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