GitLab

* Fixed issue that caused inefficient sorting when a block contained only one atom

* Add the fix to OpenCL and HIP

* Make reference/CPU minimizer into a kernel

* Add per-platform support for GPU minimization

* Initial implementation of GPU minimization

* Fixes

* Increase robustness when initial gradient is huge

* Handle overflow leading to non-finite values gracefully

* Handle large forces in single precision more robustly

* Optimize kernels

* Fix kernel launch size

* Update banner years

* Don't create MinimizeKernel until first minimization requested

* Make some compile-time constants into kernel arguments

* Consolidate scale calculation kernel

* Condense alpha/beta reduction kernels using atomics

* Condense line search dot kernels with reductions

* Remove a download, and download grad norm separately

* Asynchronously check lbfgs convergence condition

* Restructure line search to avoid download waiting

* Start line search preemptively in case CPU evaluation is not needed

* In rare cases, constraint error might not decrease after one optimization round

* Better handling of unsupported 64-bit atomics, use FLT_MAX

* Pick gradient mode based on GPU vs. CPU evaluation

* Rework getDiff/getScale reduction, remove reduceBuffer

* Older CUDA might not like float hex literals

* Fix error in a comment

* 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

* Store bounding box sizes in half precision

* Work correctly in double precision mode

It allows to use a faster float-to-int64 in the HIP platform.

* 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

* Converted more code to common platform

* Converted more code to common platform

* Frames distance calculation as matrix multiplciation

* Adds comment explaining distance calculation

* Tunes launch bound for cuda11.2

* Simplifies the effective matrix multiplication
Co-authored-by: David Clark <daclark@nvidia.com>

* Changes name of NVRTC program

* Adds launch bounds for findInteractingBlocks

* Replaces launch bound parameter with named constant
Co-authored-by: David Clark <daclark@nvidia.com>

* 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

* 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