Open Catalyst 2020 Nudged Elastic Band (OC20NEB)#
Overview#
This is a validation dataset which was used to assess model performance in CatTSunami: Accelerating Transition State Energy Calculations with Pre-trained Graph Neural Networks. It is comprised of 932 NEB relaxation trajectories. There are three different types of reactions represented: desorptions, dissociations, and transfers. NEB calculations allow us to find transition states. The rate of reaction is determined by the transition state energy, so access to transition states is very important for catalysis research. For more information, check out the paper.
File Structure and Contents#
The tar file contains 3 subdirectories: dissociations, desorptions, and transfers. As the names imply, these directories contain the converged DFT trajectories for each of the reaction classes. Within these directories, the trajectories are named to identify the contents of the file. Here is an example and the anatomy of the name:
desorption_id_83_2409_9_111-4_neb1.0.traj
desorptionindicates the reaction type (dissociation and transfer are the other possibilities)ididentifies that the material belongs to the validation in domain split (ood - out of domain is th e other possibility)83is the task id. This does not provide relavent information2409is the bulk index of the bulk used in the ocdata bulk pickle file9is the reaction index. for each reaction type there is a reaction pickle file in the repository. In this case it is the 9th entry to that pickle file111-4the first 3 numbers are the miller indices (i.e. the (1,1,1) surface), and the last number cooresponds to the shift value. In this case the 4th shift enumerated was the one used.neb1.0the number here indicates the k value used. For the full dataset, 1.0 was used so this does not distiguish any of the trajectories from one another.
The content of these trajectory files is the repeating frame sets. Despite the initial and final frames not being optimized during the NEB, the initial and final frames are saved for every iteration in the trajectory. For the dataset, 10 frames were used - 8 which were optimized over the neb. So the length of the trajectory is the number of iterations (N) * 10. If you wanted to look at the frame set prior to optimization and the optimized frame set, you could get them like this:
from __future__ import annotations
!wget https://dl.fbaipublicfiles.com/opencatalystproject/data/large_files/desorption_id_83_2409_9_111-4_neb1.0.traj
from ase.io import read
traj = read("desorption_id_83_2409_9_111-4_neb1.0.traj", ":")
unrelaxed_frames = traj[0:10]
relaxed_frames = traj[-10:]
--2025-06-05 20:17:35-- https://dl.fbaipublicfiles.com/opencatalystproject/data/large_files/desorption_id_83_2409_9_111-4_neb1.0.traj
Resolving dl.fbaipublicfiles.com (dl.fbaipublicfiles.com)...
108.156.120.77, 108.156.120.6, 108.156.120.27, ...
Connecting to dl.fbaipublicfiles.com (dl.fbaipublicfiles.com)|108.156.120.77|:443... connected.
HTTP request sent, awaiting response...
200 OK
Length: 10074935 (9.6M) [binary/octet-stream]
Saving to: ‘desorption_id_83_2409_9_111-4_neb1.0.traj’
desorptio 0%[ ] 0 --.-KB/s
desorption 7%[> ] 782.99K 3.78MB/s
desorption_id_83_24 100%[===================>] 9.61M 28.5MB/s in 0.3s
2025-06-05 20:17:36 (28.5 MB/s) - ‘desorption_id_83_2409_9_111-4_neb1.0.traj’ saved [10074935/10074935]
Download#
Splits |
Size of compressed version (in bytes) |
Size of uncompressed version (in bytes) |
MD5 checksum (download link) |
|---|---|---|---|
ASE Trajectories |
1.5G |
6.3G |
Use#
One more note: We have not prepared an lmdb for this dataset. This is because it is NEB calculations are not supported directly in ocp. You must use the ase native OCP class along with ase infrastructure to run NEB calculations. Here is an example of a use:
from ase.io import read
from ase.mep import DyNEB
from ase.optimize import BFGS
from fairchem.core import FAIRChemCalculator, pretrained_mlip
traj = read("desorption_id_83_2409_9_111-4_neb1.0.traj", ":")
images = traj[0:10]
predictor = pretrained_mlip.get_predict_unit("uma-s-1")
neb = DyNEB(images, k=1)
for image in images:
image.calc = FAIRChemCalculator(predictor, task_name="oc20")
optimizer = BFGS(
neb,
trajectory="neb.traj",
)
conv = optimizer.run(fmax=0.45, steps=200)
if conv:
neb.climb = True
conv = optimizer.run(fmax=0.05, steps=300)
/home/runner/work/_tool/Python/3.12.11/x64/lib/python3.12/site-packages/torchtnt/utils/version.py:12: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
WARNING:root:device was not explicitly set, using device='cuda'.
Step Time Energy fmax
BFGS: 0 20:17:55 -305.751993 5.179585
BFGS: 1 20:17:56 -305.678594 11.366768
BFGS: 2 20:17:57 -305.904276 1.882657
BFGS: 3 20:17:58 -305.919916 2.602309
BFGS: 4 20:17:59 -305.997627 2.277943
BFGS: 5 20:18:01 -305.991814 6.859358
BFGS: 6 20:18:02 -306.241669 9.557915
BFGS: 7 20:18:03 -306.214907 3.379464
BFGS: 8 20:18:04 -306.278913 4.739830
BFGS: 9 20:18:05 -306.303223 0.742375
BFGS: 10 20:18:06 -306.317829 0.645509
BFGS: 11 20:18:08 -306.347290 1.625525
BFGS: 12 20:18:09 -306.403376 2.013226
BFGS: 13 20:18:10 -306.437925 0.595276
BFGS: 14 20:18:11 -306.408132 0.701537
BFGS: 15 20:18:12 -306.445360 1.369152
BFGS: 16 20:18:13 -306.486215 0.859166
BFGS: 17 20:18:14 -306.484552 0.428246
BFGS: 18 20:18:16 -306.282234 9.008223
BFGS: 19 20:18:17 -306.460228 1.419491
BFGS: 20 20:18:18 -306.462902 1.053287
BFGS: 21 20:18:19 -306.349190 2.303749
BFGS: 22 20:18:20 -306.266457 3.790291
BFGS: 23 20:18:21 -306.288774 1.433890
BFGS: 24 20:18:23 -306.175075 3.202396
BFGS: 25 20:18:24 -305.943960 5.924703
BFGS: 26 20:18:25 -305.686666 6.897512
BFGS: 27 20:18:26 -305.421667 6.667293
BFGS: 28 20:18:27 -305.159447 5.585532
BFGS: 29 20:18:29 -304.896570 4.135299
BFGS: 30 20:18:30 -304.619247 2.890949
BFGS: 31 20:18:31 -304.340357 2.861278
BFGS: 32 20:18:32 -304.099026 2.709529
BFGS: 33 20:18:33 -303.917051 2.915343
BFGS: 34 20:18:34 -303.801716 4.202992
BFGS: 35 20:18:36 -303.694361 4.987354
BFGS: 36 20:18:37 -303.580620 5.458152
BFGS: 37 20:18:38 -303.416614 5.700942
BFGS: 38 20:18:39 -303.228462 5.837852
BFGS: 39 20:18:40 -302.965677 5.901061
BFGS: 40 20:18:41 -302.656380 5.944735
BFGS: 41 20:18:43 -302.324886 6.027721
BFGS: 42 20:18:44 -301.964195 6.042731
BFGS: 43 20:18:45 -301.611397 6.125480
BFGS: 44 20:18:46 -301.237858 6.404555
BFGS: 45 20:18:47 -301.080929 6.459915
BFGS: 46 20:18:49 -300.960682 6.256648
BFGS: 47 20:18:50 -300.949299 5.458165
BFGS: 48 20:18:51 -300.782455 4.737507
BFGS: 49 20:18:52 -300.644310 4.495876
BFGS: 50 20:18:53 -300.498932 5.187272
BFGS: 51 20:18:54 -300.389925 4.934961
BFGS: 52 20:18:56 -300.279694 4.955909
BFGS: 53 20:18:57 -300.166794 4.649922
BFGS: 54 20:18:58 -300.038948 4.381872
BFGS: 55 20:18:59 -299.898636 3.997375
BFGS: 56 20:19:00 -299.747764 3.596734
BFGS: 57 20:19:01 -299.595528 3.164450
BFGS: 58 20:19:03 -299.451069 3.040159
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BFGS: 60 20:19:05 -299.196962 3.313092
BFGS: 61 20:19:06 -299.086229 3.419656
BFGS: 62 20:19:07 -298.975523 3.506712
BFGS: 63 20:19:08 -298.867054 3.572035
BFGS: 64 20:19:10 -298.791403 3.566326
BFGS: 65 20:19:11 -298.768322 3.802185
BFGS: 66 20:19:12 -298.788513 4.116452
BFGS: 67 20:19:13 -298.811380 4.456981
BFGS: 68 20:19:14 -298.821234 4.719181
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BFGS: 70 20:19:17 -298.799885 5.197204
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BFGS: 76 20:19:24 -298.350916 6.083153
BFGS: 77 20:19:25 -298.214256 6.283370
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BFGS: 79 20:19:27 -297.891607 6.560536
BFGS: 80 20:19:28 -297.706393 6.641648
BFGS: 81 20:19:30 -297.504815 6.689595
BFGS: 82 20:19:31 -297.290827 6.712898
BFGS: 83 20:19:32 -297.064357 6.714312
BFGS: 84 20:19:33 -296.826185 6.696435
BFGS: 85 20:19:34 -296.576329 6.650298
BFGS: 86 20:19:35 -296.317190 6.597040
BFGS: 87 20:19:37 -296.052582 6.538816
BFGS: 88 20:19:38 -295.784615 6.473622
BFGS: 89 20:19:39 -295.518580 6.409014
BFGS: 90 20:19:40 -295.257992 6.346689
BFGS: 91 20:19:41 -295.008732 6.291408
BFGS: 92 20:19:42 -294.776363 6.243912
BFGS: 93 20:19:44 -294.568212 6.204054
BFGS: 94 20:19:45 -294.391595 6.169797
BFGS: 95 20:19:46 -294.254045 6.141650
BFGS: 96 20:19:47 -294.159330 6.117958
BFGS: 97 20:19:48 -294.105156 6.099115
BFGS: 98 20:19:49 -294.082426 6.084844
BFGS: 99 20:19:51 -294.079702 6.076011
BFGS: 100 20:19:52 -294.087135 6.070851
BFGS: 101 20:19:53 -294.095736 6.067255
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BFGS: 108 20:20:01 -294.216000 6.189148
BFGS: 109 20:20:02 -294.245057 6.220138
BFGS: 110 20:20:03 -294.270186 6.253364
BFGS: 111 20:20:05 -294.289774 6.288043
BFGS: 112 20:20:06 -294.302668 6.325827
BFGS: 113 20:20:07 -294.207485 26.246525
BFGS: 114 20:20:08 -294.480380 6.751525
BFGS: 115 20:20:09 -294.639321 6.909701
BFGS: 116 20:20:11 -294.702194 7.188622
BFGS: 117 20:20:12 -294.782121 7.333482
BFGS: 118 20:20:13 -294.794875 7.424236
BFGS: 119 20:20:14 -294.805902 7.426456
BFGS: 120 20:20:15 -294.753214 7.380703
BFGS: 121 20:20:16 -294.649669 7.298710
BFGS: 122 20:20:18 -294.475058 7.205318
BFGS: 123 20:20:19 -294.244934 7.115903
BFGS: 124 20:20:20 -293.971253 7.035012
BFGS: 125 20:20:21 -293.684897 6.949678
BFGS: 126 20:20:22 -293.414495 6.826860
BFGS: 127 20:20:23 -293.200748 6.631639
BFGS: 128 20:20:25 -293.071564 6.338629
BFGS: 129 20:20:26 -293.029471 5.970776
BFGS: 130 20:20:27 -293.037022 5.597194
BFGS: 131 20:20:28 -293.058925 5.254887
BFGS: 132 20:20:29 -293.063371 4.946568
BFGS: 133 20:20:30 -293.043063 4.657467
BFGS: 134 20:20:32 -292.978493 4.383349
BFGS: 135 20:20:33 -292.875524 4.280896
BFGS: 136 20:20:34 -292.711260 4.432528
BFGS: 137 20:20:35 -292.501675 4.265034
BFGS: 138 20:20:36 -292.292283 4.158715
BFGS: 139 20:20:37 -292.139859 4.141616
BFGS: 140 20:20:39 -292.035050 4.047718
BFGS: 141 20:20:40 -291.986808 4.529752
BFGS: 142 20:20:41 -291.938043 5.816985
BFGS: 143 20:20:42 -291.846610 6.721128
BFGS: 144 20:20:43 -291.677039 7.194946
BFGS: 145 20:20:44 -291.443552 7.350430
BFGS: 146 20:20:46 -291.194633 7.218281
BFGS: 147 20:20:47 -290.974429 6.827805
BFGS: 148 20:20:48 -290.811543 6.294397
BFGS: 149 20:20:49 -290.711912 5.667329
BFGS: 150 20:20:50 -290.662825 5.034667
BFGS: 151 20:20:51 -290.639316 5.159746
BFGS: 152 20:20:53 -290.615852 5.184211
BFGS: 153 20:20:54 -290.563208 5.097621
BFGS: 154 20:20:55 -290.442922 4.919940
BFGS: 155 20:20:56 -290.249996 4.657475
BFGS: 156 20:20:57 -290.000834 4.354749
BFGS: 157 20:20:58 -289.758858 4.742978
BFGS: 158 20:21:00 -289.518036 5.825137
BFGS: 159 20:21:01 -289.322530 6.522409
BFGS: 160 20:21:02 -289.108591 7.178073
BFGS: 161 20:21:03 -288.947768 7.443542
BFGS: 162 20:21:04 -288.772857 7.711459
BFGS: 163 20:21:06 -288.687719 7.516159
BFGS: 164 20:21:07 -288.604054 7.278931
BFGS: 165 20:21:08 -288.562737 6.738955
BFGS: 166 20:21:09 -288.500408 6.192904
BFGS: 167 20:21:10 -288.471884 5.384324
BFGS: 168 20:21:11 -288.426820 5.479667
BFGS: 169 20:21:13 -288.365833 5.645314
BFGS: 170 20:21:14 -288.262878 7.004394
BFGS: 171 20:21:15 -288.120792 8.720156
BFGS: 172 20:21:16 -287.937093 9.726650
BFGS: 173 20:21:17 -287.714129 10.076230
BFGS: 174 20:21:18 -287.461127 9.906529
BFGS: 175 20:21:20 -287.193452 9.422321
BFGS: 176 20:21:21 -286.928172 8.784325
BFGS: 177 20:21:22 -286.692034 8.128529
BFGS: 178 20:21:23 -286.490568 7.685866
BFGS: 179 20:21:24 -286.323939 7.329598
BFGS: 180 20:21:25 -286.182491 7.015240
BFGS: 181 20:21:27 -286.055020 6.740961
BFGS: 182 20:21:28 -285.934643 6.496333
BFGS: 183 20:21:29 -285.814445 6.294274
BFGS: 184 20:21:30 -285.688974 6.135602
BFGS: 185 20:21:31 -285.560493 5.987201
BFGS: 186 20:21:32 -285.426742 5.823760
BFGS: 187 20:21:34 -285.298319 5.606779
BFGS: 188 20:21:35 -285.163357 6.222800
BFGS: 189 20:21:36 -285.038979 7.068707
BFGS: 190 20:21:37 -284.944859 7.780650
BFGS: 191 20:21:38 -284.880090 8.338075
BFGS: 192 20:21:39 -284.850686 8.736976
BFGS: 193 20:21:41 -284.858853 9.041345
BFGS: 194 20:21:42 -284.894298 9.263177
BFGS: 195 20:21:43 -284.968634 9.363444
BFGS: 196 20:21:44 -285.067020 9.379523
BFGS: 197 20:21:45 -285.174906 9.324875
BFGS: 198 20:21:46 -285.271440 9.260198
BFGS: 199 20:21:48 -285.335013 9.216428
BFGS: 200 20:21:49 -285.415322 8.482714
BFGS: 201 20:21:50 -285.519859 8.266141
BFGS: 202 20:21:51 -285.613724 8.364035
BFGS: 203 20:21:52 -285.694863 8.342876
BFGS: 204 20:21:54 -285.761967 8.255380
BFGS: 205 20:21:55 -285.802574 7.920041
BFGS: 206 20:21:56 -285.793965 7.659698
BFGS: 207 20:21:57 -285.770197 7.437781
BFGS: 208 20:21:58 -285.740627 7.263793
BFGS: 209 20:22:00 -285.704623 7.113152
BFGS: 210 20:22:01 -285.715336 7.165380
BFGS: 211 20:22:02 -285.750379 6.762041
BFGS: 212 20:22:03 -285.874671 8.104122
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BFGS: 214 20:22:05 -286.163034 8.044436
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BFGS: 221 20:22:14 -287.397782 10.885038
BFGS: 222 20:22:15 -287.281162 10.552979
BFGS: 223 20:22:16 -287.125555 10.207850
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BFGS: 243 20:22:40 -289.831440 9.282884
BFGS: 244 20:22:41 -290.158489 9.856150
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BFGS: 310 20:23:58 -294.890872 4.321005
BFGS: 311 20:23:59 -294.941001 4.348109
BFGS: 312 20:24:00 -294.983446 4.337269
BFGS: 313 20:24:02 -295.019374 4.273095
BFGS: 314 20:24:03 -295.039914 4.595985
BFGS: 315 20:24:04 -295.026831 4.520617
BFGS: 316 20:24:05 -294.994735 4.582265
BFGS: 317 20:24:06 -294.955618 4.994021