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Summary

This PR closes issue #178, related to the odd values of the rovibrational entropy terms due to the moment of inertia not using the appropriate axes.

Changes

  • Diagonals of the moment of inertia tensor are now calculated using the same coordinate frame and same rotational coordinates as the torques at each level, rather than the MDAnalysis function which always employed the principal axes.

moments_of_inertia

Impact

  • The same set of axes is now used for both torques and moments of inertia. (i.e. principal for polymer or residue in a small molecule; bonding-derived axes for intramolecular levels) This ensures that axes are consistent and that they are always sorted when using the principal axes (due to sorting within MDAnalysis principal_axes function)
  • Results now match expected magnitudes and results obtained using previous release of the code. Moments of inertia corresponding to principal axis now match those obtained using previous release (with appropriate axis direction change based on sorting)
image image

ioanaapapa and others added 10 commits November 25, 2025 17:22
Bumps [actions/checkout](https://github.com/actions/checkout) from 5 to 6.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v5...v6)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 6.0.0 to 6.1.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v6.0.0...v6.1.0)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: 6.1.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
…ed for the torque calculation. Rotational axes are already sorted either due to sorting within the MDAnalysis function or from being bond-derived axes with a fixed order. This ensures that axis directions are consistent and that coordinate systems used for the torques and moments of inertia are consistent
@ioanaapapa ioanaapapa self-assigned this Dec 2, 2025
@ioanaapapa ioanaapapa mentioned this pull request Dec 2, 2025
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3 participants