 0.218994
BFGS: 18 19:14:33 -300.620125 0.176722
BFGS: 19 19:14:34 -300.621981 0.100484
BFGS: 20 19:14:34 -300.622756 0.068370
BFGS: 21 19:14:35 -300.623280 0.064074
BFGS: 22 19:14:35 -300.623856 0.079885
BFGS: 23 19:14:36 -300.624391 0.073457
BFGS: 24 19:14:36 -300.624739 0.040276
Step Time Energy fmax
BFGS: 0 19:14:36 -296.955927 4.572659
BFGS: 1 19:14:37 -297.433579 4.753241
BFGS: 2 19:14:37 -298.732553 3.798238
BFGS: 3 19:14:38 -299.081291 4.540257
BFGS: 4 19:14:38 -299.282170 1.843181
BFGS: 5 19:14:39 -299.451804 1.791755
BFGS: 6 19:14:39 -299.757050 0.908499
BFGS: 7 19:14:39 -299.782431 0.843335
BFGS: 8 19:14:40 -299.893799 0.838498
BFGS: 9 19:14:40 -299.918045 0.564904
BFGS: 10 19:14:40 -299.950176 0.591538
BFGS: 11 19:14:41 -299.962183 0.706006
BFGS: 12 19:14:41 -300.029854 1.274030
BFGS: 13 19:14:42 -300.078537 1.406361
BFGS: 14 19:14:42 -300.092286 1.848160
BFGS: 15 19:14:43 -300.225311 1.364975
BFGS: 16 19:14:43 -300.326130 1.267605
BFGS: 17 19:14:44 -300.445152 0.987727
BFGS: 18 19:14:44 -300.507978 0.958525
BFGS: 19 19:14:45 -300.546235 0.560750
BFGS: 20 19:14:45 -300.564656 0.482855
BFGS: 21 19:14:46 -300.595875 0.414236
BFGS: 22 19:14:46 -300.608890 0.293561
BFGS: 23 19:14:46 -300.614023 0.232484
BFGS: 24 19:14:47 -300.616639 0.213212
BFGS: 25 19:14:47 -300.619499 0.188755
BFGS: 26 19:14:48 -300.622223 0.139844
BFGS: 27 19:14:48 -300.623890 0.070453
BFGS: 28 19:14:48 -300.624443 0.030745
Step Time Energy fmax
BFGS: 0 19:14:49 -297.156654 4.573502
BFGS: 1 19:14:49 -297.637708 4.708478
BFGS: 2 19:14:50 -298.922212 3.568093
BFGS: 3 19:14:50 -299.140869 4.997457
BFGS: 4 19:14:51 -299.375406 1.676876
BFGS: 5 19:14:51 -299.485685 1.476341
BFGS: 6 19:14:51 -299.683928 1.863794
BFGS: 7 19:14:52 -299.728516 0.783345
BFGS: 8 19:14:52 -299.758233 0.834994
BFGS: 9 19:14:53 -299.869759 1.042094
BFGS: 10 19:14:53 -299.902442 0.785554
BFGS: 11 19:14:53 -299.933778 0.323643
BFGS: 12 19:14:53 -299.940032 0.316970
BFGS: 13 19:14:54 -299.949899 0.441836
BFGS: 14 19:14:54 -299.959100 0.484200
BFGS: 15 19:14:54 -299.967545 0.423512
BFGS: 16 19:14:55 -299.975459 0.380457
BFGS: 17 19:14:55 -299.993755 0.569020
BFGS: 18 19:14:56 -300.013722 0.711633
BFGS: 19 19:14:56 -300.029449 0.575652
BFGS: 20 19:14:57 -300.047385 0.353078
BFGS: 21 19:14:57 -300.057212 0.285773
BFGS: 22 19:14:57 -300.064914 0.310064
BFGS: 23 19:14:58 -300.071035 0.205315
BFGS: 24 19:14:58 -300.075806 0.180600
BFGS: 25 19:14:59 -300.078591 0.112026
BFGS: 26 19:14:59 -300.079430 0.073322
BFGS: 27 19:15:00 -300.079757 0.063441
BFGS: 28 19:15:00 -300.079962 0.050071
BFGS: 29 19:15:00 -300.080194 0.036276
Step Time Energy fmax
BFGS: 0 19:15:01 -297.574047 4.917622
BFGS: 1 19:15:01 -298.065859 5.020718
BFGS: 2 19:15:02 -299.288285 4.050553
BFGS: 3 19:15:02 -299.855671 2.867598
BFGS: 4 19:15:03 -300.034604 2.518772
BFGS: 5 19:15:03 -300.410734 1.166923
BFGS: 6 19:15:03 -300.462401 0.727882
BFGS: 7 19:15:04 -300.521180 0.829311
BFGS: 8 19:15:04 -300.575637 0.789262
BFGS: 9 19:15:05 -300.609184 0.436916
BFGS: 10 19:15:05 -300.619426 0.183687
BFGS: 11 19:15:06 -300.621322 0.131477
BFGS: 12 19:15:06 -300.622249 0.101452
BFGS: 13 19:15:07 -300.623429 0.093723
BFGS: 14 19:15:07 -300.624124 0.055153
BFGS: 15 19:15:08 -300.624400 0.048414
Step Time Energy fmax
BFGS: 0 19:15:08 -296.395749 4.430405
BFGS: 1 19:15:08 -296.875848 4.681842
BFGS: 2 19:15:09 -298.307512 3.354948
BFGS: 3 19:15:09 -297.889838 9.834167
BFGS: 4 19:15:10 -298.572170 1.903283
BFGS: 5 19:15:10 -298.645344 1.234099
BFGS: 6 19:15:11 -298.725919 1.505257
BFGS: 7 19:15:11 -298.780463 1.612230
BFGS: 8 19:15:11 -298.986335 1.539238
BFGS: 9 19:15:12 -299.140650 1.761871
BFGS: 10 19:15:12 -299.264364 1.938763
BFGS: 11 19:15:13 -299.406124 1.827099
BFGS: 12 19:15:14 -299.687256 1.556230
BFGS: 13 19:15:14 -299.991161 0.755415
BFGS: 14 19:15:15 -300.018839 0.790299
BFGS: 15 19:15:15 -300.032207 0.477031
BFGS: 16 19:15:15 -300.050895 0.286618
BFGS: 17 19:15:16 -300.064362 0.193358
BFGS: 18 19:15:16 -300.070723 0.177978
BFGS: 19 19:15:17 -300.073042 0.163637
BFGS: 20 19:15:17 -300.074647 0.165086
BFGS: 21 19:15:17 -300.076639 0.164011
BFGS: 22 19:15:18 -300.078162 0.148361
BFGS: 23 19:15:18 -300.079179 0.115282
BFGS: 24 19:15:18 -300.079722 0.084874
BFGS: 25 19:15:19 -300.080114 0.070566
BFGS: 26 19:15:19 -300.080501 0.047560
Step Time Energy fmax
BFGS: 0 19:15:20 -296.746639 4.496689
BFGS: 1 19:15:20 -297.217620 4.693393
BFGS: 2 19:15:20 -298.550904 3.667226
BFGS: 3 19:15:21 -298.690262 6.106581
BFGS: 4 19:15:21 -298.988109 1.993539
BFGS: 5 19:15:22 -299.105525 1.847179
BFGS: 6 19:15:22 -299.525841 1.622477
BFGS: 7 19:15:23 -299.641720 1.859730
BFGS: 8 19:15:23 -299.714239 1.017276
BFGS: 9 19:15:23 -299.759838 0.728641
BFGS: 10 19:15:24 -299.844788 0.750834
BFGS: 11 19:15:24 -299.866350 0.725637
BFGS: 12 19:15:25 -299.892329 0.432667
BFGS: 13 19:15:25 -299.901728 0.230936
BFGS: 14 19:15:25 -299.905792 0.169252
BFGS: 15 19:15:26 -299.909923 0.215005
BFGS: 16 19:15:26 -299.914623 0.236612
BFGS: 17 19:15:27 -299.917371 0.228381
BFGS: 18 19:15:27 -299.919102 0.235916
BFGS: 19 19:15:27 -299.923104 0.321859
BFGS: 20 19:15:28 -299.932368 0.760179
BFGS: 21 19:15:28 -299.959721 1.278633
BFGS: 22 19:15:29 -300.225675 1.352536
BFGS: 23 19:15:29 -300.346849 1.926905
BFGS: 24 19:15:30 -300.415890 0.982430
BFGS: 25 19:15:30 -300.462924 0.825213
BFGS: 26 19:15:30 -300.523432 0.470566
BFGS: 27 19:15:31 -300.561190 0.571659
BFGS: 28 19:15:31 -300.581673 0.532626
BFGS: 29 19:15:32 -300.596777 0.374111
BFGS: 30 19:15:32 -300.607967 0.199703
BFGS: 31 19:15:33 -300.616782 0.107346
BFGS: 32 19:15:33 -300.620473 0.144380
BFGS: 33 19:15:33 -300.621587 0.123527
BFGS: 34 19:15:34 -300.622370 0.071488
BFGS: 35 19:15:34 -300.623095 0.058643
BFGS: 36 19:15:35 -300.623901 0.060183
BFGS: 37 19:15:35 -300.624530 0.063315
BFGS: 38 19:15:35 -300.624809 0.050734
BFGS: 39 19:15:36 -300.624897 0.032138
Step Time Energy fmax
BFGS: 0 19:15:36 -296.276715 4.407332
BFGS: 1 19:15:37 -296.765786 4.691935
BFGS: 2 19:15:37 -298.255812 3.290740
BFGS: 3 19:15:38 -297.630078 11.292938
BFGS: 4 19:15:38 -298.493088 1.891958
BFGS: 5 19:15:38 -298.561918 1.127596
BFGS: 6 19:15:39 -298.616928 1.156373
BFGS: 7 19:15:39 -298.640873 1.107469
BFGS: 8 19:15:39 -298.766898 1.240587
BFGS: 9 19:15:40 -298.819149 1.405082
BFGS: 10 19:15:40 -299.296246 2.299781
BFGS: 11 19:15:41 -299.564114 2.778556
BFGS: 12 19:15:41 -299.730451 2.593626
BFGS: 13 19:15:42 -299.881417 1.104335
BFGS: 14 19:15:42 -299.919522 0.660263
BFGS: 15 19:15:42 -299.954615 0.967733
BFGS: 16 19:15:43 -299.995445 0.920025
BFGS: 17 19:15:43 -300.025620 0.560184
BFGS: 18 19:15:43 -300.033024 0.382403
BFGS: 19 19:15:44 -300.040661 0.265752
BFGS: 20 19:15:45 -300.046641 0.353331
BFGS: 21 19:15:45 -300.054950 0.377208
BFGS: 22 19:15:45 -300.061861 0.279237
BFGS: 23 19:15:46 -300.068548 0.211687
BFGS: 24 19:15:46 -300.073523 0.133254
BFGS: 25 19:15:46 -300.076457 0.149588
BFGS: 26 19:15:47 -300.078099 0.120145
BFGS: 27 19:15:47 -300.078787 0.070179
BFGS: 28 19:15:48 -300.079173 0.051991
BFGS: 29 19:15:48 -300.079574 0.053474
BFGS: 30 19:15:49 -300.079996 0.069812
BFGS: 31 19:15:49 -300.080374 0.059735
BFGS: 32 19:15:50 -300.080577 0.029079
Step Time Energy fmax
BFGS: 0 19:15:50 -297.253170 4.753477
BFGS: 1 19:15:50 -297.737264 4.894665
BFGS: 2 19:15:51 -299.009320 3.856465
BFGS: 3 19:15:51 -299.395558 4.039161
BFGS: 4 19:15:52 -299.562432 1.770523
BFGS: 5 19:15:52 -299.719061 1.664313
BFGS: 6 19:15:52 -299.868612 1.435572
BFGS: 7 19:15:53 -299.909241 1.444374
BFGS: 8 19:15:53 -300.247731 1.885443
BFGS: 9 19:15:54 -300.169420 2.676533
BFGS: 10 19:15:54 -300.334895 1.442856
BFGS: 11 19:15:54 -300.369647 1.215403
BFGS: 12 19:15:55 -300.463829 1.682354
BFGS: 13 19:15:55 -300.490616 1.236130
BFGS: 14 19:15:56 -300.538730 0.830902
BFGS: 15 19:15:56 -300.568937 0.614317
BFGS: 16 19:15:56 -300.586902 0.596602
BFGS: 17 19:15:57 -300.601928 0.451420
BFGS: 18 19:15:57 -300.609546 0.312531
BFGS: 19 19:15:58 -300.613450 0.226862
BFGS: 20 19:15:58 -300.616143 0.172499
BFGS: 21 19:15:58 -300.617876 0.168465
BFGS: 22 19:15:59 -300.619207 0.136249
BFGS: 23 19:15:59 -300.620632 0.090015
BFGS: 24 19:16:00 -300.622085 0.079515
BFGS: 25 19:16:00 -300.623059 0.065120
BFGS: 26 19:16:00 -300.623462 0.052415
BFGS: 27 19:16:01 -300.623726 0.045742
Step Time Energy fmax
BFGS: 0 19:16:01 -296.351672 4.408352
BFGS: 1 19:16:02 -296.831584 4.669751
BFGS: 2 19:16:02 -298.283116 3.376464
BFGS: 3 19:16:03 -297.847579 10.039846
BFGS: 4 19:16:03 -298.549793 1.925236
BFGS: 5 19:16:04 -298.624103 1.240690
BFGS: 6 19:16:04 -298.704972 1.546758
BFGS: 7 19:16:05 -298.763767 1.733307
BFGS: 8 19:16:05 -298.999285 1.875676
BFGS: 9 19:16:05 -299.173700 1.855861
BFGS: 10 19:16:06 -299.239960 1.780705
BFGS: 11 19:16:06 -299.374171 1.448885
BFGS: 12 19:16:07 -299.785956 0.964600
BFGS: 13 19:16:07 -299.862364 0.830147
BFGS: 14 19:16:07 -299.873920 0.461770
BFGS: 15 19:16:08 -299.886870 0.278939
BFGS: 16 19:16:08 -299.908138 0.394875
BFGS: 17 19:16:09 -299.917805 0.384146
BFGS: 18 19:16:10 -299.925053 0.360148
BFGS: 19 19:16:10 -299.931768 0.391025
BFGS: 20 19:16:10 -299.942478 0.532314
BFGS: 21 19:16:11 -299.965505 0.910520
BFGS: 22 19:16:11 -300.038789 1.638803
BFGS: 23 19:16:12 -300.003980 1.973907
BFGS: 24 19:16:12 -300.200454 1.438733
BFGS: 25 19:16:13 -300.261594 1.319090
BFGS: 26 19:16:13 -300.326694 1.349491
BFGS: 27 19:16:13 -300.355249 1.393977
BFGS: 28 19:16:14 -300.403980 1.338801
BFGS: 29 19:16:14 -300.435423 1.274195
BFGS: 30 19:16:15 -300.479698 1.020812
BFGS: 31 19:16:15 -300.497406 0.852266
BFGS: 32 19:16:16 -300.525083 0.891079
BFGS: 33 19:16:16 -300.549909 0.888116
BFGS: 34 19:16:17 -300.565199 0.771898
BFGS: 35 19:16:17 -300.571020 0.678034
BFGS: 36 19:16:18 -300.575000 0.687474
BFGS: 37 19:16:18 -300.578565 0.686039
BFGS: 38 19:16:18 -300.581989 0.656972
BFGS: 39 19:16:19 -300.584273 0.597492
BFGS: 40 19:16:19 -300.585536 0.553093
BFGS: 41 19:16:20 -300.586450 0.517228
BFGS: 42 19:16:20 -300.587438 0.530701
BFGS: 43 19:16:21 -300.588433 0.540821
BFGS: 44 19:16:21 -300.589111 0.520519
BFGS: 45 19:16:21 -300.589427 0.528153
BFGS: 46 19:16:22 -300.589617 0.541644
BFGS: 47 19:16:23 -300.589780 0.545126
BFGS: 48 19:16:23 -300.589965 0.546266
BFGS: 49 19:16:24 -300.590133 0.537386
BFGS: 50 19:16:24 -300.590231 0.528694
BFGS: 51 19:16:24 -300.590283 0.522326
BFGS: 52 19:16:25 -300.590328 0.519180
BFGS: 53 19:16:25 -300.590385 0.518791
BFGS: 54 19:16:25 -300.590450 0.523376
BFGS: 55 19:16:26 -300.590495 0.530411
BFGS: 56 19:16:26 -300.590524 0.536080
BFGS: 57 19:16:27 -300.590548 0.539938
BFGS: 58 19:16:27 -300.590578 0.542955
BFGS: 59 19:16:27 -300.590614 0.543680
BFGS: 60 19:16:28 -300.590638 0.541652
BFGS: 61 19:16:28 -300.590647 0.539024
BFGS: 62 19:16:28 -300.590656 0.536904
BFGS: 63 19:16:29 -300.590666 0.534986
BFGS: 64 19:16:29 -300.590676 0.534023
BFGS: 65 19:16:30 -300.590682 0.534542
BFGS: 66 19:16:30 -300.590686 0.535690
BFGS: 67 19:16:31 -300.590688 0.536644
BFGS: 68 19:16:31 -300.590691 0.537414
BFGS: 69 19:16:32 -300.590693 0.537862
BFGS: 70 19:16:32 -300.590696 0.537582
BFGS: 71 19:16:32 -300.590696 0.536863
BFGS: 72 19:16:33 -300.590696 0.536117
BFGS: 73 19:16:34 -300.590697 0.535486
BFGS: 74 19:16:34 -300.590699 0.534972
BFGS: 75 19:16:35 -300.590700 0.534881
BFGS: 76 19:16:35 -300.590700 0.535155
BFGS: 77 19:16:36 -300.590699 0.535515
BFGS: 78 19:16:36 -300.590699 0.535820
BFGS: 79 19:16:37 -300.590702 0.536087
BFGS: 80 19:16:37 -300.590700 0.536265
BFGS: 81 19:16:38 -300.590702 0.536238
BFGS: 82 19:16:38 -300.590702 0.536126
BFGS: 83 19:16:39 -300.590703 0.535991
BFGS: 84 19:16:39 -300.590700 0.535902
BFGS: 85 19:16:39 -300.590702 0.535820
BFGS: 86 19:16:40 -300.590700 0.535836
BFGS: 87 19:16:40 -300.590702 0.535896
BFGS: 88 19:16:41 -300.590702 0.535950
BFGS: 89 19:16:42 -300.590701 0.536009
BFGS: 90 19:16:42 -300.590699 0.536021
BFGS: 91 19:16:42 -300.590701 0.536022
BFGS: 92 19:16:43 -300.590703 0.535998
BFGS: 93 19:16:43 -300.590700 0.535947
BFGS: 94 19:16:44 -300.590702 0.535928
BFGS: 95 19:16:44 -300.590700 0.535898
BFGS: 96 19:16:45 -300.590702 0.535900
BFGS: 97 19:16:45 -300.590702 0.535868
BFGS: 98 19:16:46 -300.590702 0.535910
BFGS: 99 19:16:46 -300.590700 0.535908
BFGS: 100 19:16:47 -300.590703 0.535920
BFGS: 101 19:16:47 -300.590701 0.535929
BFGS: 102 19:16:47 -300.590702 0.535899
BFGS: 103 19:16:47 -300.590700 0.535910
BFGS: 104 19:16:48 -300.590701 0.535921
BFGS: 105 19:16:48 -300.590702 0.535909
BFGS: 106 19:16:49 -300.590700 0.535916
BFGS: 107 19:16:49 -300.590701 0.535905
BFGS: 108 19:16:50 -300.590702 0.535909
BFGS: 109 19:16:50 -300.590701 0.535913
BFGS: 110 19:16:51 -300.590702 0.535911
BFGS: 111 19:16:51 -300.590700 0.535906
BFGS: 112 19:16:51 -300.590700 0.535903
BFGS: 113 19:16:52 -300.590700 0.535921
BFGS: 114 19:16:52 -300.590702 0.535899
BFGS: 115 19:16:53 -300.590702 0.535900
BFGS: 116 19:16:53 -300.590700 0.535906
BFGS: 117 19:16:53 -300.590701 0.535917
BFGS: 118 19:16:54 -300.590701 0.535917
BFGS: 119 19:16:54 -300.590701 0.535907
BFGS: 120 19:16:55 -300.590700 0.535903
BFGS: 121 19:16:55 -300.590701 0.535916
BFGS: 122 19:16:56 -300.590700 0.535903
BFGS: 123 19:16:56 -300.590701 0.535896
BFGS: 124 19:16:57 -300.590702 0.535910
BFGS: 125 19:16:57 -300.590701 0.535907
BFGS: 126 19:16:57 -300.590700 0.535911
BFGS: 127 19:16:58 -300.590700 0.535908
BFGS: 128 19:16:58 -300.590702 0.535903
BFGS: 129 19:16:59 -300.590701 0.535915
BFGS: 130 19:16:59 -300.590702 0.535904
BFGS: 131 19:17:00 -300.590701 0.535909
BFGS: 132 19:17:00 -300.590701 0.535897
BFGS: 133 19:17:01 -300.590702 0.535919
BFGS: 134 19:17:01 -300.590702 0.535904
BFGS: 135 19:17:01 -300.590701 0.535909
BFGS: 136 19:17:02 -300.590702 0.535917
BFGS: 137 19:17:02 -300.590701 0.535900
BFGS: 138 19:17:03 -300.590702 0.535910
BFGS: 139 19:17:03 -300.590702 0.535904
BFGS: 140 19:17:04 -300.590701 0.535917
BFGS: 141 19:17:04 -300.590701 0.535911
BFGS: 142 19:17:05 -300.590702 0.535902
BFGS: 143 19:17:05 -300.590701 0.535904
BFGS: 144 19:17:05 -300.590701 0.535918
BFGS: 145 19:17:06 -300.590699 0.535911
BFGS: 146 19:17:06 -300.590702 0.535900
BFGS: 147 19:17:07 -300.590701 0.535904
BFGS: 148 19:17:07 -300.590702 0.535904
BFGS: 149 19:17:08 -300.590701 0.535899
BFGS: 150 19:17:08 -300.590701 0.535911
BFGS: 151 19:17:09 -300.590700 0.535910
BFGS: 152 19:17:09 -300.590703 0.535896
BFGS: 153 19:17:09 -300.590702 0.535898
BFGS: 154 19:17:10 -300.590702 0.535911
BFGS: 155 19:17:10 -300.590700 0.535905
BFGS: 156 19:17:11 -300.590701 0.535914
BFGS: 157 19:17:11 -300.590700 0.535898
BFGS: 158 19:17:12 -300.590702 0.535912
BFGS: 159 19:17:12 -300.590702 0.535905
BFGS: 160 19:17:12 -300.590700 0.535914
BFGS: 161 19:17:13 -300.590702 0.535907
BFGS: 162 19:17:13 -300.590701 0.535906
BFGS: 163 19:17:14 -300.590702 0.535898
BFGS: 164 19:17:14 -300.590700 0.535913
BFGS: 165 19:17:15 -300.590701 0.535919
BFGS: 166 19:17:15 -300.590702 0.535896
BFGS: 167 19:17:16 -300.590701 0.535898
BFGS: 168 19:17:16 -300.590700 0.535927
BFGS: 169 19:17:16 -300.590700 0.535912
BFGS: 170 19:17:16 -300.590702 0.535911
BFGS: 171 19:17:17 -300.590701 0.535903
BFGS: 172 19:17:17 -300.590701 0.535903
BFGS: 173 19:17:18 -300.590701 0.535897
BFGS: 174 19:17:18 -300.590702 0.535905
BFGS: 175 19:17:19 -300.590701 0.535906
BFGS: 176 19:17:19 -300.590702 0.535914
BFGS: 177 19:17:19 -300.590701 0.535902
BFGS: 178 19:17:20 -300.590702 0.535906
BFGS: 179 19:17:20 -300.590701 0.535900
BFGS: 180 19:17:21 -300.590702 0.535912
BFGS: 181 19:17:21 -300.590702 0.535922
BFGS: 182 19:17:22 -300.590702 0.535905
BFGS: 183 19:17:22 -300.590702 0.535898
BFGS: 184 19:17:22 -300.590702 0.535920
BFGS: 185 19:17:23 -300.590700 0.535921
BFGS: 186 19:17:23 -300.590700 0.535900
BFGS: 187 19:17:24 -300.590700 0.535904
BFGS: 188 19:17:24 -300.590702 0.535918
BFGS: 189 19:17:25 -300.590700 0.535917
BFGS: 190 19:17:25 -300.590701 0.535913
BFGS: 191 19:17:26 -300.590700 0.535910
BFGS: 192 19:17:26 -300.590702 0.535903
BFGS: 193 19:17:26 -300.590701 0.535898
BFGS: 194 19:17:27 -300.590702 0.535901
BFGS: 195 19:17:27 -300.590701 0.535899
BFGS: 196 19:17:28 -300.590700 0.535922
BFGS: 197 19:17:28 -300.590700 0.535911
BFGS: 198 19:17:28 -300.590702 0.535900
BFGS: 199 19:17:29 -300.590702 0.535897
BFGS: 200 19:17:29 -300.590700 0.535921
BFGS: 201 19:17:30 -300.590700 0.535922
BFGS: 202 19:17:30 -300.590702 0.535901
BFGS: 203 19:17:30 -300.590702 0.535900
BFGS: 204 19:17:31 -300.590702 0.535922
BFGS: 205 19:17:31 -300.590701 0.535911
BFGS: 206 19:17:32 -300.590702 0.535904
BFGS: 207 19:17:32 -300.590702 0.535900
BFGS: 208 19:17:32 -300.590701 0.535917
BFGS: 209 19:17:33 -300.590699 0.535922
BFGS: 210 19:17:33 -300.590701 0.535898
BFGS: 211 19:17:33 -300.590701 0.535904
BFGS: 212 19:17:34 -300.590702 0.535905
BFGS: 213 19:17:34 -300.590701 0.535904
BFGS: 214 19:17:34 -300.590699 0.535904
BFGS: 215 19:17:35 -300.590701 0.535905
BFGS: 216 19:17:35 -300.590702 0.535913
BFGS: 217 19:17:36 -300.590702 0.535898
BFGS: 218 19:17:36 -300.590699 0.535903
BFGS: 219 19:17:36 -300.590702 0.535921
BFGS: 220 19:17:37 -300.590701 0.535900
BFGS: 221 19:17:37 -300.590700 0.535910
BFGS: 222 19:17:38 -300.590701 0.535923
BFGS: 223 19:17:38 -300.590701 0.535927
BFGS: 224 19:17:38 -300.590702 0.535897
BFGS: 225 19:17:39 -300.590700 0.535904
BFGS: 226 19:17:39 -300.590702 0.535905
BFGS: 227 19:17:39 -300.590701 0.535906
BFGS: 228 19:17:40 -300.590702 0.535898
BFGS: 229 19:17:40 -300.590700 0.535910
BFGS: 230 19:17:41 -300.590702 0.535912
BFGS: 231 19:17:41 -300.590700 0.535909
BFGS: 232 19:17:42 -300.590701 0.535904
BFGS: 233 19:17:42 -300.590702 0.535920
BFGS: 234 19:17:42 -300.590701 0.535917
BFGS: 235 19:17:43 -300.590702 0.535909
BFGS: 236 19:17:43 -300.590702 0.535910
BFGS: 237 19:17:44 -300.590699 0.535921
BFGS: 238 19:17:44 -300.590702 0.535907
BFGS: 239 19:17:45 -300.590699 0.535918
BFGS: 240 19:17:45 -300.590701 0.535910
BFGS: 241 19:17:45 -300.590702 0.535914
BFGS: 242 19:17:46 -300.590702 0.535914
BFGS: 243 19:17:46 -300.590701 0.535903
BFGS: 244 19:17:47 -300.590701 0.535909
BFGS: 245 19:17:48 -300.590702 0.535914
BFGS: 246 19:17:48 -300.590701 0.535919
BFGS: 247 19:17:49 -300.590702 0.535908
BFGS: 248 19:17:49 -300.590703 0.535909
BFGS: 249 19:17:49 -300.590701 0.535913
BFGS: 250 19:17:50 -300.590700 0.535917
BFGS: 251 19:17:50 -300.590702 0.535900
BFGS: 252 19:17:50 -300.590702 0.535909
BFGS: 253 19:17:51 -300.590701 0.535914
BFGS: 254 19:17:51 -300.590700 0.535911
BFGS: 255 19:17:52 -300.590700 0.535903
BFGS: 256 19:17:52 -300.590702 0.535910
BFGS: 257 19:17:53 -300.590700 0.535912
BFGS: 258 19:17:53 -300.590702 0.535903
BFGS: 259 19:17:54 -300.590701 0.535906
BFGS: 260 19:17:54 -300.590700 0.535909
BFGS: 261 19:17:55 -300.590700 0.535910
BFGS: 262 19:17:55 -300.590699 0.535909
BFGS: 263 19:17:55 -300.590702 0.535904
BFGS: 264 19:17:56 -300.590701 0.535919
BFGS: 265 19:17:56 -300.590699 0.535913
BFGS: 266 19:17:57 -300.590702 0.535909
BFGS: 267 19:17:57 -300.590699 0.535911
BFGS: 268 19:17:58 -300.590702 0.535913
BFGS: 269 19:17:58 -300.590701 0.535900
BFGS: 270 19:17:58 -300.590702 0.535906
BFGS: 271 19:17:58 -300.590699 0.535910
BFGS: 272 19:17:59 -300.590702 0.535910
BFGS: 273 19:17:59 -300.590700 0.535909
BFGS: 274 19:18:00 -300.590700 0.535911
BFGS: 275 19:18:00 -300.590701 0.535913
BFGS: 276 19:18:00 -300.590702 0.535900
BFGS: 277 19:18:01 -300.590700 0.535859
BFGS: 278 19:18:01 -300.590700 0.535909
BFGS: 279 19:18:02 -300.590699 0.535913
BFGS: 280 19:18:02 -300.590702 0.535909
BFGS: 281 19:18:03 -300.590702 0.535898
BFGS: 282 19:18:03 -300.590702 0.535904
BFGS: 283 19:18:04 -300.590702 0.535898
BFGS: 284 19:18:04 -300.590702 0.535904
BFGS: 285 19:18:05 -300.590701 0.535903
BFGS: 286 19:18:05 -300.590702 0.535904
BFGS: 287 19:18:05 -300.590700 0.535911
BFGS: 288 19:18:06 -300.590702 0.535903
BFGS: 289 19:18:06 -300.590700 0.535909
BFGS: 290 19:18:07 -300.590702 0.535905
BFGS: 291 19:18:07 -300.590702 0.535899
BFGS: 292 19:18:08 -300.590702 0.535909
BFGS: 293 19:18:08 -300.590701 0.535906
BFGS: 294 19:18:09 -300.590702 0.535904
BFGS: 295 19:18:09 -300.590699 0.535917
BFGS: 296 19:18:10 -300.590702 0.535906
BFGS: 297 19:18:10 -300.590700 0.535904
BFGS: 298 19:18:10 -300.590701 0.535909
BFGS: 299 19:18:11 -300.590702 0.535905
BFGS: 300 19:18:12 -300.590702 0.535905
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 19:18:12 -295.171043 1.552835
BFGS: 1 19:18:12 -295.271140 1.404952
BFGS: 2 19:18:13 -295.456149 2.239829
BFGS: 3 19:18:13 -295.538812 0.467623
BFGS: 4 19:18:14 -295.552929 0.583775
BFGS: 5 19:18:14 -295.574823 0.555681
BFGS: 6 19:18:15 -295.585631 0.314094
BFGS: 7 19:18:15 -295.591007 0.261293
BFGS: 8 19:18:16 -295.596008 0.311699
BFGS: 9 19:18:16 -295.600951 0.285263
BFGS: 10 19:18:17 -295.605161 0.202145
BFGS: 11 19:18:17 -295.606978 0.151896
BFGS: 12 19:18:18 -295.607790 0.179378
BFGS: 13 19:18:18 -295.609357 0.241646
BFGS: 14 19:18:19 -295.613656 0.374652
BFGS: 15 19:18:19 -295.641502 0.739805
BFGS: 16 19:18:19 -295.715981 0.768273
BFGS: 17 19:18:20 -295.780992 0.543517
BFGS: 18 19:18:20 -295.794460 0.623697
BFGS: 19 19:18:21 -295.824380 0.324854
BFGS: 20 19:18:21 -295.843055 0.315833
BFGS: 21 19:18:21 -295.846541 0.283032
BFGS: 22 19:18:22 -295.849826 0.226912
BFGS: 23 19:18:22 -295.854777 0.132383
BFGS: 24 19:18:22 -295.858206 0.140712
BFGS: 25 19:18:23 -295.860033 0.150327
BFGS: 26 19:18:23 -295.861336 0.156020
BFGS: 27 19:18:23 -295.863447 0.160904
BFGS: 28 19:18:24 -295.866367 0.171700
BFGS: 29 19:18:24 -295.869924 0.207480
BFGS: 30 19:18:25 -295.874026 0.265242
BFGS: 31 19:18:25 -295.880280 0.340481
BFGS: 32 19:18:26 -295.893731 0.444346
BFGS: 33 19:18:26 -295.901849 0.388973
BFGS: 34 19:18:26 -295.922603 0.363912
BFGS: 35 19:18:27 -295.945148 0.249400
BFGS: 36 19:18:27 -295.955018 0.220219
BFGS: 37 19:18:28 -295.958100 0.197965
BFGS: 38 19:18:28 -295.963464 0.119908
BFGS: 39 19:18:29 -295.966451 0.067437
BFGS: 40 19:18:29 -295.967550 0.048585
Step Time Energy fmax
BFGS: 0 19:18:29 -295.097398 1.782214
BFGS: 1 19:18:30 -295.216761 1.603826
BFGS: 2 19:18:30 -295.378479 2.798031
BFGS: 3 19:18:31 -295.497824 0.490952
BFGS: 4 19:18:31 -295.516817 0.604504
BFGS: 5 19:18:31 -295.535957 0.675417
BFGS: 6 19:18:32 -295.554914 0.491579
BFGS: 7 19:18:32 -295.562760 0.204147
BFGS: 8 19:18:33 -295.567354 0.268394
BFGS: 9 19:18:33 -295.573265 0.298295
BFGS: 10 19:18:34 -295.577173 0.230422
BFGS: 11 19:18:34 -295.579549 0.106761
BFGS: 12 19:18:34 -295.579939 0.024363
Step Time Energy fmax
BFGS: 0 19:18:35 -295.160140 1.577400
BFGS: 1 19:18:35 -295.262085 1.425932
BFGS: 2 19:18:35 -295.444965 2.287382
BFGS: 3 19:18:36 -295.530727 0.455862
BFGS: 4 19:18:36 -295.545214 0.585315
BFGS: 5 19:18:36 -295.566456 0.574624
BFGS: 6 19:18:37 -295.577904 0.338616
BFGS: 7 19:18:37 -295.583303 0.245391
BFGS: 8 19:18:38 -295.587952 0.301145
BFGS: 9 19:18:38 -295.592551 0.279919
BFGS: 10 19:18:39 -295.596361 0.186339
BFGS: 11 19:18:39 -295.597881 0.111048
BFGS: 12 19:18:39 -295.598354 0.123231
BFGS: 13 19:18:40 -295.599006 0.152891
BFGS: 14 19:18:40 -295.600578 0.212070
BFGS: 15 19:18:41 -295.605146 0.325969
BFGS: 16 19:18:41 -295.626243 0.488766
BFGS: 17 19:18:42 -295.686325 0.754116
BFGS: 18 19:18:42 -295.726065 0.668256
BFGS: 19 19:18:43 -295.749808 0.590412
BFGS: 20 19:18:43 -295.830488 0.454262
BFGS: 21 19:18:43 -295.824557 0.618787
BFGS: 22 19:18:44 -295.848784 0.387026
BFGS: 23 19:18:44 -295.853692 0.338948
BFGS: 24 19:18:45 -295.871444 0.264564
BFGS: 25 19:18:45 -295.874509 0.264076
BFGS: 26 19:18:46 -295.881718 0.242218
BFGS: 27 19:18:46 -295.887655 0.223552
BFGS: 28 19:18:47 -295.894108 0.228321
BFGS: 29 19:18:47 -295.898563 0.247527
BFGS: 30 19:18:48 -295.903737 0.265532
BFGS: 31 19:18:48 -295.910720 0.261305
BFGS: 32 19:18:48 -295.918026 0.214920
BFGS: 33 19:18:49 -295.924341 0.162407
BFGS: 34 19:18:49 -295.928229 0.134118
BFGS: 35 19:18:49 -295.930228 0.122612
BFGS: 36 19:18:49 -295.932574 0.090136
BFGS: 37 19:18:50 -295.934562 0.063472
BFGS: 38 19:18:50 -295.935661 0.050395
BFGS: 39 19:18:51 -295.936129 0.046061
Step Time Energy fmax
BFGS: 0 19:18:51 -295.309796 1.281793
BFGS: 1 19:18:51 -295.388826 1.169553
BFGS: 2 19:18:52 -295.597501 1.470078
BFGS: 3 19:18:52 -295.637847 0.568084
BFGS: 4 19:18:52 -295.648344 0.510657
BFGS: 5 19:18:53 -295.683257 0.459662
BFGS: 6 19:18:53 -295.689099 0.461722
BFGS: 7 19:18:53 -295.741987 0.767402
BFGS: 8 19:18:54 -295.757851 0.562019
BFGS: 9 19:18:54 -295.781227 0.698271
BFGS: 10 19:18:55 -295.797827 0.681720
BFGS: 11 19:18:55 -295.823353 0.443883
BFGS: 12 19:18:55 -295.830002 0.315096
BFGS: 13 19:18:56 -295.837090 0.206119
BFGS: 14 19:18:56 -295.838780 0.192967
BFGS: 15 19:18:57 -295.840920 0.203642
BFGS: 16 19:18:57 -295.843112 0.186585
BFGS: 17 19:18:58 -295.845071 0.114184
BFGS: 18 19:18:58 -295.845966 0.081843
BFGS: 19 19:18:58 -295.846386 0.081388
BFGS: 20 19:18:59 -295.846765 0.083935
BFGS: 21 19:18:59 -295.847513 0.096635
BFGS: 22 19:19:00 -295.848732 0.118682
BFGS: 23 19:19:00 -295.850213 0.110086
BFGS: 24 19:19:00 -295.851686 0.124484
BFGS: 25 19:19:01 -295.853883 0.152377
BFGS: 26 19:19:01 -295.858649 0.284026
BFGS: 27 19:19:02 -295.872531 0.535767
BFGS: 28 19:19:02 -295.883495 0.674895
BFGS: 29 19:19:02 -295.897539 0.632814
BFGS: 30 19:19:03 -295.921321 0.351686
BFGS: 31 19:19:03 -295.939416 0.279675
BFGS: 32 19:19:03 -295.953733 0.164489
BFGS: 33 19:19:04 -295.957215 0.141604
BFGS: 34 19:19:04 -295.961577 0.119143
BFGS: 35 19:19:05 -295.964484 0.086698
BFGS: 36 19:19:05 -295.967104 0.047965
Step Time Energy fmax
BFGS: 0 19:19:05 -295.631138 0.748114
BFGS: 1 19:19:06 -295.681469 0.664581
BFGS: 2 19:19:06 -295.851315 0.297271
BFGS: 3 19:19:07 -295.864428 0.339522
BFGS: 4 19:19:07 -295.867290 0.331385
BFGS: 5 19:19:08 -295.888596 0.239662
BFGS: 6 19:19:08 -295.891974 0.223369
BFGS: 7 19:19:08 -295.898525 0.215391
BFGS: 8 19:19:09 -295.903454 0.248192
BFGS: 9 19:19:09 -295.909055 0.308224
BFGS: 10 19:19:09 -295.913304 0.327528
BFGS: 11 19:19:10 -295.917587 0.298430
BFGS: 12 19:19:10 -295.921905 0.226804
BFGS: 13 19:19:11 -295.926340 0.132445
BFGS: 14 19:19:11 -295.929392 0.169543
BFGS: 15 19:19:12 -295.931194 0.182259
BFGS: 16 19:19:12 -295.932834 0.164344
BFGS: 17 19:19:12 -295.934541 0.112388
BFGS: 18 19:19:13 -295.935804 0.058939
BFGS: 19 19:19:13 -295.936349 0.031530
Step Time Energy fmax
BFGS: 0 19:19:14 -295.296241 1.304613
BFGS: 1 19:19:14 -295.376824 1.188830
BFGS: 2 19:19:14 -295.583881 1.527789
BFGS: 3 19:19:15 -295.626924 0.563262
BFGS: 4 19:19:15 -295.637461 0.519553
BFGS: 5 19:19:16 -295.670951 0.430759
BFGS: 6 19:19:16 -295.676499 0.440307
BFGS: 7 19:19:16 -295.713127 0.653890
BFGS: 8 19:19:17 -295.730566 0.625978
BFGS: 9 19:19:17 -295.756263 0.698538
BFGS: 10 19:19:17 -295.770486 0.741274
BFGS: 11 19:19:18 -295.808163 0.585321
BFGS: 12 19:19:18 -295.818853 0.403771
BFGS: 13 19:19:19 -295.829952 0.212708
BFGS: 14 19:19:19 -295.833617 0.194869
BFGS: 15 19:19:19 -295.835323 0.222233
BFGS: 16 19:19:20 -295.837757 0.218663
BFGS: 17 19:19:20 -295.839815 0.157882
BFGS: 18 19:19:21 -295.841036 0.073101
BFGS: 19 19:19:21 -295.841502 0.042769
Step Time Energy fmax
BFGS: 0 19:19:21 -295.119663 1.695375
BFGS: 1 19:19:22 -295.232011 1.529099
BFGS: 2 19:19:22 -295.401352 2.623435
BFGS: 3 19:19:23 -295.509131 0.436857
BFGS: 4 19:19:23 -295.526570 0.599540
BFGS: 5 19:19:23 -295.546323 0.647074
BFGS: 6 19:19:24 -295.562006 0.442400
BFGS: 7 19:19:24 -295.568622 0.206622
BFGS: 8 19:19:24 -295.573095 0.281210
BFGS: 9 19:19:25 -295.577971 0.291038
BFGS: 10 19:19:25 -295.581780 0.206093
BFGS: 11 19:19:26 -295.583635 0.086639
BFGS: 12 19:19:26 -295.583923 0.036332
Step Time Energy fmax
BFGS: 0 19:19:26 -295.497634 1.010698
BFGS: 1 19:19:27 -295.558349 0.945148
BFGS: 2 19:19:27 -295.767463 0.827863
BFGS: 3 19:19:27 -295.789185 0.513353
BFGS: 4 19:19:28 -295.799514 0.529239
BFGS: 5 19:19:28 -295.851927 0.569034
BFGS: 6 19:19:28 -295.864074 0.570939
BFGS: 7 19:19:29 -295.916337 0.539000
BFGS: 8 19:19:29 -295.929952 0.361275
BFGS: 9 19:19:29 -295.940609 0.351262
BFGS: 10 19:19:30 -295.945113 0.306529
BFGS: 11 19:19:30 -295.951254 0.246958
BFGS: 12 19:19:31 -295.957248 0.171592
BFGS: 13 19:19:31 -295.960642 0.166827
BFGS: 14 19:19:31 -295.962337 0.151124
BFGS: 15 19:19:32 -295.963709 0.116051
BFGS: 16 19:19:32 -295.965310 0.075269
BFGS: 17 19:19:32 -295.966892 0.049565
Step Time Energy fmax
BFGS: 0 19:19:33 -295.283185 1.331253
BFGS: 1 19:19:33 -295.364626 1.211610
BFGS: 2 19:19:34 -295.568362 1.570181
BFGS: 3 19:19:34 -295.613327 0.553939
BFGS: 4 19:19:35 -295.623748 0.525251
BFGS: 5 19:19:35 -295.655074 0.387431
BFGS: 6 19:19:35 -295.660222 0.405878
BFGS: 7 19:19:35 -295.681767 0.478585
BFGS: 8 19:19:36 -295.696722 0.575842
BFGS: 9 19:19:36 -295.721035 0.579480
BFGS: 10 19:19:36 -295.739254 0.798867
BFGS: 11 19:19:37 -295.766722 1.003320
BFGS: 12 19:19:37 -295.797632 0.892622
BFGS: 13 19:19:38 -295.842873 0.528136
BFGS: 14 19:19:38 -295.859643 0.289867
BFGS: 15 19:19:39 -295.867217 0.362520
BFGS: 16 19:19:39 -295.872923 0.406332
BFGS: 17 19:19:39 -295.880906 0.386364
BFGS: 18 19:19:39 -295.890783 0.257436
BFGS: 19 19:19:40 -295.897203 0.257940
BFGS: 20 19:19:40 -295.901868 0.242883
BFGS: 21 19:19:40 -295.905431 0.235463
BFGS: 22 19:19:41 -295.910982 0.309814
BFGS: 23 19:19:41 -295.919381 0.309024
BFGS: 24 19:19:41 -295.925323 0.175983
BFGS: 25 19:19:42 -295.928825 0.124997
BFGS: 26 19:19:42 -295.930597 0.091523
BFGS: 27 19:19:42 -295.932110 0.089018
BFGS: 28 19:19:43 -295.933828 0.086149
BFGS: 29 19:19:43 -295.935271 0.056637
BFGS: 30 19:19:43 -295.935940 0.038079
Step Time Energy fmax
BFGS: 0 19:19:44 -295.616319 0.736842
BFGS: 1 19:19:44 -295.668417 0.657051
BFGS: 2 19:19:45 -295.848458 0.382066
BFGS: 3 19:19:45 -295.864153 0.431650
BFGS: 4 19:19:45 -295.869148 0.425220
BFGS: 5 19:19:45 -295.907024 0.358477
BFGS: 6 19:19:46 -295.910998 0.322052
BFGS: 7 19:19:46 -295.925760 0.183249
BFGS: 8 19:19:47 -295.926878 0.182375
BFGS: 9 19:19:47 -295.929528 0.165345
BFGS: 10 19:19:47 -295.931495 0.129754
BFGS: 11 19:19:48 -295.932878 0.088277
BFGS: 12 19:19:48 -295.933616 0.081012
BFGS: 13 19:19:48 -295.934153 0.095061
BFGS: 14 19:19:49 -295.934846 0.094295
BFGS: 15 19:19:49 -295.935709 0.075791
BFGS: 16 19:19:50 -295.936349 0.049730
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 19:19:50 -303.714907 0.929596
BFGS: 1 19:19:51 -303.737850 0.701083
BFGS: 2 19:19:51 -303.786774 0.582224
BFGS: 3 19:19:51 -303.814515 0.679529
BFGS: 4 19:19:52 -303.844908 0.789887
BFGS: 5 19:19:52 -303.868074 0.586145
BFGS: 6 19:19:52 -303.906583 0.274623
BFGS: 7 19:19:53 -303.910139 0.264005
BFGS: 8 19:19:53 -303.916177 0.143545
BFGS: 9 19:19:54 -303.919268 0.124721
BFGS: 10 19:19:54 -303.920933 0.110481
BFGS: 11 19:19:55 -303.921999 0.149512
BFGS: 12 19:19:55 -303.923175 0.152299
BFGS: 13 19:19:55 -303.924317 0.108979
BFGS: 14 19:19:56 -303.925228 0.111471
BFGS: 15 19:19:56 -303.925828 0.086226
BFGS: 16 19:19:56 -303.926273 0.093723
BFGS: 17 19:19:57 -303.926776 0.086602
BFGS: 18 19:19:57 -303.927443 0.119423
BFGS: 19 19:19:58 -303.928305 0.142964
BFGS: 20 19:19:58 -303.929043 0.106619
BFGS: 21 19:19:58 -303.929398 0.046964
Step Time Energy fmax
BFGS: 0 19:19:59 -304.433350 0.275735
BFGS: 1 19:19:59 -304.436714 0.222458
BFGS: 2 19:20:00 -304.448592 0.126996
BFGS: 3 19:20:00 -304.451295 0.106044
BFGS: 4 19:20:00 -304.452635 0.070914
BFGS: 5 19:20:01 -304.453115 0.060697
BFGS: 6 19:20:01 -304.453623 0.053787
BFGS: 7 19:20:01 -304.454136 0.051241
BFGS: 8 19:20:02 -304.454531 0.056595
BFGS: 9 19:20:02 -304.454800 0.050063
BFGS: 10 19:20:03 -304.455023 0.044288
Step Time Energy fmax
BFGS: 0 19:20:03 -304.434692 0.248835
BFGS: 1 19:20:03 -304.438370 0.224641
BFGS: 2 19:20:04 -304.449070 0.132755
BFGS: 3 19:20:04 -304.451655 0.100184
BFGS: 4 19:20:05 -304.452967 0.077667
BFGS: 5 19:20:05 -304.453566 0.077579
BFGS: 6 19:20:05 -304.454218 0.069822
BFGS: 7 19:20:06 -304.454823 0.058071
BFGS: 8 19:20:06 -304.455272 0.076657
BFGS: 9 19:20:07 -304.455559 0.065723
BFGS: 10 19:20:07 -304.455789 0.040161
Step Time Energy fmax
BFGS: 0 19:20:08 -303.801845 1.299975
BFGS: 1 19:20:08 -303.841827 0.768833
BFGS: 2 19:20:08 -303.880440 0.707828
BFGS: 3 19:20:09 -303.908837 0.917772
BFGS: 4 19:20:09 -304.001155 1.707825
BFGS: 5 19:20:09 -304.045328 1.118867
BFGS: 6 19:20:10 -304.130223 0.814605
BFGS: 7 19:20:10 -304.193478 1.132836
BFGS: 8 19:20:10 -304.219617 0.782650
BFGS: 9 19:20:11 -304.301461 0.734285
BFGS: 10 19:20:11 -304.368723 1.627063
BFGS: 11 19:20:11 -304.424723 1.665620
BFGS: 12 19:20:12 -304.497492 0.916708
BFGS: 13 19:20:12 -304.551195 0.737998
BFGS: 14 19:20:12 -304.574895 0.975242
BFGS: 15 19:20:13 -304.581785 0.814225
BFGS: 16 19:20:13 -304.597768 0.411013
BFGS: 17 19:20:14 -304.607684 0.412517
BFGS: 18 19:20:14 -304.647364 0.489580
BFGS: 19 19:20:14 -304.659772 0.325702
BFGS: 20 19:20:15 -304.668103 0.261809
BFGS: 21 19:20:15 -304.675227 0.230823
BFGS: 22 19:20:16 -304.682429 0.192690
BFGS: 23 19:20:16 -304.686371 0.139135
BFGS: 24 19:20:16 -304.688034 0.115419
BFGS: 25 19:20:17 -304.689055 0.094603
BFGS: 26 19:20:18 -304.690258 0.071198
BFGS: 27 19:20:18 -304.691035 0.053145
BFGS: 28 19:20:19 -304.691448 0.049280
Step Time Energy fmax
BFGS: 0 19:20:19 -303.942255 0.300526
BFGS: 1 19:20:19 -303.946802 0.230845
BFGS: 2 19:20:20 -303.956201 0.134515
BFGS: 3 19:20:20 -303.958664 0.120342
BFGS: 4 19:20:20 -303.960287 0.097201
BFGS: 5 19:20:21 -303.961236 0.080144
BFGS: 6 19:20:21 -303.962097 0.078601
BFGS: 7 19:20:22 -303.962864 0.070900
BFGS: 8 19:20:22 -303.963469 0.077429
BFGS: 9 19:20:22 -303.963825 0.063220
BFGS: 10 19:20:23 -303.964028 0.034549
Step Time Energy fmax
BFGS: 0 19:20:23 -303.945453 0.266733
BFGS: 1 19:20:24 -303.948720 0.202784
BFGS: 2 19:20:24 -303.956616 0.125990
BFGS: 3 19:20:24 -303.958882 0.127758
BFGS: 4 19:20:25 -303.960577 0.101897
BFGS: 5 19:20:25 -303.961449 0.070669
BFGS: 6 19:20:26 -303.962145 0.058575
BFGS: 7 19:20:26 -303.962772 0.064213
BFGS: 8 19:20:26 -303.963314 0.078621
BFGS: 9 19:20:27 -303.963696 0.062529
BFGS: 10 19:20:27 -303.963948 0.039048
Step Time Energy fmax
BFGS: 0 19:20:27 -303.180634 0.887952
BFGS: 1 19:20:28 -303.205718 0.726757
BFGS: 2 19:20:28 -303.274564 0.699145
BFGS: 3 19:20:28 -303.309201 0.706486
BFGS: 4 19:20:28 -303.340716 0.752353
BFGS: 5 19:20:29 -303.371401 0.559117
BFGS: 6 19:20:29 -303.416531 0.404562
BFGS: 7 19:20:29 -303.420608 0.301308
BFGS: 8 19:20:30 -303.429842 0.171799
BFGS: 9 19:20:30 -303.432485 0.191250
BFGS: 10 19:20:30 -303.434653 0.170013
BFGS: 11 19:20:31 -303.436763 0.191074
BFGS: 12 19:20:31 -303.438647 0.139995
BFGS: 13 19:20:32 -303.439964 0.128383
BFGS: 14 19:20:32 -303.441061 0.110223
BFGS: 15 19:20:32 -303.441794 0.082671
BFGS: 16 19:20:32 -303.442488 0.078086
BFGS: 17 19:20:33 -303.443249 0.098411
BFGS: 18 19:20:33 -303.444002 0.114556
BFGS: 19 19:20:34 -303.444549 0.078539
BFGS: 20 19:20:34 -303.444809 0.055238
BFGS: 21 19:20:34 -303.444954 0.047841
Step Time Energy fmax
BFGS: 0 19:20:35 -303.243055 3.041630
BFGS: 1 19:20:35 -303.426060 1.591164
BFGS: 2 19:20:36 -303.530994 0.976552
BFGS: 3 19:20:36 -303.583838 0.859716
BFGS: 4 19:20:36 -303.660717 1.034415
BFGS: 5 19:20:37 -303.707040 1.143044
BFGS: 6 19:20:37 -303.774271 1.065016
BFGS: 7 19:20:37 -303.886174 0.922414
BFGS: 8 19:20:37 -303.949520 1.420234
BFGS: 9 19:20:38 -304.006722 1.434223
BFGS: 10 19:20:38 -304.143235 1.079488
BFGS: 11 19:20:39 -304.165522 0.687568
BFGS: 12 19:20:39 -304.190568 0.594667
BFGS: 13 19:20:39 -304.225499 0.639525
BFGS: 14 19:20:40 -304.258347 0.512451
BFGS: 15 19:20:40 -304.280042 0.388996
BFGS: 16 19:20:41 -304.293062 0.339475
BFGS: 17 19:20:41 -304.306795 0.425391
BFGS: 18 19:20:41 -304.323913 0.498068
BFGS: 19 19:20:42 -304.339740 0.360429
BFGS: 20 19:20:42 -304.347384 0.285932
BFGS: 21 19:20:43 -304.351890 0.216430
BFGS: 22 19:20:43 -304.354160 0.226852
BFGS: 23 19:20:43 -304.355531 0.133063
BFGS: 24 19:20:44 -304.356066 0.051467
BFGS: 25 19:20:44 -304.356352 0.046067
/home/runner/work/_tool/Python/3.12.12/x64/lib/python3.12/site-packages/fairchem/applications/cattsunami/core/autoframe.py:1551: UserWarning: torch.range is deprecated and will be removed in a future release because its behavior is inconsistent with Python's range builtin. Instead, use torch.arange, which produces values in [start, end).
alpha = torch.range(0, num_frames - 1, device=device) / (num_frames - 1)
Run NEBs¶
## This will run all NEBs enumerated - to just run one, run the code cell below.
# On GPU, each NEB takes an average of ~1 minute so this could take around a half hour on GPU
# But much longer on CPU
# Remember that not all NEBs will converge -- the k, nframes would be adjusted to achieve convergence
fmax = 0.05 # [eV / ang**2]
delta_fmax_climb = 0.4
converged_idxs = []
for idx, frame_set in enumerate(frame_sets):
neb = DyNEB(frame_set, k=1)
for image in frame_set:
image.calc = FAIRChemCalculator(predictor, task_name="oc20")
optimizer = BFGS(
neb,
trajectory=f"ch_dissoc_on_Ru_{idx}.traj",
)
conv = optimizer.run(fmax=fmax + delta_fmax_climb, steps=optimization_steps)
if conv:
neb.climb = True
conv = optimizer.run(fmax=fmax, steps=optimization_steps)
if conv:
converged_idxs.append(idx)
print(converged_idxs)This cell will run a shorter calculations for just a single one of the enumerated transition state pathways. You can adapt this code to run transition state searches via nudged elastic band (NEB) calculations for any reaction.
# If you run the above cell -- dont run this one
fmax = 0.05 # [eV / ang**2]
delta_fmax_climb = 0.4
images = frame_sets[0]
neb = DyNEB(images, k=1)
for image in images:
image.calc = FAIRChemCalculator(predictor, task_name="oc20")
optimizer = BFGS(
neb,
trajectory="ch_dissoc_on_Ru_0.traj",
)
conv = optimizer.run(fmax=fmax + delta_fmax_climb, steps=optimization_steps)
if conv:
neb.climb = True
conv = optimizer.run(fmax=fmax, steps=optimization_steps) Step Time Energy fmax
BFGS: 0 19:21:34 -303.011788 3.696740
BFGS: 1 19:21:38 -303.135071 2.872989
BFGS: 2 19:21:41 -303.339503 11.071499
BFGS: 3 19:21:43 -303.308315 1.993122
BFGS: 4 19:21:47 -303.366484 1.692478
BFGS: 5 19:21:50 -303.504461 2.642542
BFGS: 6 19:21:52 -303.536043 1.038063
BFGS: 7 19:21:56 -303.601513 0.922081
BFGS: 8 19:21:59 -303.626080 0.920036
BFGS: 9 19:22:02 -303.665217 0.593949
BFGS: 10 19:22:06 -303.682075 0.649364
BFGS: 11 19:22:13 -303.694324 0.462832
BFGS: 12 19:22:16 -303.691847 0.400078
BFGS: 13 19:22:19 -303.687705 0.380448
BFGS: 14 19:22:24 -303.688146 0.348373
BFGS: 15 19:22:26 -303.686076 0.292962
BFGS: 16 19:22:28 -303.681808 0.230670
BFGS: 17 19:22:33 -303.678081 0.172262
BFGS: 18 19:22:36 -303.676437 0.132752
BFGS: 19 19:22:38 -303.675701 0.136490
BFGS: 20 19:22:41 -303.675060 0.117915
BFGS: 21 19:22:44 -303.674848 0.113669
BFGS: 22 19:22:46 -303.675182 0.116318
BFGS: 23 19:22:52 -303.675974 0.108578
BFGS: 24 19:22:57 -303.676967 0.123860
BFGS: 25 19:23:01 -303.676719 0.113012
BFGS: 26 19:23:03 -303.676167 0.111815
BFGS: 27 19:23:05 -303.675527 0.137264
BFGS: 28 19:23:11 -303.675527 0.091267
BFGS: 29 19:23:13 -303.675527 0.056347
BFGS: 30 19:23:18 -303.675527 0.053138
BFGS: 31 19:23:19 -303.675527 0.037649
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_10358/3247994494.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")