Consolidate WiSE benchmark per PR ddmms#445 review

- Merge density / rdf / xray_sf into a single litfsi_h2o_21m benchmark
  under ml_peg/{calcs,analysis,app}/wise_electrolytes/litfsi_h2o_21m/.
- Adopt the standard ml-peg patterns in the analysis and calc scripts:
  load_models(current_models) for model discovery, @build_table for
  the metrics table, and metrics.yml for thresholds/tooltips/weights.
- Add a Janus recast of the LAMMPS+symmetrix Adastra production protocol
  in ml_peg/calcs/wise_electrolytes/md_reference/calc_md_reference.py
  (pytest-skipped reference; documents the exact MD parameters).
- Add the docs page docs/source/user_guide/benchmarks/wise_electrolytes.rst
  (and toctree entry) and wire the app docs_url to it.
- Update the parent wise_electrolytes.yml to a single benchmark weight.

Author: luca

docs/source/user_guide/benchmarks/index.rst

@@ -17,3 +17,4 @@ Benchmarks
     tm_complexes
     conformers
     molecular_dynamics
+    wise_electrolytes

docs/source/user_guide/benchmarks/wise_electrolytes.rst

@@ -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).