Upstream GROMACS atom type merging

[mattwthompson]

Description

This is #962

Checklist

• Add tests
  • Test in general that merging atom types doesn't seem to affect energies
  • Test that non-bonded parameters topology files written with molecules with common moieties look similar to ParmEd, including one with water
• Lint
• Update docstrings
  • Not a part of the public API, so not documented

[codecov]

Codecov Report

Merging #973 (c8b3bfb) into main (0afa0b3) will increase coverage by 0.05%.
The diff coverage is 100.00%.

Additional details and impacted files