Support non-periodic trajectories without box dimensions

[harryswift01]

Summary

This PR allows CodeEntropy to run on non-periodic trajectories, such as gas-phase simulations of isolated molecules. These trajectories have no box dimensions, so merge_forces failed with AttributeError: 'NoneType' object has no attribute 'copy' when loading them. The axes and covariance code also assumes a box when applying the minimum image convention and unwrapping molecules, so skipping the dimensions alone would not have been enough.

Changes

Handle trajectories without box dimensions:

• merge_forces now checks whether the trajectory has box dimensions before extracting them.
• When there are none, a cubic box is built for every frame, with 90° angles. Its side is max(10 × largest coordinate span, 100 Å), which is far more than twice any interatomic distance, so the minimum image and unwrap steps have no effect.
• A warning is logged when this box is used, giving the box size.
• Trajectories that have a box follow the same path as before.

Add unit tests:

• Check that the generated box has the right shape, is larger than twice the largest extent, and has 90° angles.
• Check that merge_forces passes a per-frame box to load_new when the trajectory has no dimensions.

Impact

• Non-periodic trajectories can now be processed instead of failing at trajectory loading.
• No change for trajectories that have a box, so existing results are unaffected.

[jimboid]

Fast turn around on this user reported bug. Happy with eyeballing of the numbers by Jas in the chat. Happy for this to merge and new minor release to be made on this basis.

[HafizSaqibAli]

Hi @harryswift01,

Thank you so much for sorting this out so quickly. I’ve updated to v2.5.0 and can confirm that it’s now working perfectly on my gas-phase simulations, with no more AttributeError.

I really appreciate the fast turnaround.

Thanks,
Hafiz