Class GaussianReader

Method Details

• initializeReader

  protected void initializeReader() throws Exception

  Overrides:

  initializeReader in class MOReader

  Throws:

  Exception

• checkLine

  protected boolean checkLine() throws 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:

  Exception

• finalizeSubclassReader

  public void finalizeSubclassReader() throws Exception

  Overrides:

  finalizeSubclassReader in class AtomSetCollectionReader

  Throws:

  Exception

• readAtoms

  protected void readAtoms() throws Exception

  Throws:

  Exception

• readBasis

  protected void readBasis() throws Exception

  Throws:

  Exception

• readMolecularOrbitals

  protected void readMolecularOrbitals() throws Exception

  Throws:

  Exception

• readFrequencies

  protected void readFrequencies(String key, boolean mustHave) throws 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:

  key -

  mustHave -

  Throws:

  Exception - If no frequencies were encountered