Rotate MPCD coordinate system

[mphoward]

Description

For legacy reasons from another implementation, many of the geometries and features in MPCD are defined in the xz plane, including mpcd.stream.slit, mpcd.stream.slit_pore, mpcd.integrate.slit, mpcd.integrate.slit_pore, and everything in mpcd.force. As pointed out by @j-proc in PR #443, it would be smarter to rotate everything into the xy plane so that these features still work in 2d simulations, if such a collision rule is later implemented.

This is a breaking change that I didn't want to tackle before, but I think it would be smart to adjust in v3.0.

Proposed solution

Swap out z coordinates for y coordinates everywhere in those classes. Alot of it should be localized to the geometry files.

Developer

Yes, I can take care of it when I go through this code for v3.

[github-actions[bot]]

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

[github-actions[bot]]

This issue has been automatically closed because it has not had recent activity.

[mphoward]

Completed in #1714