IntegratorDimerRT

java.lang.Object
- etomica.integrator.Integrator
- - etomica.integrator.IntegratorBox
  - - etomica.dimer.IntegratorDimerRT

All Implemented Interfaces:

AtomLeafAgentManager.AgentSource<Vector>
```
public class IntegratorDimerRT
extends IntegratorBox
implements AtomLeafAgentManager.AgentSource<Vector>
```
Henkelman's Dimer Method (Rotation and Translation). | Finding saddle points on high dimensional surfaces. | J. Chem. Phys., Vol. 111, No. 15, 15 October 1999.

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

Field Summary

Fields
Modifier and Type	Field	Description
`IteratorDirective`	`allatoms`
`AtomLeafAgentManager<Vector>`	`atomAgent0`
`AtomLeafAgentManager<Vector>`	`atomAgent1`
`AtomLeafAgentManager<Vector>`	`atomAgent2`
`Box`	`box1`
`Box`	`box2`
`int`	`counter`
`double`	`curvature`
`double`	`deltaR`
`double`	`deltaTheta`
`Vector[]`	`deltaV`
`double`	`deltaXl`
`double`	`deltaXmax`
`double`	`dFrot`
`double`	`dFsq`
`double`	`dTheta`
`double`	`dXl`
`MeterPotentialEnergy`	`energyBox0`
`MeterPotentialEnergy`	`energyBox1`
`MeterPotentialEnergy`	`energyBox2`
`Vector[]`	`F`
`Vector[]`	`F1`
`Vector[]`	`F1perp`
`Vector[]`	`F1star`
`Vector[]`	`F2`
`Vector[]`	`F2perp`
`Vector[]`	`F2star`
`Vector[]`	`Feff`
`Vector[]`	`Feffstar`
`java.lang.String`	`file`
`PotentialCalculationForceSum`	`force0`
`PotentialCalculationForceSum`	`force1`
`PotentialCalculationForceSum`	`force2`
`Vector[]`	`Fpara`
`Vector[]`	`Fperp`
`Vector[]`	`Fperplast`
`double`	`Fprimerot`
`Vector[]`	`Fr`
`double`	`Frot`
`double`	`Frot2`
`Vector[]`	`Fstar`
`Vector[]`	`Fstarperp`
`double`	`gammai`
`Vector[]`	`Gperp`
`Vector[]`	`Gperplast`
`AtomArrayList`	`list`
`AtomArrayList`	`list1`
`AtomArrayList`	`list2`
`int`	`movableAtoms`
`ISpecies[]`	`movableSpecies`
`Vector[]`	`N`
`Vector[]`	`N1`
`Vector`	`NDelta`
`Vector[]`	`Neff`
`Vector[]`	`newPosition`
`Vector[]`	`Nstar`
`Vector`	`NstarDelta`
`boolean`	`ortho`
`boolean`	`ortho2`
`IRandom`	`random1`
`boolean`	`rotate`
`int`	`rotCounter`
`int`	`rotNum`
`double`	`saddleEnergy`
`boolean`	`saddleFound`
`double`	`saddleT`
`Simulation`	`sim`
`boolean`	`startOrtho`
`Vector[]`	`THETA`
`Vector[]`	`THETAstar`
`Vector[]`	`THETAstarstar`
`Vector[]`	`V`
`CalcVibrationalModes`	`vib`
`Vector`	`workVector`
`Vector[]`	`workVector3`

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
`IntegratorDimerRT(Simulation sim, PotentialMaster potentialMaster, ISpecies[] species, Box box)`
`IntegratorDimerRT(Simulation aSim, PotentialMaster potentialMaster, IRandom random, double temperature, ISpecies[] aspecies, Box box)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`dimerCurvature(Vector[] aN, Vector[] aF1, Vector[] aF2)`	Computes curvature value, C, for the energy surface.
`protected void`	`dimerForceCenter(Vector[] aF)`
`protected void`	`dimerForceEff(Vector[] aF, Vector[] aFeff, Vector[] aNeff)`
`protected void`	`dimerForcePerp(Vector[] aN, Vector[] aF1, Vector[] aF2, Vector[] aFperp)`
`protected void`	`dimerForces(Vector[] aF1, Vector[] aF2, Vector[] aF)`
`protected void`	`dimerForcesStar(Vector[] aF1star, Vector[] aF2star, Vector[] aF)`
`protected void`	`dimerNormal()`
`protected void`	`dimerSaddleTolerance()`
`protected void`	`dimerUpdatePositions(double a1, Vector[] normal)`
`protected void`	`doStepInternal()`	Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.
`Vector`	`makeAgent(IAtom a, Box agentBox)`	Returns an agent for the given Atom.
`void`	`releaseAgent(Vector agent, IAtom atom, Box agentBox)`	This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements.
`void`	`reset()`	Performs superclass reset actions and recalculated currentPotentialEnergy
`protected void`	`resizeDimer()`
`void`	`rotateDimerNewton()`	Rotates the dimer in potential energy hyperspace and aligns it with the surface's lowest curvature mode.
`void`	`setFileName(java.lang.String fileName)`	Set's the filename of the output of this integrator.
`void`	`setOrtho(boolean orthoON, boolean o2)`	Set's the Dimer search's orthogonality criteria.
`void`	`setRotNum(int num)`
`protected void`	`setup()`	Takes in a current configuration of atoms (Rc) and creates a dimer of their positions (R1 and R2).
`protected void`	`testOrthoCurvature(Vector[] aN1, Vector[] aNortho)`	Checks the curvature value at dimer orientation along a vector orthogonal to lowest curvature mode's (lcm) vector with the lcm's unit vector.
`void`	`translateDimerQuickmin()`	Moves the dimer along the lowest curvature mode of the energy surface, Quickmin style.

Methods inherited from class etomica.integrator.Integrator
doStep, getEventInterval, getEventManager, getStepCount, isInitialized, resetStepCount, setEventInterval

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

box1
```
public Box box1
```

box2
```
public Box box2
```

sim
```
public Simulation sim
```

deltaR
```
public double deltaR
```

dTheta
```
public double dTheta
```

deltaXl
```
public double deltaXl
```

dXl
```
public double dXl
```

deltaTheta
```
public double deltaTheta
```

curvature
```
public double curvature
```

deltaXmax
```
public double deltaXmax
```

Frot
```
public double Frot
```

Frot2
```
public double Frot2
```

Fprimerot
```
public double Fprimerot
```

dFrot
```
public double dFrot
```

saddleT
```
public double saddleT
```

dFsq
```
public double dFsq
```

gammai
```
public double gammai
```

saddleEnergy
```
public double saddleEnergy
```

rotNum
```
public int rotNum
```

counter
```
public int counter
```

rotCounter
```
public int rotCounter
```

movableAtoms
```
public int movableAtoms
```

rotate
```
public boolean rotate
```

ortho
```
public boolean ortho
```

ortho2
```
public boolean ortho2
```

startOrtho
```
public boolean startOrtho
```

saddleFound
```
public boolean saddleFound
```

energyBox1
```
public MeterPotentialEnergy energyBox1
```

energyBox2
```
public MeterPotentialEnergy energyBox2
```

energyBox0
```
public MeterPotentialEnergy energyBox0
```

THETA
```
public Vector[] THETA
```

THETAstar
```
public Vector[] THETAstar
```

THETAstarstar
```
public Vector[] THETAstarstar
```

F
```
public Vector[] F
```

F1
```
public Vector[] F1
```

F2
```
public Vector[] F2
```

Fperp
```
public Vector[] Fperp
```

F1perp
```
public Vector[] F1perp
```

F2perp
```
public Vector[] F2perp
```

Gperp
```
public Vector[] Gperp
```

Gperplast
```
public Vector[] Gperplast
```

Fperplast
```
public Vector[] Fperplast
```

Fstar
```
public Vector[] Fstar
```

F1star
```
public Vector[] F1star
```

F2star
```
public Vector[] F2star
```

Fstarperp
```
public Vector[] Fstarperp
```

Feff
```
public Vector[] Feff
```

Feffstar
```
public Vector[] Feffstar
```

Fr
```
public Vector[] Fr
```

Fpara
```
public Vector[] Fpara
```

deltaV
```
public Vector[] deltaV
```

V
```
public Vector[] V
```

newPosition
```
public Vector[] newPosition
```

workVector3
```
public Vector[] workVector3
```

N
```
public Vector[] N
```

Nstar
```
public Vector[] Nstar
```

Neff
```
public Vector[] Neff
```

N1
```
public Vector[] N1
```

NDelta
```
public Vector NDelta
```

NstarDelta
```
public Vector NstarDelta
```

workVector
```
public Vector workVector
```

random1
```
public IRandom random1
```

movableSpecies
```
public ISpecies[] movableSpecies
```

force0

public PotentialCalculationForceSum force0

force1

public PotentialCalculationForceSum force1

force2

public PotentialCalculationForceSum force2

list
```
public AtomArrayList list
```

list1
```
public AtomArrayList list1
```

list2
```
public AtomArrayList list2
```

atomAgent0

public AtomLeafAgentManager<Vector> atomAgent0

atomAgent1

public AtomLeafAgentManager<Vector> atomAgent1

atomAgent2

public AtomLeafAgentManager<Vector> atomAgent2

allatoms
```
public IteratorDirective allatoms
```

file
```
public java.lang.String file
```

vib
```
public CalcVibrationalModes vib
```

Constructor Detail

IntegratorDimerRT

public IntegratorDimerRT(Simulation sim,
                         PotentialMaster potentialMaster,
                         ISpecies[] species,
                         Box box)

IntegratorDimerRT

public IntegratorDimerRT(Simulation aSim,
                         PotentialMaster potentialMaster,
                         IRandom random,
                         double temperature,
                         ISpecies[] aspecies,
                         Box box)

Method Detail
- setRotNum
```
public void setRotNum(int num)
```
- setOrtho
```
public void setOrtho(boolean orthoON,
                     boolean o2)
```
  Set's the Dimer search's orthogonality criteria.
  
  Parameters:
  
  orthoON - (if true) Once the rotation scheme has converged to a small enough Frot value, the orthogonal search is started.
  
  o2 - (if true) Launches another orthogonal path search after the primary orthogonal search.
- setFileName
```
public void setFileName(java.lang.String fileName)
```
  Set's the filename of the output of this integrator. "-minimum" is appended to the string.
  
  Parameters:
  
  fileName - String
- 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
- reset
```
public void reset()
```
  Description copied from class: IntegratorBox
  
  Performs superclass reset actions and recalculated currentPotentialEnergy
  
  Overrides:
  
  reset in class IntegratorBox
- setup
```
protected void setup()
```
  Takes in a current configuration of atoms (Rc) and creates a dimer of their positions (R1 and R2). (R2)-------[Rc]-------(R1) ===> N
  
  Overrides:
  
  setup in class Integrator
- rotateDimerNewton
```
public void rotateDimerNewton()
```
  Rotates the dimer in potential energy hyperspace and aligns it with the surface's lowest curvature mode. Using Newton's finite difference method, the rotational force perpendicular to the dimer's orientation is minimized. Minimization criteria is dependent on dFrot and rotCounter.
- translateDimerQuickmin
```
public void translateDimerQuickmin()
```
  Moves the dimer along the lowest curvature mode of the energy surface, Quickmin style. Step length is determined using a line search (Newton) and the step direction is obtained by a calculation of the effective force on the dimer.
- dimerCurvature
```
protected void dimerCurvature(Vector[] aN,
                              Vector[] aF1,
                              Vector[] aF2)
```
  Computes curvature value, C, for the energy surface. Quantifies the difference in forces at each end of the dimer into a single number.
- testOrthoCurvature
```
protected void testOrthoCurvature(Vector[] aN1,
                                  Vector[] aNortho)
```
  Checks the curvature value at dimer orientation along a vector orthogonal to lowest curvature mode's (lcm) vector with the lcm's unit vector. When the ortho vector returns a curvature less than that of the lcm vector, ORTHO is turned off.
- dimerNormal
```
protected void dimerNormal()
```
- dimerForces
```
protected void dimerForces(Vector[] aF1,
                           Vector[] aF2,
                           Vector[] aF)
```
- dimerForcesStar
```
protected void dimerForcesStar(Vector[] aF1star,
                               Vector[] aF2star,
                               Vector[] aF)
```
- dimerForceCenter
```
protected void dimerForceCenter(Vector[] aF)
```
- dimerForcePerp
```
protected void dimerForcePerp(Vector[] aN,
                              Vector[] aF1,
                              Vector[] aF2,
                              Vector[] aFperp)
```
- dimerForceEff
```
protected void dimerForceEff(Vector[] aF,
                             Vector[] aFeff,
                             Vector[] aNeff)
```
- dimerUpdatePositions
```
protected void dimerUpdatePositions(double a1,
                                    Vector[] normal)
```
- resizeDimer
```
protected void resizeDimer()
```
- dimerSaddleTolerance
```
protected void dimerSaddleTolerance()
```
- makeAgent
```
public Vector makeAgent(IAtom a,
                        Box agentBox)
```
  Description copied from interface: AtomLeafAgentManager.AgentSource
  
  Returns an agent for the given Atom. The agentBox is provided for convenience for agent sources that handle multiple boxes.
  
  Specified by:
  
  makeAgent in interface AtomLeafAgentManager.AgentSource<Vector>
  
  agentBox - TODO
- releaseAgent
```
public void releaseAgent(Vector agent,
                         IAtom atom,
                         Box agentBox)
```
  Description copied from interface: AtomLeafAgentManager.AgentSource
  
  This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements. The agentBox is provided for convenience for agent sources that handle multiple boxes.
  
  Specified by:
  
  releaseAgent in interface AtomLeafAgentManager.AgentSource<Vector>

Class IntegratorDimerRT

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

box1

box2

sim

deltaR

dTheta

deltaXl

dXl

deltaTheta

curvature

deltaXmax

Frot

Frot2

Fprimerot

dFrot

saddleT

dFsq

gammai

saddleEnergy

rotNum

counter

rotCounter

movableAtoms

rotate

ortho

ortho2

startOrtho

saddleFound

energyBox1

energyBox2

energyBox0

THETA

THETAstar

THETAstarstar

F

F1

F2

Fperp

F1perp

F2perp

Gperp

Gperplast

Fperplast

Fstar

F1star

F2star

Fstarperp

Feff

Feffstar

Fr

Fpara

deltaV

V

newPosition

workVector3

N

Nstar

Neff

N1

NDelta

NstarDelta

workVector

random1

movableSpecies

force0

force1

force2

list

list1