etomica.action
Class IntegratorDimerApproach

java.lang.Object
  etomica.integrator.Integrator
      etomica.integrator.IntegratorBox
          etomica.action.IntegratorDimerApproach

All Implemented Interfaces:

IIntegrator, Serializable

public class IntegratorDimerApproach
extends IntegratorBox

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class etomica.integrator.Integrator

Integrator.Forcible, Integrator.Torquable

Field Summary

protected static IAtom	atom_aC_A
protected static IAtom	atom_aC_B
protected static IAtom	atom_aH_A
protected static IAtom	atom_aH_B
protected static IAtom	atom_H1_A
protected static IAtom	atom_O_A
protected static IAtom	atom_O_B
protected AtomActionRotateBy	atomActionRotateBy
protected AtomActionTranslateBy	atomActionTranslateBy
protected MoleculeChildAtomAction	atomGroupActionRotateBy
protected MoleculeChildAtomAction	atomGroupActionTranslateBy
protected IAtomList	atomSetA
protected IAtomList	atomSetB
protected double	delta
protected IMoleculeList	moleculeList
protected IMolecule	monomerA
protected IMolecule	monomerB
protected IVectorMutable	newOriginB
protected IPotentialMaster	potentialMaster
protected double	r
protected int	route
protected double[][]	routeParams
protected IVectorMutable	translationVector

Fields inherited from class etomica.integrator.IntegratorBox

box, currentPotentialEnergy, isothermal, meterPE, temperature

Fields inherited from class etomica.integrator.Integrator

eventManager, initialized, interval, stepCount

Constructor Summary

IntegratorDimerApproach(IPotentialMaster potentialMaster, ISpace space)

Method Summary

void	checkOHBondLength()
void	doStepInternal() Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.
IAtom	getAtom_aC_A()
IAtom	getAtom_aC_B()
IAtom	getAtom_aH_A()
IAtom	getAtom_aH_B()
IAtom	getAtom_H1_A()
IAtom	getAtom_O_A()
IAtom	getAtom_O_B()
void	initializeCoordinates()
void	printKeyAtomPositions()
void	setImportantAtoms()
void	setMolecules()
void	setRoute(int route)
void	setRouteParams(double[][] routeParams)
void	translateMonomerB()
void	translationVector()

Methods inherited from class etomica.integrator.IntegratorBox

getBox, getMeterPotentialEnergy, getPotentialEnergy, getPotentialMaster, getTemperature, getTemperatureDimension, isIsothermal, reset, setBox, setIsothermal, setMeterPotentialEnergy, setTemperature

Methods inherited from class etomica.integrator.Integrator

doStep, getEventInterval, getEventManager, getStepCount, resetStepCount, setEventInterval, setup

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

atomActionTranslateBy

protected AtomActionTranslateBy atomActionTranslateBy

atomActionRotateBy

protected final AtomActionRotateBy atomActionRotateBy

atomGroupActionRotateBy

protected MoleculeChildAtomAction atomGroupActionRotateBy

atomGroupActionTranslateBy

protected MoleculeChildAtomAction atomGroupActionTranslateBy

potentialMaster

protected IPotentialMaster potentialMaster

newOriginB

protected IVectorMutable newOriginB

translationVector

protected IVectorMutable translationVector

moleculeList

protected IMoleculeList moleculeList

atomSetA

protected IAtomList atomSetA

atomSetB

protected IAtomList atomSetB

monomerA

protected IMolecule monomerA

monomerB

protected IMolecule monomerB

atom_O_A

protected static IAtom atom_O_A

atom_aC_A

protected static IAtom atom_aC_A

atom_aH_A

protected static IAtom atom_aH_A

atom_H1_A

protected static IAtom atom_H1_A

atom_O_B

protected static IAtom atom_O_B

atom_aC_B

protected static IAtom atom_aC_B

atom_aH_B

protected static IAtom atom_aH_B

r

protected double r

delta

protected double delta

route

protected int route

routeParams

protected double[][] routeParams

Constructor Detail

IntegratorDimerApproach

public IntegratorDimerApproach(IPotentialMaster potentialMaster,
                               ISpace space)

Method Detail

initializeCoordinates

public void initializeCoordinates()

doStepInternal

public void doStepInternal()

Description copied from class: Integrator

Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.

Specified by:

doStepInternal in class Integrator

translationVector

public void translationVector()

translateMonomerB

public void translateMonomerB()

setRoute

public void setRoute(int route)

setRouteParams

public void setRouteParams(double[][] routeParams)

setMolecules

public void setMolecules()

setImportantAtoms

public void setImportantAtoms()

getAtom_O_A

public IAtom getAtom_O_A()

getAtom_aC_A

public IAtom getAtom_aC_A()

getAtom_aH_A

public IAtom getAtom_aH_A()

getAtom_H1_A

public IAtom getAtom_H1_A()

getAtom_O_B

public IAtom getAtom_O_B()

getAtom_aC_B

public IAtom getAtom_aC_B()

getAtom_aH_B

public IAtom getAtom_aH_B()

printKeyAtomPositions

public void printKeyAtomPositions()

checkOHBondLength

public void checkOHBondLength()