public class CsfReader extends MopacSlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
BasisFunctionReader.MOEnergySorter
Modifier and Type | Field and Description |
---|---|
private static byte |
anum |
private static byte[] |
atomFieldMap |
private static String[] |
atomFields |
private static byte |
bfxn_ang |
private static byte[] |
bondFieldMap |
private static String[] |
bondFields |
private static byte |
bondType |
private static byte |
chrg |
private static byte |
coef_indices |
private static byte[] |
connectorFieldMap |
private static String[] |
connectorFields |
private Map<String,int[]> |
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 Map<String,Bond> |
htBonds |
private static byte |
ID |
private static byte |
mo_occ |
private static byte[] |
moFieldMap |
private static 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 Map<String,Integer> |
propertyItemCounts |
private static byte |
shell |
private static byte |
sto_exp |
private String |
strAtomicNumbers |
private static byte |
sym |
private static byte |
transitionDipole |
private static byte |
vibEnergy |
private static byte[] |
vibFieldMap |
private static String[] |
vibFields |
private static byte |
xyz_coordinates |
atomicNumbers, MIN_COEF
slaterArray, slaters
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer
Constructor and Description |
---|
CsfReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkLine() |
private void |
fillCsfArray(String property,
String[] tokens,
int i0,
Object f,
boolean isInteger) |
private int |
getPropertyCount(String what) |
private int |
parseLineParameters(String[] fields,
byte[] fieldMap) |
private void |
processAtomObject() |
private void |
processBasisObject(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) |
createSphericalSlaterByType, scaleSlater
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReader, finalizeReaderASCR, getElementSymbol, getFilter, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeReader, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, read3Vectors, readDataObject, readLine, readLines, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setSpaceGroupName, setSymmetryOperator, setTransform, setU, setUnitCell, setUnitCellItem, setup, setupASCR
private int nAtoms
private String strAtomicNumbers
private int fieldCount
private int nVibrations
private int nGaussians
private int nSlaters
private final int[] fieldTypes
private static final byte objCls1
private static final byte objID1
private static final byte objCls2
private static final byte objID2
private static final String[] connectorFields
private static final byte[] connectorFieldMap
private static final byte ID
private static final byte sym
private static final byte anum
private static final byte chrg
private static final byte xyz_coordinates
private static final byte pchrg
private static final String[] atomFields
private static final byte[] atomFieldMap
private static final byte bondType
private static final String[] bondFields
private static final byte[] bondFieldMap
private int nBonds
private static final byte normalMode
private static final byte vibEnergy
private static final byte transitionDipole
private static final String[] vibFields
private static final byte[] vibFieldMap
private static final byte eig_val
private static final byte mo_occ
private static final byte eig_vec
private static final byte eig_vec_compressed
private static final byte coef_indices
private static final byte bfxn_ang
private static final byte sto_exp
private static final byte contractions
private static final byte gto_exp
private static final byte shell
private static final String[] moFields
private static final byte[] moFieldMap
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
private int getPropertyCount(String what)
private int parseLineParameters(String[] fields, byte[] fieldMap) throws Exception
Exception
private void fillCsfArray(String property, String[] tokens, int i0, Object f, boolean isInteger) throws Exception
Exception
private void setBond(Bond bond, int[] connect)
private void processMolecularOrbitalObject() throws Exception
Exception