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

* Created DPDIntegrator class

* Reference implementation of DPDIntegrator

* Build neighbor list for DPDIntegrator

* Minor fixes

* Documentation for DPDIntegrator

* Python API for DPDIntegrator

* Preliminary OpenCL implementation of DPDIntegrator

* Enable USE_PERIODIC

* Use updated positions in DPD thermostat

* Working on neighbor list for OpenCL DPDIntegrator

* ReorderListener for particle types

* Serialization for DPDIntegrator

* CUDA implementation of DPDIntegrator

* HIP implementation of DPDIntegrator

* Fixed compile error in Python wrapper

* Fixed compile error in wrappers

* Fixed uninitialized memory in reference neighbor list

* Added DPDIntegrator to C++ API docs

* Fixed incorrect launch size

* Fixed nan in DPD random number generator

* Minor optimizations

* Improved load balancing

* Fixed an indexing error

* Neighbor list uses the maximum cutoff of any force

* Fixed HIP compilation error

* Fixed access to invalid memory

* Added test case for diffusion coefficient

* Try to debug segfaults on CI

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Possible fix

* Debugging

* Debugging

* Debugging

* Use correct block size on CPU OpenCL

* Workaround for bug in Intel's OpenCL for CPUs

* Removed an unnecessary define

* Removed debugging code

* Include Dart

* More Intel workarounds

* Workaround for error in NVIDIA OpenCL

* Improved sorting of blocks when building neighbor list

* Improved block sorting for OpenCL

* Made sort keys more evenly distributed

* Use large blocks to optimize building the neighbor list

* Large blocks optimization for OpenCL

* Fix test failures

* Select whether to use large blocks based on system size

* Skip neighbor list for very small systems

* Fixed typos

* Don't skip box size check when not using neighbor list

* Made test larger to ensure it uses neighbor list

It may contain a garbage value, and if it is large then
updateNeighborListSize does not force reorder atoms after 25 steps
in extremal cases.

* Minor optimizations to computing single pairs

* Adjusted MAX_BITS_FOR_PAIRS on Ampere

* Fixed potential invalid memory access

* Fixed exception

* 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

* Began converting AMOEBA to common platform

* Beginning of OpenCL platform for AMOEBA

* Converted AmoebaVdwForce to common platform

* Cleaned up reference AMOEBA tests

* Began converting AmoebaMultipoleForce to common platform

* Continue converting AmoebaMultipoleForce to common platform

* Bug fixes

* Bug fix

* Continue converting AmoebaMultipoleForce to common platform

* Converting AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce to common platform

* Converting AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce to common platform

* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce

* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce

* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce

* Converted arrays from real3 to real

* Bug fix to OpenCL AmoebaGeneralizedKirkwoodForce

* Fixes for AMD GPUs

* Began converting HippoNonbondedForce to common platform

* Continuing to convert HippoNonbondedForce to common platform

* Continuing to convert HippoNonbondedForce to common platform

* Working on unifying PME kernels

* Fixed error on devices without 64 bit atomics

* Unified PME kernels

* Converted HippoNonbondedForce to common platform

* Creating OpenCL implementation of HippoNonbondedForce

* Continuing OpenCL implementation of HippoNonbondedForce

* Mostly finished OpenCL implementation of HippoNonbondedForce

* Eliminated three component vector types in host code

* Fix errors on CPU OpenCL

* Skip double precision tests for AMOEBA on OpenCL

* Bug fixes

* Bug fixes

* Fixed compilation error

* Fixed range overflow with very large numbers of atoms

* More fixes to overflow with large numbers of atoms

* Fix test failures

* 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

* Created API for HIPPO force field

* Beginning of reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Completed reference of HIPPO with no cutoff

* Beginning cutoffs/PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Completed reference implementation of HIPPO

* Cleanup and optimization to HIPPO reference

* Further cleanup to HIPPO

* Combined direct space interactions into a single loop

* Compute direct space interactions in quasi-internal frame

* Beginning of CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Finished CUDA implementation of HIPPO

* More features and test cases for HippoNonbondedForce

* Serialization and Python API for HippoNonbondedForce

* Fixed sign error in computing forces