org.jmol.adapter.readers.quantum
Class GamessReader

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.MOReader
              extended by org.jmol.adapter.readers.quantum.GamessReader
Direct Known Subclasses:
GamessUKReader, GamessUSReader

public abstract class GamessReader
extends MOReader


Field Summary
protected  java.util.List atomNames
           
private  java.util.Hashtable calcOptions
           
private  boolean isTypeSet
           
 
Fields inherited from class org.jmol.adapter.readers.quantum.MOReader
energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
 
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
GamessReader()
           
 
Method Summary
protected static java.lang.String fixBasisLine(java.lang.String line)
           
protected abstract  java.lang.String fixShellTag(java.lang.String tag)
           
protected abstract  void readAtomsInBohrCoordinates()
           
protected  void readBasisInfo()
           
private  void readCalculationInfo(java.lang.String type)
           
protected  void readControlInfo()
           
protected  void readFrequencies()
           
protected  void readGaussianBasis(java.lang.String initiator, java.lang.String terminator)
           
protected  void setCalculationType()
           
 
Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addMOData, checkNboLine, getMOHeader, getNboTypes, initializeReader, readMolecularOrbitals, setMOData, setMOType
 
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, checkLine, 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

atomNames

protected java.util.List atomNames

calcOptions

private java.util.Hashtable calcOptions

isTypeSet

private boolean isTypeSet
Constructor Detail

GamessReader

public GamessReader()
Method Detail

readAtomsInBohrCoordinates

protected abstract void readAtomsInBohrCoordinates()
                                            throws java.lang.Exception
Throws:
java.lang.Exception

readGaussianBasis

protected void readGaussianBasis(java.lang.String initiator,
                                 java.lang.String terminator)
                          throws java.lang.Exception
Throws:
java.lang.Exception

fixShellTag

protected abstract java.lang.String fixShellTag(java.lang.String tag)

readFrequencies

protected void readFrequencies()
                        throws java.lang.Exception
Throws:
java.lang.Exception

fixBasisLine

protected static java.lang.String fixBasisLine(java.lang.String line)

setCalculationType

protected void setCalculationType()

readControlInfo

protected void readControlInfo()
                        throws java.lang.Exception
Throws:
java.lang.Exception

readBasisInfo

protected void readBasisInfo()
                      throws java.lang.Exception
Throws:
java.lang.Exception

readCalculationInfo

private void readCalculationInfo(java.lang.String type)
                          throws java.lang.Exception
Throws:
java.lang.Exception