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java.lang.Objectorg.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.GaussianReader
public class GaussianReader
Reader for Gaussian 94/98/03 output files.
Field Summary | |
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(package private) int |
atomCount
|
private 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 static int |
FREQ_FIRST_VECTOR_OFFSET
Word index of the first X vector of the first frequency in the frequency output. |
(package private) int |
gaussianCount
|
(package private) java.util.Hashtable |
moData
|
(package private) java.util.Vector |
orbitals
|
private int |
scanPoint
The scan point, where -1 denotes no scan information. |
(package private) int |
shellCount
|
private static int |
STD_ORIENTATION_ATOMIC_NUMBER_OFFSET
Word index of atomic number in line with atom coordinates in an orientation block. |
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
---|
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, desiredModelNumber, desiredSpaceGroupIndex, doApplySymmetry, filter, getHeader, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveDesiredModel, iHaveSymmetryOperators, iHaveUnitCell, latticeCells, line, modelNumber, needToApplySymmetry, next, notionalUnitCell, prevline, primitiveLatticeVectors, ptLine, reader, readerName, spaceGroup |
Constructor Summary | |
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GaussianReader()
|
Method Summary | |
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(package private) void |
addMOData(int nColumns,
java.util.Vector[] data,
java.util.Hashtable[] mos)
|
private void |
readAtoms()
|
AtomSetCollection |
readAtomSetCollection(java.io.BufferedReader reader)
Reads a Collection of AtomSets from a BufferedReader. |
(package private) void |
readBasis()
|
(package private) void |
readDipoleMoment()
|
private void |
readFrequencies()
Interprets the Harmonic frequencies section. |
(package private) 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 |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private static final int STD_ORIENTATION_ATOMIC_NUMBER_OFFSET
private static final int FREQ_FIRST_VECTOR_OFFSET
private java.lang.String energyString
private java.lang.String energyKey
private int calculationNumber
private int scanPoint
private int equivalentAtomSets
Needed to associate identical properties to multiple atomsets
int atomCount
int shellCount
int gaussianCount
java.util.Hashtable moData
java.util.Vector orbitals
Constructor Detail |
---|
public GaussianReader()
Method Detail |
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public AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
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.
readAtomSetCollection
in class AtomSetCollectionReader
reader
- BufferedReader associated with the Gaussian output text.
private void readSCFDone() throws java.lang.Exception
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.
java.lang.Exception
- If an error occursprivate void setEnergy()
private void readAtoms() throws java.lang.Exception
java.lang.Exception
void readBasis() throws java.lang.Exception
java.lang.Exception
void readMolecularOrbitals() throws java.lang.Exception
java.lang.Exception
void addMOData(int nColumns, java.util.Vector[] data, java.util.Hashtable[] mos)
private void readFrequencies() throws java.lang.Exception, java.io.IOException
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.
java.lang.Exception
- If no frequences were encountered
java.io.IOException
- If an I/O error occursvoid readDipoleMoment() throws java.lang.Exception
java.lang.Exception
void readPartialCharges() throws java.lang.Exception
java.lang.Exception
- When an I/O error or discardlines error occurs
|
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