Package etomica.normalmode

Class SimOverlapSoftSphereSoftness

java.lang.Object

etomica.simulation.Simulation

etomica.normalmode.SimOverlapSoftSphereSoftness

public class SimOverlapSoftSphereSoftness
extends Simulation

Conduct Bennett's Overlap Sampling to quantify the free-energy difference between soft-sphere model with different softness Soft-Sphere potential: U = epsilon*(sigma/r)^n where n is the exponent, s = 1/n (where s is softness) epsilon and sigma is set to 1

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SimOverlapSoftSphereSoftness.SimOverlapParam	Inner class for parameters understood by the HSMD3D constructor

Field Summary

Fields

Modifier and Type	Field	Description
DataPump[]	accumulatorPumps
AccumulatorVirialOverlapSingleAverage[]	accumulators
protected MCMoveAtomCoupled	atomMoveRef
protected MCMoveAtomCoupled	atomMoveTarg
Basis	basis
Boundary	boundaryRef
Boundary	boundaryTarg
Box	boxRef
Box	boxTarg
DataSourceVirialOverlap	dsvo
java.lang.String	fname
IntegratorOverlap	integratorOverlap
IntegratorBox[]	integrators
protected double	latticeEnergyRef
protected double	latticeEnergyTarg
IDataSource[]	meters
int[]	nCells
protected PotentialMaster	potentialMasterRef
protected PotentialMaster	potentialMasterTarg
Primitive	primitive
Primitive	primitiveUnitCell
double	refPref

Fields inherited from class etomica.simulation.Simulation

eventManager, random, seeds, space

Constructor Summary

Constructors

Constructor	Description
SimOverlapSoftSphereSoftness(Space _space, int numAtoms, double density, double temperature, double harmonicFudge, int[] exponent, double alpha, double alphaSpan, int numAlpha)

Method Summary

Modifier and Type	Method	Description
void	equilibrate(long initSteps)
static void	main(java.lang.String[] args)
void	setAccumulator(AccumulatorVirialOverlapSingleAverage newAccumulator, int iBox)
void	setRefPref(double alpha, double alphaSpan)

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

boxTarg

public Box boxTarg

boxRef

public Box boxRef

boundaryTarg

public Boundary boundaryTarg

boundaryRef

public Boundary boundaryRef

nCells

public int[] nCells

basis

public Basis basis

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

atomMoveTarg

protected MCMoveAtomCoupled atomMoveTarg

atomMoveRef

protected MCMoveAtomCoupled atomMoveRef

potentialMasterTarg

protected PotentialMaster potentialMasterTarg

potentialMasterRef

protected PotentialMaster potentialMasterRef

latticeEnergyTarg

protected double latticeEnergyTarg

latticeEnergyRef

protected double latticeEnergyRef

Constructor Detail

SimOverlapSoftSphereSoftness

public SimOverlapSoftSphereSoftness(Space _space,
                                    int numAtoms,
                                    double density,
                                    double temperature,
                                    double harmonicFudge,
                                    int[] exponent,
                                    double alpha,
                                    double alphaSpan,
                                    int numAlpha)

Method Detail

main

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

Parameters:

args - filename containing simulation parameters

See Also:

SimOverlapSoftSphereSoftness.SimOverlapParam

setRefPref

public void setRefPref(double alpha,
                       double alphaSpan)

setAccumulator

public void setAccumulator(AccumulatorVirialOverlapSingleAverage newAccumulator,
                           int iBox)

equilibrate

public void equilibrate(long initSteps)