org.jmol.adapter.readers.more

Class GaussianReader

public class GaussianReader extends AtomSetCollectionReader

Reader for Gaussian 94/98/03 output files.
Field Summary
intatomCount
intcalculationNumber
The number of the calculation being interpreted.
StringenergyKey
Type of energy calculated, e.g., E(RB+HF-PW91).
StringenergyString
Calculated energy with units (if possible).
intequivalentAtomSets
The number of equivalent atom sets.
static intFREQ_FIRST_VECTOR_OFFSET
Word index of the first X vector of the first frequency in the frequency output.
intgaussianCount
HashtablemoData
Vectororbitals
intscanPoint
The scan point, where -1 denotes no scan information.
intshellCount
static intSTD_ORIENTATION_ATOMIC_NUMBER_OFFSET
Word index of atomic number in line with atom coordinates in an orientation block.
Method Summary
voidaddMOData(int nColumns, Vector[] data, Hashtable[] mos)
voidreadAtoms()
AtomSetCollectionreadAtomSetCollection(BufferedReader reader)
Reads a Collection of AtomSets from a BufferedReader.
voidreadBasis()
voidreadDipoleMoment()
voidreadFrequencies()
Interprets the Harmonic frequencies section.
voidreadMolecularOrbitals()
voidreadPartialCharges()
Reads partial charges and assigns them only to the last atom set.
voidreadSCFDone()
Interprets the SCF Done: section.
voidsetEnergy()
Interpret the Energy= line for non SCF type energy output

Field Detail

atomCount

int atomCount

calculationNumber

private int calculationNumber
The number of the calculation being interpreted.

energyKey

private String energyKey
Type of energy calculated, e.g., E(RB+HF-PW91).

energyString

private String energyString
Calculated energy with units (if possible).

equivalentAtomSets

private int equivalentAtomSets
The number of equivalent atom sets.

Needed to associate identical properties to multiple atomsets

FREQ_FIRST_VECTOR_OFFSET

private static final int FREQ_FIRST_VECTOR_OFFSET
Word index of the first X vector of the first frequency in the frequency output.

gaussianCount

int gaussianCount

moData

Hashtable moData

orbitals

Vector orbitals

scanPoint

private int scanPoint
The scan point, where -1 denotes no scan information.

shellCount

int shellCount

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.

Method Detail

addMOData

void addMOData(int nColumns, Vector[] data, Hashtable[] mos)

readAtoms

private void readAtoms()

readAtomSetCollection

public AtomSetCollection readAtomSetCollection(BufferedReader reader)
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.

Parameters: reader BufferedReader associated with the Gaussian output text.

Returns: The AtomSetCollection representing the interpreted Gaussian text.

readBasis

void readBasis()

readDipoleMoment

void readDipoleMoment()

readFrequencies

private void 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.

Throws: Exception If no frequences were encountered IOException If an I/O error occurs

readMolecularOrbitals

void readMolecularOrbitals()

readPartialCharges

void readPartialCharges()
Reads partial charges and assigns them only to the last atom set.

Throws: Exception When an I/O error or discardlines error occurs

readSCFDone

private void 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

setEnergy

private void setEnergy()
Interpret the Energy= line for non SCF type energy output