basic.io

Class Restart

java.lang.Object

basic.io.Restart

public class Restart
extends java.lang.Object

Author:

J. Alberdi-Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private long[]	co2C Current moment CO2 amount.
private long[]	co2P Previous moment CO2 amount.
private int	counterCo2
private double	currentTime
private java.util.List<java.lang.Double>	deltaTimeBetweenTwoAttachments
private java.util.List<java.lang.Double>	deltaTimePerAtom
(package private) static java.nio.charset.Charset	ENCODING
private boolean	extraOutput Attribute to control the output of data every 1% and nucleation.
private boolean	extraOutput2 Attribute to control the output of extra data of delta time between two attachments and between an atom is deposited and attached to an island.
private java.lang.String	folder
private boolean	isCatalysis
private boolean	isConcerted
private int	iteration
static int	MAX_DIMS
private java.io.PrintWriter	outCatalysis
private java.io.PrintWriter	outData
private java.io.PrintWriter[]	outDataAe
private java.lang.String	outDataFormat
private java.io.PrintWriter	outDeltaAttachments
private java.io.PrintWriter	outPerAtom
private java.io.PrintWriter	outTof
private double	previousTime

Constructor Summary

Constructors

Constructor and Description
Restart()
Restart(boolean extraOutput, boolean extraOutput2) Creates a restart object to be used to write extra data files.
Restart(boolean catalysisOutput, java.lang.String restartFolder)
Restart(java.lang.String restartFolder)

Method Summary

Modifier and Type	Method and Description
private java.lang.String	addFolderAndSuffix(java.lang.String fileName, java.lang.String suffix) Normalises fileName with the folder and proper suffix.
private void	createFolder(java.lang.String restartFolder)
void	flushCatalysis()
void	flushExtra()
java.io.PrintWriter	getExtraWriter()
java.io.PrintWriter[]	getExtraWriters()
static java.lang.String	getGitRevision()
static java.lang.String	getJarBaseDir() Returns the base location of the JAR file (or the main executable instead).
java.lang.String	getPsdScript(java.lang.String inputFileName, java.lang.String outputFileName, float min, float max, int sizeX, int sizeY)
private void	initCatalysis(int simulationNumber)
private void	initConcerted(int simulationNumber)
java.util.ArrayList<java.util.ArrayList>	readDataTextFile(java.lang.String fileName) Reads a file to a ArrayList of unknown size aimed to be like array[][].
java.lang.String	readFile(java.lang.String fileName)
float[][]	readPsdText2D(int dimensions, int[] sizes, java.lang.String fileName)
float[][]	readSurfaceBinary2D(java.lang.String fileName)
float[][]	readSurfaceBinary2D(java.lang.String fileName, int factor) Reads a surface from a (binary) file and it reduces it surface by the given factor.
float[][]	readSurfaceText2D(int dimensions, int[] sizes, java.lang.String fileName)
float[][]	readSurfaceText2D(java.lang.String fileName)
void	reset()
void	resetCatalysis()
void	writeCatalysisAdsorptionDataText(int simulationNumber, double[][] data)
void	writeExtra2Output(AbstractGrowthLattice lattice, AbstractGrowthAtom atom, float coverage, double time, double diffusionRate)
void	writeExtraCatalysisOutput(double time, float[] coverages, long[] steps, long[] co2, int[] sizes)
void	writeExtraOutput(AbstractGrowthLattice lattice, float coverage, int nucleations, double time, double adsorptionRate, double diffusionRate, long simulatedSteps, double sumProbabilities)
void	writePsdBinary(int dimensions, int[] sizes, float[][] data, int simulationNumber) Writes float data to a file called "psd[number].mko".
void	writePsdBinary(int dimensions, int[] sizes, float[][] data, java.lang.String fileName)
void	writePsdText1D(float[] data, java.lang.String fileName)
void	writePsdText2D(int dimensions, int[] sizes, float[][] data, int simulationNumber) Function to print to text file each PSD result.
void	writePsdText2D(int dimensions, int[] sizes, float[][] data, java.lang.String fileName)
void	writeSurfaceBinary(int dimensions, int[] sizes, float[][] data, int simulationNumber) Writes float data to a file called "surface[number].mko".
void	writeSurfaceBinary2D(float[][] data, int simulationNumber)
void	writeSurfaceHexagonal(int dimensions, int[] sizes, float[][] data, int simulationNumber)
void	writeSurfaceStationary(float[][] data)
void	writeSurfaceText2D(int dimensions, int[] sizes, float[][] data, int simulationNumber)
void	writeSurfaceText2D(int dimensions, int[] sizes, float[][] data, java.lang.String fileName)
void	writeSvg(int simulationNumber, AbstractLattice lattice)
void	writeTextString(java.lang.String data, java.lang.String fileName)
void	writeXyz(int simulationNumber, AbstractLattice lattice)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MAX_DIMS

public static final int MAX_DIMS

See Also:

Constant Field Values

folder

private java.lang.String folder

ENCODING

static final java.nio.charset.Charset ENCODING

iteration

private int iteration

counterCo2

private int counterCo2

extraOutput

private boolean extraOutput

Attribute to control the output of data every 1% and nucleation.

extraOutput2

private boolean extraOutput2

Attribute to control the output of extra data of delta time between two attachments and between an atom is deposited and attached to an island.

isCatalysis

private final boolean isCatalysis

isConcerted

private final boolean isConcerted

outDataFormat

private java.lang.String outDataFormat

outData

private java.io.PrintWriter outData

outDataAe

private java.io.PrintWriter[] outDataAe

outDeltaAttachments

private java.io.PrintWriter outDeltaAttachments

outPerAtom

private java.io.PrintWriter outPerAtom

outCatalysis

private java.io.PrintWriter outCatalysis

outTof

private java.io.PrintWriter outTof

deltaTimeBetweenTwoAttachments

private java.util.List<java.lang.Double> deltaTimeBetweenTwoAttachments

deltaTimePerAtom

private java.util.List<java.lang.Double> deltaTimePerAtom

currentTime

private double currentTime

previousTime

private double previousTime

co2P

private long[] co2P

Previous moment CO2 amount.

co2C

private long[] co2C

Current moment CO2 amount.

Constructor Detail

Restart

public Restart()

Restart

public Restart(java.lang.String restartFolder)

Restart

public Restart(boolean extraOutput,
               boolean extraOutput2)

Creates a restart object to be used to write extra data files.

Parameters:

extraOutput -

extraOutput2 -

Restart

public Restart(boolean catalysisOutput,
               java.lang.String restartFolder)

Method Detail

getJarBaseDir

public static java.lang.String getJarBaseDir()

Returns the base location of the JAR file (or the main executable instead).

Returns:

base location of the executable

getGitRevision

public static java.lang.String getGitRevision()

getPsdScript

public java.lang.String getPsdScript(java.lang.String inputFileName,
                                     java.lang.String outputFileName,
                                     float min,
                                     float max,
                                     int sizeX,
                                     int sizeY)

writePsdBinary

public void writePsdBinary(int dimensions,
                           int[] sizes,
                           float[][] data,
                           int simulationNumber)

Writes float data to a file called "psd[number].mko". First of all calls to the header writing: look documentation there.

Parameters:

dimensions -

sizes -

data -

simulationNumber -

writePsdBinary

public void writePsdBinary(int dimensions,
                           int[] sizes,
                           float[][] data,
                           java.lang.String fileName)

writeSurfaceBinary

public void writeSurfaceBinary(int dimensions,
                               int[] sizes,
                               float[][] data,
                               int simulationNumber)

Writes float data to a file called "surface[number].mko". First of all calls to the header writing: look documentation there.

Parameters:

dimensions -

sizes -

data -

simulationNumber -

writeSurfaceBinary2D

public void writeSurfaceBinary2D(float[][] data,
                                 int simulationNumber)

writePsdText2D

public void writePsdText2D(int dimensions,
                           int[] sizes,
                           float[][] data,
                           int simulationNumber)

Function to print to text file each PSD result. Mainly thought to plot it with gnuplot Instructions to plot: > set dgrid3d 30,30 > splot "psd000.txt" u 1:2:3 w l

Parameters:

dimensions -

sizes -

data -

simulationNumber -

writePsdText1D

public void writePsdText1D(float[] data,
                           java.lang.String fileName)

writePsdText2D

public void writePsdText2D(int dimensions,
                           int[] sizes,
                           float[][] data,
                           java.lang.String fileName)

writeSurfaceText2D

public void writeSurfaceText2D(int dimensions,
                               int[] sizes,
                               float[][] data,
                               int simulationNumber)

writeSurfaceText2D

public void writeSurfaceText2D(int dimensions,
                               int[] sizes,
                               float[][] data,
                               java.lang.String fileName)

writeSurfaceHexagonal

public void writeSurfaceHexagonal(int dimensions,
                                  int[] sizes,
                                  float[][] data,
                                  int simulationNumber)

writeSurfaceStationary

public void writeSurfaceStationary(float[][] data)

writeTextString

public void writeTextString(java.lang.String data,
                            java.lang.String fileName)

writeCatalysisAdsorptionDataText

public void writeCatalysisAdsorptionDataText(int simulationNumber,
                                             double[][] data)

writeXyz

public void writeXyz(int simulationNumber,
                     AbstractLattice lattice)

writeSvg

public void writeSvg(int simulationNumber,
                     AbstractLattice lattice)

writeExtraOutput

public void writeExtraOutput(AbstractGrowthLattice lattice,
                             float coverage,
                             int nucleations,
                             double time,
                             double adsorptionRate,
                             double diffusionRate,
                             long simulatedSteps,
                             double sumProbabilities)

writeExtra2Output

public void writeExtra2Output(AbstractGrowthLattice lattice,
                              AbstractGrowthAtom atom,
                              float coverage,
                              double time,
                              double diffusionRate)

writeExtraCatalysisOutput

public void writeExtraCatalysisOutput(double time,
                                      float[] coverages,
                                      long[] steps,
                                      long[] co2,
                                      int[] sizes)

getExtraWriter

public java.io.PrintWriter getExtraWriter()

getExtraWriters

public java.io.PrintWriter[] getExtraWriters()

readSurfaceBinary2D

public float[][] readSurfaceBinary2D(java.lang.String fileName,
                                     int factor)
                              throws java.io.FileNotFoundException

Reads a surface from a (binary) file and it reduces it surface by the given factor.

Parameters:

fileName -

factor - how much we want to reduce the surface. A number greater than one

Returns:

reduced surface

Throws:

java.io.FileNotFoundException

readSurfaceBinary2D

public float[][] readSurfaceBinary2D(java.lang.String fileName)
                              throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

readPsdText2D

public float[][] readPsdText2D(int dimensions,
                               int[] sizes,
                               java.lang.String fileName)
                        throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

readSurfaceText2D

public float[][] readSurfaceText2D(int dimensions,
                                   int[] sizes,
                                   java.lang.String fileName)
                            throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

readSurfaceText2D

public float[][] readSurfaceText2D(java.lang.String fileName)
                            throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

readDataTextFile

public java.util.ArrayList<java.util.ArrayList> readDataTextFile(java.lang.String fileName)
                                                          throws java.io.FileNotFoundException

Reads a file to a ArrayList of unknown size aimed to be like array[][].

Parameters:

fileName -

Returns:

Throws:

java.io.FileNotFoundException

readFile

public java.lang.String readFile(java.lang.String fileName)

flushExtra

public void flushExtra()

resetCatalysis

public void resetCatalysis()

flushCatalysis

public void flushCatalysis()

reset

public void reset()

initCatalysis

private void initCatalysis(int simulationNumber)

initConcerted

private void initConcerted(int simulationNumber)

createFolder

private void createFolder(java.lang.String restartFolder)

addFolderAndSuffix

private java.lang.String addFolderAndSuffix(java.lang.String fileName,
                                            java.lang.String suffix)

Normalises fileName with the folder and proper suffix.

Parameters:

fileName - input file name.

suffix - suffix to be added.

Returns:

complete file name.