org.jmol.adapter.readers.quantum
Class PsiReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.quantum.BasisFunctionReader
          extended by org.jmol.adapter.readers.quantum.MOReader
              extended by org.jmol.adapter.readers.quantum.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.) -- not processing specified model option in LOAD command


Field Summary
(package private)  java.util.List<java.lang.String> atomNames
           
(package private)  java.util.List<java.util.List<int[]>> shellsByUniqueAtom
           
(package private)  java.util.Map<java.lang.String,java.lang.Integer> uniqueAtomMap
           
 
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
 
Constructor Summary
PsiReader()
           
 
Method Summary
protected  boolean checkLine()
           
private  void readAtoms(boolean isInitial)
           
(package private)  void readBasis()
           
private  void readFrequencies()
           
(package private)  void readPsiMolecularOrbitals()
           
private  void readSCFDone()
          Interprets the SCF Done: section.
private  void readUniqueAtoms()
           
 
Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addMOData, checkNboLine, getMOHeader, getNboTypes, initializeReader, readMolecularOrbitals, setMOData, setMOType
 
Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO
 
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, readLine, 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
 

Field Detail

atomNames

java.util.List<java.lang.String> atomNames

shellsByUniqueAtom

java.util.List<java.util.List<int[]>> shellsByUniqueAtom

uniqueAtomMap

java.util.Map<java.lang.String,java.lang.Integer> uniqueAtomMap
Constructor Detail

PsiReader

public PsiReader()
Method Detail

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

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

readFrequencies

private void readFrequencies()
                      throws java.lang.Exception
Throws:
java.lang.Exception