GitLab

* Created ReplicaExchangeReporter

* Documentation for ReplicaExchangeReporter

* Created ReplicaExchangeSampler

* Improvements to ReplicaExchangeSampler

* PythonForce can be restricted to a subset of particles

* Fix exception with CUDA

* Infrastructure for multistate sampling

* Added computeRelativeEnergies()

* optimization, switch to unordered map

* Remove emplace, reduce reserve allocation

* Cache coefficients for long range correction

* updateParametersInContext() clears cache

* fix 5234 and add test

* clean up docstring and standardize test name

* Fixed issue that caused inefficient sorting when a block contained only one atom

* Add the fix to OpenCL and HIP

* Added two more synonyms for HOH

* Change H20 to H2O

* Update patch documentation

Clarified the definition and purpose of patches.

* Fix typo in RemoveExternalBond tag description

* Update wording in patches

* A few edits to the description of patches

---------
Co-authored-by: Peter Eastman <peter.eastman@gmail.com>

* Make reference/CPU minimizer into a kernel

* Add per-platform support for GPU minimization

* Initial implementation of GPU minimization

* Fixes

* Increase robustness when initial gradient is huge

* Handle overflow leading to non-finite values gracefully

* Handle large forces in single precision more robustly

* Optimize kernels

* Fix kernel launch size

* Update banner years

* Don't create MinimizeKernel until first minimization requested

* Make some compile-time constants into kernel arguments

* Consolidate scale calculation kernel

* Condense alpha/beta reduction kernels using atomics

* Condense line search dot kernels with reductions

* Remove a download, and download grad norm separately

* Asynchronously check lbfgs convergence condition

* Restructure line search to avoid download waiting

* Start line search preemptively in case CPU evaluation is not needed

* In rare cases, constraint error might not decrease after one optimization round

* Better handling of unsupported 64-bit atomics, use FLT_MAX

* Pick gradient mode based on GPU vs. CPU evaluation

* Rework getDiff/getScale reduction, remove reduceBuffer

* Older CUDA might not like float hex literals

* Fix error in a comment

* Residue templates can specify constraints

* Patched template generation preserves constraints

* API for querying devices

* CUDA and HIP implementations of getDevices()

* Fix test failures

* Fix test failures

* CUDA returns correct devices even if no context has been created

* Return a single device for Reference and CPU

* Fix CI failure

* Templates can match whole molecules

* addExtraParticles() supports molecule templates

* Documentation on molecule templates

* Bug fix

* Remove std::enable_if, warpRotateLeft is always used with TILE_SIZE

* Do not use built-in warpSize in constexpr contexts

Starting from ROCm 7 warpSize is no longer constexpr.
findInteractingBlocks.hip uses it for sizes of __shared__ arrays.

* Check if hipHostMallocNumaUser is allowed before using it

adaptFrictionPart1 is executed first, it reads randomForce and
segmentVelocity buffers before other kernels write them so they can
contain garbage after allocation (cuMemAlloc/hipMalloc/clCreateBuffer
do not clear allocated memory).

* Prevent running out of disk space in OpenCL CI build

* Removed incorrect lines

* Delete more

* Fixed incorrect paths

* Removed some paths

* Basic LCPO support

* Add basic test for LCPO from a prmtop file

* API for LCPOForce

* Started LCPO reference implementation

* Finished reference forces & test cases

* Use other test for finite difference since grid might have discontinuous forces

* Reference platform formatting

* Initial implementation of CPU platform

* Bugfixes

* More vectorization and improve neighbor list query speed

* Parallelize part of neighbor search

* Check box size for LCPO with periodic boundary conditions

* Fixes for updating parameters in context

* GBSAOBCForce doesn't use first & last indices for updates, so no need for this optimization here

* Changes to neighbor checking and optimization

* Fixes and minor changes

* Add global surface tension parameter

* Only process half of the pairs in the neighbor list

* Remove unnecessary checks

* Initial version of common platform implementation

* Asynchronously download neighbor list size

* Debugging

* Do pair precomputation in copyPairsToNeighborList

* Recompute interactions instead of scanning neighbor list in inner loop

* Condense position array before computations

* Also make neighbor count download asynchronous on device

* Fixes for kernel launching

* Topology-based LCPO parameter assignment

* Fixes, and use test system for LCPO with nucleic acids

* Always raise instead of warn when LCPO parameters can't be assigned

* Use Amber convention for phosphates

* Minor optimization to PME

* Minor simplification

Added pythonforce.i to SWIG input files for Python.

* Initial implementation of PythonForce

* Continuing implementation of PythonForce

* Tests for PythonForce

* Fix memory leaks

* Documentation for PythonForce

* Fixed incorrect return type

* Fix compilation error on Python older than 3.12

* Handle all dtypes

* Optimizations to PythonForce

* Optimized getPositions()

* Test all platforms

* Fix test failures