Package etomica.simulation

Class Simulation

java.lang.Object

etomica.simulation.Simulation

Direct Known Subclasses:

Adsorption, AshtonWildingLJ, AshtonWildingOsmoticVirial, AshtonWildingVirial, Catalysis, CH4NVT, ChainEquilibriumSim, ChainHSMD3D, ClathrateHarmonicFE, ColloidSim, DCVGCMD, DCVGCMD, DHS_NVT, DHS_NVT, DimerApproach, DipoleBox, DipoleBoxMatrix, DLJ_NVT_1site, DLJ_NVT_1site, Droplet, DropletAtomic, EFSTungsten, FindBetaN2AngleFromParameter, FreeRadicalPolymerizationSim, GCRestrictedGibbsHS, GCWidomInsertHS, GEMCWithRotation, HarmonicAlphaNitrogenModel, HarmonicAlphaNitrogenModelDecomposed, HarmonicAlphaNitrogenModelLatticeSum, HarmonicAlphaNitrogenModelPairMolecule, HarmonicAlphaNitrogenModelPairMoleculeSequential, HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2, HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS, HarmonicAlphaNitrogenModelPairMoleculeSequentialLS, HarmonicBetaNitrogenModel, HarmonicBetaNitrogenModelDecomposed, HarmonicBetaNitrogenModelLatticeSum, HarmonicBetaNitrogenModelPairMoleculeSequential, HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS, HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2, HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS, HarmonicBetaNitrogenModelPairMoleculeSequentialLS, HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS, HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS, Heisenberg, Heisenberg3Pair, HeisenbergPair, HessianDB, HSDimerNPT, HSMC2D, HSMD2D, HSMD2D_noNbr, HSMD3D, HSMD3DNoNbr, HSMDCavity, HSMDWidom, HSNPT, HSNPT2DSim, HTTPSoftSphereSim, Insertion, InterfacialSW, Ising, LJMC, LJMC, LJMC, LjMC3D, LJMC3D, LJMC3DDimer, Ljmd, LJMD, LJMD2D, LjMd3D, LJMD3D, LJMD3DNbr, LJmuVT, LJNPT, LJNVT, LJVacancyMin, MappedU, MappedVirialLJ, MappedVirialLJVGr, MaterialFracture, MinimizationBetaNitrogenModel, MinimizationBetaNitrogenModelLS, MinimizationTIP4P, MinimizeBetaNitrogenLatticeParameter, MinimizeBetaNitrogenLatticeParameterFromFile, MinimizeBetaNitrogenLatticeParameterLSFromFile, MinimizeBetaNitrogenTranslationDOF, MinimizeGammaNitrogenLatticeParameter, MinimizeHCP, Mu, Multiharmonic, MultiharmonicMC, MultiharmonicMC, MultiharmonicMC, MultiharmonicMC, NormalModeAnalysisDisplay1D, NormalModeAnalysisDisplay2D, NormalModeAnalysisDisplay3D, NVTWidomInsertLJ, OsmosisSim, PistonCylinder, PolydisperseHS, ProtonDisorderGenerator, ReactionEquilibrium, ReverseOsmosis, ReverseOsmosisWater, Sam, SelfAssemblySim, SimBennet, SimCalcJ, SimCalcS, SimCalcSLJ, SimCalcSMorse, SimCalcSSoftSphere2D, SimCalcSSoftSphereFCC, SimCalcSSoftSphereFCCSuperBox, SimDimerLJadatom, SimDirectBetaN2RP, SimDirectBetaN2RPAngleToNoAngle, SimDirectBetaN2RPInitPert, SimDirectDisorderedAlphaN2RPInitPert, SimEinStep1, SimEinStep1HCP, SimEinStep2, SimEinStep2HCP, SimFe, SimFluidSoftSphere, SimGCPMWaterMCNPT, SimGCPMWaterMCNVT, SimGlass, SimHarmonic, SimHarmonicUmbrella, SimHSMDVacancy, SimIdealGas, SimKMCLJadatom, SimLattice, SimLJ, SimLJHTTISuper, SimLJHTTISuperHCP, SimLJHTTISuperHCP2, SimLJHTTISuperSFMD, SimLJVacancy, SimMappedRdf, SimModesJ, SimOverlap, SimOverlapAlphaN2TP, SimOverlapBetaN2RP, SimOverlapBetaN2RPScaling, SimOverlapBetaN2TP, SimOverlapDisorderedAlphaN2RPScaling, SimOverlapDisorderedAlphaN2TP, SimOverlapLJ, SimOverlapNitrogenModel, SimOverlapSoftSphere, SimOverlapSoftSphereDP, SimOverlapSoftSphereEin, SimOverlapSoftSphereEinHarm, SimOverlapSoftSphereHCP, SimOverlapSoftSphereReweighting, SimOverlapSoftSphereSoftness, SimOverlapSoftSphereSuperBox, SimOverlapSoftSphereTP, SimOverlapSoftSphereTPHCP, SimOverlapSoftSphereTPSlantedBox, SimOverlapSSnxy, SimTarget, SimTargetUmbrella, SimulationAlphaNitrogenModel, SimulationBetaNitrogenModel, SimulationBetaNitrogenModelTest, SimulationGammaNitrogenModel, SimulationRheology, SimulationVirial, SimulationVirialOverlap2, SimUmbrella, SimUmbrellaSoftSphere, SoftSphere3d, StarPolymerMC, StarPolymerMD, Swmd, SWMD2D, SWMD3D, SWVLESim, TestAceticAcidMC3D_NPT, TestEwaldTIP4PWater, TestHSMD3D, TestIGAssociationMC3D_NPT_DoubleSites, TestLammpsLJ, TestLJAssociationMC3D_NPT, TestLJAssociationMC3D_NPT, TestLJAssociationMC3D_NPT_DoubleSites, TestLJAssociationMC3D_NVTOld, TestLJGCMC3D, TestLJMC3D, TestLJMD3D, TestSWChain, TIP4P_NVT, VLESim, VLESim, ZeoliteSimulation

public class Simulation
extends java.lang.Object

The main class that organizes the elements of a molecular simulation. It contains boxes, species, an integrator, a random number generator, and a controller.

Field Summary

Fields

Modifier and Type	Field	Description
protected SimulationEventManager	eventManager
protected IRandom	random
protected int[]	seeds
protected Space	space

Constructor Summary

Constructors

Constructor	Description
Simulation(Space space)	Creates a new simulation using the given space

Method Summary

Modifier and Type	Method	Description
Box	addBox(Box newBox)	Adds a Box to the simulation.
void	addSpecies(ISpecies species)	Adds species to the list of all ISpecies in the simulation, and notifies all Boxes of the addition.
Box	box()	Convenience method to retrieve the first (and typically only) Box in the simulation.
Box	getBox(int index)	Returns one of the simulation Boxes.
int	getBoxCount()
java.util.List<Box>	getBoxes()	Get all boxes in the simulation.
Controller	getController()
SimulationEventManager	getEventManager()
Integrator	getIntegrator()
IRandom	getRandom()
int[]	getRandomSeeds()
Space	getSpace()
ISpecies	getSpecies(int index)	Returns one of the simulation ISpecies.
int	getSpeciesCount()
java.util.List<ISpecies>	getSpeciesList()
Box	makeBox()	Creates a new Box with the default Boundary and adds it to the Simulation.
Box	makeBox(Boundary boundary)	Creates a new Box and adds it to the Simulation.
java.lang.String	makeUniqueElementSymbol(java.lang.String symbolBase)	Method to allow generation of unique string to identify Elements in the Simulation.
void	removeBox(Box oldBox)	Removes a Box to the simulation.
void	setRandom(IRandom newRandom)	Set the simulation's random number generator to the given one.
ISpecies	species()	Convenience method to return the first (and often only) ISpecies in the simulation.

Methods inherited from class java.lang.Object

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

Field Detail

space

protected final Space space

eventManager

protected final SimulationEventManager eventManager

seeds

protected int[] seeds

random

protected IRandom random

Constructor Detail

Simulation

public Simulation(Space space)

Creates a new simulation using the given space

Parameters:

space - the space used to construct Vectors etc.

Method Detail

getRandomSeeds

public int[] getRandomSeeds()

Returns:

the seeds that were used for the random number generator at construction. If the random number generator has been set manually since then, this method returns null.

getBoxes

public final java.util.List<Box> getBoxes()

Get all boxes in the simulation.

Attempts to add or remove boxes from this list will throw UnsupportedOperationException, you must use the addBox and removeBox methods on Simulation.

Returns:

a read-only list of Boxes

box

public final Box box()

Convenience method to retrieve the first (and typically only) Box in the simulation.

Returns:

the Box at index 0

addBox

public final Box addBox(Box newBox)

Adds a Box to the simulation. This method may not be called until all Species have been added to the simulation.

Parameters:

newBox - the Box being added.

Throws:

java.lang.IllegalArgumentException - if newBox was already added to the simulation.

makeBox

public Box makeBox()

Creates a new Box with the default Boundary and adds it to the Simulation.

Returns:

the new Box.

makeBox

public Box makeBox(Boundary boundary)

Creates a new Box and adds it to the Simulation.

Parameters:

boundary - the boundary to use when constructing the Box.

Returns:

the new Box.

removeBox

public final void removeBox(Box oldBox)

Removes a Box to the simulation.

Parameters:

oldBox - the Box being removed.

Throws:

java.lang.IllegalArgumentException - if oldBox was not previously added to the simulation.

getBox

public final Box getBox(int index)

Returns one of the simulation Boxes. Boxes are numbered in the order that they are added, beginning with 0.

Parameters:

index - specifies the Box to be returned.

Returns:

the specified Box.

getBoxCount

public final int getBoxCount()

Returns:

the number of boxes that have been added to the Simulation.

getController

public final Controller getController()

Returns:

the Controller used to run the simulation's Actions and Activities.

getSpace

public final Space getSpace()

Returns:

the Space that was specified in the constructor.

getRandom

public final IRandom getRandom()

Returns:

the Simulation's random number generator.

setRandom

public void setRandom(IRandom newRandom)

Set the simulation's random number generator to the given one.

Parameters:

newRandom - the new random number generator.

getEventManager

public final SimulationEventManager getEventManager()

Returns:

the Simulation's event manager, which fires events for Boxes and Species being added and removed.

addSpecies

public final void addSpecies(ISpecies species)

Adds species to the list of all ISpecies in the simulation, and notifies all Boxes of the addition.

Parameters:

species - the Species being added.

Throws:

java.lang.IllegalArgumentException - if species was already added.

java.lang.IllegalStateException - if a Box has already been added to the simulation.

getSpeciesCount

public final int getSpeciesCount()

Returns:

the number of Species in the Simulation.

getSpecies

public final ISpecies getSpecies(int index)

Returns one of the simulation ISpecies. ISpecies are numbered in the order that they are added, beginning with 0.

Parameters:

index - specifies the ISpecies to be returned.

Returns:

the specified ISpecies.

getSpeciesList

public final java.util.List<ISpecies> getSpeciesList()

species

public final ISpecies species()

Convenience method to return the first (and often only) ISpecies in the simulation.

Returns:

the ISpecies at index 0

makeUniqueElementSymbol

public java.lang.String makeUniqueElementSymbol(java.lang.String symbolBase)

Method to allow generation of unique string to identify Elements in the Simulation.

Parameters:

symbolBase - the base string.

Returns:

an Element symbol starting with symbolBase that does not yet exist in the Simulation. Return values will be like "base0, base1, base2..."

getIntegrator

public Integrator getIntegrator()

Returns:

the Simulation's primary integrator. If the controller holds multiple integrators, the first is returned. If the first integrator holds sub-integrators, the top-level integrator is still returned. This method assumes the controller holds an ActivityIntegrate. Returns null if no integrator is found.