org.jmol.adapter.readers.more
Class QchemReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.MOReader
org.jmol.adapter.readers.more.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.more.MOReader |
alphaBeta, continuing, energyUnits, gaussianCount, gaussians, haveNboCharges, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, ignoreMOs, iHaveAtoms, moData, moTypes, orbitals, shellCount, shells |
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, doApplySymmetry, filter, getHeader, haveAtomFilter, havePartialChargeFilter, htParams, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isTrajectory, latticeCells, line, modelNumber, needToApplySymmetry, next, prevline, reader, readerName, spaceGroup, templateAtomCount |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetryAndSetTrajectory, checkLineForScript, checkLineForScript, clearLatticeParameters, deducePdbElementSymbol, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, fillDataBlock, filterAtom, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readData, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, 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
QchemReader.MOInfo[] alphas
betas
QchemReader.MOInfo[] betas
nShell
int nShell
nBasis
int nBasis
QchemReader
public QchemReader()
readAtomSetCollection
public void readAtomSetCollection(java.io.BufferedReader reader)
- Specified by:
readAtomSetCollection
in class MOReader
checkLine
protected boolean checkLine()
throws java.lang.Exception
- Specified by:
checkLine
in class MOReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
readCalculationType
private void readCalculationType()
readAtoms
void readAtoms()
throws java.lang.Exception
- Throws:
java.lang.Exception
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 encountered
java.io.IOException
- If an I/O error occurs
readPartialCharges
void readPartialCharges()
throws java.lang.Exception
- Throws:
java.lang.Exception
readBasis
private void readBasis()
throws java.lang.Exception
- Throws:
java.lang.Exception
readESym
protected void readESym(boolean haveSym)
throws java.lang.Exception
- Throws:
java.lang.Exception
readQchemMolecularOrbitals
private void readQchemMolecularOrbitals()
throws java.lang.Exception
- Throws:
java.lang.Exception
readMOs
private int readMOs(boolean restricted,
java.lang.String[] aoLabels,
java.util.Vector orbitals,
QchemReader.MOInfo[] moInfos)
throws java.lang.Exception
- Throws:
java.lang.Exception