| cosRatioPot |
index |
potential terms to restrain values of Da
NOTE: these are not fully tested!
These were developed to restrain the orientational 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.]
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.
Accessor:
useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights
or to use those of the underlying EnsembleSimulation.
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
# 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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