CustomBondForce Class Reference

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

#include <CustomBondForce.h>

Inheritance diagram for CustomBondForce:

List of all members.

Classes
class	BondInfo
	This is an internal class used to record information about a bond.
class	BondParameterInfo
	This is an internal class used to record information about a per-bond parameter.
class	GlobalParameterInfo
	This is an internal class used to record information about a global parameter.
Public Member Functions
	CustomBondForce (const std::string &energy)
	Create a CustomBondForce.
int	getNumBonds () const
	Get the number of bonds for which force field parameters have been defined.
int	getNumPerBondParameters () const
	Get the number of per-bond parameters that the interaction depends on.
int	getNumGlobalParameters () const
	Get the number of global parameters that the interaction depends on.
const std::string &	getEnergyFunction () const
	Get the algebraic expression that gives the interaction energy for each bond.
void	setEnergyFunction (const std::string &energy)
	Set the algebraic expression that gives the interaction energy for each bond.
int	addPerBondParameter (const std::string &name)
	Add a new per-bond parameter that the interaction may depend on.
const std::string &	getPerBondParameterName (int index) const
	Get the name of a per-bond parameter.
void	setPerBondParameterName (int index, const std::string &name)
	Set the name of a per-bond parameter.
int	addGlobalParameter (const std::string &name, double defaultValue)
	Add a new global parameter that the interaction may depend on.
const std::string &	getGlobalParameterName (int index) const
	Get the name of a global parameter.
void	setGlobalParameterName (int index, const std::string &name)
	Set the name of a global parameter.
double	getGlobalParameterDefaultValue (int index) const
	Get the default value of a global parameter.
void	setGlobalParameterDefaultValue (int index, double defaultValue)
	Set the default value of a global parameter.
int	addBond (int particle1, int particle2, const std::vector< double > &parameters)
	Add a bond term to the force field.
void	getBondParameters (int index, int &particle1, int &particle2, std::vector< double > &parameters) const
	Get the force field parameters for a bond term.
void	setBondParameters (int index, int particle1, int particle2, const std::vector< double > &parameters)
	Set the force field parameters for a bond term.
Protected Member Functions
ForceImpl *	createImpl ()
	When a Context is created, it invokes this method on each Force in the System.

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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, 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.

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Constructor & Destructor Documentation

CustomBondForce

(

const std::string &

energy

)

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

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Member Function Documentation

int addBond	(	int	particle1,
		int	particle2,
		const std::vector< double > &	parameters
	)

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

Returns:

the index of the bond that was added

int addGlobalParameter	(	const std::string &	name,
		double	defaultValue
	)

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

Returns:

the index of the parameter that was added

int addPerBondParameter

(

const std::string &

name

)

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

Parameters:

name

the name of the parameter

Returns:

the index of the parameter that was added

ForceImpl* createImpl

(

)

[protected, virtual]

When a Context is created, it invokes this method on each Force in the System.

It should create a new ForceImpl object which can be used by the context for calculating forces. The ForceImpl will be deleted automatically when the Context is deleted.

Implements Force.

void getBondParameters	(	int	index,
		int &	particle1,
		int &	particle2,
		std::vector< double > &	parameters
	)			const

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

const std::string& getEnergyFunction

(

)

const

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

double getGlobalParameterDefaultValue

(

int

index

)

const

Get the default value of a global parameter.

Parameters:

index

the index of the parameter for which to get the default value

Returns:

the parameter default value

const std::string& getGlobalParameterName

(

int

index

)

const

Get the name of a global parameter.

Parameters:

index

the index of the parameter for which to get the name

Returns:

the parameter name

int getNumBonds

(

)

const [inline]

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

int getNumGlobalParameters

(

)

const [inline]

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

int getNumPerBondParameters

(

)

const [inline]

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

const std::string& getPerBondParameterName

(

int

index

)

const

Get the name of a per-bond parameter.

Parameters:

index

the index of the parameter for which to get the name

Returns:

the parameter name

void setBondParameters	(	int	index,
		int	particle1,
		int	particle2,
		const std::vector< double > &	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

void setEnergyFunction

(

const std::string &

energy

)

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

void setGlobalParameterDefaultValue	(	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

void setGlobalParameterName	(	int	index,
		const std::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

void setPerBondParameterName	(	int	index,
		const std::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

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The documentation for this class was generated from the following file:

• CustomBondForce.h