Package etomica.potential

Class PotentialMaster

java.lang.Object

etomica.potential.PotentialMaster

Direct Known Subclasses:

PotentialMasterMonatomic, PotentialMasterNbr, PotentialMasterNbrMolecular

public class PotentialMaster
extends java.lang.Object

Manager of all potentials in simulation. Most calls to compute the energy or other potential calculations begin with the calculate method of this class. It then passes the calculation on to the contained potentials.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PotentialMaster.AtomIterator0
static class	PotentialMaster.MoleculeIterator0
static class	PotentialMaster.PotentialLinker

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	enabled
protected boolean	isPotentialHard
protected IteratorFactory	iteratorFactory
protected PotentialMasterLrc	lrcMaster
protected java.util.List<PotentialMaster.PotentialLinker>	potentialList

Constructor Summary

Constructors

Constructor	Description
PotentialMaster()
PotentialMaster(IteratorFactory iteratorFactory)

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, MoleculesetIteratorPDT iterator, ISpecies[] types)
void	addPotential(IPotentialMolecular potential, ISpecies[] species)	Indicates to the PotentialMaster that the given potential should apply to the specified species.
void	calculate(Box box, IteratorDirective id, PotentialCalculation pc)	Performs the given PotentialCalculation on the atoms of the given Box.
PotentialGroup	getPotential(ISpecies[] types)	Returns the potential that applies to the specified types, or null of no existing potential applies.
IPotentialMolecular[]	getPotentials()	Returns an array containing all molecular Potentials.
ISpecies[]	getSpecies(IPotentialMolecular potential)
boolean	isEnabled()
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	isEnabled(IPotentialMolecular 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	isPotentialHard()	Flag indicating indicating that the only energetic interactions are based on hard potentials, which prohibit overlap but otherwise have zero energy.
PotentialMasterLrc	lrcMaster()	Returns the object that oversees the long-range correction zero-body potentials.
PotentialGroup	makePotentialGroup(int nBody)	Returns an nBody PotentialGroup appropriate for this type of PotentialMaster.
void	potentialAddedNotify(IPotentialAtomic subPotential, PotentialGroup pGroup)	Notifies the PotentialMaster that the sub-potential has been added to the given PotentialGroup, which is associated (but not necessarily held by) this PotentialMaster.
void	removePotential(IPotentialAtomic potential)	Removes given potential from the group.
void	removePotential(IPotentialMolecular potential)	Removes given potential from the group.
void	setEnabled(boolean enabled)	Permits enabling/disabling of all potentials.
void	setEnabled(IPotentialAtomic potential, boolean enabled)	Indicates that the specified potential should not contribute to potential calculations.
void	setEnabled(IPotentialMolecular potential, boolean enabled)	Indicates that the specified potential should not contribute to potential calculations.
void	setPotentialHard(boolean potentialHard)

Methods inherited from class java.lang.Object

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

Field Detail

lrcMaster

protected PotentialMasterLrc lrcMaster

iteratorFactory

protected IteratorFactory iteratorFactory

potentialList

protected java.util.List<PotentialMaster.PotentialLinker> potentialList

enabled

protected boolean enabled

isPotentialHard

protected boolean isPotentialHard

Constructor Detail

PotentialMaster

public PotentialMaster()

PotentialMaster

public PotentialMaster(IteratorFactory iteratorFactory)

Method Detail

lrcMaster

public PotentialMasterLrc lrcMaster()

Returns the object that oversees the long-range correction zero-body potentials.

makePotentialGroup

public PotentialGroup makePotentialGroup(int nBody)

Returns an nBody PotentialGroup appropriate for this type of PotentialMaster.

calculate

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

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.

addPotential

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

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).

addPotential

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

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.

potentialAddedNotify

public void potentialAddedNotify(IPotentialAtomic subPotential,
                                 PotentialGroup pGroup)

Notifies the PotentialMaster that the sub-potential has been added to the given PotentialGroup, which is associated (but not necessarily held by) this PotentialMaster. This method is called by PotentialGroup and should not be called in other circumstances.

getPotential

public PotentialGroup getPotential(ISpecies[] types)

Returns the potential that applies to the specified types, or null of no existing potential applies.

getSpecies

public ISpecies[] getSpecies(IPotentialMolecular potential)

addPotential

public void addPotential(IPotentialMolecular potential,
                         MoleculesetIteratorPDT iterator,
                         ISpecies[] types)

removePotential

public void removePotential(IPotentialMolecular potential)

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

removePotential

public void removePotential(IPotentialAtomic potential)

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

isEnabled

public boolean isEnabled()

Returns:

Returns enabled flag.

setEnabled

public void setEnabled(boolean enabled)

Permits enabling/disabling of all potentials. Default is enabled (true).

Parameters:

enabled - flags if potentials are enabled.

setEnabled

public void setEnabled(IPotentialMolecular 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.

isPotentialHard

public boolean isPotentialHard()

Flag indicating indicating that the only energetic interactions are based on hard potentials, which prohibit overlap but otherwise have zero energy. If this flag is true, then it is assumed that the energy of an equilibriated configuration (e.g., not an initial configuration; not a configuration generated by an unprocessed MC trial; etc.) is zero, and thus it need not be computed. Value is established solely via setPotentialHard method, and is not determined by any analysis of potentials in simulation. Default is false.

Returns:

true if simulations elements can assume an equilibrated configuration has zero energy

setPotentialHard

public void setPotentialHard(boolean potentialHard)

Parameters:

potentialHard - new value of field indicating that simulation involves only hard potentials. No check is made to ensure that they are indeed only hard potentials.

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.

isEnabled

public boolean isEnabled(IPotentialMolecular 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 IPotentialMolecular[] getPotentials()

Returns an array containing all molecular Potentials.