public class QchemReader extends MOReader
Molecular coordinates, normal coordinates of vibrations and MOs are read.
In order to get the output required for MO reading make sure that the $rem block has
print_general_basis TRUE
print_orbitals TRUE
This reader was developed from only a few output files, and therefore, is not guaranteed to properly read all Q-chem output. If you have problems, please contact the author of this code, not the developers of Q-chem.
This is a hacked version of Miguel's GaussianReader
Modifier and Type | Class and Description |
---|---|
protected class |
QchemReader.MOInfo |
BasisFunctionReader.MOEnergySorter
Modifier and Type | Field and Description |
---|---|
private QchemReader.MOInfo[] |
alphas |
private QchemReader.MOInfo[] |
betas |
private int |
calculationNumber
The number of the job being interpreted.
|
private static String |
DC_LIST |
private boolean |
dFixed |
(package private) String |
dList |
private static String |
DS_LIST |
(package private) boolean |
dSpherical |
private static String |
FC_LIST |
private boolean |
fFixed |
(package private) String |
fList |
private static String |
FS_LIST |
(package private) boolean |
fSpherical |
private boolean |
isFirstJob |
private int |
nBasis |
allowNoOrbitals, energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
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QchemReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkLine() |
protected void |
initializeReader() |
private void |
readAtoms() |
private void |
readBasis() |
private void |
readCalculationType() |
private void |
readEnergy() |
private void |
readESym(boolean haveSym) |
private void |
readFrequencies()
Interprets the Harmonic frequencies section.
|
private int |
readMOs(boolean restricted,
QchemReader.MOInfo[] moInfos) |
private void |
readPartialCharges() |
private void |
readQchemMolecularOrbitals() |
addCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData
canonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR
private int calculationNumber
private boolean isFirstJob
private QchemReader.MOInfo[] alphas
private QchemReader.MOInfo[] betas
private int nBasis
private boolean dFixed
private boolean fFixed
private static String DC_LIST
private static String DS_LIST
private static String FC_LIST
private static String FS_LIST
String dList
String fList
boolean dSpherical
boolean fSpherical
protected void initializeReader()
initializeReader
in class MOReader
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
private void readCalculationType()
private void readFrequencies() throws Exception, IOException
The vectors are added to a clone of the last read AtomSet. Only the Frequencies, reduced masses, force constants and IR intensities are set as properties for each of the frequency type AtomSet generated.
Exception
- If no frequences were encounteredIOException
- If an I/O error occursprivate void readEnergy()
private void readQchemMolecularOrbitals() throws Exception
Exception
private int readMOs(boolean restricted, QchemReader.MOInfo[] moInfos) throws Exception
Exception