potential terms to restrain values of Da

NOTE: these are not fully tested!

These were developed to restrain the orientational <m
varTensor>.VarTensor Da values to be close to oneanother (but not
necessarily identical). 

CosRatioPot
          1/2 * scale * (cos(theta1) - ratio*cos(theta2))^2

 where theta1 is one bond angle, theta2 is a second bond angle, and
 scale and ratio are constants.

 use:
  from potCosAngleRatio import CosAngleRatioPot

  term = CosRatioPot("name",             
                     AtomSel("atom 01"),
                     AtomSel("atom a1"),
                     AtomSel("atom b1"),
                     AtomSel("atom 02"),
                     AtomSel("atom a2"),
                     AtomSel("atom b2"),
                     [simulation])

 theta1 is given by the angle a1 - 01 - b1
 theta2 is given by the angle a2 - 02 - b2
  [simulation is an optional simulation parameter - usually not needed.]

 to set the scale factor:
   term.scale = 100

 to set the constant ratio:
   term.ratio = 0.2

 remember to add this to the terms to be evaluated:
   simulation.addPot(term)

##################################################


Cos2RatioPot
 potential term #2:
       1/2 * scale * (cos(theta1)*cos(theta4) - cos(theta2)*cos(theta3))^2

 where theta1, theta2, theta3, and theta4 are bond angles, and
 scale is a constant. Note that the minimum of this potential occurs when

    cos(theta1)/cos(theta2) = cos(theta3)/cos(theta4)

 use:
  from potCosAngleRatio import CosAngleRatioPot

  term = Cos2RatioPot("name",             
                      AtomSel("atom 01"),
                      AtomSel("atom a1"),
                      AtomSel("atom b1"),
                      AtomSel("atom 02"),
                      AtomSel("atom a2"),
                      AtomSel("atom b2"),
                      AtomSel("atom 03"),
                      AtomSel("atom a3"),
                      AtomSel("atom b3"),
                      AtomSel("atom 04"),
                      AtomSel("atom a4"),
                      AtomSel("atom b4"),
                      [simulation])

 theta1 is given by the angle a1 - 01 - b1
 theta2 is given by the angle a2 - 02 - b2
  [simulation is an optional simulation parameter - usually not needed.]

 to set the scale factor:
   term.scale = 100

 to set the constant ratio:
   term.ratio = 0.2