Added flat-bottom cylindrical restraints in x and y.

Added flat-bottom cylindrical restraints in x and y.

The code previously only allowed the long axis of the cylinder
to be aligned along z.  This patch allows the cylinder to be
aligned along any axis.

Old topologies and .tpr files will still work for all geometries with
g values from 2 to 5, as 2 is now just a synonym for a z-directional
cylinder.  The new values are g=6 for x, g=7 for y, and g=8 for z.
The manual has been updated to reflect these changes.

Introduced a new static function that computes forces and energy for the
flat-bottom restraint.

Refs #1577

Change-Id: I40e0bd35225170e13a18ee54f6798470e697f29d