Package etomica.potential

Class P2HardBond

java.lang.Object

etomica.potential.Potential

etomica.potential.Potential2

etomica.potential.Potential2HardSpherical

etomica.potential.P2HardBond

All Implemented Interfaces:

IPotential, IPotentialAtomic, Potential2Spherical, PotentialHard

public class P2HardBond
extends Potential2HardSpherical

Potential that acts like a hard string connecting the centers of two atoms. Meant for use as an intra-molecular interaction. Atoms can fluctuate between a minimum and maximum separation. Atoms undergo an attractive collision when attempting to separate by more than the maximum and an repulsive collision when attempting to come together closer than the min distance. P2Tether is similar to this potential, but does not have the repulsive core.

Field Summary

Fields inherited from class etomica.potential.Potential

space

Fields inherited from class etomica.potential.Potential2HardSpherical

boundary, dr

Constructor Summary

Constructors

Constructor	Description
P2HardBond(Space space)
P2HardBond(Space space, double bondLength, double bondDelta, boolean ignoreOverlap)

Method Summary

Modifier and Type	Method	Description
void	bump(IAtomList pair, double falseTime)	Implements collision dynamics for pair attempting to separate beyond tether distance
double	collisionTime(IAtomList pair, double falseTime)	Time at which two atoms will reach the end of their tether, assuming free-flight kinematics
double	energyChange()	returns change in potential energy due to the last collision
double	getBondDelta()	Accessor method for the bond extension factor
double	getBondLength()	Accessor method for the bond length
Dimension	getBondLengthDimension()
double	getRange()	Returns infinity.
double	lastCollisionVirial()	Value of the virial from the most recent collision.
Tensor	lastCollisionVirialTensor()	Value of the virial from the most recent collision, decomposed into it tensoral elements.
void	setBondDelta(double d)	Sets the bond extension factor (max = length * (1+delta))
void	setBondLength(double l)	Setter method for the bond length
double	u(double r2)	Returns 0 if the bond is within the required distance, infinity if not.

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.Potential

nBody

Methods inherited from class etomica.potential.Potential2HardSpherical

energy, setBox

Constructor Detail

P2HardBond

public P2HardBond(Space space)

P2HardBond

public P2HardBond(Space space,
                  double bondLength,
                  double bondDelta,
                  boolean ignoreOverlap)

Method Detail

getBondLength

public final double getBondLength()

Accessor method for the bond length

getBondDelta

public final double getBondDelta()

Accessor method for the bond extension factor

setBondLength

public final void setBondLength(double l)

Setter method for the bond length

setBondDelta

public final void setBondDelta(double d)

Sets the bond extension factor (max = length * (1+delta))

getBondLengthDimension

public final Dimension getBondLengthDimension()

bump

public final void bump(IAtomList pair,
                       double falseTime)

Implements collision dynamics for pair attempting to separate beyond tether distance

lastCollisionVirial

public final double lastCollisionVirial()

Description copied from interface: PotentialHard

Value of the virial from the most recent collision.

Returns:

double virial value

lastCollisionVirialTensor

public final Tensor lastCollisionVirialTensor()

Description copied from interface: PotentialHard

Value of the virial from the most recent collision, decomposed into it tensoral elements.

Returns:

Tensor

collisionTime

public final double collisionTime(IAtomList pair,
                                  double falseTime)

Time at which two atoms will reach the end of their tether, assuming free-flight kinematics

u

public double u(double r2)

Returns 0 if the bond is within the required distance, infinity if not.

Specified by:

u in interface Potential2Spherical

Specified by:

u in class Potential2HardSpherical

Parameters:

r2 - the square of the distance between the particles.

getRange

public double getRange()

Returns infinity.

Specified by:

getRange in interface IPotential

Specified by:

getRange in class Potential

energyChange

public double energyChange()

Description copied from interface: PotentialHard

returns change in potential energy due to the last collision