Shape Potential term

This term includes potential terms to constrain the shape tensor of a
atom selection. The shape tensor is defined as

            ( y_i^2+z_i^2  -x_i*y_i      -x_i*z_i     )
            (  -x_i*y_i    x_i^2+z_i^2   -y_i*z_i     )
            (  -x_i*z_i    -y_i*z_i     x_i^2+y_i^2   )

where (x_i,y_i,z_i) is the position of atom i relative to the center
of the atom selection. Thus, the shape tensor is analogous to the
inertia tensor: only it contains no mass information.

  There are separate potential terms which target the eigen values of
this tensor (which correspond to size), and the eigenvectors of the
tensor, which contain orientational information.

Constructor:
  ShapePot(name, sel, sim)   with arguments: 
    name - a name for this potential term
    sel  - (optional) an <m atomSel>.AtomSel. Defaults to all atoms
    sim  - (optional) a <m simulation>.Simulation Object. 
           Defaults to <m simulation>.currentSimulation.


Methods:
  calcEnergy()                    - calcs energy
  calcEnergyAndDerivs(DerivList)  - calcs energy and derivative info
    note that these routines also update all other potential-specific data.

Read-Write accessors:
  sizeScale         - scale factor for the size term
  orientScale       - scale factor for the orientation term
  targetSel         - atom selection for target. Used if targetType=='molecule'
  sizeTol           - error in size term. Used if sizePotType=='square'
  orientTol         - error (in degrees) in orient term. 
                      Used if orientPotType=='square'
  targetType        - specifies the target tensor
                        'molecule' : target specified by targetSel
                        'average'  : target is the ensemble average of
                                      the shape tensor.
                        'pairwise' : the pairwise difference of the shape
				     tensor between each ensemble member is
                                     minimized.
  sizePotType       - potential type for size term: 'harmonic' or 'square'
  orientPotType     - potential type for orient term: 'harmonic' or 'square'
  degenerateTol     - if the difference between eigenvalues drops below this
                      number, eigenvalue/eigenvector pairs are sorted such 
                      that the eigenvector overlap with the target is 
                      maximized, instead of by eigenvalue.


Read-only accessors
  simulation()   - simulation used by this shape term. Is an EnsembleSimulation
  atomSel()      - atom selection defining the shape tensor.

  qCenter(index) - center of the atomSelection for ensemble given by index.
  qCenterTarget()- center position of the target selection.
  rotation(index)- rotation angle (in degrees) of shape tensor to target. 
                   The optional argument specifies the ensemble member 
                   (defaults to the current ensemble).

  getContrib(index,i)
                 - get EigenPair for ensemble member index, number i.
  getTarget(i)   - get EigenPair target shape tensor. EigenPair
                   objects contain two members:
                     value, vector

  info()         - return string synopsis of potential info.
  showValues()   - return pretty-printed eigenvalue info.
  showVectors()  - return pretty-printed eigenvector info.


The potential term is defined as

  E = sizeScale * ( V(ds_x,sizeTol) +
		    V(ds_y,sizeTol) +
		    V(ds_z,sizeTol) ) +
      orientScale * V(dTheta,orienTol)

where
  ds_i = eigenValue(i) - target_eigenValue(i)
  dTheta = overall rotation of shapeTensor, relative to target

and
  V(x,tol) = x^2             if potType=='harmonic'
             (abs(x)-tol)^2  if potType=='square'