CustomBondForce Class Reference

This class implements bonded interactions between pairs of particles. More...

Inheritance diagram for CustomBondForce:
Force

List of all members.

Public Member Functions

def getNumBonds
 getNumBonds(self) -> int
def getNumPerBondParameters
 getNumPerBondParameters(self) -> int
def getNumGlobalParameters
 getNumGlobalParameters(self) -> int
def getEnergyFunction
 getEnergyFunction(self) -> string
def setEnergyFunction
 setEnergyFunction(self, string energy)
def addPerBondParameter
 addPerBondParameter(self, string name) -> int
def getPerBondParameterName
 getPerBondParameterName(self, int index) -> string
def setPerBondParameterName
 setPerBondParameterName(self, int index, string name)
def addGlobalParameter
 addGlobalParameter(self, string name, double defaultValue) -> int
def getGlobalParameterName
 getGlobalParameterName(self, int index) -> string
def setGlobalParameterName
 setGlobalParameterName(self, int index, string name)
def getGlobalParameterDefaultValue
 getGlobalParameterDefaultValue(self, int index) -> double
def setGlobalParameterDefaultValue
 setGlobalParameterDefaultValue(self, int index, double defaultValue)
def addBond
 addBond(self, int particle1, int particle2, vectord parameters) -> int
def getBondParameters
 getBondParameters(self, int index)
def setBondParameters
 setBondParameters(self, int index, int particle1, int particle2, vectord parameters)
def __init__
 __init__(self, string energy) -> CustomBondForce __init__(self, CustomBondForce other) -> CustomBondForce
def __del__
 __del__(self)

Public Attributes

 this

Detailed Description

This class implements bonded interactions between pairs of particles.

Unlike HarmonicBondForce, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions. It may depend on the distance between particles, as well as on arbitrary global and per-bond parameters.

To use this class, create a CustomBondForce object, passing an algebraic expression to the constructor that defines the interaction energy between each pair of bonded particles. The expression may depend on r, the distance between the particles, as well as on any parameters you choose. Then call addPerBondParameter() to define per-bond parameters, and addGlobalParameter() to define global parameters. The values of per-bond parameters are specified as part of the system definition, while values of global parameters may be modified during a simulation by calling Context.setParameter(). Finally, call addBond() once for each bond. After a bond has been added, you can modify its parameters by calling setBondParameters().

As an example, the following code creates a CustomBondForce that implements a harmonic potential:

CustomBondForce* force = new CustomBondForce("0.5*k*(r-r0)^2");

This force depends on two parameters: the spring constant k and equilibrium distance r0. The following code defines these parameters:

     force->addPerBondParameter("k");
     force->addPerBondParameter("r0");

Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step. All trigonometric functions are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise.

Member Function Documentation

def __del__ (   self  ) 

__del__(self)

Reimplemented from Force.

def __init__ (   self,
  args 
)

__init__(self, string energy) -> CustomBondForce __init__(self, CustomBondForce other) -> CustomBondForce

Create a CustomBondForce.

Parameters:
energy an algebraic expression giving the interaction energy between two bonded particles as a function of r, the distance between them
def addBond (   self,
  args 
)

addBond(self, int particle1, int particle2, vectord parameters) -> int

Add a bond term to the force field.

Parameters:
particle1 the index of the first particle connected by the bond
particle2 the index of the second particle connected by the bond
parameters the list of parameters for the new bond
def addGlobalParameter (   self,
  args 
)

addGlobalParameter(self, string name, double defaultValue) -> int

Add a new global parameter that the interaction may depend on.

Parameters:
name the name of the parameter
defaultValue the default value of the parameter
def addPerBondParameter (   self,
  args 
)

addPerBondParameter(self, string name) -> int

Add a new per-bond parameter that the interaction may depend on.

Parameters:
name the name of the parameter
def getBondParameters (   self,
  args 
)

getBondParameters(self, int index)

Get the force field parameters for a bond term.

Parameters:
index the index of the bond for which to get parameters
particle1 the index of the first particle connected by the bond
particle2 the index of the second particle connected by the bond
parameters the list of parameters for the bond
def getEnergyFunction (   self  ) 

getEnergyFunction(self) -> string

Get the algebraic expression that gives the interaction energy for each bond

def getGlobalParameterDefaultValue (   self,
  args 
)

getGlobalParameterDefaultValue(self, int index) -> double

Get the default value of a global parameter.

Parameters:
index the index of the parameter for which to get the default value
def getGlobalParameterName (   self,
  args 
)

getGlobalParameterName(self, int index) -> string

Get the name of a global parameter.

Parameters:
index the index of the parameter for which to get the name
def getNumBonds (   self  ) 

getNumBonds(self) -> int

Get the number of bonds for which force field parameters have been defined.

def getNumGlobalParameters (   self  ) 

getNumGlobalParameters(self) -> int

Get the number of global parameters that the interaction depends on.

def getNumPerBondParameters (   self  ) 

getNumPerBondParameters(self) -> int

Get the number of per-bond parameters that the interaction depends on.

def getPerBondParameterName (   self,
  args 
)

getPerBondParameterName(self, int index) -> string

Get the name of a per-bond parameter.

Parameters:
index the index of the parameter for which to get the name
def setBondParameters (   self,
  args 
)

setBondParameters(self, int index, int particle1, int particle2, vectord parameters)

Set the force field parameters for a bond term.

Parameters:
index the index of the bond for which to set parameters
particle1 the index of the first particle connected by the bond
particle2 the index of the second particle connected by the bond
parameters the list of parameters for the bond
def setEnergyFunction (   self,
  args 
)

setEnergyFunction(self, string energy)

Set the algebraic expression that gives the interaction energy for each bond

def setGlobalParameterDefaultValue (   self,
  args 
)

setGlobalParameterDefaultValue(self, int index, double defaultValue)

Set the default value of a global parameter.

Parameters:
index the index of the parameter for which to set the default value
name the default value of the parameter
def setGlobalParameterName (   self,
  args 
)

setGlobalParameterName(self, int index, string name)

Set the name of a global parameter.

Parameters:
index the index of the parameter for which to set the name
name the name of the parameter
def setPerBondParameterName (   self,
  args 
)

setPerBondParameterName(self, int index, string name)

Set the name of a per-bond parameter.

Parameters:
index the index of the parameter for which to set the name
name the name of the parameter

Member Data Documentation

this
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