GitLab

* Avoid overflow in large XTC files

* Also cast box indices to size_t

* Created DebuggingReporter class

* Fixed description

* Update references to "openmmforcefields" project

* Org name, too

* Revised code from installing CUDA on CI

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

LoongArch is a new architecture, already supported by linux-6.1, gcc-12.
Signed-off-by: Zang Ruochen <zangruochen@loongson.cn>
Co-authored-by: Zang Ruochen <zangruochen@loongson.cn>

* Minor optimization to validating exclusions

* Optimizations to findMoleculeGroups()

* Improved performance of CustomHbondForce on large systems

* Fixed CUDA compilation errors

* Made LangevinIntegrator identical to LangevinMiddleIntegrator

* Removed unused code

* VariableLangevinIntegrator uses LFMiddle

* Can use getPlatform() instead of getPlatformByName()

* More concise arguments for getState()

* Reference platform supports nested virtual sites

* Common platform supports nested virtual sites

* Fixed force distribution from nested virtual sites

* Fixed test failures

* Improve numerical stability for edge cases

* Undo checking of derivative factors

* Undo checking for NaNs

causing warnings by Clang

Type in 'implementation'

* Replaces sub tags for python API docs

* Changes string to pathlib

* Adds support for sup html tags

* Corrects function description

* Faster algorithm for DrudeSCFIntegrator

* Minor code simplification

* Reduced default error tolerance

* Fixed errors on NVIDIA

* Use portable SIMD vectors as a backup

* Remove old file

* Try to fix compilation error on Windows

* Common implementation of BondedUtilities

* Common implementation of UpdateStateDataKernel

* Improved sorting of blocks when building neighbor list

* Improved block sorting for OpenCL

* Made sort keys more evenly distributed

Added CustomCentroidBondForce.addTabulatedFunction to STEAL_OWNERSHIP table in Python wrapper configuration script (#4340)
Co-authored-by: Evan Pretti <evan@pretti.net>

* Updated to new version of libLBFGS

* Enable SSE code for LBFGS

* Optimizations to reporters

* Removed unneeded imports

* Py wrapper: preserve bond data in Modeller operations

* regression tests for add(), delete(), deleteWater(), addSolvent()

* Tests for addHydrogens and addExtraParticles

* Cosmetic

* A single regression test spanning a whole workflow

* Remove now-redundant tests

* Test also deleteWater and addHydrogens. Remove excessive assertions.

* Fixed some incorrect comments

* Fixed some incorrect comments

* Fixed typo