GitLab

Fixed units in swigInputConfig.py for new Alchemical AMOEBA vdW methods exposed in the OpenMM API; implemented the getDefaultParameters() on the AmoebaVdwForceImpl to return 1.0 for AmoebaVdwAlpha; Use AmoebaVdwForce::Lambda() to refer to this parameter rather than the String AmoebaVdwAlpha

AMOEBA vdW softcore is propogated through the Reference platform; pending some feedback adding it to the CUDA code can begin

from all .cpp and .h files.

Simple fix to combining rules allowing AMOEBA VdW parameters to be zero.  Zero parameter excludes all interactions involving that particle, in agreement with TINKER.

added tests to TestCudaAmoebaVdwForce for dispersion correction using box of 216 water molecules
AmoebaVdwForce and AmoebaMultipoleForce now throw execptions if cutoff > 0.5*(box size)

Moved AMOEBA include files to plugins/amoeba/openmmapi/include/openmm to be consistent w/ outlay other plugins, ...

Added checks for nonbonded methods
Removed unused functionality from GK force
Moved non-accessor methods from Force classes to ForceImpl classes

Refactored ForceImpl, lots of KernelImpl subclasses, and other related classes to avoid redundant calculations when requesting a State with both forces and energies

Changed how kernels get initialized.  StandardMMForceField now has you set the 1-4 interactions explicitly.  CMMotionRemover allows the removal frequency to be set.

Modified the initialization order of ForceImpls to prevent them from trying to initialize themselves before the Platform had been chosen

Continuing to implement ReferencePlatform (implemented GBSA kernels, added test case for SHAKE and fixed some bugs in it)