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@skfegan skfegan commented Nov 7, 2025

Summary

Adding options to allow for reading in forces from a separate trajectory file to the coordinates.

Changes

  • Adding force_file option so the user can point to where the force part of the trajectory is.
  • Adding file_format option
  • Adding the kcal_force_units option because MDAnalysis typically converts units from the various MD programs into MDAnalysis standard units, but this seems to be missed when the forces are in a separate file

Impact

  • Easier for LAMMPS users and others with coordinates / forces in separate files to use CodeEntropy
  • Correct vibrational entropy results when the forces are in kcal and in a separate file (also works for SI units)
  • Users can add the file format information for cases when MDAnalysis fails to automatically identify the type of trajectory file.

@skfegan skfegan requested a review from harryswift01 November 7, 2025 11:14
harryswift01 and others added 9 commits November 10, 2025 09:18
- Update `.github/workflows/release.yaml` to bump `CITATION.cff` version and date-released automatically
- Keep version in `__init__.py` and `CITATION.cff` in sync during releases
- Fully automated in CI, no manaul edits needed
Bumps [softprops/action-gh-release](https://github.com/softprops/action-gh-release) from 2.4.1 to 2.4.2.
- [Release notes](https://github.com/softprops/action-gh-release/releases)
- [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md)
- [Commits](softprops/action-gh-release@v2.4.1...v2.4.2)

---
updated-dependencies:
- dependency-name: softprops/action-gh-release
  dependency-version: 2.4.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
- `test_merges_forcefile_correctly`: verifies that coordinate and force universes are merged and loaded correctly
- `test_converts_kcal_to_kj`: checks that forces are scaled by 4.184 when `kcal_force_units=True`
- `test_logs_debug_messages`: ensures expected debug logs are emitted during force merge
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@harryswift01 harryswift01 left a comment

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Thanks @skfegan, this looks like a great addition that will allow us to support even more file formats within CodeEntropy. I have added in a couple of tests to make sure we keep coverage up but I am more than happy to approve this, thank you!

@harryswift01 harryswift01 added the feature request New feature or request label Nov 10, 2025
@harryswift01 harryswift01 added this to the v1.0.4 milestone Nov 10, 2025
@harryswift01 harryswift01 linked an issue Nov 10, 2025 that may be closed by this pull request
@harryswift01 harryswift01 changed the title 172 coordinates and forces in separate files Add Support for Calculating Entropy When Forces and Coordinates Are Within Seperate Files Nov 10, 2025
@skfegan skfegan merged commit dff1fb7 into main Nov 10, 2025
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@skfegan skfegan deleted the 172-coordinates-and-forces-in-separate-files branch November 10, 2025 11:10
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Difficulties when coordinates and forces are in separate files

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