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, 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 |
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, initializeReader, 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 |
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.Map<java.lang.String,Bond> htBonds
propertyItemCounts
private java.util.Map<java.lang.String,java.lang.Integer> 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.Map<java.lang.String,int[]> 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
CsfReader
public CsfReader()
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