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Use explicit 128-thread block launches for selected HIP PME kernels that
benefit from larger blocks.  Keep the platform default block size unchanged,
and leave small-system grid indexing and charge spreading on the existing
default launch configuration.

The heuristic applies 128-thread launches to finishSpreadCharge on HIP, and
uses 128-thread launches for findAtomGridIndex and gridSpreadCharge only for
larger systems.  Coulomb PME and LJPME dispersion paths are handled in
parallel, while interpolation and energy evaluation remain unchanged.

Apply heuristics for HIP neighbor-list construction:
use fewer nonbonded force blocks for small neighbor-list systems, use two
tiles per batch for larger atom-block counts, and increase the
findBlocksWithInteractions thread block size for small atom-block counts.

Standard concurrent validation shows no clear per-case regression and a
small geomean throughput improvement over the current blocksPerCU baseline.

- Use bitwise prefix accounting when storing sparse interactions as single pairs in the HIP pair-list kernel. This reduces the number of ballot operations needed to compute per-lane single-pair offsets.
- For HIP CDNA single precision, raise MAX_BITS_FOR_PAIRS to 8 so more sparse interactions are emitted as single pairs instead of full tiles. Keep the existing double precision and RDNA thresholds unchanged.
- Also simplify the HIP LJPME direct correction by computing alpha^2*r2

Avoid forcing Coulomb PME to re-sort whenever LJ-PME is enabled, and give dispersion PME its own atom-grid index and sort state so the performance impact can be measured independently.

* 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