etomica.dimer

Class SimDimerLJadatom

java.lang.Object

etomica.simulation.Simulation

etomica.dimer.SimDimerLJadatom

All Implemented Interfaces:

ISimulation

public class SimDimerLJadatom
extends Simulation

Simulation using Henkelman's Dimer method to find a saddle point for an adatom on a surface, modeled with LJ.

Field Summary

Fields

Modifier and Type	Field and Description
ActivityIntegrate	activityIntegrateDimer
ActivityIntegrate	activityIntegrateMD
ActivityIntegrate	activityIntegrateMin
IVectorMutable	adAtomPos
IBox	box
CalcGradientDifferentiable	calcGradientDifferentiable
java.lang.Boolean	calcModes
CalcVibrationalModes	calcVibrationalModes
int[]	d
double[][]	dForces
SpeciesSpheresMono	fixed
double[]	frequencies
IntegratorDimerRT	integratorDimer
IntegratorDimerMin	integratorDimerMin
IntegratorVelocityVerlet	integratorMD
double[]	lambdas
java.lang.Boolean	minSearch
int[]	modeSigns
SpeciesSpheresMono	movable
IMoleculeList	movableSet
IVectorMutable[]	normal
java.lang.Boolean	normalDir
double[]	positions
PotentialMaster	potentialMaster
IVectorMutable[]	saddle
java.lang.Boolean	saddleFine

Fields inherited from class etomica.simulation.Simulation

eventManager, random, seeds, space

Constructor Summary

Constructors

Constructor and Description
SimDimerLJadatom()

Method Summary

Modifier and Type	Method and Description
void	enableDimerSearch(java.lang.String fileName, long maxSteps, java.lang.Boolean orthoSearch, java.lang.Boolean fine)
void	enableMinimumSearch(java.lang.String fileName, java.lang.Boolean normalDir)
void	enableMolecularDynamics(long maxSteps)
void	generateConfigs(java.lang.String fileName, double percentd)
void	initializeConfiguration(java.lang.String fileName)
static void	main(java.lang.String[] args)
void	randomizePositions()
void	removeAtoms(double distance, IVectorMutable center)
void	setMovableAtoms(double distance, IVectorMutable center)

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

potentialMaster

public final PotentialMaster potentialMaster

integratorMD

public IntegratorVelocityVerlet integratorMD

integratorDimer

public IntegratorDimerRT integratorDimer

integratorDimerMin

public IntegratorDimerMin integratorDimerMin

box

public IBox box

saddle

public IVectorMutable[] saddle

normal

public IVectorMutable[] normal

fixed

public SpeciesSpheresMono fixed

movable

public SpeciesSpheresMono movable

activityIntegrateMD

public ActivityIntegrate activityIntegrateMD

activityIntegrateDimer

public ActivityIntegrate activityIntegrateDimer

activityIntegrateMin

public ActivityIntegrate activityIntegrateMin

calcGradientDifferentiable

public CalcGradientDifferentiable calcGradientDifferentiable

calcVibrationalModes

public CalcVibrationalModes calcVibrationalModes

dForces

public double[][] dForces

d

public int[] d

modeSigns

public int[] modeSigns

positions

public double[] positions

lambdas

public double[] lambdas

frequencies

public double[] frequencies

movableSet

public IMoleculeList movableSet

adAtomPos

public IVectorMutable adAtomPos

saddleFine

public java.lang.Boolean saddleFine

calcModes

public java.lang.Boolean calcModes

minSearch

public java.lang.Boolean minSearch

normalDir

public java.lang.Boolean normalDir

Constructor Detail

SimDimerLJadatom

public SimDimerLJadatom()

Method Detail

setMovableAtoms

public void setMovableAtoms(double distance,
                            IVectorMutable center)

removeAtoms

public void removeAtoms(double distance,
                        IVectorMutable center)

initializeConfiguration

public void initializeConfiguration(java.lang.String fileName)

generateConfigs

public void generateConfigs(java.lang.String fileName,
                            double percentd)

enableMolecularDynamics

public void enableMolecularDynamics(long maxSteps)

enableDimerSearch

public void enableDimerSearch(java.lang.String fileName,
                              long maxSteps,
                              java.lang.Boolean orthoSearch,
                              java.lang.Boolean fine)

enableMinimumSearch

public void enableMinimumSearch(java.lang.String fileName,
                                java.lang.Boolean normalDir)

randomizePositions

public void randomizePositions()

main

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