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* Common implementation of BondedUtilities

* Common implementation of UpdateStateDataKernel

* Improved sorting of blocks when building neighbor list

* Improved block sorting for OpenCL

* Made sort keys more evenly distributed

* Fixed some incorrect comments

* Fixed some incorrect comments

* Fixed typo

Closes #2986

* Enable flush on Windows

- Implements perm 5 from https://github.com/openmm/openmm/issues/3937#issuecomment-1413872621

Co-Authored-By: Philip Turner <philipturner.AR@gmail.com>

* Add brackets for clarification
Co-authored-by: Philip Turner <philipturner.AR@gmail.com>

* Make this optimization only apply to AMD GPUs

* Switch to perm 1

- Flush before call to computeNonbonded since it works well on Windows and Linux

* Update OpenCLNonbondedUtilities.cpp

* Perm 4 is now significantly faster on Windows

* Use isAMD

* Fix indentation

* Fix missed variable

* Remove Mac check

* Remove isAMD out of Mac code

* Consistent (lack of) brackets style

---------
Co-authored-by: Philip Turner <philipturner.AR@gmail.com>

WIP - looking for a way to optimise performance of creating contexts by removing temporary arrays (and their associated mallocs/frees) (#4261)

* Suggesting a "haveSameParameters" function for CustomNonbondedForce which could be
used to avoid creating temporary copies of arrays when testing if particles are
the same.

Also updating "getParticleParameters" so that it re-uses the memory of the
passed vector argument, rather than deallocating and reallocating it
via a copy.

* Revert "Suggesting a "haveSameParameters" function for CustomNonbondedForce which could be"

This reverts commit e80ec2d2e9981abb90711636bf3a78d0c49e43fc.

* Moved to `thread_local static` as suggested to prevent new vector allocations on each function call.

Updated `getParameters` and `getBondParameters` to re-use the memory from the argument rather
than re-allocating via the copy.

* Forgot to reuse the memory for the groups...

* Reverted back the manual copies via memcpy as they aren't needed. Looking at the header
file and benchmarking shows that std::vector does the right thing.

* Confined `thread_local static` only to ForceInfo methods, and have also put declarations
for multiple variables back onto a single line

* Removed `thread_local static` from the constructor

* Moved constructor declarations back into the for loop

The nonbonded kernel uses USE_NEIGHBOR_LIST (useNeighborList)
so host code also must check it instead of useCutoff.

See also https://github.com/openmm/openmm/issues/3462

* Implemented CustomCPPForceImpl

* Documentation for CustomCPPForceImpl

* Attempt at fixing Windows compilation error

* Improved documentation

* remove std::binary_function from ConstraintOrderer functor

* whoops whitespace

* Amoeba minor cleanup

- Fix variable name in string
- Remove odd space between variable and period that is inconsistently styled

* Replaces random tabs with spaces in ATM Force

* Draft integration of the Alchemical Transfer Method (ATM) plugin

* Attempt to store and retrieve forces--does not compile

* Implement addForce()/getForce() methods

* Throw exception when specifying properties without a Platform (#4130)

* Fixed DOF calculation for NoseHooverIntegrator (#4128)

* Fix variance in documentation of VerletIntegrator (#4138)

* Python API for ATMForce

* Fixed compilation error

* Minor cleanup of formatting and documentation

* Files for ATMForce test cases

* More cleanup

* Removed variable groups

* Test ATMForce with two particles

* More tests for ATMForce plus fixes

* Added missing header

* Rework interface to pass displacements as vector of parameters

* Revert "Rework interface to pass displacements as vector of parameters"

This reverts commit 5e092031f31ded1137b677588f007add1c2d6f82.

* Test with nonbonded force

* Allow energy expression to be customized

* Optional displacements at the initial state

* Fixed compilation error build C wrapper

* Address edge case of default energy expression

* Consistent naming of the variables of the displacement states

* Test of soft core function of the default energy expression

* Mark addForce() as taking ownership

* initial python test for ATMForce

* Test custom expressions

* Expanded C++ API documentation for ATMForce

* Energy parameter derivatives

* Serialization for ATMForce

* Documentation, cleanup, and fixes

* Fixed typos

* getPerturbationEnergy() computes energy

* Another test case

* Minor edits

---------
Co-authored-by: Peter Eastman <peastman@stanford.edu>
Co-authored-by: Michael Plainer <plainer@ymail.com>

* Use large blocks to optimize building the neighbor list

* Large blocks optimization for OpenCL

* Fix test failures

* Select whether to use large blocks based on system size

* Always use nvrtc for compilation

* Install nvrtc on CI

* Workaround for compiler error

* Set empty values for deprecated properties

* save atomIndex order in MCBarostat kernel

* Update device indices

* Only setAtomIndex if there was a reorder

* Attempt at fixing errors with barostat

* Missing ContextSelector

* Skip neighbor list for very small systems

* Fixed typos

* Don't skip box size check when not using neighbor list

* Made test larger to ensure it uses neighbor list

* Faster implementation of CustomHbondForce

* Minor optimization

* Optimized writing forces, which are often zero

* Fix test failure on CPU OpenCL

* Bug fix

* Store bounding box sizes in half precision

* Work correctly in double precision mode

It may contain a garbage value, and if it is large then
updateNeighborListSize does not force reorder atoms after 25 steps
in extremal cases.

* Use 768 instead of 384 threads in generic kernels

* Use 1536 instead of 1024 threads in force kernels.

- Appear to be copy and pasted from getPositions and were not removed

* Flushing optimization

* Remove unnecessary checks