q_makefep - Couplings and Torsion output

- Angle/Torsion/Improper couplings added to q_makefep.
- Torsion changes are now condensed into as few lines
  as possible:

Old
  $1.C1$     $1.C2$     $1.C3$     $1.H4$       5     0
  $1.C1$     $1.C2$     $1.C3$     $1.H4$       6     0
  $1.C1$     $1.C2$     $1.C3$     $1.H4$       7     0
  $1.C1$     $1.C2$     $1.C3$     $1.H4$       0     8

New
  $1.C1$     $1.C2$     $1.C3$     $1.H4$       5     8
  $1.C1$     $1.C2$     $1.C3$     $1.H4$       6     0
  $1.C1$     $1.C2$     $1.C3$     $1.H4$       7     0

- Adapted the tests.
- Confirmed that qdyn5_r8 gives identical results between
  old and new versions if couplings are removed.

packages/Qpyl/core/qtopology.py

@@ -495,6 +495,8 @@ class _TopoBonding(object):
 
     def __init__(self, atoms, prm):
         self.prm = prm
+
+        # order the atoms
         atom_indexes = [(a.index, a) for a in atoms]
         if isinstance(self, _TopoBond):
             atom_indexes.sort()
@@ -505,7 +507,6 @@ def __init__(self, atoms, prm):
         elif isinstance(self, _TopoImproper):
             # order is defined in the library
             pass
-
         self.atoms = [a for (i,a) in atom_indexes]
 
         for a in self.atoms: