org.jmol.adapter.readers.more
Class PsiReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by 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.)


Field Summary
(package private)  java.util.Vector atomNames
           
(package private)  int gaussianCount
           
(package private)  java.util.Hashtable moData
           
(package private)  java.util.Vector orbitals
           
(package private)  int shellCount
           
(package private)  java.util.Vector shellsByUniqueAtom
           
(package private)  java.util.Hashtable uniqueAtomMap
           
 
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
 
Constructor Summary
PsiReader()
           
 
Method Summary
(package private)  void addMOData(int nColumns, java.util.Vector[] data, java.util.Hashtable[] mos)
           
private  void readAtoms(boolean isInitial)
           
 AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
           
(package private)  void readBasis()
           
(package private)  void readMolecularOrbitals()
           
private  void readSCFDone()
          Interprets the SCF Done: section.
private  void readUniqueAtoms()
           
 
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
 

Field Detail

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
Constructor Detail

PsiReader

public PsiReader()
Method Detail

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)