GitLab

Improve the performance of sending the AmoebaVdwLambda to Cuda using pinned host memory; Updated the AmoebaVdwForceProxy to version 3, and added backward compatibility to version 2; updated TestAPIUnits.py to handle the per particle lambda flag

changed the type of the isAlchemical Cuda array to float, which is needed for the CudaNonbondedUtilities.addParameter method to work; the TestCudaAmoebaVdwForce now passes for its current set of tests, but new tests are needed to check the softcore behavior

Rough draft AmoebaVdwForce Cuda code; next steps are to add CUDA kernal compilation support for USE_SOFTCORE, VDW_LAMBDA, VDW_SOFTCORE_POWER, VDW_SOFTCORE_ALPHA, and per particle isAlchemicalI / isAlchemicalJ flags

Fixed units in swigInputConfig.py for new Alchemical AMOEBA vdW methods exposed in the OpenMM API; implemented the getDefaultParameters() on the AmoebaVdwForceImpl to return 1.0 for AmoebaVdwAlpha; Use AmoebaVdwForce::Lambda() to refer to this parameter rather than the String AmoebaVdwAlpha

AMOEBA vdW softcore is propogated through the Reference platform; pending some feedback adding it to the CUDA code can begin

for the AmoebaVdwLambda global parameter was added that returns the parameter's name; added the value None to the AlchemicalMethod enumeration; provided default values for the isAlchemical flag

* 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).

CUDA Extrapolated polaraization test now obeys precision argument, and handles finite difference checks appropriately.

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