COM pulling options per coord, improved cylinder

COM pulling options per coord, improved cylinder

The COM pull type (potential/constraint), geometry, dimensions
and pull-start can now be set differently for each pull coordinate.
Also added a flat-bottom potential.

Cylinder geometry now uses a smooth radial weight function and
adds radial forces so it now conserves energy.
Fixes #1590.

There is now also an option for printing the COM of the second group,
as well as the reference value for all pull coordinates.
Writing the distance components to the pull coordinate output is now
optional (off by default).

gmx wham currently only supports input with the old restrictions
(and it checks for this). These restrctions should be removed.

Change-Id: I86e443b225accb85cc7fe0aa6c23d937f15b2efb