Overhaul of Thole screening.

Reverted to old style of using 4 atoms in Thole directive; this ultimately
makes organization easier and the topologies are shorter and more convenient.
This update also corrects some issues within the Thole screening functions.
Outside of the Drude branch, there is nothing that uses Thole screening,
so changes in these functions should not affect anything.

Necessary updates to thole_pol() and do_1_thole() in bondfree.c alleviated a
problem in which massive forces accumulated on the Drude-atom pairs, leading
to ridiculous geometries.  The current code defines the Thole screening exactly
as it is in CHARMM and calculates the forces in the same way.

Force field updates to follow when DNA has been properly converted.

Change-Id: I9be302fe07ae5e84da84b4f7bf942cd132e20382