GitLab

* Use common API for kernels

* More code uses common interface

* Bug fixes

* Unified interface for sorting

* Simplified interface for FFT

* Use common event API for synchronization

* Minor changes to make code more consistent between platforms

* Common implementation of NonbondedForce

* Bug fixes

* Flag to enable list of single pairs

* CUDA and OpenCL use common implementation of NonbondedForce

* Fixed compilation error

* HIP uses common implementation of NonbondedForce

* Always use nvrtc for compilation

* Install nvrtc on CI

* Workaround for compiler error

* Set empty values for deprecated properties

* Optimized CudaSort for non-uniformly distributed data

* Optimized OpenCLSort for non-uniformly distributed data

* Further tuned distributing elements between buckets

* Copied optimizations over to OpenCL

* Use cuCtxPushCurrent() and cuCtxPopCurrent() for selecting CUDA context

* Fixed errors in amoeba coda

* Fixed more errors in context selection

* Use command line compiler if it is explicitly specified

* Don't set OPENMM_CUDA_COMPILER on Jenkins

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

Continuing to implement new CUDA platform: constraints, LangevinIntegrator, BrownianIntegrator, VariableLangevinIntegrator, VariableVerletIntegrator

Moved SFMT into libraries folder, and restructured it to allow multiple independent random number generators

Modified the API for lots of classes so that the number of particles/bonds/etc. need not be specified in the constructor.

Continuing to implement ReferencePlatform (implemented kinetic energy calculation and LangevinIntegrator)

Created a test case for StandardMMForceFieldImpl's findExclusions() method.  Fixed some bugs that it found.  Created a CMake script and configured it for building and running test cases.