Package etomica.modules.chainequilibrium

Class P2SquareWellRadical

java.lang.Object

etomica.potential.Potential

etomica.potential.Potential2

etomica.potential.Potential2HardSpherical

etomica.potential.P2SquareWell

etomica.modules.chainequilibrium.P2SquareWellRadical

All Implemented Interfaces:

IPotential, IPotentialAtomic, Potential2Spherical, PotentialHard

public class P2SquareWellRadical
extends P2SquareWell

Similar to square-well potential, but considers and alters bonding states with collisions based on free radical reactions. Fully reacted atoms are inert. A radical can react (bond) with a monomer. If two radicals meet, they can bond or disproportionate (become unreactive without forming a bond) based on the combinationProbability.

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomLeafAgentManager	agentManager
protected double	combinationProbability
protected IRandom	random
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
P2SquareWellRadical(Space space, AtomLeafAgentManager aam, double coreDiameter, double lambda, double epsilon, IRandom random)

Method Summary

Modifier and Type	Method	Description
protected boolean	areBonded(IAtom a, IAtom b)	This function tells you if two atoms are bonded
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.
double	collisionTime(IAtomList atoms, double falseTime)	Computes next time of collision of the two atoms, assuming free-flight kinematics.
protected void	disproportionate(IAtom a, IAtom b)	this function will makes a and b unreactive by setting both to be bonded to themselves (a-a, b-b).
double	getCombinationProbability()	Returns the probability that two radicals will bond instead of becoming unreactive.
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 boolean	isEmpty(IAtom a)
protected boolean	isRadical(IAtom a)	This function return true if the given atom is a radical (meaning that it has only one unreacted site).
protected int	lowest(IAtom a)	This will tell you what the lowest open space is in atom a
void	setCombinationProbability(double newCombinationProbability)	Sets the probability that two radicals will bond instead of becoming unreactive.
void	setSolventThermoFrac(double newSolventThermoFrac)	Sets the fraction of well energy that is gained by an atom pair when they hop in their well.

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 final AtomLeafAgentManager agentManager

random

protected final IRandom random

combinationProbability

protected double combinationProbability

solventThermoFrac

protected double solventThermoFrac

Constructor Detail

P2SquareWellRadical

public P2SquareWellRadical(Space space,
                           AtomLeafAgentManager aam,
                           double coreDiameter,
                           double lambda,
                           double epsilon,
                           IRandom random)

Method Detail

setCombinationProbability

public void setCombinationProbability(double newCombinationProbability)

Sets the probability that two radicals will bond instead of becoming unreactive.

getCombinationProbability

public double getCombinationProbability()

Returns the probability that two radicals will bond instead of becoming unreactive.

isRadical

protected boolean isRadical(IAtom a)

This function return true if the given atom is a radical (meaning that it has only one unreacted site).

isEmpty

protected boolean isEmpty(IAtom a)

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

bond

protected void bond(IAtom a,
                    IAtom b)

this function will bond atoms a & b together

disproportionate

protected void disproportionate(IAtom a,
                                IAtom b)

this function will makes a and b unreactive by setting both to be bonded to themselves (a-a, b-b).

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.