Class GaussianFchkReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader

    public class GaussianFchkReader
    extends GaussianReader
    Reader for Gaussian fchk files for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot) also allows appended freq data
    Author:
    hansonr Bob Hanson hansonr@stolaf.edu
    • Field Detail

      • fileData

        private java.util.Map<java.lang.String,​java.lang.Object> fileData
      • atomCount

        private int atomCount
      • AO_TYPES

        private static java.lang.String[] AO_TYPES
    • Constructor Detail

      • GaussianFchkReader

        public GaussianFchkReader()
    • Method Detail

      • initializeReader

        protected void initializeReader()
                                 throws java.lang.Exception
        Overrides:
        initializeReader in class GaussianReader
        Throws:
        java.lang.Exception
      • checkForFreq

        private void checkForFreq()
                           throws java.lang.Exception
        Throws:
        java.lang.Exception
      • fillFloat

        private float[] fillFloat​(float[] f0,
                                  int i,
                                  int n)
      • readAllData

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

        protected void readAtoms()
                          throws java.lang.Exception
        Overrides:
        readAtoms in class GaussianReader
        Throws:
        java.lang.Exception
      • readBonds

        protected void readBonds()
      • readDipoleMoment

        protected void readDipoleMoment()
                                 throws java.lang.Exception
        Overrides:
        readDipoleMoment in class GaussianReader
        Throws:
        java.lang.Exception
      • readPartialCharges

        protected void readPartialCharges()
                                   throws java.lang.Exception
        Description copied from class: GaussianReader
        Reads partial charges and assigns them only to the last atom set.
        Overrides:
        readPartialCharges in class GaussianReader
        Throws:
        java.lang.Exception - When an I/O error or discardlines error occurs
      • readBasis

        protected void readBasis()
                          throws java.lang.Exception
        Overrides:
        readBasis in class GaussianReader
        Throws:
        java.lang.Exception
      • readMolecularObitals

        protected void readMolecularObitals()
                                     throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getOrbitals

        private void getOrbitals​(float[] e,
                                 float[] c,
                                 int occ,
                                 int nElec)