GitLab

* set box vectors of the inner contexts before atom reordering

* test for changing box vectors

* Optimized setPositions() and setVelocities()

* Fix test failures

* Improved residue indexing in error messages

* Fixed another one

* Fix GPU memory leak

* Undo CUDA change

Add new CHARMM and Amber force fields

* 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 queues

* Simplified stream handling in CudaFFT3D

* HIP implementation of ComputeQueue

* Created CustomVolumeForce

* Serialization for CustomVolumeForce

* Documentation for CustomVolumeForce

* Code simplification

* Removed unused code

* Added computeCurrentPressure() to MonteCarloBarostat

* Use instantaneous temperature to compute pressure

* Added computeCurrentPressure() to MonteCarloAnisotropicBarostat

* Added computeCurrentPressure() to MonteCarloMembraneBarostat

* Fixed compilation error

* Fixed error in typemap

* Added documentation on computing pressure

* Fixed CUDA compilation errors

* Made test case more robust

* Made a test case more robust

* Added computeCurrentPressure() to MonteCarloFlexibleBarostat

* Fixed compilation error

* More documentation on computing pressure

* Unified interface for FFTs

* AMOEBA uses unified interface for FFTs

* HIP implementation of common FFT interface

* 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

* Use newer docker container for PPC

* Try different syntax

* Create bonds based on chem_comp_bond records

* Fixed a test that assumed bonds would be in a particular order

Check comment block length from DCD when appending

* 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

* modifiy CMakeLists.txt to generate drude fortran wrapper

* modify doxyfile and wrapper generation wrapper

* add tests for correctness of step and time written in XTC and DCD

* improve tests

* improve xtc tests

* fix XTC/DCD time/step writing

* different approach by changing the reporters to not pass currentStep as firstStep but instead interval

* undo change

* Remove includes for Dart

* Fix CMake error

* Fixed broken link

* Pin to cmake<4.0

* Try to make the link checker stop complaining

Correctly assign CMAPs to torsions across multiple CMAPTorsionForce sections

* Began splitting CommonKernels into multiple files

* Moved two more kernels into separate files

* Moved two integrators into separate files

* Fix compilation error on Windows

* reset overflowed state energies at the alchemical endpoints

* address formatting, complete clash test

* Fixed indentation

---------
Co-authored-by: Peter Eastman <peter.eastman@gmail.com>

* Replace pthreads with C++ threads

* Try to fix CI errors

* Try including -pthread linker option