Add position restraints for Site

[daico007]

Add position_restraints for site and write it out in GROMACS top writer. Pending unit test.

[codecov]

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (b728c99) 92.82% compared to head (93d501d) 92.79%.

Files	Patch %	Lines
gmso/formats/top.py	90.90%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #770      +/-   ##
==========================================
- Coverage   92.82%   92.79%   -0.03%     
==========================================
  Files          66       66              
  Lines        6845     6859      +14     
==========================================
+ Hits         6354     6365      +11     
- Misses        491      494       +3     

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[CalCraven]

I think the tests should go in test_atom.py and test_top.py. One that you can add a restraint to a site and parse it, and one that a topology with restraints will properly be id'd in gromacs. I think the best way to do that would be to make a restrained_water_topology in base_test.py for other engines to use, and then call that.

[daico007]

This PR includes the fix for the current failing CI tests.

[daico007]

All unit tests has been added.

[CalCraven]

Just remove the duplicate files and it should be good to go!

[CalCraven]

Once tests pass, lets merge it.