GitLab

* Minor optimization to validating exclusions

* Optimizations to findMoleculeGroups()

* Improved performance of CustomHbondForce on large systems

* Fixed CUDA compilation errors

* Made LangevinIntegrator identical to LangevinMiddleIntegrator

* Removed unused code

* VariableLangevinIntegrator uses LFMiddle

* Can use getPlatform() instead of getPlatformByName()

* More concise arguments for getState()

* Reference platform supports nested virtual sites

* Common platform supports nested virtual sites

* Fixed force distribution from nested virtual sites

* Fixed test failures

* Improve numerical stability for edge cases

* Undo checking of derivative factors

* Undo checking for NaNs

causing warnings by Clang

Type in 'implementation'

* Replaces sub tags for python API docs

* Changes string to pathlib

* Adds support for sup html tags

* Corrects function description

* Faster algorithm for DrudeSCFIntegrator

* Minor code simplification

* Reduced default error tolerance

* Fixed errors on NVIDIA

* Use portable SIMD vectors as a backup

* Remove old file

* Try to fix compilation error on Windows

* 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

Added CustomCentroidBondForce.addTabulatedFunction to STEAL_OWNERSHIP table in Python wrapper configuration script (#4340)
Co-authored-by: Evan Pretti <evan@pretti.net>

* Updated to new version of libLBFGS

* Enable SSE code for LBFGS

* Optimizations to reporters

* Removed unneeded imports

* Py wrapper: preserve bond data in Modeller operations

* regression tests for add(), delete(), deleteWater(), addSolvent()

* Tests for addHydrogens and addExtraParticles

* Cosmetic

* A single regression test spanning a whole workflow

* Remove now-redundant tests

* Test also deleteWater and addHydrogens. Remove excessive assertions.

* Fixed some incorrect comments

* Fixed some incorrect comments

* Fixed typo

Fix CI deprecation warnings

- Upgrade actions/checkout to v3 and actions/cache to v3.3.2 to address node.js 12 warnings
- https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
- Replace usages of set-output with `>> $GITHUB_OUTPUT` for Unix and `>> %GITHUB_OUTPUT` for Windows

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>