Add support for writing rigid bodies when converting to HOOMD formats.

[chrisjonesBSU]

rigid IDs are ints assigned to particles/atoms that signal which rigid body they belong to which is needed when recording rigid body information in HOOMD Frames and/or GSD files. The mBuild hoomd writers handled this, but we still need to implement them here.

In mBuild, rigid_id is a property at the particle level, so we can treat it the same here, at the site level.

This is a draft for now. Remaining TODOs are:

• handle cases where some molecules are rigid and others aren't
• throw an error if rigid particle type is found in the topology already

[CalCraven]

A remaining question to figure out: What if only some molecules are rigid in a hoomd simulation? How does the list of rigid body indices change?
https://hoomd-blue.readthedocs.io/en/v3.6.0/tutorial/06-Modelling-Rigid-Bodies/00-index.html

[CalCraven]

Was playing around with the rigid bodies in HOOMD. Got a working simulation with some rigid particles and some non-rigid particles. Looks like the body argument, shown now in line, get's a tag of -1 if the particle is not rigid. The rigid particles get the rigid ID for that particle, and the rigid COM particle, named "dimer" here, also get's that same ID.

[codecov]

Codecov Report

Attention: Patch coverage is 96.15385% with 2 lines in your changes missing coverage. Please review.

Project coverage is 93.51%. Comparing base (c8c62ae) to head (4eaf697).
Report is 8 commits behind head on main.

Files with missing lines	Patch %	Lines
gmso/external/convert_hoomd.py	96.15%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #850      +/-   ##
==========================================
- Coverage   94.07%   93.51%   -0.57%     
==========================================
  Files          65       65              
  Lines        6953     6998      +45     
==========================================
+ Hits         6541     6544       +3     
- Misses        412      454      +42     

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[chrisjonesBSU]

Was playing around with the rigid bodies in HOOMD. Got a working simulation with some rigid particles and some non-rigid particles. Looks like the body argument, shown now in line, get's a tag of -1 if the particle is not rigid. The rigid particles get the rigid ID for that particle, and the rigid COM particle, named "dimer" here, also get's that same ID.

I believe this is correctly implemented now, but I still need to test it out.