org.jmol.adapter.readers.quantum
Class CsfReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.quantum.BasisFunctionReader
org.jmol.adapter.readers.quantum.SlaterReader
org.jmol.adapter.readers.quantum.MopacSlaterReader
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
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 |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, 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 |
nAtoms
private int nAtoms
strAtomicNumbers
private String strAtomicNumbers
fieldCount
private int fieldCount
nVibrations
private int nVibrations
nGaussians
private int nGaussians
nSlaters
private int nSlaters
htBonds
private Hashtable htBonds
propertyItemCounts
private 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 String[] connectorFields
connectorFieldMap
private static final byte[] connectorFieldMap
connectors
private 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 String[] atomFields
atomFieldMap
private static final byte[] atomFieldMap
bondType
private static final byte bondType
- See Also:
- Constant Field Values
bondFields
private static final 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 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 String[] moFields
moFieldMap
private static final byte[] moFieldMap
CsfReader
public CsfReader()
checkLine
protected boolean checkLine()
throws Exception
- Overrides:
checkLine
in class AtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
processLocalTransform
private void processLocalTransform()
throws Exception
- Throws:
Exception
getPropertyCount
private int getPropertyCount(String what)
parseLineParameters
private int parseLineParameters(String[] fields,
byte[] fieldMap)
throws Exception
- Throws:
Exception
fillCsfArray
private void fillCsfArray(String property,
String[] tokens,
int i0,
Object f)
throws Exception
- Throws:
Exception
processConnectorObject
private void processConnectorObject()
throws Exception
- Throws:
Exception
setBond
private void setBond(Bond bond,
int[] connect)
processAtomObject
private void processAtomObject()
throws Exception
- Throws:
Exception
processBondObject
private void processBondObject()
throws Exception
- Throws:
Exception
processVibrationObject
private void processVibrationObject()
throws Exception
- Throws:
Exception
processMolecularOrbitalObject
private void processMolecularOrbitalObject()
throws Exception
- Throws:
Exception
processBasisObject
private void processBasisObject(String sto_gto)
throws Exception
- Throws:
Exception