org.jmol.adapter.readers.quantum
Class QchemReader
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.QchemReader
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 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
- Version:
- 1.1, 1.0
- Author:
- Rene P.F Kanters (rkanters@richmond.edu), Steven E. Wheeler (swheele2@ccqc.uga.edu)
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, nOrbitals, orbitals, shells |
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
calculationNumber
private int calculationNumber
- The number of the calculation being interpreted.
alphas
private QchemReader.MOInfo[] alphas
betas
private QchemReader.MOInfo[] betas
nBasis
private int nBasis
dFixed
private boolean dFixed
fFixed
private boolean fFixed
DC_LIST
private static String DC_LIST
DS_LIST
private static String DS_LIST
FC_LIST
private static String FC_LIST
FS_LIST
private static String FS_LIST
dList
String dList
fList
String fList
dSpherical
boolean dSpherical
fSpherical
boolean fSpherical
QchemReader
public QchemReader()
initializeReader
protected void initializeReader()
- Overrides:
initializeReader
in class MOReader
checkLine
protected boolean checkLine()
throws Exception
- Overrides:
checkLine
in class AtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
readCalculationType
private void readCalculationType()
readAtoms
private void readAtoms()
throws Exception
- Throws:
Exception
readFrequencies
private void readFrequencies()
throws Exception,
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:
Exception
- If no frequences were encountered
IOException
- If an I/O error occurs
readPartialCharges
private void readPartialCharges()
throws Exception
- Throws:
Exception
readBasis
private void readBasis()
throws Exception
- Throws:
Exception
readESym
private void readESym(boolean haveSym)
throws Exception
- Throws:
Exception
readQchemMolecularOrbitals
private void readQchemMolecularOrbitals()
throws Exception
- Throws:
Exception
readMOs
private int readMOs(boolean restricted,
QchemReader.MOInfo[] moInfos)
throws Exception
- Throws:
Exception