GitLab

* Big fix to QTB

* Fixed race condition

* Created OrientationRestraintForce

* Python API

* Documentation

* Serialization

* GPU implementation of OrientationRestraintForce

* Bug fix

* Remove unused code

* fix to correctly read Gromacs topology files for CHARMM force field

* updated fix to correctly read topology files with NBFIX and different combination rules

* fixes to read topology files with NBFIX and different combination rules

* changed default for useDispersionCorrection to True

* changed docstring default for useDispersionCorrection to 'True'

* fix scaling of 1-4 LJ pairs when NBFIX is used

* apply NBFIXes to 1-4 pairs if no pair parameters are given

* rerun CI

* Reference implementation of RGForce

* GPU implementation of RGForce

* Serialization

* Documentation

* Fix compilation error

* Fixed error building API docs

* Replace C++ code examples in Python API docs

* Use newer Python for building docs

* Remove sphinx version pin

* Add Python versions of code examples

* Minor edit

* Add Python version of one more code example

* Variable displacements based on particle positions

* set variable displacements when adding particles

* update documentation

* address compilation error in OpenMMFortranWrapper

* update python API tests

* fix stray 'and'

* addParticle() without arguments add a particle that is not displaced

* pack displacement particles into int4

* put back default displacement removed in error

* ATMForce interface with coordinate transformation objects

* revise variable displacement API

* documentation, formatting, serialization

* Fixed C and Fortran wrappers

* Fixed Python wrappers

* Fixed factory

* Sort files to ensure classes are listed in the correct order

* Converted APIUnits test to new ATMForce API

* write class name

* skip the documentation for forward declarations

* undo 9e91d0b since it does not fix the doc build

* remove temporary doc files for nested classes

* Clean away tabs

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Co-authored-by: Peter Eastman <peastman@stanford.edu>

* Convert C++ types to Python types in API docs

* Translate some more types

* Convert return types that are STL containers

* Began implementing QTBIntegrator

* Adaptation and deconvolution

* Continuing reference implementation

* Continuing to implement QTBIntegrator

* Use common thread pool

* More tests, documentation, and threading

* Fix segfault

* Serialize adapted friction when creating a State

* Beginning of GPU implementation

* Added missing files

* Bug fixes

* Fixed inverse FFT

* Continuing GPU implementation

* Checkpointing

* Bug fixes

* Test cases run faster

* Changes needed for latest main branch

* Minor optimizations

* Documentation

* Fixed atom reordering

* Added parahydrogen test case

* Workaround for bug in Microsoft's compiler

* Added a Python test

* Normalize kernel in deconvolution

* Minor documentation improvements

* fix to correctly read Gromacs topology files for CHARMM force field

* updated fix to correctly read topology files with NBFIX and different combination rules

* fixes to read topology files with NBFIX and different combination rules

* changed default for useDispersionCorrection to True

* changed docstring default for useDispersionCorrection to 'True'

* fix scaling of 1-4 LJ pairs when NBFIX is used

* fix to correctly read Gromacs topology files for CHARMM force field

* updated fix to correctly read topology files with NBFIX and different combination rules

* fixes to read topology files with NBFIX and different combination rules

* changed default for useDispersionCorrection to True

* changed docstring default for useDispersionCorrection to 'True'

Cleanup examples, documentation, and README files

Always safely overwrite checkpoint and state files

Output more detailed messages when template matching fails

* Reference implementation of SymmetrySite

* Common implementation of SymmetrySite

* Removed duplicated code

* Serialization for SymmetrySite

* Fixed compilation error building C wrapper

* Added SymmetrySite to user guide

* Bug fix

* Added P21 test case

Update AWS S3 bucket region

Don't reinitialize CustomIntegrator on every step when no computations are present

Fixes #5001.
Signed-off-by: Yannick Lemke <yannick.lemke@posteo.de>

* Unified storage of global parameters

* Fixes to CUDA and HIP

* Store global parameters as real instead of float

Update CHARMM36 2024 and add water models