| shapePot |
index |
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 atomSel.AtomSel. Defaults to all atoms
sim - (optional) a simulation.Simulation Object.
Defaults to simulation.currentSimulation.
Methods:
calcEnergy() - calcs energy
calcEnergyAndDerivs(DerivList) - calcs energy and derivative info
note that these routines also update all other potential-specific data.
ensWeigth(index) - return the ensemble weight associated with the
specified member.
setEnsWeights(vals) - use the specified ensemble weights instead of those
in the underlying EnsembleSimulation.
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.
useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights
or to use those of the underlying EnsembleSimulation.
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'
# This file was automatically generated by SWIG (http://www.swig.org).
# Version 4.0.2
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.
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