cct.siesta
Class SiestaInput

java.lang.Object
  extended by cct.siesta.SiestaInput
All Implemented Interfaces:
SiestaInterface

public class SiestaInput
extends java.lang.Object
implements SiestaInterface

Title: Computational Chemistry Tookit

Description:

Copyright: Copyright (c) 2005-2008 Dr. Vladislav Vassiliev

Company: ANU


Nested Class Summary
(package private)  class SiestaInput.SiestaAtom
           
 
Field Summary
static java.lang.String BLOCK_TOKEN
           
 
Fields inherited from interface cct.siesta.SiestaInterface
SIESTA_INTERFACE, SIESTA_SPECIES_LABEL, SIESTA_SPECIES_NUMBER
 
Constructor Summary
SiestaInput()
           
 
Method Summary
 float[][] calcAbsoluteCoordinates(java.util.ArrayList<SiestaInput.SiestaAtom> atoms, double[][] vectors)
           
 void centerContentsInCell()
           
static void centerContentsInCell(double[][] fracCoord, int nCenters)
           
 java.lang.String getAtomicCoordinatesAsString()
           
 java.lang.String getAtomicCoordinatesAsString(MoleculeInterface molec)
           
 java.util.HashMap<java.lang.Integer,ChemicalSpeciesLabel> getChemicalSpeciesLabels()
           
 double[][] getFractionalCoordinates(double[][] transMatrix)
           
static float[] getFractionalCoordinates(float x, float y, float z, float[][] transMatrix)
           
 java.lang.String getInputAsString()
           
 double[][] getLatticeVectors()
           
 void getMolecularInterface(MoleculeInterface molec)
           
 java.util.ArrayList<java.lang.String> getOtherOptions()
           
 java.lang.String getOtherOptionsAsString()
           
 java.lang.String getSpeciesLabelsAsString()
           
 java.lang.String getSystemLabel()
           
static void main(java.lang.String[] args)
           
 void parseAtomicCoordinatesAndAtomicSpecies(java.io.BufferedReader in)
           
 void parseAtomicCoordinatesAndAtomicSpecies(java.lang.String text)
           
 void parseChemicalSpeciesLabel(java.io.BufferedReader in)
           
 void parseChemicalSpeciesLabel(java.lang.String text)
           
 void parseFDF(java.lang.String filename, int fileType)
           
 void setAtomicCoordinatesFormat(AtomicCoordinatesFormat format)
           
 void setChemicalSpeciesLabels(java.util.Map<java.lang.Integer,ChemicalSpeciesLabel> speciesLabels)
           
 void setLatticeConstant(double latticeConst)
           
 void setLatticeParameters(double a, double b, double c, double alpha, double beta, double gamma)
           
 void setLatticeParameters(float a, float b, float c, float alpha, float beta, float gamma)
           
 void setOtherOptions(java.util.ArrayList<java.lang.String> other)
           
 void setOtherOptions(java.lang.String other)
           
 void setSystemLabel(java.lang.String name)
           
 void setSystemName(java.lang.String name)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

BLOCK_TOKEN

public static final java.lang.String BLOCK_TOKEN
See Also:
Constant Field Values
Constructor Detail

SiestaInput

public SiestaInput()
Method Detail

main

public static void main(java.lang.String[] args)

getLatticeVectors

public double[][] getLatticeVectors()

setLatticeConstant

public void setLatticeConstant(double latticeConst)

getMolecularInterface

public void getMolecularInterface(MoleculeInterface molec)
                           throws java.lang.Exception
Throws:
java.lang.Exception

calcAbsoluteCoordinates

public float[][] calcAbsoluteCoordinates(java.util.ArrayList<SiestaInput.SiestaAtom> atoms,
                                         double[][] vectors)
                                  throws java.lang.Exception
Throws:
java.lang.Exception

parseFDF

public void parseFDF(java.lang.String filename,
                     int fileType)
              throws java.lang.Exception
Throws:
java.lang.Exception

parseAtomicCoordinatesAndAtomicSpecies

public void parseAtomicCoordinatesAndAtomicSpecies(java.lang.String text)
                                            throws java.lang.Exception
Throws:
java.lang.Exception

parseAtomicCoordinatesAndAtomicSpecies

public void parseAtomicCoordinatesAndAtomicSpecies(java.io.BufferedReader in)
                                            throws java.lang.Exception
Throws:
java.lang.Exception

parseChemicalSpeciesLabel

public void parseChemicalSpeciesLabel(java.lang.String text)
                               throws java.lang.Exception
Throws:
java.lang.Exception

parseChemicalSpeciesLabel

public void parseChemicalSpeciesLabel(java.io.BufferedReader in)
                               throws java.lang.Exception
Throws:
java.lang.Exception

setLatticeParameters

public void setLatticeParameters(float a,
                                 float b,
                                 float c,
                                 float alpha,
                                 float beta,
                                 float gamma)

setLatticeParameters

public void setLatticeParameters(double a,
                                 double b,
                                 double c,
                                 double alpha,
                                 double beta,
                                 double gamma)

setSystemLabel

public void setSystemLabel(java.lang.String name)

setSystemName

public void setSystemName(java.lang.String name)

setAtomicCoordinatesFormat

public void setAtomicCoordinatesFormat(AtomicCoordinatesFormat format)

setChemicalSpeciesLabels

public void setChemicalSpeciesLabels(java.util.Map<java.lang.Integer,ChemicalSpeciesLabel> speciesLabels)

setOtherOptions

public void setOtherOptions(java.util.ArrayList<java.lang.String> other)

setOtherOptions

public void setOtherOptions(java.lang.String other)

getOtherOptionsAsString

public java.lang.String getOtherOptionsAsString()

getSpeciesLabelsAsString

public java.lang.String getSpeciesLabelsAsString()

getAtomicCoordinatesAsString

public java.lang.String getAtomicCoordinatesAsString()

getAtomicCoordinatesAsString

public java.lang.String getAtomicCoordinatesAsString(MoleculeInterface molec)

getInputAsString

public java.lang.String getInputAsString()
                                  throws java.lang.Exception
Throws:
java.lang.Exception

centerContentsInCell

public static void centerContentsInCell(double[][] fracCoord,
                                        int nCenters)

centerContentsInCell

public void centerContentsInCell()
                          throws java.lang.Exception
Throws:
java.lang.Exception

getFractionalCoordinates

public double[][] getFractionalCoordinates(double[][] transMatrix)

getFractionalCoordinates

public static float[] getFractionalCoordinates(float x,
                                               float y,
                                               float z,
                                               float[][] transMatrix)

getSystemLabel

public java.lang.String getSystemLabel()
Specified by:
getSystemLabel in interface SiestaInterface

getChemicalSpeciesLabels

public java.util.HashMap<java.lang.Integer,ChemicalSpeciesLabel> getChemicalSpeciesLabels()
Specified by:
getChemicalSpeciesLabels in interface SiestaInterface

getOtherOptions

public java.util.ArrayList<java.lang.String> getOtherOptions()
Specified by:
getOtherOptions in interface SiestaInterface