Fix/ring fragments

[rsdefever]

Description

This PR has two major changes:

1. A bug fix for the MCF generation for fragment library generation. The MCFs previously used the LJ parameters from the first fragment atom for all the atoms in the fragment. Since branched fragments only contain 1-2 interactions, which are normally set to 0.0, this fix has no material impact in those systems. However, ring fragments can contain 1-4, 1-5, etc. interactions which may be non-zero. In ring fragments with multiple atom types the interactions were therefore incorrect. This resulted in incorrect bond angle distributions in the fragment libraries for certain molecules, e.g., all atom benzene.
2. The ability to generate ring fragments for (simple) fused ring systems. The current code attempts ring flip moves on all ring atoms. In a fused-ring system (e.g., naphthalene), this results in the bond lengths being not preserved. The PR implements the identification of so-called "multiring" atoms, which participate in multiple rings. No ring flip moves are attempted on the multiring atoms. This at least preserves the bond lengths and generates the correct bond angle distribution for a simple test cases (naphthalene). I suspect this scheme will fail for more complex (i.e., larger) fused ring systems. However, in this case the fragments will be so large as to render the CBMC scheme nearly useless anyway. Warnings have been added to the user manual that care should be taken when simulating fused-ring systems.

How Has This Been Tested?

The bugfix was tested by comparing the bond angle distributions for all atom benzene with constrained MD before and after the bugfix. Before the bugfix the bond angle distributions did not match. After the bugfix they agreed with constrained MD. The "multiring" atom scheme was tested via the same approach with all atom naphthalene. Once again, the distributions matched.

Backward Compatibility

Input file backward compatibility is maintained.

Post Submission Checklist

Please check the fields below as they are completed

• Suitable new documentation files and/or updates to the existing docs are included.