Package etomica.normalmode

Class SimOverlapLJ

java.lang.Object

etomica.simulation.Simulation

etomica.normalmode.SimOverlapLJ

public class SimOverlapLJ
extends Simulation

Simulation to run sampling with the LJ potential, but measuring the harmonic potential based on normal mode data from a previous simulation.

Nested Class Summary

Nested Classes

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

Field Summary

Fields

Modifier and Type	Field	Description
DataPump[]	accumulatorPumps
AccumulatorVirialOverlapSingleAverage[]	accumulators
Basis	basis
Boundary	boundaryHarmonic
Boundary	boundaryTarget
Box	boxHarmonic
Box	boxTarget
DataSourceVirialOverlap	dsvo
IntegratorOverlap	integratorOverlap
IntegratorBox[]	integrators
IDataSource[]	meters
int[]	nCells
NormalModes	normalModes
P1Constraint	p1Constraint
Primitive	primitive
Primitive	primitiveUnitCell
double	refPref

Fields inherited from class etomica.simulation.Simulation

eventManager, random, seeds, space

Constructor Summary

Constructors

Constructor	Description
SimOverlapLJ(Space _space, int numAtoms, double density, double temperature, double harmonicFudge)

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

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

p1Constraint

public P1Constraint p1Constraint

Constructor Detail

SimOverlapLJ

public SimOverlapLJ(Space _space,
                    int numAtoms,
                    double density,
                    double temperature,
                    double harmonicFudge)

Method Detail

main

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

Parameters:

args - filename containing simulation parameters

See Also:

SimOverlapLJ.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)