GitLab

* Created API for HIPPO force field

* Beginning of reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Completed reference of HIPPO with no cutoff

* Beginning cutoffs/PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Completed reference implementation of HIPPO

* Cleanup and optimization to HIPPO reference

* Further cleanup to HIPPO

* Combined direct space interactions into a single loop

* Compute direct space interactions in quasi-internal frame

* Beginning of CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Finished CUDA implementation of HIPPO

* More features and test cases for HippoNonbondedForce

* Serialization and Python API for HippoNonbondedForce

* Fixed sign error in computing forces

Fixed an edge case bug for Gyrcuk Radii. If the radius (ri) of the atom being descreened is larger than sum of the separation distance (r) and scaled descreening radius (sk), then there is no descreening. This could happen for carbon atom (ri ~= 2) engulfing its bonded hydrogens (sk < 1).

o Variable renaming in multipole electrostatics code, to avoid confusion.
o CUDA test case only runs finite difference test for the double precision test.

Modified dummy cuda getLabFramePermanentDipoles from getSystemMultipoles to getInducedDipoles Implementation

Added LabFramePermanentDipole function to the cuda kernels files, but it currently works as getSystemMultipoleMoments

Added LabFramePermanentDipole function to the cuda kernels files, but it currently works as getSystemMultipoleMoments

errors.

This copies the fix for the AmoebaTorsionTorsionForce over to the other two
forces that calculate angles via the inverse cosine -- specifically the in-plane
angle force and the stretch-bend force.  The TorsionTorsion fix did not
completely solve the occasional simulation blowup, although it did make it a
*lot* less frequent (it went from happening within 5 minutes to happening ~once
per day).