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element.

fix the remaining CI issues.

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

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.

Again, this will need to be done in the future anyway for general triclinic
support.

    - 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.

Fixed incorrect units in AmoebaStretchBendForce.getStretchBendParameters()

Implemented AMOEBA 2013 force field

Fixed typo in modeller docstring.

Python 3 compatibility

Fixed a bug in a test case

Fixed bug using multiple devices with PME

DrudeForce was ignoring force groups (see bug 2012)

Additional changes to support LocalCoordinatesSite

VS2013 compile errors

This reverts commit fa806957.

This reverts commit a3998cae.

This reverts commit 5dfab798.