public class GamessUSReader extends GamessReader
atomNames
energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
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, 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 and Description |
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GamessUSReader() |
Modifier and Type | Method and Description |
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protected boolean |
checkLine() |
protected java.lang.String |
fixShellTag(java.lang.String tag) |
private void |
readAtomsInAngstromCoordinates() |
protected void |
readAtomsInBohrCoordinates() |
(package private) void |
readDipoleMoment() |
protected void |
readEFPInBohrCoordinates() |
protected void |
readMolecularOrbitals(int headerType) |
(package private) void |
readPartialCharges() |
fixBasisLine, readBasisInfo, readControlInfo, readFrequencies, readGaussianBasis, setCalculationType
addMOData, checkNboLine, getMOHeader, getNboTypes, initializeReader, setMOData, setMOType
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDFMap, isQuantumBasisSupported, setMO
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, 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
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
protected void readMolecularOrbitals(int headerType) throws java.lang.Exception
readMolecularOrbitals
in class MOReader
java.lang.Exception
protected void readEFPInBohrCoordinates() throws java.lang.Exception
java.lang.Exception
protected void readAtomsInBohrCoordinates() throws java.lang.Exception
readAtomsInBohrCoordinates
in class GamessReader
java.lang.Exception
private void readAtomsInAngstromCoordinates() throws java.lang.Exception
java.lang.Exception
protected java.lang.String fixShellTag(java.lang.String tag)
fixShellTag
in class GamessReader
void readPartialCharges() throws java.lang.Exception
java.lang.Exception
void readDipoleMoment() throws java.lang.Exception
java.lang.Exception