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* updateParametersInContext() can modify parameter offsets

* Reordering respects parameter offsets

* Implemented for CUDA and HIP

* PME_ORDER threads process one atom;
* PME_ORDER threads access consecutive addresses;
* No need to permute z indices with zindexTable;
* finishSpreadCharge is needed only with fixed point charge spreading;

* Unified lots of parallel computation code between platforms

* Unified test code between platforms

* Eliminated duplicated timing code

* Optimize CustomNonbondedForce.updateParametersInContext()

* Optimized uploading changed values to GPU

* Optimized updateParametersInContext() for lots of bonded forces

* Optimized updateParametersInContext() for CustomExternalForce

* Optimized updateParametersInContext() for NonbondedForce

* Code changes for HIP platform

* Fixed error on GPUs with SIMT width 64

* Interpret sortedBlocks correctly

* Made LangevinIntegrator identical to LangevinMiddleIntegrator

* Removed unused code

* VariableLangevinIntegrator uses LFMiddle

* Reference platform supports nested virtual sites

* Common platform supports nested virtual sites

* Fixed force distribution from nested virtual sites

* Fixed test failures

* 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

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>

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

* 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

* 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

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

* Profiling of OpenCL kernels

* Minor improvements to profiling

* Use VkFFT for OpenCL

* Updated comments for OpenCLFFT3D

This initialization is needed to prevent segfault during object destruction in certain circumstances (e.g., when a `Force` is changed before calling `Context.reinitialize()` and this change causes the corresponding `ForceImpl` to throw an exception).

* Use PocketFFT instead of FFTW

* Minor cleanup

* Use PocketFFT instead of fftpack for reference platform

* Remove FFTW as a dependency

* Converted a test case to use PocketFFT

* Fixed an incorrect comment

Without this fix, we see cases in which not all work-items in a thread group end up hitting the same number of barriers, which leads to a hang in OpenCL GPU execution.