Package org.jmol.adapter.readers.quantum

Class 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 Detail

      • calculationNumber

        private int calculationNumber
        The number of the job being interpreted.

      • isFirstJob

        private boolean isFirstJob

      • nBasis

        private int nBasis

      • dFixed

        private boolean dFixed

      • fFixed

        private boolean fFixed

      • DC_LIST

        private static java.lang.String DC_LIST

      • DS_LIST

        private static java.lang.String DS_LIST

      • FC_LIST

        private static java.lang.String FC_LIST

      • FS_LIST

        private static java.lang.String FS_LIST

      • dList

        java.lang.String dList

      • fList

        java.lang.String fList

      • dSpherical

        boolean dSpherical

      • fSpherical

        boolean fSpherical

    • Constructor Detail

      • QchemReader

        public QchemReader()

    • Method Detail

      • checkLine

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

      • readCalculationType

        private void readCalculationType()

      • readAtoms

        private void readAtoms()
                throws java.lang.Exception
        Throws:
        java.lang.Exception

      • readFrequencies

        private void readFrequencies()
                      throws java.lang.Exception,
                             java.io.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:
        java.lang.Exception - If no frequences were encountered
        java.io.IOException - If an I/O error occurs

      • readPartialCharges

        private void readPartialCharges()
                         throws java.lang.Exception
        Throws:
        java.lang.Exception

      • readEnergy

        private void readEnergy()

      • readBasis

        private void readBasis()
                throws java.lang.Exception
        Throws:
        java.lang.Exception

      • readESym

        private void readESym​(boolean haveSym)
               throws java.lang.Exception
        Throws:
        java.lang.Exception

      • readQchemMolecularOrbitals

        private void readQchemMolecularOrbitals()
                                 throws java.lang.Exception
        Throws:
        java.lang.Exception

      • readMOs

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