cct.adf
Class ADFOutput

java.lang.Object
  extended by cct.adf.ADFOutput
All Implemented Interfaces:
OutputResultsInterface, StructureManagerInterface

public class ADFOutput
extends java.lang.Object
implements OutputResultsInterface, StructureManagerInterface

Title: Computational Chemistry Tookit

Description:

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

Company: ANU


Constructor Summary
ADFOutput()
           
 
Method Summary
 VIBRATIONAL_SPECTRUM[] availableVibrationalSpectra()
           
 int countFrequencies()
           
 int countSectionsWithGeometry()
           
 int countSpectra()
           
 double[] getAllTerms(java.lang.String term)
           
 java.lang.String[] getAvailPropToChart()
           
 float[][] getDisplacementVectors(int n)
           
 double getFrequency(int n)
           
 void getMolecularInterface(MoleculeInterface molec, int section_number)
           
 ADFOutputSection getSection(int section_number)
           
 int[] getSectionsWithGeometry()
           
 void getSpectrum(double[] x, double[] y, int dim, VIBRATIONAL_SPECTRUM type)
           
 double getSpectrumValue(int n, VIBRATIONAL_SPECTRUM spectrum)
           
 float[][] getStructure(int n)
           
 float[][] getStructure(int n, java.lang.String term)
           
 boolean hasDisplacementVectors()
           
 boolean hasInfraredSpectrum()
           
 boolean hasInteractiveChart()
           
 boolean hasJobSummary()
           
 boolean hasPDepolSpectrum()
           
 boolean hasRamanSpectrum()
           
 boolean hasUDepolSpectrum()
           
 boolean hasVCDSpectrum()
           
static void main(java.lang.String[] args)
           
 java.util.ArrayList<ADFAtom> parseCoordinates(java.io.BufferedReader in)
           
 void parseFile(java.lang.String fileName)
          Parses ADF output file
 java.util.ArrayList<ADFAtom> parseInitialGeometry(java.io.BufferedReader in)
           
 boolean parseLogInfo(ADFOutputSection section, java.io.BufferedReader in)
           
 boolean parseSection(java.io.BufferedReader in)
           
 void selectSection(int n)
           
 void selectStructure(int number)
           
 void selectStructure(int number, java.lang.String term)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ADFOutput

public ADFOutput()
Method Detail

selectSection

public void selectSection(int n)

getSection

public ADFOutputSection getSection(int section_number)
                            throws java.lang.Exception
Throws:
java.lang.Exception

getMolecularInterface

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

parseFile

public void parseFile(java.lang.String fileName)
               throws java.lang.Exception
Parses ADF output file

Parameters:
fileName - String - file name
Throws:
java.lang.Exception

parseSection

public boolean parseSection(java.io.BufferedReader in)
                     throws java.lang.Exception
Throws:
java.lang.Exception

parseLogInfo

public boolean parseLogInfo(ADFOutputSection section,
                            java.io.BufferedReader in)
                     throws java.lang.Exception
Throws:
java.lang.Exception

parseInitialGeometry

public java.util.ArrayList<ADFAtom> parseInitialGeometry(java.io.BufferedReader in)
                                                  throws java.lang.Exception
Throws:
java.lang.Exception

parseCoordinates

public java.util.ArrayList<ADFAtom> parseCoordinates(java.io.BufferedReader in)
                                              throws java.lang.Exception
Throws:
java.lang.Exception

countSectionsWithGeometry

public int countSectionsWithGeometry()

getSectionsWithGeometry

public int[] getSectionsWithGeometry()

getAvailPropToChart

public java.lang.String[] getAvailPropToChart()

getAllTerms

public double[] getAllTerms(java.lang.String term)

hasJobSummary

public boolean hasJobSummary()
Specified by:
hasJobSummary in interface OutputResultsInterface

hasInteractiveChart

public boolean hasInteractiveChart()
Specified by:
hasInteractiveChart in interface OutputResultsInterface

hasVCDSpectrum

public boolean hasVCDSpectrum()
Specified by:
hasVCDSpectrum in interface OutputResultsInterface

hasUDepolSpectrum

public boolean hasUDepolSpectrum()
Specified by:
hasUDepolSpectrum in interface OutputResultsInterface

hasPDepolSpectrum

public boolean hasPDepolSpectrum()
Specified by:
hasPDepolSpectrum in interface OutputResultsInterface

hasRamanSpectrum

public boolean hasRamanSpectrum()
Specified by:
hasRamanSpectrum in interface OutputResultsInterface

hasInfraredSpectrum

public boolean hasInfraredSpectrum()
Specified by:
hasInfraredSpectrum in interface OutputResultsInterface

getStructure

public float[][] getStructure(int n)
Specified by:
getStructure in interface StructureManagerInterface

getStructure

public float[][] getStructure(int n,
                              java.lang.String term)
Specified by:
getStructure in interface StructureManagerInterface

selectStructure

public void selectStructure(int number)
                     throws java.lang.Exception
Specified by:
selectStructure in interface StructureManagerInterface
Throws:
java.lang.Exception

selectStructure

public void selectStructure(int number,
                            java.lang.String term)
                     throws java.lang.Exception
Specified by:
selectStructure in interface StructureManagerInterface
Throws:
java.lang.Exception

availableVibrationalSpectra

public VIBRATIONAL_SPECTRUM[] availableVibrationalSpectra()
Specified by:
availableVibrationalSpectra in interface OutputResultsInterface

countFrequencies

public int countFrequencies()
Specified by:
countFrequencies in interface OutputResultsInterface

countSpectra

public int countSpectra()
Specified by:
countSpectra in interface OutputResultsInterface

getFrequency

public double getFrequency(int n)
Specified by:
getFrequency in interface OutputResultsInterface

getSpectrumValue

public double getSpectrumValue(int n,
                               VIBRATIONAL_SPECTRUM spectrum)
Specified by:
getSpectrumValue in interface OutputResultsInterface

hasDisplacementVectors

public boolean hasDisplacementVectors()
Specified by:
hasDisplacementVectors in interface OutputResultsInterface

getDisplacementVectors

public float[][] getDisplacementVectors(int n)
Specified by:
getDisplacementVectors in interface OutputResultsInterface

getSpectrum

public void getSpectrum(double[] x,
                        double[] y,
                        int dim,
                        VIBRATIONAL_SPECTRUM type)
                 throws java.lang.Exception
Specified by:
getSpectrum in interface OutputResultsInterface
Throws:
java.lang.Exception

main

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