IntegratorDimerMin

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

```
public class IntegratorDimerMin
extends IntegratorBox
```
Henkelman's Dimer Method (Minimum Energy Path). | 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>`	`atomAgentMin`
`Box`	`boxMin`
`double`	`cosDtheta`
`int`	`counter`
`double`	`deltaR`
`double`	`deltaTheta`
`double`	`dFrot`
`double`	`dTheta`
`double`	`e0`
`double`	`eMin`
`double`	`energy`
`MeterPotentialEnergy`	`energyBox0`
`MeterPotentialEnergy`	`energyBoxMin`
`Vector[]`	`F0`
`java.lang.String`	`file`
`java.io.FileWriter`	`fileWriter`
`Vector[]`	`Fmin`
`Vector[]`	`Fmin2`
`Vector[]`	`Fmin2perp`
`Vector[]`	`Fmin2star`
`Vector[]`	`Fminperp`
`Vector[]`	`Fminstar`
`PotentialCalculationForceSum`	`force0`
`PotentialCalculationForceSum`	`forceMin`
`Vector[]`	`Fpara`
`Vector[]`	`Fperp`
`double`	`Fprimerot`
`double`	`Frot`
`Vector[]`	`Fstar`
`Vector[]`	`Fstarperp`
`AtomArrayList`	`list`
`AtomArrayList`	`listMin`
`boolean`	`minFound`
`int`	`movableAtoms`
`ISpecies[]`	`movableSpecies`
`Vector[]`	`N`
`Vector`	`NDelta`
`boolean`	`normalD`
`Vector[]`	`Nstar`
`Vector`	`NstarDelta`
`boolean`	`rotate`
`int`	`rotCounter`
`Vector[]`	`saddle`
`Simulation`	`sim`
`double`	`sinDtheta`
`double`	`stepLength`
`Vector[]`	`THETA`
`Vector[]`	`THETAstar`
`CalcVibrationalModes`	`vib`
`Vector`	`workVector`
`WriteConfiguration`	`writer`

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
`IntegratorDimerMin(Simulation aSim, PotentialMaster potentialMaster, double temperature, ISpecies[] aspecies, java.lang.Boolean normalDir, Box box)`
`IntegratorDimerMin(Simulation sim, PotentialMaster potentialMaster, ISpecies[] species, java.lang.Boolean normalDir, Box box)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`dimerForcePerp(Vector[] aN, Vector[] aF1, Vector[] aFperp)`	Finds the component of the dimer's total force that is perpendicular to the normal vector.
`protected void`	`dimerForces(Vector[] aF1, Vector[] aF, Vector[] aF2)`	Resets forces in boxes 0 and min, calls potential.calculate, and copies over the new forces to local arrays.
`protected void`	`dimerForcesStar(Vector[] aF1star, Vector[] aF2star, Vector[] aF)`	Used in the middle of the rotateDimer method.
`protected void`	`dimerNormal()`	Computes an n-dimensional vector in potential energy hyperspace, pointing in the direction of the dimer (intersecting both simulation boxes).
`protected void`	`doStepInternal()`	Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.
`void`	`quitSearch()`	Called after criteria is met in the rotateDimer method.
`void`	`reset()`	Performs superclass reset actions and recalculated currentPotentialEnergy
`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.
`protected void`	`setup()`	Perform initialization.
`void`	`walkDimer()`	Moves the half-dimer stepLength*N towards the energy minimum.

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
  - sim
```
public Simulation sim
```
  - boxMin
```
public Box boxMin
```
  - atomAgent0
```
public AtomLeafAgentManager<Vector> atomAgent0
```
  - atomAgentMin
```
public AtomLeafAgentManager<Vector> atomAgentMin
```
  - force0
```
public PotentialCalculationForceSum force0
```
  - forceMin
```
public PotentialCalculationForceSum forceMin
```
  - allatoms
```
public IteratorDirective allatoms
```
  - fileWriter
```
public java.io.FileWriter fileWriter
```
  - energyBox0
```
public MeterPotentialEnergy energyBox0
```
  - energyBoxMin
```
public MeterPotentialEnergy energyBoxMin
```
  - N
```
public Vector[] N
```
  - Nstar
```
public Vector[] Nstar
```
  - NDelta
```
public Vector NDelta
```
  - NstarDelta
```
public Vector NstarDelta
```
  - workVector
```
public Vector workVector
```
  - saddle
```
public Vector[] saddle
```
  - F0
```
public Vector[] F0
```
  - Fmin
```
public Vector[] Fmin
```
  - Fmin2
```
public Vector[] Fmin2
```
  - THETA
```
public Vector[] THETA
```
  - THETAstar
```
public Vector[] THETAstar
```
  - Fperp
```
public Vector[] Fperp
```
  - Fminperp
```
public Vector[] Fminperp
```
  - Fmin2perp
```
public Vector[] Fmin2perp
```
  - Fstar
```
public Vector[] Fstar
```
  - Fminstar
```
public Vector[] Fminstar
```
  - Fmin2star
```
public Vector[] Fmin2star
```
  - Fstarperp
```
public Vector[] Fstarperp
```
  - Fpara
```
public Vector[] Fpara
```
  - movableSpecies
```
public ISpecies[] movableSpecies
```
  - list
```
public AtomArrayList list
```
  - listMin
```
public AtomArrayList listMin
```
  - movableAtoms
```
public int movableAtoms
```
  - energy
```
public double energy
```
  - deltaR
```
public double deltaR
```
  - deltaTheta
```
public double deltaTheta
```
  - stepLength
```
public double stepLength
```
  - dTheta
```
public double dTheta
```
  - Frot
```
public double Frot
```
  - dFrot
```
public double dFrot
```
  - Fprimerot
```
public double Fprimerot
```
  - sinDtheta
```
public double sinDtheta
```
  - cosDtheta
```
public double cosDtheta
```
  - eMin
```
public double eMin
```
  - e0
```
public double e0
```
  - rotCounter
```
public int rotCounter
```
  - counter
```
public int counter
```
  - rotate
```
public boolean rotate
```
  - normalD
```
public boolean normalD
```
  - minFound
```
public boolean minFound
```
  - file
```
public java.lang.String file
```
  - writer
```
public WriteConfiguration writer
```
  - vib
```
public CalcVibrationalModes vib
```
- Constructor Detail
  - IntegratorDimerMin
```
public IntegratorDimerMin(Simulation sim,
                          PotentialMaster potentialMaster,
                          ISpecies[] species,
                          java.lang.Boolean normalDir,
                          Box box)
```
  - IntegratorDimerMin
```
public IntegratorDimerMin(Simulation aSim,
                          PotentialMaster potentialMaster,
                          double temperature,
                          ISpecies[] aspecies,
                          java.lang.Boolean normalDir,
                          Box box)
```
- Method Detail
  - 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
  - reset
```
public void reset()
```
    Description copied from class: IntegratorBox
    
    Performs superclass reset actions and recalculated currentPotentialEnergy
    
    Overrides:
    
    reset in class IntegratorBox
  - 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
  - setup
```
protected void setup()
```
    Description copied from class: Integrator
    
    Perform initialization. Subclasses can override this method to set up before integration begins.
    
    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. For minimum energy path tracing, rotCounter criteria is commented out to ensure convergence to lowest curvature mode before stepping the dimer.
  - walkDimer
```
public void walkDimer()
```
    Moves the half-dimer stepLength*N towards the energy minimum.
  - quitSearch
```
public void quitSearch()
```
    Called after criteria is met in the rotateDimer method. If F0dotN is negative, the dimer has reached the minimum in an energy basin.
  - dimerNormal
```
protected void dimerNormal()
```
    Computes an n-dimensional vector in potential energy hyperspace, pointing in the direction of the dimer (intersecting both simulation boxes).
  - dimerForces
```
protected void dimerForces(Vector[] aF1,
                           Vector[] aF,
                           Vector[] aF2)
```
    Resets forces in boxes 0 and min, calls potential.calculate, and copies over the new forces to local arrays. Approximates the force in virtual box 2.
    
    Parameters:
    
    aF1 - Array of vectors holding the forces in box min
    
    aF - Array of vectors holding the forces in box 0
    
    aF2 - Array of vectors holding the forces in virtual box 2
  - dimerForcesStar
```
protected void dimerForcesStar(Vector[] aF1star,
                               Vector[] aF2star,
                               Vector[] aF)
```
    Used in the middle of the rotateDimer method. Resets forces in box min only (we are rotating the dimer around a fixed center). Calls potential.calculate, and copies over the new forces to local array. Approximates the force in virtual box 2.
    
    Parameters:
    
    aF1star - Array of vectors holding the forces in box min
    
    aF2star - Array of vectors holding the forces in virtual box 2
    
    aF - Array of vectors holding the forces in box 0
  - dimerForcePerp
```
protected void dimerForcePerp(Vector[] aN,
                              Vector[] aF1,
                              Vector[] aFperp)
```
    Finds the component of the dimer's total force that is perpendicular to the normal vector.
    
    Parameters:
    
    aN - Array of vectors that create an n-dimensional vector parallel to the orientation of the dimer.
    
    aF1 - Array of vectors holding the forces in box min
    
    aFperp - Array of vectors that create an n-dimensional vector perpendicular to the orientation of the dimer.

Class IntegratorDimerMin

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

sim

boxMin

atomAgent0

atomAgentMin

force0

forceMin

allatoms

fileWriter

energyBox0

energyBoxMin

N

Nstar

NDelta

NstarDelta

workVector

saddle

F0

Fmin

Fmin2

THETA

THETAstar

Fperp

Fminperp

Fmin2perp

Fstar

Fminstar

Fmin2star

Fstarperp

Fpara

movableSpecies

list

listMin

movableAtoms

energy

deltaR

deltaTheta

stepLength

dTheta

Frot

dFrot

Fprimerot

sinDtheta

cosDtheta

eMin

e0

rotCounter

counter

rotate

normalD

minFound

file

writer

vib

Constructor Detail

IntegratorDimerMin

IntegratorDimerMin

Method Detail

setFileName

reset

doStepInternal

setup

rotateDimerNewton

walkDimer

quitSearch

dimerNormal

dimerForces

dimerForcesStar

dimerForcePerp