Package org.jmol.adapter.readers.quantum

Class QchemReader

java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.quantum.BasisFunctionReader
org.jmol.adapter.readers.quantum.MOReader
org.jmol.adapter.readers.quantum.QchemReader
All Implemented Interfaces:
javajs.api.GenericLineReader
public class QchemReader extends MOReader
A reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc. (http://www.q-chem.com/)

Molecular coordinates, normal coordinates of vibrations and MOs are read.

In order to get the output required for MO reading make sure that the $rem block has

print_general_basis TRUE
print_orbitals TRUE

This reader was developed from only a few output files, and therefore, is not guaranteed to properly read all Q-chem output. If you have problems, please contact the author of this code, not the developers of Q-chem.

This is a hacked version of Miguel's GaussianReader

Version:
1.1, 1.0
Author:
Rene P.F Kanters (rkanters@richmond.edu), Steven E. Wheeler (swheele2@ccqc.uga.edu)

  • Field Details

    • calculationNumber

      private int calculationNumber
      The number of the job being interpreted.

    • isFirstJob

      private boolean isFirstJob

    • alphas

      private QchemReader.MOInfo[] alphas

    • betas

      private QchemReader.MOInfo[] betas

    • nBasis

      private int nBasis

    • dFixed

      private boolean dFixed

    • fFixed

      private boolean fFixed

    • DC_LIST

      private static String DC_LIST

    • DS_LIST

      private static String DS_LIST

    • FC_LIST

      private static String FC_LIST

    • FS_LIST

      private static String FS_LIST

    • dList

      String dList

    • fList

      String fList

    • dSpherical

      boolean dSpherical

    • fSpherical

      boolean fSpherical

  • Constructor Details

    • QchemReader

      public QchemReader()

  • Method Details

    • initializeReader

      protected void initializeReader()
      Overrides:
      initializeReader in class MOReader

    • checkLine

      protected boolean checkLine() throws Exception
      Overrides:
      checkLine in class AtomSetCollectionReader
      Returns:
      true if need to read new line
      Throws:
      Exception

    • readCalculationType

      private void readCalculationType()

    • readAtoms

      private void readAtoms() throws Exception
      Throws:
      Exception

    • readFrequencies

      private void readFrequencies() throws Exception, IOException
      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

    • readPartialCharges

      private void readPartialCharges() throws Exception
      Throws:
      Exception

    • readEnergy

      private void readEnergy()

    • readBasis

      private void readBasis() throws Exception
      Throws:
      Exception

    • readESym

      private void readESym(boolean haveSym) throws Exception
      Throws:
      Exception

    • readQchemMolecularOrbitals

      private void readQchemMolecularOrbitals() throws Exception
      Throws:
      Exception

    • readMOs

      private int readMOs(boolean restricted, QchemReader.MOInfo[] moInfos) throws Exception
      Throws:
      Exception