Package gov.nih.mipav.model.structures

Class Voro.voro_base_unitcell

java.lang.Object
gov.nih.mipav.model.structures.Voro.voro_base_unitcell
Direct Known Subclasses:
Voro.container_periodic_base
Enclosing class:
Voro
class Voro.voro_base_unitcell extends Object

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    double
    boxx
    The size of a computational block in the x direction.
    double
    boxy
    The size of a computational block in the y direction.
    double
    boxz
    The size of a computational block in the z direction.
    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.
    double[]
    mrad
    An array to hold the minimum distances associated with the worklists.
    int
    nx
    The number of blocks in the x direction.
    int
    nxy
    A finalant, set to the value of nx multiplied by ny, which is used in the routines that step through blocks in sequence.
    int
    nxyz
    A finalant, set to the value of nx*ny*nz, which is used in the routines that step through blocks in sequence.
    int
    ny
    The number of blocks in the y direction.
    int
    nz
    The number of blocks in the z direction.
    Voro.voronoicell
    unit_voro
    The computed unit Voronoi cell corresponding the given 3D non-rectangular periodic domain geometry.
    double
    xsp
    The inverse box length in the x direction.
    double
    ysp
    The inverse box length in the y direction.
    double
    zsp
    The inverse box length in the z direction.

  • Constructor Summary

    Constructors
    Constructor
    Description
    voro_base_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.
    voro_base_unitcell(double bx_, double bxy_, double by_, double bxz_, double byz_, double bz_, int nx_, int ny_, int nz_, double boxx_, double boxy_, double boxz_)
     
    voro_base_unitcell(int nx_, int ny_, int nz_, double boxx_, double boxy_, double boxz_)
    This function is called during container finalruction.

  • Method Summary

    Modifier and Type
    Method
    Description
    (package private) void
    compute_minimum(double[] minr, double xlo, double xhi, double ylo, double yhi, double zlo, double zhi, int ti, int tj, int tk)
    Computes the minimum distance from a subregion to a given block.
    (package private) boolean
    contains_neighbor(byte[] format)
    Checks to see whether "%n" appears in a format sequence to determine whether neighbor information is required or not.
    (package private) boolean
    contains_neighbor(char[] format)
     
    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.
    protected int
    step_div(int a, int b)
    A custom Double division function that returns consistent stepping for negative numbers.
    protected int
    step_int(double a)
    A custom int function that returns consistent stepping for negative numbers, so that (-1.5, -0.5, 0.5, 1.5) maps to (-2,-1,0,1).
    protected int
    step_mod(int a, int b)
    A custom modulo function that returns consistent stepping for negative numbers.
    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

    • nx

      public int nx
      The number of blocks in the x direction.

    • ny

      public int ny
      The number of blocks in the y direction.

    • nz

      public int nz
      The number of blocks in the z direction.

    • nxy

      public int nxy
      A finalant, set to the value of nx multiplied by ny, which is used in the routines that step through blocks in sequence.

    • nxyz

      public int nxyz
      A finalant, set to the value of nx*ny*nz, which is used in the routines that step through blocks in sequence.

    • boxx

      public double boxx
      The size of a computational block in the x direction.

    • boxy

      public double boxy
      The size of a computational block in the y direction.

    • boxz

      public double boxz
      The size of a computational block in the z direction.

    • xsp

      public double xsp
      The inverse box length in the x direction.

    • ysp

      public double ysp
      The inverse box length in the y direction.

    • zsp

      public double zsp
      The inverse box length in the z direction.

    • mrad

      public double[] mrad
      An array to hold the minimum distances associated with the worklists. This array is initialized during container finalruction, by the initialize_radii() routine.

    • 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

    • voro_base_unitcell

      public voro_base_unitcell(int nx_, int ny_, int nz_, double boxx_, double boxy_, double boxz_)
      This function is called during container finalruction. The routine scans all of the worklists in the wl[] array. For a given worklist of blocks labeled \f$w_1\f$ to \f$w_n\f$, it computes a sequence \f$r_0\f$ to \f$r_n\f$ so that $r_i$ is the minimum distance to all the blocks \f$w_{j}\f$ where \f$j>i\f$ and all blocks outside the worklist. The values of \f$r_n\f$ is calculated first, as the minimum distance to any block in the shell surrounding the worklist. The \f$r_i\f$ are then computed in reverse order by considering the distance to \f$w_{i+1}\f$.

    • voro_base_unitcell

      public voro_base_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.

    • voro_base_unitcell

      public voro_base_unitcell(double bx_, double bxy_, double by_, double bxz_, double byz_, double bz_, int nx_, int ny_, int nz_, double boxx_, double boxy_, double boxz_)

  • Method Details

    • step_int

      protected int step_int(double a)
      A custom int function that returns consistent stepping for negative numbers, so that (-1.5, -0.5, 0.5, 1.5) maps to (-2,-1,0,1). \param[in] a the number to consider. \return The value of the custom int operation.

    • step_mod

      protected int step_mod(int a, int b)
      A custom modulo function that returns consistent stepping for negative numbers. For example, (-2,-1,0,1,2) step_mod 2 is (0,1,0,1,0). \param[in] (a,b) the input Doubles. \return The value of a modulo b, consistent for negative numbers.

    • step_div

      protected int step_div(int a, int b)
      A custom Double division function that returns consistent stepping for negative numbers. For example, (-2,-1,0,1,2) step_div 2 is (-1,-1,0,0,1). \param[in] (a,b) the input Doubles. \return The value of a div b, consistent for negative numbers.

    • compute_minimum

      void compute_minimum(double[] minr, double xlo, double xhi, double ylo, double yhi, double zlo, double zhi, int ti, int tj, int tk)
      Computes the minimum distance from a subregion to a given block. If this distance is smaller than the value of minr, then it passes \param[in,out] minr a pointer to the current minimum distance. If the distance computed in this function is smaller, then this distance is set to the new one. \param[out] (xlo,ylo,zlo) the lower coordinates of the subregion being considered. \param[out] (xhi,yhi,zhi) the upper coordinates of the subregion being considered. \param[in] (ti,tj,tk) the coordinates of the block.

    • contains_neighbor

      boolean contains_neighbor(byte[] format)
      Checks to see whether "%n" appears in a format sequence to determine whether neighbor information is required or not. \param[in] format the format string to check. \return True if a "%n" is found, false otherwise.

    • contains_neighbor

      boolean contains_neighbor(char[] format)

    • 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.