GitLab

* Converted RPMD plugin to common platform

* Merged RPMD tests for different platforms

* Try to fix errors on CPU OpenCL

* Converted more code to common platform

* Converted more code to common platform

* Made ComputeContext worker threads rethrow encountered exceptions into the main thread.

* Changed misleading variable names.

* Changed a misleading exception description

* Began implementing geometric functions on points

* Started common implementation of point functions

* Completed implementation of point functions for CustomCompoundBondForce

* Implemented point functions for CustomCentroidBondForce

* Implemented point functions for CustomManyParticleForce

* Use point functions to simplify implementation of custom forces

* Removed unnecessary code

* Fixed typo

* Update IntegrationUtilities.cpp

* Use pinned buffer and for context download
* use template to reduce duplicate code

* Remove template and only add PinnedBuffer for minor performance improvement

* Use pinned buffer for minor performance improvement

Co-authored-by: xxx <yyy>

* CCMA with a small number of constraints uses a single kernel

* Fixed compilation errors in kernel

* Fixed compilation errors in kernel

* Further optimizations to CCMA with few constraints

* Fixed range overflow with very large numbers of atoms

* More fixes to overflow with large numbers of atoms

* Fix test failures

This ensures that the correct argument size is used when calling clSetKernelArg.

Explicitly cast the second parameter to the type of the first one so the compiler can pick an overload that is supported in device code (fixes error: calling a __host__ function("fmin<float, int, (int)0> ") from a __global__ function("computeBondedForces") is not allowed).

Naming the argument list of a variadic macro is a GNU extension which is not supported by msvc. Since CUDA uses the system preprocessor this will fail to build kernels on Windows (fixes error C2010: '.': unexpected in macro parameter list).

* Cleaned up checkpointing code for NoseHooverIntegrator

* Fixed compilation error

* Fixed OpenCL compiler errors

* Fixed incorrect references to BAOAB

* Fixed a method that was incorrectly made public

* Convert Nose-Hoover into LF middle scheme by copying NH kernels

* Rebrand VelocityVerletIntegrator as NoseHooverIntegrator

* Consolidate NH tests

* NoseHooverChainKernel begone

* Make Windows builds happy

* Add missing header for Windows build

* Fix mistake in CommonKernels header

* Add 6th Yoshida-Suzuki and make it the default

* 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