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 String[]

AO_TYPES

private int

atomCount

private Map<String,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, forceMOPAC, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, lastMoData, moTypes, orbitalsRead, shellCount

Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells, slaterArray, slaters

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor Summary

Constructors

Constructor

Description

GaussianFchkReader()
Method Summary

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, addSlaterBasis, 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, checkAndRemoveFilterKey, 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, getFilterWithCase, 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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- fileData
  
  private Map<String,Object> fileData
- atomCount
  
  private int atomCount
- AO_TYPES
  
  private static String[] AO_TYPES
Constructor Details
- GaussianFchkReader
  
  public GaussianFchkReader()
Method Details
- initializeReader
  
  protected void initializeReader() throws Exception
  
  Overrides:
  
  initializeReader in class GaussianReader
  
  Throws:
  
  Exception
- checkForFreq
  
  private void checkForFreq() throws Exception
  
  Throws:
  
  Exception
- fillFloat
  
  private float[] fillFloat(float[] f0, int i, int n)
- readAllData
  
  private void readAllData() throws Exception
  
  Throws:
  
  Exception
- readAtoms
  
  protected void readAtoms() throws Exception
  
  Overrides:
  
  readAtoms in class GaussianReader
  
  Throws:
  
  Exception
- readBonds
  
  protected void readBonds()
- readDipoleMoment
  
  protected void readDipoleMoment() throws Exception
  
  Overrides:
  
  readDipoleMoment in class GaussianReader
  
  Throws:
  
  Exception
- readPartialCharges
  
  protected void readPartialCharges() throws Exception
  
  Description copied from class: GaussianReader
  
  Reads partial charges and assigns them only to the last atom set.
  
  Overrides:
  
  readPartialCharges in class GaussianReader
  
  Throws:
  
  Exception - When an I/O error or discardlines error occurs
- readBasis
  
  protected void readBasis() throws Exception
  
  Overrides:
  
  readBasis in class GaussianReader
  
  Throws:
  
  Exception
- readMolecularObitals
  
  protected void readMolecularObitals() throws Exception
  
  Throws:
  
  Exception
- getOrbitals
  
  private void getOrbitals(float[] e, float[] c, int occ, int nElec)

Class GaussianFchkReader

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Field Summary

Fields inherited from class org.jmol.adapter.readers.quantum.GaussianReader

Fields inherited from class org.jmol.adapter.readers.quantum.MOReader

Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.quantum.GaussianReader

Methods inherited from class org.jmol.adapter.readers.quantum.MOReader

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Methods inherited from class java.lang.Object

Field Details

fileData

atomCount

AO_TYPES

Constructor Details

GaussianFchkReader

Method Details

initializeReader

checkForFreq

fillFloat

readAllData

readAtoms

readBonds

readDipoleMoment

readPartialCharges

readBasis

readMolecularObitals

getOrbitals