Skip to content

Add WiSE electrolyte benchmark (density, X-ray S(q), Li-O RDF) #445

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
LucaBrugnoli wants to merge 3 commits into
base: main
Choose a base branch
from
Draft

Add WiSE electrolyte benchmark (density, X-ray S(q), Li-O RDF) #445

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
ef5aecc
Add WiSE electrolyte benchmark (density, X-ray S(q), Li-O RDF)
LucaBrugnoli Apr 3, 2026
8387cec
Consolidate WiSE benchmark per PR #445 review
Apr 26, 2026
ff0db5c
Use NPT_MTK and very_slow marker in WiSE MD reference
Apr 28, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions docs/source/user_guide/benchmarks/index.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,3 +17,4 @@ Benchmarks
tm_complexes
conformers
molecular_dynamics
wise_electrolytes
87 changes: 87 additions & 0 deletions docs/source/user_guide/benchmarks/wise_electrolytes.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,87 @@
==================
WiSE electrolytes
==================

LiTFSI/H2O 21 m
===============

Summary
-------

Performance in predicting structural and thermodynamic properties of the 21 molal
LiTFSI/H2O "water-in-salt" electrolyte (WiSE). The benchmark consolidates three
experimental observables for the same chemistry: NPT equilibrium density, Li-O
coordination from the radial distribution function, and the X-ray static
structure factor S(q).

Two simulation cells are used: a small cell (16 LiTFSI + 42 H2O, 382 atoms) for
the NPT density, and a large cubic cell (64 LiTFSI + 170 H2O, 1534 atoms,
27.4938 A) for the NVT trajectories that feed the RDF and S(q).

Metrics
-------

1. Density error

Absolute error in NPT density vs the experimental value
(1.7126 g/cm3, Gilbert et al., *J. Chem. Eng. Data* 62, 2056 (2017)).
The density is the average over the production NPT trajectory at
298.15 K and 1 atm.

2. Li-O_water coordination number error

Absolute error in the Li-O_water coordination number, computed by
integrating the Li-O_water radial distribution function up to the first
minimum (R_cut = 2.83 A, from r2SCAN AIMD reference). Water oxygens are
identified from the first frame as those bonded to a hydrogen
(d_OH < 1.25 A). Reference value: 2.0 (Watanabe et al.,
*J. Phys. Chem. B* 125, 7477 (2021), neutron diffraction with isotopic
substitution at ~18.5 m).

3. Li-O_TFSI coordination number error

Same definition as above, restricted to TFSI oxygens (those bonded to a
sulfur, d_OS < 1.75 A). Reference value: 2.0 (same source).

4. S(q) R-factor

R-factor between the computed and experimental X-ray structure factor,
``sum(|S_exp - S_calc|) / sum(|S_exp|)``. S(q) is computed via dynasor
in the Faber-Ziman convention with Cromer-Mann 4-Gaussian form factors
(including hydrogen) and Savitzky-Golay smoothing
(window = 27, order = 3, dq = 0.02 A^-1). Reference: SAXS data of
Zhang et al., *J. Phys. Chem. B* 125, 4501 (2021).

Computational cost
------------------

High: production trajectories require a GPU MD code (e.g. LAMMPS + symmetrix
or Janus + MACE) and several hours per model on a single MI250X / A100 GPU.
Re-extracting metrics from pre-computed trajectories is cheap (seconds per
model).

Data availability
-----------------

Input structures:

* p64_w170 cubic cell (1534 atoms, 27.4938 A) for NVT trajectories.
* p16_w42 cell (382 atoms) for NPT density.

Production trajectories were generated with LAMMPS + symmetrix on Adastra
(MI250X) using a MACE foundation model. The reference Janus recast of the
same protocol (Min -> NVT 50 ps -> NPT 200 ps, dt = 0.5 fs, T = 298.15 K,
P = 1.01325 bar, NH thermostat tau = 50 fs, NH barostat tau = 500 fs) lives
in ``ml_peg/calcs/wise_electrolytes/md_reference/``.

Reference data:

* Density: Gilbert et al., *J. Chem. Eng. Data* 62, 2056 (2017),
DOI: 10.1021/acs.jced.7b00135.
* Li-O coordination numbers: Watanabe et al., *J. Phys. Chem. B* 125, 7477
(2021), DOI: 10.1021/acs.jpcb.1c04693.
* X-ray S(q): Zhang et al., *J. Phys. Chem. B* 125, 4501 (2021),
DOI: 10.1021/acs.jpcb.1c02189.

Further details on the simulation protocol and MLIP assessment for this
system: L. Brugnoli, arXiv:2603.22099 (2026).
301 changes: 301 additions & 0 deletions ml_peg/analysis/wise_electrolytes/data/saxs_maginn.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,301 @@
# 10.1021/acs.jpcb.1c02189
# q / A-1 S(q)
0.20849 -0.14530
0.27792 -0.13506
0.34735 -0.12067
0.41678 -0.10336
0.45728 -0.08727
0.49200 -0.06776
0.52671 -0.04801
0.55178 -0.02997
0.57493 -0.00949
0.59036 0.01014
0.61598 0.03412
0.64243 0.06049
0.65400 0.08160
0.66557 0.10150
0.67714 0.12052
0.68293 0.13778
0.69797 0.15855
0.70800 0.17996
0.72012 0.20988
0.73170 0.24081
0.74465 0.27042
0.75484 0.30330
0.73500 0.28700
0.76641 0.34761
0.76586 0.32650
0.77798 0.38731
0.77550 0.36819
0.79286 0.42909
0.78708 0.40842
0.80113 0.46380
0.78129 0.44792
0.81022 0.50741
0.81215 0.48840
0.82427 0.56746
0.82526 0.54096
0.81601 0.52692
0.83584 0.62473
0.83336 0.60080
0.81601 0.59129
0.84741 0.67948
0.84493 0.65675
0.82758 0.64688
0.85899 0.73424
0.85651 0.71161
0.83915 0.70247
0.87001 0.79805
0.86808 0.77562
0.86808 0.75989
0.87965 0.86242
0.88312 0.83911
0.87386 0.82146
0.89370 0.93738
0.89122 0.91350
0.88544 0.89753
0.88544 0.88241
0.90527 0.99757
0.89701 0.97555
0.89701 0.96141
0.91436 1.05943
0.90858 1.03504
0.90858 1.01993
0.92842 1.12024
0.92015 1.09454
0.92015 1.07991
0.93999 1.17479
0.93172 1.15208
0.92015 1.14135
0.95156 1.21659
0.94329 1.19840
0.96258 1.25522
0.95487 1.23790
0.97470 1.28555
0.98727 1.31134
1.01272 1.33234
1.05323 1.30934
1.04744 1.33153
1.06595 1.28501
1.07637 1.26497
1.08794 1.24156
1.10067 1.21596
1.11108 1.19365
1.12150 1.17119
1.13307 1.14808
1.14580 1.12380
1.15853 1.10039
1.17010 1.07815
1.18630 1.05913
1.19980 1.03724
1.23259 1.01286
1.27226 0.99067
1.34252 0.98092
1.41195 0.97409
1.46237 0.95577
1.49874 0.93595
1.51417 0.92045
1.53577 0.90319
1.54965 0.88446
1.57395 0.86291
1.59710 0.83755
1.62024 0.81219
1.64338 0.78586
1.66653 0.76026
1.69380 0.73737
1.71667 0.71637
1.75332 0.69589
1.79299 0.67865
1.86325 0.66980
1.93846 0.67614
1.99748 0.69413
2.04261 0.71832
2.07154 0.73685
2.09468 0.75441
2.12554 0.77245
2.14868 0.79293
2.17183 0.81439
2.19497 0.83584
2.21040 0.85462
2.23354 0.87558
2.26247 0.90216
2.27983 0.92593
2.30297 0.94776
2.33190 0.97567
2.35697 1.00091
2.37587 1.01876
2.39555 1.03748
2.42448 1.05796
2.46498 1.08027
2.52284 1.09893
2.59227 1.09722
2.64665 1.08137
2.68484 1.06363
2.72534 1.04480
2.76502 1.02682
2.79477 1.01056
2.82949 0.99506
2.86420 0.97750
2.89892 0.95995
2.93859 0.94156
2.96835 0.92630
3.00885 0.90893
3.05513 0.88918
3.10060 0.87154
3.15019 0.85357
3.19400 0.83804
3.25764 0.82126
3.29236 0.80890
3.34443 0.79342
3.40807 0.77854
3.47172 0.76148
3.54115 0.74636
3.61058 0.73295
3.68001 0.72198
3.74944 0.71491
3.81887 0.71076
3.88830 0.71101
3.95773 0.71539
4.02716 0.72612
4.09080 0.74051
4.14866 0.75709
4.19660 0.77541
4.23958 0.79547
4.27132 0.81512
4.30901 0.83455
4.34075 0.85491
4.37431 0.87607
4.40787 0.89792
4.43217 0.91752
4.46303 0.93459
4.48617 0.95214
4.50932 0.97019
4.53246 0.98921
4.55560 1.00822
4.57875 1.02724
4.60189 1.04724
4.62503 1.06698
4.64818 1.08747
4.66708 1.10595
4.69446 1.12623
4.71761 1.14476
4.74075 1.16305
4.76389 1.18231
4.78511 1.20279
4.80825 1.22298
4.83718 1.24193
4.86611 1.26180
4.90083 1.28374
4.93554 1.30447
4.97604 1.32440
5.02150 1.34407
5.08019 1.36420
5.14962 1.37444
5.21905 1.37225
5.28269 1.36225
5.34055 1.34558
5.38105 1.32586
5.42155 1.30788
5.45627 1.29057
5.49098 1.27301
5.52570 1.25546
5.56041 1.23717
5.59513 1.21742
5.62985 1.19694
5.66456 1.17719
5.69928 1.15671
5.73399 1.13647
5.76871 1.11721
5.80342 1.09795
5.83814 1.07991
5.87285 1.06235
5.90757 1.04650
5.94724 1.02975
5.99353 1.01199
6.06379 0.99359
6.13322 0.97799
6.20265 0.96604
6.27208 0.96043
6.34151 0.95726
6.41094 0.95775
6.48037 0.96043
6.54980 0.96507
6.61923 0.97043
6.68866 0.97458
6.75809 0.97897
6.82752 0.98140
6.89695 0.98287
6.96638 0.98213
7.03581 0.98067
7.10524 0.97823
7.17467 0.97531
7.24410 0.97238
7.31353 0.96872
7.38296 0.96580
7.45239 0.96287
7.52182 0.96043
7.59125 0.95775
7.66068 0.95629
7.73011 0.95434
7.79954 0.95288
7.86898 0.95214
7.93841 0.95117
8.00784 0.95214
8.07727 0.95263
8.14670 0.95385
8.21613 0.95653
8.28556 0.96019
8.35499 0.96458
8.42442 0.97019
8.49385 0.97604
8.56328 0.98238
8.63271 0.98896
8.70214 0.99530
8.77157 1.00262
8.84100 1.00944
8.91043 1.01603
8.97986 1.02432
9.04929 1.03261
9.11872 1.04163
9.18815 1.05162
9.25758 1.06284
9.32701 1.07527
9.39644 1.08747
9.46587 1.10088
9.53530 1.11404
9.60473 1.12745
9.67417 1.14038
9.74360 1.15305
9.81303 1.16329
9.88246 1.17158
9.95189 1.17646
10.02132 1.18061
10.09075 1.17987
10.16018 1.17670
10.22961 1.16890
10.29904 1.15744
10.36847 1.14184
10.43211 1.12584
10.48997 1.10917
10.54204 1.08887
10.60238 1.06946
10.65583 1.05065
10.70488 1.03288
10.76046 1.01389
10.81629 0.99652
10.87184 0.98043
10.92970 0.96346
10.99334 0.94776
11.06277 0.93240
11.13220 0.92069
11.20163 0.91265
11.27106 0.90557
11.34049 0.90314
11.40992 0.90289
11.47936 0.90411
11.54879 0.90704
11.61822 0.91167
11.68765 0.91703
11.75708 0.92362
11.82651 0.92996
11.89594 0.93678
Loading