GitLab

Variable step size integrators were scaling the step size incorrectly

Make it so that random forces and integrators generate unique seeds each time a Context is made

Fix for #780

principle -> principal... I'm a bozo.

Catch nan coordinates before they can produce a segfault

random numbers.  Add 2 citations about Langevin synchronization.  Convert the
references.bib file to UNIX line endings.

Some windows changes

Fix typemap for str/bytes -> std::string

Fixed bug in reference CustomCompoundBondForce

stripUnits behavior with bytes

.message -> str()

to 0 here as well.

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

This commit hits the CPU platform (I had previously thought it just used the
Reference generator) as well as the CustomIntegrator stream that is set
separately from the standard "integrator" stream attached to each platform for
CUDA and OpenCL platforms (it seemed to me that the Reference platform's
CustomIntegrator just used the integrator random stream).

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).

Add a check and raise an exception if someone tries to use a CHAMBER-style prmtop

Implements `usesPeriodicBoundaryConditions` on `Force`s and `System`

topology file with the Amber file parsers. These do *not* currently work for
creating a system.