AmoebaBondForce Class Reference

This class implements an interaction between pairs of particles that varies with the distance between them. More...

#include <AmoebaBondForce.h>

Inheritance diagram for AmoebaBondForce:

Public Member Functions
	AmoebaBondForce ()
	Create an AmoebaBondForce. More...
int	getNumBonds () const
	Get the number of bond stretch terms in the potential function. More...
void	setAmoebaGlobalBondCubic (double cubicK)
	Set the global cubic term. More...
double	getAmoebaGlobalBondCubic () const
	Get the global cubic term. More...
void	setAmoebaGlobalBondQuartic (double quarticK)
	Set the global quartic term. More...
double	getAmoebaGlobalBondQuartic () const
	Get the global quartic term. More...
int	addBond (int particle1, int particle2, double length, double quadraticK)
	Add a bond term to the force field. More...
void	getBondParameters (int index, int &particle1, int &particle2, double &length, double &quadraticK) const
	Get the force field parameters for a bond term. More...
void	setBondParameters (int index, int particle1, int particle2, double length, double quadraticK)
	Set the force field parameters for a bond term. More...
void	updateParametersInContext (Context &context)
	Update the per-bond parameters in a Context to match those stored in this Force object. More...
bool	usesPeriodicBoundaryConditions () const
	Returns whether or not this force makes use of periodic boundary conditions. More...
Public Member Functions inherited from Force
	Force ()
virtual	~Force ()
int	getForceGroup () const
	Get the force group this Force belongs to. More...
void	setForceGroup (int group)
	Set the force group this Force belongs to. More...

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

Protected Attributes
double	_globalQuarticK
double	_globalCubicK

Detailed Description

This class implements an interaction between pairs of particles that varies with the distance between them.

The interaction is defined by a 4th order polynomial. Only the quadratic term is set per-bond. The coefficients of the higher order terms each have a single value that is set globally.

To use it, create an AmoebaBondForce object then call addBond() once for each bond. After a bond has been added, you can modify its force field parameters by calling setBondParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

Constructor & Destructor Documentation

AmoebaBondForce

(

)

Create an AmoebaBondForce.

Member Function Documentation

int addBond	(	int	particle1,
		int	particle2,
		double	length,
		double	quadraticK
	)

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
length	the equilibrium length of the bond, measured in nm
k	the quadratic force constant for the bond

Returns

the index of the bond 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.

double getAmoebaGlobalBondCubic

(

)

const

Get the global cubic term.

Returns

global cubicK term

double getAmoebaGlobalBondQuartic

(

)

const

Get the global quartic term.

Returns

global quartic term

void getBondParameters	(	int	index,
		int &	particle1,
		int &	particle2,
		double &	length,
		double &	quadraticK
	)		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
length	the equilibrium length of the bond, measured in nm
quadratic	k the quadratic force constant for the bond

int getNumBonds ( ) const

inline

Get the number of bond stretch terms in the potential function.

void setAmoebaGlobalBondCubic

(

double

cubicK

)

Set the global cubic term.

Parameters

cubicK

the cubic force constant for the bond

void setAmoebaGlobalBondQuartic

(

double

quarticK

)

Set the global quartic term.

Parameters

quarticK

the quartic force constant for the bond

void setBondParameters	(	int	index,
		int	particle1,
		int	particle2,
		double	length,
		double	quadraticK
	)

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
length	the equilibrium length of the bond, measured in nm
k	the quadratic force constant for the bond

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 updateParametersInContext() to copy them over to the Context.

The only information this method updates is the values of per-bond parameters. The set of particles involved in a bond cannot be changed, nor can new bonds be added.

bool usesPeriodicBoundaryConditions ( ) const

inlinevirtual

Returns whether or not this force makes use of periodic boundary conditions.

Returns

true if nonbondedMethod uses PBC and false otherwise

Reimplemented from Force.

Member Data Documentation

double _globalCubicK

protected

double _globalQuarticK

protected

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

• AmoebaBondForce.h