org.jmol.adapter.readers.quantum
Class JaguarReader
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.JaguarReader
public class JaguarReader
- extends MOReader
Jaguar reader tested for the two samples files in CVS. Both
these files were created with Jaguar version 4.0, release 20.
MO reader corrected 9/28/11 by Bob Hanson -- reading NORMALIZED set
TODO: slight question about application of SQRT(3) in XY XZ YZ set
if that turns out to be an issue, we can multiply coefficients
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, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, 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, processBinaryDocument, processXml, read3Vectors, readData, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
moCount
private int moCount
lumoEnergy
private float lumoEnergy
ROOT3
private static final float ROOT3
- See Also:
- Constant Field Values
haveLine
private boolean haveLine
JaguarReader
public JaguarReader()
checkLine
protected boolean checkLine()
throws java.lang.Exception
- Overrides:
checkLine
in class AtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
readAtoms
private void readAtoms()
throws java.lang.Exception
- Throws:
java.lang.Exception
readCharges
private void readCharges()
throws java.lang.Exception
- Throws:
java.lang.Exception
readUnnormalizedBasis
private void readUnnormalizedBasis()
throws java.lang.Exception
- Throws:
java.lang.Exception
readBasisNormalized
private void readBasisNormalized()
throws java.lang.Exception
- Throws:
java.lang.Exception
readJaguarMolecularOrbitals
private void readJaguarMolecularOrbitals()
throws java.lang.Exception
- Throws:
java.lang.Exception
readFrequencies
private void readFrequencies()
throws java.lang.Exception
- Throws:
java.lang.Exception
readLine
public java.lang.String readLine()
throws java.lang.Exception
- Overrides:
readLine
in class AtomSetCollectionReader
- Throws:
java.lang.Exception