GitLab

* Vectorize NonbondedForce with no cutoff

* Vectorize CustomNonbondedForce with no cutoff

* Memory efficient dense neighbor list

* Fixed errors

* Began vectorizing CustomNonbondedForce

* Refactored CpuCustomNonbondedForce to support multiple vector sizes

* AVX implementation of CpuCustomNonbondedForce

* Fixed compilation errors

* Began implementing vectorization of Lepton expressions

* Tests for vector expressions

* Implemented CompiledVectorExpression for x86

* Bug fix

* Optimized select() on ARM

* Optimized select() on x86

* CompiledVectorExpression supports AVX

* Bug fix

* Updated docs

* Use VEX encoded instructions for CompiledExpression

* Optimized min() and max() on x86

* Optimized min() and max() on ARM

* Fixed compilation error

* Upgrade AsmJit

* Fix #3557 : Generate more informative error message if residue template not found.

* Fix test failures

* Prevent child integrators from accessing deleted context

* Prevent reading property names from nullptr platform

* Don't check properties in a loop, but only when there's a Platform

* Clarified condition in "if" block
Co-authored-by: Peter Eastman <peter.eastman@gmail.com>

* Optimized computing powers in CompiledExpression

* Fixed compilation error

* Attempt at fixing compilation error

* Upgraded to new version of asmjit

* JIT compilation for ARM

* Updated CMake script

* computeDrudeTemperature

* cleanup

* revert drude temperature computation in DrudeNoseHoover

* Do not add constraints involving extra particles

* Added test case

* Max Drude distance defaults to 0.2 nm

* Fixed incorrect number in docs

* Fixed a test case

* Access atom element field

* Update GB-Neck2 force regression test

It allows to use a faster float-to-int64 in the HIP platform.

* Use importlib_metadata instead of pkg_resources

* Use built in importlib when available

* Revert change that didn't work

* Minor optimizations to computing single pairs

* Adjusted MAX_BITS_FOR_PAIRS on Ampere

* Ensure bond lengths are set before creating forces that depend on them

* Minor formatting

* Only call set switching function/distance on nonbonded force(s)

* Also catch CustomNonbondedForce

* Fix logic around setEwaldErrorTolerance

* DrudeLangevinIntegrator has getSystemTemperature()

* DrudeNoseHooverIntegrator has getSystemTemperature()

* StateDataReporter reports system temperature for Drude systems

* Fixed incorrect return type

* Add library path with os.add_dll_directory()

* Update path for Visual Studio

* Improved handling of CRYST1 records #3446

* Apply suggestions from code review
Co-authored-by: Jason Swails <jason@entos.ai>
Co-authored-by: Jason Swails <jason@entos.ai>

* Added documentation to clarify behavior of nonbonded exceptions

* Added documentation to clarify behavior of nonbonded exceptions