Package etomica.modules.chainequilibrium

Class P2SquareWellBonded

java.lang.Object

etomica.potential.Potential

etomica.potential.Potential2

etomica.potential.Potential2HardSpherical

etomica.potential.P2SquareWell

etomica.modules.chainequilibrium.P2SquareWellBonded

All Implemented Interfaces:

IPotential, IPotentialAtomic, Potential2Spherical, PotentialHard

public class P2SquareWellBonded
extends P2SquareWell

Similar to square-well potential, but considers and alters bonding states with collisions. Each atom may bind, in the form of the square-well attraction, to one other atom. Two atoms approaching each other with this potential may interact as follows:

• If neither is bound, or if they are bound to each other, they will interact as square-well atoms.
• If one or both is bound, each to another atom, they will act as hard spheres of diameter equal to the well diameter.

The potential is similar to P2SquareWellBondedBarrier, but there is no accounting for a barrier, and no possibility for one atom to dislodge the bonding partner of another directly in a single collision.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected static class	P2SquareWellBonded.RingResult

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomLeafAgentManager	agentManager
protected Box	box
protected P2SquareWellBonded.RingResult	ringResult
protected double	solventThermoFrac

Fields inherited from class etomica.potential.P2SquareWell

coreDiameter, coreDiameterSquared, dv, epsilon, ignoreOverlap, lambda, lastCollisionVirial, lastCollisionVirialr2, lastCollisionVirialTensor, lastEnergyChange, wellDiameter, wellDiameterSquared

Fields inherited from class etomica.potential.Potential

space

Fields inherited from class etomica.potential.Potential2HardSpherical

boundary, dr

Constructor Summary

Constructors

Constructor	Description
P2SquareWellBonded(Space space, AtomLeafAgentManager aam, double coreDiameter, double lambda, double epsilon)

Method Summary

Modifier and Type	Method	Description
protected boolean	areBonded(IAtom a, IAtom b)	This function tells you if two atoms are bonded This could probably be public, although a public version would need to first re-retrieve agents
protected void	bond(IAtom a, IAtom b)	this function will bond atoms a & b together
void	bump(IAtomList pair, double falseTime)	Implements collision dynamics between two square-well atoms.
protected void	checkRing(IAtom a, IAtom b, int maxBondCount)	this function will bond atoms a & b together
double	collisionTime(IAtomList atoms, double falseTime)	Computes next time of collision of the two atoms, assuming free-flight kinematics.
protected boolean	full(IAtom a)	This function will tell the user, if passed an atom weither or not that atom can bond
double	getSolventThermoFrac()	Returns the fraction of well energy that is gained or lost by an atom pair when they hop in or leave their well.
protected int	lowest(IAtom a)	This will tell you what the lowest open space is in atom a
void	setBox(Box newBox)	Informs the potential of the box on which it acts.
void	setSolventThermoFrac(double newSolventThermoFrac)	Sets the fraction of well energy that is gained by an atom pair when they hop in their well.
protected void	unbond(IAtom a, IAtom b)	this function unbonds two atoms

Methods inherited from interface etomica.potential.IPotential

nBody

Methods inherited from class java.lang.Object

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

Methods inherited from class etomica.potential.P2SquareWell

energyChange, getCoreDiameter, getCoreDiameterDimension, getEpsilon, getEpsilonDimension, getLambda, getLambdaDimension, getRange, lastCollisionVirial, lastCollisionVirialTensor, setCoreDiameter, setEpsilon, setLambda, u

Methods inherited from class etomica.potential.Potential

nBody

Methods inherited from class etomica.potential.Potential2HardSpherical

energy

Field Detail

agentManager

protected final AtomLeafAgentManager agentManager

box

protected Box box

solventThermoFrac

protected double solventThermoFrac

ringResult

protected final P2SquareWellBonded.RingResult ringResult

Constructor Detail

P2SquareWellBonded

public P2SquareWellBonded(Space space,
                          AtomLeafAgentManager aam,
                          double coreDiameter,
                          double lambda,
                          double epsilon)

Method Detail

setBox

public void setBox(Box newBox)

Description copied from class: Potential

Informs the potential of the box on which it acts. Typically this requires at least that it update the nearestImageTransformer of its coordinatePair (if it uses one), e.g.: cPair.setNearestImageTransformer(box.boundary());

Specified by:

setBox in interface IPotential

Overrides:

setBox in class Potential2HardSpherical

full

protected boolean full(IAtom a)

This function will tell the user, if passed an atom weither or not that atom can bond

lowest

protected int lowest(IAtom a)

This will tell you what the lowest open space is in atom a

areBonded

protected boolean areBonded(IAtom a,
                            IAtom b)

This function tells you if two atoms are bonded This could probably be public, although a public version would need to first re-retrieve agents

bond

protected void bond(IAtom a,
                    IAtom b)

this function will bond atoms a & b together

checkRing

protected void checkRing(IAtom a,
                         IAtom b,
                         int maxBondCount)

this function will bond atoms a & b together

unbond

protected void unbond(IAtom a,
                      IAtom b)

this function unbonds two atoms

collisionTime

public double collisionTime(IAtomList atoms,
                            double falseTime)

Computes next time of collision of the two atoms, assuming free-flight kinematics.

Specified by:

collisionTime in interface PotentialHard

Overrides:

collisionTime in class P2SquareWell

bump

public void bump(IAtomList pair,
                 double falseTime)

Description copied from class: P2SquareWell

Implements collision dynamics between two square-well atoms. Includes all possibilities involving collision of hard cores, and collision of wells both approaching and diverging

Specified by:

bump in interface PotentialHard

Overrides:

bump in class P2SquareWell

getSolventThermoFrac

public double getSolventThermoFrac()

Returns the fraction of well energy that is gained or lost by an atom pair when they hop in or leave their well.

setSolventThermoFrac

public void setSolventThermoFrac(double newSolventThermoFrac)

Sets the fraction of well energy that is gained by an atom pair when they hop in their well. This is also the fraction of energy they give up when they leave the well. The pair does still need to have sufficient energy to escape the well at its full strength.