Package etomica.models.nitrogen

Class SimOverlapNitrogenModel

java.lang.Object

etomica.simulation.Simulation

etomica.models.nitrogen.SimOverlapNitrogenModel

public class SimOverlapNitrogenModel
extends Simulation

Simulation to run sampling with the nitrogen model to find the free energy difference between the harmonic reference system and the target system The Bennett's Overlapping Sampling Simulation - used to check for the computation time

Nested Class Summary

Nested Classes

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

Field Summary

Fields

Modifier and Type	Field	Description
DataPump[]	accumulatorPumps
AccumulatorVirialOverlapSingleAverage[]	accumulators
Boundary	boundaryHarmonic
Boundary	boundaryTarget
Box	boxHarmonic
Box	boxTarget
DataSourceVirialOverlap	dsvo
java.lang.String	fname
protected IntegratorMC	integratorHarmonic
IntegratorOverlap	integratorOverlap
IntegratorBox[]	integrators
protected IntegratorMC	integratorTarget
protected double	latticeEnergy
protected MeterHarmonicEnergy	meterHarmonicEnergy
IDataSource[]	meters
protected MCMoveHarmonic	moveHarmonic
protected int	nCell
NormalModes	normalModes
protected PotentialMaster	potentialMasterTarget
Primitive	primitive
Primitive	primitiveUnitCell
double	refPref
protected SpeciesGeneral	species

Fields inherited from class etomica.simulation.Simulation

eventManager, random, seeds, space

Constructor Summary

Constructors

Constructor	Description
SimOverlapNitrogenModel(Space _space, int numMolecules, double temperature, java.lang.String filename, double scale)

Method Summary

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

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

moveHarmonic

protected MCMoveHarmonic moveHarmonic

potentialMasterTarget

protected PotentialMaster potentialMasterTarget

meterHarmonicEnergy

protected MeterHarmonicEnergy meterHarmonicEnergy

latticeEnergy

protected double latticeEnergy

species

protected SpeciesGeneral species

nCell

protected int nCell

integratorHarmonic

protected IntegratorMC integratorHarmonic

integratorTarget

protected IntegratorMC integratorTarget

Constructor Detail

SimOverlapNitrogenModel

public SimOverlapNitrogenModel(Space _space,
                               int numMolecules,
                               double temperature,
                               java.lang.String filename,
                               double scale)

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:

SimOverlapNitrogenModel.SimOverlapParam