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Fixed a race condition in OpenCL

Simplification to reference platform tests

Fixed an error in doxygen comments

Fix HAngles with Amber prmtop files

Adds a test for it as well.

files.

CMAPTorsionForce implements updateParametersInContext()

Modified travis logic to only fail if retested tests fail.

Fixing multiple bugs in dcdfile / dcdreporter.

Fix very subtle bug in Amber prmtop with NBFIX

Some topology files have some of the nonbonded pairs in the Lennard-Jones matrix
pointing to a 0 entry in the HBOND_ACOEF and HBOND_BCOEF arrays. This commit
simply skips over those entries, having previously checked that all entries in
the 10-12 sections are 0.  There is actually an example of this already in the
test suite (see ff14ipq.parm7), but this fortuitously did not cause any
difference in those test results.

The reason this bug is not evident in that test case is because the A- and
B-coefficients pulled when the index was -1 (later decremented to -2) was also
coincidentally 0. However, if this was not the case (as it does not *have* to
be), then who knows what could happen.

This also adds more of a check against 10-12 topology files. ParmEd actually
supports using the 10-12 potential in OpenMM when specified in the Amber prmtop,
but it is sufficiently rare that it is not worth porting to OpenMM, IMO.

Fixed a performance regression in multi-GPU on CUDA

Bug fixes to multi-GPU simulations

Cleanup and simplification to reference AMOEBA multipole force

Update `Topology` creation from CHARMM parsers and fix Amber prmtop parsing when %COMMENT sections are present

flags. This can cause a KeyError when trying to look up the format of the
current section when it's reading the %COMMENT line (before any Format has been
assigned).

Added keepIds flag to PDBFile.writeFile()

Fixed exception in addExtraParticles()