GitLab

Update the Python application layer to use both force constants when building
the AmoebaStretchBendForce.

stretch-bend test correctly.

The potential energy calculation done in the ReferenceStretchBendTest file was
updated to mirror that of the Reference kernel, but first I made sure that the
test passed *before* updating to the new energy expression, just to make sure
that the energies and forces didn't *change* with the new expression.

of just 1.  Backwards compatibility is provided by making the 2nd force constant
default to -1, which is reinterpreted as "copy the first force constant".

Updates both the reference and CUDA kernels.

typo fix

typo fix

typo fix

Removed 'void' declarations from getCutoff/getCutoffDistance methods so that swigInputBuilder.py would correctly wrap return values.

from all .cpp and .h files.

Modified the AmoebaMultipoleForce.getSystemMultipoleMoments method with two extra arguments; toggle whether to evaluate energy/force and select maximum multipole order.

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)

Added new tests to TestCudaAmoebaVdwForce; fixed bug in AmoebaVdw tapering; non-default AmoebaVdw rules for calculating combinded epsilon 
value changed to agree w/ TINKER

Added AmoebaMultipoleForce::getSystemMultipoleMoments() to get system multipole moments; based on TINKER subroutine moments()

TorsionTorsion grids reordered, if needed, so that first angle is the 'slow' index
Fixes for MonteCarloBarostat 

WCA force now written directly to cuda.force4 array