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

typo fix

@rmcgibbo and @mpharrigan convinced me I should have just fixed it myself.

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.

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)

Added tests for system of 2 ions and 2 water molecules;
Removed TestCudaAmoebaPME.cpp

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()