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.

} 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

Created reference implementation of DIIS for converging AMOEBA dipoles.  Also some minor code cleanup.

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

Platform specific header files get installed.  This allows plugins to be built with just an OpenMM installation, not a full source tree.

Fixed units for AMOEBA dipole and quadrupole moment (now returns Debye and Debye * Angstrom, not Debye/10 and Debye*Angstrom/100.)  Rationale is that Debye/10 is not a common physical unit.  Note that CUDA platform still gets quadrupole to be incorrect.

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