fix a bug in rigid body align

there was a typo in _cdef_MeasureAngleAxisCluster.align().  x1 was
passed as both x1 and x2.

Add tests for rigid body measure.align and transform.rotate.

Ensure exceptions are handled in some of the cdef functions.

Ensure findrotation returns a real object

Fix the documentation for rotations.rotate_aa.  The order of the inputs
is non-intuitive.
add lj minimization benchmark
update README

so that cython is installed from pip because the Ubuntu version is too
old
update README
fix small issue in README
Merge pull request #107 from js850/aamindist

fix a bug in rigid body align
Merge branch 'master' into periodic_boundaries