GitLab

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

typo fix

typo fix

typo fix

typo fix

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

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

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