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.

} else { -->
}
else {

However, these were not my additions originally, but rather part of the Amoeba
test cases that have been around for awhile. I figured while I was at it, I
might as well update these styles as well.

function call.

Plugins work with CPU platform.  This involved separating the reference implementations of plugins into their own libraries.

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

Fixed test failures caused by linking to the same library twice, once statically and once dynamically

Modified Reference platform of AmoebaVdwForce to handle PBC, cutoffs, tapering and dispersion correction

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)