Precedence of torsions defined using "type" vs. "class" about foyer HOT 4 CLOSED

Agreed.

We want bonded parameters that references atom_types to take precedence of bond_classes, as they would be the most specific cases. Given that our atom-typing approach does not rely upon the physical order in which rules are evaluated, we don't want to require bonded interactions to be defined in a specific order.

from foyer.

In testing, a few things I found:
1- "type" and "class" can be mixed in a single definition
2- if the parameters for two separately defined bonded interactions are the same, the code considers them to only be a single type when it dumps to lammps (I didn't check gromacs, but I assume it's the same behavior). I'm not sure if this makes things cleaner or potentially more confusing.

from foyer.

Regarding those two findings:

1. If "type" and "class" can be mixed, then perhaps we want to set the order of precedence based on the number of "type" definitions in a listed dihedral.
2. I implemented this behavior when writing the LAMMPS writer simply to make the data file a bit cleaner. I had been thinking of going back on this, however, and having the LAMMPS writer write all dihedral parameters (even duplicates) with a comment added at the end that specifies what the dihedral corresponds to (at this point we are dealing with a ParmEd Structure so we will have lost the bond type information, but could at least have a comment at the end of the line that details what elements are involved in the dihedral).

from foyer.

1. That's a good idea, the highest precedence is the maximum number of "type" and minimum number of "none" definitions
2. Ok, so that's an easy change. I think we should have an option that is "descriptive" output, where we put a comment at the end of each line to say which dihedral parameters these correspond to (so like basically dump the definition string, class1="x" class2="") I probably wouldn't want that in every file, but might be useful to have for validation purposes (of say, a single molecule).

from foyer.