GitLab

* Optimize CustomNonbondedForce.updateParametersInContext()

* Optimized uploading changed values to GPU

* Optimized updateParametersInContext() for lots of bonded forces

* Optimized updateParametersInContext() for CustomExternalForce

* Optimized updateParametersInContext() for NonbondedForce

* Code changes for HIP platform

Swigged python docstrings now include documented return values and type
information or their arguments. They are generated in numpydoc format.
Furthermore, all of the Python app layer docstrings have been changed
to numpydoc format. The filterPythonFiles.py script which helps to
generate the Doxygen Python API docs has been updated to reflect these
changes.

the barostats and andersen thermostat.

the System. The System inspects all of its forces and calls
usePeriodicBoundaryConditions -- it reports 'true' if at least one of its Forces
returns 'true' for usesPeriodicBoundaryConditions.

The default Force implementation is to raise an exception (NotImplementedError).
The System implementation will return true if at least one of its Forces returns
'true' for usesPeriodicBoundaryConditions, _regardless_ of whether or not one or
more of the forces does not implement the method. If at least one of the forces
does not implement usesPeriodicBoundaryConditions and all forces return false,
an OpenMMException is thrown.

from all .cpp and .h files.

Modified the API for lots of classes so that the number of particles/bonds/etc. need not be specified in the constructor.