Package etomica.potential

Class P1HarmonicSite

java.lang.Object

etomica.potential.Potential

etomica.potential.Potential1

etomica.potential.P1HarmonicSite

All Implemented Interfaces:

IPotential, IPotentialAtomic, PotentialSoft

public class P1HarmonicSite
extends Potential1
implements PotentialSoft

Potential in which attaches a harmonic spring between each affected atom a nominal site for that atom, as defined by an agent manager.

Nested Class Summary

Nested classes/interfaces inherited from class etomica.potential.Potential1

Potential1.Intramolecular

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomLeafAgentManager<? extends Vector>	atomAgentManager
protected java.util.Map<Box,AtomLeafAgentManager<? extends Vector>>	boxAgentManager

Fields inherited from class etomica.potential.Potential

space

Fields inherited from class etomica.potential.Potential1

boundary

Constructor Summary

Constructors

Constructor	Description
P1HarmonicSite(Space space)

Method Summary

Modifier and Type	Method	Description
double	energy(IAtomList a)	Returns the interaction energy between the given atoms.
double	getSpringConstant()
Dimension	getSpringConstantDimension()
Vector[]	gradient(IAtomList a)	Returns the gradient of the potential as it applies to each atom in the given AtomSet, indicating how the energy would change as the position of the first atom is varied.
Vector[]	gradient(IAtomList a, Tensor pressureTensor)	Returns the same gradient as gradient(AtomSet) and also adds in the contribution of the AtomSet to the pressureTensor.
void	setAtomAgentManager(Box box, AtomLeafAgentManager<? extends Vector> agentManager)
void	setBox(Box box)	Informs the potential of the box on which it acts.
void	setSpringConstant(double springConstant)
double	virial(IAtomList a)

Methods inherited from interface etomica.potential.IPotential

getRange, 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.Potential1

getRange

Field Detail

boxAgentManager

protected final java.util.Map<Box,AtomLeafAgentManager<? extends Vector>> boxAgentManager

atomAgentManager

protected AtomLeafAgentManager<? extends Vector> atomAgentManager

Constructor Detail

P1HarmonicSite

public P1HarmonicSite(Space space)

Method Detail

setAtomAgentManager

public void setAtomAgentManager(Box box,
                                AtomLeafAgentManager<? extends Vector> agentManager)

setBox

public void setBox(Box box)

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 Potential1

setSpringConstant

public void setSpringConstant(double springConstant)

getSpringConstant

public double getSpringConstant()

getSpringConstantDimension

public Dimension getSpringConstantDimension()

energy

public double energy(IAtomList a)

Description copied from class: Potential

Returns the interaction energy between the given atoms. There might be 0, 1, 2 or more atoms in the AtomSet.

Specified by:

energy in interface IPotentialAtomic

Specified by:

energy in class Potential

virial

public double virial(IAtomList a)

Specified by:

virial in interface PotentialSoft

gradient

public Vector[] gradient(IAtomList a)

Description copied from interface: PotentialSoft

Returns the gradient of the potential as it applies to each atom in the given AtomSet, indicating how the energy would change as the position of the first atom is varied. The method is allowed to return an array of Vectors with fewer elements than the number of atoms in the AtomSet.

Specified by:

gradient in interface PotentialSoft

Returns:

gradient

public Vector[] gradient(IAtomList a,
                         Tensor pressureTensor)

Description copied from interface: PotentialSoft

Returns the same gradient as gradient(AtomSet) and also adds in the contribution of the AtomSet to the pressureTensor. Their contribution is added to the given Tensor. This combined method exists for computational efficiency. Calculating the pressureTensor is generally trivial once the gradient is known but often requires intermediate information.

Specified by:

gradient in interface PotentialSoft