Package gov.nih.mipav.model.structures

Class Voro.unitcell

java.lang.Object
gov.nih.mipav.model.structures.Voro.unitcell
Enclosing class:
Voro
class Voro.unitcell extends Object
\brief Class for computation of the unit Voronoi cell associated with a 3D non-rectangular periodic domain.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    double
    bx
    The x coordinate of the first vector defining the periodic domain.
    double
    bxy
    The x coordinate of the second vector defining the periodic domain.
    double
    bxz
    The x coordinate of the third vector defining the periodic domain.
    double
    by
    The y coordinate of the second vector defining the periodic domain.
    double
    byz
    The y coordinate of the third vector defining the periodic domain.
    double
    bz
    The z coordinate of the third vector defining the periodic domain.
    protected double
    max_uv_y
    The maximum y-coordinate that could possibly cut the computed unit Voronoi cell.
    protected double
    max_uv_z
    The maximum z-coordinate that could possibly cut the computed unit Voronoi cell.
    Voro.voronoicell
    unit_voro
    The computed unit Voronoi cell corresponding the given 3D non-rectangular periodic domain geometry.

  • Constructor Summary

    Constructors
    Constructor
    Description
    unitcell(double bx_, double bxy_, double by_, double bxz_, double byz_, double bz_)
    Initializes the unit cell class for a particular non-orthogonal periodic geometry, corresponding to a parallelepiped with sides given by three vectors.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    draw_domain_gnuplot(RandomAccessFile fp)
    Draws the periodic domain in gnuplot format.
    void
    draw_domain_gnuplot(String filename)
    Draws an outline of the domain in Gnuplot format.
    void
    draw_domain_pov(RandomAccessFile fp)
    Draws the periodic domain in POV-Ray format.
    void
    draw_domain_pov(String filename)
     
    void
    images(Vector<Integer> vi, Vector<Double> vd)
    Computes a list of periodic domain images that intersect the unit Voronoi cell.
    boolean
    intersects_image(double dx, double dy, double dz, double[] vol)
    Calculates whether the unit Voronoi cell intersects a given periodic image of the domain.
    private void
    unit_voro_apply(int i, int j, int k)
    Applies a pair of opposing plane cuts from a periodic image point to the unit Voronoi cell.
    private boolean
    unit_voro_intersect(int l)
    Tests to see if a shell of periodic images could possibly cut the periodic unit cell.
    private boolean
    unit_voro_test(int i, int j, int k)
    Tests to see if a plane cut from a particular periodic image will cut th unit Voronoi cell.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • bx

      public double bx
      The x coordinate of the first vector defining the periodic domain.

    • bxy

      public double bxy
      The x coordinate of the second vector defining the periodic domain.

    • by

      public double by
      The y coordinate of the second vector defining the periodic domain.

    • bxz

      public double bxz
      The x coordinate of the third vector defining the periodic domain.

    • byz

      public double byz
      The y coordinate of the third vector defining the periodic domain.

    • bz

      public double bz
      The z coordinate of the third vector defining the periodic domain.

    • unit_voro

      public Voro.voronoicell unit_voro
      The computed unit Voronoi cell corresponding the given 3D non-rectangular periodic domain geometry.

    • max_uv_y

      protected double max_uv_y
      The maximum y-coordinate that could possibly cut the computed unit Voronoi cell.

    • max_uv_z

      protected double max_uv_z
      The maximum z-coordinate that could possibly cut the computed unit Voronoi cell.

  • Constructor Details

    • unitcell

      public unitcell(double bx_, double bxy_, double by_, double bxz_, double byz_, double bz_)
      Initializes the unit cell class for a particular non-orthogonal periodic geometry, corresponding to a parallelepiped with sides given by three vectors. The class constructs the unit Voronoi cell corresponding to this geometry. \param[in] (bx_) The x coordinate of the first unit vector. \param[in] (bxy_,by_) The x and y coordinates of the second unit vector. \param[in] (bxz_,byz_,bz_) The x, y, and z coordinates of the third unit vector.

  • Method Details

    • draw_domain_gnuplot

      public void draw_domain_gnuplot(String filename)
      Draws an outline of the domain in Gnuplot format. \param[in] filename the filename to write to.

    • draw_domain_gnuplot

      public void draw_domain_gnuplot(RandomAccessFile fp)
      Draws the periodic domain in gnuplot format. \param[in] fp the file handle to write to.

    • draw_domain_pov

      public void draw_domain_pov(String filename)

    • draw_domain_pov

      public void draw_domain_pov(RandomAccessFile fp)
      Draws the periodic domain in POV-Ray format. \param[in] fp the file handle to write to.

    • intersects_image

      public boolean intersects_image(double dx, double dy, double dz, double[] vol)
      Calculates whether the unit Voronoi cell intersects a given periodic image of the domain. \param[in] (dx,dy,dz) the displacement of the periodic image. \param[out] vol the proportion of the unit cell volume within this image, only computed in the case that the two intersect. \return True if they intersect, false otherwise.

    • images

      public void images(Vector<Integer> vi, Vector<Double> vd)
      Computes a list of periodic domain images that intersect the unit Voronoi cell. \param[out] vi a vector containing triplets (i,j,k) corresponding to domain images that intersect the unit Voronoi cell, when it is centered in the middle of the primary domain. \param[out] vd a vector containing the fraction of the Voronoi cell volume within each corresponding image listed in vi.

    • unit_voro_apply

      private void unit_voro_apply(int i, int j, int k)
      Applies a pair of opposing plane cuts from a periodic image point to the unit Voronoi cell. \param[in] (i,j,k) the index of the periodic image to consider.

    • unit_voro_intersect

      private boolean unit_voro_intersect(int l)
      Tests to see if a shell of periodic images could possibly cut the periodic unit cell. \param[in] l the index of the shell to consider. \return True if a point in the shell cuts the cell, false otherwise.

    • unit_voro_test

      private boolean unit_voro_test(int i, int j, int k)
      Tests to see if a plane cut from a particular periodic image will cut th unit Voronoi cell. \param[in] (i,j,k) the index of the periodic image to consider. \return True if the image cuts the cell, false otherwise.