Package etomica.potential

Class PotentialGroup

java.lang.Object

etomica.potential.PotentialMolecular

etomica.potential.PotentialGroup

All Implemented Interfaces:

IPotential, IPotentialMolecular

Direct Known Subclasses:

P2AceticAcidTwoSite, P2HardAssociationRefAceticAcidTwoSite, PotentialGroup3PI, PotentialGroupNbr, PotentialGroupPI, PotentialGroupSoft

public class PotentialGroup
extends PotentialMolecular

Collection of potentials that act between the atoms contained in one or more groups of atoms. This group iterates over all such atom-groups assigned to it. For each group it iterates over the potentials it contains, instructing these sub-potentials to perform their calculations over the atoms relevant to them in the groups.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected static class	PotentialGroup.PotentialLinker

Field Summary

Fields

Modifier and Type	Field	Description
protected Box	box
protected NeighborCriterion	criterion
protected PotentialGroup.PotentialLinker	first
protected PotentialMaster	potentialMaster

Fields inherited from class etomica.potential.PotentialMolecular

nBody, space

Constructor Summary

Constructors

Constructor	Description
PotentialGroup(int nBody)	Makes a potential group defined on the position of nBody atom or atom groups.
PotentialGroup(int nBody, Space space)

Method Summary

Modifier and Type	Method	Description
void	addPotential(IPotentialAtomic potential, AtomType[] types)	Adds the given potential and sets it up to apply to the atoms in the basis having the given types.
void	addPotential(IPotentialAtomic potential, AtomsetIteratorBasisDependent iterator)	Adds the given potential to this group, defining it to apply to the atoms provided by the given basis-dependent iterator.
protected void	addPotential(IPotentialAtomic potential, AtomsetIteratorBasisDependent iterator, AtomType[] types)
void	calculate(MoleculesetIterator iterator, IteratorDirective.Direction direction, IAtom targetAtom, PotentialCalculation pc)	Performs the specified calculation over the iterates given by the iterator, using the directive to set up the iterators for the sub-potentials of this group.
boolean	contains(IPotentialAtomic potential)	Indicates if a given potential is a sub-potential of this group.
double	energy(IMoleculeList basisAtoms)	Returns the interaction energy between the given molecules.
AtomType[]	getAtomTypes(IPotential potential)	Returns the AtomTypes that the given potential applies to if the given potential is within this potential group.
IPotentialAtomic[]	getPotentials()
double	getRange()	Returns the maximum of the range of all potentials in the group.
boolean	isEnabled(IPotentialAtomic potential)	Returns true if the potential is in this group and has not been disabled via a previous call to setEnabled; returns false otherwise.
boolean	removePotential(IPotentialAtomic potential)	Removes given potential from the group.
void	setBox(Box box)	Informs the potential of the box on which it acts.
void	setEnabled(IPotentialAtomic potential, boolean enabled)	Indicates that the specified potential should not contribute to potential calculations.
void	setPotentialMaster(PotentialMaster newPotentialMaster)

Methods inherited from class java.lang.Object

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

Methods inherited from class etomica.potential.PotentialMolecular

nBody

Field Detail

first

protected PotentialGroup.PotentialLinker first

box

protected Box box

potentialMaster

protected PotentialMaster potentialMaster

criterion

protected NeighborCriterion criterion

Constructor Detail

PotentialGroup

public PotentialGroup(int nBody)

Makes a potential group defined on the position of nBody atom or atom groups. This constructor should only be called by the PotentialMaster. Use potentialMaster.makePotentialGroup method to create PotentialGroups.

PotentialGroup

public PotentialGroup(int nBody,
                      Space space)

Method Detail

setPotentialMaster

public void setPotentialMaster(PotentialMaster newPotentialMaster)

contains

public boolean contains(IPotentialAtomic potential)

Indicates if a given potential is a sub-potential of this group.

Parameters:

potential - the potential in question

Returns:

boolean true if potential has been added to this group

addPotential

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

Adds the given potential and sets it up to apply to the atoms in the basis having the given types. Another addPotential method should be used if iteration is not based on atom types. Length of types array must not exceed the order of the potential (as given by the nBody method, and set in the constructor).
If length of types array is 1, this must be a one-body potential and iteration is done over the atoms of the basis having the given type. If types is of length 2 and this is a one-body potential, pairs are formed from atoms in the (single) basis having the two given types (which might be the same); if this is a two-body potential, pairs are formed from the first-type atoms taken from the first basis atom, with the second-type atoms taken from the second basis.

addPotential

public void addPotential(IPotentialAtomic potential,
                         AtomsetIteratorBasisDependent iterator)

Adds the given potential to this group, defining it to apply to the atoms provided by the given basis-dependent iterator.

addPotential

protected void addPotential(IPotentialAtomic potential,
                            AtomsetIteratorBasisDependent iterator,
                            AtomType[] types)

getAtomTypes

public AtomType[] getAtomTypes(IPotential potential)

Returns the AtomTypes that the given potential applies to if the given potential is within this potential group. If the potential is not within this group or does not apply to specific AtomTypes, null is returned.

energy

public double energy(IMoleculeList basisAtoms)

Description copied from class: PotentialMolecular

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

Specified by:

energy in interface IPotentialMolecular

Specified by:

energy in class PotentialMolecular

getRange

public double getRange()

Returns the maximum of the range of all potentials in the group.

Specified by:

getRange in interface IPotential

Specified by:

getRange in class PotentialMolecular

removePotential

public boolean removePotential(IPotentialAtomic potential)

Removes given potential from the group. No error is generated if potential is not in group. Returns true if the given Potential was found and removed.

calculate

public void calculate(MoleculesetIterator iterator,
                      IteratorDirective.Direction direction,
                      IAtom targetAtom,
                      PotentialCalculation pc)

Performs the specified calculation over the iterates given by the iterator, using the directive to set up the iterators for the sub-potentials of this group.

setBox

public void setBox(Box box)

Description copied from class: PotentialMolecular

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

Specified by:

setBox in class PotentialMolecular

setEnabled

public void setEnabled(IPotentialAtomic potential,
                       boolean enabled)

Indicates that the specified potential should not contribute to potential calculations. If potential is not in this group, no action is taken.

isEnabled

public boolean isEnabled(IPotentialAtomic potential)

Returns true if the potential is in this group and has not been disabled via a previous call to setEnabled; returns false otherwise.

getPotentials

public IPotentialAtomic[] getPotentials()