feat: add bond length distribution benchmark

[lwalew]

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Summary

Migrates the bond length distribution benchmark from the MLIP Audit suite. For each of a set of small organic molecules — covering the C-C, C=C, C#C, C-N, C-O, C=O and C-F bond types — an NVT molecular dynamics simulation is run at 300 K starting from a QM-optimised reference geometry (selected from QM9), and the deviation of a tracked covalent bond from its reference length is measured over the trajectory. A well behaved potential keeps bonds close to their reference length, so a lower average deviation is better.

The analysis reports the average bond length deviation per model in the metrics table and shows the distribution of sampled deviations as a histogram.

Linked issue

Resolves #665

Progress

• Calculations
• Analysis
• Application
• Documentation

Testing

Not yet run end-to-end: the benchmark input data still needs to be uploaded to the ML-PEG S3 bucket at inputs/molecular_dynamics/bond_length_distribution/bond_length_distribution.zip (layout bond_length_distribution/bond_length_distribution.json). Kept as a draft until the data is available. Style checks (pre-commit) pass locally.

New decorators/callbacks

No new callbacks required; uses the existing plot_hist and build_table decorators and the plot_from_table_column callback.

Note for reviewers

This is the first MLIP Audit migration, so it also adds the shared mlipaudit wiring: the mlipaudit optional extra and git source in pyproject.toml, the mlip_audit framework badge in frameworks.yml, and ml_peg/calcs/utils/mlipaudit.py. This overlaps with the other in-flight MLIP Audit migration PRs (e.g. #660, #644); whichever lands first introduces this wiring and the others can drop it.