GitLab

* Replace SimTK-containing file headers

* Update file headers for new Tinker reader files added

CustomCPPForceImpl for writing forces in C++

    https://github.com/openmm/openmm/commit/9a0db72
    https://github.com/openmm/openmm/pull/4231

Virtual sites can depend on other virtual sites

    https://github.com/openmm/openmm/commit/71f4b3f

Use LF-Middle for LangevinIntegrator and VariableLangevinIntegrator

    https://github.com/openmm/openmm/commit/86988b9

Merged more code into common platform

    https://github.com/openmm/openmm/commit/5739788

    * Common implementation of BondedUtilities
    * Common implementation of UpdateStateDataKernel

Fixed periodic box changing from rectangular to triclinic

    https://github.com/openmm/openmm/commit/75d4f29

Port changes in CUDA backend to HIP

Fix a warning about arithmetic operations on void* in HipArray::uploadSubArray

Fix "Error Initializing context ROCm 5.3.0"

    https://github.com/StreamHPC/openmm-hip/issues/3


    hipDeviceSetCacheConfig returns hipErrorNotSupported on 5.3
Co-authored-by: Nick Curtis <nicholas.curtis@amd.com>

* Common implementation of BondedUtilities

* Common implementation of UpdateStateDataKernel

* Proof of concept matching current behaviour with Breathe

* Reorganise C++ API docs to work without autosummary

* Revert to Sphinx-native search

* Move remaining pip deps to conda

* Remove unnecessary lunrsearch templates

* Remove lunrsearch from cmake

* Tidy up layout of API docs

* Get code blocks to work with Breathe

Breathe doesn't seem to support the Doxygen <preformatted> tag.
It does support the <code> tag, but better yet it supports using
<verbatim> tags to embed rst into docstrings. This commit changes
all <pre> tags to use RST verbatim, and updates the Python
documentation machinery to support it too.

* Clarified some language

* Have doxygen exclude undocumented classes and have sphinx fail on warnings for C++ API docs

* List custom forces and integrators last

* Add breathe to documentation CI

* Typo

* Fix link to custom forces in extras.rst

* Have Breathe process only public classes

* Strip OpenMM:: prefix from rst files to avoid colons in links

* Remove existing private classes from EXCLUDE_SYMBOLS

* Add comment to C++ cmake describing why we promote warnings to errors

* Revise documentation build instructions for new dependencies

* 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

Platform specific header files get installed.  This allows plugins to be built with just an OpenMM installation, not a full source tree.