Package org.jmol.adapter.readers.quantum
Class GaussianFchkReader
- java.lang.Object
-
- org.jmol.adapter.smarter.AtomSetCollectionReader
-
- org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- org.jmol.adapter.readers.quantum.MOReader
-
- org.jmol.adapter.readers.quantum.GaussianReader
-
- org.jmol.adapter.readers.quantum.GaussianFchkReader
-
- All Implemented Interfaces:
javajs.api.GenericLineReader
public class GaussianFchkReader extends GaussianReader
Reader for Gaussian fchk files for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot) also allows appended freq data- Author:
- hansonr Bob Hanson hansonr@stolaf.edu
-
-
Nested Class Summary
-
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
-
-
Field Summary
Fields Modifier and Type Field Description private static java.lang.String[]
AO_TYPES
private int
atomCount
private java.util.Map<java.lang.String,java.lang.Object>
fileData
-
Fields inherited from class org.jmol.adapter.readers.quantum.GaussianReader
calculationNumber, namedSets
-
Fields inherited from class org.jmol.adapter.readers.quantum.MOReader
allowNoOrbitals, energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
-
Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells
-
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
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, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
-
-
Constructor Summary
Constructors Constructor Description GaussianFchkReader()
-
Method Summary
All Methods Instance Methods Concrete Methods 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.-
Methods inherited from class org.jmol.adapter.readers.quantum.GaussianReader
checkLine, finalizeSubclassReader, readFrequencies, readMolecularOrbitals
-
Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData
-
Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
-
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, 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
-
-
-
-
Method Detail
-
initializeReader
protected void initializeReader() throws java.lang.Exception
- Overrides:
initializeReader
in classGaussianReader
- Throws:
java.lang.Exception
-
checkForFreq
private void checkForFreq() throws java.lang.Exception
- Throws:
java.lang.Exception
-
fillFloat
private float[] fillFloat(float[] f0, int i, int n)
-
readAllData
private void readAllData() throws java.lang.Exception
- Throws:
java.lang.Exception
-
readAtoms
protected void readAtoms() throws java.lang.Exception
- Overrides:
readAtoms
in classGaussianReader
- Throws:
java.lang.Exception
-
readBonds
protected void readBonds()
-
readDipoleMoment
protected void readDipoleMoment() throws java.lang.Exception
- Overrides:
readDipoleMoment
in classGaussianReader
- Throws:
java.lang.Exception
-
readPartialCharges
protected void readPartialCharges() throws java.lang.Exception
Description copied from class:GaussianReader
Reads partial charges and assigns them only to the last atom set.- Overrides:
readPartialCharges
in classGaussianReader
- Throws:
java.lang.Exception
- When an I/O error or discardlines error occurs
-
readBasis
protected void readBasis() throws java.lang.Exception
- Overrides:
readBasis
in classGaussianReader
- Throws:
java.lang.Exception
-
readMolecularObitals
protected void readMolecularObitals() throws java.lang.Exception
- Throws:
java.lang.Exception
-
getOrbitals
private void getOrbitals(float[] e, float[] c, int occ, int nElec)
-
-