GitLab

* 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

* Use fixed point spread charge on RDNA4 as it is faster

Even though RDNA4 (gfx12) has global_atomic_add_f32, micro-benchmarks and OpenMM benchmarks show
that it is very slow compared to global_atomic_add_u64.

* Add a workaround for fixed point gridSpreadCharge on RDNA4

Workaround for rare cases when few values of pmeGrid are very large and
incorrect. The cause is unknown. Why this workaround or other irrelevant
changes like printf help is also unknown.

* Add a workaround for infinite loop in computeNonbonded (HIP)

computeNonbonded hangs in some tests (without neighbor list).
Reproducible on ROCm 6.4 and 6.4.1 (maybe on older versions too) on various architectures (both CDNA and RDNA).
Affected tests: TestHipATMForce, TestHipMonteCarloBarostat, TestHipNonbondedForce, TestHipVirtualSites.

Disassembly shows that the compiler splits branches of `if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS)` and does
`SHFL(skipTiles, TILE_SIZE-1) < pos` checks in them separately, even though `__builtin_amdgcn_ds_bpermute`
is a convergent function. Apparently in this case not all lanes participate in each call.

* Simplify includeTile check using ballot

Handle relative include paths from force fields in data directories