GitLab

* Reference implementation of SymmetrySite

* Common implementation of SymmetrySite

* Removed duplicated code

* Serialization for SymmetrySite

* Fixed compilation error building C wrapper

* Added SymmetrySite to user guide

* Bug fix

* Added P21 test case

* 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

* Unified interface for FFTs

* AMOEBA uses unified interface for FFTs

* HIP implementation of common FFT interface

* Replace pthreads with C++ threads

* Try to fix CI errors

* Try including -pthread linker option

* Cleanup of AMOEBA code

* Fixed another compilation error

* More Windows compilation errors

* Fixed incorrect syntax

* Update the AMOEBA OpenMM API for vdW, GK and WCA

* Changes needed for the Corrigan et al Generalized Kirkwood model and minor changes to the vdW force to support CpHMD

* Add casts to real for uses of POW in GK; Pass force by reference within the WCA kernel

* Update swigInputConfig for Amoeba vdW and GK forces

* Update TestAPIUnits.testAmoebaVdwForce

* Set the units for getSolventDielectric and getSoluteDielectric to None

* Update default dispersion offset parameter for the AmoebaWcaDispersionForce

* Remove overloaded getParticleParameters and setParticleParameters from AmoebaGeneralizedKirkwoodForce

* Update the AmoebaWcaDispersionForce TestAPIUnits tests to reflect using the correct units for the C++ parameter default values; Update the alanine-dipeptide-amoeba-forces to reflect the updated GK model

* Move neck descreening constants into AmoebaGeneralizedKirkwoodForceImpl; set the default GK dielecticOffset to 0.09; set the default WCA shctd parameter to 0.82

* Fix Python test cases for WCA and GK

* Load AMOEBA/GK parameters into an array of float4

* Cleaned up the AmoebaGeneralizedKirkwoodForce based on feedback from Peter; the one case where backwards compatibility remains a challenge is application of the dielectric offset parameter - in the prior code this was only applied to the nonpolar cavity term, but not to calculation of Born radii; in this revision the dielectric offset is applied to BOTH the nonpolar cavity term and to calculation of Born radii. At this point I can't think of elegant way to maintain backwards compatibility that isn't confusing, nor does it make sense (at least to me) to only apply the concept of the dieletric offset to one aspect (i.e. only to nonpolar cavity or only to Born radii calculation) but not to both.

* Remove 'using std::vector' from AmoebaGeneralizedKirkwoodForceImpl.h; divide by 10 instead of multiplying by 0.1f in amoebaGk.cc

* Added a parameter called descreenOffset, which is applied during calculation of effective Born radii for GK. The parameter dielectricOffset is only used for the nonpolar cavity term consistent with its prior use. All tests in TestAmoebaGeneralizedKirkwoodForce.h are now backwards compatible with their behavior prior to this PR.

* Change two constants in amoebaGk.cc to single precision; Improved the documentation for getNeckConstants in AmoebaGeneralizedKirkwoodForceImpl.h

* Fix comment for setTanhRescaling in AmoebaGeneralizedKirkwoodForce.h, Fix comment for setTanhParameters in AmoebaReferenceGeneralizedKirkwoodForce.h; set the type of parameter GeneralizedKirkwoodTanhRescaling to bool in AmoebaGeneralizedKirkwoodForceProxy.cpp; In ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel return references of per particle parameters instead of copies; update AmoebaReferenceKernels.h method signatures for per particle parameters to return const vector references

* Minor tweaks to the documentation for the tanh rescaling flag

* Improve the comments for the get and setTanhParameters in AmoebaGeneralizedKirkwoodForce.h and AmoebaReferenceGeneralizedKirkwoodForce.h

* PME_ORDER threads process one atom;
* PME_ORDER threads access consecutive addresses;
* No need to permute z indices with zindexTable;
* finishSpreadCharge is needed only with fixed point charge spreading;

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

    https://github.com/openmm/openmm/pull/3258

Fixed uninitialized memory access

    https://github.com/openmm/openmm/issues/3392
    https://github.com/openmm/openmm/pull/3399

Fixed potential invalid memory access

    See https://github.com/openmm/openmm/pull/3428

Improved temperature reporting for Drude particles

    https://github.com/openmm/openmm/pull/3486
    https://github.com/openmm/openmm/commit/a5e42f5

Fixed race condition with multiple GPUs

    https://github.com/openmm/openmm/commit/6fb1c8a41edff980862750bc086f6a204eb50941

Use blocking sync when creating events

    https://github.com/openmm/openmm/commit/fe21d5ee4f14673a4ea38b7244991772a64ceec2

Very minor optimizations

    https://github.com/openmm/openmm/commit/109f6b2535da4e0c0dd88007d6ca06b4add2ce81

Use PocketFFT

    https://github.com/openmm/openmm/commit/1dac981a63300a2a53a7925f570995914f7163ed

Improved logic for deciding when to reorder atoms

    https://github.com/openmm/openmm/commit/48664a1f1a4490a4dabc277757545ac070e7b898

Ensure valid atom order after loading a checkpoint

    https://github.com/openmm/openmm/commit/a056d5a3754e193105409afa12c9f0c9a2d972a2

Improve performance running on multiple GPUs

    https://github.com/openmm/openmm/commit/0c82c2647de98da5c6dab7bf7a7b8b19705aadc0

Fixed errors when running on multiple GPUs

    https://github.com/openmm/openmm/commit/ed9df876d43c037c08d4762721e73e5caae086d9

Optimized reducing energy

    https://github.com/openmm/openmm/commit/2975f44

* VkFFT-based 3D FFT;
* Caching of compiled VkFFT kernels;
* Extend FFT tests with more sizes.

* Compile with -munsafe-fp-atomics to enable fast hardware f32 atomic
  add on global memory on pre-MI100 GPUs;
* Use fixed point charge spreading on other GPUs, otherwise float atomic
  add will be compiled as a slow CAS loop;
* Tune block sizes, use executeKernelFlat;
* Tune launch bounds of PME grid-related kernels: force the compiler to
  use all registers by limiting max waves per EU to 1.

* 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;

* Amoeba minor cleanup

- Fix variable name in string
- Remove odd space between variable and period that is inconsistently styled

* Replaces random tabs with spaces in ATM Force

* Always use nvrtc for compilation

* Install nvrtc on CI

* Workaround for compiler error

* Set empty values for deprecated properties

* Support kernel files with extensions of any length (like .hip)

* Do not allow to replace symbols in single-line comments

* Add OPENMM_BUILD_COMMON CMake option

It allows to build and install common platform files even if
CUDA or OpenCL platforms are not built.
This is required for HIP platform (openmm-hip) if ROCm OpenCL
packages are not installed.

* Add an option for Python wrapper to install into user packages

OPENMM_PYTHON_USER_INSTALL is OFF be default.

* Support FFT backends in Amoeba plugin

The HIP platform supports FFT backends, this commit moves
findLegalFFTDimension to ComputeContext, so platforms can have their own
implementations.

* Compatibility for common platform w/ new HIP platform

* Do not use volatile with private and local AtomData parameters on HIP

The generated code is not optimal, for example, the compiler generates
flat_load instructions instead of ds_read.

* Tune launch bounds for PME grid-related kernels and add WA for RDNA

Force the compiler to use all registers for gridSpreadCharge and
gridInterpolateForce by limiting max waves per EU to 1 on CDNA GPUs,
RDNA GPUs work better without it.

* Optimize atom data structs in GBSA and Amoeba on HIP

Manually rearrange fields, add paddings and force alignments to
have faster accesses to shared memory: ds_read and ds_write may
work slower if addresses are not aligned by 16 bytes.
Co-authored-by: Anton Gorenko <anton@streamhpc.com>
Co-authored-by: Nick Curtis <nicholas.curtis@amd.com>

* 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

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

* Fixed potential invalid memory access

* Fixed exception

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

* Fixed errors in amoeba coda

* Fixed more errors in context selection

* 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

* Cleanup to CUDA AmoebaMultipoleForce

* Deleted obsolete SOR code

* Replaced several AMOEBA bonded forces with custom forces

* Deleted obsolete AMOEBA forces

* Replaced AmoebaPiTorsionForce with custom force

* 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