SimOverlapSoftSphereHCP

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

```
public class SimOverlapSoftSphereHCP
extends Simulation
```
Simulation to run sampling with the soft-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 Description

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

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

Field Summary

Fields
Modifier and Type	Field	Description
`DataPump[]`	`accumulatorPumps`
`AccumulatorVirialOverlapSingleAverage[]`	`accumulators`
`protected MCMoveAtomCoupled`	`atomMove`
`Basis`	`basis`
`Boundary`	`boundaryHarmonic`
`Boundary`	`boundaryTarget`
`Box`	`boxHarmonic`
`Box`	`boxTarget`
`DataSourceVirialOverlap`	`dsvo`
`java.lang.String`	`fname`
`IntegratorOverlap`	`integratorOverlap`
`IntegratorBox[]`	`integrators`
`protected double`	`latticeEnergy`
`protected MeterHarmonicEnergy`	`meterHarmonicEnergy`
`IDataSource[]`	`meters`
`protected MCMoveHarmonic`	`move`
`int[]`	`nCells`
`NormalModes`	`normalModes`
`protected P1Constraint`	`p1Constraint`
`protected PotentialMaster`	`potentialMasterTarget`
`Primitive`	`primitive`
`Primitive`	`primitiveUnitCell`
`double`	`refPref`

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

Constructor Summary

Constructors
Constructor	Description
`SimOverlapSoftSphereHCP(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	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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from class etomica.simulation.Simulation
addBox, addSpecies, box, getBox, getBoxCount, getBoxes, getController, getEventManager, getIntegrator, getRandom, getRandomSeeds, getSpace, getSpecies, getSpeciesCount, getSpeciesList, makeBox, makeBox, makeUniqueElementSymbol, removeBox, setRandom, species

Field Detail

integratorOverlap

public IntegratorOverlap integratorOverlap

dsvo
```
public DataSourceVirialOverlap dsvo
```

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

boxTarget
```
public Box boxTarget
```

boxHarmonic
```
public Box 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 IDataSource[] 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
```

p1Constraint
```
protected P1Constraint p1Constraint
```

Constructor Detail

SimOverlapSoftSphereHCP

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

Method Detail

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

args - filename containing simulation parameters

See Also:

SimOverlapSoftSphereHCP.SimOverlapParam

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)

Class SimOverlapSoftSphereHCP

Nested Class Summary

Field Summary

Fields inherited from class etomica.simulation.Simulation

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from class etomica.simulation.Simulation

Field Detail

integratorOverlap

dsvo

integrators

boxTarget

boxHarmonic

boundaryTarget

boundaryHarmonic

nCells

basis

normalModes

primitive

primitiveUnitCell

refPref

accumulators

accumulatorPumps

meters

fname

move

atomMove

potentialMasterTarget

meterHarmonicEnergy

latticeEnergy

p1Constraint

Constructor Detail

SimOverlapSoftSphereHCP

Method Detail

main

setRefPref

setAccumulator

setRefPref

initRefPref

equilibrate