public class GaussianFchkReader extends MOReader
BasisFunctionReader.MOEnergySorter
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 |
energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells
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 and Description |
---|
GaussianFchkReader() |
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() |
addMOData, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData, setMOType
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO
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
private java.util.Map<java.lang.String,java.lang.Object> fileData
private int atomCount
private static java.lang.String[] AO_TYPES
protected void initializeReader() throws java.lang.Exception
initializeReader
in class MOReader
java.lang.Exception
private void readAllData() throws java.lang.Exception
java.lang.Exception
private void readAtoms() throws java.lang.Exception
java.lang.Exception
private void readBonds()
private void readDipoleMoment() throws java.lang.Exception
java.lang.Exception
private void readPartialCharges() throws java.lang.Exception
java.lang.Exception
private void readBasis() throws java.lang.Exception
java.lang.Exception
private void readMOs() throws java.lang.Exception
java.lang.Exception
private void getOrbitals(float[] e, float[] c, int occ, int nElec)
private void readFrequencies() throws java.lang.Exception, java.io.IOException
java.lang.Exception
java.io.IOException