Class GaussianReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
GaussianFchkReader
-
Nested Class Summary
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
-
Field Summary
FieldsModifier and TypeFieldDescriptionprivate boolean
protected int
The number of the calculation being interpreted.private String
Type of energy calculated, e.g., E(RB+HF-PW91).private String
Calculated energy with units (if possible).private int
The number of equivalent atom sets.private boolean
private boolean
private int
protected javajs.util.BS
private String
private boolean
private int
The scan point, where -1 denotes no scan information.private static final int
Word index of atomic number in line with atom coordinates in an orientation block.private int
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 -
Method Summary
Modifier and TypeMethodDescriptionprivate void
protected boolean
Reads a Collection of AtomSets from a BufferedReader.void
optional reader-specific method run first.private void
getSpinDensities
(int pt) protected void
protected void
protected void
private void
private void
(package private) void
protected void
readFrequencies
(String key, boolean mustHave) Interprets the Harmonic frequencies section.protected void
(package private) void
Reads partial charges and assigns them only to the last atom set.private void
Interprets the SCF Done: section.private void
Interpret the Energy= line for non SCF type energy outputprivate void
private void
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
-
Field Details
-
STD_ORIENTATION_ATOMIC_NUMBER_OFFSET
private static final int STD_ORIENTATION_ATOMIC_NUMBER_OFFSETWord index of atomic number in line with atom coordinates in an orientation block.- See Also:
-
energyString
Calculated energy with units (if possible). -
energyKey
Type of energy calculated, e.g., E(RB+HF-PW91). -
calculationNumber
protected int calculationNumberThe number of the calculation being interpreted. -
scanPoint
private int scanPointThe scan point, where -1 denotes no scan information. -
equivalentAtomSets
private int equivalentAtomSetsThe number of equivalent atom sets.Needed to associate identical properties to multiple atomsets
-
stepNumber
private int stepNumber -
moModelSet
private int moModelSet -
namedSets
protected javajs.util.BS namedSets -
isHighPrecision
private boolean isHighPrecision -
haveHighPrecision
private boolean haveHighPrecision -
allowHighPrecision
private boolean allowHighPrecision -
orientationInput
private boolean orientationInput -
orientation
-
-
Constructor Details
-
GaussianReader
public GaussianReader()
-
-
Method Details
-
initializeReader
- Overrides:
initializeReader
in classMOReader
- Throws:
Exception
-
checkLine
Reads a Collection of AtomSets from a BufferedReader.New AtomSets are generated when an
Input
,Standard
orZ-Matrix
orientation is read. The occurence of these orientations seems to depend on (in pseudo-code):
if (opt=z-matrix) Z-Matrix; else Input;
if (!NoSymmetry) Standard;
Which means that ifNoSymmetry
is used with a z-matrix optimization, no other orientation besidesZ-Matrix
will be present. This is important becauseZ-Matrix
may have dummy atoms while the analysis of the calculation results will not, i.e., theCenter Numbers
in the z-matrix orientation may be different from those in the population analysis!Single point or frequency calculations always have an
Input
orientation. If symmetry is used aStandard
will be present too.- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- TRUE to read a new line
- Throws:
Exception
-
finalizeSubclassReader
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
Exception
-
getSpinDensities
- Throws:
Exception
-
readSCFDone
Interprets the SCF Done: section.The energyKey and energyString will be set for further AtomSets that have the same molecular geometry (e.g., frequencies). The energy, convergence, -V/T and S**2 values will be set as properties for the atomSet.
- Throws:
Exception
- If an error occurs
-
setProps
-
setNames
-
setEnergy
private void setEnergy()Interpret the Energy= line for non SCF type energy output -
readAtoms
- Throws:
Exception
-
readBasis
- Throws:
Exception
-
readMolecularOrbitals
- Throws:
Exception
-
readFrequencies
Interprets the Harmonic frequencies section.The vectors are added to a clone of the last read AtomSet. Only the Frequencies, reduced masses, force constants and IR intensities are set as properties for each of the frequency type AtomSet generated.
- Parameters:
key
-mustHave
-- Throws:
Exception
- If no frequencies were encountered
-
readDipoleMoment
- Throws:
Exception
-
readPartialCharges
Reads partial charges and assigns them only to the last atom set.- Throws:
Exception
- When an I/O error or discardlines error occurs
-
readCSATensors
- Throws:
Exception
-
addTensor
-
readCouplings
- Throws:
Exception
-