GitLab

* Replace SimTK-containing file headers

* Update file headers for new Tinker reader files added

* updateParametersInContext() can modify parameter offsets

* Reordering respects parameter offsets

* Implemented for CUDA and HIP

* Unified lots of parallel computation code between platforms

* Unified test code between platforms

* Eliminated duplicated timing code

* Skip neighbor list for very small systems

* Fixed typos

* Don't skip box size check when not using neighbor list

* Made test larger to ensure it uses neighbor list

* Vectorize NonbondedForce with no cutoff

* Vectorize CustomNonbondedForce with no cutoff

* Memory efficient dense neighbor list

* Fixed errors

* Fixed range overflow with very large numbers of atoms

* More fixes to overflow with large numbers of atoms

* Fix test failures

o Added C12 shift term, to match GMX.
o Added tests to compare energies and forces directly to GMX, with and without exclusions.
o Modified set/get LJPME parameters to look similar to electrostatic equivalents.

o Added C12 shift term, to match GMX.
o Added tests to compare energies and forces directly to GMX, with and without exclusions.
o Modified set/get LJPME parameters to look similar to electrostatic equivalents.

Platform specific header files get installed.  This allows plugins to be built with just an OpenMM installation, not a full source tree.

All platforms now handle nonbonded exceptions in a consistent way (they ignore cutoffs and periodic boundary conditions).  Also started OpenCL implementation of CustomHbondForce.

Use a consistent (and more accurate) value for electric constant everywhere.  Also cleaned up handling of constants and units in various places.