Package org.jmol.adapter.readers.quantum

Class DgridReader

java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.quantum.BasisFunctionReader
org.jmol.adapter.readers.quantum.MOReader
org.jmol.adapter.readers.quantum.DgridReader
All Implemented Interfaces:
GenericLineReader
public class DgridReader extends MOReader
A reader for Dgrid BASISFILE data. http://www.scm.com/News/DGrid.html http://www.scm.com/Doc/Doc2009.01/ADF/ADFUsersGuide/page430.html

  • Field Details

    • scaleSlaters

      protected boolean scaleSlaters

    • _1_4pi

      protected static final double _1_4pi
      See Also:

    • fact_2n

      protected static final double[] fact_2n

  • Constructor Details

    • DgridReader

      public DgridReader()

  • Method Details

    • checkLine

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

    • addSlater

      protected final SlaterData addSlater(int iAtom, int a, int b, int c, int d, double zeta, double coef)
      We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
      Parameters:
      iAtom - now 1-based
      a -
      b -
      c -
      d -
      zeta -
      coef -

    • getSlaters

      protected Lst<SlaterData> getSlaters()

    • addSlater

      protected void addSlater(SlaterData sd, int n)

    • setSlaters

      protected final void setSlaters(boolean doSort)
      after the vectors intinfo and floatinfo are completed, we
      Parameters:
      doSort - TODO

    • setMOs

      protected final void setMOs(String units)

    • sortOrbitalCoefficients

      protected void sortOrbitalCoefficients(int[] pointers)
      sorts coefficients by atomic number for speed later
      Parameters:
      pointers -

    • sortOrbitals

      protected void sortOrbitals()
      sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"

    • scaleSlater

      protected double scaleSlater(int ex, int ey, int ez, int er, double zeta)
      Perform implementation-specific scaling. This method is subclassed in MopacSlaterReader to handle spherical slaters
      Parameters:
      ex -
      ey -
      ez -
      er -
      zeta -
      Returns:
      scaling factor

    • fact

      protected static double fact(double f, double zeta, int n)
      Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents. sqrt[(2zeta)^(2n + 1) * f / 4pi / (2n)!] where f = (2 el + 1)!! / (2 ex - 1)!! / (2 ey - 1)!! / (2 ez - 1)!! The double factorials are precalculated.
      Parameters:
      f -
      zeta -
      n -
      Returns:
      scaled exponent

    • getSlaterConstCartesian

      protected static final double getSlaterConstCartesian(int n, double zeta, int el, int ex, int ey, int ez)
      scales slater using double factorials involving quantum number n, l, and xyz exponents. fact2[x] is (2x - 1)!! Since x!! = 1 for x = 1, 0 or -1, we can just ignore this part for s and p orbitals, where x, y, and z are all 0 or 1. 7!! = 105 5!! = 15 3!! = 3 Numerators/4pi: all d orbitals: fact2[3] = (2*2 + 1)!! = 5!! = 15/4pi all f orbitals: fact2[4] = (2*3 + 1)!! = 7!! = 105/4pi Denominators: dxy, dyz, dxz all are 1 giving 15/4pi dx2, dy2, and dz2 all have one "2", giving 15/3!!/4pi or 5/4pi
      Parameters:
      n -
      zeta -
      el -
      ex -
      ey -
      ez -
      Returns:
      scaled exponent