Fix some issues with FF hierarchy, SMIRKS patterns

[davidlmobley]

• Tag issue being addressed
  (https://github.com/openforcefield/openforcefield/tree/master/docs), if applicable
• Update changelog

Addresses #367 . Changes ultimately to be propagated to smirnoff99frosst repo; this is an interim fix to get the FF ready for use in testing.

Fixes some problems with the test force field (changes later to be propagated to smirnoff99Frosst).

[davidlmobley]

@j-wags this is ready to go.

@yudongqiu the force field we're going to want to be fitting is here. (edit by Jeff, to remove ambiguity: The new FF is in test_forcefields/smirnoff99Frosst_experimental.offxml)

[davidlmobley]

(That said, @j-wags this is "good to go" in the sense of "this is the force field I want put in here", but it does not deal with the issue of the regression tests. Do you want me to put in some alternate FFs for use in the tests? Or you can do it...)

[j-wags]

Thanks, I'll get the tests fixed up :-)

[codecov-io]

Codecov Report

Merging #368 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #368   +/-   ##
=======================================
  Coverage   76.54%   76.54%           
=======================================
  Files          19       19           
  Lines        5585     5585           
=======================================
  Hits         4275     4275           
  Misses       1310     1310

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 1c1abc7...2dc6167. Read the comment docs.

[j-wags]

Looks good. I've moved the new FF to test_forcefields/smirnoff99Frosst_experimental.offxml. I know we make no guarantees about the contents of test_forcefields/smirnoff99Frosst.offxml, but I figure that we want to minimize changes to it if possible. We can consider merging them in once the new FF gets a release/official version in s99F.

@yudongqiu Note that the new FF is at test_forcefields/smirnoff99Frosst_experimental.offxml.