Class CubeReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader

    public class CubeReader
    extends AtomSetCollectionReader
    Gaussian cube file format http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html this is good because it is source code http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm distances are in Bohrs because we are reading Gaussian cube OUTPUT files not Gaussian cube INPUT files. Miguel 2005 07 17 a negative atom count means that it is molecular orbital (MO) data with MO data, the extra line contains the number of orbitals and the orbital number these orbitals are interspersed -- all orbital values are given together for each coordinate point. also used for older JVXL and JVXL+ file format
    • Field Detail

      • ac

        private int ac
      • isAngstroms

        private boolean isAngstroms
    • Constructor Detail

      • CubeReader

        public CubeReader()
    • Method Detail

      • readTitleLines

        private void readTitleLines()
                             throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readAtomCountAndOrigin

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

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