GitLab

* 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

* 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

* Updated to latest values for physical constants

* Updated documentation on physical constants

* Updated Python unit definitions

* Fixed constants in test case

* Added a comment

This helps pave the way to test wider SIMD ISAs, such as AVX-512.

* 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

* CPU: Refactored code to be generic across vector CPU platforms.

Ewald and non-Ewald interactions now share a common code base, templated on
their interaction type.

The vec4 and vec8 implementations have been replaced by a single generic implementation
class which is templated on SIMD type. Currently works for SIMD4 and SIMD8 types, but
can be extended in future to support other types (e.g., AVX-512).

Modified runtime CPU support to lay groundwork for future SIMD types.

Pulled out some vector utility functions (gather pair, reduce),
and refactored the AVX CPU code to make use of them.

* CPU: Fixed coding standards and incorrect header include.

* CPU: Fixed code review comments from PR #2661

* CPU: Fixed CI build issues.

* CPU: Further CI fixes.

* CPU: Fix for unit test failure on MacOS.

Reverted optimised code to go back to a version which is thought to work
on MacOS. The optimisation will be reapplied in future after the failure is
understood better.

* 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