org.jmol.adapter.readers.quantum
Class MopacGraphfReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.quantum.BasisFunctionReader
          extended by org.jmol.adapter.readers.quantum.SlaterReader
              extended by org.jmol.adapter.readers.quantum.MopacSlaterReader
                  extended by org.jmol.adapter.readers.quantum.MopacGraphfReader

public class MopacGraphfReader
extends MopacSlaterReader

Reads Mopac 2007 GRAPHF output files

Author:
Bob Hanson

Nested Class Summary
 
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
 
Field Summary
private  int atomCount
           
private  float[][] invMatrix
           
private  boolean isNewFormat
           
private  int nCoefficients
           
private  java.util.List orbitalData
           
private  java.util.List orbitalInfo
           
 
Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
atomicNumbers, MIN_COEF
 
Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader
slaterArray, slaters
 
Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, shells
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer
 
Constructor Summary
MopacGraphfReader()
           
 
Method Summary
protected  boolean checkLine()
           
protected  void initializeReader()
           
private  void readAtoms()
           
private  boolean readKeywords()
           
private  void readMolecularOrbitals(boolean isBeta)
           
private  void readSlaterBasis()
           
 
Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
createSphericalSlaterByType, scaleSlater
 
Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
 
Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDFMap, isQuantumBasisSupported, setMO
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

atomCount

private int atomCount

nCoefficients

private int nCoefficients

invMatrix

private float[][] invMatrix

isNewFormat

private boolean isNewFormat

orbitalData

private java.util.List orbitalData

orbitalInfo

private java.util.List orbitalInfo
Constructor Detail

MopacGraphfReader

public MopacGraphfReader()
Method Detail

initializeReader

protected void initializeReader()
Overrides:
initializeReader in class AtomSetCollectionReader

checkLine

protected boolean checkLine()
                     throws java.lang.Exception
Overrides:
checkLine in class AtomSetCollectionReader
Returns:
true if need to read new line
Throws:
java.lang.Exception

readAtoms

private void readAtoms()
                throws java.lang.Exception
Throws:
java.lang.Exception

readSlaterBasis

private void readSlaterBasis()
                      throws java.lang.Exception
Throws:
java.lang.Exception

readMolecularOrbitals

private void readMolecularOrbitals(boolean isBeta)
                            throws java.lang.Exception
Throws:
java.lang.Exception

readKeywords

private boolean readKeywords()
                      throws java.lang.Exception
Throws:
java.lang.Exception