CatalysisRates (Morphokinetics)

java.lang.Object
- ratesLibrary.CatalysisRates

All Implemented Interfaces:

IRates

Direct Known Subclasses:

CatalysisFarkasRates, CatalysisFarkasTestRates, CatalysisKiejnaRates, CatalysisReuterOverRates, CatalysisReuterRates, CatalysisSeitsonenRates
```
public abstract class CatalysisRates
extends java.lang.Object
implements IRates
```
Author:

K. Valencia, J. Alberdi-Rodriguez

Field Summary

Fields
Modifier and Type	Field and Description
`private double[]`	`adsorptionRates`
`private double`	`correctionFactor`
`private double[]`	`desorptionEnergiesCo`
`private double[]`	`desorptionEnergiesCoCusCoCus`
`private double[][]`	`desorptionEnergiesO2`
`private double[][][]`	`diffusionEnergies`
`private double[]`	`diffusionEnergiesCoCusCoCus`
`private double[]`	`mass` Mass of molecule (kg/molecule).
`private double[]`	`mu` Chemical potential (eV).
`private double`	`prefactor`
`private double[]`	`pressures` Partial pressures in Pascal (Pa).
`private double[]`	`R` Molecular interdistance (m).
`private double[][]`	`reactionEnergiesCoO`
`private double[]`	`reactionEnergiesCoOCoCusCoCus`
`private double[]`	`reducedMass`
`private double[]`	`sigma` Symmetry number.
`private float`	`temperature` Temperature (K).
`private double[]`	`V` Vibrational frequency (Hz).

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

Constructor Summary

Constructors
Constructor and Description

CatalysisRates(float temperature)

Constructors
Constructor and Description
`CatalysisRates(float temperature)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private double`	`computeAdsorptionRate(int sourceType)` Equation (3) of Reuter & Scheffler, PRB 73, 2006.
`void`	`computeAdsorptionRates()` Compute all adsorptions.
`double`	`getAdsorptionRate(int atomType)` Adsorption rate for CO or O.
`double`	`getDepositionRatePerSite()`
`private double`	`getDesorptionRate(byte type, double energy)` mu_{A} = -K_{B} T log( k_{B} T / p_{A} * (2 pi m_{A} k_{B} T / h^2)^(3/2) * (8 pi^2 I k_{B} T / sigma h^2) * 1/ ( 1 - exp( -h v / k_{B} T ) )) )
`double[]`	`getDesorptionRates()` Only for Farkas and repulsion.
`double[]`	`getDesorptionRates(int type)`
`double[]`	`getDiffusionRates()` Only for Farkas and repulsion.
`double[]`	`getDiffusionRates(int type)`
`double`	`getEnergy(int i, int j)`
`double`	`getIslandDensity(double temperature)` Returns the island density mono layer depending on the temperature.
`private double`	`getRate(int index)` Only for Farkas and repulsion.
`private double`	`getRate(int sourceType, int sourceSite, int destinationSite)`
`double[]`	`getRates(double temperature)`
`double[]`	`getReactionRates()`
`double[]`	`getReactionRates(boolean fake)` Only for Farkas and repulsion.
`void`	`setCorrectionFactor(double factor)` Scales prefactor.
`void`	`setDepositionFlux(double diffusionMl)`
`void`	`setDesorptionEnergiesCo(double[] desorptionEnergiesCo)`
`void`	`setDesorptionEnergiesCoCusCoCus(double[] desorptionEnergiesCoCusCoCus)`
`void`	`setDesorptionEnergiesO2(double[][] desorptionEnergiesO2)`
`void`	`setDiffusionEnergies(double[][][] diffusionEnergies)`
`void`	`setDiffusionEnergiesCoCusCoCus(double[] diffusionEnergiesCoCusCoCus)`
`private void`	`setPressure(byte type, double pressure)`
`void`	`setPressureCO(double pressureCO)` Sets pressure for CO given in atmospheres and saved in Pa.
`void`	`setPressureO2(double pressureO)` Sets pressure for O2 given in atmospheres and saved in Pa.
`void`	`setReactionEnergiesCoO(double[][] reactionEnergiesCoO)`
`void`	`setReactionEnergiesCoOcoCusCoCus(double[] reactionEnergiesCoOCoCusCoCus)`

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

- Field Detail
  - diffusionEnergies
```
private double[][][] diffusionEnergies
```
  - desorptionEnergiesCo
```
private double[] desorptionEnergiesCo
```
  - desorptionEnergiesO2
```
private double[][] desorptionEnergiesO2
```
  - reactionEnergiesCoO
```
private double[][] reactionEnergiesCoO
```
  - desorptionEnergiesCoCusCoCus
```
private double[] desorptionEnergiesCoCusCoCus
```
  - reactionEnergiesCoOCoCusCoCus
```
private double[] reactionEnergiesCoOCoCusCoCus
```
  - diffusionEnergiesCoCusCoCus
```
private double[] diffusionEnergiesCoCusCoCus
```
  - prefactor
```
private final double prefactor
```
  - correctionFactor
```
private double correctionFactor
```
  - mass
```
private final double[] mass
```
    Mass of molecule (kg/molecule).
  - pressures
```
private final double[] pressures
```
    Partial pressures in Pascal (Pa). Pa = atm * 101325 (Pa: kg/m/s^2)
  - adsorptionRates
```
private final double[] adsorptionRates
```
  - mu
```
private final double[] mu
```
    Chemical potential (eV).
  - R
```
private final double[] R
```
    Molecular interdistance (m). Distance between atoms in the molecule.
  - V
```
private final double[] V
```
    Vibrational frequency (Hz).
  - reducedMass
```
private final double[] reducedMass
```
  - sigma
```
private final double[] sigma
```
    Symmetry number.
  - temperature
```
private final float temperature
```
    Temperature (K).
- Constructor Detail
  - CatalysisRates
```
public CatalysisRates(float temperature)
```
- Method Detail
  - setCorrectionFactor
```
public final void setCorrectionFactor(double factor)
```
    Scales prefactor. By default is kB * temperature / hEv
    
    Parameters:
    
    factor - 1.0 or 0.5
  - setDiffusionEnergies
```
public final void setDiffusionEnergies(double[][][] diffusionEnergies)
```
  - setDiffusionEnergiesCoCusCoCus
```
public final void setDiffusionEnergiesCoCusCoCus(double[] diffusionEnergiesCoCusCoCus)
```
  - setDesorptionEnergiesCo
```
public final void setDesorptionEnergiesCo(double[] desorptionEnergiesCo)
```
  - setDesorptionEnergiesCoCusCoCus
```
public final void setDesorptionEnergiesCoCusCoCus(double[] desorptionEnergiesCoCusCoCus)
```
  - setDesorptionEnergiesO2
```
public final void setDesorptionEnergiesO2(double[][] desorptionEnergiesO2)
```
  - setReactionEnergiesCoO
```
public final void setReactionEnergiesCoO(double[][] reactionEnergiesCoO)
```
  - setReactionEnergiesCoOcoCusCoCus
```
public final void setReactionEnergiesCoOcoCusCoCus(double[] reactionEnergiesCoOCoCusCoCus)
```
  - getDepositionRatePerSite
```
public double getDepositionRatePerSite()
```
    Specified by:
    
    getDepositionRatePerSite in interface IRates
  - setDepositionFlux
```
public void setDepositionFlux(double diffusionMl)
```
    Specified by:
    
    setDepositionFlux in interface IRates
  - getIslandDensity
```
public double getIslandDensity(double temperature)
```
    Description copied from interface: IRates
    
    Returns the island density mono layer depending on the temperature. How many islands per area site are generated at current temperature. Usually with higher temperature less islands are created, and thus, island density is lower. And the other way around.
    
    Specified by:
    
    getIslandDensity in interface IRates
    
    Parameters:
    
    temperature - temperature in Kelvin.
    
    Returns:
    
    island density
  - getEnergy
```
public double getEnergy(int i,
                        int j)
```
    Specified by:
    
    getEnergy in interface IRates
  - setPressureO2
```
public void setPressureO2(double pressureO)
```
    Sets pressure for O2 given in atmospheres and saved in Pa.
    
    Parameters:
    
    pressureO - in atm.
  - setPressureCO
```
public void setPressureCO(double pressureCO)
```
    Sets pressure for CO given in atmospheres and saved in Pa.
    
    Parameters:
    
    pressureCO - in atm.
  - getAdsorptionRate
```
public double getAdsorptionRate(int atomType)
```
    Adsorption rate for CO or O.
    
    Parameters:
    
    atomType - CO or O.
    
    Returns:
    
    adsorption rate.
  - getRates
```
public double[] getRates(double temperature)
```
    Specified by:
    
    getRates in interface IRates
  - getDesorptionRates
```
public double[] getDesorptionRates(int type)
```
  - getDesorptionRates
```
public double[] getDesorptionRates()
```
    Only for Farkas and repulsion.
    
    Returns:
    
    rates.
  - getReactionRates
```
public double[] getReactionRates()
```
  - getReactionRates
```
public double[] getReactionRates(boolean fake)
```
    Only for Farkas and repulsion.
    
    Parameters:
    
    fake - fake parameter.
    
    Returns:
    
    rates.
  - getDiffusionRates
```
public double[] getDiffusionRates(int type)
```
  - getDiffusionRates
```
public double[] getDiffusionRates()
```
    Only for Farkas and repulsion.
    
    Returns:
    
    rates.
  - computeAdsorptionRates
```
public void computeAdsorptionRates()
```
    Compute all adsorptions.
  - setPressure
```
private void setPressure(byte type,
                         double pressure)
```
  - getRate
```
private double getRate(int sourceType,
                       int sourceSite,
                       int destinationSite)
```
  - getRate
```
private double getRate(int index)
```
    Only for Farkas and repulsion.
    
    Returns:
    
    rate.
  - computeAdsorptionRate
```
private double computeAdsorptionRate(int sourceType)
```
    Equation (3) of Reuter & Scheffler, PRB 73, 2006. k_i = \frac{p_A A_s}{\sqrt{2\pi m_A K_B T}}
    
    Parameters:
    
    sourceType -
    
    pressures -
    
    temperature -
    
    Returns:
  - getDesorptionRate
```
private double getDesorptionRate(byte type,
                                 double energy)
```
    mu_{A} = -K_{B} T log( k_{B} T / p_{A} * (2 pi m_{A} k_{B} T / h^2)^(3/2) * (8 pi^2 I k_{B} T / sigma h^2) * 1/ ( 1 - exp( -h v / k_{B} T ) )) )
    
    Parameters:
    
    type -
    
    energy -
    
    Returns:

Class CatalysisRates

Field Summary

Fields inherited from interface ratesLibrary.IRates

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

diffusionEnergies

desorptionEnergiesCo

desorptionEnergiesO2

reactionEnergiesCoO

desorptionEnergiesCoCusCoCus

reactionEnergiesCoOCoCusCoCus

diffusionEnergiesCoCusCoCus

prefactor

correctionFactor

mass

pressures

adsorptionRates

mu

R

V

reducedMass

sigma

temperature

Constructor Detail

CatalysisRates

Method Detail

setCorrectionFactor

setDiffusionEnergies

setDiffusionEnergiesCoCusCoCus

setDesorptionEnergiesCo

setDesorptionEnergiesCoCusCoCus

setDesorptionEnergiesO2

setReactionEnergiesCoO

setReactionEnergiesCoOcoCusCoCus

getDepositionRatePerSite

setDepositionFlux

getIslandDensity

getEnergy

setPressureO2

setPressureCO

getAdsorptionRate

getRates

getDesorptionRates

getDesorptionRates

getReactionRates

getReactionRates

getDiffusionRates

getDiffusionRates

computeAdsorptionRates

setPressure

getRate

getRate

computeAdsorptionRate

getDesorptionRate