CustomBondForce Class Reference

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

#include <CustomBondForce.h>

Inheritance diagram for CustomBondForce:

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.
void	updateParametersInContext (Context &context)
	Update the per-bond parameters in a Context to match those stored in this Force object.
Public Member Functions inherited from Force
	Force ()
virtual	~Force ()
int	getForceGroup () const
	Get the force group this Force belongs to.
void	setForceGroup (int group)
	Set the force group this Force belongs to.

Protected Member Functions
ForceImpl *	createImpl ()
	When a Context is created, it invokes this method on each Force in the System.
Protected Member Functions inherited from Force
ForceImpl &	getImplInContext (Context &context)
	Get the ForceImpl corresponding to this Force in a Context.
ContextImpl &	getContextImpl (Context &context)
	Get the ContextImpl corresponding to a Context.

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(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

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, delta. All trigonometric functions are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise. delta(x) = 1 if x is 0, 0 otherwise.

Constructor & Destructor Documentation

CustomBondForce ( const std::string &  energy )

explicit

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

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 ( )

protectedvirtual

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

void updateParametersInContext

(

Context &

context

)

Update the per-bond parameters in a Context to match those stored in this Force object.

This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call setBondParameters() to modify this object's parameters, then call updateParametersInState() to copy them over to the Context.

This method has several limitations. The only information it updates is the values of per-bond parameters. All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing the Context. The set of particles involved in a bond cannot be changed, nor can new bonds be added.

---

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

• CustomBondForce.h