GitLab

* Add correction for self energy of neutralizing plasma

* Fixed compilation errors

* Update total charge in copyParametersToContext()

* Bug fixes

* Fixed compilation errors in HIP

* Bug fix

* 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

* CPU platform checkpoints random number generator

* Fix Windows compilation error

* Another Windows compilation error

* updateParametersInContext() can modify parameter offsets

* Reordering respects parameter offsets

* Implemented for CUDA and HIP

* Optimize CustomNonbondedForce.updateParametersInContext()

* Optimized uploading changed values to GPU

* Optimized updateParametersInContext() for lots of bonded forces

* Optimized updateParametersInContext() for CustomExternalForce

* Optimized updateParametersInContext() for NonbondedForce

* Code changes for HIP platform

* Made LangevinIntegrator identical to LangevinMiddleIntegrator

* Removed unused code

* VariableLangevinIntegrator uses LFMiddle

* Reference platform supports nested virtual sites

* Common platform supports nested virtual sites

* Fixed force distribution from nested virtual sites

* Fixed test failures

* Added FAQ links to error messages

* Added missing Windows export

* Vectorize NonbondedForce with no cutoff

* Vectorize CustomNonbondedForce with no cutoff

* Memory efficient dense neighbor list

* Fixed errors

* Began vectorizing CustomNonbondedForce

* Refactored CpuCustomNonbondedForce to support multiple vector sizes

* AVX implementation of CpuCustomNonbondedForce

* Fixed compilation errors

* Reference implementation of computed values for CustomNonbondedForce

* CPU implementation of computed values for CustomNonbondedForce

* Common implementation of computed values for CustomNonbondedForce

* Serialization of computed values

* ForceField supports computed values

* updateParametersInContext() can change tabulated functions

* Fixed error in building C wrappers

* updateParametersInContext() can change tabulated functions for CustomCentroidBondForce

* CustomNonbondedForce can update tabulated functions

* CustomGBForce can update tabulated functions

* CustomManyParticleForce can update tabulated functions

* CustomHbondForce can update tabulated functions

* 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

The exclusion mask was 8-bits wide, but future CPU support will require
more bits than this (e.g., AVX-512 will be 16-bit).

* 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 ...

* Remove unused variable from CpuCustomGBForce::calculateIxn

* Remove unused variable from CpuCalcCustomManyParticleForceKernel::initialize

* Remove unused variable from CudaCalcCustomCVForceKernel::initialize

* Remove unused variable from ReferenceCalcCustomManyParticleForceKernel::initialize

* Remove unused variables from ReferenceObc::computeBornEnergyForces

* Remove unused variable from AmoebaTorsionTorsionForceProxy::serialize

* 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