org.jmol.adapter.readers.more
Class PsiReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.MOReader
org.jmol.adapter.readers.more.PsiReader
public class PsiReader
- extends MOReader
Reader for Psi3 output files. -- http://www.psicode.org/
preliminary version:
-- coordinates only
-- final geometry only; not reading steps
-- no charges
-- no frequencies
-- no orbitals (Can't handle irreducible representations here.)
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 |
atomNames
java.util.Vector atomNames
shellsByUniqueAtom
java.util.Vector shellsByUniqueAtom
uniqueAtomMap
java.util.Hashtable uniqueAtomMap
PsiReader
public PsiReader()
readAtomSetCollection
public void readAtomSetCollection(java.io.BufferedReader reader)
- Specified by:
readAtomSetCollection
in class MOReader
- Parameters:
reader
- BufferedReader associated with the Gaussian output text.
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
readSCFDone
private void readSCFDone()
throws java.lang.Exception
- Interprets the SCF Done: section.
- Throws:
java.lang.Exception
- If an error occurs
readAtoms
private void readAtoms(boolean isInitial)
throws java.lang.Exception
- Throws:
java.lang.Exception
readBasis
void readBasis()
throws java.lang.Exception
- Throws:
java.lang.Exception
readUniqueAtoms
private void readUniqueAtoms()
throws java.lang.Exception
- Throws:
java.lang.Exception
readPsiMolecularOrbitals
void readPsiMolecularOrbitals()
throws java.lang.Exception
- Throws:
java.lang.Exception