GitLab

* Fixed error on GPUs with SIMT width 64

* Interpret sortedBlocks correctly

* fix formal charge reading and writing in pdb files; store formal charge in topology

* use formalCharge in public api

* permissive reading

* fix writing

* fix

* add test for formal charges

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Co-authored-by: Alex Izvorski <alex@genesistherapeutics.ai>

* Support numpy 2

* Debugging

* Removed debugging code

* Don't require importlib_metadata

* Handle older versions of importlib

* Fix import of netcdf_file for scipy 1.14

* Fix indentation

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Co-authored-by: Timothy Palpant <tim@atommapper.com>

* Run Mac tests on ARM and Intel

* Added missing environment file

* Removed obsolete code for M1 runner

* Removed obsolete code for M1 runner

* Debug CI failures

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Removed build that was failing

* Fixed URL that had changed

* addHydrogens() allows specifying exactly what hydrogens to add

* Prevent CI from using numpy 2.0

* Allow multiple registrations of the same atom type if definitions identical

* Different short-circuiting logic

* DrudeForce supports periodic boundary conditions

* Fixed uninitialized memory

Co-authored-by: FloLangenfeld <florent.langenfeld@peptinov.fr>

* added type checking for Simulation.step()

* changed how to check if step is an integer number

* ATMForce reorders inner contexts for better performance

* Fixed obsolete comments

* 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