javajs.api.GenericLineReader
public class GaussianFchkReader extends GaussianReader
BasisFunctionReader.MOEnergySorter
Modifier and Type | Field | Description |
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private static java.lang.String[] |
AO_TYPES |
|
private int |
atomCount |
|
private java.util.Map<java.lang.String,java.lang.Object> |
fileData |
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells
calculationNumber, namedSets
allowNoOrbitals, energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
Constructor | Description |
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GaussianFchkReader() |
Modifier and Type | Method | Description |
---|---|---|
private void |
checkForFreq() |
|
private float[] |
fillFloat(float[] f0,
int i,
int n) |
|
private void |
getOrbitals(float[] e,
float[] c,
int occ,
int nElec) |
|
protected void |
initializeReader() |
|
private void |
readAllData() |
|
protected void |
readAtoms() |
|
protected void |
readBasis() |
|
protected void |
readBonds() |
|
protected void |
readDipoleMoment() |
|
protected void |
readMolecularObitals() |
|
protected void |
readPartialCharges() |
Reads partial charges and assigns them only to the last atom set.
|
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR
canonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
checkLine, readFrequencies, readMolecularOrbitals
addCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData
private java.util.Map<java.lang.String,java.lang.Object> fileData
private int atomCount
private static java.lang.String[] AO_TYPES
protected void initializeReader() throws java.lang.Exception
initializeReader
in class GaussianReader
java.lang.Exception
private void checkForFreq() throws java.lang.Exception
java.lang.Exception
private float[] fillFloat(float[] f0, int i, int n)
private void readAllData() throws java.lang.Exception
java.lang.Exception
protected void readAtoms() throws java.lang.Exception
readAtoms
in class GaussianReader
java.lang.Exception
protected void readBonds()
protected void readDipoleMoment() throws java.lang.Exception
readDipoleMoment
in class GaussianReader
java.lang.Exception
protected void readPartialCharges() throws java.lang.Exception
GaussianReader
readPartialCharges
in class GaussianReader
java.lang.Exception
- When an I/O error or discardlines error occursprotected void readBasis() throws java.lang.Exception
readBasis
in class GaussianReader
java.lang.Exception
protected void readMolecularObitals() throws java.lang.Exception
java.lang.Exception
private void getOrbitals(float[] e, float[] c, int occ, int nElec)