CustomAngleForce Class Reference

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

#include <CustomAngleForce.h>

Inheritance diagram for CustomAngleForce:

Public Member Functions
	CustomAngleForce (const std::string &energy)
	Create a CustomAngleForce.
int	getNumAngles () const
	Get the number of angles for which force field parameters have been defined.
int	getNumPerAngleParameters () const
	Get the number of per-angle 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 angle.
void	setEnergyFunction (const std::string &energy)
	Set the algebraic expression that gives the interaction energy for each angle.
int	addPerAngleParameter (const std::string &name)
	Add a new per-angle parameter that the interaction may depend on.
const std::string &	getPerAngleParameterName (int index) const
	Get the name of a per-angle parameter.
void	setPerAngleParameterName (int index, const std::string &name)
	Set the name of a per-angle 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	addAngle (int particle1, int particle2, int particle3, const std::vector< double > &parameters)
	Add an angle term to the force field.
void	getAngleParameters (int index, int &particle1, int &particle2, int &particle3, std::vector< double > &parameters) const
	Get the force field parameters for an angle term.
void	setAngleParameters (int index, int particle1, int particle2, int particle3, const std::vector< double > &parameters)
	Set the force field parameters for an angle term.
void	updateParametersInContext (Context &context)
	Update the per-angle 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 () const
	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 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(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

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, 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

CustomAngleForce ( const std::string &  energy )

explicit

Create a CustomAngleForce.

Parameters

energy

an algebraic expression giving the interaction energy between three particles as a function of theta, the angle between them

Member Function Documentation

int addAngle	(	int	particle1,
		int	particle2,
		int	particle3,
		const std::vector< double > &	parameters
	)

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

Returns

the index of the angle 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 addPerAngleParameter

(

const std::string &

name

)

Add a new per-angle 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 ( ) const

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 getAngleParameters	(	int	index,
		int &	particle1,
		int &	particle2,
		int &	particle3,
		std::vector< double > &	parameters
	)		const

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

const std::string& getEnergyFunction

(

)

const

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

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 getNumAngles ( ) const

inline

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

int getNumGlobalParameters ( ) const

inline

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

int getNumPerAngleParameters ( ) const

inline

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

const std::string& getPerAngleParameterName

(

int

index

)

const

Get the name of a per-angle parameter.

Parameters

index

the index of the parameter for which to get the name

Returns

the parameter name

void setAngleParameters	(	int	index,
		int	particle1,
		int	particle2,
		int	particle3,
		const std::vector< double > &	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

void setEnergyFunction

(

const std::string &

energy

)

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

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 setPerAngleParameterName	(	int	index,
		const std::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

void updateParametersInContext

(

Context &

context

)

Update the per-angle 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 setAngleParameters() 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-angle 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 angle cannot be changed, nor can new angles be added.

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

• CustomAngleForce.h