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

* modifiy CMakeLists.txt to generate drude fortran wrapper

* modify doxyfile and wrapper generation wrapper

* Remove includes for Dart

* Fix CMake error

* Fixed broken link

* Pin to cmake<4.0

* Try to make the link checker stop complaining

* Replace pthreads with C++ threads

* Try to fix CI errors

* Try including -pthread linker option

* 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;

* DrudeForce supports periodic boundary conditions

* Fixed uninitialized memory

* Reference platform supports nested virtual sites

* Common platform supports nested virtual sites

* Fixed force distribution from nested virtual sites

* Fixed test failures

* Faster algorithm for DrudeSCFIntegrator

* Minor code simplification

* Reduced default error tolerance

* Fixed errors on NVIDIA

* computeDrudeTemperature

* cleanup

* revert drude temperature computation in DrudeNoseHoover

* Max Drude distance defaults to 0.2 nm

* Fixed incorrect number in docs

* Fixed a test case

* DrudeLangevinIntegrator has getSystemTemperature()

* DrudeNoseHooverIntegrator has getSystemTemperature()

* StateDataReporter reports system temperature for Drude systems

* Fixed incorrect return type

* Added lots of checks for invalid parameter values

* Fixed test failures

* More checks for incorrect parameters

* Fixed test failures

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

* Fixed errors in amoeba coda

* Fixed more errors in context selection

* Updated to latest values for physical constants

* Updated documentation on physical constants

* Updated Python unit definitions

* Fixed constants in test case

* Added a comment

This ensures that the correct argument size is used when calling clSetKernelArg.

This is required by msvc when standard conformance mode is not enabled (DrudeNoseHooverIntegratorProxy.cpp(53): error C2065: 'not': undeclared identifier).

* Convert Nose-Hoover into LF middle scheme by copying NH kernels

* Rebrand VelocityVerletIntegrator as NoseHooverIntegrator

* Consolidate NH tests

* NoseHooverChainKernel begone

* Make Windows builds happy

* Add missing header for Windows build

* Fix mistake in CommonKernels header

* Add 6th Yoshida-Suzuki and make it the default