Implement triclinic and general hyperparallelepiped boxes

[janbridley]

No description provided.

[github-actions]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[github-actions]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[github-actions]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[github-actions]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[github-actions]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[tfteague]

Description

This PR implements sheared boxes in hoomd-rs via three new structs: triclinic, rhomboid, and hyperparallelepiped, supporting 3D, 2D, and arbitrary-dimension simulations respectively. triclinic and rhomboid are preferred over hyperparallelepiped, which relies on more expensive particle-wrapping operations.

To maintain numerical stability in simulations using hyperparallelepiped, QR decomposition was also implemented in the linear algebra module. This factorizes the general box-vector matrix into a rotation and an upper-triangular box matrix, analogous to those used by triclinic and rhomboid.

Motivation and Context

Non-orthogonal boxes are needed for simulating non-cubic crystals and for boundary-shearing workflows such as floppy box MC.

How Has This Been Tested?

Unit tests cover added functions and structs. Hard-polyhedra simulations in a sheared box were run using all three structs and appear to work as intended.

Checklist:

• I have reviewed the Contributor Guidelines.
• I agree with the terms of the hoomd-rs Contributor Agreement.
• My name is on the list of contributors (doc/src/credits.md) in the pull request source branch.
• I have summarized these changes in release-notes.md following the established format.