GitLab

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

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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

* remove std::binary_function from ConstraintOrderer functor

* whoops whitespace

Test no longer runs and prints out a warning when running benchmark.py with --verbose. Fixes #3391

* 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

* Support GROMOS bond and angle types

* Support NBFIX with geometric combining rule

* Continuing GROMOS support

* Bug fixes

* Fixes to test case

* Update wrappers/python/openmm/app/gromacstopfile.py
Co-authored-by: Jason Swails <jason@entos.ai>

* Improve logic for handling dihedraltypes

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Co-authored-by: Jason Swails <jason@entos.ai>

Fix bad link that directs to unsafe HTTP and then HTTP-HTTPS redirect

* 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 custom...