feat: use NPT sims for water + solvent benchmarks

[mcarobene-id]

Pull Request Title

Description

This PR updates the benchmarks (WaterRadialDistributionBenchmark, SolventRadialDistributionBenchmark) to use the NPT ensemble rather than NVT, as an NPT integrator was recently added to mlip v2.

Checklist for adding a new benchmark

• Benchmark class is fully implemented, including
  all abstract method implementations.
• Benchmark is fully tested following our standard
  testing pattern.
• Input data uploaded to HF is validated and correct.
• The corresponding documentation is added and up to date.
• The UI code is added and up-to-date and has been tested.
• Our license has been added to any Python file.

[CLAassistant]

Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you all sign our Contributor License Agreement before we can accept your contribution.
1 out of 2 committers have signed the CLA.

✅ lwalew
❌ Marco Carobene

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[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
src/mlipaudit
__init__.py	2	0	100%
benchmark.py	77	7	90%	147, 166, 232, 238–239, 249, 263
exceptions.py	2	0	100%
io.py	100	25	75%	117, 121, 146–150, 152, 154, 171–172, 174–175, 192–193, 195, 213–221
io_helpers.py	52	0	100%
run_mode.py	5	0	100%
scoring.py	29	7	75%	101–102, 104, 107, 111–112, 114
src/mlipaudit/benchmarks
__init__.py	29	0	100%
src/mlipaudit/benchmarks/bond_length_distribution
bond_length_distribution.py	95	3	96%	208, 211, 276
src/mlipaudit/benchmarks/conformer_selection
conformer_selection.py	132	5	96%	249, 252, 295, 300, 340
src/mlipaudit/benchmarks/dihedral_scan
dihedral_scan.py	116	5	95%	222, 225, 259, 262, 304
src/mlipaudit/benchmarks/folding_stability
folding_stability.py	106	4	96%	212, 270, 275, 339
helpers.py	35	0	100%
src/mlipaudit/benchmarks/noncovalent_interactions
noncovalent_interactions.py	168	10	94%	245, 248, 272, 283, 407, 424, 441, 525–527
src/mlipaudit/benchmarks/nudged_elastic_band
engine.py	126	94	25%	62, 81–82, 84–89, 91, 93, 95–96, 98–99, 101–103, 112–113, 115–116, 120–121, 123, 130, 132, 134–136, 138–139, 141, 143–145, 147–151, 153, 159–163, 165–167, 169–171, 173–175, 177–180, 182, 185, 189–190, 192, 194–195, 197, 201–202, 205–210, 212–213, 229, 234, 236–238, 240, 242–243, 246–247, 253, 256–257, 261–262, 267
nudged_elastic_band.py	121	6	95%	290–291, 298, 310, 316, 323
src/mlipaudit/benchmarks/reactivity
reactivity.py	117	3	97%	239–240, 272
src/mlipaudit/benchmarks/reference_geometry_stability
reference_geometry_stability.py	122	3	97%	233, 305, 328
src/mlipaudit/benchmarks/ring_planarity
ring_planarity.py	99	6	93%	229, 232, 264, 267–268, 287
src/mlipaudit/benchmarks/sampling
helpers.py	64	4	93%	46, 67, 97, 129
sampling.py	225	10	95%	303, 344, 385, 388–390, 440, 707, 825–826
src/mlipaudit/benchmarks/scaling
scaling.py	103	34	66%	128–130, 138–139, 141–144, 154–156, 193–198, 201–203, 209–210, 212–213, 215–216, 219–220, 222, 243, 252, 271, 284
src/mlipaudit/benchmarks/solvent_radial_distribution
solvent_radial_distribution.py	118	8	93%	206–207, 209, 248, 253–254, 329, 357
src/mlipaudit/benchmarks/stability
stability.py	150	18	88%	166, 169, 201–202, 205–206, 208, 210, 213, 215, 431–432, 442, 478, 487, 522, 537, 548
src/mlipaudit/benchmarks/tautomers
tautomers.py	92	5	94%	182, 208, 211–212, 231
src/mlipaudit/benchmarks/water_radial_distribution
water_radial_distribution.py	112	2	98%	199, 285
src/mlipaudit/ui
__init__.py	16	0	100%
bond_length_distribution.py	58	11	81%	89–90, 95–96, 141–142, 147, 150, 176, 188, 192
conformer_selection.py	100	7	93%	133–134, 139–140, 195, 320, 324
dihedral_scan.py	115	12	89%	141–142, 147–148, 259–260, 302, 313, 353, 355, 365, 369
folding_stability.py	96	7	92%	44, 226–227, 232–233, 406, 410
leaderboard.py	80	10	87%	67, 74, 78, 85, 287–289, 291, 293, 303
noncovalent_interactions.py	152	9	94%	205–206, 211–212, 392, 397, 432, 454, 458
nudged_elastic_band.py	55	39	29%	42–46, 50–51, 53, 66, 68, 75, 82, 89–90, 93, 97–99, 101, 103–105, 107–109, 111–113, 115, 117, 119, 121–122, 124, 135, 137, 149, 159, 163
page_wrapper.py	14	2	85%	36, 46
reactivity.py	59	6	89%	96–97, 102–103, 173, 177
reference_geometry_stability.py	66	9	86%	62, 131–132, 137–138, 199, 226, 236, 240
ring_planarity.py	56	9	83%	71–72, 77–78, 123–124, 160, 170, 174
sampling.py	87	9	89%	85, 129–130, 135–136, 166, 234, 265, 269
scaling.py	52	6	88%	135–136, 147–148, 162, 166
solvent_radial_distribution.py	84	20	76%	122–123, 128–129, 155, 161, 167–171, 173–174, 180, 183, 195, 202, 204, 216, 220
stability.py	60	10	83%	106–107, 112–113, 134–135, 138, 148, 177, 181
tautomers.py	62	6	90%	82–83, 88–89, 194, 198
utils.py	106	19	82%	69, 73–74, 130, 192–195, 201, 251, 269–270, 273–274, 277, 287–289, 291
water_radial_distribution.py	97	6	93%	130–131, 136–137, 277, 281
src/mlipaudit/utils
__init__.py	4	0	100%
inference.py	27	7	74%	54–56, 65–66, 69, 72
molecular_liquids.py	11	0	100%
simulation.py	55	4	92%	139, 177–179
stability.py	31	5	83%	61, 68, 92, 99, 103
trajectory_helpers.py	42	0	100%
unallowed_elements.py	10	0	100%
TOTAL	3992	472	88%

Tests	Skipped	Failures	Errors	Time
128	0 💤	0 ❌	0 🔥	13.155s ⏱️

[mcarobene-id]

TODO: Add details RE how the densities are computed and (below) what experimental values we compare to