GaussianReader

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

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

GaussianFchkReader
```
public class GaussianReader
extends MOReader
```
Reader for Gaussian 94/98/03/09 output files. 4/11/2009 -- hansonr -- added NBO support as extension of MOReader

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 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`

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, 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

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

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

Constructor Summary

Constructors
Constructor Description

GaussianReader()

Constructors
Constructor	Description
`GaussianReader()`

Method Summary

All Methods Instance Methods Concrete Methods
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)`

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

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData

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

- Field Detail
  - STD_ORIENTATION_ATOMIC_NUMBER_OFFSET
```
private static final int STD_ORIENTATION_ATOMIC_NUMBER_OFFSET
```
    Word index of atomic number in line with atom coordinates in an orientation block.
    
    See Also:
    
    Constant Field Values
  - energyString
```
private java.lang.String energyString
```
    Calculated energy with units (if possible).
  - energyKey
```
private java.lang.String energyKey
```
    Type of energy calculated, e.g., E(RB+HF-PW91).
  - calculationNumber
```
protected int calculationNumber
```
    The number of the calculation being interpreted.
  - scanPoint
```
private int scanPoint
```
    The scan point, where -1 denotes no scan information.
  - equivalentAtomSets
```
private int equivalentAtomSets
```
    The number of equivalent atom sets.
    Needed to associate identical properties to multiple atomsets
  - stepNumber
```
private int stepNumber
```
  - moModelSet
```
private int moModelSet
```
  - namedSets
```
protected BS namedSets
```
  - isHighPrecision
```
private boolean isHighPrecision
```
  - haveHighPrecision
```
private boolean haveHighPrecision
```
  - allowHighPrecision
```
private boolean allowHighPrecision
```
- Constructor Detail
  - GaussianReader
```
public GaussianReader()
```
- Method Detail
  - initializeReader
```
protected void initializeReader()
                         throws java.lang.Exception
```
    Overrides:
    
    initializeReader in class MOReader
    
    Throws:
    
    java.lang.Exception
  - checkLine
```
protected boolean checkLine()
                     throws java.lang.Exception
```
    Reads a Collection of AtomSets from a BufferedReader.
    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.
    
    Overrides:
    
    checkLine in class AtomSetCollectionReader
    
    Returns:
    
    TRUE to read a new line
    
    Throws:
    
    java.lang.Exception
  - getSpinDensities
```
private void getSpinDensities(int pt)
                       throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - readSCFDone
```
private void readSCFDone()
                  throws java.lang.Exception
```
    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:
    
    java.lang.Exception - If an error occurs
  - setProps
```
private void setProps(java.lang.String key,
                      java.lang.String value,
                      int n)
```
  - setNames
```
private void setNames(java.lang.String atomSetName,
                      BS namedSets,
                      int n)
```
  - setEnergy
```
private void setEnergy()
```
    Interpret the Energy= line for non SCF type energy output
  - readAtoms
```
protected void readAtoms()
                  throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - readBasis
```
protected void readBasis()
                  throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - readMolecularOrbitals
```
protected void readMolecularOrbitals()
                              throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - readFrequencies
```
protected void readFrequencies(java.lang.String key,
                               boolean mustHave)
                        throws java.lang.Exception
```
    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:
    
    mustHave -
    
    key -
    
    Throws:
    
    java.lang.Exception - If no frequencies were encountered
  - readDipoleMoment
```
void readDipoleMoment()
               throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - readPartialCharges
```
void readPartialCharges()
                 throws java.lang.Exception
```
    Reads partial charges and assigns them only to the last atom set.
    
    Throws:
    
    java.lang.Exception - When an I/O error or discardlines error occurs

Class GaussianReader

Nested Class Summary

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

Field Summary

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

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

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

Constructor Summary

Method Summary

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

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

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

Methods inherited from class java.lang.Object

Field Detail

STD_ORIENTATION_ATOMIC_NUMBER_OFFSET

energyString

energyKey

calculationNumber

scanPoint

equivalentAtomSets

stepNumber

moModelSet

namedSets

isHighPrecision

haveHighPrecision

allowHighPrecision

Constructor Detail

GaussianReader

Method Detail

initializeReader

checkLine

getSpinDensities

readSCFDone

setProps

setNames

setEnergy

readAtoms

readBasis

readMolecularOrbitals

readFrequencies

readDipoleMoment

readPartialCharges