GitLab

Switched to a new Windows pthreads library

Conflicts:
	libraries/pthreads/include/pthread.h

Implemented runForClockTime()

Added checkpointing functions to Simulation

Update setup.py

Improved accuracy of correction for exclusions with PME

mingw has STRUCT_TIMESPEC

Implemented select() in custom expressions

fix mingw build

Fixed failing test cases.  Increased default minimizer tolerance to 10.

Added option to add a fixed number of solvent molecules

fix swig build

Better error catch for using chamber prmtops

Prints out a more helpful error message than a weird regex-based missing
"groups" attribute on NoneType.

Optimization for AMD

CPU PME plugin respects OPENMM_CPU_THREADS environment variable

Improve CHARMM parsing when resnums have inscodes

Fixed bug in CustomIntegrator

This also removes assert statements, since those can't be relied upon to *not*
be optimized away -- they should never be used to check user input sanity.

Masses do not increase monotonically with atomic number

Also fixes the test case.  Everything should pass now.