GitLab

Removed debugging code

Fixed problem w/ AmoebaVdwForce.areParticlesIdentical() that was preventing particles from being reordered

Reduced memory footprint

Add logging guards 

Set nonbondThreadsPerBlock to gpu->sim.nonbond_threads_per_block

-This line, and th -se below, will be ignored--

M    amoebaCudaGpu.cpp
M    kCalculateAmoebaCudaMapTorques.cu
M    kCalculateAmoebaCudaRotateFrame.cu

Modified cudaLoadCudaFloatArray() call
Minor optimizations

Converted CUDAStream SysStream[0] and DevStream[0] references to SysData & Devdata

Added diagnostics for handling reorder of atoms

Added support for missing axis types (Cuda only)
Removed rotationMatrix

Renamed files to be consistent w/ other file names

Removal SASA code
Versioning introduced in AmoebaTinkerParameterFile
Decomposition of PME forces included in prm files 

An exception is now thrown if the multipole axis type is not Bisector or Z-then-X
Redid velocity initialization in test code