Package etomica.association

Class BiasVolume2SiteAceticAcid

java.lang.Object

etomica.association.BiasVolume2SiteAceticAcid

All Implemented Interfaces:

AssociationDefinitionMolecule

public class BiasVolume2SiteAceticAcid
extends java.lang.Object
implements AssociationDefinitionMolecule

Field Summary

Fields

Modifier and Type	Field	Description
protected Vector	C1CH31
protected Vector	C1DBO1
protected Vector	C1SBO1
protected Vector	C2C1
protected Vector	C2CH32
protected Vector	C2DBO2
protected Vector	C2SBO2
protected Vector	DBO2C2
protected Vector	DBO2H1
protected Vector	dv
protected Vector	groupTranslationVector
protected Vector	H1DBO2
protected Vector	H1O2
protected Vector	H1SBO1
protected Vector	H2O1
protected MoleculeChildAtomAction	moveMoleculeAction
protected Vector	newPositionC
protected Vector	OO1
protected Vector	OO2
protected MoleculePair	pair
protected RotationTensor3D	rotationTensor
protected Vector	secondAxis
protected Vector	thirdAxis
protected Vector	work1
protected Vector	work2

Constructor Summary

Constructors

Constructor	Description
BiasVolume2SiteAceticAcid(Space space, IRandom random)

Method Summary

Modifier and Type	Method	Description
protected double	calcAngle(Vector v1, Vector v2)
protected void	doFlip(IMolecule molecule)
protected void	doTransform(IMolecule molecule, Vector r0, Vector axis, double theta)
double	getBiasSphereRadius()
boolean	isAssociated(IMolecule molecule1, IMolecule molecule2)	Function to check for bonding calculate the distance between atom1 and atom2
void	setBiasSphereInnerRadius(double innerRadius)
void	setBiasSphereRadius(double radius)
void	setBox(Box box)
void	setmaxCosPhi(double maxCosPhi)
void	setmaxCosTheta(double maxCosTheta)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

pair

protected final MoleculePair pair

H1O2

protected final Vector H1O2

H2O1

protected final Vector H2O1

C1CH31

protected final Vector C1CH31

C2CH32

protected final Vector C2CH32

OO1

protected final Vector OO1

OO2

protected final Vector OO2

C2C1

protected final Vector C2C1

secondAxis

protected final Vector secondAxis

thirdAxis

protected final Vector thirdAxis

newPositionC

protected final Vector newPositionC

work1

protected final Vector work1

work2

protected final Vector work2

C1SBO1

protected final Vector C1SBO1

C1DBO1

protected final Vector C1DBO1

C2SBO2

protected final Vector C2SBO2

C2DBO2

protected final Vector C2DBO2

dv

protected final Vector dv

H1DBO2

protected final Vector H1DBO2

H1SBO1

protected final Vector H1SBO1

DBO2H1

protected final Vector DBO2H1

DBO2C2

protected final Vector DBO2C2

groupTranslationVector

protected Vector groupTranslationVector

moveMoleculeAction

protected MoleculeChildAtomAction moveMoleculeAction

rotationTensor

protected final RotationTensor3D rotationTensor

Constructor Detail

BiasVolume2SiteAceticAcid

public BiasVolume2SiteAceticAcid(Space space,
                                 IRandom random)

Method Detail

setBox

public void setBox(Box box)

setBiasSphereRadius

public void setBiasSphereRadius(double radius)

setBiasSphereInnerRadius

public void setBiasSphereInnerRadius(double innerRadius)

setmaxCosPhi

public void setmaxCosPhi(double maxCosPhi)

setmaxCosTheta

public void setmaxCosTheta(double maxCosTheta)

getBiasSphereRadius

public double getBiasSphereRadius()

doFlip

protected void doFlip(IMolecule molecule)

calcAngle

protected double calcAngle(Vector v1,
                           Vector v2)

doTransform

protected void doTransform(IMolecule molecule,
                           Vector r0,
                           Vector axis,
                           double theta)

isAssociated

public boolean isAssociated(IMolecule molecule1,
                            IMolecule molecule2)

Function to check for bonding calculate the distance between atom1 and atom2

Specified by:

isAssociated in interface AssociationDefinitionMolecule