Package etomica.potential

Class PotentialMasterMonatomic

java.lang.Object

etomica.potential.PotentialMaster

etomica.potential.PotentialMasterMonatomic

All Implemented Interfaces:

AtomTypeAgentManager.AgentSource<PotentialArrayByType>

public class PotentialMasterMonatomic
extends PotentialMaster
implements AtomTypeAgentManager.AgentSource<PotentialArrayByType>

PotentialMaster suitable for monatomic molecules without using neighbor lists and avoids PotentialMaster's performance problems. Potentials should be added via the method taking IAtomTypeLeafs. This currently only handles 1 and 2 body potentials. This class assumes that only one 2-body potential applies to any given pair of leaf atoms, but more than one 1-body potential may apply to any atom. PotentialGroups are not created to hold the leaf potentials. Calling addPotential with an ISpecies array will fail.

Nested Class Summary

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

PotentialMaster.AtomIterator0, PotentialMaster.MoleculeIterator0, PotentialMaster.PotentialLinker

Field Summary

Fields

Modifier and Type	Field	Description
protected IPotential[]	allPotentials
protected AtomPair	atomPair
protected AtomSetSinglet	atomSetSinglet
protected AtomTypeAgentManager<PotentialArrayByType>	potentialAgentManager

Fields inherited from class etomica.potential.PotentialMaster

enabled, isPotentialHard, iteratorFactory, lrcMaster, potentialList

Constructor Summary

Constructors

Constructor	Description
PotentialMasterMonatomic(Simulation sim)

Method Summary

Modifier and Type	Method	Description
void	addPotential(IPotentialAtomic potential, AtomType[] atomTypes)	Indicates to the PotentialMaster that the given potential should apply to the specified atom types.
void	addPotential(IPotentialMolecular potential, ISpecies[] species)	Indicates to the PotentialMaster that the given potential should apply to the specified species.
protected void	calculate(IAtom leafAtom, IAtomList leafList, int leafIndex, PotentialArrayByType potentialArray, IteratorDirective.Direction direction, PotentialCalculation pc)
void	calculate(Box box, IteratorDirective id, PotentialCalculation pc)	Performs the given PotentialCalculation on the atoms of the given Box.
PotentialArrayByType	makeAgent(AtomType type)	Returns an agent for the given AtomType.
void	releaseAgent(PotentialArrayByType agent, AtomType type)	This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements.
void	removePotential(IPotentialAtomic potential)	Removes given potential from the group.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from class etomica.potential.PotentialMaster

addPotential, getPotential, getPotentials, getSpecies, isEnabled, isEnabled, isEnabled, isPotentialHard, lrcMaster, makePotentialGroup, potentialAddedNotify, removePotential, setEnabled, setEnabled, setEnabled, setPotentialHard

Field Detail

potentialAgentManager

protected final AtomTypeAgentManager<PotentialArrayByType> potentialAgentManager

atomSetSinglet

protected final AtomSetSinglet atomSetSinglet

atomPair

protected final AtomPair atomPair

allPotentials

protected IPotential[] allPotentials

Constructor Detail

PotentialMasterMonatomic

public PotentialMasterMonatomic(Simulation sim)

Method Detail

addPotential

public void addPotential(IPotentialMolecular potential,
                         ISpecies[] species)

Description copied from class: PotentialMaster

Indicates to the PotentialMaster that the given potential should apply to the specified species. Exception is thrown if the potential.nBody() value is different from the length of the species array. Thus, for example, if giving a 2-body potential, then the array should contain exactly two species; the species may refer to the same instance (appropriate for an intra-species potential, defining the interactions between molecules of the same species).

Overrides:

addPotential in class PotentialMaster

addPotential

public void addPotential(IPotentialAtomic potential,
                         AtomType[] atomTypes)

Description copied from class: PotentialMaster

Indicates to the PotentialMaster that the given potential should apply to the specified atom types. The potential is assumed to be intermolecular. The given types should not include any type which is the descendent of another. Potential group hierarchy will be constructed as needed above the level of the given atom types.

Overrides:

addPotential in class PotentialMaster

removePotential

public void removePotential(IPotentialAtomic potential)

Description copied from class: PotentialMaster

Removes given potential from the group. No error is generated if potential is not in group.

Overrides:

removePotential in class PotentialMaster

calculate

public void calculate(Box box,
                      IteratorDirective id,
                      PotentialCalculation pc)

Description copied from class: PotentialMaster

Performs the given PotentialCalculation on the atoms of the given Box. Sets the box for all molecule iterators and potentials, sets target and direction for iterators as specified by given IteratorDirective, and applies doCalculation of given PotentialCalculation with the iterators and potentials.

Overrides:

calculate in class PotentialMaster

calculate

protected void calculate(IAtom leafAtom,
                         IAtomList leafList,
                         int leafIndex,
                         PotentialArrayByType potentialArray,
                         IteratorDirective.Direction direction,
                         PotentialCalculation pc)

makeAgent

public PotentialArrayByType makeAgent(AtomType type)

Description copied from interface: AtomTypeAgentManager.AgentSource

Returns an agent for the given AtomType.

Specified by:

makeAgent in interface AtomTypeAgentManager.AgentSource<PotentialArrayByType>

releaseAgent

public void releaseAgent(PotentialArrayByType agent,
                         AtomType type)

Description copied from interface: AtomTypeAgentManager.AgentSource

This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements.

Specified by:

releaseAgent in interface AtomTypeAgentManager.AgentSource<PotentialArrayByType>