javajs.api.GenericLineReader
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 | Description |
---|---|---|
protected class |
QchemReader.MOInfo |
BasisFunctionReader.MOEnergySorter
Modifier and Type | Field | Description |
---|---|---|
private QchemReader.MOInfo[] |
alphas |
|
private QchemReader.MOInfo[] |
betas |
|
private int |
calculationNumber |
The number of the job being interpreted.
|
private static java.lang.String |
DC_LIST |
|
private boolean |
dFixed |
|
(package private) java.lang.String |
dList |
|
private static java.lang.String |
DS_LIST |
|
(package private) boolean |
dSpherical |
|
private static java.lang.String |
FC_LIST |
|
private boolean |
fFixed |
|
(package private) java.lang.String |
fList |
|
private static java.lang.String |
FS_LIST |
|
(package private) boolean |
fSpherical |
|
private boolean |
isFirstJob |
|
private int |
nBasis |
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
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells
allowNoOrbitals, energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
Constructor | Description |
---|---|
QchemReader() |
Modifier and Type | Method | 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() |
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
canonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
addCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData
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 java.lang.String DC_LIST
private static java.lang.String DS_LIST
private static java.lang.String FC_LIST
private static java.lang.String FS_LIST
java.lang.String dList
java.lang.String fList
boolean dSpherical
boolean fSpherical
protected void initializeReader()
initializeReader
in class MOReader
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private void readCalculationType()
private void readAtoms() throws java.lang.Exception
java.lang.Exception
private void readFrequencies() throws java.lang.Exception, java.io.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.
java.lang.Exception
- If no frequences were encounteredjava.io.IOException
- If an I/O error occursprivate void readPartialCharges() throws java.lang.Exception
java.lang.Exception
private void readEnergy()
private void readBasis() throws java.lang.Exception
java.lang.Exception
private void readESym(boolean haveSym) throws java.lang.Exception
java.lang.Exception
private void readQchemMolecularOrbitals() throws java.lang.Exception
java.lang.Exception
private int readMOs(boolean restricted, QchemReader.MOInfo[] moInfos) throws java.lang.Exception
java.lang.Exception