GitLab

* add tests for correctness of step and time written in XTC and DCD

* improve tests

* improve xtc tests

* fix XTC/DCD time/step writing

* different approach by changing the reporters to not pass currentStep as firstStep but instead interval

* undo change

* In CharmmPsfFile, add lonepair exceptions even when no Drude particles
  are present

* In ForceField, correctly update the indices of virtual site exclusion
  reference particles in a residue when applying a patch to it

* Properly handle duplicate atom type definitions without elements

* Correct the description of a test in a docstring

* Correctly handle existing type without element and duplicate type with element

* Try to update actions/cache to v4

* Ensure that in_prec will never be uninitialized

* Add a test case that uses a system size below the compression threshold

* Compare and track openmm.unit.BaseUnit objects by name

* Retrieve _conversion_factors as a class attribute

* Include more cases in TestForceField.test_NBFix

* Reduce LennardJonesGenerator NBFIX memory consumption

* Restored test case to use multiple elements to avoid ambiguity

This is similar to https://github.com/openmm/openmm/pull/4528 but was
missed out. When the membrane and protein are combined a new topology
is created. This invalidates the residueTemplates dict so it must be
recreated before calling addSolvent.

* Update the AMOEBA OpenMM API for vdW, GK and WCA

* Changes needed for the Corrigan et al Generalized Kirkwood model and minor changes to the vdW force to support CpHMD

* Add casts to real for uses of POW in GK; Pass force by reference within the WCA kernel

* Update swigInputConfig for Amoeba vdW and GK forces

* Update TestAPIUnits.testAmoebaVdwForce

* Set the units for getSolventDielectric and getSoluteDielectric to None

* Update default dispersion offset parameter for the AmoebaWcaDispersionForce

* Remove overloaded getParticleParameters and setParticleParameters from AmoebaGeneralizedKirkwoodForce

* Update the AmoebaWcaDispersionForce TestAPIUnits tests to reflect using the correct units for the C++ parameter default values; Update the alanine-dipeptide-amoeba-forces to reflect the updated GK model

* Move neck descreening constants into AmoebaGeneralizedKirkwoodForceImpl; set the default GK dielecticOffset to 0.09; set the default WCA shctd parameter to 0.82

* Fix Python test cases for WCA and GK

* Load AMOEBA/GK parameters into an array of float4

* Cleaned up the AmoebaGeneralizedKirkwoodForce based on feedback from Peter; the one case where backwards compatibility remains a challenge is application of the dielectric offset parameter - in the prior code this was only applied to the nonpolar cavity term, but not to calculation of Born radii; in this revision the dielectric offset is applied to BOTH the nonpolar cavity term and to calculation of Born radii. At this point I can't think of elegant way to maintain backwards compatibility that isn't confusing, nor does it make sense (at least to me) to only apply the concept of the dieletric offset to one aspect (i.e. only to nonpolar cavity or only to Born radii calculation) but not to both.

* Remove 'using std::vector' from AmoebaGeneralizedKirkwoodForceImpl.h; divide by 10 instead of multiplying by 0.1f in amoebaGk.cc

* Added a parameter called descreenOffset, which is applied during calculation of effective Born radii for GK. The parameter dielectricOffset is only used for the nonpolar cavity term consistent with its prior use. All tests in TestAmoebaGeneralizedKirkwoodForce.h are now backwards compatible with their behavior prior to this PR.

* Change two constants in amoebaGk.cc to single precision; Improved the documentation for getNeckConstants in AmoebaGeneralizedKirkwoodForceImpl.h

* Fix comment for setTanhRescaling in AmoebaGeneralizedKirkwoodForce.h, Fix comment for setTanhParameters in AmoebaReferenceGeneralizedKirkwoodForce.h; set the type of parameter GeneralizedKirkwoodTanhRescaling to bool in AmoebaGeneralizedKirkwoodForceProxy.cpp; In ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel return references of per particle parameters instead of copies; update AmoebaReferenceKernels.h method signatures for per particle parameters to return const vector references

* Minor tweaks to the documentation for the tanh rescaling flag

* Improve the comments for the get and setTanhParameters in AmoebaGeneralizedKirkwoodForce.h and AmoebaReferenceGeneralizedKirkwoodForce.h

* added type checking for Simulation.step()

* changed how to check if step is an integer number

* allow for dicts to be returned from Reporter.describeNextReport
remove deprecated getState parameters ( #4437 )

* convert old format into new format

* update docstring

* nested set comprehension to set.union

* Allow 'periodic':None
update describeNextReport in all occurrences in the code

* debug

* update documentation

* add a reporter for energyParameterDerivative

* Revert "add a reporter for energyParameterDerivative"

This reverts commit 1d44dc3f60153defb6252ab56a3b85350fa24826.

* Edit documentation

* XTCReporter overwrite existing xtc file

* add position size check for xtcfile

* 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

---------
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

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

* 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

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

* added type checking for Simulation.step()

* changed how to check if step is an integer number

* Avoid overflow in large XTC files

* Also cast box indices to size_t

* Created DebuggingReporter class

* Fixed description