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:]
--2025-06-18 14:34:08-- 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)...
18.238.192.99, 18.238.192.60, 18.238.192.122, ...
Connecting to dl.fbaipublicfiles.com (dl.fbaipublicfiles.com)|18.238.192.99|: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 83%[===============> ] 8.00M 29.1MB/s
desorption_id_83_24 100%[===================>] 9.61M 33.9MB/s in 0.3s
2025-06-18 14:34:08 (33.9 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 14:34:24 -305.751997 5.179585
BFGS: 1 14:34:25 -305.678596 11.366769
BFGS: 2 14:34:26 -305.904274 1.882657
BFGS: 3 14:34:27 -305.919916 2.602309
BFGS: 4 14:34:28 -305.997625 2.277943
BFGS: 5 14:34:29 -305.991819 6.859359
BFGS: 6 14:34:31 -306.241671 9.557948
BFGS: 7 14:34:32 -306.214908 3.379573
BFGS: 8 14:34:33 -306.278919 4.739883
BFGS: 9 14:34:34 -306.303228 0.742368
BFGS: 10 14:34:35 -306.317829 0.645264
BFGS: 11 14:34:36 -306.347292 1.625757
BFGS: 12 14:34:37 -306.403383 2.013868
BFGS: 13 14:34:39 -306.437923 0.595247
BFGS: 14 14:34:40 -306.408136 0.705192
BFGS: 15 14:34:41 -306.445282 1.372755
BFGS: 16 14:34:42 -306.486189 0.854076
BFGS: 17 14:34:43 -306.484566 0.428320
BFGS: 18 14:34:44 -306.281544 9.125462
BFGS: 19 14:34:45 -306.460533 1.417865
BFGS: 20 14:34:47 -306.463280 1.051390
BFGS: 21 14:34:48 -306.351564 2.334730
BFGS: 22 14:34:49 -306.270340 3.786557
BFGS: 23 14:34:50 -306.294540 1.427301
BFGS: 24 14:34:51 -306.188530 3.115916
BFGS: 25 14:34:52 -305.962940 5.878541
BFGS: 26 14:34:53 -305.710041 6.851119
BFGS: 27 14:34:54 -305.448500 6.567751
BFGS: 28 14:34:56 -305.190399 5.392535
BFGS: 29 14:34:57 -304.935068 3.842170
BFGS: 30 14:34:58 -304.671394 2.734126
BFGS: 31 14:34:59 -304.411434 2.780117
BFGS: 32 14:35:00 -304.189175 2.618870
BFGS: 33 14:35:01 -304.019625 3.095736
BFGS: 34 14:35:03 -303.909305 4.322395
BFGS: 35 14:35:04 -303.800432 5.058592
BFGS: 36 14:35:05 -303.683979 5.492490
BFGS: 37 14:35:06 -303.510622 5.698408
BFGS: 38 14:35:07 -303.315550 5.807897
BFGS: 39 14:35:08 -303.042068 5.850423
BFGS: 40 14:35:09 -302.717363 5.877101
BFGS: 41 14:35:10 -302.362955 5.930020
BFGS: 42 14:35:12 -301.965973 5.940001
BFGS: 43 14:35:13 -301.552250 5.985605
BFGS: 44 14:35:14 -301.110157 6.146882
BFGS: 45 14:35:15 -300.776688 6.385990
BFGS: 46 14:35:16 -300.972778 6.034767
BFGS: 47 14:35:17 -300.861561 5.046716
BFGS: 48 14:35:18 -300.803415 4.100813
BFGS: 49 14:35:20 -300.670116 4.691816
BFGS: 50 14:35:21 -300.663177 4.289832
BFGS: 51 14:35:22 -300.663807 4.562983
BFGS: 52 14:35:23 -300.595198 3.833212
BFGS: 53 14:35:24 -300.511551 3.854820
BFGS: 54 14:35:25 -300.375988 4.079554
BFGS: 55 14:35:26 -300.233013 4.118357
BFGS: 56 14:35:27 -300.080198 4.044491
BFGS: 57 14:35:29 -299.928619 3.896747
BFGS: 58 14:35:30 -299.784265 3.694881
BFGS: 59 14:35:31 -299.646690 3.467095
BFGS: 60 14:35:32 -299.504589 3.249350
BFGS: 61 14:35:33 -299.348434 3.140039
BFGS: 62 14:35:34 -299.190132 3.343379
BFGS: 63 14:35:35 -299.070000 3.591612
BFGS: 64 14:35:37 -299.027872 3.672315
BFGS: 65 14:35:38 -299.069954 4.430005
BFGS: 66 14:35:39 -299.181742 5.001501
BFGS: 67 14:35:40 -299.305044 5.382055
BFGS: 68 14:35:41 -299.389391 5.668052
BFGS: 69 14:35:42 -299.407738 5.691513
BFGS: 70 14:35:43 -299.375423 5.593985
BFGS: 71 14:35:44 -299.321178 5.417364
BFGS: 72 14:35:46 -299.262230 5.205491
BFGS: 73 14:35:47 -299.207491 4.995058
BFGS: 74 14:35:48 -299.146803 4.804477
BFGS: 75 14:35:49 -299.072637 4.645102
BFGS: 76 14:35:50 -298.985914 4.508088
BFGS: 77 14:35:51 -298.886721 4.371045
BFGS: 78 14:35:52 -298.771337 4.236062
BFGS: 79 14:35:54 -298.655952 4.083562
BFGS: 80 14:35:55 -298.564400 3.930572
BFGS: 81 14:35:56 -298.497480 3.766889
BFGS: 82 14:35:57 -298.451507 3.621720
BFGS: 83 14:35:58 -298.419142 3.475254
BFGS: 84 14:35:59 -298.392364 3.371453
BFGS: 85 14:36:00 -298.364973 3.524727
BFGS: 86 14:36:02 -298.331762 4.029002
BFGS: 87 14:36:03 -298.286466 4.447284
BFGS: 88 14:36:04 -298.227676 4.867840
BFGS: 89 14:36:05 -298.150305 5.189667
BFGS: 90 14:36:06 -298.055921 5.506477
BFGS: 91 14:36:07 -297.940906 5.764251
BFGS: 92 14:36:08 -297.804714 5.989054
BFGS: 93 14:36:10 -297.646170 6.170612
BFGS: 94 14:36:11 -297.463913 6.314513
BFGS: 95 14:36:12 -297.256404 6.419111
BFGS: 96 14:36:13 -297.022742 6.486026
BFGS: 97 14:36:14 -296.762841 6.517731
BFGS: 98 14:36:15 -296.476454 6.518214
BFGS: 99 14:36:16 -296.163617 6.484715
BFGS: 100 14:36:18 -295.825180 6.424899
BFGS: 101 14:36:19 -295.462803 6.340613
BFGS: 102 14:36:20 -295.078546 6.231403
BFGS: 103 14:36:21 -294.674727 6.101545
BFGS: 104 14:36:22 -294.254717 5.950826
BFGS: 105 14:36:23 -293.823242 5.779688
BFGS: 106 14:36:24 -293.386684 5.592644
BFGS: 107 14:36:26 -292.952050 5.393141
BFGS: 108 14:36:27 -292.524431 5.187044
BFGS: 109 14:36:28 -292.109192 4.976302
BFGS: 110 14:36:29 -291.713185 4.785156
BFGS: 111 14:36:30 -291.339586 4.843581
BFGS: 112 14:36:31 -290.985568 4.911133
BFGS: 113 14:36:32 -290.642259 4.977214
BFGS: 114 14:36:34 -290.300152 5.032003
BFGS: 115 14:36:35 -289.953740 5.070847
BFGS: 116 14:36:36 -289.600652 5.093106
BFGS: 117 14:36:37 -289.239069 5.099436
BFGS: 118 14:36:38 -288.866993 5.090187
BFGS: 119 14:36:39 -288.483854 5.064533
BFGS: 120 14:36:41 -288.090595 5.020142
BFGS: 121 14:36:42 -287.688314 4.953238
BFGS: 122 14:36:43 -287.278039 4.960165
BFGS: 123 14:36:44 -286.861767 5.124053
BFGS: 124 14:36:45 -286.442058 5.272077
BFGS: 125 14:36:46 -286.021759 5.403789
BFGS: 126 14:36:47 -285.603523 5.520214
BFGS: 127 14:36:49 -285.188380 5.631916
BFGS: 128 14:36:50 -284.777136 5.789363
BFGS: 129 14:36:51 -284.392787 5.887674
BFGS: 130 14:36:52 -284.010064 5.934777
BFGS: 131 14:36:53 -283.632913 6.023956
BFGS: 132 14:36:54 -283.262353 6.110120
BFGS: 133 14:36:55 -282.898248 6.194447
BFGS: 134 14:36:57 -282.540691 6.276842
BFGS: 135 14:36:58 -282.101758 6.375357
BFGS: 136 14:36:59 -281.695464 6.458852
BFGS: 137 14:37:00 -281.307849 6.531172
BFGS: 138 14:37:01 -280.941184 6.681297
BFGS: 139 14:37:02 -280.594590 6.931446
BFGS: 140 14:37:04 -280.267860 7.158994
BFGS: 141 14:37:05 -279.957745 7.348140
BFGS: 142 14:37:06 -279.661869 7.491121
BFGS: 143 14:37:07 -279.377719 7.573011
BFGS: 144 14:37:08 -279.105585 7.563769
BFGS: 145 14:37:09 -278.848191 7.415536
BFGS: 146 14:37:10 -278.613659 7.063231
BFGS: 147 14:37:12 -278.405995 7.172911
BFGS: 148 14:37:13 -278.231431 7.342077
BFGS: 149 14:37:14 -278.093239 7.527584
BFGS: 150 14:37:15 -277.986935 7.758623
BFGS: 151 14:37:16 -277.917101 8.064655
BFGS: 152 14:37:17 -277.884477 8.413619
BFGS: 153 14:37:18 -277.883565 8.851371
BFGS: 154 14:37:20 -277.904317 9.304932
BFGS: 155 14:37:21 -277.955784 9.832757
BFGS: 156 14:37:22 -278.023983 10.122661
BFGS: 157 14:37:23 -278.118318 10.219844
BFGS: 158 14:37:24 -278.250482 9.988359
BFGS: 159 14:37:25 -278.429600 9.697521
BFGS: 160 14:37:27 -278.665860 9.383339
BFGS: 161 14:37:28 -278.956453 9.095147
BFGS: 162 14:37:29 -279.285358 8.855175
BFGS: 163 14:37:30 -279.633726 9.526032
BFGS: 164 14:37:31 -279.979620 10.075938
BFGS: 165 14:37:33 -280.299614 10.420508
BFGS: 166 14:37:34 -280.588268 10.603022
BFGS: 167 14:37:35 -280.830742 10.658484
BFGS: 168 14:37:36 -281.013079 10.646706
BFGS: 169 14:37:37 -281.124248 10.572913
BFGS: 170 14:37:38 -281.160971 10.461680
BFGS: 171 14:37:39 -281.111747 10.321001
BFGS: 172 14:37:41 -280.992872 10.152760
BFGS: 173 14:37:42 -280.817468 9.963685
BFGS: 174 14:37:43 -280.598428 9.766789
BFGS: 175 14:37:44 -280.353240 9.564391
BFGS: 176 14:37:45 -280.103510 9.350678
BFGS: 177 14:37:46 -279.962004 9.049541
BFGS: 178 14:37:48 -279.893787 9.221679
BFGS: 179 14:37:49 -280.084705 9.348490
BFGS: 180 14:37:50 -280.376070 9.521127
BFGS: 181 14:37:51 -280.471366 9.575539
BFGS: 182 14:37:52 -280.464377 9.620071
BFGS: 183 14:37:53 -280.399441 9.659474
BFGS: 184 14:37:54 -280.184905 9.706169
BFGS: 185 14:37:56 -279.798408 9.723506
BFGS: 186 14:37:57 -279.255155 9.709318
BFGS: 187 14:37:58 -278.626530 9.675148
BFGS: 188 14:37:59 -277.949592 9.630718
BFGS: 189 14:38:00 -277.194444 9.565775
BFGS: 190 14:38:01 -276.377630 9.476157
BFGS: 191 14:38:03 -275.642245 9.356320
BFGS: 192 14:38:04 -274.996846 9.223189
BFGS: 193 14:38:05 -274.445835 9.088888
BFGS: 194 14:38:06 -273.841928 8.957783
BFGS: 195 14:38:07 -273.303872 8.791905
BFGS: 196 14:38:08 -272.858058 8.657247
BFGS: 197 14:38:10 -272.409642 8.470602
BFGS: 198 14:38:11 -271.982956 8.397922
BFGS: 199 14:38:12 -271.581454 8.257087
BFGS: 200 14:38:13 -271.189741 8.010430
BFGS: 201 14:38:14 -271.048777 7.618147
BFGS: 202 14:38:16 -271.117348 7.356795
BFGS: 203 14:38:17 -271.246765 7.509110
BFGS: 204 14:38:18 -271.368793 7.607163
BFGS: 205 14:38:19 -271.498010 7.709455
BFGS: 206 14:38:20 -271.699728 7.838984
BFGS: 207 14:38:21 -271.964604 7.968263
BFGS: 208 14:38:23 -272.263061 8.085011
BFGS: 209 14:38:24 -272.586657 8.084403
BFGS: 210 14:38:25 -272.915183 8.054060
BFGS: 211 14:38:26 -273.281582 7.908693
BFGS: 212 14:38:27 -273.701825 8.030814
BFGS: 213 14:38:28 -274.205115 8.359205
BFGS: 214 14:38:30 -274.861142 9.181370
BFGS: 215 14:38:31 -275.764403 10.280328
BFGS: 216 14:38:32 -276.582500 10.408885
BFGS: 217 14:38:33 -277.488142 10.822386
BFGS: 218 14:38:34 -278.131040 10.062499
BFGS: 219 14:38:35 -278.483250 9.476072
BFGS: 220 14:38:37 -278.939478 9.323689
BFGS: 221 14:38:38 -279.228961 9.706339
BFGS: 222 14:38:39 -279.425662 10.373426
BFGS: 223 14:38:40 -279.661333 10.806636
BFGS: 224 14:38:41 -280.283510 11.082577
BFGS: 225 14:38:42 -280.860143 11.034770
BFGS: 226 14:38:44 -280.691462 11.566847
BFGS: 227 14:38:45 -279.917855 12.052370
BFGS: 228 14:38:46 -279.134258 12.296504
BFGS: 229 14:38:47 -278.436746 12.422442
BFGS: 230 14:38:48 -278.034049 12.371940
BFGS: 231 14:38:49 -277.979044 12.259945
BFGS: 232 14:38:51 -278.250655 12.124573
BFGS: 233 14:38:52 -278.388100 12.057904
BFGS: 234 14:38:53 -278.166474 11.978041
BFGS: 235 14:38:54 -277.697212 11.966547
BFGS: 236 14:38:55 -277.212114 12.002120
BFGS: 237 14:38:57 -276.786794 12.131158
BFGS: 238 14:38:58 -276.306053 12.161356
BFGS: 239 14:38:59 -275.786016 12.149778
BFGS: 240 14:39:00 -275.266892 12.146047
BFGS: 241 14:39:01 -274.733916 12.215017
BFGS: 242 14:39:02 -274.230104 12.242084
BFGS: 243 14:39:04 -273.803747 12.172743
BFGS: 244 14:39:05 -273.571749 11.666065
BFGS: 245 14:39:06 -273.313960 11.282742
BFGS: 246 14:39:07 -273.709343 10.546539
BFGS: 247 14:39:08 -274.543423 9.917477
BFGS: 248 14:39:09 -274.626395 9.571817
BFGS: 249 14:39:11 -274.157844 9.451679
BFGS: 250 14:39:12 -273.586667 9.620856
BFGS: 251 14:39:13 -272.912583 9.656736
BFGS: 252 14:39:14 -272.389512 9.684677
BFGS: 253 14:39:15 -272.020875 9.719091
BFGS: 254 14:39:16 -271.666489 11.087652
BFGS: 255 14:39:18 -271.487815 11.124374
BFGS: 256 14:39:19 -271.463331 11.171039
BFGS: 257 14:39:20 -271.487554 11.154497
BFGS: 258 14:39:21 -271.874413 11.134522
BFGS: 259 14:39:22 -272.566259 10.811517
BFGS: 260 14:39:23 -273.734818 10.781848
BFGS: 261 14:39:25 -274.220876 10.477770
BFGS: 262 14:39:26 -274.458358 10.505292
BFGS: 263 14:39:27 -274.567471 13.986198
BFGS: 264 14:39:28 -273.817635 18.132024
BFGS: 265 14:39:29 -272.106557 22.743114
BFGS: 266 14:39:30 -271.935886 25.229473
BFGS: 267 14:39:32 -272.579899 26.254481
BFGS: 268 14:39:33 -273.334465 26.377122
BFGS: 269 14:39:34 -273.951318 25.352365
BFGS: 270 14:39:35 -274.533764 24.028669
BFGS: 271 14:39:36 -275.067366 20.615566
BFGS: 272 14:39:37 -275.628189 18.165747
BFGS: 273 14:39:39 -276.172210 16.562812
BFGS: 274 14:39:40 -276.511970 15.368924
BFGS: 275 14:39:41 -276.578775 14.019692
BFGS: 276 14:39:42 -276.676292 13.642705
BFGS: 277 14:39:43 -276.480681 13.555614
BFGS: 278 14:39:45 -276.126171 12.092261
BFGS: 279 14:39:46 -275.920549 12.279351
BFGS: 280 14:39:47 -276.337877 12.296310
BFGS: 281 14:39:48 -277.610026 10.635877
BFGS: 282 14:39:49 -277.180584 10.329642
BFGS: 283 14:39:51 -276.745185 10.100150
BFGS: 284 14:39:52 -276.472645 9.896514
BFGS: 285 14:39:53 -276.240210 9.677580
BFGS: 286 14:39:54 -276.051915 9.433171
BFGS: 287 14:39:55 -275.944962 9.542423
BFGS: 288 14:39:56 -275.892876 9.544060
BFGS: 289 14:39:58 -275.903897 9.541152
BFGS: 290 14:39:59 -275.963469 9.754072
BFGS: 291 14:40:00 -276.039730 9.980710
BFGS: 292 14:40:01 -276.072159 10.127743
BFGS: 293 14:40:02 -276.112040 10.252981
BFGS: 294 14:40:03 -276.178656 10.376428
BFGS: 295 14:40:05 -276.276811 10.457043
BFGS: 296 14:40:06 -276.046029 11.497249
BFGS: 297 14:40:07 -275.571247 11.324128
BFGS: 298 14:40:08 -275.184069 12.363022
BFGS: 299 14:40:09 -274.831624 12.608093
BFGS: 300 14:40:10 -274.687228 12.395818
BFGS: 301 14:40:12 -274.662172 11.782207
BFGS: 302 14:40:13 -274.690143 11.055881
BFGS: 303 14:40:14 -274.744181 10.778456
BFGS: 304 14:40:15 -274.856745 11.082242
BFGS: 305 14:40:16 -275.225542 11.283419
BFGS: 306 14:40:17 -276.622144 11.417250
BFGS: 307 14:40:19 -276.510848 11.337659
BFGS: 308 14:40:20 -276.094790 10.989208
BFGS: 309 14:40:21 -275.538930 10.323553
BFGS: 310 14:40:22 -275.059483 9.618803
BFGS: 311 14:40:23 -274.611047 9.961645
BFGS: 312 14:40:24 -274.215778 10.398064
BFGS: 313 14:40:26 -273.904516 11.539599
BFGS: 314 14:40:27 -273.700079 12.271411
BFGS: 315 14:40:28 -273.520143 12.583075
BFGS: 316 14:40:29 -273.364092 12.707693
BFGS: 317 14:40:30 -273.214249 12.633095