GitLab

Created API and reference implementation of restricting CustomNonbondedForce to selected interaction groups

Converted the routine for identifying molecules from a recursion to a loop.  This avoids stack overflows with very long linear molecules.

Platform specific header files get installed.  This allows plugins to be built with just an OpenMM installation, not a full source tree.

Using a const Vec3& instead of three doubles for the AnisotropicBarostat API.  Still figuring out SWIG issues.

Long range correction for both NonbondedForce and CustomNonbondedForce takes the switching function into account

Completed support for serialization of all integrator types. Modified Assertion utilities to allow ASSERT_EQUAL to work on strings. Updated unit tests for testSerializeIntegrators. 

CustomNonbondedForce.cpp, CudaNonbondedUtilities.cpp and CudaKernels.cpp are now fully reverted to 3478.

LPW attempted bugfixes: (1) Changed unit multipliers in AmoebaVdwForce::getParticleParameters (2) Sorted vectors in exclusionLists so it agrees with atomExclusions