GitLab

* Remove setting of link libraries, include and link dirs and compile
  flags for each target, instead let Cmake deal with them by linking the
  main library to hip::host hiprtc::hiprtc hip::hipfft;
* Fix: custom command without ADD_CUSTOM_TARGET and ADD_DEPENDENCIES is
  executed for both static and shared targets;
* Remove IF(APPLE) parts.

Fix SegFault in HipCalcHippoNonbondedForceKernel

    HipSort was created using a temporary ref. Adding `HipContext& cu`
    field to HipCalcHippoNonbondedForceKernel fixes the issue;

* Attempt at fixing errors with barostat

* Missing ContextSelector

* Use PocketFFT instead of FFTW

* Minor cleanup

* Use PocketFFT instead of fftpack for reference platform

* Remove FFTW as a dependency

* Converted a test case to use PocketFFT

* Fixed an incorrect comment

* Added lots of checks for invalid parameter values

* Fixed test failures

* More checks for incorrect parameters

* Fixed test failures

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

* Fixed errors in amoeba coda

* Fixed more errors in context selection

* Allow querying current step count

* Fixed error building Python wrapper

* Converted RPMD plugin to common platform

* Merged RPMD tests for different platforms

* Try to fix errors on CPU OpenCL

* Updated to latest values for physical constants

* Updated documentation on physical constants

* Updated Python unit definitions

* Fixed constants in test case

* Added a comment

* Began creating common compute framework to unify code between CUDA and OpenCL

* Began OpenCL implementation of common compute framework

* Common implementation of CMMotionRemover

* CUDA implementation of common compute interface

* Converted HarmonicBondForce to common compute API

* Converted standard bonded forces to common compute API

* Converted ExpressionUtilities to common compute API

* Created ComputeParameterSet

* Converted custom bonded forces to common compute API

* Converted CustomCentroidBondForce to common compute API

* Converted CustomManyParticleForce to common compute API

* Moved lots of duplicate code from CudaContext and OpenCLContext to ComputeContext

* Converted GayBerneForce to common compute API

* Removed obsolete kernels

* Converted verlet integrators to common compute API

* Converted Langevin and Brownian integrators to common compute API

* Converted CustomIntegrator to common compute API

* Converted CustomNonbondedForce to common compute API

* Removed uses of a deprecated API

* Fixed failing test cases

* Converted GBSAOBCForce to common compute API

* Began converting CustomGBForce to common compute API

* Finished converting CustomGBForce to common compute API

* Merged duplicated code in CudaIntegrationUtilities and OpenCLIntegrationUtilities

* Converted RMSDForce and AndersenThermostat to common compute API

* Converted CustomHbondForce to common compute API

* Merged scripts for encoding kernel sources

* Converted Drude plugin to common compute API

* Fixed errors in CMake scripts

* Attempt at fixing errors on Windows

* Added discussion of common compute API to developer guide

* Added Windows export macro for common classes

* Fixed error in CMMotionRemover

* Ubdated travis to newer Ubuntu version

* Fixed errors on CPU OpenCL

* Fixed Windows linking errors

* Added missing pragma for 32 bit atomics

* Replaced long long with mm_long

* More fixes to Windows linking

* Bug fix

New advanced options OPENMM_BUILD_CPU_TESTS, OPENMM_BUILD_SERIALIZATION_TESTS,
OPENMM_BUILD_REFERENCE_TESTS were added to the cmake configuration and disabled
in the OpenCL test matrix element to increase speed. Redundant or unnecessary
apt packages removed from the travis installation.

to 0 here as well.