Package etomica.modules.reactionequilibrium

Class P2SquareWellBonded

java.lang.Object

etomica.potential.Potential

etomica.potential.Potential2

etomica.potential.Potential2HardSpherical

etomica.potential.P2SquareWell

etomica.modules.reactionequilibrium.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.

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomLeafAgentManager<IAtom>	agentManager

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<IAtom> aam, double coreDiameter, double lambda, double epsilon, boolean ignoreOverlap)

Method Summary

Modifier and Type	Method	Description
void	bump(IAtomList pair, double falseTime)	Implements collision dynamics between two square-well atoms.
double	collisionTime(IAtomList atoms, double falseTime)	Computes next time of collision of the two atoms, assuming free-flight kinematics.
double	getBarrier()
Dimension	getBarrierDimension()
void	setBarrier(double b)

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, setBox

Field Detail

agentManager

protected AtomLeafAgentManager<IAtom> agentManager

Constructor Detail

P2SquareWellBonded

public P2SquareWellBonded(Space space,
                          AtomLeafAgentManager<IAtom> aam,
                          double coreDiameter,
                          double lambda,
                          double epsilon,
                          boolean ignoreOverlap)

Method Detail

setBarrier

public void setBarrier(double b)

getBarrier

public double getBarrier()

getBarrierDimension

public Dimension getBarrierDimension()

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