GaussianFchkReader
public class GaussianReader extends MOReader
BasisFunctionReader.MOEnergySorter
Modifier and Type | Field | Description |
---|---|---|
private boolean |
allowHighPrecision |
|
protected int |
calculationNumber |
The number of the calculation being interpreted.
|
private java.lang.String |
energyKey |
Type of energy calculated, e.g., E(RB+HF-PW91).
|
private java.lang.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 |
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
allowNoOrbitals, energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
Constructor | Description |
---|---|
GaussianReader() |
Modifier and Type | Method | 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(java.lang.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(java.lang.String atomSetName,
BS namedSets,
int n) |
|
private void |
setProps(java.lang.String key,
java.lang.String value,
int n) |
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
addCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData
private static final int STD_ORIENTATION_ATOMIC_NUMBER_OFFSET
private java.lang.String energyString
private java.lang.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 java.lang.Exception
initializeReader
in class MOReader
java.lang.Exception
protected boolean checkLine() throws java.lang.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
java.lang.Exception
private void getSpinDensities(int pt) throws java.lang.Exception
java.lang.Exception
private void readSCFDone() throws java.lang.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.
java.lang.Exception
- If an error occursprivate void setProps(java.lang.String key, java.lang.String value, int n)
private void setNames(java.lang.String atomSetName, BS namedSets, int n)
private void setEnergy()
protected void readAtoms() throws java.lang.Exception
java.lang.Exception
protected void readBasis() throws java.lang.Exception
java.lang.Exception
protected void readMolecularOrbitals() throws java.lang.Exception
java.lang.Exception
protected void readFrequencies(java.lang.String key, boolean mustHave) throws java.lang.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
- java.lang.Exception
- If no frequencies were encounteredvoid readDipoleMoment() throws java.lang.Exception
java.lang.Exception
void readPartialCharges() throws java.lang.Exception
java.lang.Exception
- When an I/O error or discardlines error occurs