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 22:42:14 -300.885256 4.036973
BFGS: 1 22:42:14 -301.278400 3.438302
BFGS: 2 22:42:14 -302.422891 3.423166
BFGS: 3 22:42:14 -302.192101 8.717020
BFGS: 4 22:42:14 -302.727058 2.856669
BFGS: 5 22:42:14 -302.878867 1.989686
BFGS: 6 22:42:14 -303.013329 2.152452
BFGS: 7 22:42:15 -303.059602 0.827330
BFGS: 8 22:42:15 -303.098738 0.732579
BFGS: 9 22:42:15 -303.158770 1.435822
BFGS: 10 22:42:15 -303.177582 0.877205
BFGS: 11 22:42:15 -303.192659 0.132653
BFGS: 12 22:42:15 -303.194067 0.137350
BFGS: 13 22:42:15 -303.195758 0.114233
BFGS: 14 22:42:15 -303.197530 0.079238
BFGS: 15 22:42:15 -303.198725 0.087037
BFGS: 16 22:42:15 -303.199236 0.073548
BFGS: 17 22:42:15 -303.199489 0.058366
BFGS: 18 22:42:15 -303.199936 0.053759
BFGS: 19 22:42:16 -303.200661 0.080606
BFGS: 20 22:42:16 -303.201531 0.086642
BFGS: 21 22:42:16 -303.202158 0.082135
BFGS: 22 22:42:16 -303.202606 0.083173
BFGS: 23 22:42:16 -303.203194 0.084205
BFGS: 24 22:42:16 -303.204658 0.113635
BFGS: 25 22:42:16 -303.209453 0.215496
BFGS: 26 22:42:16 -303.222780 0.517843
BFGS: 27 22:42:16 -303.240453 0.977038
BFGS: 28 22:42:16 -303.249747 1.459819
BFGS: 29 22:42:16 -303.229457 1.339162
BFGS: 30 22:42:17 -303.258091 1.521025
BFGS: 31 22:42:17 -303.262596 1.356936
BFGS: 32 22:42:17 -303.269259 1.371653
BFGS: 33 22:42:17 -303.274762 1.406020
BFGS: 34 22:42:17 -303.283442 1.456196
BFGS: 35 22:42:17 -303.290140 1.599722
BFGS: 36 22:42:17 -303.297091 1.756895
BFGS: 37 22:42:17 -303.302714 1.820198
BFGS: 38 22:42:17 -303.309734 1.811059
BFGS: 39 22:42:17 -303.321396 1.910011
BFGS: 40 22:42:17 -303.336828 1.726181
BFGS: 41 22:42:17 -303.355924 2.073526
BFGS: 42 22:42:18 -303.379599 2.024704
BFGS: 43 22:42:18 -303.411508 2.167642
BFGS: 44 22:42:18 -303.438662 2.135357
BFGS: 45 22:42:18 -303.475837 2.114299
BFGS: 46 22:42:18 -303.504986 1.926419
BFGS: 47 22:42:18 -303.536687 1.928545
BFGS: 48 22:42:18 -303.587396 1.776232
BFGS: 49 22:42:18 -303.646430 1.558411
BFGS: 50 22:42:18 -303.728529 1.339313
BFGS: 51 22:42:18 -303.804896 1.178846
BFGS: 52 22:42:18 -303.876872 0.954810
BFGS: 53 22:42:19 -303.943462 0.974421
BFGS: 54 22:42:19 -304.006969 1.036047
BFGS: 55 22:42:19 -304.067636 1.051468
BFGS: 56 22:42:19 -304.124118 0.847120
BFGS: 57 22:42:19 -304.175522 0.805376
BFGS: 58 22:42:19 -304.232233 0.599079
BFGS: 59 22:42:19 -304.285412 0.416916
BFGS: 60 22:42:19 -304.322475 0.340155
BFGS: 61 22:42:19 -304.329738 0.453742
BFGS: 62 22:42:19 -304.337026 0.275381
BFGS: 63 22:42:19 -304.342799 0.219445
BFGS: 64 22:42:19 -304.350808 0.111118
BFGS: 65 22:42:20 -304.353231 0.078490
BFGS: 66 22:42:20 -304.354503 0.068033
BFGS: 67 22:42:20 -304.355143 0.060461
BFGS: 68 22:42:20 -304.355751 0.050231
BFGS: 69 22:42:20 -304.356177 0.037671
Step Time Energy fmax
BFGS: 0 22:42:20 -301.505836 4.084397
BFGS: 1 22:42:20 -301.886154 3.432745
BFGS: 2 22:42:20 -302.895263 3.215040
BFGS: 3 22:42:20 -302.992779 4.799333
BFGS: 4 22:42:21 -303.291080 2.373720
BFGS: 5 22:42:21 -303.513247 1.935754
BFGS: 6 22:42:21 -303.651546 2.665568
BFGS: 7 22:42:21 -303.950261 1.950190
BFGS: 8 22:42:21 -303.947137 1.800027
BFGS: 9 22:42:21 -304.078883 0.945941
BFGS: 10 22:42:21 -304.124239 0.850947
BFGS: 11 22:42:21 -304.214349 0.579619
BFGS: 12 22:42:21 -304.228225 0.439917
BFGS: 13 22:42:21 -304.253125 0.361522
BFGS: 14 22:42:21 -304.262085 0.387597
BFGS: 15 22:42:22 -304.276483 0.406755
BFGS: 16 22:42:22 -304.287884 0.354793
BFGS: 17 22:42:22 -304.298062 0.243284
BFGS: 18 22:42:22 -304.305317 0.267413
BFGS: 19 22:42:22 -304.313424 0.338140
BFGS: 20 22:42:22 -304.322736 0.357463
BFGS: 21 22:42:22 -304.330354 0.274508
BFGS: 22 22:42:22 -304.334203 0.202297
BFGS: 23 22:42:22 -304.337403 0.221387
BFGS: 24 22:42:22 -304.341162 0.231041
BFGS: 25 22:42:22 -304.344848 0.228097
BFGS: 26 22:42:23 -304.348877 0.250398
BFGS: 27 22:42:23 -304.352248 0.169744
BFGS: 28 22:42:23 -304.353850 0.092499
BFGS: 29 22:42:23 -304.354747 0.099510
BFGS: 30 22:42:23 -304.355360 0.086490
BFGS: 31 22:42:23 -304.355993 0.066398
BFGS: 32 22:42:23 -304.356588 0.057078
BFGS: 33 22:42:23 -304.356874 0.029686
Step Time Energy fmax
BFGS: 0 22:42:23 -300.688645 4.024666
BFGS: 1 22:42:23 -301.137687 3.753506
BFGS: 2 22:42:23 -302.503727 3.693567
BFGS: 3 22:42:23 -302.330977 8.645473
BFGS: 4 22:42:24 -302.812412 3.158830
BFGS: 5 22:42:24 -302.992231 2.166274
BFGS: 6 22:42:24 -303.097790 2.298605
BFGS: 7 22:42:24 -303.132855 0.601973
BFGS: 8 22:42:24 -303.141908 0.425896
BFGS: 9 22:42:24 -303.158218 0.626385
BFGS: 10 22:42:24 -303.169190 0.580642
BFGS: 11 22:42:24 -303.175420 0.288542
BFGS: 12 22:42:24 -303.176782 0.158436
BFGS: 13 22:42:24 -303.178516 0.248812
BFGS: 14 22:42:24 -303.180940 0.336923
BFGS: 15 22:42:25 -303.184076 0.331812
BFGS: 16 22:42:25 -303.186606 0.203346
BFGS: 17 22:42:25 -303.187837 0.122898
BFGS: 18 22:42:25 -303.188384 0.154016
BFGS: 19 22:42:25 -303.189162 0.189537
BFGS: 20 22:42:25 -303.190197 0.176703
BFGS: 21 22:42:25 -303.190878 0.092120
BFGS: 22 22:42:25 -303.191075 0.022715
Step Time Energy fmax
BFGS: 0 22:42:25 -301.998776 4.140970
BFGS: 1 22:42:25 -302.382199 3.181895
BFGS: 2 22:42:25 -303.299114 3.242164
BFGS: 3 22:42:25 -303.466303 3.013382
BFGS: 4 22:42:26 -303.756238 2.006788
BFGS: 5 22:42:26 -303.891471 2.546779
BFGS: 6 22:42:26 -303.977140 1.682759
BFGS: 7 22:42:26 -304.168831 1.365290
BFGS: 8 22:42:26 -304.223648 1.167593
BFGS: 9 22:42:26 -304.428656 1.712277
BFGS: 10 22:42:26 -304.524709 1.207478
BFGS: 11 22:42:26 -304.602925 0.703094
BFGS: 12 22:42:26 -304.613830 0.438965
BFGS: 13 22:42:26 -304.624661 0.309895
BFGS: 14 22:42:26 -304.638807 0.317612
BFGS: 15 22:42:27 -304.650806 0.216148
BFGS: 16 22:42:27 -304.654592 0.224398
BFGS: 17 22:42:27 -304.657902 0.225072
BFGS: 18 22:42:27 -304.665220 0.213968
BFGS: 19 22:42:27 -304.673778 0.244402
BFGS: 20 22:42:27 -304.680851 0.229276
BFGS: 21 22:42:27 -304.684637 0.151400
BFGS: 22 22:42:27 -304.686160 0.104201
BFGS: 23 22:42:27 -304.687159 0.092396
BFGS: 24 22:42:27 -304.688595 0.096873
BFGS: 25 22:42:27 -304.690227 0.092106
BFGS: 26 22:42:27 -304.691298 0.059389
BFGS: 27 22:42:28 -304.691702 0.050654
BFGS: 28 22:42:28 -304.691863 0.047832
Step Time Energy fmax
BFGS: 0 22:42:28 -301.000238 4.002768
BFGS: 1 22:42:28 -301.401124 3.203538
BFGS: 2 22:42:28 -302.557240 3.667701
BFGS: 3 22:42:28 -302.625670 5.260755
BFGS: 4 22:42:28 -302.955832 2.448966
BFGS: 5 22:42:28 -303.060210 2.546871
BFGS: 6 22:42:28 -303.105003 0.533953
BFGS: 7 22:42:28 -303.119513 0.441859
BFGS: 8 22:42:28 -303.186059 0.699411
BFGS: 9 22:42:29 -303.198933 0.422098
BFGS: 10 22:42:29 -303.203696 0.243714
BFGS: 11 22:42:29 -303.209656 0.304687
BFGS: 12 22:42:29 -303.216928 0.394412
BFGS: 13 22:42:29 -303.223927 0.396049
BFGS: 14 22:42:29 -303.229734 0.353165
BFGS: 15 22:42:29 -303.234050 0.336025
BFGS: 16 22:42:29 -303.246956 0.600784
BFGS: 17 22:42:29 -303.330199 1.498138
BFGS: 18 22:42:29 -303.582781 1.811356
BFGS: 19 22:42:29 -303.915062 1.768237
BFGS: 20 22:42:30 -304.019978 2.461518
BFGS: 21 22:42:30 -304.148607 1.660902
BFGS: 22 22:42:30 -304.220127 1.168722
BFGS: 23 22:42:30 -304.303100 0.872147
BFGS: 24 22:42:30 -304.395845 0.991417
BFGS: 25 22:42:30 -304.459866 0.718067
BFGS: 26 22:42:30 -304.501824 0.548538
BFGS: 27 22:42:30 -304.519612 0.480174
BFGS: 28 22:42:30 -304.547621 0.506929
BFGS: 29 22:42:30 -304.574133 0.512707
BFGS: 30 22:42:30 -304.593752 0.415936
BFGS: 31 22:42:30 -304.608478 0.366466
BFGS: 32 22:42:31 -304.624544 0.401096
BFGS: 33 22:42:31 -304.641834 0.388413
BFGS: 34 22:42:31 -304.659483 0.255541
BFGS: 35 22:42:31 -304.669558 0.248453
BFGS: 36 22:42:31 -304.675112 0.225837
BFGS: 37 22:42:31 -304.679597 0.187751
BFGS: 38 22:42:31 -304.684136 0.129002
BFGS: 39 22:42:31 -304.687322 0.076305
BFGS: 40 22:42:31 -304.689118 0.083318
BFGS: 41 22:42:31 -304.689945 0.073564
BFGS: 42 22:42:31 -304.690390 0.085381
BFGS: 43 22:42:32 -304.690928 0.087287
BFGS: 44 22:42:32 -304.691530 0.062960
BFGS: 45 22:42:32 -304.691990 0.036207
Step Time Energy fmax
BFGS: 0 22:42:32 -300.982492 4.034743
BFGS: 1 22:42:32 -301.384154 3.161276
BFGS: 2 22:42:32 -302.539693 3.627417
BFGS: 3 22:42:32 -302.556663 6.022340
BFGS: 4 22:42:32 -302.904712 2.677244
BFGS: 5 22:42:32 -303.069200 1.354959
BFGS: 6 22:42:32 -303.096220 0.969314
BFGS: 7 22:42:32 -303.130888 1.012486
BFGS: 8 22:42:32 -303.153120 1.063757
BFGS: 9 22:42:33 -303.201773 0.524074
BFGS: 10 22:42:33 -303.207015 0.209034
BFGS: 11 22:42:33 -303.210421 0.265979
BFGS: 12 22:42:33 -303.217763 0.429459
BFGS: 13 22:42:33 -303.223457 0.417868
BFGS: 14 22:42:33 -303.228679 0.341407
BFGS: 15 22:42:33 -303.232414 0.313526
BFGS: 16 22:42:33 -303.241325 0.540654
BFGS: 17 22:42:33 -303.274543 1.175158
BFGS: 18 22:42:33 -303.369714 1.201914
BFGS: 19 22:42:33 -303.575726 1.911020
BFGS: 20 22:42:34 -303.635979 3.574935
BFGS: 21 22:42:34 -303.737140 2.795809
BFGS: 22 22:42:34 -303.856846 2.313143
BFGS: 23 22:42:34 -304.038467 1.638056
BFGS: 24 22:42:34 -304.138121 1.004696
BFGS: 25 22:42:34 -304.219342 0.863224
BFGS: 26 22:42:34 -304.248342 0.888670
BFGS: 27 22:42:34 -304.336791 1.035849
BFGS: 28 22:42:34 -304.347760 1.656096
BFGS: 29 22:42:34 -304.437801 0.936482
BFGS: 30 22:42:34 -304.473894 0.812914
BFGS: 31 22:42:34 -304.500945 1.057591
BFGS: 32 22:42:35 -304.539890 0.436026
BFGS: 33 22:42:35 -304.553695 0.356484
BFGS: 34 22:42:35 -304.591742 0.532729
BFGS: 35 22:42:35 -304.605351 0.495433
BFGS: 36 22:42:35 -304.622069 0.354916
BFGS: 37 22:42:35 -304.630713 0.349236
BFGS: 38 22:42:35 -304.644406 0.568240
BFGS: 39 22:42:35 -304.661747 0.625719
BFGS: 40 22:42:35 -304.676312 0.370886
BFGS: 41 22:42:35 -304.681670 0.146342
BFGS: 42 22:42:35 -304.683952 0.114315
BFGS: 43 22:42:36 -304.685627 0.094757
BFGS: 44 22:42:36 -304.687590 0.136026
BFGS: 45 22:42:36 -304.689549 0.122214
BFGS: 46 22:42:36 -304.690647 0.064302
BFGS: 47 22:42:36 -304.691105 0.045764
Step Time Energy fmax
BFGS: 0 22:42:36 -301.502950 4.070814
BFGS: 1 22:42:36 -301.887739 3.388053
BFGS: 2 22:42:36 -302.915958 3.258788
BFGS: 3 22:42:36 -303.019914 4.835571
BFGS: 4 22:42:36 -303.321755 2.389113
BFGS: 5 22:42:36 -303.546981 2.013786
BFGS: 6 22:42:37 -303.675268 2.612256
BFGS: 7 22:42:37 -303.974129 1.929707
BFGS: 8 22:42:37 -304.075612 1.149333
BFGS: 9 22:42:37 -304.147357 1.023374
BFGS: 10 22:42:37 -304.231954 0.837704
BFGS: 11 22:42:37 -304.286753 0.681960
BFGS: 12 22:42:37 -304.304211 0.504532
BFGS: 13 22:42:37 -304.317639 0.243457
BFGS: 14 22:42:37 -304.327989 0.194779
BFGS: 15 22:42:37 -304.333369 0.198688
BFGS: 16 22:42:37 -304.337100 0.189157
BFGS: 17 22:42:37 -304.339992 0.163713
BFGS: 18 22:42:38 -304.341798 0.144589
BFGS: 19 22:42:38 -304.343362 0.133629
BFGS: 20 22:42:38 -304.345348 0.198580
BFGS: 21 22:42:38 -304.348302 0.259557
BFGS: 22 22:42:38 -304.351873 0.248922
BFGS: 23 22:42:38 -304.354344 0.162431
BFGS: 24 22:42:38 -304.355629 0.079898
BFGS: 25 22:42:38 -304.356086 0.071606
BFGS: 26 22:42:38 -304.356337 0.056523
BFGS: 27 22:42:38 -304.356710 0.038735
Step Time Energy fmax
BFGS: 0 22:42:38 -301.131141 4.088279
BFGS: 1 22:42:39 -301.519628 3.289951
BFGS: 2 22:42:39 -302.592720 3.475675
BFGS: 3 22:42:39 -302.611321 5.662992
BFGS: 4 22:42:39 -302.936302 2.652932
BFGS: 5 22:42:39 -303.099855 1.024673
BFGS: 6 22:42:39 -303.145452 1.383566
BFGS: 7 22:42:39 -303.191002 0.979912
BFGS: 8 22:42:39 -303.248068 1.454271
BFGS: 9 22:42:39 -303.321292 1.268628
BFGS: 10 22:42:39 -303.363527 0.926419
BFGS: 11 22:42:39 -303.439383 1.028225
BFGS: 12 22:42:39 -303.577769 2.100260
BFGS: 13 22:42:40 -303.662283 3.220157
BFGS: 14 22:42:40 -303.801470 2.352692
BFGS: 15 22:42:40 -303.909457 1.488751
BFGS: 16 22:42:40 -304.020334 1.247991
BFGS: 17 22:42:40 -304.049536 0.987151
BFGS: 18 22:42:40 -304.079925 0.662554
BFGS: 19 22:42:40 -304.135251 0.331838
BFGS: 20 22:42:40 -304.144822 0.379882
BFGS: 21 22:42:40 -304.158174 0.454151
BFGS: 22 22:42:40 -304.173261 0.456352
BFGS: 23 22:42:40 -304.189331 0.348942
BFGS: 24 22:42:41 -304.201344 0.310919
BFGS: 25 22:42:41 -304.209694 0.419121
BFGS: 26 22:42:41 -304.222074 0.513241
BFGS: 27 22:42:41 -304.243136 0.505231
BFGS: 28 22:42:41 -304.255266 0.272139
BFGS: 29 22:42:41 -304.264629 0.279298
BFGS: 30 22:42:41 -304.271151 0.330231
BFGS: 31 22:42:41 -304.278819 0.398497
BFGS: 32 22:42:41 -304.288786 0.354015
BFGS: 33 22:42:41 -304.310179 0.287710
BFGS: 34 22:42:41 -304.320141 0.246981
BFGS: 35 22:42:42 -304.327378 0.222729
BFGS: 36 22:42:42 -304.331961 0.233894
BFGS: 37 22:42:42 -304.338863 0.174324
BFGS: 38 22:42:42 -304.344450 0.175423
BFGS: 39 22:42:42 -304.348725 0.148988
BFGS: 40 22:42:42 -304.351076 0.106175
BFGS: 41 22:42:42 -304.352254 0.093417
BFGS: 42 22:42:42 -304.353245 0.070285
BFGS: 43 22:42:42 -304.354450 0.095061
BFGS: 44 22:42:42 -304.355549 0.086613
BFGS: 45 22:42:42 -304.356170 0.057024
BFGS: 46 22:42:42 -304.356476 0.037629
Step Time Energy fmax
BFGS: 0 22:42:43 -301.490370 4.090055
BFGS: 1 22:42:43 -301.865652 3.118333
BFGS: 2 22:42:43 -302.823427 3.445878
BFGS: 3 22:42:43 -302.971799 3.296902
BFGS: 4 22:42:43 -303.254107 2.027275
BFGS: 5 22:42:43 -303.391695 3.466228
BFGS: 6 22:42:43 -303.501175 1.987173
BFGS: 7 22:42:43 -303.757398 1.174907
BFGS: 8 22:42:43 -304.109331 2.209693
BFGS: 9 22:42:43 -304.229886 2.689340
BFGS: 10 22:42:43 -304.340448 2.159875
BFGS: 11 22:42:44 -304.545279 1.164454
BFGS: 12 22:42:44 -304.595307 0.780749
BFGS: 13 22:42:44 -304.620261 0.485047
BFGS: 14 22:42:44 -304.633152 0.399195
BFGS: 15 22:42:44 -304.647851 0.238585
BFGS: 16 22:42:44 -304.652552 0.209403
BFGS: 17 22:42:44 -304.658833 0.213742
BFGS: 18 22:42:44 -304.664866 0.197991
BFGS: 19 22:42:44 -304.669760 0.190742
BFGS: 20 22:42:44 -304.673041 0.189063
BFGS: 21 22:42:44 -304.676284 0.158325
BFGS: 22 22:42:44 -304.680031 0.151376
BFGS: 23 22:42:45 -304.683954 0.174282
BFGS: 24 22:42:45 -304.686814 0.128566
BFGS: 25 22:42:45 -304.688320 0.108538
BFGS: 26 22:42:45 -304.689167 0.090147
BFGS: 27 22:42:45 -304.689879 0.069207
BFGS: 28 22:42:45 -304.690688 0.090927
BFGS: 29 22:42:45 -304.691395 0.077808
BFGS: 30 22:42:45 -304.691781 0.044543
Step Time Energy fmax
BFGS: 0 22:42:45 -301.920035 4.088148
BFGS: 1 22:42:45 -302.297502 2.916490
BFGS: 2 22:42:45 -303.220192 3.453780
BFGS: 3 22:42:46 -303.399660 3.190571
BFGS: 4 22:42:46 -303.770249 2.000802
BFGS: 5 22:42:46 -303.856931 1.803981
BFGS: 6 22:42:46 -303.942701 1.613535
BFGS: 7 22:42:46 -304.039883 0.904978
BFGS: 8 22:42:46 -304.065518 0.691627
BFGS: 9 22:42:46 -304.131206 0.698925
BFGS: 10 22:42:46 -304.168210 0.394222
BFGS: 11 22:42:46 -304.178118 0.248918
BFGS: 12 22:42:46 -304.183547 0.257183
BFGS: 13 22:42:46 -304.190844 0.299555
BFGS: 14 22:42:46 -304.200298 0.278491
BFGS: 15 22:42:47 -304.206100 0.274036
BFGS: 16 22:42:47 -304.210611 0.257185
BFGS: 17 22:42:47 -304.217674 0.306200
BFGS: 18 22:42:47 -304.230067 0.568678
BFGS: 19 22:42:47 -304.244658 0.871691
BFGS: 20 22:42:47 -304.262050 0.545291
BFGS: 21 22:42:47 -304.278485 0.314096
BFGS: 22 22:42:47 -304.283237 0.363780
BFGS: 23 22:42:47 -304.290237 0.347688
BFGS: 24 22:42:47 -304.304625 0.303429
BFGS: 25 22:42:48 -304.318414 0.273770
BFGS: 26 22:42:48 -304.327080 0.249763
BFGS: 27 22:42:48 -304.331842 0.213415
BFGS: 28 22:42:48 -304.335961 0.177677
BFGS: 29 22:42:48 -304.342718 0.201397
BFGS: 30 22:42:48 -304.349125 0.168393
BFGS: 31 22:42:48 -304.352612 0.099123
BFGS: 32 22:42:48 -304.353796 0.076447
BFGS: 33 22:42:48 -304.354551 0.079986
BFGS: 34 22:42:48 -304.355193 0.081576
BFGS: 35 22:42:49 -304.355873 0.059017
BFGS: 36 22:42:49 -304.356366 0.042165
# 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 22:42:49 -296.499385 4.449457
BFGS: 1 22:42:49 -296.974153 4.674884
BFGS: 2 22:42:49 -298.364071 3.406785
BFGS: 3 22:42:49 -298.098416 8.772037
BFGS: 4 22:42:49 -298.655977 1.917779
BFGS: 5 22:42:49 -298.734331 1.354764
BFGS: 6 22:42:49 -298.856668 1.869049
BFGS: 7 22:42:49 -298.973616 2.126500
BFGS: 8 22:42:49 -299.218742 2.127447
BFGS: 9 22:42:49 -299.424030 1.812626
BFGS: 10 22:42:50 -299.527787 1.507413
BFGS: 11 22:42:50 -299.622384 1.289225
BFGS: 12 22:42:50 -299.989028 1.023361
BFGS: 13 22:42:50 -300.007803 0.732582
BFGS: 14 22:42:50 -300.030901 0.532913
BFGS: 15 22:42:50 -300.041723 0.381649
BFGS: 16 22:42:50 -300.053479 0.323419
BFGS: 17 22:42:50 -300.061812 0.416784
BFGS: 18 22:42:50 -300.068135 0.407900
BFGS: 19 22:42:50 -300.073477 0.315080
BFGS: 20 22:42:50 -300.076447 0.199279
BFGS: 21 22:42:51 -300.077975 0.112645
BFGS: 22 22:42:51 -300.078839 0.088944
BFGS: 23 22:42:51 -300.079331 0.064833
BFGS: 24 22:42:51 -300.079909 0.071019
BFGS: 25 22:42:51 -300.080462 0.053826
BFGS: 26 22:42:51 -300.080710 0.022506
Step Time Energy fmax
BFGS: 0 22:42:51 -297.192316 4.733490
BFGS: 1 22:42:51 -297.669131 4.889116
BFGS: 2 22:42:51 -298.823653 4.198896
BFGS: 3 22:42:51 -299.464121 2.046880
BFGS: 4 22:42:51 -299.654872 2.773361
BFGS: 5 22:42:52 -300.043876 2.158989
BFGS: 6 22:42:52 -300.190234 1.619320
BFGS: 7 22:42:52 -300.316971 1.299581
BFGS: 8 22:42:52 -300.426261 1.525567
BFGS: 9 22:42:52 -300.505014 1.457799
BFGS: 10 22:42:52 -300.558023 0.773193
BFGS: 11 22:42:52 -300.587014 0.466753
BFGS: 12 22:42:52 -300.594121 0.385123
BFGS: 13 22:42:52 -300.603440 0.349502
BFGS: 14 22:42:52 -300.611369 0.295310
BFGS: 15 22:42:52 -300.616629 0.164677
BFGS: 16 22:42:52 -300.618896 0.151322
BFGS: 17 22:42:53 -300.620446 0.153235
BFGS: 18 22:42:53 -300.621751 0.119460
BFGS: 19 22:42:53 -300.623070 0.061170
BFGS: 20 22:42:53 -300.624097 0.035075
Step Time Energy fmax
BFGS: 0 22:42:53 -296.003675 4.354725
BFGS: 1 22:42:53 -296.532035 4.728174
BFGS: 2 22:42:53 -298.206787 3.042665
BFGS: 3 22:42:53 -296.794654 16.900455
BFGS: 4 22:42:53 -298.383441 1.863903
BFGS: 5 22:42:53 -298.445929 1.044773
BFGS: 6 22:42:53 -298.481229 0.592884
BFGS: 7 22:42:54 -298.485630 0.314092
BFGS: 8 22:42:54 -298.491169 0.134091
BFGS: 9 22:42:54 -298.493133 0.169161
BFGS: 10 22:42:54 -298.493886 0.136451
BFGS: 11 22:42:54 -298.494416 0.110752
BFGS: 12 22:42:54 -298.495695 0.137485
BFGS: 13 22:42:54 -298.499087 0.230347
BFGS: 14 22:42:54 -298.517247 0.569655
BFGS: 15 22:42:54 -298.509104 0.965163
BFGS: 16 22:42:54 -298.625884 0.805950
BFGS: 17 22:42:54 -298.690920 1.920485
BFGS: 18 22:42:54 -298.753461 2.127751
BFGS: 19 22:42:55 -298.858431 1.518897
BFGS: 20 22:42:55 -299.002780 1.940942
BFGS: 21 22:42:55 -299.225974 2.590730
BFGS: 22 22:42:55 -299.400002 2.496099
BFGS: 23 22:42:55 -299.590047 2.322212
BFGS: 24 22:42:55 -300.022182 1.716588
BFGS: 25 22:42:55 -300.188543 1.606715
BFGS: 26 22:42:55 -300.294338 1.451582
BFGS: 27 22:42:55 -300.443146 1.129853
BFGS: 28 22:42:55 -300.518738 0.716516
BFGS: 29 22:42:55 -300.574380 0.608448
BFGS: 30 22:42:56 -300.582665 0.331726
BFGS: 31 22:42:56 -300.594914 0.332600
BFGS: 32 22:42:56 -300.609140 0.264372
BFGS: 33 22:42:56 -300.615868 0.149158
BFGS: 34 22:42:56 -300.618351 0.118288
BFGS: 35 22:42:56 -300.619217 0.112084
BFGS: 36 22:42:56 -300.620762 0.109597
BFGS: 37 22:42:56 -300.622444 0.109396
BFGS: 38 22:42:56 -300.623976 0.091796
BFGS: 39 22:42:56 -300.624632 0.056700
BFGS: 40 22:42:56 -300.624812 0.029371
Step Time Energy fmax
BFGS: 0 22:42:57 -296.300203 4.411115
BFGS: 1 22:42:57 -296.787170 4.689755
BFGS: 2 22:42:57 -298.264735 3.301398
BFGS: 3 22:42:57 -297.680289 10.998199
BFGS: 4 22:42:57 -298.506540 1.892721
BFGS: 5 22:42:57 -298.575987 1.143047
BFGS: 6 22:42:57 -298.634387 1.211851
BFGS: 7 22:42:57 -298.661967 1.185280
BFGS: 8 22:42:57 -298.803751 1.208300
BFGS: 9 22:42:57 -298.870582 1.561315
BFGS: 10 22:42:57 -299.011104 2.200969
BFGS: 11 22:42:57 -299.139826 2.487664
BFGS: 12 22:42:58 -299.255923 2.635670
BFGS: 13 22:42:58 -299.470699 2.498204
BFGS: 14 22:42:58 -299.901832 1.487684
BFGS: 15 22:42:58 -299.936717 1.259489
BFGS: 16 22:42:58 -299.993123 0.970347
BFGS: 17 22:42:58 -300.039981 0.348232
BFGS: 18 22:42:58 -300.056664 0.222405
BFGS: 19 22:42:58 -300.064096 0.233318
BFGS: 20 22:42:58 -300.069509 0.222004
BFGS: 21 22:42:58 -300.073388 0.173026
BFGS: 22 22:42:58 -300.075949 0.097590
BFGS: 23 22:42:59 -300.077024 0.081417
BFGS: 24 22:42:59 -300.077501 0.075793
BFGS: 25 22:42:59 -300.078090 0.065232
BFGS: 26 22:42:59 -300.078945 0.080876
BFGS: 27 22:42:59 -300.079774 0.073431
BFGS: 28 22:42:59 -300.080231 0.051069
BFGS: 29 22:42:59 -300.080417 0.050463
BFGS: 30 22:42:59 -300.080534 0.040629
Step Time Energy fmax
BFGS: 0 22:42:59 -297.306456 4.771646
BFGS: 1 22:42:59 -297.794579 4.900629
BFGS: 2 22:42:59 -299.054237 3.825396
BFGS: 3 22:42:59 -299.463611 3.698697
BFGS: 4 22:43:00 -299.620167 1.772221
BFGS: 5 22:43:00 -299.810876 1.524538
BFGS: 6 22:43:00 -299.979397 1.398922
BFGS: 7 22:43:00 -300.039397 1.461349
BFGS: 8 22:43:00 -300.335420 1.397389
BFGS: 9 22:43:00 -300.420436 1.352913
BFGS: 10 22:43:00 -300.512122 0.924900
BFGS: 11 22:43:00 -300.545649 0.682843
BFGS: 12 22:43:00 -300.574625 0.445542
BFGS: 13 22:43:00 -300.590316 0.462699
BFGS: 14 22:43:00 -300.602592 0.342972
BFGS: 15 22:43:01 -300.608221 0.203770
BFGS: 16 22:43:01 -300.612839 0.250190
BFGS: 17 22:43:01 -300.616621 0.246099
BFGS: 18 22:43:01 -300.620024 0.182805
BFGS: 19 22:43:01 -300.622201 0.130656
BFGS: 20 22:43:01 -300.623107 0.089163
BFGS: 21 22:43:01 -300.623524 0.064537
BFGS: 22 22:43:01 -300.623988 0.078829
BFGS: 23 22:43:01 -300.624481 0.065655
BFGS: 24 22:43:01 -300.624774 0.038324
Step Time Energy fmax
BFGS: 0 22:43:01 -296.462343 4.434470
BFGS: 1 22:43:01 -296.929781 4.678212
BFGS: 2 22:43:02 -298.326444 3.494634
BFGS: 3 22:43:02 -298.134893 8.364893
BFGS: 4 22:43:02 -298.641043 1.940601
BFGS: 5 22:43:02 -298.722892 1.380939
BFGS: 6 22:43:02 -298.868843 2.184028
BFGS: 7 22:43:02 -299.058785 2.761238
BFGS: 8 22:43:02 -299.331022 2.856431
BFGS: 9 22:43:02 -299.520324 2.412220
BFGS: 10 22:43:02 -299.591788 1.874372
BFGS: 11 22:43:02 -299.730432 1.798203
BFGS: 12 22:43:02 -300.385924 1.247870
BFGS: 13 22:43:03 -300.452950 1.307709
BFGS: 14 22:43:03 -300.489388 1.353079
BFGS: 15 22:43:03 -300.570046 0.890675
BFGS: 16 22:43:03 -300.593007 0.564402
BFGS: 17 22:43:03 -300.603703 0.346190
BFGS: 18 22:43:03 -300.610385 0.201009
BFGS: 19 22:43:03 -300.615613 0.221675
BFGS: 20 22:43:03 -300.618918 0.208229
BFGS: 21 22:43:03 -300.620727 0.164729
BFGS: 22 22:43:03 -300.621825 0.109514
BFGS: 23 22:43:03 -300.622723 0.102467
BFGS: 24 22:43:03 -300.623556 0.092016
BFGS: 25 22:43:04 -300.624204 0.062458
BFGS: 26 22:43:04 -300.624559 0.045340
Step Time Energy fmax
BFGS: 0 22:43:04 -296.781846 4.480540
BFGS: 1 22:43:04 -297.248011 4.652190
BFGS: 2 22:43:04 -298.553998 3.517385
BFGS: 3 22:43:04 -298.591500 6.565120
BFGS: 4 22:43:04 -298.928501 1.933713
BFGS: 5 22:43:04 -299.025239 1.665001
BFGS: 6 22:43:04 -299.366590 2.005738
BFGS: 7 22:43:04 -299.649184 1.961318
BFGS: 8 22:43:04 -299.795937 1.215847
BFGS: 9 22:43:05 -299.875325 0.915571
BFGS: 10 22:43:05 -300.020165 0.821373
BFGS: 11 22:43:05 -300.033051 0.646930
BFGS: 12 22:43:05 -300.056654 0.256235
BFGS: 13 22:43:05 -300.060463 0.258403
BFGS: 14 22:43:05 -300.068491 0.263005
BFGS: 15 22:43:05 -300.074209 0.197722
BFGS: 16 22:43:05 -300.077110 0.122650
BFGS: 17 22:43:05 -300.078030 0.091782
BFGS: 18 22:43:05 -300.078554 0.087511
BFGS: 19 22:43:05 -300.079144 0.072281
BFGS: 20 22:43:06 -300.079854 0.049080
Step Time Energy fmax
BFGS: 0 22:43:06 -297.687532 4.513171
BFGS: 1 22:43:06 -298.160703 4.533018
BFGS: 2 22:43:06 -299.313751 3.011162
BFGS: 3 22:43:06 -299.460505 3.926848
BFGS: 4 22:43:06 -299.661138 1.292239
BFGS: 5 22:43:06 -299.749318 1.153889
BFGS: 6 22:43:06 -299.996566 0.603422
BFGS: 7 22:43:06 -300.017111 0.506843
BFGS: 8 22:43:06 -300.067964 0.367225
BFGS: 9 22:43:06 -300.075900 0.208454
BFGS: 10 22:43:06 -300.079002 0.085176
BFGS: 11 22:43:07 -300.079335 0.061155
BFGS: 12 22:43:07 -300.079741 0.059462
BFGS: 13 22:43:07 -300.080086 0.055122
BFGS: 14 22:43:07 -300.080256 0.043247
Step Time Energy fmax
BFGS: 0 22:43:07 -296.335916 4.421415
BFGS: 1 22:43:07 -296.820085 4.686840
BFGS: 2 22:43:07 -298.279844 3.352585
BFGS: 3 22:43:07 -297.798770 10.325850
BFGS: 4 22:43:07 -298.538294 1.910432
BFGS: 5 22:43:07 -298.610780 1.204341
BFGS: 6 22:43:07 -298.683020 1.422452
BFGS: 7 22:43:08 -298.728610 1.523479
BFGS: 8 22:43:08 -298.939160 1.563677
BFGS: 9 22:43:08 -299.086324 1.866161
BFGS: 10 22:43:08 -299.187748 1.832649
BFGS: 11 22:43:08 -299.361561 1.662239
BFGS: 12 22:43:08 -299.826444 1.240076
BFGS: 13 22:43:08 -299.854513 0.604301
BFGS: 14 22:43:08 -299.866066 0.647284
BFGS: 15 22:43:08 -299.883900 0.422239
BFGS: 16 22:43:08 -299.907405 0.380684
BFGS: 17 22:43:08 -299.915403 0.305253
BFGS: 18 22:43:08 -299.919956 0.236525
BFGS: 19 22:43:09 -299.924787 0.261046
BFGS: 20 22:43:09 -299.929594 0.346388
BFGS: 21 22:43:09 -299.934964 0.412355
BFGS: 22 22:43:09 -299.942927 0.450882
BFGS: 23 22:43:09 -299.955264 0.430006
BFGS: 24 22:43:09 -299.971636 0.471760
BFGS: 25 22:43:09 -299.989271 0.465794
BFGS: 26 22:43:09 -300.009967 0.559459
BFGS: 27 22:43:09 -300.032963 0.474827
BFGS: 28 22:43:09 -300.035711 0.703387
BFGS: 29 22:43:09 -300.060578 0.240841
BFGS: 30 22:43:10 -300.066424 0.187537
BFGS: 31 22:43:10 -300.073283 0.109914
BFGS: 32 22:43:10 -300.075216 0.126685
BFGS: 33 22:43:10 -300.077304 0.117584
BFGS: 34 22:43:10 -300.078818 0.083441
BFGS: 35 22:43:10 -300.079683 0.043711
Step Time Energy fmax
BFGS: 0 22:43:10 -296.632256 4.495458
BFGS: 1 22:43:10 -297.093134 4.712604
BFGS: 2 22:43:10 -298.429699 3.665272
BFGS: 3 22:43:10 -298.513533 6.469540
BFGS: 4 22:43:10 -298.832505 1.979717
BFGS: 5 22:43:10 -298.934004 1.722695
BFGS: 6 22:43:11 -299.330777 2.351045
BFGS: 7 22:43:11 -299.699331 2.714273
BFGS: 8 22:43:11 -299.961434 2.038922
BFGS: 9 22:43:11 -300.071464 1.670436
BFGS: 10 22:43:11 -300.244778 1.530663
BFGS: 11 22:43:11 -300.544433 0.867090
BFGS: 12 22:43:11 -300.562642 0.670425
BFGS: 13 22:43:11 -300.586931 0.372461
BFGS: 14 22:43:11 -300.603442 0.322591
BFGS: 15 22:43:11 -300.610127 0.283406
BFGS: 16 22:43:11 -300.614031 0.232249
BFGS: 17 22:43:12 -300.617361 0.156017
BFGS: 18 22:43:12 -300.619830 0.170758
BFGS: 19 22:43:12 -300.621041 0.172910
BFGS: 20 22:43:12 -300.622134 0.145849
BFGS: 21 22:43:12 -300.623161 0.089940
BFGS: 22 22:43:12 -300.623922 0.075678
BFGS: 23 22:43:12 -300.624363 0.069682
BFGS: 24 22:43:12 -300.624639 0.056755
BFGS: 25 22:43:12 -300.624859 0.044215
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 22:43:12 -295.312888 1.276168
BFGS: 1 22:43:12 -295.391530 1.164782
BFGS: 2 22:43:12 -295.600068 1.460538
BFGS: 3 22:43:13 -295.640067 0.566893
BFGS: 4 22:43:13 -295.650573 0.507122
BFGS: 5 22:43:13 -295.685539 0.463377
BFGS: 6 22:43:13 -295.691427 0.464914
BFGS: 7 22:43:13 -295.747174 0.768991
BFGS: 8 22:43:13 -295.763557 0.585624
BFGS: 9 22:43:13 -295.787385 0.698332
BFGS: 10 22:43:13 -295.805012 0.676235
BFGS: 11 22:43:13 -295.831029 0.438105
BFGS: 12 22:43:13 -295.838779 0.279644
BFGS: 13 22:43:13 -295.844356 0.230376
BFGS: 14 22:43:14 -295.846067 0.208573
BFGS: 15 22:43:14 -295.848858 0.186782
BFGS: 16 22:43:14 -295.851695 0.148554
BFGS: 17 22:43:14 -295.854273 0.127379
BFGS: 18 22:43:14 -295.855622 0.129087
BFGS: 19 22:43:14 -295.856455 0.137674
BFGS: 20 22:43:14 -295.857648 0.153830
BFGS: 21 22:43:14 -295.860317 0.186186
BFGS: 22 22:43:14 -295.865123 0.224203
BFGS: 23 22:43:14 -295.871760 0.252330
BFGS: 24 22:43:14 -295.880802 0.327046
BFGS: 25 22:43:14 -295.894980 0.450916
BFGS: 26 22:43:15 -295.915726 0.501966
BFGS: 27 22:43:15 -295.944326 0.333833
BFGS: 28 22:43:15 -295.951418 0.192316
BFGS: 29 22:43:15 -295.955868 0.171627
BFGS: 30 22:43:15 -295.961266 0.109955
BFGS: 31 22:43:15 -295.962908 0.095896
BFGS: 32 22:43:15 -295.964538 0.075233
BFGS: 33 22:43:15 -295.965973 0.063392
BFGS: 34 22:43:15 -295.967289 0.049461
Step Time Energy fmax
BFGS: 0 22:43:15 -295.434155 1.067804
BFGS: 1 22:43:15 -295.500415 0.985679
BFGS: 2 22:43:16 -295.709294 0.996262
BFGS: 3 22:43:16 -295.733331 0.527926
BFGS: 4 22:43:16 -295.743367 0.472407
BFGS: 5 22:43:16 -295.785192 0.530788
BFGS: 6 22:43:16 -295.793158 0.494513
BFGS: 7 22:43:16 -295.827656 0.375109
BFGS: 8 22:43:16 -295.838669 0.243336
BFGS: 9 22:43:16 -295.841892 0.228806
BFGS: 10 22:43:16 -295.846377 0.203068
BFGS: 11 22:43:16 -295.849323 0.183820
BFGS: 12 22:43:16 -295.853888 0.155199
BFGS: 13 22:43:17 -295.855753 0.146973
BFGS: 14 22:43:17 -295.856954 0.145602
BFGS: 15 22:43:17 -295.858648 0.148914
BFGS: 16 22:43:17 -295.861995 0.164042
BFGS: 17 22:43:17 -295.867366 0.199841
BFGS: 18 22:43:17 -295.873750 0.246710
BFGS: 19 22:43:17 -295.879740 0.318376
BFGS: 20 22:43:17 -295.886491 0.326008
BFGS: 21 22:43:17 -295.895983 0.296993
BFGS: 22 22:43:17 -295.909742 0.243127
BFGS: 23 22:43:17 -295.921700 0.228537
BFGS: 24 22:43:17 -295.927532 0.150887
BFGS: 25 22:43:18 -295.928282 0.128807
BFGS: 26 22:43:18 -295.930804 0.100334
BFGS: 27 22:43:18 -295.932525 0.075362
BFGS: 28 22:43:18 -295.934820 0.049454
Step Time Energy fmax
BFGS: 0 22:43:18 -295.564411 0.754227
BFGS: 1 22:43:18 -295.619773 0.671763
BFGS: 2 22:43:18 -295.803645 0.474329
BFGS: 3 22:43:18 -295.817650 0.300345
BFGS: 4 22:43:18 -295.821216 0.295937
BFGS: 5 22:43:18 -295.836668 0.233959
BFGS: 6 22:43:18 -295.838369 0.203479
BFGS: 7 22:43:19 -295.842568 0.146139
BFGS: 8 22:43:19 -295.843758 0.080245
BFGS: 9 22:43:19 -295.844263 0.075248
BFGS: 10 22:43:19 -295.844609 0.081097
BFGS: 11 22:43:19 -295.845231 0.086534
BFGS: 12 22:43:19 -295.845929 0.088454
BFGS: 13 22:43:19 -295.846559 0.090426
BFGS: 14 22:43:19 -295.847103 0.095971
BFGS: 15 22:43:19 -295.847943 0.130587
BFGS: 16 22:43:19 -295.850041 0.207927
BFGS: 17 22:43:19 -295.856421 0.405939
BFGS: 18 22:43:19 -295.861756 0.662405
BFGS: 19 22:43:20 -295.871686 0.514933
BFGS: 20 22:43:20 -295.903598 0.326347
BFGS: 21 22:43:20 -295.910206 0.232403
BFGS: 22 22:43:20 -295.915650 0.239312
BFGS: 23 22:43:20 -295.922815 0.168734
BFGS: 24 22:43:20 -295.929837 0.110867
BFGS: 25 22:43:20 -295.931259 0.101057
BFGS: 26 22:43:20 -295.932128 0.094919
BFGS: 27 22:43:20 -295.933401 0.092953
BFGS: 28 22:43:20 -295.934825 0.060665
BFGS: 29 22:43:20 -295.935682 0.049805
Step Time Energy fmax
BFGS: 0 22:43:21 -295.686865 0.718851
BFGS: 1 22:43:21 -295.736021 0.640443
BFGS: 2 22:43:21 -295.908003 0.384161
BFGS: 3 22:43:21 -295.920993 0.396307
BFGS: 4 22:43:21 -295.924115 0.382096
BFGS: 5 22:43:21 -295.953359 0.189610
BFGS: 6 22:43:21 -295.955688 0.182847
BFGS: 7 22:43:21 -295.958781 0.171514
BFGS: 8 22:43:21 -295.960611 0.160001
BFGS: 9 22:43:21 -295.963364 0.133170
BFGS: 10 22:43:21 -295.965032 0.106088
BFGS: 11 22:43:22 -295.965842 0.083846
BFGS: 12 22:43:22 -295.966253 0.069799
BFGS: 13 22:43:22 -295.966821 0.050367
BFGS: 14 22:43:22 -295.967541 0.037523
Step Time Energy fmax
BFGS: 0 22:43:22 -295.217337 1.452511
BFGS: 1 22:43:22 -295.308593 1.316734
BFGS: 2 22:43:22 -295.503918 1.919984
BFGS: 3 22:43:22 -295.567341 0.510903
BFGS: 4 22:43:22 -295.579220 0.561231
BFGS: 5 22:43:22 -295.604244 0.411248
BFGS: 6 22:43:22 -295.611674 0.275460
BFGS: 7 22:43:22 -295.617514 0.330666
BFGS: 8 22:43:23 -295.624222 0.347323
BFGS: 9 22:43:23 -295.631741 0.343893
BFGS: 10 22:43:23 -295.638219 0.260744
BFGS: 11 22:43:23 -295.642283 0.345169
BFGS: 12 22:43:23 -295.647798 0.491358
BFGS: 13 22:43:23 -295.672963 0.941492
BFGS: 14 22:43:23 -295.709364 1.327334
BFGS: 15 22:43:23 -295.682921 1.365583
BFGS: 16 22:43:23 -295.719089 1.316487
BFGS: 17 22:43:23 -295.721800 1.319642
BFGS: 18 22:43:23 -295.727451 1.306089
BFGS: 19 22:43:24 -295.730805 1.312950
BFGS: 20 22:43:24 -295.740846 1.319584
BFGS: 21 22:43:24 -295.742146 1.316190
BFGS: 22 22:43:24 -295.752705 1.249270
BFGS: 23 22:43:24 -295.764804 1.112730
BFGS: 24 22:43:24 -295.780801 0.990874
BFGS: 25 22:43:24 -295.811228 0.898950
BFGS: 26 22:43:24 -295.827398 0.839531
BFGS: 27 22:43:24 -295.838269 0.756683
BFGS: 28 22:43:24 -295.856713 0.821461
BFGS: 29 22:43:24 -295.867967 0.715503
BFGS: 30 22:43:24 -295.873497 0.668074
BFGS: 31 22:43:25 -295.874907 0.678635
BFGS: 32 22:43:25 -295.876948 0.686125
BFGS: 33 22:43:25 -295.879115 0.681999
BFGS: 34 22:43:25 -295.880133 0.668752
BFGS: 35 22:43:25 -295.880486 0.657964
BFGS: 36 22:43:25 -295.880728 0.650038
BFGS: 37 22:43:25 -295.880999 0.643402
BFGS: 38 22:43:25 -295.881228 0.641374
BFGS: 39 22:43:25 -295.881358 0.643897
BFGS: 40 22:43:25 -295.881425 0.647204
BFGS: 41 22:43:25 -295.881491 0.650414
BFGS: 42 22:43:26 -295.881554 0.652704
BFGS: 43 22:43:26 -295.881614 0.652608
BFGS: 44 22:43:26 -295.881645 0.650345
BFGS: 45 22:43:26 -295.881663 0.647838
BFGS: 46 22:43:26 -295.881675 0.645591
BFGS: 47 22:43:26 -295.881684 0.643977
BFGS: 48 22:43:26 -295.881694 0.643203
BFGS: 49 22:43:26 -295.881702 0.643898
BFGS: 50 22:43:26 -295.881709 0.645588
BFGS: 51 22:43:26 -295.881713 0.647424
BFGS: 52 22:43:26 -295.881716 0.649070
BFGS: 53 22:43:26 -295.881720 0.650347
BFGS: 54 22:43:27 -295.881724 0.651038
BFGS: 55 22:43:27 -295.881729 0.650887
BFGS: 56 22:43:27 -295.881733 0.650256
BFGS: 57 22:43:27 -295.881735 0.649817
BFGS: 58 22:43:27 -295.881736 0.649678
BFGS: 59 22:43:27 -295.881737 0.649825
BFGS: 60 22:43:27 -295.881737 0.650257
BFGS: 61 22:43:27 -295.881740 0.650696
BFGS: 62 22:43:27 -295.881740 0.650895
BFGS: 63 22:43:27 -295.881740 0.650886
BFGS: 64 22:43:27 -295.881741 0.650752
BFGS: 65 22:43:28 -295.881741 0.650541
BFGS: 66 22:43:28 -295.881741 0.650283
BFGS: 67 22:43:28 -295.881740 0.650164
BFGS: 68 22:43:28 -295.881740 0.650151
BFGS: 69 22:43:28 -295.881741 0.650191
BFGS: 70 22:43:28 -295.881742 0.650229
BFGS: 71 22:43:28 -295.881742 0.650255
BFGS: 72 22:43:28 -295.881740 0.650254
BFGS: 73 22:43:28 -295.881741 0.650208
BFGS: 74 22:43:28 -295.881742 0.650165
BFGS: 75 22:43:28 -295.881742 0.650131
BFGS: 76 22:43:29 -295.881741 0.650105
BFGS: 77 22:43:29 -295.881741 0.650080
BFGS: 78 22:43:29 -295.881740 0.650083
BFGS: 79 22:43:29 -295.881740 0.650093
BFGS: 80 22:43:29 -295.881741 0.650110
BFGS: 81 22:43:29 -295.881742 0.650117
BFGS: 82 22:43:29 -295.881742 0.650126
BFGS: 83 22:43:29 -295.881743 0.650131
BFGS: 84 22:43:29 -295.881742 0.650133
BFGS: 85 22:43:29 -295.881741 0.650110
BFGS: 86 22:43:29 -295.881742 0.650108
BFGS: 87 22:43:29 -295.881742 0.650095
BFGS: 88 22:43:30 -295.881742 0.650102
BFGS: 89 22:43:30 -295.881741 0.650108
BFGS: 90 22:43:30 -295.881742 0.650108
BFGS: 91 22:43:30 -295.881740 0.650104
BFGS: 92 22:43:30 -295.881741 0.650104
BFGS: 93 22:43:30 -295.881740 0.650105
BFGS: 94 22:43:30 -295.881740 0.650086
BFGS: 95 22:43:30 -295.881741 0.650087
BFGS: 96 22:43:30 -295.881742 0.650087
BFGS: 97 22:43:30 -295.881740 0.650105
BFGS: 98 22:43:30 -295.881740 0.650098
BFGS: 99 22:43:31 -295.881742 0.650115
BFGS: 100 22:43:31 -295.881740 0.650120
BFGS: 101 22:43:31 -295.881740 0.650151
BFGS: 102 22:43:31 -295.881742 0.650193
BFGS: 103 22:43:31 -295.881741 0.650277
BFGS: 104 22:43:31 -295.881742 0.650385
BFGS: 105 22:43:31 -295.881743 0.650484
BFGS: 106 22:43:31 -295.881743 0.650570
BFGS: 107 22:43:31 -295.881745 0.650618
BFGS: 108 22:43:31 -295.881750 0.650614
BFGS: 109 22:43:31 -295.881759 0.650479
BFGS: 110 22:43:31 -295.881778 0.650112
BFGS: 111 22:43:32 -295.881818 0.649335
BFGS: 112 22:43:32 -295.881881 0.648132
BFGS: 113 22:43:32 -295.881972 0.646736
BFGS: 114 22:43:32 -295.882092 0.645398
BFGS: 115 22:43:32 -295.882296 0.643781
BFGS: 116 22:43:32 -295.882716 0.640927
BFGS: 117 22:43:32 -295.883668 0.634469
BFGS: 118 22:43:32 -295.885741 0.619435
BFGS: 119 22:43:32 -295.889743 0.586944
BFGS: 120 22:43:32 -295.895978 0.526030
BFGS: 121 22:43:32 -295.903390 0.451764
BFGS: 122 22:43:33 -295.911120 0.414128
BFGS: 123 22:43:33 -295.919900 0.345127
BFGS: 124 22:43:33 -295.928631 0.220148
BFGS: 125 22:43:33 -295.933707 0.119256
BFGS: 126 22:43:33 -295.935702 0.065745
BFGS: 127 22:43:33 -295.936292 0.044078
Step Time Energy fmax
BFGS: 0 22:43:33 -295.143128 1.622282
BFGS: 1 22:43:33 -295.248946 1.465306
BFGS: 2 22:43:33 -295.426696 2.416558
BFGS: 3 22:43:33 -295.520872 0.435063
BFGS: 4 22:43:33 -295.536446 0.591520
BFGS: 5 22:43:34 -295.556946 0.608309
BFGS: 6 22:43:34 -295.569974 0.383480
BFGS: 7 22:43:34 -295.575747 0.226459
BFGS: 8 22:43:34 -295.580231 0.291679
BFGS: 9 22:43:34 -295.584734 0.282597
BFGS: 10 22:43:34 -295.588435 0.183221
BFGS: 11 22:43:34 -295.589944 0.080465
BFGS: 12 22:43:34 -295.590246 0.074924
BFGS: 13 22:43:34 -295.590453 0.085031
BFGS: 14 22:43:34 -295.590891 0.105370
BFGS: 15 22:43:34 -295.591816 0.135003
BFGS: 16 22:43:34 -295.593706 0.165127
BFGS: 17 22:43:35 -295.597014 0.183001
BFGS: 18 22:43:35 -295.604140 0.348493
BFGS: 19 22:43:35 -295.614867 0.675612
BFGS: 20 22:43:35 -295.611337 0.997916
BFGS: 21 22:43:35 -295.624731 0.832520
BFGS: 22 22:43:35 -295.633608 0.866105
BFGS: 23 22:43:35 -295.716979 1.120071
BFGS: 24 22:43:35 -295.757234 1.054476
BFGS: 25 22:43:35 -295.779544 0.719064
BFGS: 26 22:43:35 -295.801816 0.682741
BFGS: 27 22:43:35 -295.831040 0.551049
BFGS: 28 22:43:36 -295.856225 0.388931
BFGS: 29 22:43:36 -295.880660 0.295912
BFGS: 30 22:43:36 -295.889878 0.321469
BFGS: 31 22:43:36 -295.898962 0.312896
BFGS: 32 22:43:36 -295.906802 0.218737
BFGS: 33 22:43:36 -295.913410 0.212482
BFGS: 34 22:43:36 -295.917290 0.209290
BFGS: 35 22:43:36 -295.920263 0.193651
BFGS: 36 22:43:36 -295.923172 0.174784
BFGS: 37 22:43:36 -295.926648 0.141700
BFGS: 38 22:43:36 -295.929949 0.107562
BFGS: 39 22:43:36 -295.932146 0.088854
BFGS: 40 22:43:37 -295.933211 0.107776
BFGS: 41 22:43:37 -295.934009 0.104284
BFGS: 42 22:43:37 -295.935010 0.082374
BFGS: 43 22:43:37 -295.935877 0.053581
BFGS: 44 22:43:37 -295.936327 0.037625
Step Time Energy fmax
BFGS: 0 22:43:37 -295.211410 1.463761
BFGS: 1 22:43:37 -295.304047 1.327415
BFGS: 2 22:43:37 -295.497793 1.994084
BFGS: 3 22:43:37 -295.565555 0.504441
BFGS: 4 22:43:37 -295.577991 0.567325
BFGS: 5 22:43:37 -295.602346 0.446688
BFGS: 6 22:43:38 -295.610436 0.261340
BFGS: 7 22:43:38 -295.616090 0.318508
BFGS: 8 22:43:38 -295.622498 0.343460
BFGS: 9 22:43:38 -295.629473 0.332591
BFGS: 10 22:43:38 -295.635678 0.256284
BFGS: 11 22:43:38 -295.639471 0.319237
BFGS: 12 22:43:38 -295.643838 0.442083
BFGS: 13 22:43:38 -295.660574 0.804367
BFGS: 14 22:43:38 -295.703764 1.289418
BFGS: 15 22:43:38 -295.754636 1.276392
BFGS: 16 22:43:38 -295.773279 1.101226
BFGS: 17 22:43:38 -295.827148 0.693906
BFGS: 18 22:43:39 -295.854097 0.417352
BFGS: 19 22:43:39 -295.864046 0.402317
BFGS: 20 22:43:39 -295.872092 0.399474
BFGS: 21 22:43:39 -295.884551 0.329006
BFGS: 22 22:43:39 -295.896484 0.276118
BFGS: 23 22:43:39 -295.904198 0.290473
BFGS: 24 22:43:39 -295.909129 0.288613
BFGS: 25 22:43:39 -295.914063 0.281629
BFGS: 26 22:43:39 -295.921527 0.275967
BFGS: 27 22:43:39 -295.932395 0.272212
BFGS: 28 22:43:39 -295.942505 0.255894
BFGS: 29 22:43:40 -295.949480 0.228772
BFGS: 30 22:43:40 -295.954500 0.204903
BFGS: 31 22:43:40 -295.959161 0.162492
BFGS: 32 22:43:40 -295.963350 0.111136
BFGS: 33 22:43:40 -295.965599 0.070049
BFGS: 34 22:43:40 -295.966598 0.066639
BFGS: 35 22:43:40 -295.967078 0.055488
BFGS: 36 22:43:40 -295.967371 0.039200
Step Time Energy fmax
BFGS: 0 22:43:40 -295.448984 1.076012
BFGS: 1 22:43:40 -295.513852 0.998215
BFGS: 2 22:43:40 -295.725479 0.984535
BFGS: 3 22:43:41 -295.749977 0.521068
BFGS: 4 22:43:41 -295.760408 0.502212
BFGS: 5 22:43:41 -295.807090 0.568341
BFGS: 6 22:43:41 -295.817221 0.538720
BFGS: 7 22:43:41 -295.877134 0.488345
BFGS: 8 22:43:41 -295.887815 0.381653
BFGS: 9 22:43:41 -295.895897 0.370443
BFGS: 10 22:43:41 -295.902910 0.335985
BFGS: 11 22:43:41 -295.912708 0.302015
BFGS: 12 22:43:41 -295.921367 0.286267
BFGS: 13 22:43:41 -295.927268 0.306899
BFGS: 14 22:43:41 -295.932840 0.289439
BFGS: 15 22:43:42 -295.940515 0.287942
BFGS: 16 22:43:42 -295.951037 0.209359
BFGS: 17 22:43:42 -295.958834 0.147024
BFGS: 18 22:43:42 -295.962069 0.118208
BFGS: 19 22:43:42 -295.963181 0.109689
BFGS: 20 22:43:42 -295.964270 0.095697
BFGS: 21 22:43:42 -295.965881 0.064486
BFGS: 22 22:43:42 -295.967157 0.051727
BFGS: 23 22:43:42 -295.967687 0.042113
Step Time Energy fmax
BFGS: 0 22:43:42 -295.315684 1.284481
BFGS: 1 22:43:42 -295.393587 1.173762
BFGS: 2 22:43:43 -295.600725 1.488379
BFGS: 3 22:43:43 -295.642417 0.562153
BFGS: 4 22:43:43 -295.652845 0.510774
BFGS: 5 22:43:43 -295.686783 0.444865
BFGS: 6 22:43:43 -295.692552 0.451686
BFGS: 7 22:43:43 -295.740639 0.765120
BFGS: 8 22:43:43 -295.760865 0.697676
BFGS: 9 22:43:43 -295.798707 0.886326
BFGS: 10 22:43:43 -295.823043 0.914148
BFGS: 11 22:43:43 -295.879521 0.691276
BFGS: 12 22:43:43 -295.892353 0.464170
BFGS: 13 22:43:44 -295.910643 0.320573
BFGS: 14 22:43:44 -295.916403 0.297749
BFGS: 15 22:43:44 -295.922986 0.336157
BFGS: 16 22:43:44 -295.933064 0.327621
BFGS: 17 22:43:44 -295.942621 0.289956
BFGS: 18 22:43:44 -295.948646 0.259405
BFGS: 19 22:43:44 -295.953588 0.208769
BFGS: 20 22:43:44 -295.956720 0.196053
BFGS: 21 22:43:44 -295.959627 0.211484
BFGS: 22 22:43:44 -295.963745 0.165937
BFGS: 23 22:43:44 -295.965960 0.089045
BFGS: 24 22:43:44 -295.966732 0.059031
BFGS: 25 22:43:45 -295.967087 0.053628
BFGS: 26 22:43:45 -295.967433 0.044898
Step Time Energy fmax
BFGS: 0 22:43:45 -295.381625 1.187851
BFGS: 1 22:43:45 -295.452096 1.093128
BFGS: 2 22:43:45 -295.662980 1.224982
BFGS: 3 22:43:45 -295.694257 0.560628
BFGS: 4 22:43:45 -295.704650 0.458441
BFGS: 5 22:43:45 -295.745631 0.544481
BFGS: 6 22:43:45 -295.753883 0.536221
BFGS: 7 22:43:45 -295.842253 0.553534
BFGS: 8 22:43:45 -295.878710 0.827824
BFGS: 9 22:43:46 -295.893437 0.657985
BFGS: 10 22:43:46 -295.924076 0.575725
BFGS: 11 22:43:46 -295.952108 0.313328
BFGS: 12 22:43:46 -295.956525 0.217276
BFGS: 13 22:43:46 -295.959379 0.211064
BFGS: 14 22:43:46 -295.961678 0.214637
BFGS: 15 22:43:46 -295.964379 0.190088
BFGS: 16 22:43:46 -295.966560 0.136800
BFGS: 17 22:43:46 -295.967620 0.069331
BFGS: 18 22:43:46 -295.967971 0.024526
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 22:43:46 -303.943842 0.297200
BFGS: 1 22:43:47 -303.947968 0.235104
BFGS: 2 22:43:47 -303.957740 0.126439
BFGS: 3 22:43:47 -303.960167 0.112638
BFGS: 4 22:43:47 -303.961640 0.088802
BFGS: 5 22:43:47 -303.962459 0.086117
BFGS: 6 22:43:47 -303.963299 0.073974
BFGS: 7 22:43:47 -303.964051 0.067924
BFGS: 8 22:43:47 -303.964563 0.071791
BFGS: 9 22:43:47 -303.964823 0.051075
BFGS: 10 22:43:47 -303.964985 0.035789
Step Time Energy fmax
BFGS: 0 22:43:47 -303.942056 0.289849
BFGS: 1 22:43:48 -303.946346 0.246755
BFGS: 2 22:43:48 -303.956601 0.128861
BFGS: 3 22:43:48 -303.959145 0.109829
BFGS: 4 22:43:48 -303.960665 0.087310
BFGS: 5 22:43:48 -303.961533 0.085517
BFGS: 6 22:43:48 -303.962442 0.076261
BFGS: 7 22:43:48 -303.963220 0.059221
BFGS: 8 22:43:48 -303.963717 0.069115
BFGS: 9 22:43:48 -303.963964 0.053615
BFGS: 10 22:43:48 -303.964135 0.033808
Step Time Energy fmax
BFGS: 0 22:43:49 -303.937377 0.355083
BFGS: 1 22:43:49 -303.942949 0.298402
BFGS: 2 22:43:49 -303.954957 0.144936
BFGS: 3 22:43:49 -303.957891 0.106818
BFGS: 4 22:43:49 -303.959569 0.093603
BFGS: 5 22:43:49 -303.960564 0.099827
BFGS: 6 22:43:49 -303.961732 0.092790
BFGS: 7 22:43:49 -303.962793 0.071428
BFGS: 8 22:43:49 -303.963483 0.073121
BFGS: 9 22:43:49 -303.963793 0.053474
BFGS: 10 22:43:49 -303.963969 0.039151
Step Time Energy fmax
BFGS: 0 22:43:50 -303.144279 0.963688
BFGS: 1 22:43:50 -303.173381 0.718601
BFGS: 2 22:43:50 -303.227875 0.666582
BFGS: 3 22:43:50 -303.259680 0.696689
BFGS: 4 22:43:50 -303.304584 0.941738
BFGS: 5 22:43:50 -303.334748 0.810963
BFGS: 6 22:43:50 -303.408502 0.604892
BFGS: 7 22:43:50 -303.415391 0.382125
BFGS: 8 22:43:50 -303.423216 0.173562
BFGS: 9 22:43:50 -303.429918 0.147694
BFGS: 10 22:43:50 -303.432694 0.143962
BFGS: 11 22:43:51 -303.434597 0.166599
BFGS: 12 22:43:51 -303.436974 0.142587
BFGS: 13 22:43:51 -303.439085 0.100600
BFGS: 14 22:43:51 -303.440444 0.109958
BFGS: 15 22:43:51 -303.441220 0.081682
BFGS: 16 22:43:51 -303.441848 0.064547
BFGS: 17 22:43:51 -303.442597 0.075592
BFGS: 18 22:43:51 -303.443401 0.105413
BFGS: 19 22:43:51 -303.444046 0.101764
BFGS: 20 22:43:51 -303.444422 0.057716
BFGS: 21 22:43:51 -303.444624 0.049670
/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 22:44:03 -301.657353 3.039677
BFGS: 1 22:44:04 -301.932310 2.488098
BFGS: 2 22:44:04 -302.367454 5.543548
BFGS: 3 22:44:05 -302.566859 2.054287
BFGS: 4 22:44:06 -303.050889 2.419851
BFGS: 5 22:44:07 -303.136277 1.794263
BFGS: 6 22:44:08 -303.306781 1.389974
BFGS: 7 22:44:09 -303.414304 1.268804
BFGS: 8 22:44:09 -303.514034 1.813500
BFGS: 9 22:44:10 -303.515904 1.105086
BFGS: 10 22:44:11 -303.551047 1.365775
BFGS: 11 22:44:12 -303.589779 1.355423
BFGS: 12 22:44:12 -303.609501 1.052019
BFGS: 13 22:44:13 -303.621685 0.634852
BFGS: 14 22:44:14 -303.641408 0.775924
BFGS: 15 22:44:15 -303.678943 0.754808
BFGS: 16 22:44:16 -303.711403 0.968985
BFGS: 17 22:44:16 -303.733701 0.777890
BFGS: 18 22:44:17 -303.744255 0.843533
BFGS: 19 22:44:18 -303.749395 0.898126
BFGS: 20 22:44:19 -303.743894 0.743179
BFGS: 21 22:44:20 -303.740653 0.589492
BFGS: 22 22:44:20 -303.741858 0.750666
BFGS: 23 22:44:21 -303.744584 0.735160
BFGS: 24 22:44:22 -303.742064 0.648752
BFGS: 25 22:44:23 -303.738467 0.584084
BFGS: 26 22:44:23 -303.742835 0.661462
BFGS: 27 22:44:24 -303.752362 0.666396
BFGS: 28 22:44:25 -303.757856 0.502785
BFGS: 29 22:44:26 -303.761471 0.488596
BFGS: 30 22:44:27 -303.766796 0.572678
BFGS: 31 22:44:27 -303.771350 0.672732
BFGS: 32 22:44:28 -303.764636 1.174695
BFGS: 33 22:44:29 -303.776902 0.810588
BFGS: 34 22:44:30 -303.779994 0.639480
BFGS: 35 22:44:31 -303.782836 1.140865
BFGS: 36 22:44:31 -303.787136 1.080500
BFGS: 37 22:44:32 -303.790870 0.638445
BFGS: 38 22:44:33 -303.792865 0.601805
BFGS: 39 22:44:34 -303.790537 1.009402
BFGS: 40 22:44:34 -303.794110 0.586576
BFGS: 41 22:44:35 -303.795021 0.578993
BFGS: 42 22:44:36 -303.789929 0.529393
BFGS: 43 22:44:37 -303.782261 0.618285
BFGS: 44 22:44:38 -303.780525 0.561242
BFGS: 45 22:44:38 -303.777491 0.549953
BFGS: 46 22:44:39 -303.775979 0.465247
BFGS: 47 22:44:40 -303.777389 0.436729
BFGS: 48 22:44:41 -303.777708 0.360012
BFGS: 49 22:44:42 -303.776945 0.379027
BFGS: 50 22:44:42 -303.773374 0.576702
BFGS: 51 22:44:43 -303.772902 0.593006
BFGS: 52 22:44:44 -303.773355 0.746378
BFGS: 53 22:44:45 -303.775725 0.750629
BFGS: 54 22:44:46 -303.777922 0.771834
BFGS: 55 22:44:46 -303.780067 0.783121
BFGS: 56 22:44:47 -303.781109 0.841388
BFGS: 57 22:44:48 -303.781003 0.900640
BFGS: 58 22:44:49 -303.779683 0.806720
BFGS: 59 22:44:49 -303.782052 0.737220
BFGS: 60 22:44:50 -303.783559 0.570028
BFGS: 61 22:44:51 -303.784136 0.781357
BFGS: 62 22:44:52 -303.784102 0.697933
BFGS: 63 22:44:53 -303.783956 0.583071
BFGS: 64 22:44:53 -303.783700 0.434993
BFGS: 65 22:44:54 -303.783599 0.402484
BFGS: 66 22:44:55 -303.783054 0.714380
BFGS: 67 22:44:56 -303.781101 1.159226
BFGS: 68 22:44:57 -303.783092 0.506249
BFGS: 69 22:44:57 -303.783914 0.700448
BFGS: 70 22:44:58 -303.783896 0.692328
BFGS: 71 22:44:59 -303.782211 0.457095
BFGS: 72 22:45:00 -303.783847 0.400970
BFGS: 73 22:45:00 -303.784392 0.308589
BFGS: 74 22:45:01 -303.784729 0.239474
BFGS: 75 22:45:02 -303.784729 0.223542
BFGS: 76 22:45:02 -303.784729 0.247763
BFGS: 77 22:45:03 -303.784729 0.147199
BFGS: 78 22:45:03 -303.784729 0.136341
BFGS: 79 22:45:04 -303.784729 0.117656
BFGS: 80 22:45:04 -303.784729 0.104066
BFGS: 81 22:45:05 -303.784729 0.121939
BFGS: 82 22:45:05 -303.784729 0.112342
BFGS: 83 22:45:06 -303.784729 0.114066
BFGS: 84 22:45:06 -303.784729 0.161230
BFGS: 85 22:45:07 -303.784729 0.222650
BFGS: 86 22:45:07 -303.784729 0.190022
BFGS: 87 22:45:07 -303.784729 0.119538
BFGS: 88 22:45:08 -303.784729 0.095303
BFGS: 89 22:45:08 -303.784729 0.092491
BFGS: 90 22:45:09 -303.784729 0.070327
BFGS: 91 22:45:09 -303.784729 0.026566
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_7419/3247994494.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")