Package etomica.modules.rosmosis

Class P1Tether

java.lang.Object

etomica.potential.Potential

etomica.potential.Potential1

etomica.modules.rosmosis.P1Tether

All Implemented Interfaces:

AtomLeafAgentManager.AgentSource<Vector>, IPotential, IPotentialAtomic, PotentialSoft

public class P1Tether
extends Potential1
implements AtomLeafAgentManager.AgentSource<Vector>, PotentialSoft

Potential for a harmonic tether. U = 0.5 eps r^2

Nested Class Summary

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

Potential1.Intramolecular

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomLeafAgentManager<Vector>	agentManager
protected double	epsilon
protected Vector[]	gradient
protected ISpecies	species
protected Vector	work

Fields inherited from class etomica.potential.Potential

space

Fields inherited from class etomica.potential.Potential1

boundary

Constructor Summary

Constructors

Constructor	Description
P1Tether(Box box, ISpecies species, Space _space)

Method Summary

Modifier and Type	Method	Description
double	energy(IAtomList atoms)	Returns the interaction energy between the given atoms.
double	getEpsilon()
Vector[]	gradient(IAtomList atoms)	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 atoms, Tensor pressureTensor)	Returns the same gradient as gradient(AtomSet) and also adds in the contribution of the AtomSet to the pressureTensor.
Vector	makeAgent(IAtom a, Box agentBox)	Returns an agent for the given Atom.
void	releaseAgent(Vector agent, IAtom atom, Box agentBox)	This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements.
void	setEpsilon(double newEpsilon)
double	virial(IAtomList atoms)

Methods inherited from interface etomica.potential.IPotential

getRange, nBody, setBox

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, setBox

Field Detail

agentManager

protected final AtomLeafAgentManager<Vector> agentManager

species

protected final ISpecies species

work

protected final Vector work

gradient

protected final Vector[] gradient

epsilon

protected double epsilon

Constructor Detail

P1Tether

public P1Tether(Box box,
                ISpecies species,
                Space _space)

Method Detail

setEpsilon

public void setEpsilon(double newEpsilon)

getEpsilon

public double getEpsilon()

energy

public double energy(IAtomList atoms)

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

gradient

public Vector[] gradient(IAtomList atoms)

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 atoms,
                         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

virial

public double virial(IAtomList atoms)

Specified by:

virial in interface PotentialSoft

makeAgent

public Vector makeAgent(IAtom a,
                        Box agentBox)

Description copied from interface: AtomLeafAgentManager.AgentSource

Returns an agent for the given Atom. The agentBox is provided for convenience for agent sources that handle multiple boxes.

Specified by:

makeAgent in interface AtomLeafAgentManager.AgentSource<Vector>

agentBox - TODO

releaseAgent

public void releaseAgent(Vector agent,
                         IAtom atom,
                         Box agentBox)

Description copied from interface: AtomLeafAgentManager.AgentSource

This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements. The agentBox is provided for convenience for agent sources that handle multiple boxes.

Specified by:

releaseAgent in interface AtomLeafAgentManager.AgentSource<Vector>