public class GaussianReader extends MOReader
BasisFunctionReader.MOEnergySorter
Modifier and Type | Field and Description |
---|---|
private boolean |
allowHighPrecision |
protected int |
calculationNumber
The number of the calculation being interpreted.
|
private String |
energyKey
Type of energy calculated, e.g., E(RB+HF-PW91).
|
private String |
energyString
Calculated energy with units (if possible).
|
private int |
equivalentAtomSets
The number of equivalent atom sets.
|
private boolean |
haveHighPrecision |
private boolean |
isHighPrecision |
private int |
moModelSet |
protected BS |
namedSets |
private int |
scanPoint
The scan point, where -1 denotes no scan information.
|
private static int |
STD_ORIENTATION_ATOMIC_NUMBER_OFFSET
Word index of atomic number in line with atom coordinates in an
orientation block.
|
private int |
stepNumber |
allowNoOrbitals, energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells
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
Constructor and Description |
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GaussianReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkLine()
Reads a Collection of AtomSets from a BufferedReader.
|
private void |
getSpinDensities(int pt) |
protected void |
initializeReader() |
protected void |
readAtoms() |
protected void |
readBasis() |
(package private) void |
readDipoleMoment() |
protected void |
readFrequencies(String key,
boolean mustHave)
Interprets the Harmonic frequencies section.
|
protected void |
readMolecularOrbitals() |
(package private) void |
readPartialCharges()
Reads partial charges and assigns them only to the last atom set.
|
private void |
readSCFDone()
Interprets the SCF Done: section.
|
private void |
setEnergy()
Interpret the Energy= line for non SCF type energy output
|
private void |
setNames(String atomSetName,
BS namedSets,
int n) |
private void |
setProps(String key,
String value,
int n) |
addCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData
canonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
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
private static final int STD_ORIENTATION_ATOMIC_NUMBER_OFFSET
private String energyString
private String energyKey
protected int calculationNumber
private int scanPoint
private int equivalentAtomSets
Needed to associate identical properties to multiple atomsets
private int stepNumber
private int moModelSet
protected BS namedSets
private boolean isHighPrecision
private boolean haveHighPrecision
private boolean allowHighPrecision
protected void initializeReader() throws Exception
initializeReader
in class MOReader
Exception
protected boolean checkLine() throws Exception
New AtomSets are generated when an Input
,
Standard
or Z-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 if NoSymmetry
is used with a z-matrix
optimization, no other orientation besides Z-Matrix
will be
present. This is important because Z-Matrix
may have dummy
atoms while the analysis of the calculation results will not, i.e., the
Center 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 a Standard
will be present
too.
checkLine
in class AtomSetCollectionReader
Exception
private void readSCFDone() throws Exception
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.
Exception
- If an error occursprivate void setEnergy()
protected void readFrequencies(String key, boolean mustHave) throws Exception
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.
mustHave
- key
- Exception
- If no frequencies were encountered