Class MOReader

All Implemented Interfaces:
javajs.api.GenericLineReader
Direct Known Subclasses:
GaussianReader, GenNBOReader, JaguarReader, NWChemReader, OrcaReader, PsiReader, QchemReader, SlaterReader

public abstract class MOReader extends BasisFunctionReader
General methods for reading molecular orbital data, including embedded output from the NBO program. In particular, when the AONBO keyword is included. requires the following sort of construct: public AtomSetCollection readAtomSetCollection(BufferedReader reader) { readAtomSetCollection(reader, "some type"); } protected boolean checkLine() { if (line.indexOf(...)) { doThis(); return true/false; } if (line.indexOf(...)) { doThat(); return true/false; } return checkNboLine(); }
  • Field Details

    • shellCount

      public int shellCount
    • gaussianCount

      public int gaussianCount
    • gaussians

      public float[][] gaussians
    • energyUnits

      protected String energyUnits
    • moTypes

      protected javajs.util.Lst<String> moTypes
    • getNBOs

      private boolean getNBOs
    • getNBOCharges

      private boolean getNBOCharges
    • haveNboCharges

      protected boolean haveNboCharges
    • haveNboOrbitals

      protected boolean haveNboOrbitals
    • orbitalsRead

      protected boolean orbitalsRead
    • lastMoData

      protected Map<String,Object> lastMoData
    • allowNoOrbitals

      protected boolean allowNoOrbitals
    • forceMOPAC

      protected boolean forceMOPAC
    • HEADER_GAMESS_UK_MO

      protected final int HEADER_GAMESS_UK_MO
      See Also:
    • HEADER_GAMESS_OCCUPANCIES

      protected final int HEADER_GAMESS_OCCUPANCIES
      See Also:
    • HEADER_GAMESS_ORIGINAL

      protected final int HEADER_GAMESS_ORIGINAL
      See Also:
    • HEADER_NONE

      protected final int HEADER_NONE
      See Also:
    • haveCoeffMap

      private boolean haveCoeffMap
    • P_LIST

      private static final String P_LIST
      See Also:
    • DS_LIST

      private static final String DS_LIST
      See Also:
    • DC_LIST

      private static final String DC_LIST
      See Also:
    • FS_LIST

      private static final String FS_LIST
      See Also:
    • FC_LIST

      private static String FC_LIST
    • iMo0

      private int iMo0
  • Constructor Details

    • MOReader

      public MOReader()
  • Method Details

    • initializeReader

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

      protected boolean checkNboLine() throws Exception
      Returns:
      true if need to read line
      Throws:
      Exception
    • getNboCharges

      private void getNboCharges() throws Exception
      Throws:
      Exception
    • getNboTypes

      protected void getNboTypes() throws Exception
      Throws:
      Exception
    • readMolecularOrbitals

      protected void readMolecularOrbitals(int headerType) throws Exception
      Throws:
      Exception
    • addSlaterBasis

      protected void addSlaterBasis()
      See MopacSlaterReader
    • addCoef

      public void addCoef(Map<String,Object> mo, float[] coefs, String type, float energy, float occ, int moCount)
    • getMOHeader

      protected void getMOHeader(int headerType, String[] tokens, Map<String,Object>[] mos, int nThisLine) throws Exception
      Throws:
      Exception
    • addMOData

      protected void addMOData(int nColumns, javajs.util.Lst<String>[] data, Map<String,Object>[] mos)
    • setMOData

      public void setMOData(boolean clearOrbitals)
    • readSecondOrderData

      private void readSecondOrderData() throws Exception
      Throws:
      Exception