AgRatesFromPrbCox (Morphokinetics)

java.lang.Object
- ratesLibrary.AgRatesFromPrbCox

All Implemented Interfaces:

IRates
```
public class AgRatesFromPrbCox
extends java.lang.Object
implements IRates
```
Etch rates data obtained from Cox et al. - PHYSICAL REVIEW B 71, 11541 2005

Author:

N. Ferrando, J. Alberdi-Rodriguez

Field Summary

Fields
Modifier and Type	Field and Description
`private double`	`diffusionMl` Diffusion Mono Layer (F).
`private double`	`Eaa` Energy from edge A to edge A
`private double`	`Eacb` Energy from edge A to edge B, across corner
`private double`	`Eack` Energy from edge A to kink, across corner
`private double`	`Ebb` Energy from edge B to edge B
`private double`	`Ebca` Energy from edge B to edge A, across corner
`private double`	`Ebck` Energy from edge B to kink, across corner
`private double`	`Eca` Energy from corner to edge A
`private double`	`Ecak` Energy from corner to kink A
`private double`	`Ecb` Energy from corner to edge B
`private double`	`Ecbk` Energy from corner to kink B
`private double`	`Ecc` Energy from corner to corner
`private double`	`Ed`
`private double`	`Einf` Infinite energy.
`private double[][]`	`energies`
`private double`	`P`
`private double`	`Pd`
`private double[][]`	`prefactors`

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

Constructor Summary

Constructors
Constructor and Description

AgRatesFromPrbCox()
Atom types are documented in class AbstractAtom.

Constructors
Constructor and Description
`AgRatesFromPrbCox()` Atom types are documented in class AbstractAtom.

Method Summary

All Methods Static 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`	`getEnergy(int i, int j)`
`double`	`getIslandDensity(double temperature)` Returns the island density mono layer depending on the temperature.
`static double`	`getRate(double temperature, double energy)` Giving energy it returns a rate with a prefactor of 1e13
`private double`	`getRate(int i, int j, double temperature)`
`double[]`	`getRates(double temperature)`
`double[]`	`getReduced6Energies()`
`double[]`	`getReduced6Rates(float temperature)` This is tuned to work with only 6 "genes".
`void`	`setDepositionFlux(double diffusionMl)` Diffusion Mono Layer (F).

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

- Field Detail
  - diffusionMl
```
private 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.
  - P
```
private final double P
```
  - Pd
```
private final double Pd
```
  - Eaa
```
private final double Eaa
```
    Energy from edge A to edge A
  - Ebb
```
private final double Ebb
```
    Energy from edge B to edge B
  - Eca
```
private final double Eca
```
    Energy from corner to edge A
  - Ecb
```
private final double Ecb
```
    Energy from corner to edge B
  - Ecc
```
private final double Ecc
```
    Energy from corner to corner
  - Eacb
```
private final double Eacb
```
    Energy from edge A to edge B, across corner
  - Ebca
```
private final double Ebca
```
    Energy from edge B to edge A, across corner
  - Eack
```
private final double Eack
```
    Energy from edge A to kink, across corner
  - Ebck
```
private final double Ebck
```
    Energy from edge B to kink, across corner
  - Ecak
```
private final double Ecak
```
    Energy from corner to kink A
  - Ecbk
```
private final double Ecbk
```
    Energy from corner to kink B
  - Ed
```
private final double Ed
```
  - Einf
```
private final double Einf
```
    Infinite energy. To make impossible the transition.
  - prefactors
```
private final double[][] prefactors
```
  - energies
```
private final double[][] energies
```
- Constructor Detail
  - AgRatesFromPrbCox
```
public AgRatesFromPrbCox()
```
    Atom types are documented in class AbstractAtom. In any case are; 0: terrace | 1: corner | 2: A side | 3: kink A | 4: bulk | 5: B side | 6: kink B edge island edge
- Method Detail
  - getRate
```
private double getRate(int i,
                       int j,
                       double temperature)
```
  - getRate
```
public static double getRate(double temperature,
                             double energy)
```
    Giving energy it returns a rate with a prefactor of 1e13
    
    Parameters:
    
    temperature - system temperature
    
    energy - input energy
    
    Returns:
    
    rate
  - 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 section 4 of the paper of Cox et al. (But are not consistent with, for example, the multi-flake simulations: 180K, 250x250)
    
    Specified by:
    
    getIslandDensity in interface IRates
    
    Parameters:
    
    temperature -
    
    Returns:
    
    a double value from 1e-4 to 2e-5
  - 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
  - getReduced6Rates
```
public double[] getReduced6Rates(float temperature)
```
    This is tuned to work with only 6 "genes". Gene 0 from Ed (0,j) Gene 1 from Ec (1,1)(1,2)(1,6) Gene 2 from Ee (1,3)(1,5) Gene 3 from Ef (2,3)(5,2)(5,3)(5,4)(5,6) Gene 4 from Ea (2,2) Gene 5 from Eb (5,5)
    
    Parameters:
    
    temperature -
    
    Returns:
    
    rates[6]
  - getReduced6Energies
```
public double[] getReduced6Energies()
```

Class AgRatesFromPrbCox

Field Summary

Fields inherited from interface ratesLibrary.IRates

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

diffusionMl

P

Pd

Eaa

Ebb

Eca

Ecb

Ecc

Eacb

Ebca

Eack

Ebck

Ecak

Ecbk

Ed

Einf

prefactors

energies

Constructor Detail

AgRatesFromPrbCox

Method Detail

getRate

getRate

getDepositionRatePerSite

getIslandDensity

getEnergy

setDepositionFlux

getRates

getReduced6Rates

getReduced6Energies