IntegratorDimerApproach

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

public class IntegratorDimerApproach
extends IntegratorBox

Nested Class Summary
- Nested classes/interfaces inherited from class etomica.integrator.Integrator
  Integrator.Forcible, Integrator.Torquable

Field Summary

Fields
Modifier and Type	Field	Description
`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 Vector`	`newOriginB`
`protected double`	`r`
`protected int`	`route`
`protected double[][]`	`routeParams`
`protected Vector`	`translationVector`

Fields inherited from class etomica.integrator.Integrator
eventManager, initialized, interval, stepCount

Fields inherited from class etomica.integrator.IntegratorBox
box, currentPotentialEnergy, isothermal, meterPE, potentialMaster, space, temperature

Constructor Summary

Constructors
Constructor Description

IntegratorDimerApproach(PotentialMaster potentialMaster, Box box)

Constructors
Constructor	Description
`IntegratorDimerApproach(PotentialMaster potentialMaster, Box box)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`checkOHBondLength()`
`protected 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.Integrator
doStep, getEventInterval, getEventManager, getStepCount, isInitialized, resetStepCount, setEventInterval, setup

Methods inherited from class etomica.integrator.IntegratorBox
getBox, getMeterPotentialEnergy, getPotentialEnergy, getPotentialMaster, getTemperature, getTemperatureDimension, isIsothermal, reset, setBox, setIsothermal, setMeterPotentialEnergy, setTemperature

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

newOriginB
```
protected Vector newOriginB
```

translationVector
```
protected Vector 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(PotentialMaster potentialMaster,
                               Box box)

Method Detail

initializeCoordinates

public void initializeCoordinates()

doStepInternal
```
protected 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()
```

Class IntegratorDimerApproach

Nested Class Summary

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

Field Summary

Fields inherited from class etomica.integrator.Integrator

Fields inherited from class etomica.integrator.IntegratorBox

Constructor Summary

Method Summary

Methods inherited from class etomica.integrator.Integrator

Methods inherited from class etomica.integrator.IntegratorBox

Methods inherited from class java.lang.Object

Field Detail

atomActionTranslateBy

atomActionRotateBy

atomGroupActionRotateBy

atomGroupActionTranslateBy

newOriginB

translationVector

moleculeList

atomSetA

atomSetB

monomerA

monomerB

atom_O_A

atom_aC_A

atom_aH_A

atom_H1_A

atom_O_B

atom_aC_B

atom_aH_B

r

delta

route

routeParams

Constructor Detail

IntegratorDimerApproach

Method Detail

initializeCoordinates

doStepInternal

translationVector

translateMonomerB

setRoute

setRouteParams

setMolecules

setImportantAtoms

getAtom_O_A

getAtom_aC_A

getAtom_aH_A

getAtom_H1_A

getAtom_O_B

getAtom_aC_B

getAtom_aH_B

printKeyAtomPositions

checkOHBondLength