feat: add solvent radial distribution benchmark - #728
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Migrate the solvent radial distribution benchmark from the MLIP Audit suite. A short NVT molecular dynamics simulation is run for boxes of carbon tetrachloride, methanol and acetonitrile, and the radial distribution function of the characteristic atom is compared to the experimental first solvent peak position. Adds the shared mlipaudit wiring (optional extra, uv source, framework badge and calculator adapter). # Conflicts: # ml_peg/calcs/utils/mlipaudit.py
Guard the module-level `mlipaudit` imports with `pytest.importorskip` so collection skips instead of erroring when the optional `mlipaudit` extra is not installed. Placed ahead of the `ml_peg.calcs.utils.mlipaudit` import, which pulls in `mlipaudit` unconditionally. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Save the downloaded input data to the calculation outputs and read it from there during analysis, so the analysis no longer re-downloads from S3. Raise a clear error if the calculation has not been run. Store elements as one list per structure rather than a single union, so individual structures can be excluded once partial filtering is supported. Report a failed model as NaN rather than None. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Summary
Migrates the solvent radial distribution benchmark from the MLIP Audit suite. For each of
carbon tetrachloride, methanol and acetonitrile, a short NVT molecular dynamics simulation
is run from an equilibrated box, and the radial distribution function of the characteristic
atom (C-C, O-O and N-N respectively) is computed from the trajectory. The position of the
first solvent peak is compared to the experimental reference peak position and the absolute
deviation is averaged across the solvents. The interactive feature is a line plot of the
RDF profiles for each model and solvent.
This PR also adds the shared
mlipauditwiring (optional extra, uv git source,mlip_auditframework badge and the
ml_peg/calcs/utils/mlipaudit.pycalculator adapter). This overlapswith other in-flight MLIP Audit benchmark PRs (e.g. #666, #660); whichever merges first
introduces the shared wiring, and the others will need a rebase to drop the duplicate.
Linked issue
Resolves #723
Progress
Testing
The end-to-end run is pending the upload of the input data to S3
(
inputs/molecular_dynamics/solvent_radial_distribution/solvent_radial_distribution.zip).All pre-commit hooks (ruff check, ruff format, numpydoc-validation, whitespace/EOF) pass
locally.
New decorators/callbacks
None. The benchmark reuses the existing
plot_scatter/build_tabledecorators and theplot_from_table_columncallback.