org.jmol.adapter.readers.quantum
Class DgridReader

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.SlaterReader
              extended by org.jmol.adapter.readers.quantum.DgridReader

public class DgridReader
extends SlaterReader

A reader for Dgrid BASISFILE data. http://www.scm.com/News/DGrid.html http://www.scm.com/Doc/Doc2009.01/ADF/ADFUsersGuide/page430.html


Nested Class Summary
 
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
 
Field Summary
(package private)  java.util.Hashtable htExponents
           
private  java.util.Hashtable htFuncMap
           
private  java.lang.String title
           
 
Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader
slaterArray, slaters
 
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, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer
 
Constructor Summary
DgridReader()
           
 
Method Summary
protected  boolean checkLine()
           
private  SlaterData createSlaterData(int iAtom, java.lang.String atomSymbol, java.lang.String xyz)
           
private  void readCoordinates()
          Reads a set of coordinates
private  void readMolecularOrbitals()
           
private  void readSlaterBasis()
           
 
Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, scaleSlater, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
 
Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDFMap, isQuantumBasisSupported, setMO
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeReader, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, 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
 

Field Detail

title

private java.lang.String title

htExponents

java.util.Hashtable htExponents

htFuncMap

private java.util.Hashtable htFuncMap
Constructor Detail

DgridReader

public DgridReader()
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

readCoordinates

private void readCoordinates()
                      throws java.lang.Exception
Reads a set of coordinates

Throws:
java.lang.Exception - if an I/O error occurs

readSlaterBasis

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

readMolecularOrbitals

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

createSlaterData

private SlaterData createSlaterData(int iAtom,
                                    java.lang.String atomSymbol,
                                    java.lang.String xyz)