Package org.jmol.adapter.readers.simple

Class MopacReader

java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.simple.MopacReader
All Implemented Interfaces:
javajs.api.GenericLineReader
public class MopacReader extends AtomSetCollectionReader
Reads Mopac 93, 6, 7, 2002, or 2009 output files
Author:
Egon Willighagen <egonw@jmol.org>

  • Field Details

    • chargesFound

      private boolean chargesFound

    • haveHeader

      private boolean haveHeader

    • mopacVersion

      private int mopacVersion

  • Constructor Details

    • MopacReader

      public MopacReader()

  • Method Details

    • initializeReader

      protected void initializeReader() throws Exception
      Overrides:
      initializeReader in class AtomSetCollectionReader
      Throws:
      Exception

    • checkLine

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

    • processTotalEnergy

      void processTotalEnergy()

    • processAtomicCharges

      void processAtomicCharges() throws Exception
      Reads the section in MOPAC files with atomic charges. These sections look like: 
                     NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS
 
          ATOM NO.   TYPE          CHARGE        ATOM  ELECTRON DENSITY
            1          C          -0.077432        4.0774
            2          C          -0.111917        4.1119
            3          C           0.092081        3.9079
      They are expected to be found in the file before the cartesian coordinate section.
      Throws:
      Exception

    • processCoordinates

      void processCoordinates() throws Exception
      Reads the section in MOPAC files with cartesian coordinates. These sections look like: 
                 CARTESIAN COORDINATES
 
     NO.       ATOM         X         Y         Z
 
      1         C        0.0000    0.0000    0.0000
      2         C        1.3952    0.0000    0.0000
      3         C        2.0927    1.2078    0.0000
      In a MOPAC2002 file the columns are different: 
                CARTESIAN COORDINATES
 
 NO.       ATOM           X             Y             Z
 
  1         H        0.00000000    0.00000000    0.00000000
  2         O        0.95094500    0.00000000    0.00000000
  3         H        1.23995160    0.90598439    0.00000000
      Throws:
      Exception

    • readFrequencies

      private void readFrequencies() throws Exception
      Interprets the Harmonic frequencies section. 
           THE LAST 6 VIBRATIONS ARE THE TRANSLATION AND ROTATION MODES
    THE FIRST THREE OF THESE BEING TRANSLATIONS IN X, Y, AND Z, RESPECTIVELY
              NORMAL COORDINATE ANALYSIS
   
       ROOT NO.    1           2           3           4           5           6
   
              370.51248   370.82204   618.03031   647.68700   647.74806   744.32662
     
            1   0.00002     0.00001    -0.00002    -0.05890     0.07204    -0.00002
            2   0.00001    -0.00006    -0.00001     0.01860     0.13517     0.00000
            3   0.00421    -0.11112     0.06838    -0.00002    -0.00003    -0.02449
   
            4   0.00002     0.00001    -0.00002    -0.04779     0.07977    -0.00001
            5  -0.00002     0.00002     0.00001     0.13405    -0.02908     0.00004
            6  -0.10448     0.05212    -0.06842    -0.00005    -0.00002    -0.02447

      The vectors are added to a clone of the last read AtomSet. Only the Frequencies are set as properties for each of the frequency type AtomSet generated.

      Throws:
      Exception - If an I/O error occurs