public class MopacGraphfReader extends MopacSlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
Modifier and Type | Field and Description |
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private int |
atomCount |
private float[][] |
invMatrix |
private boolean |
isNewFormat |
private int |
nCoefficients |
private java.util.List<float[]> |
orbitalData |
private java.util.List<java.lang.String> |
orbitalInfo |
atomicNumbers, MIN_COEF
slaterArray, slaters
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, shells
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
Constructor and Description |
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MopacGraphfReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkLine() |
protected void |
initializeReader() |
private void |
readAtoms() |
private boolean |
readKeywords() |
private void |
readMolecularOrbitals(boolean isBeta) |
private void |
readSlaterBasis() |
createSphericalSlaterByType, scaleSlater
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO
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, 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
private int atomCount
private int nCoefficients
private float[][] invMatrix
private boolean isNewFormat
private java.util.List<float[]> orbitalData
private java.util.List<java.lang.String> orbitalInfo
protected void initializeReader()
initializeReader
in class AtomSetCollectionReader
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private void readAtoms() throws java.lang.Exception
java.lang.Exception
private void readSlaterBasis() throws java.lang.Exception
java.lang.Exception
private void readMolecularOrbitals(boolean isBeta) throws java.lang.Exception
java.lang.Exception
private boolean readKeywords() throws java.lang.Exception
java.lang.Exception