AbstractConcertedRates (Morphokinetics)

java.lang.Object
- ratesLibrary.concerted.AbstractConcertedRates

All Implemented Interfaces:

IRates

Direct Known Subclasses:

ConcertedAgAgRates, ConcertedCuCuRates, ConcertedCuNiRates, ConcertedNiCuRates, ConcertedNiNiRates, ConcertedPdPdRates
```
public class AbstractConcertedRates
extends java.lang.Object
implements IRates
```
Author:

J. Alberdi-Rodriguez

Field Summary

Fields
Modifier and Type	Field and Description
`private double[]`	`concertedEnergies`
`private double`	`diffusionMl`
`private double[][]`	`energies`
`private double[]`	`multiAtomEnergies`
`private double`	`prefactor`
`private float`	`temperature` Temperature (K).

Fields inherited from interface ratesLibrary.IRates
h, hEv, kB, kBInt, Na

Constructor Summary

Constructors
Constructor and Description

AbstractConcertedRates(float temperature)

Constructors
Constructor and Description
`AbstractConcertedRates(float temperature)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double`	`getDepositionRatePerSite()` In principle, deposition rate is constant to 0.0035 ML/s.
`double[][]`	`getDiffusionRates()`
`double`	`getEnergy(int i, int j)`
`double`	`getIslandDensity(double temperature)` Returns the island density mono layer depending on the temperature.
`double[]`	`getIslandDiffusionRates()`
`private double`	`getMultiAtomRate(int size, double temperature)` Multi atom version.
`double[]`	`getMultiAtomRates()`
`private double`	`getRate(int size, double temperature)` Concerted version.
`private double`	`getRate(int sourceType, int destinationType, double temperature)`
`double[]`	`getRates(double temperature)`
`(package private) void`	`setConcertedEnergies(double[] energies)`
`void`	`setDepositionFlux(double diffusionMl)` Diffusion Mono Layer (F).
`(package private) void`	`setEnergies(double[][] energies)`
`(package private) void`	`setMultiAtomEnergies(double[] energies)`

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

- Field Detail
  - diffusionMl
```
private double diffusionMl
```
  - energies
```
private double[][] energies
```
  - concertedEnergies
```
private double[] concertedEnergies
```
  - multiAtomEnergies
```
private double[] multiAtomEnergies
```
  - prefactor
```
private final double prefactor
```
  - temperature
```
private final float temperature
```
    Temperature (K).
- Constructor Detail
  - AbstractConcertedRates
```
public AbstractConcertedRates(float temperature)
```
- Method Detail
  - setEnergies
```
final void setEnergies(double[][] energies)
```
  - setConcertedEnergies
```
final void setConcertedEnergies(double[] energies)
```
  - setMultiAtomEnergies
```
final void setMultiAtomEnergies(double[] energies)
```
  - getRate
```
private double getRate(int sourceType,
                       int destinationType,
                       double temperature)
```
  - getRate
```
private double getRate(int size,
                       double temperature)
```
    Concerted version.
  - getMultiAtomRate
```
private double getMultiAtomRate(int size,
                                double temperature)
```
    Multi atom version.
  - getDepositionRatePerSite
```
public double getDepositionRatePerSite()
```
    In principle, deposition rate is constant to 0.0035 ML/s. What changes is island density. Consequently, deposition rate in practice varies with the temperature.
    
    Specified by:
    
    getDepositionRatePerSite in interface IRates
    
    Returns:
    
    diffusion mono layer (or deposition flux)
  - getIslandDensity
```
public double getIslandDensity(double temperature)
```
    Returns the island density mono layer depending on the temperature. These values are taken from many run of multi flake with 200x200 lattice points. The formula to get the number of islands is: N = F^{0.23}·c·(r_tt/F^{1/3})^x Therefore, we can get island density for single flake.
    
    Specified by:
    
    getIslandDensity in interface IRates
    
    Parameters:
    
    temperature -
    
    Returns:
    
    a double density value
  - getEnergy
```
public double getEnergy(int i,
                        int j)
```
    Specified by:
    
    getEnergy in interface IRates
  - setDepositionFlux
```
public void setDepositionFlux(double diffusionMl)
```
    Diffusion Mono Layer (F). Utilised to calculate absorption rate. Cox et al. define to be F=0.0035 ML/s. The perimeter deposition is calculated multiplying F (this) and island density.
    
    Specified by:
    
    setDepositionFlux in interface IRates
    
    Parameters:
    
    diffusionMl - diffusion mono layer (deposition flux)
  - getRates
```
public double[] getRates(double temperature)
```
    Specified by:
    
    getRates in interface IRates
  - getDiffusionRates
```
public double[][] getDiffusionRates()
```
  - getIslandDiffusionRates
```
public double[] getIslandDiffusionRates()
```
  - getMultiAtomRates
```
public double[] getMultiAtomRates()
```

Class AbstractConcertedRates

Field Summary

Fields inherited from interface ratesLibrary.IRates

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

diffusionMl

energies

concertedEnergies

multiAtomEnergies

prefactor

temperature

Constructor Detail

AbstractConcertedRates

Method Detail

setEnergies

setConcertedEnergies

setMultiAtomEnergies

getRate

getRate

getMultiAtomRate

getDepositionRatePerSite

getIslandDensity

getEnergy

setDepositionFlux

getRates

getDiffusionRates

getIslandDiffusionRates

getMultiAtomRates