SimOverlapSoftSphere

java.lang.Object
- etomica.simulation.Simulation
- - etomica.normalmode.SimOverlapSoftSphere

All Implemented Interfaces:

ISimulation
```
public class SimOverlapSoftSphere
extends Simulation
```
Simulation to run sampling with the hard sphere potential, but measuring the harmonic potential based on normal mode data from a previous simulation. The original Bennett's Overlapping Sampling Simulation - used to check for the computation time

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class SimOverlapSoftSphere.SimOverlapParam
Inner class for parameters understood by the HSMD3D constructor

Nested Classes
Modifier and Type	Class and Description
`static class`	`SimOverlapSoftSphere.SimOverlapParam` Inner class for parameters understood by the HSMD3D constructor

Field Summary

Fields
Modifier and Type	Field and Description
`DataPump[]`	`accumulatorPumps`
`AccumulatorVirialOverlapSingleAverage[]`	`accumulators`
`ActivityIntegrate`	`activityIntegrate`
`protected MCMoveAtomCoupled`	`atomMove`
`Basis`	`basis`
`Boundary`	`boundaryHarmonic`
`Boundary`	`boundaryTarget`
`IBox`	`boxHarmonic`
`IBox`	`boxTarget`
`DataSourceVirialOverlap`	`dsvo`
`java.lang.String`	`fname`
`etomica.overlap.IntegratorOverlap`	`integratorOverlap`
`IntegratorBox[]`	`integrators`
`protected double`	`latticeEnergy`
`protected MeterHarmonicEnergy`	`meterHarmonicEnergy`
`IEtomicaDataSource[]`	`meters`
`protected MCMoveHarmonic`	`move`
`int[]`	`nCells`
`NormalModes`	`normalModes`
`protected PotentialMaster`	`potentialMasterTarget`
`Primitive`	`primitive`
`Primitive`	`primitiveUnitCell`
`double`	`refPref`

Fields inherited from class etomica.simulation.Simulation
eventManager, random, seeds, space

Constructor Summary

Constructors
Constructor and Description
`SimOverlapSoftSphere(Space _space, int numAtoms, double density, double temperature, java.lang.String filename, double harmonicFudge, int exponent)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`equilibrate(java.lang.String fileName, long initSteps)`
`void`	`initRefPref(java.lang.String fileName, long initSteps)`
`static void`	`main(java.lang.String[] args)`
`void`	`setAccumulator(AccumulatorVirialOverlapSingleAverage newAccumulator, int iBox)`
`void`	`setRefPref(double newRefPref)`
`void`	`setRefPref(double refPrefCenter, double span)`

Methods inherited from class etomica.simulation.Simulation
addBox, addSpecies, atomTypeAddedNotify, atomTypeRemovedNotify, getBox, getBoxCount, getController, getEventManager, getIntegrator, getRandom, getRandomSeeds, getSpace, getSpecies, getSpeciesCount, makeUniqueElementSymbol, removeBox, removeSpecies, setRandom

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

Field Detail

integratorOverlap

public etomica.overlap.IntegratorOverlap integratorOverlap

dsvo
```
public DataSourceVirialOverlap dsvo
```

integrators
```
public IntegratorBox[] integrators
```

activityIntegrate

public ActivityIntegrate activityIntegrate

boxTarget
```
public IBox boxTarget
```

boxHarmonic
```
public IBox boxHarmonic
```

boundaryTarget
```
public Boundary boundaryTarget
```

boundaryHarmonic
```
public Boundary boundaryHarmonic
```

nCells
```
public int[] nCells
```

basis
```
public Basis basis
```

normalModes
```
public NormalModes normalModes
```

primitive
```
public Primitive primitive
```

primitiveUnitCell
```
public Primitive primitiveUnitCell
```

refPref
```
public double refPref
```

accumulators

public AccumulatorVirialOverlapSingleAverage[] accumulators

accumulatorPumps
```
public DataPump[] accumulatorPumps
```

meters
```
public IEtomicaDataSource[] meters
```

fname
```
public java.lang.String fname
```

move
```
protected MCMoveHarmonic move
```

atomMove
```
protected MCMoveAtomCoupled atomMove
```

potentialMasterTarget

protected PotentialMaster potentialMasterTarget

meterHarmonicEnergy

protected MeterHarmonicEnergy meterHarmonicEnergy

latticeEnergy
```
protected double latticeEnergy
```

Constructor Detail

SimOverlapSoftSphere

public SimOverlapSoftSphere(Space _space,
                            int numAtoms,
                            double density,
                            double temperature,
                            java.lang.String filename,
                            double harmonicFudge,
                            int exponent)

Method Detail

setRefPref

public void setRefPref(double refPrefCenter,
                       double span)

setAccumulator

public void setAccumulator(AccumulatorVirialOverlapSingleAverage newAccumulator,
                           int iBox)

setRefPref

public void setRefPref(double newRefPref)

initRefPref

public void initRefPref(java.lang.String fileName,
                        long initSteps)

equilibrate

public void equilibrate(java.lang.String fileName,
                        long initSteps)

main
```
public static void main(java.lang.String[] args)
```
Parameters:

args - filename containing simulation parameters

See Also:

SimOverlapSoftSphere.SimOverlapParam

Class SimOverlapSoftSphere

Nested Class Summary

Field Summary

Fields inherited from class etomica.simulation.Simulation

Constructor Summary

Method Summary

Methods inherited from class etomica.simulation.Simulation

Methods inherited from class java.lang.Object

Field Detail

integratorOverlap

dsvo

integrators

activityIntegrate

boxTarget

boxHarmonic

boundaryTarget

boundaryHarmonic

nCells

basis

normalModes

primitive

primitiveUnitCell

refPref

accumulators

accumulatorPumps

meters

fname

move

atomMove

potentialMasterTarget

meterHarmonicEnergy

latticeEnergy

Constructor Detail

SimOverlapSoftSphere

Method Detail

setRefPref

setAccumulator

setRefPref

initRefPref

equilibrate

main