org.jmol.adapter.readers.more
public class GaussianReader extends AtomSetCollectionReader
| Field Summary | |
|---|---|
| int | atomCount |
| int | calculationNumber The number of the calculation being interpreted. |
| String | energyKey
Type of energy calculated, e.g., E(RB+HF-PW91). |
| String | energyString Calculated energy with units (if possible). |
| int | equivalentAtomSets
The number of equivalent atom sets.
|
| static int | FREQ_FIRST_VECTOR_OFFSET
Word index of the first X vector of the first frequency in the
frequency output. |
| int | gaussianCount |
| Hashtable | moData |
| Vector | orbitals |
| int | scanPoint The scan point, where -1 denotes no scan information. |
| int | shellCount |
| static int | STD_ORIENTATION_ATOMIC_NUMBER_OFFSET
Word index of atomic number in line with atom coordinates in an
orientation block. |
| Method Summary | |
|---|---|
| void | addMOData(int nColumns, Vector[] data, Hashtable[] mos) |
| void | readAtoms() |
| AtomSetCollection | readAtomSetCollection(BufferedReader reader)
Reads a Collection of AtomSets from a BufferedReader.
|
| void | readBasis() |
| void | readDipoleMoment() |
| void | readFrequencies()
Interprets the Harmonic frequencies section.
|
| void | readMolecularOrbitals() |
| void | readPartialCharges()
Reads partial charges and assigns them only to the last atom set. |
| void | readSCFDone()
Interprets the SCF Done: section.
|
| void | setEnergy()
Interpret the Energy= line for non SCF type energy output
|
Needed to associate identical properties to multiple atomsets
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.
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
Throws: Exception When an I/O error or discardlines error occurs
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