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* 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>

* Added FAQ links to error messages

* Added missing Windows export

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

* DrudeLangevinIntegrator has getSystemTemperature()

* DrudeNoseHooverIntegrator has getSystemTemperature()

* StateDataReporter reports system temperature for Drude systems

* Fixed incorrect return type

* 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

* Fixed potential invalid memory access

* Fixed exception

* 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

* Created MonteCarloFlexibleBarostat

* Improved test cases

* Documentation for MonteCarloFlexibleBarostat

* Added a missing include

* Serialization for MonteCarloFlexibleBarostat

* Added MonteCarloFlexibleBarostat to C++ API docs index

* Added citation for MonteCarloFlexibleBarostat

* Further optimization to updating long range correction

* Bug fix

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

* Fixed errors in amoeba coda

* Fixed more errors in context selection

* Allow querying current step count

* Fixed error building Python wrapper

* Simplified derivatives of min() and max()

* Fixed compilation error in kernel

* 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 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

* Converted RPMD plugin to common platform

* Merged RPMD tests for different platforms

* Try to fix errors on CPU OpenCL