GitLab

"truly" random seed being generated from the wall clock upon Context creation.

Context into the platform rather than hacked into getRandomNumberSeed...

Someone please check this.

rather than some pre-set seed generated at construction time.

Any call to "setRandomNumberSeed" prevents this behavior (unless the generator
is seeded with 0).

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.

/usr/local/openmm/include/openmm/CustomHbondForce.h:477:25: warning: field 'p3' will be initialized after field 'parameters' [-Wreorder]
        p1(p1), p2(p2), p3(p3), parameters(parameters) {
                            ^
I believe that the initializer is supposed to assign variables in the same
order they're declared in the class definition (not the same order they're
defined in the constructor argument list.

CustomManyParticleForce offers two different "permutation modes".  Implemented it for Reference and CPU platforms.