Parser (Morphokinetics)

java.lang.Object
- basic.Parser

```
public class Parser
extends java.lang.Object
```
This class will read an input file called "parameters" with all the parameters for the execution. The format of this file is JSON. If "parameters" file is missing in the launch directory, default values are taken. Only desired options can be specified, default ones are used for the rest. In all cases, the used options are printed to the main screen and they can be copied to a "parameters" file.

Author:

J. Alberdi-Rodriguez

Field Summary

Fields
Modifier and Type	Field and Description
`private boolean`	`automaticCollections` See `areCollectionsAutomatic()`.
`private int`	`binsLevels` See `getBinsLevels()`.
`private java.lang.String`	`calculationMode` See `getCalculationMode()`.
`private java.lang.String`	`calculationType` See `getCalculationType()`.
`private int`	`cartSizeX` See `getCartSizeX()`.
`private int`	`cartSizeY` See `getCartSizeY()`.
`private int`	`cartSizeZ` See `getCartSizeZ()`.
`private java.lang.String`	`catalysisAdsorption` See `doCatalysisAdsorption()`
`private java.lang.String`	`catalysisDesorption` See `doCatalysisDesorption()`
`private java.lang.String`	`catalysisDiffusion` See `doCatalysisDiffusion()`
`private boolean`	`catalysisO2Dissociation` See `doCatalysisO2Dissociation()`
`private java.lang.String`	`catalysisReaction` See `doCatalysisReaction()`
`private java.lang.String`	`catalysisStart` See `#calalysisStart()`
`private boolean[]`	`catalysisTree` Attribute to control the use of trees for catalysis.
`private double`	`coverage` See `getCoverage()`.
`private double`	`depositionFlux` See `getDepositionFlux()`.
`private boolean`	`devita` See `useDevita()`
`private boolean`	`doIslandDiffusion` See `()`.
`private boolean`	`doMultiAtomDiffusion` See `()`.
`private double`	`endTime` See `getEndTime()`.
`private org.json.JSONArray`	`evaluator`
`private EvaluatorType`	`evaluatorType` To have the possibility to choose between different evaluators.
`private java.lang.String`	`evolutionaryAlgorithm` Can be original or dcma.
`private java.lang.String`	`evolutionarySearchType` Search for "rates" or "energies".
`private boolean`	`expDistribution` Chooses between exponential distribution of the random genes (true) or linear distribution (false).
`private int`	`extraLevels` See `getExtraLevels()`.
`private boolean`	`fixDiffusion` Decides if diffusion must be fixed.
`private boolean`	`forceNucleation` See `forceNucleation()`
`private double`	`goMultiplier` Gets O desorption rate multiplied by a factor for plotting resolution problems.
`private java.lang.String`	`hierarchyEvaluator` If a hierarchy evaluator has been chosen, select the type of hierarchy evaluator.
`private boolean`	`justCentralFlake` See `justCentralFlake()`.
`private java.lang.String`	`listType` See `getListType()`.
`private double`	`maxValueGene` Maximum possible value that a gene can have.
`private int`	`millerX`
`private int`	`millerY`
`private int`	`millerZ`
`private double`	`minValueGene` Minimum possible value that a gene can have.
`private boolean`	`multithreaded`
`private int`	`numberOfCo2` See `getNumberOfCo2()`.
`private int`	`numberOfSimulations` See `getNumberOfSimulations()`.
`private long`	`numberOfSteps` See `getNumberOfSteps()`.
`private long`	`numericFormatCode` This numbers reflect the power of two and gives the chance to choose between inclusively among TXT(0), MKO(1), PNG(2), EXTRA(3), AE(4), XYZ(5), EXTRA2(6), CAT(7), AETOTAL(8) and SVG(9).
`private long`	`numericStatusCode` This numbers reflect the power of two and gives the chance to choose between inclusively among PSD(0), TIME(1) and HIERARCHY(2).
`private int`	`offspringSize`
`private boolean`	`outputData` See `outputData()` and `getOutputFormats()`.
`private org.json.JSONArray`	`outputDataFormat`
`private int`	`outputEvery` See {@link #getOutputEvery()].
`private OutputType`	`outputType` See `getOutputFormats()`.
`private boolean`	`parallelEvaluator` Can be serial or threaded.
`private java.lang.String`	`perimeterType` See `getPerimeterType()`.
`private boolean`	`periodicSingleFlake` See `isPeriodicSingleFlake()`.
`private int`	`populationReplacement`
`private int`	`populationSize`
`private double`	`pressureCO` See `getPressureO2()` and `getPressureCO()`.
`private double`	`pressureO2`
`private boolean`	`printAllIterations` See `doPrintAllIterations()`
`private boolean`	`printToImage` See `printToImage()`.
`private boolean`	`psd` See `doPsd()`.
`private double`	`psdExtend` See `getPsdExtend()`.
`private double`	`psdScale` See `getPsdScale()`.
`private boolean`	`psdSymmetry` See `isPsdSymmetric()`.
`private boolean`	`randomSeed` See `randomSeed()`.
`private java.lang.String`	`ratesLibrary` See `getRatesLibrary()`.
`private boolean`	`readReference`
`private int`	`repetitions`
`private Restart`	`restart` Restart object to read "parameters" file.
`private double`	`stopError`
`private java.lang.String`	`surfaceType` See `getSurfaceType()`.
`private float`	`temperature` See `getTemperature()`.
`private int`	`totalIterations` See `getTotalIterations()`.
`private boolean`	`useMaxPerimeter` See `useMaxPerimeter()`.
`private boolean`	`visualise` See `visualise()`.
`private boolean`	`withGui` See `withGui()`.

Constructor Summary

Constructors
Constructor and Description

Parser()
Constructor

Constructors
Constructor and Description
`Parser()` Constructor

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`areCollectionsAutomatic()` Allow to change between tree and array collections, when the code decides to do so.
`java.lang.String`	`catalysisStart()` Starts a catalysis run given coverage.
`private void`	`computeTree()`
`boolean`	`doCatalysisAdsorption()` Adsorb atoms during catalysis simulation.
`boolean`	`doCatalysisDesorption()` Desorb atoms during catalysis simulation.
`boolean`	`doCatalysisDiffusion()` Diffuse atom during catalysis simulation.
`boolean`	`doCatalysisO2Dissociation()` Dissociates O2 atoms during catalysis simulation Input "parameters" variable: `catalysisO2Dissociation`.
`boolean`	`doCatalysisReaction()` Allow to react atoms during catalysis simulation.
`boolean`	`doIslandDiffusion()` In concerted calculation mode, allow to island to move.
`boolean`	`doMultiAtomDiffusion()` In concerted calculation mode, allow to atoms on the edge to move.
`boolean`	`doPrintAllIterations()` Print all iterations during catalysis simulation.
`boolean`	`doPsd()` Selects to do a PSD analysis of the simulated system.
`boolean`	`forceNucleation()` If two terraces are together freeze them, in multi-flake simulation mode.
`int`	`getBinsLevels()` Selects the number of bin levels.
`java.lang.String`	`getCalculationMode()` Selects the type of system to be calculated.
`java.lang.String`	`getCalculationType()` Morphokinetics has two main calculation modes: one called batch, for arbitrarily chosen input parameters, and the other called evolutionary, which tries to find the best input parameters for a target system.
`int`	`getCartSizeX()` Selects the Cartesian size in X direction.
`int`	`getCartSizeY()` Selects the Cartesian size in Y direction.
`int`	`getCartSizeZ()` Selects the Cartesian size in Z direction.
`double`	`getCoverage()` Returns the maximum coverage until a simulation is allowed to grow.
`double`	`getDepositionFlux()` Number of atoms that is coming per second and per area.
`double`	`getEndTime()` Returns the maximum simulation time that each run has to do or -1 if there is no time limit.
`java.util.EnumSet<EvaluatorType.evaluatorFlag>`	`getEvaluatorTypes()` To have the possibility to choose between different evaluators in genetic algorithm runs.
`java.lang.String`	`getEvolutionaryAlgorithm()`
`java.lang.String`	`getEvolutionarySearchType()`
`int`	`getExtraLevels()`
`double`	`getGOMultiplier()` GO multiplier for plotting resolution problem solving.
`int`	`getHexaSizeI()` Selects the lattice size in I direction.
`int`	`getHexaSizeJ()` Selects the lattice size in J direction.
`java.lang.String`	`getHierarchyEvaluator()` If a hierarchy evaluator has been chosen, select the type of hierarchy evaluator.
`java.lang.String`	`getListType()` Selects the internal list type to be used between linear and binned.
`double`	`getMaxValueGene()` For evolutionary algorithm, maximum possible value of a gene.
`int`	`getMillerX()`
`int`	`getMillerY()`
`int`	`getMillerZ()`
`double`	`getMinValueGene()` For evolutionary algorithm, minimum possible value of a gene.
`int`	`getNumberOfCo2()` Selects the number of CO2 molecules that will be created at most. -1 by default, which means that it will run until another criteria is reached.
`int`	`getNumberOfSimulations()` Selects the number of simulations that has to be done with the same parameters.
`long`	`getNumberOfSteps()` Selects the number of steps that each simulation will at most. -1 by default, which means that it will run until another criteria is reached.
`int`	`getOffspringSize()`
`int`	`getOutputEvery()` How frequently should be printed extra file of catalysis.
`java.util.EnumSet<OutputType.formatFlag>`	`getOutputFormats()` To have the possibility to output to different file formats.
`short`	`getPerimeterType()` Input "parameters" variable: `perimeterType`.
`int`	`getPopulationReplacement()`
`int`	`getPopulationSize()`
`double`	`getPressureCO()` Partial pressure for CO in atm.
`double`	`getPressureO2()` Partial pressure for O2 in atm.
`(package private) double`	`getPsdExtend()` Factor which has to be added as empty area to the surface.
`double`	`getPsdScale()` Factor with which has to be multiplied the size of the surface to calculate the PSD.
`java.lang.String`	`getRatesLibrary()` Selects which rates are used for the simulation.
`boolean`	`getReadReference()` Chooses between to read a reference PSD or doing an initial run to be the objective for the Evolutionary run
`int`	`getRepetitions()` Number of repetitions or evaluations that a single Gene has to do.
`double`	`getStopError()` For evolutionary algorithm run mode target minimum error
`java.lang.String`	`getSurfaceType()` The options below are for "Ag" calculationMode (see `getCalculationMode()`).
`float`	`getTemperature()` Simulation temperature.
`int`	`getTotalIterations()` Total number of iterations that the evolutionary algorithm has to do.
`boolean`	`isDiffusionFixed()` Decides if diffusion must be fixed.
`boolean`	`isEnergySearch()`
`boolean`	`isEvaluatorParallel()`
`boolean`	`isExpDistribution()` Chooses between exponential distribution of the random genes (true) or linear distribution (false)
`boolean`	`isMultithreaded()`
`boolean`	`isPeriodicSingleFlake()` Returns if single-flake simulation is periodic.
`boolean`	`isPsdSymmetric()` Returns if the PSD (`doPsd()`) has to be symmetrised.
`boolean`	`justCentralFlake()` Selects to run a single flake simulation (faster and usually with Devita acceleration) or not.
`boolean`	`outputData()` Chooses to output data or not.
`void`	`print()` Prints all the parameters; either read from "parameter" file or the default value.
`boolean`	`printToImage()` Selects to print the simulated system (the canvas of the frame) to a PNG file.
`boolean`	`randomSeed()` Selects to use randomSeed, based on the current time in ms.
`int`	`readFile(java.lang.String fileName)` Read the execution parameters from the given file.
`void`	`setBinsLevels(int binsLevels)`
`void`	`setCalculationMode(java.lang.String mode)`
`void`	`setCartSizeX(int sizeX)`
`void`	`setCartSizeY(int sizeY)`
`void`	`setCartSizeZ(int sizeZ)`
`void`	`setEvolutionaryAlgorithm(java.lang.String name)`
`void`	`setExtraLevels(int extraLevels)`
`void`	`setListType(java.lang.String listType)` Sets the internal list type to be used.
`void`	`setMillerX(int sizeX)`
`void`	`setMillerY(int sizeY)`
`void`	`setMillerZ(int sizeZ)`
`void`	`setNumberOfSimulations(int numberOfSimulations)`
`void`	`setPopulation(int populationSize)`
`void`	`setTemperature(float temperature)`
`boolean`	`useCatalysisTree(byte process)` Instead of writing "true", one can use the word "tree" to use a tree to store catalysis processes.
`boolean`	`useDevita()` Devita accelerator makes execution much faster, it may change results a bit.
`boolean`	`useMaxPerimeter()` In single flake simulation mode (`justCentralFlake()`) selects the initial size of the simulation area.
`boolean`	`visualise()` If GUI is enabled (see `withGui()`), selects to visualise the GUI.
`boolean`	`withGui()` Selects to enable all the GUI with its windows.

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

- Field Detail
  - catalysisTree
```
private boolean[] catalysisTree
```
    Attribute to control the use of trees for catalysis.
  - restart
```
private final Restart restart
```
    Restart object to read "parameters" file.
  - calculationType
```
private java.lang.String calculationType
```
    See getCalculationType().
  - ratesLibrary
```
private java.lang.String ratesLibrary
```
    See getRatesLibrary().
  - listType
```
private java.lang.String listType
```
    See getListType().
  - perimeterType
```
private java.lang.String perimeterType
```
    See getPerimeterType().
  - calculationMode
```
private java.lang.String calculationMode
```
    See getCalculationMode().
  - surfaceType
```
private java.lang.String surfaceType
```
    See getSurfaceType().
  - temperature
```
private float temperature
```
    See getTemperature().
  - pressureCO
```
private double pressureCO
```
    See getPressureO2() and getPressureCO().
  - pressureO2
```
private double pressureO2
```
  - depositionFlux
```
private double depositionFlux
```
    See getDepositionFlux().
  - endTime
```
private double endTime
```
    See getEndTime().
  - coverage
```
private double coverage
```
    See getCoverage().
  - psdScale
```
private double psdScale
```
    See getPsdScale().
  - psdExtend
```
private double psdExtend
```
    See getPsdExtend().
  - numberOfSimulations
```
private int numberOfSimulations
```
    See getNumberOfSimulations().
  - numberOfSteps
```
private long numberOfSteps
```
    See getNumberOfSteps().
  - numberOfCo2
```
private int numberOfCo2
```
    See getNumberOfCo2().
  - cartSizeX
```
private int cartSizeX
```
    See getCartSizeX().
  - cartSizeY
```
private int cartSizeY
```
    See getCartSizeY().
  - cartSizeZ
```
private int cartSizeZ
```
    See getCartSizeZ().
  - millerX
```
private int millerX
```
  - millerY
```
private int millerY
```
  - millerZ
```
private int millerZ
```
  - binsLevels
```
private int binsLevels
```
    See getBinsLevels().
  - extraLevels
```
private int extraLevels
```
    See getExtraLevels().
  - multithreaded
```
private boolean multithreaded
```
  - visualise
```
private boolean visualise
```
    See visualise().
  - withGui
```
private boolean withGui
```
    See withGui().
  - justCentralFlake
```
private boolean justCentralFlake
```
    See justCentralFlake().
  - printToImage
```
private boolean printToImage
```
    See printToImage().
  - psd
```
private boolean psd
```
    See doPsd().
  - psdSymmetry
```
private boolean psdSymmetry
```
    See isPsdSymmetric().
  - periodicSingleFlake
```
private boolean periodicSingleFlake
```
    See isPeriodicSingleFlake().
  - outputData
```
private boolean outputData
```
    See outputData() and getOutputFormats().
  - randomSeed
```
private boolean randomSeed
```
    See randomSeed().
  - useMaxPerimeter
```
private boolean useMaxPerimeter
```
    See useMaxPerimeter().
  - forceNucleation
```
private boolean forceNucleation
```
    See forceNucleation()
  - devita
```
private boolean devita
```
    See useDevita()
  - catalysisAdsorption
```
private java.lang.String catalysisAdsorption
```
    See doCatalysisAdsorption()
  - catalysisDesorption
```
private java.lang.String catalysisDesorption
```
    See doCatalysisDesorption()
  - catalysisReaction
```
private java.lang.String catalysisReaction
```
    See doCatalysisReaction()
  - catalysisDiffusion
```
private java.lang.String catalysisDiffusion
```
    See doCatalysisDiffusion()
  - catalysisStart
```
private java.lang.String catalysisStart
```
    See #calalysisStart()
  - printAllIterations
```
private boolean printAllIterations
```
    See doPrintAllIterations()
  - catalysisO2Dissociation
```
private boolean catalysisO2Dissociation
```
    See doCatalysisO2Dissociation()
  - automaticCollections
```
private boolean automaticCollections
```
    See areCollectionsAutomatic().
  - doIslandDiffusion
```
private boolean doIslandDiffusion
```
    See ().
  - doMultiAtomDiffusion
```
private boolean doMultiAtomDiffusion
```
    See ().
  - outputDataFormat
```
private org.json.JSONArray outputDataFormat
```
  - outputType
```
private final OutputType outputType
```
    See getOutputFormats().
  - numericFormatCode
```
private long numericFormatCode
```
    This numbers reflect the power of two and gives the chance to choose between inclusively among TXT(0), MKO(1), PNG(2), EXTRA(3), AE(4), XYZ(5), EXTRA2(6), CAT(7), AETOTAL(8) and SVG(9). So a number between 0 and 2⁸ has to be chosen.
  - outputEvery
```
private int outputEvery
```
    See {@link #getOutputEvery()].
  - evolutionaryAlgorithm
```
private java.lang.String evolutionaryAlgorithm
```
    Can be original or dcma.
  - parallelEvaluator
```
private boolean parallelEvaluator
```
    Can be serial or threaded.
  - populationSize
```
private int populationSize
```
  - offspringSize
```
private int offspringSize
```
  - populationReplacement
```
private int populationReplacement
```
  - totalIterations
```
private int totalIterations
```
    See getTotalIterations().
  - repetitions
```
private int repetitions
```
  - readReference
```
private boolean readReference
```
  - stopError
```
private double stopError
```
  - minValueGene
```
private double minValueGene
```
    Minimum possible value that a gene can have.
  - maxValueGene
```
private double maxValueGene
```
    Maximum possible value that a gene can have.
  - goMultiplier
```
private double goMultiplier
```
    Gets O desorption rate multiplied by a factor for plotting resolution problems.
  - expDistribution
```
private boolean expDistribution
```
    Chooses between exponential distribution of the random genes (true) or linear distribution (false).
  - evaluatorType
```
private final EvaluatorType evaluatorType
```
    To have the possibility to choose between different evaluators. For the moment only PSD, TIME and HIERARCHY.
  - numericStatusCode
```
private long numericStatusCode
```
    This numbers reflect the power of two and gives the chance to choose between inclusively among PSD(0), TIME(1) and HIERARCHY(2). So a number between 0 (no evaluator) and 7 (all the evaluators) has to be chosen.
  - evaluator
```
private org.json.JSONArray evaluator
```
  - hierarchyEvaluator
```
private java.lang.String hierarchyEvaluator
```
    If a hierarchy evaluator has been chosen, select the type of hierarchy evaluator. Options: "basic", "step", "reference" and "Frobenius".
  - evolutionarySearchType
```
private java.lang.String evolutionarySearchType
```
    Search for "rates" or "energies".
  - fixDiffusion
```
private boolean fixDiffusion
```
    Decides if diffusion must be fixed.
- Constructor Detail
  - Parser
```
public Parser()
```
    Constructor
- Method Detail
  - readFile
```
public int readFile(java.lang.String fileName)
             throws org.json.JSONException
```
    Read the execution parameters from the given file. If nothing found, default values are assigned.
    
    Parameters:
    
    fileName -
    
    Returns:
    
    0 if success, negative otherwise
    
    Throws:
    
    org.json.JSONException
  - print
```
public void print()
           throws org.json.JSONException
```
    Prints all the parameters; either read from "parameter" file or the default value.
    
    Throws:
    
    org.json.JSONException
  - getCalculationType
```
public java.lang.String getCalculationType()
```
    Morphokinetics has two main calculation modes: one called batch, for arbitrarily chosen input parameters, and the other called evolutionary, which tries to find the best input parameters for a target system. Additionally, it has an utility which does PSD analysis from given surfaces. Input "parameters" variable: calculationType.
    
    Returns:
    
    "batch", "evolutionary" or "psd".
  - getRatesLibrary
```
public java.lang.String getRatesLibrary()
```
    Selects which rates are used for the simulation. Available options for graphene are: "GaillardSimple", "Gaillard1Neighbour", "Gaillard2Neighbours", "Schoenhalz" or anything else for synthetic rates. Available options for basic growth are: "simple", "version2", "version3" or anything else for original synthetic rates. Available options for AgUc growth are: "simple" or anything else for original Cox et al. rates. Input "parameters" variable: ratesLibrary.
    
    Returns:
    
    "GaillardSimple", "Gaillard1Neighbour", "Gaillard2Neighbours", "Schoenhalz" or anything else for synthetic rates for graphene. "simple", "version2", "version3" or anything else for basic growth. "simple" or anything else for AgUc.
  - getListType
```
public java.lang.String getListType()
```
    Selects the internal list type to be used between linear and binned. Input "parameters" variable: listType.
    
    Returns:
    
    "linear" or "binned".
  - setListType
```
public void setListType(java.lang.String listType)
```
    Sets the internal list type to be used. Should be linear or binned.
    
    Parameters:
    
    listType - linear or binned.
  - getPerimeterType
```
public short getPerimeterType()
```
    Input "parameters" variable: perimeterType.
    
    Returns:
    
    properly formated "SQUARE" or "CIRCLE" (default option).
  - setTemperature
```
public void setTemperature(float temperature)
```
  - getTemperature
```
public float getTemperature()
```
    Simulation temperature. Input "parameters" variable: temperature.
    
    Returns:
    
    temperature
  - getPressureO2
```
public double getPressureO2()
```
    Partial pressure for O2 in atm.
    
    Returns:
    
    O2 pressure.
  - getGOMultiplier
```
public double getGOMultiplier()
```
    GO multiplier for plotting resolution problem solving.
    
    Returns:
    
    GO multiplier.
  - getPressureCO
```
public double getPressureCO()
```
    Partial pressure for CO in atm.
    
    Returns:
    
    CO pressure.
  - getDepositionFlux
```
public double getDepositionFlux()
```
    Number of atoms that is coming per second and per area. Synonym of deposition rate and diffusionMl. Input "parameters" variable: depositionFlux.
    
    Returns:
    
    deposition flux
    
    See Also:
    
    IRates.getDepositionRatePerSite()
  - getEndTime
```
public double getEndTime()
```
    Returns the maximum simulation time that each run has to do or -1 if there is no time limit. Input "parameters" variable: endTime.
    
    Returns:
    
    ending time of simulation or -1 (no time limit).
  - getCoverage
```
public double getCoverage()
```
    Returns the maximum coverage until a simulation is allowed to grow. Only valid for multi-flake simulations Input "parameters" variable: coverage.
    
    Returns:
    
    final coverage.
  - getPsdScale
```
public double getPsdScale()
```
    Factor with which has to be multiplied the size of the surface to calculate the PSD. I recommend to be 1. Converts this island:
```
                                                                  
                       'H                                   
       :H    ;HH;                                 
        HH.   #HH                                 
         HH`#HHH`     #HHHHH                      
         .HHHHHH      ,HHHHH                      
          #HHHH;H;`     #H'``              HHH`   
              HHHHH#H`   HHHH`       #HHH#HHHHH   
            :#HHHHHHH  ` :H;;#H   ;:`:#HHHHH;:    
              #HHHHH :HH; :HHH   :HHHHHHHHHHH;    
                HHHHHHHH` :#H;    HHHHHH;,HHHH;   
                  #HHHHHHHHHHH #HHHHHH#H   HHHH`  
                  :HHHHHHHHHHHHHHHHHH`      :H:`  
                  :HH`  HHHHHHH HHHHHH            
                  HH` :HHH::HHH:`#HHHH:`          
                    HHHHHHH`#HHHH  #HHH`          
                    HHH;#HH; HHH;                 
                     HHHHHH                       
                      #HHHH`                      
                :#'`  :HH'                        
                :HHH#HHHH;                        
                 ;HHHHHHH`                        
                  `.+HHHHH`                         
          
```
    to this smaller one:
```
   
               H  H.                
              `HHH   HHH           
               ;HHH:  H';      ;H: 
                ,HHH;;.H+; #`HHH,  
                  +HHH +H .HH';HH' 
                   +HHHHHHH#H   .. 
                   + ,H'+# HH+     
                    HHHH`+.        
                     H+#           
                  ;HHHH            
                    ;HH    
     
```
    Returns:
    
    psdScale
  - getPsdExtend
```
double getPsdExtend()
```
    Factor which has to be added as empty area to the surface. Used to decide the scale from this island:
```
  
:::::::::::::::::::::::::
:::::::::::::::::::::::::
::::@::@.::::::::::::::::
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```
    and this filled one:
```
 
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```
    Returns:
    
    psdExtend
    
    See Also:
    
    kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc#increaseEmptyArea(float[][], double)
  - setNumberOfSimulations
```
public void setNumberOfSimulations(int numberOfSimulations)
```
  - getNumberOfSimulations
```
public int getNumberOfSimulations()
```
    Selects the number of simulations that has to be done with the same parameters. Input "parameters" variable: numberOfSimulations.
    
    Returns:
    
    number of simulations.
  - getNumberOfSteps
```
public long getNumberOfSteps()
```
    Selects the number of steps that each simulation will at most. -1 by default, which means that it will run until another criteria is reached. Input "parameters" variable: numberOfSteps.
    
    Returns:
    
    number of simulations.
  - getNumberOfCo2
```
public int getNumberOfCo2()
```
    Selects the number of CO2 molecules that will be created at most. -1 by default, which means that it will run until another criteria is reached. Input "parameters" variable: numberOfCo2.
    
    Returns:
    
    number of simulations.
  - getCartSizeX
```
public int getCartSizeX()
```
    Selects the Cartesian size in X direction. Input "parameters" variable: cartSizeX.
    
    Returns:
    
    Cartesian size in X direction.
  - setCartSizeX
```
public void setCartSizeX(int sizeX)
```
  - getCartSizeY
```
public int getCartSizeY()
```
    Selects the Cartesian size in Y direction. Input "parameters" variable: cartSizeY.
    
    Returns:
    
    Cartesian size in Y direction.
  - setCartSizeY
```
public void setCartSizeY(int sizeY)
```
  - getCartSizeZ
```
public int getCartSizeZ()
```
    Selects the Cartesian size in Z direction. Next methods are only meaningful in etching, ignored in 2D surface growth. Input "parameters" variable: cartSizeZ.
    
    Returns:
    
    Cartesian size in Z direction.
  - setCartSizeZ
```
public void setCartSizeZ(int sizeZ)
```
  - getMillerX
```
public int getMillerX()
```
  - setMillerX
```
public void setMillerX(int sizeX)
```
  - getMillerY
```
public int getMillerY()
```
  - setMillerY
```
public void setMillerY(int sizeY)
```
  - getMillerZ
```
public int getMillerZ()
```
  - setMillerZ
```
public void setMillerZ(int sizeZ)
```
  - getHexaSizeI
```
public int getHexaSizeI()
```
    Selects the lattice size in I direction. Can not be directly set from "parameters" file.
    
    Returns:
    
    lattice size in I direction.
  - getHexaSizeJ
```
public int getHexaSizeJ()
```
    Selects the lattice size in J direction. Can not be directly set from "parameters" file.
    
    Returns:
    
    lattice size in J direction.
  - getBinsLevels
```
public int getBinsLevels()
```
    Selects the number of bin levels. Useful only if binned list is selected. Input "parameters" variable: binsLevels.
    
    Returns:
    
    number of levels of the bin.
  - setBinsLevels
```
public void setBinsLevels(int binsLevels)
```
  - getExtraLevels
```
public int getExtraLevels()
```
  - setExtraLevels
```
public void setExtraLevels(int extraLevels)
```
  - isMultithreaded
```
public boolean isMultithreaded()
```
  - visualise
```
public boolean visualise()
```
    If GUI is enabled (see withGui()), selects to visualise the GUI. Input "parameters" variable: visualise.
    
    Returns:
    
    whether to show the GUI.
  - justCentralFlake
```
public boolean justCentralFlake()
```
    Selects to run a single flake simulation (faster and usually with Devita acceleration) or not. If not selected, usually a multi-flake simulation will happen in a periodic simulation box. Input "parameters" variable: justCentralFlake.
    
    Returns:
    
    whether to simulate just a single flake.
  - withGui
```
public boolean withGui()
```
    Selects to enable all the GUI with its windows. Input "parameters" variable: withGui. See also visualise() to also show the GUI.
    
    Returns:
    
    whether to enable GUI.
  - printToImage
```
public boolean printToImage()
```
    Selects to print the simulated system (the canvas of the frame) to a PNG file. Can be only be used if GUI is enabled (see withGui()). Input "parameters" variable: printToImage.
    
    Returns:
    
    whether to print to a PNG file.
  - getCalculationMode
```
public java.lang.String getCalculationMode()
```
    Selects the type of system to be calculated. Can be Si (for silicon etching), Ag (2D Ag/Ag growth in former mode), AgUc (same as previous Ag/Ag growth, with correct periodicity), basic (synthetic simulation mode in a square lattice), graphene (graphene 2D growth simulation) or Catalysis (CO2 catalysis on RuO2 (110)). For the graphene and catalysis pay attention to the used rates library with getRatesLibrary(). The temperature (getTemperature()) has to be between 120 and 180 for Ag, between 120 and 220 for basic and 1273 for graphene. Input "parameters" variable: calculationMode.
    
    Returns:
    
    calculation mode. Either: "Si", "Ag", "AgUc", "basic", "graphene" or "catalysis"
  - getSurfaceType
```
public java.lang.String getSurfaceType()
```
    The options below are for "Ag" calculationMode (see getCalculationMode()). Instead of using this calculation mode, it is recommended to use "AgUc" calculation mode, which has the correct periodicity and shape. Can be "cartesian" or "periodic". If "cartesian" is chosen, the surface (islands) will have the same shape as in the GUI, but the periodicity will not be correct in top-bottom (there is a shift of 60º). If "periodic" is chosen, the shape will be shifted by 60º and periodicity will be correct in 2D. This option will change the PSD; "cartesian" will have vertical and horizontal symmetry and in "periodic" the symmetry will be shifted by 60º. This variable can be also used for the PSD utility (see getCalculationType()) to choose between to do the tents for the surfaces or not.
    
    Returns:
    
    surface type. For "Ag" either: "cartesian" or "periodic". For PSD utility: "tent" or "plane".
  - doPsd
```
public boolean doPsd()
```
    Selects to do a PSD analysis of the simulated system. If many repetitions are used (see getNumberOfSimulations()), the PSD will be smoother and better defined. I recommend to use getPsdScale() == 1 and getPsdExtend() == 1. Input "parameters" variable: doPsd.
    
    Returns:
    
    whether to do a PSD.
  - isPsdSymmetric
```
public boolean isPsdSymmetric()
```
    Returns if the PSD (doPsd()) has to be symmetrised. If the periodicity is correctly implemented, the PSD tents to be symmetric circularly. If this option is enabled, helps to that symmetry. Or, the other way around, one can obtain properly defined PSD with less repetitions (getNumberOfSimulations()) Input "parameters" variable: isPsdSymmetric.
    
    Returns:
    
    psdSymmetry
  - isPeriodicSingleFlake
```
public boolean isPeriodicSingleFlake()
```
    Returns if single-flake simulation is periodic. If yes, a simulation size of selected size is created and it will be periodic. If not, a circular region will be created in the selected region and when current atom exits the perimeter it will be inserted by a prefixed statistics. Input "parameters" variable: periodicSingleFlake.
    
    Returns:
    
    whether periodic in single flake.
  - outputData
```
public boolean outputData()
```
    Chooses to output data or not. Input "parameters" variable: outputData. It has to be used in combination with getOutputFormats() to chose the proper format for the output.
    
    Returns:
    
    whether to output data.
  - getOutputFormats
```
public java.util.EnumSet<OutputType.formatFlag> getOutputFormats()
```
    To have the possibility to output to different file formats. Available options are: TXT, PNG, MKO, EXTRA, EXTRA2, AE (extra information for activation energy runs) or XYZ. Input "parameters" variable: outputDataFormat.
    
    Returns:
    
    output format. Either: TXT, PNG, MKO, EXTRA, EXTRA2, AE, XYZ or AETOTAL
  - getOutputEvery
```
public int getOutputEvery()
```
    How frequently should be printed extra file of catalysis.
    
    Returns:
    
    output frequency.
  - randomSeed
```
public boolean randomSeed()
```
    Selects to use randomSeed, based on the current time in ms. Input "parameters" variable: randomSeed.
    
    Returns:
    
    whether to use random seed.
  - useMaxPerimeter
```
public boolean useMaxPerimeter()
```
    In single flake simulation mode (justCentralFlake()) selects the initial size of the simulation area. If this option is enabled, biggest possible area is used since the beginning. Input "parameters" variable: useMaxPerimeter.
    
    Returns:
    
    whether to use maximum possible perimeter.
  - forceNucleation
```
public boolean forceNucleation()
```
    If two terraces are together freeze them, in multi-flake simulation mode. Should be only disabled for debugging purposes because slows down significantly the execution time. Input "parameters" variable: forceNucleation.
    
    Returns:
    
    whether to force nucleation.
  - useDevita
```
public boolean useDevita()
```
    Devita accelerator makes execution much faster, it may change results a bit. It is tested for single-flake simulations and seems to work fine. Nothing tried yet for multi-flake simulations. Input "parameters" variable: devita.
    
    Returns:
    
    whether to use Devita accelerator.
  - doCatalysisAdsorption
```
public boolean doCatalysisAdsorption()
```
    Adsorb atoms during catalysis simulation. Input "parameters" variable: catalysisAdsorption.
    
    Returns:
    
    do adsorption.
  - doCatalysisDesorption
```
public boolean doCatalysisDesorption()
```
    Desorb atoms during catalysis simulation. Input "parameters" variable: catalysisDesorption.
    
    Returns:
    
    do desorption.
  - doPrintAllIterations
```
public boolean doPrintAllIterations()
```
    Print all iterations during catalysis simulation. Input "parameters" variable: printAllIterations.
    
    Returns:
    
    print all iterations.
  - doCatalysisReaction
```
public boolean doCatalysisReaction()
```
    Allow to react atoms during catalysis simulation. Input "parameters" variable: catalysisReaction.
    
    Returns:
    
    do reaction.
  - doCatalysisDiffusion
```
public boolean doCatalysisDiffusion()
```
    Diffuse atom during catalysis simulation. Input "parameters" variable: catalysisDiffusion.
    
    Returns:
    
    do diffusion.
  - computeTree
```
private void computeTree()
```
  - useCatalysisTree
```
public boolean useCatalysisTree(byte process)
```
    Instead of writing "true", one can use the word "tree" to use a tree to store catalysis processes.
    
    Parameters:
    
    process -
    
    Returns:
  - catalysisStart
```
public java.lang.String catalysisStart()
```
    Starts a catalysis run given coverage. Can be "O" (Oxygen covered), "CO" (CO covered), "empty" or "random" (randomly covered surface). Input "parameters" variable: catalysisStart.
    
    Returns:
    
    do diffusion.
  - doCatalysisO2Dissociation
```
public boolean doCatalysisO2Dissociation()
```
    Dissociates O2 atoms during catalysis simulation Input "parameters" variable: catalysisO2Dissociation.
    
    Returns:
    
    do O2 dissociation.
  - areCollectionsAutomatic
```
public boolean areCollectionsAutomatic()
```
    Allow to change between tree and array collections, when the code decides to do so. Input "parameters" variable: automaticCollections.
    
    Returns:
    
    "automatically" change between tree/array.
  - doIslandDiffusion
```
public boolean doIslandDiffusion()
```
    In concerted calculation mode, allow to island to move. Input "parameter" variable: doIslandDiffusion.
    
    Returns:
    
    island moving
  - doMultiAtomDiffusion
```
public boolean doMultiAtomDiffusion()
```
    In concerted calculation mode, allow to atoms on the edge to move. For example, two atoms can diffuse together. Input "parameter" variable: doMultiAtomDiffusion.
    
    Returns:
    
    multi-atom moving
  - getEvolutionaryAlgorithm
```
public java.lang.String getEvolutionaryAlgorithm()
```
  - isEvaluatorParallel
```
public boolean isEvaluatorParallel()
```
  - getPopulationSize
```
public int getPopulationSize()
```
  - getOffspringSize
```
public int getOffspringSize()
```
  - getPopulationReplacement
```
public int getPopulationReplacement()
```
  - getTotalIterations
```
public int getTotalIterations()
```
    Total number of iterations that the evolutionary algorithm has to do.
    
    Returns:
    
    total number of iterations.
  - getRepetitions
```
public int getRepetitions()
```
    Number of repetitions or evaluations that a single Gene has to do.
    
    Returns:
    
    by default 18.
  - getReadReference
```
public boolean getReadReference()
```
    Chooses between to read a reference PSD or doing an initial run to be the objective for the Evolutionary run
    
    Returns:
    
    read reference?
  - setCalculationMode
```
public void setCalculationMode(java.lang.String mode)
```
  - setPopulation
```
public void setPopulation(int populationSize)
```
  - setEvolutionaryAlgorithm
```
public void setEvolutionaryAlgorithm(java.lang.String name)
```
  - getStopError
```
public double getStopError()
```
    For evolutionary algorithm run mode target minimum error
    
    Returns:
    
    minimum error
  - getMinValueGene
```
public double getMinValueGene()
```
    For evolutionary algorithm, minimum possible value of a gene.
    
    Returns:
    
    minimum error
  - getMaxValueGene
```
public double getMaxValueGene()
```
    For evolutionary algorithm, maximum possible value of a gene.
    
    Returns:
    
    minimum error
  - isExpDistribution
```
public boolean isExpDistribution()
```
    Chooses between exponential distribution of the random genes (true) or linear distribution (false)
    
    Returns:
    
    true exponential distribution; false linear
  - getEvaluatorTypes
```
public java.util.EnumSet<EvaluatorType.evaluatorFlag> getEvaluatorTypes()
```
    To have the possibility to choose between different evaluators in genetic algorithm runs. For the moment only PSD, TIME and HIERARCHY.
    
    Returns:
    
    evaluator type. Either: PSD, TIME and HIERARCHY.
  - getHierarchyEvaluator
```
public java.lang.String getHierarchyEvaluator()
```
    If a hierarchy evaluator has been chosen, select the type of hierarchy evaluator. Options: "basic", "step", "reference" and "Frobenius".
    
    Returns:
    
    "basic", "step", "reference" or "Frobenius".
  - getEvolutionarySearchType
```
public java.lang.String getEvolutionarySearchType()
```
  - isEnergySearch
```
public boolean isEnergySearch()
```
  - isDiffusionFixed
```
public boolean isDiffusionFixed()
```
    Decides if diffusion must be fixed.
    
    Returns:
    
    true if fixed, false otherwise

Class Parser

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

catalysisTree

restart

calculationType

ratesLibrary

listType

perimeterType

calculationMode

surfaceType

temperature

pressureCO

pressureO2

depositionFlux

endTime

coverage

psdScale

psdExtend

numberOfSimulations

numberOfSteps

numberOfCo2

cartSizeX

cartSizeY

cartSizeZ

millerX

millerY

millerZ

binsLevels

extraLevels

multithreaded

visualise

withGui

justCentralFlake

printToImage

psd

psdSymmetry

periodicSingleFlake

outputData

randomSeed

useMaxPerimeter

forceNucleation

devita

catalysisAdsorption

catalysisDesorption

catalysisReaction

catalysisDiffusion

catalysisStart

printAllIterations

catalysisO2Dissociation

automaticCollections

doIslandDiffusion

doMultiAtomDiffusion

outputDataFormat

outputType

numericFormatCode

outputEvery

evolutionaryAlgorithm

parallelEvaluator

populationSize

offspringSize

populationReplacement

totalIterations

repetitions

readReference

stopError

minValueGene

maxValueGene

goMultiplier

expDistribution

evaluatorType

numericStatusCode

evaluator

hierarchyEvaluator

evolutionarySearchType

fixDiffusion

Constructor Detail