Package org.jmol.quantum

Class NciCalculation

java.lang.Object
org.jmol.quantum.QuantumCalculation
org.jmol.quantum.QuantumPlaneCalculation
org.jmol.quantum.NciCalculation
public class NciCalculation extends QuantumPlaneCalculation

  • Field Details

    • havePoints

      private boolean havePoints

    • isReducedDensity

      private boolean isReducedDensity

    • DEFAULT_RHOPLOT_SCF

      private double DEFAULT_RHOPLOT_SCF

    • DEFAULT_RHOPLOT_PRO

      private double DEFAULT_RHOPLOT_PRO

    • DEFAULT_RHOPARAM

      private double DEFAULT_RHOPARAM

    • rhoMin

      private double rhoMin

    • rhoPlot

      private double rhoPlot

    • rhoParam

      private double rhoParam

    • TYPE_ALL

      private static final int TYPE_ALL
      See Also:

    • TYPE_INTRA

      private static final int TYPE_INTRA
      See Also:

    • TYPE_INTER

      private static final int TYPE_INTER
      See Also:

    • TYPE_LIGAND

      private static final int TYPE_LIGAND
      See Also:

    • NO_VALUE

      private static final double NO_VALUE
      See Also:

    • dataScaling

      private float dataScaling

    • dataIsReducedDensity

      private boolean dataIsReducedDensity

    • eigen

      private javajs.util.Eigen eigen

    • rhoMolecules

      private double[] rhoMolecules

    • type

      private int type

    • nMolecules

      private int nMolecules

    • isPromolecular

      private boolean isPromolecular

    • bsOK

      private javajs.util.BS bsOK

    • noValuesAtAll

      private boolean noValuesAtAll

    • useAbsolute

      private boolean useAbsolute

    • c

      private static double c

    • rpower

      private static double rpower

    • hess

      private double[][] hess

    • grad

      private double grad

    • gxTemp

      private double gxTemp

    • gyTemp

      private double gyTemp

    • gzTemp

      private double gzTemp

    • gxxTemp

      private double gxxTemp

    • gyyTemp

      private double gyyTemp

    • gzzTemp

      private double gzzTemp

    • gxyTemp

      private double gxyTemp

    • gyzTemp

      private double gyzTemp

    • gxzTemp

      private double gxzTemp

    • eigenValues

      private float[] eigenValues

    • test1

      double test1

    • yzPlanesRaw

      private float[][] yzPlanesRaw

    • yzCount

      private int yzCount

    • yzPlanesRho

      private float[][] yzPlanesRho

    • p0

      private float[] p0

    • p1

      private float[] p1

    • p2

      private float[] p2

    • coef1

      private static double[] coef1

    • coef2

      private static double[] coef2

    • coef3

      private static double[] coef3

    • zeta1

      private static double[] zeta1

    • zeta2

      private static double[] zeta2

    • zeta3

      private static double[] zeta3

    • dMax

      private static double[] dMax

  • Constructor Details

    • NciCalculation

      public NciCalculation()

  • Method Details

    • getNoValue

      public float getNoValue()
      Description copied from class: QuantumPlaneCalculation
      Get that value that represents "no value" so that it can be disregarded in terms of recording and reporting the min/max/mean.
      Specified by:
      getNoValue in class QuantumPlaneCalculation
      Returns:
      NO_VALUE

    • setupCalculation

      public boolean setupCalculation(VolumeData volumeData, javajs.util.BS bsSelected, javajs.util.BS bsExcluded, javajs.util.BS[] bsMolecules, javajs.util.T3[] atomCoordAngstroms, int firstAtomOffset, boolean isReducedDensity, javajs.util.T3[] points, float[] parameters, int testFlags)

    • getParameter

      private static double getParameter(float[] parameters, int i, double def, String name)

    • getBsOK

      private void getBsOK()
      grid-based discrete SCF calculation needs to know which atoms to consider inter and which intramolecular

    • createCube

      public void createCube()
      Specified by:
      createCube in class QuantumCalculation

    • initializeOnePoint

      protected void initializeOnePoint()
      Overrides:
      initializeOnePoint in class QuantumCalculation

    • initializeEigen

      private void initializeEigen()

    • getPlane

      public void getPlane(int ix, float[] yzPlane)
      Specified by:
      getPlane in class QuantumPlaneCalculation

    • process

      protected void process()
      Specified by:
      process in class QuantumCalculation

    • getValue

      private float getValue(double rho, boolean isReducedDensity)

    • processAtoms

      private double processAtoms(int ix, int iy, int iz, int index)
      At each grid point we need to calculate the sum of the atom-based promolecular data. We partition this calculation into molecular subsets if necessary, and we check for atoms that are too far away to make a difference before we waste time doing exponentiation. If index >= 0, then this is just a check for intra- vs. inter- molecularity based on promolecular density. This is needed for applying intra- and inter-molecular filters to SCF CUBE data.
      Parameters:
      ix -
      iy -
      iz -
      index -
      Returns:
      rho value or NO_VALUE

    • setPlanes

      public void setPlanes(float[][] planes)
      Raw file data planes are passed to us here from VolumeFileReader
      Specified by:
      setPlanes in class QuantumPlaneCalculation
      Parameters:
      planes -

    • calcPlane

      public void calcPlane(int x, float[] plane)
      For reduced density only; coloring is done point by point.
      Specified by:
      calcPlane in class QuantumPlaneCalculation
      Parameters:
      x -
      plane - an OUTPUT plane, to be filled here and used by MarchingCubes

    • process

      public float process(int vA, int vB, float f)
      Passing the grid points of the two ends of an edge and a fraction to this method returns the value at a triangle point. This way we do not need to calculate this for EVERY point on the grid, only the ones that are part of the surface.
      Specified by:
      process in class QuantumPlaneCalculation
      Parameters:
      vA -
      vB -
      f -
      Returns:
      value at point f-way between vA and vB

    • getPlaneValue

      private double getPlaneValue(int vA)
      We always have four raw planes in hand; we just need to know which three to use in any particular case.
      Parameters:
      vA -
      Returns:
      value of sign(lambda2)*rho at this grid point