GitLab

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.

Reduces time taken from 15.7 seconds (last commit) to 2.2 seconds by avoiding
Quantity comparisons altogether.

The old approach iterated through the entire periodic table by atomic number and
subtracted the provided mass by the element's mass and kept track of the
smallest difference. The new approach steps through the elements in order of
atomic number and bails once it hits an element with a higher mass than the
target mass (assuming masses are monotonically increasing).

On my desktop, processing 4TVP-dmj_wat-ion.psf dropped from 297 s to 15.4 s. But
15.4 s is still a bit too long...

Fix SWIG 3 support for the Python wrappers.

See swig/swig#387 for a discussion.  It would actually be nice to *not* set the
"compactdefaultargs" feature globally, since that would allow us to actually see
the real API at the Python level the same as you would see by looking at the C++
header files. But this is the only way to support both SWIG 2 and SWIG 3 easily
and avoid a lot of retooling for the SWIG input code generator.