org.jmol.adapter.readers.more
Class PsiReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.PsiReader
public class PsiReader
- extends AtomSetCollectionReader
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.smarter.AtomSetCollectionReader |
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, desiredModelNumber, desiredSpaceGroupIndex, doApplySymmetry, filter, getHeader, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveDesiredModel, iHaveSymmetryOperators, iHaveUnitCell, latticeCells, line, modelNumber, needToApplySymmetry, next, notionalUnitCell, prevline, primitiveLatticeVectors, ptLine, reader, readerName, spaceGroup |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetry, checkLineForScript, checkLineForScript, clearLatticeParameters, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, fillDataBlock, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, initialize, initialize, initializeCartesianToFractional, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
shellCount
int shellCount
gaussianCount
int gaussianCount
moData
java.util.Hashtable moData
orbitals
java.util.Vector orbitals
atomNames
java.util.Vector atomNames
shellsByUniqueAtom
java.util.Vector shellsByUniqueAtom
uniqueAtomMap
java.util.Hashtable uniqueAtomMap
PsiReader
public PsiReader()
readAtomSetCollection
public AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
- Specified by:
readAtomSetCollection
in class AtomSetCollectionReader
- Parameters:
reader
- BufferedReader associated with the Gaussian output text.
- Returns:
- The AtomSetCollection representing the interpreted Gaussian text.
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
readMolecularOrbitals
void readMolecularOrbitals()
throws java.lang.Exception
- Throws:
java.lang.Exception
addMOData
void addMOData(int nColumns,
java.util.Vector[] data,
java.util.Hashtable[] mos)