Merge branch 'amoeba' of github.com:peastman/openmm
Merge branch 'master' of github.com:SimTk/openmm
Merge branch 'amoeba' of github.com:peastman/openmm
Added tip3p-fb and tip4p-fb parameter files.
Merge branch 'master' of github.com:SimTk/openmm
Seed the rng from urandom
separate files
fix path
rename
rename
fix capitalization
Rewrite Amber inpcrd/restart file handling. Among the improvements:
    - existence of velocities and box vectors is auto-detected, so
      loadVelocities and loadBoxVectors are unnecessary
    - recognizes NetCDF-format Amber restart files (which can be written by
      tleap, sander, pmemd, and cpptraj).
    - Restart files coordinate/velocity/box fields have a hard width of 12
      characters and does not ensure that fields are whitespace delimited. This
      commit will correctly parse (valid) Amber restart files in which a
      particular coordinate is <= -100 A or >= 1000 A (not uncommon for restart
      files from sander/pmemd).
    - File format (ASCII vs. NetCDF) is auto-detected.

I deprecated the loadVelocities and loadBoxVectors arguments, since the behavior
does not change (and is correct) whether these variables are set or not. A
DeprecationWarning is emitted if users specify these variables.
Add a natom attribute to AmberNetcdfRestart.
Add tests for Amber inpcrd file parsing.
Remove the hard-coded orthogonal box vector code in the PrmtopLoader class.
Again, this will need to be done in the future anyway for general triclinic
support.
Finish the last commit. Make sure the box vector calculation from the lengths
and angles makes numbers exactly 0 that _should_ be zero (but aren't due to
precision and round-off issues).

Now the box vector code in the prmtop file is fully general for every type of
box that Amber supports.
Get rid of some comments that I had forgotten to get rid of earlier.
Merge pull request #460 from rmcgibbo/seed-random

Seed default RNG from /dev/urandom
Copy over all parm7 and rst7 files as well...
The natom attribute is only part of the private objects -- this should hopefully
fix the remaining CI issues.

Also make sure .ncrst files are copied over in the test directory.