Lammps charmm dihedrals

[CalCraven]

No description provided.

[codecov]

Codecov Report

Attention: 7 lines in your changes are missing coverage. Please review.

Comparison is base (fce6f42) 92.36% compared to head (11bbf15) 92.42%.

Files	Patch %	Lines
gmso/utils/compatibility.py	79.16%	5 Missing ⚠️
gmso/formats/lammpsdata.py	98.76%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #787      +/-   ##
==========================================
+ Coverage   92.36%   92.42%   +0.06%     
==========================================
  Files          66       66              
  Lines        6864     7024     +160     
==========================================
+ Hits         6340     6492     +152     
- Misses        524      532       +8     

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[CalCraven]

Noting two issues still to deal with:

1. We need to make sure that we want this way to deal with potentials that have terms, such as charmm dihedrals and cvff params that need to be given multiple lines for the same dihedal types
2. There is a lot of optimization to be done, this still takes on the order of 15 minutes for 1000 atoms, which doesn't scale great.

[daico007]

Got some comments, but I will need to come back to this later this week, still probably have a bit of the lammps writer (the smaller utilities).

[daico007]

I think I went through all the changes (and some local tests). Most of the logic is sound, only some minor suggestion with code styling. The only issue I think we need to resolve is with the priority of grabbing value for site.charge (see comment above).

[CalCraven]

All comments look great @daico007. Will incorporate these tomorrow. Agreed about some of the messiness of those loops. I'll see if I can think of a cleaner way to write it, because even I look at it and my eyes glaze over.

[daico007]

LGTM! Will merge once all tests pass.