GitLab

o Replaced Cartesians in the reciprocal and self PME terms.
o Added non-PME spherical harmonics field generation and force evaluation routines.
o Added spherical harmonic potential evaluation, to allow removal of the Cartesian moments.

o Permanent and induced moment energies, forces and torques are implemented, for PME direct space.
o The code is activated by a preprocessor macro at the top of AmoebaReferenceMultipoleForce.h, and can be completely disabled.
o Currently, the Cartesian momenents are stored alongside the spherical harmonic moments, but these can eventually be removed when the reciprocal and self terms have been adapted to use spherical harmonics (in progress) and the non-PME routines have been coded.

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

one in the Reference platform (pulled over via meld to limit possible mistakes).

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.

} 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.

typo fix