Detect and remove duplicate dihedrals with the same periodicity

[LSchwiebert]

Resolves issue #529 by issuing a warning when dihedrals with matching periodicities are found. The duplicates are removed and a warning is generated. The warning looks like this:

Warning: Skipping duplicate periodicity of 3 for dihedral HCCTCTHC!

[LSchwiebert]

Updated patch to generate an error and exit, instead of a warning, if the duplicate dihedrals have different parameter values.

[bc118]

Tested code and functioned as intended.

[bc118]

This patch works as intended per my testing.

I looked at what NAMD does. It appears they take the last one input. We may want to be consistent with them for py-mcmd.

My last comment, is more of a question, and this would go for non-bonded and all bonded parameters.

Do we want to more than NAMD and check if the parameters are the same or different (this would be more than NAMD):

• if the same, skip it
• if different, throw an error or overwrite with the last one.

[bc118]

I tested is and it Looks like it is working as intended.

[LSchwiebert]

I updated the patch so that it throws an error if the parameters differ by more than 0.001. I have to imagine that would be a mistake. Since it only proceeds if they match, then which one we save doesn't matter.

So, we do the same thing as NAMD if the parameters match except we also issue a warning, and we terminate with an error if the parameters differ.

[bc118]

Reviewed and it looks good. My only suggested change is some wording. Change the below "Using first entry." to "found duplicate entry" or similar, as it errors out if the entries are different, other than the n-value, which the n-value has to be allowed to be different in this periodic form because it is listed as n entries.

Reading DIHEDRALS parameters.
Warning: Ignoring duplicate periodicity of 3 for dihedral HCCTCTHC in GOMC_pdb_psf_ff_files_dihedrals_zeroed.inp. Using first entry.

[LSchwiebert]

Thanks for the feedback. I have revised the error messages per your suggestions.