CustomAngleForce Class Reference

This class implements interactions between sets of three particles that depend on the angle between them. More...

Inheritance diagram for CustomAngleForce:
Force

List of all members.

Public Member Functions

def getNumAngles
 getNumAngles(self) -> int
def getNumPerAngleParameters
 getNumPerAngleParameters(self) -> int
def getNumGlobalParameters
 getNumGlobalParameters(self) -> int
def getEnergyFunction
 getEnergyFunction(self) -> string
def setEnergyFunction
 setEnergyFunction(self, string energy)
def addPerAngleParameter
 addPerAngleParameter(self, string name) -> int
def getPerAngleParameterName
 getPerAngleParameterName(self, int index) -> string
def setPerAngleParameterName
 setPerAngleParameterName(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 addAngle
 addAngle(self, int particle1, int particle2, int particle3, vectord parameters) -> int
def getAngleParameters
 getAngleParameters(self, int index)
def setAngleParameters
 setAngleParameters(self, int index, int particle1, int particle2, int particle3, vectord parameters)
def __init__
 __init__(self, string energy) -> CustomAngleForce __init__(self, CustomAngleForce other) -> CustomAngleForce
def __del__
 __del__(self)

Public Attributes

 this

Detailed Description

This class implements interactions between sets of three particles that depend on the angle between them.

Unlike HarmonicAngleForce, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions. In addition to the angle formed by the particles, it may depend on arbitrary global and per-angle parameters.

To use this class, create a CustomAngleForce object, passing an algebraic expression to the constructor that defines the interaction energy between each set of particles. The expression may depend on theta, the angle formed by the particles, as well as on any parameters you choose. Then call addPerAngleParameter() to define per-angle parameters, and addGlobalParameter() to define global parameters. The values of per-angle 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 addAngle() once for each angle. After an angle has been added, you can modify its parameters by calling setAngleParameters().

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

CustomAngleForce* force = new CustomAngleForce("0.5*k*(theta-theta0)^2");

This force depends on two parameters: the spring constant k and equilibrium angle theta0. The following code defines these parameters:

     force->addPerAngleParameter("k");
     force->addPerAngleParameter("theta0");

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) -> CustomAngleForce __init__(self, CustomAngleForce other) -> CustomAngleForce

Create a CustomAngleForce.

Parameters:
energy an algebraic expression giving the interaction energy between three particles as a function of theta, the angle between them
def addAngle (   self,
  args 
)

addAngle(self, int particle1, int particle2, int particle3, vectord parameters) -> int

Add an angle term to the force field.

Parameters:
particle1 the index of the first particle connected by the angle
particle2 the index of the second particle connected by the angle
particle3 the index of the third particle connected by the angle
parameters the list of parameters for the new angle
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 addPerAngleParameter (   self,
  args 
)

addPerAngleParameter(self, string name) -> int

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

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

getAngleParameters(self, int index)

Get the force field parameters for an angle term.

Parameters:
index the index of the angle for which to get parameters
particle1 the index of the first particle connected by the angle
particle2 the index of the second particle connected by the angle
particle3 the index of the third particle connected by the angle
parameters the list of parameters for the angle
def getEnergyFunction (   self  ) 

getEnergyFunction(self) -> string

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

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 getNumAngles (   self  ) 

getNumAngles(self) -> int

Get the number of angles 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 getNumPerAngleParameters (   self  ) 

getNumPerAngleParameters(self) -> int

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

def getPerAngleParameterName (   self,
  args 
)

getPerAngleParameterName(self, int index) -> string

Get the name of a per-angle parameter.

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

setAngleParameters(self, int index, int particle1, int particle2, int particle3, vectord parameters)

Set the force field parameters for an angle term.

Parameters:
index the index of the angle for which to set parameters
particle1 the index of the first particle connected by the angle
particle2 the index of the second particle connected by the angle
particle3 the index of the third particle connected by the angle
parameters the list of parameters for the angle
def setEnergyFunction (   self,
  args 
)

setEnergyFunction(self, string energy)

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

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 setPerAngleParameterName (   self,
  args 
)

setPerAngleParameterName(self, int index, string name)

Set the name of a per-angle 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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