GitLab

* 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>

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

* Note that w_cross has units of inverse distance

* Grammar

* Remove support for Gromacs implicit solvent

* Removed tests of implicit solvent

* Replace distutils with setuptools

* Replace more uses of distutils

* Implemented MinimizationReporter

* PythonAPI for MinimizationReporter

* Improved test case

* SWIG fix

* Reporter returns a bool instead of throwing an exception

* Implemented CustomCPPForceImpl

* Documentation for CustomCPPForceImpl

* Attempt at fixing Windows compilation error

* Improved documentation