Simulation

java.lang.Object
- etomica.simulation.Simulation

All Implemented Interfaces:

ISimulation

Direct Known Subclasses:

ChainHSMD3D, GEMCWithRotation, HsMc2d, HSMD2D, HSMD2D_noNbr, HSMD3D, HSMD3DNoNbr, LjMd2D, LjMd3D, SoftSphere3d, SwMd2D, SWMD3D, TestEwaldTIP4PWater, TestHSMD3D, TestLJMC3D, TestSWChain
```
public class Simulation
extends java.lang.Object
implements ISimulation
```
The main class that organizes the elements of a molecular simulation. Holds a single Space instance that is referenced in many places to obtain spatial elements such as vectors and boundaries.

Field Summary

Fields
Modifier and Type Field and Description

protected SimulationEventManager eventManager

protected IRandom random

protected int[] seeds

protected ISpace space

Fields
Modifier and Type	Field and Description
`protected SimulationEventManager`	`eventManager`
`protected IRandom`	`random`
`protected int[]`	`seeds`
`protected ISpace`	`space`

Constructor Summary

Constructors
Constructor and Description

Simulation(ISpace space)
Creates a new simulation using the given space

Constructors
Constructor and Description
`Simulation(ISpace space)` Creates a new simulation using the given space

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addBox(IBox newBox)` Adds a Box to the simulation.
`void`	`addSpecies(ISpecies species)` Adds species to the list of all ISpecies in the simulation, and adds notifies all IBoxes of the new ISpecies.
`protected void`	`atomTypeAddedNotify(IAtomType newChildType)`
`protected void`	`atomTypeRemovedNotify(IAtomType removedType)`
`IBox`	`getBox(int index)` Returns an array of Boxs contained in the Simulation
`int`	`getBoxCount()` Returns number of boxes contained in the Simulation
`Controller`	`getController()` Returns the Controller used to run the simulation's Actions and Activities.
`ISimulationEventManager`	`getEventManager()` Returns the Simulation's event manager, which fires events for Boxes and Species being added and removed.
`IIntegrator`	`getIntegrator()` Returns the Simulation's primary integrator.
`IRandom`	`getRandom()` Returns the Simulation's random number generator.
`int[]`	`getRandomSeeds()` Returns the seeds that were used for the random number generator at construction.
`ISpace`	`getSpace()`
`ISpecies`	`getSpecies(int index)` Returns the Species in the Simulation for the specified index.
`int`	`getSpeciesCount()` Returns the number of Species in the Simulation.
`java.lang.String`	`makeUniqueElementSymbol(java.lang.String symbolBase)` Returns an Element symbol starting with symbolBase that does not yet exist in the Simulation.
`void`	`removeBox(IBox oldBox)` Removes a Box to the simulation.
`void`	`removeSpecies(ISpecies removedSpecies)` Removes the given ISpecies from the ISimulation.
`void`	`setRandom(IRandom newRandom)` Set the simulation's random number generator to the given one.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - space
```
protected final ISpace space
```
  - seeds
```
protected int[] seeds
```
  - eventManager
```
protected final SimulationEventManager eventManager
```
  - random
```
protected IRandom random
```
- Constructor Detail
  - Simulation
```
public Simulation(ISpace space)
```
    Creates a new simulation using the given space
- 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.
  - addBox
```
public final void addBox(IBox newBox)
```
    Description copied from interface: ISimulation
    
    Adds a Box to the simulation. This method should not be called if newBox is already held by the simulation.
    
    Specified by:
    
    addBox in interface ISimulation
  - removeBox
```
public final void removeBox(IBox oldBox)
```
    Description copied from interface: ISimulation
    
    Removes a Box to the simulation. This method should not be called if oldBox is not held by the simulation.
    
    Specified by:
    
    removeBox in interface ISimulation
  - getBox
```
public final IBox getBox(int index)
```
    Returns an array of Boxs contained in the Simulation
    
    Specified by:
    
    getBox in interface ISimulation
  - getBoxCount
```
public int getBoxCount()
```
    Description copied from interface: ISimulation
    
    Returns number of boxes contained in the Simulation
    
    Specified by:
    
    getBoxCount in interface ISimulation
  - getController
```
public Controller getController()
```
    Returns the Controller used to run the simulation's Actions and Activities.
  - getSpace
```
public final ISpace getSpace()
```
    Returns:
    
    the space
  - getRandom
```
public IRandom getRandom()
```
    Description copied from interface: ISimulation
    
    Returns the Simulation's random number generator.
    
    Specified by:
    
    getRandom in interface ISimulation
  - setRandom
```
public void setRandom(IRandom newRandom)
```
    Set the simulation's random number generator to the given one.
  - getEventManager
```
public ISimulationEventManager getEventManager()
```
    Description copied from interface: ISimulation
    
    Returns the Simulation's event manager, which fires events for Boxes and Species being added and removed.
    
    Specified by:
    
    getEventManager in interface ISimulation
  - addSpecies
```
public void addSpecies(ISpecies species)
```
    Description copied from interface: ISimulation
    
    Adds species to the list of all ISpecies in the simulation, and adds notifies all IBoxes of the new ISpecies.
    
    Specified by:
    
    addSpecies in interface ISimulation
  - removeSpecies
```
public void removeSpecies(ISpecies removedSpecies)
```
    Description copied from interface: ISimulation
    
    Removes the given ISpecies from the ISimulation.
    
    Specified by:
    
    removeSpecies in interface ISimulation
  - getSpeciesCount
```
public int getSpeciesCount()
```
    Description copied from interface: ISimulation
    
    Returns the number of Species in the Simulation.
    
    Specified by:
    
    getSpeciesCount in interface ISimulation
  - getSpecies
```
public ISpecies getSpecies(int index)
```
    Description copied from interface: ISimulation
    
    Returns the Species in the Simulation for the specified index.
    
    Specified by:
    
    getSpecies in interface ISimulation
  - atomTypeAddedNotify
```
protected void atomTypeAddedNotify(IAtomType newChildType)
```
  - atomTypeRemovedNotify
```
protected void atomTypeRemovedNotify(IAtomType removedType)
```
  - makeUniqueElementSymbol
```
public java.lang.String makeUniqueElementSymbol(java.lang.String symbolBase)
```
    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 IIntegrator 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 or an ActionIntegrate.
    
    Specified by:
    
    getIntegrator in interface ISimulation

Class Simulation

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

space

seeds

eventManager

random

Constructor Detail

Simulation

Method Detail

getRandomSeeds

addBox

removeBox

getBox

getBoxCount

getController

getSpace

getRandom

setRandom

getEventManager

addSpecies

removeSpecies

getSpeciesCount

getSpecies

atomTypeAddedNotify

atomTypeRemovedNotify

makeUniqueElementSymbol

getIntegrator