org.jmol.adapter.readers.quantum
Class CsfReader

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.MopacSlaterReader
                  extended by org.jmol.adapter.readers.quantum.CsfReader

public class CsfReader
extends MopacSlaterReader

CSF file reader based on CIF idea -- fluid property fields. note that, like CIF, the order of fields is totally unpredictable in addition, ID numbers are not sequential, requiring atomNames first crack at this 2006/04/13 added DGAUSS, MOPAC, EHT orbital/basis reading 2007/04/09 streamlined CSF dataset reading capabilities 2007/04/09

Author:
hansonr

Nested Class Summary
 
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
 
Field Summary
private static byte anum
           
private static byte[] atomFieldMap
           
private static java.lang.String[] atomFields
           
private static byte bfxn_ang
           
private static byte[] bondFieldMap
           
private static java.lang.String[] bondFields
           
private static byte bondType
           
private static byte chrg
           
private static byte coef_indices
           
private static byte[] connectorFieldMap
           
private static java.lang.String[] connectorFields
           
private  java.util.Hashtable connectors
           
private static byte contractions
           
private static byte eig_val
           
private static byte eig_vec
           
private static byte eig_vec_compressed
           
private  int fieldCount
           
private  int[] fieldTypes
           
private static byte gto_exp
           
private  java.util.Hashtable htBonds
           
private static byte ID
           
private static byte mo_occ
           
private static byte[] moFieldMap
           
private static java.lang.String[] moFields
           
private  int nAtoms
           
private  int nBonds
           
private  int nGaussians
           
private static byte normalMode
           
private  int nSlaters
           
private  int nVibrations
           
private static byte objCls1
           
private static byte objCls2
           
private static byte objID1
           
private static byte objID2
           
private static byte pchrg
           
private  java.util.Hashtable propertyItemCounts
           
private static byte shell
           
private static byte sto_exp
           
private  java.lang.String strAtomicNumbers
           
private static byte sym
           
private static byte transitionDipole
           
private static byte vibEnergy
           
private static byte[] vibFieldMap
           
private static java.lang.String[] vibFields
           
private static byte xyz_coordinates
           
 
Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
atomicNumbers, MIN_COEF
 
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
CsfReader()
           
 
Method Summary
protected  boolean checkLine()
           
private  void fillCsfArray(java.lang.String property, java.lang.String[] tokens, int i0, java.lang.Object f)
           
private  int getPropertyCount(java.lang.String what)
           
private  int parseLineParameters(java.lang.String[] fields, byte[] fieldMap)
           
private  void processAtomObject()
           
private  void processBasisObject(java.lang.String sto_gto)
           
private  void processBondObject()
           
private  void processConnectorObject()
           
private  void processLocalTransform()
           
private  void processMolecularOrbitalObject()
           
private  void processVibrationObject()
           
private  void setBond(Bond bond, int[] connect)
           
 
Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
createSphericalSlaterByType, scaleSlater
 
Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, 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

nAtoms

private int nAtoms

strAtomicNumbers

private java.lang.String strAtomicNumbers

fieldCount

private int fieldCount

nVibrations

private int nVibrations

nGaussians

private int nGaussians

nSlaters

private int nSlaters

htBonds

private java.util.Hashtable htBonds

propertyItemCounts

private java.util.Hashtable propertyItemCounts

fieldTypes

private final int[] fieldTypes

objCls1

private static final byte objCls1
See Also:
Constant Field Values

objID1

private static final byte objID1
See Also:
Constant Field Values

objCls2

private static final byte objCls2
See Also:
Constant Field Values

objID2

private static final byte objID2
See Also:
Constant Field Values

connectorFields

private static final java.lang.String[] connectorFields

connectorFieldMap

private static final byte[] connectorFieldMap

connectors

private java.util.Hashtable connectors

ID

private static final byte ID
See Also:
Constant Field Values

sym

private static final byte sym
See Also:
Constant Field Values

anum

private static final byte anum
See Also:
Constant Field Values

chrg

private static final byte chrg
See Also:
Constant Field Values

xyz_coordinates

private static final byte xyz_coordinates
See Also:
Constant Field Values

pchrg

private static final byte pchrg
See Also:
Constant Field Values

atomFields

private static final java.lang.String[] atomFields

atomFieldMap

private static final byte[] atomFieldMap

bondType

private static final byte bondType
See Also:
Constant Field Values

bondFields

private static final java.lang.String[] bondFields

bondFieldMap

private static final byte[] bondFieldMap

nBonds

private int nBonds

normalMode

private static final byte normalMode
See Also:
Constant Field Values

vibEnergy

private static final byte vibEnergy
See Also:
Constant Field Values

transitionDipole

private static final byte transitionDipole
See Also:
Constant Field Values

vibFields

private static final java.lang.String[] vibFields

vibFieldMap

private static final byte[] vibFieldMap

eig_val

private static final byte eig_val
See Also:
Constant Field Values

mo_occ

private static final byte mo_occ
See Also:
Constant Field Values

eig_vec

private static final byte eig_vec
See Also:
Constant Field Values

eig_vec_compressed

private static final byte eig_vec_compressed
See Also:
Constant Field Values

coef_indices

private static final byte coef_indices
See Also:
Constant Field Values

bfxn_ang

private static final byte bfxn_ang
See Also:
Constant Field Values

sto_exp

private static final byte sto_exp
See Also:
Constant Field Values

contractions

private static final byte contractions
See Also:
Constant Field Values

gto_exp

private static final byte gto_exp
See Also:
Constant Field Values

shell

private static final byte shell
See Also:
Constant Field Values

moFields

private static final java.lang.String[] moFields

moFieldMap

private static final byte[] moFieldMap
Constructor Detail

CsfReader

public CsfReader()
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

processLocalTransform

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

getPropertyCount

private int getPropertyCount(java.lang.String what)

parseLineParameters

private int parseLineParameters(java.lang.String[] fields,
                                byte[] fieldMap)
                         throws java.lang.Exception
Throws:
java.lang.Exception

fillCsfArray

private void fillCsfArray(java.lang.String property,
                          java.lang.String[] tokens,
                          int i0,
                          java.lang.Object f)
                   throws java.lang.Exception
Throws:
java.lang.Exception

processConnectorObject

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

setBond

private void setBond(Bond bond,
                     int[] connect)

processAtomObject

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

processBondObject

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

processVibrationObject

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

processMolecularOrbitalObject

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

processBasisObject

private void processBasisObject(java.lang.String sto_gto)
                         throws java.lang.Exception
Throws:
java.lang.Exception