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mdtraj) does *not* fully reduce the vectors.

Also adds a test for this.

Also added a test suite for them.

truncated octahedron inpcrd and prmtop file.

cutoff GB.

found in doctests.py (and quite a bit more, too)

Make sure files are appropriately closed by PDBFile()

can't validate the that this object does anything more than simply write without
exceptions (i.e., we can't tell if the DCD file is actually _valid_)

Add a test for the various numpy attributes (and the arguments they take) for
the unit module.

Traceback (most recent call last):
  File ".../python/tests/TestNumpyCompatibility.py", line 87, in testNumpyAttributes
    d = self.data.reshape((100, 3))
  File ".../simtk/unit/quantity.py", line 575, in reshape
    return Quantity(self._value.reshape(shape, order=order))
  File ".../simtk/unit/quantity.py", line 142, in __init__
    if value == first_item:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

Also add a test for new unit numpy capabilities.

simtk.openmm.app namespace to allow users to filter that warning out if they
want to.

necessitated creating a Copy method to do that on TabulatedFunction classes.

- Convert coordinates, velocities, and box vectors into Vec3 objects to avoid a
  subtle bug in the units module with respect to silently modifying mutable
  collections in-place when converting to a new set of units.

added.

correction by default. Then add a test for using the long-range correction and
_not_ using the long-range correction.  Comment out the test using the
long-range correction since it currently segfaults.  When the fix for the
segfault is added, this test can be reinstated (but the energy has to be
updated)

This change in default makes it consistent with the default behavior for the
classical NonbondedForce, and I would have set that as the default to begin with
if I had known it was supposed to work.

TestAmberPrmtopFile.py tests take 17 seconds combined on my laptop).

force field utilizes nbfix functionality. Without this commit, using a ff14IPQ
topology file (or one modified by ParmEd to contain off-diagonal LJ elements),
would happily run, but ignore off-diagonal elements.

The new Chen and Garcia RNA force field (see doi:10.1073/pnas.1309392110) also
utilizes off-diagonal terms in its parametrization scheme.

One shortcoming is that the approach taken here -- using a pair parameter lookup
table -- cannot be currently used with a long-range correction because it is not
a `Continuous1DFunction' by virtue of using two `Discrete2DFunction'
TabulatedFunction classes.

Energies here match the values obtained with Amber to 0.01 -- 0.1 kcal/mol
(within 0.1% of the total).

itself. This way each parm is only read once for every test (rather than being
read for every test, even when they're not used, as part of the setUp routine).
For large systems, this makes the tests run a lot faster (for small systems it's
not a large speedup).

All tests continue to pass. This change also tests that the various calls to
createSystem and such do not actually change the object in a detrimental way.