Package gov.nih.mipav.model.structures

Class Voro.container_periodic_base

java.lang.Object
gov.nih.mipav.model.structures.Voro.voro_base_unitcell
gov.nih.mipav.model.structures.Voro.container_periodic_base
Direct Known Subclasses:
Voro.container_periodic_poly_radius_poly, Voro.container_periodic_radius_mono
Enclosing class:
Voro
class Voro.container_periodic_base extends Voro.voro_base_unitcell
\brief Class for representing a particle system in a 3D periodic non-orthogonal periodic domain. This class represents a particle system in a three-dimensional non-orthogonal periodic domain. The domain is defined by three periodicity vectors (bx,0,0), (bxy,by,0), and (bxz,byz,bz) that represent a parallelepiped. Internally, the class stores particles in the box 0invalid input: '<'xinvalid input: '<'bx, 0invalid input: '<'yinvalid input: '<'by, 0invalid input: '<'zinvalid input: '<'bz, and constructs periodic images of particles that displaced by the three periodicity vectors when they are necessary for the computation. The internal memory structure for this class is significantly different from the container_base class in order to handle the dynamic construction of these periodic images. The class is derived from the unitcell class, which encapsulates information about the domain geometry, and the voro_base class, which encapsulates information about the underlying computational grid.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    int[]
    co
    This array holds the number of particles within each computational box of the container.
    int
    ey
    The lower y index (inclusive) of the primary domain within the block structure.
    int
    ez
    The lower z index (inclusive) of the primary domain within the block structure.
    int[][]
    id
    This array holds the numerical IDs of each particle in each computational box.
    byte[]
    img
    An array holding information about periodic image construction at a given location.
    int
    init_mem
    The initial amount of memory to allocate for particles for each block.
    double
    max_len_sq
     
    int[]
    mem
    This array holds the maximum amount of particle memory for each computational box of the container.
    int
    oxyz
    The total number of blocks.
    int
    oy
    The total size of the block structure (including images) in the y direction.
    int
    oz
    The total size of the block structure (including images) in the z direction.
    double[][]
    p
    A two dimensional array holding particle positions.
    int
    ps
    The amount of memory in the array structure for each particle.
    int
    wy
    The upper y index (exclusive) of the primary domain within the block structure.
    int
    wz
    The upper z index (exclusive) of the primary domain within the block structure.

    Fields inherited from class gov.nih.mipav.model.structures.Voro.voro_base_unitcell

    boxx, boxy, boxz, bx, bxy, bxz, by, byz, bz, max_uv_y, max_uv_z, mrad, nx, nxy, nxyz, ny, nz, unit_voro, xsp, ysp, zsp

  • Constructor Summary

    Constructors
    Constructor
    Description
    container_periodic_base(double bx_, double bxy_, double by_, double bxz_, double byz_, double bz_, int nx_, int ny_, int nz_, int init_mem_, int ps_)
    The class constructor sets up the geometry of container, initializing the minimum and maximum coordinates in each direction, and setting whether each direction is periodic or not.

  • Method Summary

    Modifier and Type
    Method
    Description
    protected void
    add_particle_memory(int i)
    Increase memory for a particular region.
    void
    check_compartmentalized()
    Checks that the particles within each block lie within that block's bounds.
    void
    create_all_images()
    This routine creates all periodic images of the particles.
    void
    create_periodic_image(int di, int dj, int dk)
    Creates particles within an image block by copying them from the primary domain and shifting them.
    void
    create_side_image(int di, int dj, int dk)
    Creates particles within an image block that is aligned with the primary domain in the z axis.
    void
    create_vertical_image(int di, int dj, int dk)
    Creates particles within an image block that is not aligned with the primary domain in the z axis.
    void
    delete()
    The container destructor frees the dynamically allocated memory.
    void
    frac_pos(double x, double y, double z, double ci, double cj, double ck, double[] fx, double[] fy, double[] fz)
    Returns the position of a particle currently being computed relative to the computational block that it is within.
    void
    initialize_search(int ci, int cj, int ck, int ijk, int[] i, int[] j, int[] k, int[] disp)
    Initializes parameters for a find_voronoi_cell call within the voro_compute template.
    boolean
    initialize_voronoicell(Voro.voronoicell_neighbor c, int ijk, int q, int ci, int cj, int ck, int[] i, int[] j, int[] k, double[] x, double[] y, double[] z, int[] disp)
     
    boolean
    initialize_voronoicell(Voro.voronoicell c, int ijk, int q, int ci, int cj, int ck, int[] i, int[] j, int[] k, double[] x, double[] y, double[] z, int[] disp)
    Initializes the Voronoi cell prior to a compute_cell operation for a specific particle being carried out by a voro_compute class.
    void
    print_all_particles()
    Prints all particles in the container, including those that have been constructed in image blocks.
    void
    put_image(int reg, int fijk, int l, double dx, double dy, double dz)
    Copies a particle position from the primary domain into an image block.
    protected void
    put_locate_block(int[] ijk, double[] x, double[] y, double[] z)
    Takes a particle position vector and computes the region index into which it should be stored.
    protected void
    put_locate_block(int[] ijk, double[] x, double[] y, double[] z, int[] ai, int[] aj, int[] ak)
    Takes a particle position vector and computes the region index into which it should be stored.
    void
    region_count()
    Outputs the a list of all the container regions along with the number of particles stored within each.
    int
    region_index(int ci, int cj, int ck, int ei, int ej, int ek, double[] qx, double[] qy, double[] qz, int[] disp)
    Calculates the index of block in the container structure corresponding to given coordinates.
    protected void
    remap(int[] ai, int[] aj, int[] ak, int[] ci, int[] cj, int[] ck, double[] x, double[] y, double[] z, int[] ijk)
    Takes a position vector and remaps it into the primary domain.

    Methods inherited from class gov.nih.mipav.model.structures.Voro.voro_base_unitcell

    compute_minimum, contains_neighbor, contains_neighbor, draw_domain_gnuplot, draw_domain_gnuplot, draw_domain_pov, draw_domain_pov, images, intersects_image, step_div, step_int, step_mod

    Methods inherited from class java.lang.Object

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

  • Field Details

    • max_len_sq

      public double max_len_sq

    • ey

      public int ey
      The lower y index (inclusive) of the primary domain within the block structure.

    • ez

      public int ez
      The lower z index (inclusive) of the primary domain within the block structure.

    • wy

      public int wy
      The upper y index (exclusive) of the primary domain within the block structure.

    • wz

      public int wz
      The upper z index (exclusive) of the primary domain within the block structure.

    • oy

      public int oy
      The total size of the block structure (including images) in the y direction.

    • oz

      public int oz
      The total size of the block structure (including images) in the z direction.

    • oxyz

      public int oxyz
      The total number of blocks.

    • id

      public int[][] id
      This array holds the numerical IDs of each particle in each computational box.

    • p

      public double[][] p
      A two dimensional array holding particle positions. For the derived container_poly class, this also holds particle radii.

    • co

      public int[] co
      This array holds the number of particles within each computational box of the container.

    • mem

      public int[] mem
      This array holds the maximum amount of particle memory for each computational box of the container. If the number of particles in a particular box ever approaches this limit, more is allocated using the add_particle_memory() function.

    • img

      public byte[] img
      An array holding information about periodic image construction at a given location.

    • init_mem

      public int init_mem
      The initial amount of memory to allocate for particles for each block.

    • ps

      public int ps
      The amount of memory in the array structure for each particle. This is set to 3 when the basic class is initialized, so that the array holds (x,y,z) positions. If the container class is initialized as part of the derived class container_poly, then this is set to 4, to also hold the particle radii.

  • Constructor Details

    • container_periodic_base

      public container_periodic_base(double bx_, double bxy_, double by_, double bxz_, double byz_, double bz_, int nx_, int ny_, int nz_, int init_mem_, int ps_)
      The class constructor sets up the geometry of container, initializing the minimum and maximum coordinates in each direction, and setting whether each direction is periodic or not. It divides the container into a rectangular grid of blocks, and allocates memory for each of these for storing particle positions and IDs. \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. \param[in] (nx_,ny_,nz_) the number of grid blocks in each of the three coordinate directions. \param[in] init_mem_ the initial memory allocation for each block. \param[in] ps_ the number of floating point entries to store for each particle.

  • Method Details

    • delete

      public void delete()
      The container destructor frees the dynamically allocated memory.

    • region_count

      public void region_count()
      Outputs the a list of all the container regions along with the number of particles stored within each.

    • initialize_voronoicell

      public boolean initialize_voronoicell(Voro.voronoicell c, int ijk, int q, int ci, int cj, int ck, int[] i, int[] j, int[] k, double[] x, double[] y, double[] z, int[] disp)
      Initializes the Voronoi cell prior to a compute_cell operation for a specific particle being carried out by a voro_compute class. The cell is initialized to be the pre-computed unit Voronoi cell based on planes formed by periodic images of the particle. \param[in,out] c a reference to a voronoicell object. \param[in] ijk the block that the particle is within. \param[in] q the index of the particle within its block. \param[in] (ci,cj,ck) the coordinates of the block in the container coordinate system. \param[out] (i,j,k) the coordinates of the test block relative to the voro_compute coordinate system. \param[out] (x,y,z) the position of the particle. \param[out] disp a block displacement used internally by the compute_cell routine. \return False if the plane cuts applied by walls completely removed the cell, true otherwise.

    • initialize_voronoicell

      public boolean initialize_voronoicell(Voro.voronoicell_neighbor c, int ijk, int q, int ci, int cj, int ck, int[] i, int[] j, int[] k, double[] x, double[] y, double[] z, int[] disp)

    • initialize_search

      public void initialize_search(int ci, int cj, int ck, int ijk, int[] i, int[] j, int[] k, int[] disp)
      Initializes parameters for a find_voronoi_cell call within the voro_compute template. \param[in] (ci,cj,ck) the coordinates of the test block in the container coordinate system. \param[in] ijk the index of the test block \param[out] (i,j,k) the coordinates of the test block relative to the voro_compute coordinate system. \param[out] disp a block displacement used internally by the find_voronoi_cell routine (but not needed in this instance.)

    • frac_pos

      public void frac_pos(double x, double y, double z, double ci, double cj, double ck, double[] fx, double[] fy, double[] fz)
      Returns the position of a particle currently being computed relative to the computational block that it is within. It is used to select the optimal worklist entry to use. \param[in] (x,y,z) the position of the particle. \param[in] (ci,cj,ck) the block that the particle is within. \param[out] (fx,fy,fz) the position relative to the block.

    • region_index

      public int region_index(int ci, int cj, int ck, int ei, int ej, int ek, double[] qx, double[] qy, double[] qz, int[] disp)
      Calculates the index of block in the container structure corresponding to given coordinates. \param[in] (ci,cj,ck) the coordinates of the original block in the current computation, relative to the container coordinate system. \param[in] (ei,ej,ek) the displacement of the current block from the original block. \param[in,out] (qx,qy,qz) the periodic displacement that must be added to the particles within the computed block. \param[in] disp a block displacement used internally by the find_voronoi_cell and compute_cell routines (but not needed in this instance.) \return The block index.

    • create_all_images

      public void create_all_images()
      This routine creates all periodic images of the particles. It is meant for diagnostic purposes only, since usually periodic images are dynamically created in when they are referenced.

    • check_compartmentalized

      public void check_compartmentalized()
      Checks that the particles within each block lie within that block's bounds. This is useful for diagnosing problems with periodic image computation.

    • add_particle_memory

      protected void add_particle_memory(int i)
      Increase memory for a particular region. \param[in] i the index of the region to reallocate.

    • put_locate_block

      protected void put_locate_block(int[] ijk, double[] x, double[] y, double[] z)
      Takes a particle position vector and computes the region index into which it should be stored. If the container is periodic, then the routine also maps the particle position to ensure it is in the primary domain. If the container is not periodic, the routine bails out. \param[out] ijk the region index. \param[in,out] (x,y,z) the particle position, remapped into the primary domain if necessary. \return True if the particle can be successfully placed into the container, false otherwise.

    • put_locate_block

      protected void put_locate_block(int[] ijk, double[] x, double[] y, double[] z, int[] ai, int[] aj, int[] ak)
      Takes a particle position vector and computes the region index into which it should be stored. If the container is periodic, then the routine also maps the particle position to ensure it is in the primary domain. If the container is not periodic, the routine bails out. \param[out] ijk the region index. \param[in,out] (x,y,z) the particle position, remapped into the primary domain if necessary. \param[out] (ai,aj,ak) the periodic image displacement that the particle is in, with (0,0,0) corresponding to the primary domain. \return True if the particle can be successfully placed into the container, false otherwise.

    • create_periodic_image

      public void create_periodic_image(int di, int dj, int dk)
      Creates particles within an image block by copying them from the primary domain and shifting them. If the given block is aligned with the primary domain in the z-direction, the routine calls the simpler create_side_image routine where the image block may comprise of particles from up to two primary blocks. Otherwise is calls the more complex create_vertical_image where the image block may comprise of particles from up to four primary blocks. \param[in] (di,dj,dk) the coordinates of the image block to create.

    • create_side_image

      public void create_side_image(int di, int dj, int dk)
      Creates particles within an image block that is aligned with the primary domain in the z axis. In this case, the image block may be comprised of particles from two primary blocks. The routine considers these two primary blocks, and adds the needed particles to the image. The remaining particles from the primary blocks are also filled into the neighboring images. \param[in] (di,dj,dk) the index of the block to consider. The z index must satisfy ezinvalid input: '<'=dkinvalid input: '<'wz.

    • create_vertical_image

      public void create_vertical_image(int di, int dj, int dk)
      Creates particles within an image block that is not aligned with the primary domain in the z axis. In this case, the image block may be comprised of particles from four primary blocks. The routine considers these four primary blocks, and adds the needed particles to the image. The remaining particles from the primary blocks are also filled into the neighboring images. \param[in] (di,dj,dk) the index of the block to consider. The z index must satisfy dk=wz.

    • put_image

      public void put_image(int reg, int fijk, int l, double dx, double dy, double dz)
      Copies a particle position from the primary domain into an image block. \param[in] reg the block index within the primary domain that the particle is within. \param[in] fijk the index of the image block. \param[in] l the index of the particle entry within the primary block. \param[in] (dx,dy,dz) the displacement vector to add to the particle.

    • remap

      protected void remap(int[] ai, int[] aj, int[] ak, int[] ci, int[] cj, int[] ck, double[] x, double[] y, double[] z, int[] ijk)
      Takes a position vector and remaps it into the primary domain. \param[out] (ai,aj,ak) the periodic image displacement that the vector is in, with (0,0,0) corresponding to the primary domain. \param[out] (ci,cj,ck) the index of the block that the position vector is within, once it has been remapped. \param[in,out] (x,y,z) the position vector to consider, which is remapped into the primary domain during the routine. \param[out] ijk the block index that the vector is within.