Package org.jmol.adapter.readers.quantum
Class QchemReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.quantum.BasisFunctionReader
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- org.jmol.adapter.readers.quantum.MOReader
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- org.jmol.adapter.readers.quantum.QchemReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class QchemReader extends MOReader
A reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc. (http://www.q-chem.com/)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 TRUEThis 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
- Version:
- 1.1, 1.0
- Author:
- Rene P.F Kanters (rkanters@richmond.edu), Steven E. Wheeler (swheele2@ccqc.uga.edu)
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Nested Class Summary
Nested Classes Modifier and Type Class Description protected class
QchemReader.MOInfo
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Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
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Field Summary
Fields 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
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Fields inherited from class org.jmol.adapter.readers.quantum.MOReader
allowNoOrbitals, energyUnits, forceMOPAC, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, lastMoData, moTypes, orbitalsRead, shellCount
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Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells, slaterArray, slaters
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Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, noPack, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description QchemReader()
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Method Summary
All Methods Instance Methods Concrete Methods 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()
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Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, addSlaterBasis, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData
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Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, 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
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Field Detail
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calculationNumber
private int calculationNumber
The number of the job being interpreted.
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isFirstJob
private boolean isFirstJob
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alphas
private QchemReader.MOInfo[] alphas
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betas
private QchemReader.MOInfo[] betas
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nBasis
private int nBasis
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dFixed
private boolean dFixed
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fFixed
private boolean fFixed
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DC_LIST
private static java.lang.String DC_LIST
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DS_LIST
private static java.lang.String DS_LIST
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FC_LIST
private static java.lang.String FC_LIST
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FS_LIST
private static java.lang.String FS_LIST
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dList
java.lang.String dList
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fList
java.lang.String fList
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dSpherical
boolean dSpherical
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fSpherical
boolean fSpherical
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Method Detail
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initializeReader
protected void initializeReader()
- Overrides:
initializeReader
in classMOReader
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checkLine
protected boolean checkLine() throws java.lang.Exception
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
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readCalculationType
private void readCalculationType()
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readAtoms
private void readAtoms() throws java.lang.Exception
- Throws:
java.lang.Exception
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readFrequencies
private void readFrequencies() throws java.lang.Exception, java.io.IOException
Interprets the Harmonic frequencies section.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.
- Throws:
java.lang.Exception
- If no frequences were encounteredjava.io.IOException
- If an I/O error occurs
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readPartialCharges
private void readPartialCharges() throws java.lang.Exception
- Throws:
java.lang.Exception
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readEnergy
private void readEnergy()
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readBasis
private void readBasis() throws java.lang.Exception
- Throws:
java.lang.Exception
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readESym
private void readESym(boolean haveSym) throws java.lang.Exception
- Throws:
java.lang.Exception
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readQchemMolecularOrbitals
private void readQchemMolecularOrbitals() throws java.lang.Exception
- Throws:
java.lang.Exception
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readMOs
private int readMOs(boolean restricted, QchemReader.MOInfo[] moInfos) throws java.lang.Exception
- Throws:
java.lang.Exception
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