org.jmol.adapter.readers.quantum

Class GaussianFchkReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.quantum.BasisFunctionReader

org.jmol.adapter.readers.quantum.MOReader

org.jmol.adapter.readers.quantum.GaussianFchkReader

public class GaussianFchkReader
extends MOReader

Reader for Gaussian fchk files

Author:

hansonr Bob Hanson hansonr@stolaf.edu

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

BasisFunctionReader.MOEnergySorter

Field Summary

Fields

Modifier and Type	Field and Description
private static java.lang.String[]	AO_TYPES
private int	atomCount
private java.util.Map<java.lang.String,java.lang.Object>	fileData

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, nCoef, nOrbitals, orbitals, shells

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, vwr

Constructor Summary

Constructors

Constructor and Description
GaussianFchkReader()

Method Summary

Modifier and Type	Method and Description
private void	getOrbitals(float[] e, float[] c, int occ, int nElec)
protected void	initializeReader()
private void	readAllData()
private void	readAtoms()
private void	readBasis()
private void	readBonds()
private void	readDipoleMoment()
private void	readFrequencies()
private void	readMOs()
private void	readPartialCharges()

Methods inherited from class org.jmol.adapter.readers.quantum.MOReader

addMOData, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData, setMOType

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReader, finalizeReaderASCR, getElementSymbol, getFilter, getFortranFormatLengths, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setSpaceGroupName, setSymmetryOperator, setTransform, setU, setUnitCell, setUnitCellItem, setup, setupASCR

Methods inherited from class java.lang.Object

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

Field Detail

fileData

private java.util.Map<java.lang.String,java.lang.Object> fileData

atomCount

private int atomCount

AO_TYPES

private static java.lang.String[] AO_TYPES

Constructor Detail

GaussianFchkReader

public GaussianFchkReader()

Method Detail

initializeReader

protected void initializeReader()
                         throws java.lang.Exception

Overrides:

initializeReader in class MOReader

Throws:

java.lang.Exception

readAllData

private void readAllData()
                  throws java.lang.Exception

Throws:

java.lang.Exception

readAtoms

private void readAtoms()
                throws java.lang.Exception

Throws:

java.lang.Exception

readBonds

private void readBonds()

readDipoleMoment

private void readDipoleMoment()
                       throws java.lang.Exception

Throws:

java.lang.Exception

readPartialCharges

private void readPartialCharges()
                         throws java.lang.Exception

Throws:

java.lang.Exception

readBasis

private void readBasis()
                throws java.lang.Exception

Throws:

java.lang.Exception

readMOs

private void readMOs()
              throws java.lang.Exception

Throws:

java.lang.Exception

getOrbitals

private void getOrbitals(float[] e,
                         float[] c,
                         int occ,
                         int nElec)

readFrequencies

private void readFrequencies()
                      throws java.lang.Exception,
                             java.io.IOException

Throws:

java.lang.Exception

java.io.IOException