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 19:48:32 -301.930956 4.140496
BFGS: 1 19:48:32 -302.315220 3.192805
BFGS: 2 19:48:32 -303.271828 3.278811
BFGS: 3 19:48:32 -303.465260 3.153763
BFGS: 4 19:48:32 -303.745434 2.143583
BFGS: 5 19:48:33 -303.970059 2.818247
BFGS: 6 19:48:33 -304.071360 1.520383
BFGS: 7 19:48:33 -304.235810 0.910649
BFGS: 8 19:48:33 -304.369090 1.643784
BFGS: 9 19:48:33 -304.457277 1.679189
BFGS: 10 19:48:33 -304.579773 1.212311
BFGS: 11 19:48:33 -304.646099 0.549518
BFGS: 12 19:48:33 -304.658479 0.343371
BFGS: 13 19:48:33 -304.664852 0.285392
BFGS: 14 19:48:33 -304.670158 0.207110
BFGS: 15 19:48:33 -304.674583 0.186162
BFGS: 16 19:48:33 -304.677799 0.167251
BFGS: 17 19:48:34 -304.679321 0.136444
BFGS: 18 19:48:34 -304.680368 0.125801
BFGS: 19 19:48:34 -304.681478 0.135619
BFGS: 20 19:48:34 -304.683314 0.152826
BFGS: 21 19:48:34 -304.686192 0.145815
BFGS: 22 19:48:34 -304.689140 0.126278
BFGS: 23 19:48:34 -304.690439 0.077241
BFGS: 24 19:48:34 -304.690908 0.058040
BFGS: 25 19:48:34 -304.691239 0.060278
BFGS: 26 19:48:34 -304.691649 0.064719
BFGS: 27 19:48:34 -304.692103 0.056201
BFGS: 28 19:48:34 -304.692367 0.033021
Step Time Energy fmax
BFGS: 0 19:48:35 -301.674507 4.155677
BFGS: 1 19:48:35 -302.059101 3.262488
BFGS: 2 19:48:35 -303.009519 3.290347
BFGS: 3 19:48:35 -303.161338 3.155145
BFGS: 4 19:48:35 -303.445242 2.007353
BFGS: 5 19:48:35 -303.623975 3.619254
BFGS: 6 19:48:35 -303.745243 1.748246
BFGS: 7 19:48:35 -303.882840 0.702220
BFGS: 8 19:48:35 -303.952710 1.130918
BFGS: 9 19:48:35 -303.984542 0.830785
BFGS: 10 19:48:35 -304.066347 1.014192
BFGS: 11 19:48:36 -304.116336 1.249435
BFGS: 12 19:48:36 -304.153300 0.670831
BFGS: 13 19:48:36 -304.167888 0.376514
BFGS: 14 19:48:36 -304.184381 0.640566
BFGS: 15 19:48:36 -304.203617 0.842781
BFGS: 16 19:48:36 -304.222139 0.756192
BFGS: 17 19:48:36 -304.237147 0.592018
BFGS: 18 19:48:36 -304.268416 0.854231
BFGS: 19 19:48:36 -304.330636 1.415100
BFGS: 20 19:48:36 -304.385715 1.663772
BFGS: 21 19:48:36 -304.461057 1.312110
BFGS: 22 19:48:36 -304.479718 0.965235
BFGS: 23 19:48:37 -304.513679 0.840345
BFGS: 24 19:48:37 -304.533124 0.428080
BFGS: 25 19:48:37 -304.547335 0.358608
BFGS: 26 19:48:37 -304.590901 0.436219
BFGS: 27 19:48:37 -304.611095 0.417399
BFGS: 28 19:48:37 -304.625637 0.381464
BFGS: 29 19:48:37 -304.637284 0.342895
BFGS: 30 19:48:37 -304.650376 0.383087
BFGS: 31 19:48:37 -304.663627 0.341569
BFGS: 32 19:48:37 -304.673288 0.197613
BFGS: 33 19:48:37 -304.676920 0.206425
BFGS: 34 19:48:37 -304.679917 0.200404
BFGS: 35 19:48:38 -304.683946 0.146144
BFGS: 36 19:48:38 -304.687425 0.099742
BFGS: 37 19:48:38 -304.689850 0.057036
BFGS: 38 19:48:38 -304.690928 0.044270
Step Time Energy fmax
BFGS: 0 19:48:38 -300.930711 4.036996
BFGS: 1 19:48:38 -301.330886 3.434153
BFGS: 2 19:48:38 -302.507599 3.446532
BFGS: 3 19:48:38 -302.215762 9.352031
BFGS: 4 19:48:38 -302.811679 2.904366
BFGS: 5 19:48:38 -302.955467 2.121118
BFGS: 6 19:48:38 -303.083979 2.025483
BFGS: 7 19:48:39 -303.121102 0.648840
BFGS: 8 19:48:39 -303.141940 0.595532
BFGS: 9 19:48:39 -303.197491 0.913364
BFGS: 10 19:48:39 -303.210942 0.599228
BFGS: 11 19:48:39 -303.221434 0.260007
BFGS: 12 19:48:39 -303.224816 0.361906
BFGS: 13 19:48:39 -303.235377 0.502564
BFGS: 14 19:48:39 -303.243340 0.498023
BFGS: 15 19:48:39 -303.252233 0.479198
BFGS: 16 19:48:39 -303.262816 0.550103
BFGS: 17 19:48:39 -303.295424 1.065362
BFGS: 18 19:48:39 -303.371704 2.304304
BFGS: 19 19:48:40 -303.350933 3.305362
BFGS: 20 19:48:40 -303.421306 2.429266
BFGS: 21 19:48:40 -303.443499 2.464824
BFGS: 22 19:48:40 -303.710952 2.849421
BFGS: 23 19:48:40 -303.891022 2.612456
BFGS: 24 19:48:40 -303.998438 1.140712
BFGS: 25 19:48:40 -304.053224 0.901985
BFGS: 26 19:48:40 -304.117790 0.804379
BFGS: 27 19:48:40 -304.156498 0.622743
BFGS: 28 19:48:40 -304.174751 0.670346
BFGS: 29 19:48:40 -304.184714 0.604960
BFGS: 30 19:48:41 -304.199921 0.412341
BFGS: 31 19:48:41 -304.211254 0.283939
BFGS: 32 19:48:41 -304.218529 0.261808
BFGS: 33 19:48:41 -304.224979 0.407238
BFGS: 34 19:48:41 -304.232064 0.453255
BFGS: 35 19:48:41 -304.238301 0.397524
BFGS: 36 19:48:41 -304.243755 0.544955
BFGS: 37 19:48:41 -304.249036 0.629551
BFGS: 38 19:48:41 -304.256570 0.689287
BFGS: 39 19:48:41 -304.268131 0.722838
BFGS: 40 19:48:41 -304.280664 0.665024
BFGS: 41 19:48:41 -304.291974 0.529970
BFGS: 42 19:48:42 -304.298329 0.487802
BFGS: 43 19:48:42 -304.305431 0.689938
BFGS: 44 19:48:42 -304.313090 0.714541
BFGS: 45 19:48:42 -304.319241 0.595807
BFGS: 46 19:48:42 -304.322204 0.499582
BFGS: 47 19:48:42 -304.324708 0.452066
BFGS: 48 19:48:42 -304.327509 0.460109
BFGS: 49 19:48:42 -304.329565 0.443334
BFGS: 50 19:48:42 -304.331019 0.419819
BFGS: 51 19:48:42 -304.332031 0.400788
BFGS: 52 19:48:42 -304.333226 0.376946
BFGS: 53 19:48:42 -304.334516 0.412224
BFGS: 54 19:48:43 -304.335821 0.425651
BFGS: 55 19:48:43 -304.336777 0.386424
BFGS: 56 19:48:43 -304.337383 0.398783
BFGS: 57 19:48:43 -304.338055 0.408852
BFGS: 58 19:48:43 -304.339206 0.413137
BFGS: 59 19:48:43 -304.340677 0.402234
BFGS: 60 19:48:43 -304.341818 0.382149
BFGS: 61 19:48:43 -304.342291 0.366444
BFGS: 62 19:48:43 -304.342486 0.354603
BFGS: 63 19:48:43 -304.342687 0.345734
BFGS: 64 19:48:43 -304.342994 0.341229
BFGS: 65 19:48:44 -304.343398 0.336345
BFGS: 66 19:48:44 -304.343699 0.334166
BFGS: 67 19:48:44 -304.343823 0.334235
BFGS: 68 19:48:44 -304.343881 0.334411
BFGS: 69 19:48:44 -304.343940 0.333493
BFGS: 70 19:48:44 -304.344023 0.331266
BFGS: 71 19:48:44 -304.344111 0.327598
BFGS: 72 19:48:44 -304.344174 0.325338
BFGS: 73 19:48:44 -304.344202 0.325129
BFGS: 74 19:48:44 -304.344225 0.325934
BFGS: 75 19:48:44 -304.344258 0.327398
BFGS: 76 19:48:44 -304.344305 0.329473
BFGS: 77 19:48:45 -304.344352 0.331012
BFGS: 78 19:48:45 -304.344371 0.331225
BFGS: 79 19:48:45 -304.344379 0.330740
BFGS: 80 19:48:45 -304.344386 0.330136
BFGS: 81 19:48:45 -304.344394 0.329525
BFGS: 82 19:48:45 -304.344409 0.329222
BFGS: 83 19:48:45 -304.344419 0.329757
BFGS: 84 19:48:45 -304.344424 0.330742
BFGS: 85 19:48:45 -304.344428 0.331422
BFGS: 86 19:48:45 -304.344430 0.332029
BFGS: 87 19:48:45 -304.344432 0.332580
BFGS: 88 19:48:45 -304.344434 0.333253
BFGS: 89 19:48:46 -304.344440 0.333536
BFGS: 90 19:48:46 -304.344440 0.333261
BFGS: 91 19:48:46 -304.344442 0.332843
BFGS: 92 19:48:46 -304.344443 0.332449
BFGS: 93 19:48:46 -304.344444 0.332004
BFGS: 94 19:48:46 -304.344443 0.331543
BFGS: 95 19:48:46 -304.344445 0.331153
BFGS: 96 19:48:46 -304.344445 0.331101
BFGS: 97 19:48:46 -304.344445 0.331286
BFGS: 98 19:48:47 -304.344446 0.331425
BFGS: 99 19:48:47 -304.344446 0.331510
BFGS: 100 19:48:47 -304.344445 0.331501
BFGS: 101 19:48:47 -304.344447 0.331425
BFGS: 102 19:48:47 -304.344448 0.331209
BFGS: 103 19:48:47 -304.344447 0.331046
BFGS: 104 19:48:47 -304.344447 0.331027
BFGS: 105 19:48:47 -304.344447 0.331080
BFGS: 106 19:48:47 -304.344446 0.331148
BFGS: 107 19:48:47 -304.344448 0.331260
BFGS: 108 19:48:47 -304.344447 0.331372
BFGS: 109 19:48:47 -304.344447 0.331420
BFGS: 110 19:48:48 -304.344447 0.331348
BFGS: 111 19:48:48 -304.344447 0.331270
BFGS: 112 19:48:48 -304.344445 0.331210
BFGS: 113 19:48:48 -304.344446 0.331129
BFGS: 114 19:48:48 -304.344446 0.331040
BFGS: 115 19:48:48 -304.344446 0.330970
BFGS: 116 19:48:48 -304.344446 0.330988
BFGS: 117 19:48:48 -304.344447 0.331030
BFGS: 118 19:48:48 -304.344448 0.331062
BFGS: 119 19:48:48 -304.344447 0.331119
BFGS: 120 19:48:48 -304.344447 0.331133
BFGS: 121 19:48:49 -304.344447 0.331166
BFGS: 122 19:48:49 -304.344446 0.331169
BFGS: 123 19:48:49 -304.344449 0.331129
BFGS: 124 19:48:49 -304.344447 0.331134
BFGS: 125 19:48:49 -304.344447 0.331137
BFGS: 126 19:48:49 -304.344447 0.331147
BFGS: 127 19:48:49 -304.344447 0.331136
BFGS: 128 19:48:49 -304.344447 0.331132
BFGS: 129 19:48:49 -304.344448 0.331119
BFGS: 130 19:48:49 -304.344447 0.331121
BFGS: 131 19:48:49 -304.344449 0.331115
BFGS: 132 19:48:49 -304.344448 0.331115
BFGS: 133 19:48:50 -304.344448 0.331103
BFGS: 134 19:48:50 -304.344449 0.331121
BFGS: 135 19:48:50 -304.344447 0.331124
BFGS: 136 19:48:50 -304.344447 0.331143
BFGS: 137 19:48:50 -304.344447 0.331144
BFGS: 138 19:48:50 -304.344449 0.331117
BFGS: 139 19:48:50 -304.344447 0.331120
BFGS: 140 19:48:50 -304.344449 0.331139
BFGS: 141 19:48:50 -304.344449 0.331140
BFGS: 142 19:48:50 -304.344447 0.331047
BFGS: 143 19:48:50 -304.344449 0.331124
BFGS: 144 19:48:50 -304.344448 0.331122
BFGS: 145 19:48:51 -304.344447 0.331138
BFGS: 146 19:48:51 -304.344449 0.331135
BFGS: 147 19:48:51 -304.344448 0.331109
BFGS: 148 19:48:51 -304.344448 0.331127
BFGS: 149 19:48:51 -304.344449 0.331139
BFGS: 150 19:48:51 -304.344447 0.331129
BFGS: 151 19:48:51 -304.344448 0.331128
BFGS: 152 19:48:51 -304.344447 0.331123
BFGS: 153 19:48:51 -304.344449 0.331125
BFGS: 154 19:48:51 -304.344449 0.331146
BFGS: 155 19:48:51 -304.344449 0.331144
BFGS: 156 19:48:52 -304.344448 0.331138
BFGS: 157 19:48:52 -304.344447 0.331125
BFGS: 158 19:48:52 -304.344447 0.331176
BFGS: 159 19:48:52 -304.344449 0.331129
BFGS: 160 19:48:52 -304.344446 0.331133
BFGS: 161 19:48:52 -304.344447 0.331149
BFGS: 162 19:48:52 -304.344449 0.331133
BFGS: 163 19:48:52 -304.344448 0.331130
BFGS: 164 19:48:52 -304.344448 0.331144
BFGS: 165 19:48:52 -304.344448 0.331128
BFGS: 166 19:48:52 -304.344447 0.331130
BFGS: 167 19:48:52 -304.344447 0.331128
BFGS: 168 19:48:53 -304.344447 0.331157
BFGS: 169 19:48:53 -304.344447 0.331127
BFGS: 170 19:48:53 -304.344448 0.331145
BFGS: 171 19:48:53 -304.344449 0.331133
BFGS: 172 19:48:53 -304.344447 0.331129
BFGS: 173 19:48:53 -304.344447 0.331140
BFGS: 174 19:48:53 -304.344447 0.331141
BFGS: 175 19:48:53 -304.344447 0.331129
BFGS: 176 19:48:53 -304.344448 0.331129
BFGS: 177 19:48:53 -304.344447 0.331143
BFGS: 178 19:48:53 -304.344449 0.331137
BFGS: 179 19:48:54 -304.344447 0.331142
BFGS: 180 19:48:54 -304.344447 0.331129
BFGS: 181 19:48:54 -304.344448 0.331128
BFGS: 182 19:48:54 -304.344449 0.331150
BFGS: 183 19:48:54 -304.344447 0.331138
BFGS: 184 19:48:54 -304.344447 0.331127
BFGS: 185 19:48:54 -304.344449 0.331127
BFGS: 186 19:48:54 -304.344448 0.331138
BFGS: 187 19:48:54 -304.344448 0.331134
BFGS: 188 19:48:54 -304.344448 0.331125
BFGS: 189 19:48:54 -304.344448 0.331126
BFGS: 190 19:48:54 -304.344449 0.331130
BFGS: 191 19:48:55 -304.344448 0.331135
BFGS: 192 19:48:55 -304.344448 0.331127
BFGS: 193 19:48:55 -304.344447 0.331144
BFGS: 194 19:48:55 -304.344447 0.331134
BFGS: 195 19:48:55 -304.344448 0.331140
BFGS: 196 19:48:55 -304.344448 0.331144
BFGS: 197 19:48:55 -304.344447 0.331125
BFGS: 198 19:48:55 -304.344447 0.331138
BFGS: 199 19:48:55 -304.344447 0.331126
BFGS: 200 19:48:55 -304.344447 0.331125
BFGS: 201 19:48:55 -304.344447 0.331136
BFGS: 202 19:48:56 -304.344447 0.331127
BFGS: 203 19:48:56 -304.344448 0.331126
BFGS: 204 19:48:56 -304.344447 0.331123
BFGS: 205 19:48:56 -304.344448 0.331121
BFGS: 206 19:48:56 -304.344447 0.331124
BFGS: 207 19:48:56 -304.344447 0.331144
BFGS: 208 19:48:56 -304.344447 0.331127
BFGS: 209 19:48:56 -304.344449 0.331125
BFGS: 210 19:48:56 -304.344448 0.331138
BFGS: 211 19:48:56 -304.344447 0.331150
BFGS: 212 19:48:56 -304.344447 0.331153
BFGS: 213 19:48:56 -304.344447 0.331128
BFGS: 214 19:48:57 -304.344448 0.331126
BFGS: 215 19:48:57 -304.344448 0.331148
BFGS: 216 19:48:57 -304.344447 0.331134
BFGS: 217 19:48:57 -304.344449 0.331127
BFGS: 218 19:48:57 -304.344449 0.331126
BFGS: 219 19:48:57 -304.344448 0.331151
BFGS: 220 19:48:57 -304.344448 0.331138
BFGS: 221 19:48:57 -304.344447 0.331127
BFGS: 222 19:48:57 -304.344447 0.331127
BFGS: 223 19:48:57 -304.344447 0.331134
BFGS: 224 19:48:57 -304.344449 0.331124
BFGS: 225 19:48:57 -304.344449 0.331126
BFGS: 226 19:48:58 -304.344447 0.331127
BFGS: 227 19:48:58 -304.344447 0.331152
BFGS: 228 19:48:58 -304.344448 0.331134
BFGS: 229 19:48:58 -304.344447 0.331155
BFGS: 230 19:48:58 -304.344448 0.331128
BFGS: 231 19:48:58 -304.344449 0.331132
BFGS: 232 19:48:58 -304.344447 0.331126
BFGS: 233 19:48:58 -304.344447 0.331140
BFGS: 234 19:48:58 -304.344447 0.331132
BFGS: 235 19:48:58 -304.344449 0.331136
BFGS: 236 19:48:58 -304.344447 0.331125
BFGS: 237 19:48:59 -304.344448 0.331137
BFGS: 238 19:48:59 -304.344446 0.331132
BFGS: 239 19:48:59 -304.344447 0.331124
BFGS: 240 19:48:59 -304.344448 0.331145
BFGS: 241 19:48:59 -304.344448 0.331128
BFGS: 242 19:48:59 -304.344449 0.331132
BFGS: 243 19:48:59 -304.344447 0.331126
BFGS: 244 19:48:59 -304.344447 0.331124
BFGS: 245 19:48:59 -304.344448 0.331122
BFGS: 246 19:48:59 -304.344448 0.331127
BFGS: 247 19:48:59 -304.344449 0.331139
BFGS: 248 19:48:59 -304.344448 0.331157
BFGS: 249 19:49:00 -304.344449 0.331153
BFGS: 250 19:49:00 -304.344447 0.331119
BFGS: 251 19:49:00 -304.344448 0.331127
BFGS: 252 19:49:00 -304.344448 0.331125
BFGS: 253 19:49:00 -304.344447 0.331152
BFGS: 254 19:49:00 -304.344449 0.331134
BFGS: 255 19:49:00 -304.344449 0.331126
BFGS: 256 19:49:00 -304.344448 0.331127
BFGS: 257 19:49:00 -304.344449 0.331134
BFGS: 258 19:49:00 -304.344447 0.331140
BFGS: 259 19:49:00 -304.344448 0.331124
BFGS: 260 19:49:01 -304.344446 0.331137
BFGS: 261 19:49:01 -304.344447 0.331136
BFGS: 262 19:49:01 -304.344447 0.331119
BFGS: 263 19:49:01 -304.344449 0.331124
BFGS: 264 19:49:01 -304.344447 0.331123
BFGS: 265 19:49:01 -304.344447 0.331151
BFGS: 266 19:49:01 -304.344447 0.331136
BFGS: 267 19:49:01 -304.344448 0.331119
BFGS: 268 19:49:01 -304.344447 0.331120
BFGS: 269 19:49:01 -304.344449 0.331137
BFGS: 270 19:49:01 -304.344447 0.331120
BFGS: 271 19:49:01 -304.344447 0.331124
BFGS: 272 19:49:02 -304.344447 0.331156
BFGS: 273 19:49:02 -304.344448 0.331138
BFGS: 274 19:49:02 -304.344448 0.331119
BFGS: 275 19:49:02 -304.344449 0.331120
BFGS: 276 19:49:02 -304.344446 0.331137
BFGS: 277 19:49:02 -304.344449 0.331136
BFGS: 278 19:49:02 -304.344447 0.331124
BFGS: 279 19:49:02 -304.344448 0.331124
BFGS: 280 19:49:02 -304.344449 0.331124
BFGS: 281 19:49:02 -304.344448 0.331137
BFGS: 282 19:49:02 -304.344447 0.331120
BFGS: 283 19:49:02 -304.344449 0.331139
BFGS: 284 19:49:03 -304.344447 0.331139
BFGS: 285 19:49:03 -304.344448 0.331119
BFGS: 286 19:49:03 -304.344447 0.331119
BFGS: 287 19:49:03 -304.344448 0.331135
BFGS: 288 19:49:03 -304.344447 0.331143
BFGS: 289 19:49:03 -304.344448 0.331119
BFGS: 290 19:49:03 -304.344447 0.331125
BFGS: 291 19:49:03 -304.344447 0.331134
BFGS: 292 19:49:03 -304.344447 0.331136
BFGS: 293 19:49:03 -304.344447 0.331139
BFGS: 294 19:49:03 -304.344448 0.331126
BFGS: 295 19:49:04 -304.344447 0.331119
BFGS: 296 19:49:04 -304.344449 0.331138
BFGS: 297 19:49:04 -304.344449 0.331126
BFGS: 298 19:49:04 -304.344447 0.331155
BFGS: 299 19:49:04 -304.344447 0.331138
BFGS: 300 19:49:04 -304.344449 0.331126
Step Time Energy fmax
BFGS: 0 19:49:04 -302.116038 4.100394
BFGS: 1 19:49:04 -302.487055 2.970054
BFGS: 2 19:49:04 -303.381530 3.348852
BFGS: 3 19:49:04 -303.574791 3.124895
BFGS: 4 19:49:04 -303.924664 2.214735
BFGS: 5 19:49:04 -304.098031 2.682968
BFGS: 6 19:49:05 -304.220216 1.940741
BFGS: 7 19:49:05 -304.484329 1.224831
BFGS: 8 19:49:05 -304.531584 0.850528
BFGS: 9 19:49:05 -304.599258 0.752101
BFGS: 10 19:49:05 -304.653652 0.345492
BFGS: 11 19:49:05 -304.667884 0.294077
BFGS: 12 19:49:05 -304.673628 0.243633
BFGS: 13 19:49:05 -304.678470 0.176513
BFGS: 14 19:49:05 -304.681509 0.129937
BFGS: 15 19:49:05 -304.683193 0.108793
BFGS: 16 19:49:05 -304.684034 0.100486
BFGS: 17 19:49:05 -304.684707 0.099821
BFGS: 18 19:49:06 -304.685737 0.110278
BFGS: 19 19:49:06 -304.687090 0.104051
BFGS: 20 19:49:06 -304.688450 0.125943
BFGS: 21 19:49:06 -304.689356 0.094052
BFGS: 22 19:49:06 -304.689804 0.073190
BFGS: 23 19:49:06 -304.690303 0.078834
BFGS: 24 19:49:06 -304.691082 0.068094
BFGS: 25 19:49:06 -304.691865 0.066523
BFGS: 26 19:49:06 -304.692278 0.038340
Step Time Energy fmax
BFGS: 0 19:49:06 -302.363394 3.893412
BFGS: 1 19:49:06 -302.727611 2.955349
BFGS: 2 19:49:07 -303.634730 3.128908
BFGS: 3 19:49:07 -303.813592 2.791015
BFGS: 4 19:49:07 -304.062744 1.458059
BFGS: 5 19:49:07 -304.146227 1.479917
BFGS: 6 19:49:07 -304.205763 1.301642
BFGS: 7 19:49:07 -304.292946 0.542385
BFGS: 8 19:49:07 -304.305333 0.530029
BFGS: 9 19:49:07 -304.328719 0.361681
BFGS: 10 19:49:07 -304.338750 0.206642
BFGS: 11 19:49:07 -304.343782 0.140191
BFGS: 12 19:49:07 -304.345191 0.111418
BFGS: 13 19:49:07 -304.346378 0.113754
BFGS: 14 19:49:08 -304.348763 0.107734
BFGS: 15 19:49:08 -304.350141 0.103193
BFGS: 16 19:49:08 -304.350918 0.095147
BFGS: 17 19:49:08 -304.351551 0.088433
BFGS: 18 19:49:08 -304.352593 0.116283
BFGS: 19 19:49:08 -304.354105 0.131662
BFGS: 20 19:49:08 -304.355585 0.102908
BFGS: 21 19:49:08 -304.356365 0.066521
BFGS: 22 19:49:08 -304.356636 0.042308
Step Time Energy fmax
BFGS: 0 19:49:08 -302.391366 4.033262
BFGS: 1 19:49:08 -302.752265 2.831480
BFGS: 2 19:49:08 -303.586886 3.288224
BFGS: 3 19:49:09 -303.754902 2.940094
BFGS: 4 19:49:09 -304.092131 1.569127
BFGS: 5 19:49:09 -304.168475 1.411096
BFGS: 6 19:49:09 -304.497360 0.929109
BFGS: 7 19:49:09 -304.542062 1.113739
BFGS: 8 19:49:09 -304.620122 0.884391
BFGS: 9 19:49:09 -304.655212 0.477451
BFGS: 10 19:49:09 -304.665338 0.331808
BFGS: 11 19:49:09 -304.670236 0.198562
BFGS: 12 19:49:09 -304.674132 0.160025
BFGS: 13 19:49:09 -304.677486 0.133405
BFGS: 14 19:49:10 -304.679214 0.120435
BFGS: 15 19:49:10 -304.680264 0.110999
BFGS: 16 19:49:10 -304.681530 0.111313
BFGS: 17 19:49:10 -304.683492 0.141836
BFGS: 18 19:49:10 -304.686230 0.144241
BFGS: 19 19:49:10 -304.688386 0.096453
BFGS: 20 19:49:10 -304.689513 0.067681
BFGS: 21 19:49:10 -304.690054 0.071333
BFGS: 22 19:49:10 -304.690536 0.073513
BFGS: 23 19:49:10 -304.691285 0.068893
BFGS: 24 19:49:10 -304.691921 0.047092
Step Time Energy fmax
BFGS: 0 19:49:10 -301.912514 4.117793
BFGS: 1 19:49:11 -302.285333 3.105824
BFGS: 2 19:49:11 -303.211143 3.330884
BFGS: 3 19:49:11 -303.406430 3.190593
BFGS: 4 19:49:11 -303.719461 2.215396
BFGS: 5 19:49:11 -304.018054 3.032326
BFGS: 6 19:49:11 -304.152466 1.960524
BFGS: 7 19:49:11 -304.382250 1.441613
BFGS: 8 19:49:11 -304.446563 1.110317
BFGS: 9 19:49:11 -304.507803 0.945910
BFGS: 10 19:49:11 -304.635337 0.618211
BFGS: 11 19:49:11 -304.646337 0.486006
BFGS: 12 19:49:11 -304.660389 0.321577
BFGS: 13 19:49:12 -304.668503 0.241668
BFGS: 14 19:49:12 -304.672884 0.210611
BFGS: 15 19:49:12 -304.674930 0.135229
BFGS: 16 19:49:12 -304.676228 0.144847
BFGS: 17 19:49:12 -304.678785 0.178050
BFGS: 18 19:49:12 -304.681894 0.210413
BFGS: 19 19:49:12 -304.684586 0.154603
BFGS: 20 19:49:12 -304.686060 0.102550
BFGS: 21 19:49:12 -304.687047 0.099286
BFGS: 22 19:49:12 -304.688036 0.137121
BFGS: 23 19:49:12 -304.689421 0.153228
BFGS: 24 19:49:13 -304.690791 0.114428
BFGS: 25 19:49:13 -304.691577 0.073511
BFGS: 26 19:49:13 -304.691812 0.038745
Step Time Energy fmax
BFGS: 0 19:49:13 -302.165487 4.101246
BFGS: 1 19:49:13 -302.536849 3.155083
BFGS: 2 19:49:13 -303.455933 3.207886
BFGS: 3 19:49:13 -303.670223 3.079829
BFGS: 4 19:49:13 -303.946272 2.109176
BFGS: 5 19:49:13 -304.201792 2.404405
BFGS: 6 19:49:13 -304.295563 1.517385
BFGS: 7 19:49:13 -304.483273 0.993098
BFGS: 8 19:49:13 -304.530729 1.072981
BFGS: 9 19:49:14 -304.591764 0.781354
BFGS: 10 19:49:14 -304.640965 0.520593
BFGS: 11 19:49:14 -304.663172 0.381649
BFGS: 12 19:49:14 -304.670394 0.271405
BFGS: 13 19:49:14 -304.674841 0.179424
BFGS: 14 19:49:14 -304.677825 0.164344
BFGS: 15 19:49:14 -304.680481 0.132133
BFGS: 16 19:49:14 -304.681718 0.115508
BFGS: 17 19:49:14 -304.682833 0.105682
BFGS: 18 19:49:14 -304.684353 0.112471
BFGS: 19 19:49:14 -304.686303 0.129894
BFGS: 20 19:49:14 -304.687929 0.105626
BFGS: 21 19:49:15 -304.688760 0.062416
BFGS: 22 19:49:15 -304.689226 0.072209
BFGS: 23 19:49:15 -304.689786 0.094162
BFGS: 24 19:49:15 -304.690664 0.103365
BFGS: 25 19:49:15 -304.691505 0.078096
BFGS: 26 19:49:15 -304.691913 0.034695
Step Time Energy fmax
BFGS: 0 19:49:15 -301.583559 4.116978
BFGS: 1 19:49:15 -301.972889 3.335697
BFGS: 2 19:49:15 -302.981519 3.294424
BFGS: 3 19:49:15 -303.124636 4.058261
BFGS: 4 19:49:15 -303.409599 2.334324
BFGS: 5 19:49:16 -303.660706 3.224370
BFGS: 6 19:49:16 -303.777088 2.194331
BFGS: 7 19:49:16 -304.022434 0.986917
BFGS: 8 19:49:16 -304.073438 0.952050
BFGS: 9 19:49:16 -304.201756 0.852536
BFGS: 10 19:49:16 -304.241763 0.834022
BFGS: 11 19:49:16 -304.282252 0.537756
BFGS: 12 19:49:16 -304.301500 0.419099
BFGS: 13 19:49:16 -304.312936 0.301302
BFGS: 14 19:49:16 -304.319344 0.310737
BFGS: 15 19:49:16 -304.325661 0.310709
BFGS: 16 19:49:16 -304.330788 0.249407
BFGS: 17 19:49:17 -304.334817 0.219910
BFGS: 18 19:49:17 -304.338750 0.190459
BFGS: 19 19:49:17 -304.342320 0.221792
BFGS: 20 19:49:17 -304.345334 0.190977
BFGS: 21 19:49:17 -304.347635 0.150002
BFGS: 22 19:49:17 -304.349391 0.166832
BFGS: 23 19:49:17 -304.350727 0.131471
BFGS: 24 19:49:17 -304.352396 0.123674
BFGS: 25 19:49:17 -304.354384 0.105215
BFGS: 26 19:49:17 -304.355525 0.056910
BFGS: 27 19:49:17 -304.355945 0.054005
BFGS: 28 19:49:17 -304.356160 0.042531
Step Time Energy fmax
BFGS: 0 19:49:18 -302.026882 4.093549
BFGS: 1 19:49:18 -302.408793 3.383449
BFGS: 2 19:49:18 -303.391121 3.055544
BFGS: 3 19:49:18 -303.578412 3.551502
BFGS: 4 19:49:18 -303.815478 2.169998
BFGS: 5 19:49:18 -304.016395 1.858650
BFGS: 6 19:49:18 -304.079806 1.392053
BFGS: 7 19:49:18 -304.279681 1.404699
BFGS: 8 19:49:18 -304.347936 1.250847
BFGS: 9 19:49:18 -304.480450 1.189583
BFGS: 10 19:49:18 -304.551212 1.303786
BFGS: 11 19:49:19 -304.614232 0.751944
BFGS: 12 19:49:19 -304.628118 0.329881
BFGS: 13 19:49:19 -304.639819 0.398917
BFGS: 14 19:49:19 -304.647381 0.312203
BFGS: 15 19:49:19 -304.654700 0.228769
BFGS: 16 19:49:19 -304.659892 0.266368
BFGS: 17 19:49:19 -304.664337 0.287552
BFGS: 18 19:49:19 -304.670287 0.203005
BFGS: 19 19:49:19 -304.674432 0.171055
BFGS: 20 19:49:19 -304.677927 0.153292
BFGS: 21 19:49:19 -304.681132 0.130930
BFGS: 22 19:49:19 -304.683443 0.164591
BFGS: 23 19:49:20 -304.685618 0.149966
BFGS: 24 19:49:20 -304.687947 0.103346
BFGS: 25 19:49:20 -304.689562 0.077545
BFGS: 26 19:49:20 -304.690233 0.067243
BFGS: 27 19:49:20 -304.690579 0.059348
BFGS: 28 19:49:20 -304.691012 0.040057
# 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 19:49:20 -296.240250 4.386145
BFGS: 1 19:49:20 -296.729161 4.678298
BFGS: 2 19:49:20 -298.236805 3.287276
BFGS: 3 19:49:20 -297.565651 11.658740
BFGS: 4 19:49:20 -298.470969 1.904710
BFGS: 5 19:49:21 -298.539923 1.119055
BFGS: 6 19:49:21 -298.591800 1.125179
BFGS: 7 19:49:21 -298.612894 1.061732
BFGS: 8 19:49:21 -298.749282 1.399896
BFGS: 9 19:49:21 -298.813016 1.738035
BFGS: 10 19:49:21 -298.918425 2.506831
BFGS: 11 19:49:21 -299.046210 2.366442
BFGS: 12 19:49:21 -299.455459 1.577816
BFGS: 13 19:49:21 -299.623347 2.709262
BFGS: 14 19:49:21 -299.810888 1.625945
BFGS: 15 19:49:21 -299.885350 0.809490
BFGS: 16 19:49:21 -299.923541 0.700893
BFGS: 17 19:49:22 -299.952414 0.675311
BFGS: 18 19:49:22 -300.001378 0.947222
BFGS: 19 19:49:22 -300.047681 1.217472
BFGS: 20 19:49:22 -300.131399 1.398833
BFGS: 21 19:49:22 -300.209773 1.257702
BFGS: 22 19:49:22 -300.384575 1.587631
BFGS: 23 19:49:22 -300.117998 2.282561
BFGS: 24 19:49:22 -300.439322 1.056783
BFGS: 25 19:49:22 -300.477908 0.968935
BFGS: 26 19:49:22 -300.508126 0.611623
BFGS: 27 19:49:22 -300.570258 0.412877
BFGS: 28 19:49:23 -300.592884 0.301533
BFGS: 29 19:49:23 -300.602515 0.307029
BFGS: 30 19:49:23 -300.610085 0.252931
BFGS: 31 19:49:23 -300.616418 0.160716
BFGS: 32 19:49:23 -300.620544 0.080346
BFGS: 33 19:49:23 -300.622432 0.057013
BFGS: 34 19:49:23 -300.623077 0.047333
Step Time Energy fmax
BFGS: 0 19:49:23 -296.015247 4.357064
BFGS: 1 19:49:23 -296.541236 4.728113
BFGS: 2 19:49:23 -298.206841 3.062991
BFGS: 3 19:49:23 -296.847073 16.535172
BFGS: 4 19:49:23 -298.386530 1.868565
BFGS: 5 19:49:24 -298.449321 1.046174
BFGS: 6 19:49:24 -298.484871 0.611787
BFGS: 7 19:49:24 -298.489511 0.340071
BFGS: 8 19:49:24 -298.495964 0.169376
BFGS: 9 19:49:24 -298.498158 0.203657
BFGS: 10 19:49:24 -298.499248 0.175380
BFGS: 11 19:49:24 -298.500276 0.150905
BFGS: 12 19:49:24 -298.502958 0.171262
BFGS: 13 19:49:24 -298.511664 0.349615
BFGS: 14 19:49:24 -298.541136 0.787128
BFGS: 15 19:49:24 -298.608340 1.105647
BFGS: 16 19:49:25 -298.508887 2.711286
BFGS: 17 19:49:25 -298.749103 1.684466
BFGS: 18 19:49:25 -298.935344 1.732711
BFGS: 19 19:49:25 -299.010554 2.788792
BFGS: 20 19:49:25 -299.070079 2.694844
BFGS: 21 19:49:25 -299.273171 3.094231
BFGS: 22 19:49:25 -299.310619 3.285221
BFGS: 23 19:49:25 -299.338679 3.002175
BFGS: 24 19:49:25 -299.406777 2.667011
BFGS: 25 19:49:25 -299.435885 2.535821
BFGS: 26 19:49:25 -299.448175 2.426089
BFGS: 27 19:49:25 -299.464225 2.337175
BFGS: 28 19:49:26 -299.485554 2.291679
BFGS: 29 19:49:26 -299.507520 2.333561
BFGS: 30 19:49:26 -299.525475 2.414706
BFGS: 31 19:49:26 -299.542461 2.522408
BFGS: 32 19:49:26 -299.567627 2.647985
BFGS: 33 19:49:26 -299.622021 2.894180
BFGS: 34 19:49:26 -299.702569 3.218249
BFGS: 35 19:49:26 -299.756056 3.249537
BFGS: 36 19:49:26 -299.804734 3.145625
BFGS: 37 19:49:26 -299.925436 2.765706
BFGS: 38 19:49:26 -299.962351 2.365175
BFGS: 39 19:49:26 -300.054102 2.114677
BFGS: 40 19:49:27 -300.120400 2.068424
BFGS: 41 19:49:27 -300.159469 2.185495
BFGS: 42 19:49:27 -300.179573 2.300966
BFGS: 43 19:49:27 -300.194039 2.407376
BFGS: 44 19:49:27 -300.209452 2.433468
BFGS: 45 19:49:27 -300.221719 2.425754
BFGS: 46 19:49:27 -300.229215 2.324973
BFGS: 47 19:49:27 -300.232931 2.277432
BFGS: 48 19:49:27 -300.235359 2.215936
BFGS: 49 19:49:27 -300.238811 2.196168
BFGS: 50 19:49:27 -300.242003 2.196612
BFGS: 51 19:49:28 -300.243710 2.234988
BFGS: 52 19:49:28 -300.244717 2.257341
BFGS: 53 19:49:28 -300.245853 2.278602
BFGS: 54 19:49:28 -300.247045 2.282407
BFGS: 55 19:49:28 -300.248110 2.267249
BFGS: 56 19:49:28 -300.248774 2.241375
BFGS: 57 19:49:28 -300.249213 2.219150
BFGS: 58 19:49:28 -300.249661 2.201056
BFGS: 59 19:49:28 -300.250129 2.191990
BFGS: 60 19:49:28 -300.250451 2.197168
BFGS: 61 19:49:28 -300.250597 2.207350
BFGS: 62 19:49:28 -300.250670 2.215871
BFGS: 63 19:49:29 -300.250721 2.222670
BFGS: 64 19:49:29 -300.250768 2.226802
BFGS: 65 19:49:29 -300.250813 2.227906
BFGS: 66 19:49:29 -300.250842 2.225071
BFGS: 67 19:49:29 -300.250859 2.221254
BFGS: 68 19:49:29 -300.250868 2.218123
BFGS: 69 19:49:29 -300.250882 2.215700
BFGS: 70 19:49:29 -300.250886 2.214602
BFGS: 71 19:49:29 -300.250895 2.215231
BFGS: 72 19:49:29 -300.250896 2.216820
BFGS: 73 19:49:29 -300.250903 2.218267
BFGS: 74 19:49:30 -300.250902 2.219557
BFGS: 75 19:49:30 -300.250904 2.220306
BFGS: 76 19:49:30 -300.250905 2.220334
BFGS: 77 19:49:30 -300.250909 2.219708
BFGS: 78 19:49:30 -300.250906 2.218980
BFGS: 79 19:49:30 -300.250911 2.218332
BFGS: 80 19:49:30 -300.250906 2.217884
BFGS: 81 19:49:30 -300.250907 2.217782
BFGS: 82 19:49:30 -300.250905 2.217999
BFGS: 83 19:49:30 -300.250909 2.218308
BFGS: 84 19:49:30 -300.250906 2.218584
BFGS: 85 19:49:30 -300.250907 2.218805
BFGS: 86 19:49:31 -300.250909 2.218801
BFGS: 87 19:49:31 -300.250907 2.218668
BFGS: 88 19:49:31 -300.250908 2.218500
BFGS: 89 19:49:31 -300.250907 2.218393
BFGS: 90 19:49:31 -300.250908 2.218300
BFGS: 91 19:49:31 -300.250907 2.218243
BFGS: 92 19:49:31 -300.250908 2.218280
BFGS: 93 19:49:31 -300.250907 2.218378
BFGS: 94 19:49:31 -300.250906 2.218415
BFGS: 95 19:49:31 -300.250907 2.218456
BFGS: 96 19:49:31 -300.250907 2.218475
BFGS: 97 19:49:31 -300.250909 2.218460
BFGS: 98 19:49:32 -300.250906 2.218440
BFGS: 99 19:49:32 -300.250904 2.218435
BFGS: 100 19:49:32 -300.250906 2.218386
BFGS: 101 19:49:32 -300.250907 2.218382
BFGS: 102 19:49:32 -300.250909 2.218433
BFGS: 103 19:49:32 -300.250904 2.218437
BFGS: 104 19:49:32 -300.250907 2.218389
BFGS: 105 19:49:32 -300.250908 2.218407
BFGS: 106 19:49:32 -300.250908 2.218415
BFGS: 107 19:49:32 -300.250907 2.218418
BFGS: 108 19:49:32 -300.250905 2.218440
BFGS: 109 19:49:32 -300.250904 2.218428
BFGS: 110 19:49:33 -300.250907 2.218412
BFGS: 111 19:49:33 -300.250907 2.218415
BFGS: 112 19:49:33 -300.250905 2.218428
BFGS: 113 19:49:33 -300.250906 2.218422
BFGS: 114 19:49:33 -300.250907 2.218417
BFGS: 115 19:49:33 -300.250904 2.218427
BFGS: 116 19:49:33 -300.250907 2.218413
BFGS: 117 19:49:33 -300.250906 2.218413
BFGS: 118 19:49:33 -300.250905 2.218437
BFGS: 119 19:49:33 -300.250906 2.218426
BFGS: 120 19:49:33 -300.250907 2.218413
BFGS: 121 19:49:34 -300.250907 2.218412
BFGS: 122 19:49:34 -300.250907 2.218438
BFGS: 123 19:49:34 -300.250902 2.218429
BFGS: 124 19:49:34 -300.250907 2.218413
BFGS: 125 19:49:34 -300.250907 2.218412
BFGS: 126 19:49:34 -300.250906 2.218428
BFGS: 127 19:49:34 -300.250904 2.218422
BFGS: 128 19:49:34 -300.250906 2.218410
BFGS: 129 19:49:34 -300.250906 2.218412
BFGS: 130 19:49:34 -300.250908 2.218432
BFGS: 131 19:49:34 -300.250901 2.218431
BFGS: 132 19:49:34 -300.250904 2.218413
BFGS: 133 19:49:35 -300.250904 2.218412
BFGS: 134 19:49:35 -300.250907 2.218431
BFGS: 135 19:49:35 -300.250904 2.218423
BFGS: 136 19:49:35 -300.250909 2.218388
BFGS: 137 19:49:35 -300.250905 2.218412
BFGS: 138 19:49:35 -300.250908 2.218428
BFGS: 139 19:49:35 -300.250904 2.218424
BFGS: 140 19:49:35 -300.250905 2.218413
BFGS: 141 19:49:35 -300.250905 2.218415
BFGS: 142 19:49:35 -300.250904 2.218430
BFGS: 143 19:49:35 -300.250903 2.218429
BFGS: 144 19:49:35 -300.250910 2.218395
BFGS: 145 19:49:36 -300.250905 2.218410
BFGS: 146 19:49:36 -300.250907 2.218426
BFGS: 147 19:49:36 -300.250902 2.218430
BFGS: 148 19:49:36 -300.250907 2.218400
BFGS: 149 19:49:36 -300.250905 2.218411
BFGS: 150 19:49:36 -300.250908 2.218429
BFGS: 151 19:49:36 -300.250904 2.218431
BFGS: 152 19:49:36 -300.250904 2.218346
BFGS: 153 19:49:36 -300.250905 2.218410
BFGS: 154 19:49:36 -300.250904 2.218430
BFGS: 155 19:49:36 -300.250905 2.218413
BFGS: 156 19:49:37 -300.250904 2.218414
BFGS: 157 19:49:37 -300.250903 2.218420
BFGS: 158 19:49:37 -300.250905 2.218423
BFGS: 159 19:49:37 -300.250909 2.218418
BFGS: 160 19:49:37 -300.250905 2.218412
BFGS: 161 19:49:37 -300.250904 2.218421
BFGS: 162 19:49:37 -300.250911 2.218418
BFGS: 163 19:49:37 -300.250904 2.218421
BFGS: 164 19:49:37 -300.250907 2.218400
BFGS: 165 19:49:37 -300.250904 2.218418
BFGS: 166 19:49:37 -300.250909 2.218418
BFGS: 167 19:49:37 -300.250904 2.218415
BFGS: 168 19:49:38 -300.250907 2.218425
BFGS: 169 19:49:38 -300.250906 2.218414
BFGS: 170 19:49:38 -300.250906 2.218422
BFGS: 171 19:49:38 -300.250904 2.218429
BFGS: 172 19:49:38 -300.250905 2.218418
BFGS: 173 19:49:38 -300.250909 2.218416
BFGS: 174 19:49:38 -300.250905 2.218421
BFGS: 175 19:49:38 -300.250905 2.218421
BFGS: 176 19:49:38 -300.250907 2.218412
BFGS: 177 19:49:38 -300.250908 2.218419
BFGS: 178 19:49:38 -300.250907 2.218421
BFGS: 179 19:49:39 -300.250905 2.218428
BFGS: 180 19:49:39 -300.250910 2.218404
BFGS: 181 19:49:39 -300.250908 2.218416
BFGS: 182 19:49:39 -300.250905 2.218421
BFGS: 183 19:49:39 -300.250905 2.218423
BFGS: 184 19:49:39 -300.250909 2.218398
BFGS: 185 19:49:39 -300.250907 2.218417
BFGS: 186 19:49:39 -300.250904 2.218422
BFGS: 187 19:49:39 -300.250904 2.218431
BFGS: 188 19:49:39 -300.250904 2.218421
BFGS: 189 19:49:39 -300.250905 2.218415
BFGS: 190 19:49:39 -300.250906 2.218430
BFGS: 191 19:49:40 -300.250905 2.218422
BFGS: 192 19:49:40 -300.250907 2.218415
BFGS: 193 19:49:40 -300.250904 2.218422
BFGS: 194 19:49:40 -300.250904 2.218420
BFGS: 195 19:49:40 -300.250906 2.218421
BFGS: 196 19:49:40 -300.250911 2.218401
BFGS: 197 19:49:40 -300.250908 2.218420
BFGS: 198 19:49:40 -300.250905 2.218420
BFGS: 199 19:49:40 -300.250904 2.218421
BFGS: 200 19:49:40 -300.250907 2.218421
BFGS: 201 19:49:40 -300.250902 2.218421
BFGS: 202 19:49:40 -300.250905 2.218420
BFGS: 203 19:49:41 -300.250905 2.218422
BFGS: 204 19:49:41 -300.250904 2.218423
BFGS: 205 19:49:41 -300.250904 2.218421
BFGS: 206 19:49:41 -300.250904 2.218420
BFGS: 207 19:49:41 -300.250903 2.218420
BFGS: 208 19:49:41 -300.250906 2.218421
BFGS: 209 19:49:41 -300.250902 2.218422
BFGS: 210 19:49:41 -300.250904 2.218421
BFGS: 211 19:49:41 -300.250905 2.218413
BFGS: 212 19:49:41 -300.250905 2.218420
BFGS: 213 19:49:41 -300.250903 2.218418
BFGS: 214 19:49:42 -300.250904 2.218421
BFGS: 215 19:49:42 -300.250907 2.218409
BFGS: 216 19:49:42 -300.250906 2.218422
BFGS: 217 19:49:42 -300.250904 2.218421
BFGS: 218 19:49:42 -300.250907 2.218414
BFGS: 219 19:49:42 -300.250906 2.218414
BFGS: 220 19:49:42 -300.250904 2.218413
BFGS: 221 19:49:42 -300.250905 2.218415
BFGS: 222 19:49:42 -300.250904 2.218421
BFGS: 223 19:49:42 -300.250907 2.218423
BFGS: 224 19:49:42 -300.250906 2.218422
BFGS: 225 19:49:42 -300.250904 2.218415
BFGS: 226 19:49:43 -300.250905 2.218421
BFGS: 227 19:49:43 -300.250905 2.218421
BFGS: 228 19:49:43 -300.250905 2.218431
BFGS: 229 19:49:43 -300.250907 2.218410
BFGS: 230 19:49:43 -300.250904 2.218430
BFGS: 231 19:49:43 -300.250904 2.218422
BFGS: 232 19:49:43 -300.250904 2.218429
BFGS: 233 19:49:43 -300.250905 2.218422
BFGS: 234 19:49:43 -300.250906 2.218414
BFGS: 235 19:49:43 -300.250904 2.218421
BFGS: 236 19:49:43 -300.250904 2.218422
BFGS: 237 19:49:43 -300.250904 2.218410
BFGS: 238 19:49:44 -300.250904 2.218418
BFGS: 239 19:49:44 -300.250908 2.218420
BFGS: 240 19:49:44 -300.250908 2.218418
BFGS: 241 19:49:44 -300.250906 2.218410
BFGS: 242 19:49:44 -300.250905 2.218420
BFGS: 243 19:49:44 -300.250907 2.218424
BFGS: 244 19:49:44 -300.250904 2.218422
BFGS: 245 19:49:44 -300.250902 2.218416
BFGS: 246 19:49:44 -300.250905 2.218419
BFGS: 247 19:49:44 -300.250908 2.218419
BFGS: 248 19:49:44 -300.250905 2.218415
BFGS: 249 19:49:45 -300.250906 2.218413
BFGS: 250 19:49:45 -300.250904 2.218422
BFGS: 251 19:49:45 -300.250905 2.218425
BFGS: 252 19:49:45 -300.250904 2.218419
BFGS: 253 19:49:45 -300.250907 2.218417
BFGS: 254 19:49:45 -300.250904 2.218427
BFGS: 255 19:49:45 -300.250904 2.218428
BFGS: 256 19:49:45 -300.250905 2.218423
BFGS: 257 19:49:45 -300.250910 2.218408
BFGS: 258 19:49:45 -300.250902 2.218429
BFGS: 259 19:49:45 -300.250904 2.218429
BFGS: 260 19:49:45 -300.250905 2.218412
BFGS: 261 19:49:46 -300.250904 2.218421
BFGS: 262 19:49:46 -300.250904 2.218428
BFGS: 263 19:49:46 -300.250909 2.218411
BFGS: 264 19:49:46 -300.250904 2.218428
BFGS: 265 19:49:46 -300.250908 2.218418
BFGS: 266 19:49:46 -300.250904 2.218412
BFGS: 267 19:49:46 -300.250907 2.218424
BFGS: 268 19:49:46 -300.250907 2.218426
BFGS: 269 19:49:46 -300.250907 2.218414
BFGS: 270 19:49:46 -300.250905 2.218415
BFGS: 271 19:49:46 -300.250905 2.218422
BFGS: 272 19:49:47 -300.250904 2.218422
BFGS: 273 19:49:47 -300.250905 2.218427
BFGS: 274 19:49:47 -300.250908 2.218409
BFGS: 275 19:49:47 -300.250908 2.218410
BFGS: 276 19:49:47 -300.250902 2.218429
BFGS: 277 19:49:47 -300.250902 2.218427
BFGS: 278 19:49:47 -300.250907 2.218408
BFGS: 279 19:49:47 -300.250909 2.218411
BFGS: 280 19:49:47 -300.250903 2.218430
BFGS: 281 19:49:47 -300.250902 2.218429
BFGS: 282 19:49:48 -300.250909 2.218405
BFGS: 283 19:49:48 -300.250908 2.218409
BFGS: 284 19:49:48 -300.250903 2.218431
BFGS: 285 19:49:48 -300.250902 2.218430
BFGS: 286 19:49:48 -300.250908 2.218406
BFGS: 287 19:49:48 -300.250909 2.218410
BFGS: 288 19:49:48 -300.250902 2.218432
BFGS: 289 19:49:48 -300.250902 2.218429
BFGS: 290 19:49:48 -300.250908 2.218405
BFGS: 291 19:49:48 -300.250908 2.218407
BFGS: 292 19:49:48 -300.250907 2.218421
BFGS: 293 19:49:48 -300.250902 2.218432
BFGS: 294 19:49:49 -300.250908 2.218406
BFGS: 295 19:49:49 -300.250907 2.218412
BFGS: 296 19:49:49 -300.250902 2.218431
BFGS: 297 19:49:49 -300.250904 2.218422
BFGS: 298 19:49:49 -300.250909 2.218407
BFGS: 299 19:49:49 -300.250906 2.218412
BFGS: 300 19:49:49 -300.250902 2.218429
Step Time Energy fmax
BFGS: 0 19:49:49 -297.590775 4.551878
BFGS: 1 19:49:49 -298.071708 4.589178
BFGS: 2 19:49:49 -299.251003 3.049736
BFGS: 3 19:49:49 -299.365298 4.073360
BFGS: 4 19:49:50 -299.589227 1.181832
BFGS: 5 19:49:50 -299.666486 1.043082
BFGS: 6 19:49:50 -299.907836 0.731179
BFGS: 7 19:49:50 -299.940433 0.737721
BFGS: 8 19:49:50 -299.993511 0.589879
BFGS: 9 19:49:50 -300.028559 0.413383
BFGS: 10 19:49:50 -300.043616 0.280497
BFGS: 11 19:49:50 -300.049781 0.287631
BFGS: 12 19:49:50 -300.055314 0.243773
BFGS: 13 19:49:50 -300.059695 0.186347
BFGS: 14 19:49:50 -300.063632 0.162818
BFGS: 15 19:49:50 -300.067620 0.200363
BFGS: 16 19:49:51 -300.071759 0.234128
BFGS: 17 19:49:51 -300.075472 0.208241
BFGS: 18 19:49:51 -300.077990 0.132944
BFGS: 19 19:49:51 -300.079498 0.049912
Step Time Energy fmax
BFGS: 0 19:49:51 -296.276523 4.405321
BFGS: 1 19:49:51 -296.765378 4.690360
BFGS: 2 19:49:51 -298.255434 3.285659
BFGS: 3 19:49:51 -297.622297 11.337158
BFGS: 4 19:49:51 -298.491388 1.890426
BFGS: 5 19:49:51 -298.559970 1.123236
BFGS: 6 19:49:51 -298.614133 1.140284
BFGS: 7 19:49:51 -298.637084 1.081952
BFGS: 8 19:49:52 -298.752013 1.231277
BFGS: 9 19:49:52 -298.797068 1.270844
BFGS: 10 19:49:52 -299.225975 1.689415
BFGS: 11 19:49:52 -299.597402 1.947567
BFGS: 12 19:49:52 -299.693546 2.409996
BFGS: 13 19:49:52 -299.760404 1.702361
BFGS: 14 19:49:52 -299.809129 1.376264
BFGS: 15 19:49:52 -299.989713 0.563977
BFGS: 16 19:49:52 -300.025199 0.458618
BFGS: 17 19:49:52 -300.061650 0.330964
BFGS: 18 19:49:52 -300.071421 0.169733
BFGS: 19 19:49:53 -300.075622 0.108701
BFGS: 20 19:49:53 -300.076619 0.131090
BFGS: 21 19:49:53 -300.077474 0.134160
BFGS: 22 19:49:53 -300.078767 0.110461
BFGS: 23 19:49:53 -300.079713 0.067926
BFGS: 24 19:49:53 -300.080098 0.044627
Step Time Energy fmax
BFGS: 0 19:49:53 -296.181404 4.376291
BFGS: 1 19:49:53 -296.677192 4.688597
BFGS: 2 19:49:53 -298.221148 3.237661
BFGS: 3 19:49:53 -297.401669 12.687674
BFGS: 4 19:49:53 -298.440122 1.896654
BFGS: 5 19:49:53 -298.507096 1.079650
BFGS: 6 19:49:54 -298.551097 0.951237
BFGS: 7 19:49:54 -298.563957 0.808397
BFGS: 8 19:49:54 -298.629032 0.897905
BFGS: 9 19:49:54 -298.649729 1.061821
BFGS: 10 19:49:54 -298.767690 1.997967
BFGS: 11 19:49:54 -298.861477 2.856328
BFGS: 12 19:49:54 -298.884262 3.267742
BFGS: 13 19:49:54 -298.917146 3.246288
BFGS: 14 19:49:54 -298.984125 3.369761
BFGS: 15 19:49:54 -299.163560 3.635223
BFGS: 16 19:49:54 -299.314332 4.012359
BFGS: 17 19:49:55 -299.447041 3.334439
BFGS: 18 19:49:55 -299.838049 1.867916
BFGS: 19 19:49:55 -299.966230 1.076546
BFGS: 20 19:49:55 -300.086769 1.411243
BFGS: 21 19:49:55 -300.264866 1.801217
BFGS: 22 19:49:55 -300.385533 1.429616
BFGS: 23 19:49:55 -300.456578 1.153238
BFGS: 24 19:49:55 -300.514381 0.838197
BFGS: 25 19:49:55 -300.545958 0.551010
BFGS: 26 19:49:55 -300.573012 0.471680
BFGS: 27 19:49:55 -300.594952 0.339482
BFGS: 28 19:49:55 -300.607030 0.270702
BFGS: 29 19:49:56 -300.611345 0.212912
BFGS: 30 19:49:56 -300.614339 0.156377
BFGS: 31 19:49:56 -300.618171 0.136078
BFGS: 32 19:49:56 -300.621258 0.116344
BFGS: 33 19:49:56 -300.623069 0.063121
BFGS: 34 19:49:56 -300.623692 0.064449
BFGS: 35 19:49:56 -300.623954 0.053048
BFGS: 36 19:49:56 -300.624255 0.036317
Step Time Energy fmax
BFGS: 0 19:49:56 -295.911108 4.356012
BFGS: 1 19:49:56 -296.467206 4.763370
BFGS: 2 19:49:56 -298.225398 2.889509
BFGS: 3 19:49:56 -296.357533 19.976986
BFGS: 4 19:49:57 -298.380012 1.823096
BFGS: 5 19:49:57 -298.439398 1.071631
BFGS: 6 19:49:57 -298.474529 0.549575
BFGS: 7 19:49:57 -298.478043 0.226760
BFGS: 8 19:49:57 -298.481167 0.087160
BFGS: 9 19:49:57 -298.482932 0.082832
BFGS: 10 19:49:57 -298.483330 0.039455
Step Time Energy fmax
BFGS: 0 19:49:57 -296.495218 4.440165
BFGS: 1 19:49:57 -296.968988 4.669275
BFGS: 2 19:49:57 -298.363188 3.444809
BFGS: 3 19:49:57 -298.131437 8.597256
BFGS: 4 19:49:58 -298.667251 1.940403
BFGS: 5 19:49:58 -298.748896 1.410835
BFGS: 6 19:49:58 -298.896443 2.084469
BFGS: 7 19:49:58 -299.072197 2.539001
BFGS: 8 19:49:58 -299.325323 2.465947
BFGS: 9 19:49:58 -299.434964 1.634944
BFGS: 10 19:49:58 -299.514667 1.459632
BFGS: 11 19:49:58 -299.739792 1.097200
BFGS: 12 19:49:58 -299.851405 1.039008
BFGS: 13 19:49:58 -299.897163 0.898428
BFGS: 14 19:49:58 -299.922250 0.474151
BFGS: 15 19:49:58 -299.937876 0.384520
BFGS: 16 19:49:59 -299.946982 0.460665
BFGS: 17 19:49:59 -299.963258 0.525307
BFGS: 18 19:49:59 -299.977347 0.457639
BFGS: 19 19:49:59 -299.986811 0.346152
BFGS: 20 19:49:59 -299.996477 0.374878
BFGS: 21 19:49:59 -300.008182 0.561820
BFGS: 22 19:49:59 -300.027790 0.691220
BFGS: 23 19:49:59 -300.047756 0.599466
BFGS: 24 19:49:59 -300.064235 0.307702
BFGS: 25 19:49:59 -300.070982 0.142356
BFGS: 26 19:49:59 -300.072734 0.154868
BFGS: 27 19:50:00 -300.074058 0.153245
BFGS: 28 19:50:00 -300.075709 0.143472
BFGS: 29 19:50:00 -300.078634 0.071561
BFGS: 30 19:50:00 -300.079634 0.055135
BFGS: 31 19:50:00 -300.080026 0.045132
Step Time Energy fmax
BFGS: 0 19:50:00 -296.180480 4.382236
BFGS: 1 19:50:00 -296.678641 4.696324
BFGS: 2 19:50:00 -298.224644 3.222431
BFGS: 3 19:50:00 -297.378612 12.834737
BFGS: 4 19:50:00 -298.439610 1.886415
BFGS: 5 19:50:00 -298.505661 1.071189
BFGS: 6 19:50:00 -298.548550 0.906053
BFGS: 7 19:50:01 -298.560216 0.747028
BFGS: 8 19:50:01 -298.608955 0.699380
BFGS: 9 19:50:01 -298.621845 0.805335
BFGS: 10 19:50:01 -298.711143 1.537865
BFGS: 11 19:50:01 -298.804303 2.348673
BFGS: 12 19:50:01 -298.895051 2.893542
BFGS: 13 19:50:01 -298.974817 3.370873
BFGS: 14 19:50:01 -299.115680 3.405390
BFGS: 15 19:50:01 -299.674789 2.476054
BFGS: 16 19:50:01 -299.779182 1.496320
BFGS: 17 19:50:01 -299.880676 1.098323
BFGS: 18 19:50:02 -299.952412 1.103472
BFGS: 19 19:50:02 -299.990455 0.767155
BFGS: 20 19:50:02 -300.018106 0.526905
BFGS: 21 19:50:02 -300.033194 0.446140
BFGS: 22 19:50:02 -300.045098 0.268520
BFGS: 23 19:50:02 -300.050840 0.210507
BFGS: 24 19:50:02 -300.055096 0.210944
BFGS: 25 19:50:02 -300.059357 0.251685
BFGS: 26 19:50:02 -300.065899 0.273375
BFGS: 27 19:50:02 -300.072246 0.225345
BFGS: 28 19:50:02 -300.076148 0.125546
BFGS: 29 19:50:02 -300.077861 0.097500
BFGS: 30 19:50:03 -300.078522 0.073096
BFGS: 31 19:50:03 -300.078990 0.056396
BFGS: 32 19:50:03 -300.079651 0.059068
BFGS: 33 19:50:03 -300.080208 0.053552
BFGS: 34 19:50:03 -300.080493 0.040496
Step Time Energy fmax
BFGS: 0 19:50:03 -296.428043 4.426405
BFGS: 1 19:50:03 -296.901886 4.674450
BFGS: 2 19:50:03 -298.320229 3.470195
BFGS: 3 19:50:03 -298.061506 8.860556
BFGS: 4 19:50:03 -298.622901 1.950507
BFGS: 5 19:50:03 -298.703792 1.368395
BFGS: 6 19:50:04 -298.833272 2.030614
BFGS: 7 19:50:04 -298.984063 2.553228
BFGS: 8 19:50:04 -299.242011 2.619732
BFGS: 9 19:50:04 -299.372529 1.873225
BFGS: 10 19:50:04 -299.439935 1.758432
BFGS: 11 19:50:04 -299.887060 1.217698
BFGS: 12 19:50:04 -299.940313 0.977210
BFGS: 13 19:50:04 -299.982604 0.751858
BFGS: 14 19:50:04 -300.049712 1.260953
BFGS: 15 19:50:04 -300.112132 1.609851
BFGS: 16 19:50:04 -300.232471 1.649178
BFGS: 17 19:50:04 -300.307056 1.484032
BFGS: 18 19:50:05 -300.404561 1.050223
BFGS: 19 19:50:05 -300.495924 0.783946
BFGS: 20 19:50:05 -300.517447 0.791385
BFGS: 21 19:50:05 -300.571054 0.582562
BFGS: 22 19:50:05 -300.599807 0.286973
BFGS: 23 19:50:05 -300.607436 0.254116
BFGS: 24 19:50:05 -300.612749 0.257903
BFGS: 25 19:50:05 -300.617175 0.242705
BFGS: 26 19:50:05 -300.620420 0.177593
BFGS: 27 19:50:05 -300.622170 0.108740
BFGS: 28 19:50:05 -300.622918 0.079716
BFGS: 29 19:50:05 -300.623414 0.072430
BFGS: 30 19:50:06 -300.623908 0.063784
BFGS: 31 19:50:06 -300.624351 0.043800
Step Time Energy fmax
BFGS: 0 19:50:06 -297.140086 4.528121
BFGS: 1 19:50:06 -297.611460 4.660970
BFGS: 2 19:50:06 -298.881334 3.521044
BFGS: 3 19:50:06 -299.068080 5.218711
BFGS: 4 19:50:06 -299.320410 1.799274
BFGS: 5 19:50:06 -299.439224 1.657656
BFGS: 6 19:50:06 -299.738839 1.202771
BFGS: 7 19:50:06 -299.776555 1.184583
BFGS: 8 19:50:06 -299.869419 1.142728
BFGS: 9 19:50:07 -299.919919 1.146862
BFGS: 10 19:50:07 -299.993030 0.909690
BFGS: 11 19:50:07 -300.022332 0.397936
BFGS: 12 19:50:07 -300.030554 0.308753
BFGS: 13 19:50:07 -300.036548 0.308712
BFGS: 14 19:50:07 -300.055149 0.343486
BFGS: 15 19:50:07 -300.065514 0.268098
BFGS: 16 19:50:07 -300.069452 0.184015
BFGS: 17 19:50:07 -300.070966 0.147145
BFGS: 18 19:50:07 -300.074578 0.140183
BFGS: 19 19:50:07 -300.077324 0.098845
BFGS: 20 19:50:07 -300.078823 0.055659
BFGS: 21 19:50:08 -300.079144 0.050107
BFGS: 22 19:50:08 -300.079381 0.043386
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 19:50:08 -295.136493 1.642349
BFGS: 1 19:50:08 -295.244100 1.482793
BFGS: 2 19:50:08 -295.419723 2.474841
BFGS: 3 19:50:08 -295.517560 0.426530
BFGS: 4 19:50:08 -295.533629 0.594363
BFGS: 5 19:50:08 -295.553961 0.620335
BFGS: 6 19:50:08 -295.567717 0.400547
BFGS: 7 19:50:08 -295.573705 0.220772
BFGS: 8 19:50:08 -295.578202 0.289342
BFGS: 9 19:50:09 -295.582766 0.285264
BFGS: 10 19:50:09 -295.586518 0.187941
BFGS: 11 19:50:09 -295.588106 0.076730
BFGS: 12 19:50:09 -295.588393 0.064214
BFGS: 13 19:50:09 -295.588544 0.071238
BFGS: 14 19:50:09 -295.588831 0.085264
BFGS: 15 19:50:09 -295.589417 0.105268
BFGS: 16 19:50:09 -295.590546 0.124466
BFGS: 17 19:50:09 -295.592234 0.130824
BFGS: 18 19:50:09 -295.594537 0.175614
BFGS: 19 19:50:09 -295.600449 0.394886
BFGS: 20 19:50:09 -295.613083 0.755070
BFGS: 21 19:50:10 -295.629635 1.052889
BFGS: 22 19:50:10 -295.641076 1.054044
BFGS: 23 19:50:10 -295.732352 0.614503
BFGS: 24 19:50:10 -295.693581 1.482485
BFGS: 25 19:50:10 -295.765513 0.616063
BFGS: 26 19:50:10 -295.778155 0.544792
BFGS: 27 19:50:10 -295.796079 0.481707
BFGS: 28 19:50:10 -295.823524 0.480150
BFGS: 29 19:50:10 -295.831982 0.321817
BFGS: 30 19:50:10 -295.837836 0.133939
BFGS: 31 19:50:10 -295.839841 0.095037
BFGS: 32 19:50:11 -295.841045 0.093389
BFGS: 33 19:50:11 -295.841759 0.076868
BFGS: 34 19:50:11 -295.842417 0.059103
BFGS: 35 19:50:11 -295.843055 0.058597
BFGS: 36 19:50:11 -295.843548 0.061091
BFGS: 37 19:50:11 -295.843826 0.064711
BFGS: 38 19:50:11 -295.844035 0.066825
BFGS: 39 19:50:11 -295.844355 0.069069
BFGS: 40 19:50:11 -295.844994 0.074393
BFGS: 41 19:50:11 -295.846155 0.088808
BFGS: 42 19:50:11 -295.847885 0.160505
BFGS: 43 19:50:11 -295.850582 0.244740
BFGS: 44 19:50:12 -295.856748 0.348537
BFGS: 45 19:50:12 -295.862838 0.432690
BFGS: 46 19:50:12 -295.876788 0.346035
BFGS: 47 19:50:12 -295.904912 0.324154
BFGS: 48 19:50:12 -295.910510 0.332853
BFGS: 49 19:50:12 -295.925817 0.136405
BFGS: 50 19:50:12 -295.929628 0.156123
BFGS: 51 19:50:12 -295.931831 0.117791
BFGS: 52 19:50:12 -295.934128 0.072835
BFGS: 53 19:50:12 -295.935416 0.052885
BFGS: 54 19:50:12 -295.936285 0.039114
Step Time Energy fmax
BFGS: 0 19:50:13 -295.107619 1.739599
BFGS: 1 19:50:13 -295.223612 1.567142
BFGS: 2 19:50:13 -295.389178 2.714514
BFGS: 3 19:50:13 -295.502900 0.463025
BFGS: 4 19:50:13 -295.521141 0.602459
BFGS: 5 19:50:13 -295.540614 0.662096
BFGS: 6 19:50:13 -295.557889 0.467808
BFGS: 7 19:50:13 -295.565055 0.198738
BFGS: 8 19:50:13 -295.569580 0.275474
BFGS: 9 19:50:13 -295.574894 0.295399
BFGS: 10 19:50:13 -295.578765 0.219248
BFGS: 11 19:50:13 -295.580877 0.096906
BFGS: 12 19:50:14 -295.581204 0.019736
Step Time Energy fmax
BFGS: 0 19:50:14 -295.213132 1.462516
BFGS: 1 19:50:14 -295.305456 1.326953
BFGS: 2 19:50:14 -295.498391 2.005061
BFGS: 3 19:50:14 -295.566999 0.503253
BFGS: 4 19:50:14 -295.579494 0.568102
BFGS: 5 19:50:14 -295.603632 0.452194
BFGS: 6 19:50:14 -295.611850 0.259467
BFGS: 7 19:50:14 -295.617524 0.317092
BFGS: 8 19:50:14 -295.623902 0.343949
BFGS: 9 19:50:14 -295.630875 0.335425
BFGS: 10 19:50:14 -295.637191 0.262979
BFGS: 11 19:50:15 -295.641114 0.322373
BFGS: 12 19:50:15 -295.645545 0.446073
BFGS: 13 19:50:15 -295.662171 0.803416
BFGS: 14 19:50:15 -295.707550 1.297404
BFGS: 15 19:50:15 -295.781356 1.308932
BFGS: 16 19:50:15 -295.797414 1.151675
BFGS: 17 19:50:15 -295.827348 1.069412
BFGS: 18 19:50:15 -295.854294 0.911728
BFGS: 19 19:50:15 -295.910672 0.441099
BFGS: 20 19:50:15 -295.922100 0.378374
BFGS: 21 19:50:15 -295.931553 0.389201
BFGS: 22 19:50:16 -295.941163 0.330966
BFGS: 23 19:50:16 -295.953603 0.208669
BFGS: 24 19:50:16 -295.960103 0.131350
BFGS: 25 19:50:16 -295.962913 0.105836
BFGS: 26 19:50:16 -295.964145 0.085609
BFGS: 27 19:50:16 -295.965296 0.070790
BFGS: 28 19:50:16 -295.966511 0.057993
BFGS: 29 19:50:16 -295.967307 0.045004
Step Time Energy fmax
BFGS: 0 19:50:16 -295.611133 0.777456
BFGS: 1 19:50:16 -295.664469 0.739901
BFGS: 2 19:50:16 -295.855212 0.427503
BFGS: 3 19:50:16 -295.872223 0.472532
BFGS: 4 19:50:17 -295.878260 0.466057
BFGS: 5 19:50:17 -295.923039 0.442682
BFGS: 6 19:50:17 -295.927839 0.362832
BFGS: 7 19:50:17 -295.945822 0.285652
BFGS: 8 19:50:17 -295.947765 0.284585
BFGS: 9 19:50:17 -295.956055 0.236021
BFGS: 10 19:50:17 -295.959963 0.190373
BFGS: 11 19:50:17 -295.962700 0.145050
BFGS: 12 19:50:17 -295.964107 0.133197
BFGS: 13 19:50:17 -295.965222 0.137947
BFGS: 14 19:50:17 -295.966450 0.111671
BFGS: 15 19:50:18 -295.967444 0.072144
BFGS: 16 19:50:18 -295.967931 0.040204
Step Time Energy fmax
BFGS: 0 19:50:18 -295.293366 1.312652
BFGS: 1 19:50:18 -295.374311 1.196505
BFGS: 2 19:50:18 -295.580631 1.560783
BFGS: 3 19:50:18 -295.625381 0.560139
BFGS: 4 19:50:18 -295.635984 0.523376
BFGS: 5 19:50:18 -295.668719 0.415778
BFGS: 6 19:50:18 -295.674242 0.429985
BFGS: 7 19:50:18 -295.704117 0.597101
BFGS: 8 19:50:18 -295.721521 0.644976
BFGS: 9 19:50:18 -295.749866 0.673106
BFGS: 10 19:50:19 -295.766335 0.785957
BFGS: 11 19:50:19 -295.799955 0.799724
BFGS: 12 19:50:19 -295.823599 0.586787
BFGS: 13 19:50:19 -295.842539 0.313644
BFGS: 14 19:50:19 -295.849232 0.220334
BFGS: 15 19:50:19 -295.851686 0.257819
BFGS: 16 19:50:19 -295.855125 0.265373
BFGS: 17 19:50:19 -295.859264 0.203107
BFGS: 18 19:50:19 -295.862350 0.175513
BFGS: 19 19:50:19 -295.864306 0.171780
BFGS: 20 19:50:19 -295.865712 0.166456
BFGS: 21 19:50:19 -295.867633 0.185787
BFGS: 22 19:50:20 -295.872215 0.289260
BFGS: 23 19:50:20 -295.880951 0.391103
BFGS: 24 19:50:20 -295.892710 0.411907
BFGS: 25 19:50:20 -295.906073 0.393019
BFGS: 26 19:50:20 -295.925456 0.376440
BFGS: 27 19:50:20 -295.941981 0.267482
BFGS: 28 19:50:20 -295.952575 0.218454
BFGS: 29 19:50:20 -295.956940 0.172992
BFGS: 30 19:50:20 -295.962589 0.102690
BFGS: 31 19:50:20 -295.964375 0.085966
BFGS: 32 19:50:20 -295.965365 0.078285
BFGS: 33 19:50:21 -295.966122 0.064321
BFGS: 34 19:50:21 -295.967248 0.057627
BFGS: 35 19:50:21 -295.967938 0.033736
Step Time Energy fmax
BFGS: 0 19:50:21 -295.153558 1.593899
BFGS: 1 19:50:21 -295.257005 1.440373
BFGS: 2 19:50:21 -295.438172 2.336836
BFGS: 3 19:50:21 -295.527026 0.448361
BFGS: 4 19:50:21 -295.541936 0.587939
BFGS: 5 19:50:21 -295.562903 0.588129
BFGS: 6 19:50:21 -295.574940 0.355914
BFGS: 7 19:50:21 -295.580461 0.238198
BFGS: 8 19:50:21 -295.585046 0.297788
BFGS: 9 19:50:22 -295.589588 0.281082
BFGS: 10 19:50:22 -295.593358 0.185370
BFGS: 11 19:50:22 -295.594861 0.099076
BFGS: 12 19:50:22 -295.595257 0.105425
BFGS: 13 19:50:22 -295.595697 0.126315
BFGS: 14 19:50:22 -295.596722 0.168512
BFGS: 15 19:50:22 -295.599327 0.241787
BFGS: 16 19:50:22 -295.608423 0.357934
BFGS: 17 19:50:22 -295.627090 0.487683
BFGS: 18 19:50:22 -295.565894 1.803331
BFGS: 19 19:50:22 -295.692915 0.734351
BFGS: 20 19:50:23 -295.700171 1.086845
BFGS: 21 19:50:23 -295.734002 0.532004
BFGS: 22 19:50:23 -295.747656 0.484168
BFGS: 23 19:50:23 -295.800888 0.459730
BFGS: 24 19:50:23 -295.815314 0.393459
BFGS: 25 19:50:23 -295.822862 0.365733
BFGS: 26 19:50:23 -295.833495 0.332104
BFGS: 27 19:50:23 -295.844272 0.332306
BFGS: 28 19:50:23 -295.854251 0.271328
BFGS: 29 19:50:23 -295.859270 0.183393
BFGS: 30 19:50:24 -295.861586 0.190173
BFGS: 31 19:50:24 -295.864163 0.196008
BFGS: 32 19:50:24 -295.866629 0.190347
BFGS: 33 19:50:24 -295.868696 0.181310
BFGS: 34 19:50:24 -295.871515 0.223056
BFGS: 35 19:50:24 -295.877209 0.263357
BFGS: 36 19:50:24 -295.887698 0.381455
BFGS: 37 19:50:24 -295.900414 0.499575
BFGS: 38 19:50:24 -295.913574 0.384031
BFGS: 39 19:50:24 -295.923458 0.193568
BFGS: 40 19:50:24 -295.926364 0.159209
BFGS: 41 19:50:25 -295.929626 0.112229
BFGS: 42 19:50:25 -295.934085 0.065676
BFGS: 43 19:50:25 -295.935155 0.064732
BFGS: 44 19:50:25 -295.935690 0.060272
BFGS: 45 19:50:25 -295.936056 0.047797
Step Time Energy fmax
BFGS: 0 19:50:25 -295.397686 1.144292
BFGS: 1 19:50:25 -295.466160 1.052522
BFGS: 2 19:50:25 -295.673646 1.113717
BFGS: 3 19:50:25 -295.700618 0.556804
BFGS: 4 19:50:25 -295.711108 0.463943
BFGS: 5 19:50:25 -295.753825 0.568911
BFGS: 6 19:50:26 -295.762545 0.549528
BFGS: 7 19:50:26 -295.841501 0.471377
BFGS: 8 19:50:26 -295.860686 0.577955
BFGS: 9 19:50:26 -295.876426 0.530773
BFGS: 10 19:50:26 -295.885272 0.480306
BFGS: 11 19:50:26 -295.917459 0.220394
BFGS: 12 19:50:26 -295.920897 0.226812
BFGS: 13 19:50:26 -295.923834 0.236818
BFGS: 14 19:50:26 -295.926548 0.202324
BFGS: 15 19:50:26 -295.930297 0.120627
BFGS: 16 19:50:26 -295.933590 0.087745
BFGS: 17 19:50:26 -295.935239 0.064057
BFGS: 18 19:50:27 -295.935626 0.039217
Step Time Energy fmax
BFGS: 0 19:50:27 -295.213333 1.460148
BFGS: 1 19:50:27 -295.305649 1.323680
BFGS: 2 19:50:27 -295.500695 1.958561
BFGS: 3 19:50:27 -295.566266 0.509701
BFGS: 4 19:50:27 -295.578445 0.565372
BFGS: 5 19:50:27 -295.603448 0.427255
BFGS: 6 19:50:27 -295.611218 0.272889
BFGS: 7 19:50:27 -295.617064 0.328878
BFGS: 8 19:50:27 -295.623802 0.348598
BFGS: 9 19:50:27 -295.631228 0.344034
BFGS: 10 19:50:27 -295.637737 0.259987
BFGS: 11 19:50:28 -295.641805 0.340419
BFGS: 12 19:50:28 -295.646992 0.480196
BFGS: 13 19:50:28 -295.668862 0.908585
BFGS: 14 19:50:28 -295.706422 1.313695
BFGS: 15 19:50:28 -295.680471 1.364855
BFGS: 16 19:50:28 -295.725979 1.234314
BFGS: 17 19:50:28 -295.737300 1.159600
BFGS: 18 19:50:28 -295.797401 0.529097
BFGS: 19 19:50:28 -295.818343 0.344333
BFGS: 20 19:50:28 -295.824015 0.311150
BFGS: 21 19:50:28 -295.829631 0.296988
BFGS: 22 19:50:29 -295.834291 0.259135
BFGS: 23 19:50:29 -295.838783 0.165843
BFGS: 24 19:50:29 -295.841012 0.073974
BFGS: 25 19:50:29 -295.841923 0.069488
BFGS: 26 19:50:29 -295.842348 0.062710
BFGS: 27 19:50:29 -295.842776 0.059944
BFGS: 28 19:50:29 -295.843312 0.059812
BFGS: 29 19:50:29 -295.843746 0.059203
BFGS: 30 19:50:29 -295.843988 0.063313
BFGS: 31 19:50:29 -295.844196 0.070162
BFGS: 32 19:50:29 -295.844602 0.083703
BFGS: 33 19:50:29 -295.845535 0.111057
BFGS: 34 19:50:30 -295.847605 0.162824
BFGS: 35 19:50:30 -295.851060 0.226873
BFGS: 36 19:50:30 -295.859018 0.320919
BFGS: 37 19:50:30 -295.866478 0.481988
BFGS: 38 19:50:30 -295.878742 0.472769
BFGS: 39 19:50:30 -295.905415 0.401426
BFGS: 40 19:50:30 -295.909727 0.373353
BFGS: 41 19:50:30 -295.944847 0.239622
BFGS: 42 19:50:30 -295.957138 0.242993
BFGS: 43 19:50:30 -295.961402 0.128395
BFGS: 44 19:50:30 -295.963369 0.123706
BFGS: 45 19:50:31 -295.965428 0.104721
BFGS: 46 19:50:31 -295.966897 0.072334
BFGS: 47 19:50:31 -295.968006 0.027299
Step Time Energy fmax
BFGS: 0 19:50:31 -295.167273 1.560907
BFGS: 1 19:50:31 -295.267639 1.411649
BFGS: 2 19:50:31 -295.451919 2.238900
BFGS: 3 19:50:31 -295.534779 0.462866
BFGS: 4 19:50:31 -295.548846 0.582430
BFGS: 5 19:50:31 -295.570336 0.560150
BFGS: 6 19:50:31 -295.581227 0.321111
BFGS: 7 19:50:31 -295.586534 0.252862
BFGS: 8 19:50:31 -295.591274 0.304682
BFGS: 9 19:50:32 -295.595962 0.279074
BFGS: 10 19:50:32 -295.599841 0.188223
BFGS: 11 19:50:32 -295.601406 0.125146
BFGS: 12 19:50:32 -295.601991 0.143443
BFGS: 13 19:50:32 -295.602953 0.184771
BFGS: 14 19:50:32 -295.605378 0.267592
BFGS: 15 19:50:32 -295.614241 0.445004
BFGS: 16 19:50:32 -295.641056 0.606626
BFGS: 17 19:50:32 -295.696422 0.685073
BFGS: 18 19:50:32 -295.745925 0.806893
BFGS: 19 19:50:32 -295.767946 0.940109
BFGS: 20 19:50:32 -295.812205 0.707080
BFGS: 21 19:50:33 -295.866620 0.569401
BFGS: 22 19:50:33 -295.873126 0.505880
BFGS: 23 19:50:33 -295.884574 0.536147
BFGS: 24 19:50:33 -295.901087 0.492793
BFGS: 25 19:50:33 -295.917045 0.331268
BFGS: 26 19:50:33 -295.925830 0.252745
BFGS: 27 19:50:33 -295.929448 0.168692
BFGS: 28 19:50:33 -295.932701 0.101750
BFGS: 29 19:50:33 -295.934860 0.064921
BFGS: 30 19:50:33 -295.935940 0.050994
BFGS: 31 19:50:33 -295.936285 0.038175
Step Time Energy fmax
BFGS: 0 19:50:34 -295.101442 1.764132
BFGS: 1 19:50:34 -295.219373 1.588291
BFGS: 2 19:50:34 -295.382830 2.762567
BFGS: 3 19:50:34 -295.499712 0.479129
BFGS: 4 19:50:34 -295.518387 0.603682
BFGS: 5 19:50:34 -295.537672 0.670027
BFGS: 6 19:50:34 -295.555896 0.481971
BFGS: 7 19:50:34 -295.563450 0.197717
BFGS: 8 19:50:34 -295.568012 0.271471
BFGS: 9 19:50:34 -295.573645 0.297321
BFGS: 10 19:50:34 -295.577538 0.226177
BFGS: 11 19:50:34 -295.579805 0.102782
BFGS: 12 19:50:35 -295.580168 0.022425
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 19:50:35 -303.941293 0.271642
BFGS: 1 19:50:35 -303.945360 0.212727
BFGS: 2 19:50:35 -303.956245 0.125920
BFGS: 3 19:50:35 -303.959187 0.118302
BFGS: 4 19:50:35 -303.960916 0.094916
BFGS: 5 19:50:35 -303.961658 0.074223
BFGS: 6 19:50:35 -303.962389 0.061601
BFGS: 7 19:50:35 -303.963055 0.059366
BFGS: 8 19:50:35 -303.963535 0.074771
BFGS: 9 19:50:35 -303.963840 0.061669
BFGS: 10 19:50:36 -303.964072 0.036619
Step Time Energy fmax
BFGS: 0 19:50:36 -303.943961 0.280635
BFGS: 1 19:50:36 -303.947354 0.225576
BFGS: 2 19:50:36 -303.957306 0.137541
BFGS: 3 19:50:36 -303.960150 0.131913
BFGS: 4 19:50:36 -303.961915 0.098691
BFGS: 5 19:50:36 -303.962606 0.069852
BFGS: 6 19:50:36 -303.963193 0.064502
BFGS: 7 19:50:36 -303.963772 0.067359
BFGS: 8 19:50:36 -303.964276 0.082658
BFGS: 9 19:50:37 -303.964666 0.067989
BFGS: 10 19:50:37 -303.964930 0.036644
Step Time Energy fmax
BFGS: 0 19:50:37 -303.940264 0.267863
BFGS: 1 19:50:37 -303.944405 0.234857
BFGS: 2 19:50:37 -303.955596 0.133377
BFGS: 3 19:50:37 -303.958605 0.120423
BFGS: 4 19:50:37 -303.960469 0.104469
BFGS: 5 19:50:37 -303.961347 0.075285
BFGS: 6 19:50:37 -303.962137 0.071706
BFGS: 7 19:50:37 -303.962869 0.064813
BFGS: 8 19:50:37 -303.963439 0.084344
BFGS: 9 19:50:38 -303.963793 0.072273
BFGS: 10 19:50:38 -303.964028 0.041764
Step Time Energy fmax
BFGS: 0 19:50:38 -303.941486 0.323467
BFGS: 1 19:50:38 -303.946009 0.261261
BFGS: 2 19:50:38 -303.957011 0.133917
BFGS: 3 19:50:38 -303.959471 0.109800
BFGS: 4 19:50:38 -303.960971 0.091268
BFGS: 5 19:50:38 -303.961902 0.095736
BFGS: 6 19:50:38 -303.962939 0.086953
BFGS: 7 19:50:38 -303.963834 0.070255
BFGS: 8 19:50:38 -303.964393 0.071789
BFGS: 9 19:50:39 -303.964653 0.051411
BFGS: 10 19:50:39 -303.964823 0.037677
Step Time Energy fmax
BFGS: 0 19:50:39 -303.936750 0.405996
BFGS: 1 19:50:39 -303.942700 0.304305
BFGS: 2 19:50:39 -303.954813 0.128372
BFGS: 3 19:50:39 -303.957930 0.121658
BFGS: 4 19:50:39 -303.959827 0.102356
BFGS: 5 19:50:39 -303.960952 0.097440
BFGS: 6 19:50:39 -303.962216 0.081900
BFGS: 7 19:50:39 -303.963373 0.066953
BFGS: 8 19:50:40 -303.964091 0.071267
BFGS: 9 19:50:40 -303.964408 0.053987
BFGS: 10 19:50:40 -303.964635 0.040708
Step Time Energy fmax
BFGS: 0 19:50:40 -303.937797 0.289631
BFGS: 1 19:50:40 -303.942282 0.237854
BFGS: 2 19:50:40 -303.954169 0.132950
BFGS: 3 19:50:40 -303.957350 0.106649
BFGS: 4 19:50:40 -303.959217 0.090926
BFGS: 5 19:50:40 -303.960164 0.082620
BFGS: 6 19:50:40 -303.961263 0.069486
BFGS: 7 19:50:40 -303.962366 0.078500
BFGS: 8 19:50:41 -303.963135 0.084498
BFGS: 9 19:50:41 -303.963510 0.062281
BFGS: 10 19:50:41 -303.963763 0.045006
Step Time Energy fmax
BFGS: 0 19:50:41 -303.169920 0.985183
BFGS: 1 19:50:41 -303.197176 0.756128
BFGS: 2 19:50:41 -303.258687 0.683590
BFGS: 3 19:50:41 -303.293183 0.746254
BFGS: 4 19:50:41 -303.327549 0.856729
BFGS: 5 19:50:41 -303.356884 0.681624
BFGS: 6 19:50:41 -303.415663 0.403617
BFGS: 7 19:50:41 -303.419869 0.323055
BFGS: 8 19:50:42 -303.429954 0.151584
BFGS: 9 19:50:42 -303.432382 0.162499
BFGS: 10 19:50:42 -303.434633 0.178608
BFGS: 11 19:50:42 -303.436778 0.204743
BFGS: 12 19:50:42 -303.439066 0.151027
BFGS: 13 19:50:42 -303.440418 0.121090
BFGS: 14 19:50:42 -303.441365 0.097022
BFGS: 15 19:50:42 -303.442053 0.082186
BFGS: 16 19:50:42 -303.442741 0.079937
BFGS: 17 19:50:42 -303.443598 0.111814
BFGS: 18 19:50:42 -303.444470 0.126439
BFGS: 19 19:50:43 -303.445099 0.084809
BFGS: 20 19:50:43 -303.445420 0.058162
BFGS: 21 19:50:43 -303.445627 0.050782
BFGS: 22 19:50:43 -303.445941 0.074783
BFGS: 23 19:50:43 -303.446510 0.097442
BFGS: 24 19:50:43 -303.447377 0.103708
BFGS: 25 19:50:43 -303.448450 0.125622
BFGS: 26 19:50:43 -303.449923 0.177481
BFGS: 27 19:50:43 -303.453099 0.281150
BFGS: 28 19:50:43 -303.459520 0.582313
BFGS: 29 19:50:43 -303.474601 0.871356
BFGS: 30 19:50:43 -303.525338 1.200141
BFGS: 31 19:50:44 -303.581726 1.172042
BFGS: 32 19:50:44 -303.660356 1.186129
BFGS: 33 19:50:44 -303.720805 0.814211
BFGS: 34 19:50:44 -303.757248 0.676579
BFGS: 35 19:50:44 -303.785208 0.767518
BFGS: 36 19:50:44 -303.868975 0.780047
BFGS: 37 19:50:44 -303.909039 0.672183
BFGS: 38 19:50:44 -303.917976 0.386785
BFGS: 39 19:50:44 -303.938576 0.213086
BFGS: 40 19:50:44 -303.945220 0.202488
BFGS: 41 19:50:44 -303.951879 0.197702
BFGS: 42 19:50:45 -303.957368 0.138799
BFGS: 43 19:50:45 -303.960237 0.079224
BFGS: 44 19:50:45 -303.961580 0.075577
BFGS: 45 19:50:45 -303.962491 0.079539
BFGS: 46 19:50:45 -303.963273 0.073865
BFGS: 47 19:50:45 -303.963931 0.055285
BFGS: 48 19:50:45 -303.964393 0.045048
/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 19:51:05 -301.654357 3.036014
BFGS: 1 19:51:05 -301.925790 2.539935
BFGS: 2 19:51:06 -302.354694 5.656560
BFGS: 3 19:51:07 -302.552464 2.038248
BFGS: 4 19:51:08 -303.037521 2.325257
BFGS: 5 19:51:09 -303.142328 1.802261
BFGS: 6 19:51:09 -303.308821 1.414272
BFGS: 7 19:51:10 -303.407873 1.195497
BFGS: 8 19:51:11 -303.512964 1.818943
BFGS: 9 19:51:12 -303.517064 1.097460
BFGS: 10 19:51:13 -303.548696 1.223431
BFGS: 11 19:51:13 -303.592369 1.294961
BFGS: 12 19:51:14 -303.609742 1.061042
BFGS: 13 19:51:15 -303.624169 0.650121
BFGS: 14 19:51:16 -303.644226 0.779097
BFGS: 15 19:51:16 -303.682193 0.714307
BFGS: 16 19:51:17 -303.712650 0.913275
BFGS: 17 19:51:18 -303.734241 0.746890
BFGS: 18 19:51:19 -303.745975 0.807153
BFGS: 19 19:51:20 -303.752972 0.836900
BFGS: 20 19:51:20 -303.747815 0.691538
BFGS: 21 19:51:21 -303.743814 0.557075
BFGS: 22 19:51:22 -303.744951 0.744904
BFGS: 23 19:51:23 -303.747931 0.726294
BFGS: 24 19:51:23 -303.745795 0.664852
BFGS: 25 19:51:24 -303.742758 0.584143
BFGS: 26 19:51:25 -303.747274 0.695009
BFGS: 27 19:51:26 -303.757194 0.655585
BFGS: 28 19:51:27 -303.763112 0.468339
BFGS: 29 19:51:27 -303.767404 0.463772
BFGS: 30 19:51:28 -303.772956 0.506117
BFGS: 31 19:51:29 -303.776934 0.590508
BFGS: 32 19:51:30 -303.779147 0.670779
BFGS: 33 19:51:30 -303.767624 1.247214
BFGS: 34 19:51:31 -303.779242 1.560409
BFGS: 35 19:51:32 -303.787797 0.723496
BFGS: 36 19:51:33 -303.789409 0.557936
BFGS: 37 19:51:34 -303.790989 0.624471
BFGS: 38 19:51:34 -303.774228 1.162540
BFGS: 39 19:51:35 -303.786941 1.134250
BFGS: 40 19:51:36 -303.789831 0.617585
BFGS: 41 19:51:37 -303.794074 0.586310
BFGS: 42 19:51:37 -303.779587 1.115936
BFGS: 43 19:51:38 -303.795110 0.968567
BFGS: 44 19:51:39 -303.791015 0.564117
BFGS: 45 19:51:40 -303.795065 0.565382
BFGS: 46 19:51:41 -303.787858 1.036545
BFGS: 47 19:51:41 -303.796636 0.599649
BFGS: 48 19:51:42 -303.794682 0.896431
BFGS: 49 19:51:43 -303.796982 0.607950
BFGS: 50 19:51:44 -303.797109 0.607190
BFGS: 51 19:51:44 -303.783163 0.475618
BFGS: 52 19:51:45 -303.774567 0.453803
BFGS: 53 19:51:46 -303.771864 0.412973
BFGS: 54 19:51:47 -303.770833 0.373759
BFGS: 55 19:51:47 -303.772665 0.514757
BFGS: 56 19:51:48 -303.774486 0.431827
BFGS: 57 19:51:49 -303.775089 0.295849
BFGS: 58 19:51:50 -303.775408 0.309676
BFGS: 59 19:51:51 -303.776663 0.553468
BFGS: 60 19:51:51 -303.779298 0.655900
BFGS: 61 19:51:52 -303.781835 0.559687
BFGS: 62 19:51:53 -303.782604 0.645833
BFGS: 63 19:51:54 -303.783366 0.692293
BFGS: 64 19:51:54 -303.784319 0.748915
BFGS: 65 19:51:55 -303.784696 0.912250
BFGS: 66 19:51:56 -303.782594 1.104327
BFGS: 67 19:51:57 -303.778500 1.140011
BFGS: 68 19:51:57 -303.777202 1.088018
BFGS: 69 19:51:58 -303.779937 1.372351
BFGS: 70 19:51:59 -303.782913 0.845725
BFGS: 71 19:52:00 -303.784887 0.777476
BFGS: 72 19:52:00 -303.784229 0.647229
BFGS: 73 19:52:01 -303.783186 0.526677
BFGS: 74 19:52:02 -303.783427 0.441515
BFGS: 75 19:52:03 -303.784094 0.482641
BFGS: 76 19:52:04 -303.784442 0.538538
BFGS: 77 19:52:04 -303.781116 0.937404
BFGS: 78 19:52:05 -303.781440 0.644781
BFGS: 79 19:52:06 -303.785400 0.342017
BFGS: 80 19:52:07 -303.784721 0.427323
BFGS: 81 19:52:07 -303.781215 1.150146
BFGS: 82 19:52:08 -303.782630 0.748053
BFGS: 83 19:52:09 -303.781692 0.689116
BFGS: 84 19:52:10 -303.782784 0.353720
BFGS: 85 19:52:10 -303.784406 0.292552
BFGS: 86 19:52:11 -303.786303 0.454917
BFGS: 87 19:52:12 -303.786303 0.230805
BFGS: 88 19:52:12 -303.786303 0.248715
BFGS: 89 19:52:13 -303.786303 0.657743
BFGS: 90 19:52:14 -303.786303 0.267122
BFGS: 91 19:52:14 -303.786303 0.208401
BFGS: 92 19:52:15 -303.786303 0.191777
BFGS: 93 19:52:16 -303.786303 0.167884
BFGS: 94 19:52:16 -303.786303 0.116294
BFGS: 95 19:52:17 -303.786303 0.107289
BFGS: 96 19:52:17 -303.786303 0.106632
BFGS: 97 19:52:18 -303.786303 0.157174
BFGS: 98 19:52:18 -303.786303 0.143258
BFGS: 99 19:52:19 -303.786303 0.101834
BFGS: 100 19:52:20 -303.786303 0.089561
BFGS: 101 19:52:20 -303.786303 0.263226
BFGS: 102 19:52:21 -303.786303 0.133619
BFGS: 103 19:52:21 -303.786303 0.091022
BFGS: 104 19:52:22 -303.786303 0.070991
BFGS: 105 19:52:22 -303.786303 0.070369
BFGS: 106 19:52:22 -303.786303 0.073744
BFGS: 107 19:52:23 -303.786303 0.033694
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_5378/3247994494.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")