feat: add bond length distribution benchmark#666
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Migrate the bond length distribution benchmark from the MLIP Audit suite. An NVT molecular dynamics simulation is run for each of a set of small organic molecules, and the deviation of a tracked covalent bond from its QM-optimised reference length is measured over the trajectory. Lower average deviation is better. Adds the calculation, analysis (histogram of deviations plus a metrics table), Dash app, documentation, and the mlipaudit dependency wiring (optional extra, git source and MLIP Audit framework badge).
ElliottKasoar
added
the
new benchmark
joehart2001
reviewed
Jul 9, 2026
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| High: one MD simulation per molecule, each 1,000,000 steps. Faster inference can be achieved |
Collaborator
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Thanks for the pr! same as #658 could you send the data + have a look at the element filtering? docs: https://ddmms.github.io/ml-peg/developer_guide/filter.html |
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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 #671
Progress
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(layoutbond_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_histandbuild_tabledecorators and theplot_from_table_columncallback.Note for reviewers