Package gov.nih.mipav.model.structures

Class Voro.pre_container_base

java.lang.Object
gov.nih.mipav.model.structures.Voro.pre_container_base
Direct Known Subclasses:
Voro.pre_container, Voro.pre_container_poly
Enclosing class:
Voro
class Voro.pre_container_base extends Object
\brief A class for storing an arbitrary number of particles, prior to setting up a container geometry. The pre_container_base class can dynamically import and store an arbitrary number of particles. Once the particles have been read in, an appropriate container class can be set up with the optimal grid size, and the particles can be transferred. The pre_container_base class is not intended for direct use, but forms the base of the pre_container and pre_container_poly classes, that add routines depending on whether particle radii need to be tracked or not.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    double
    ax
    The minimum x coordinate of the container.
    double
    ay
    The minimum y coordinate of the container.
    double
    az
    The minimum z coordinate of the container.
    double
    bx
    The maximum x coordinate of the container.
    double
    by
    The maximum y coordinate of the container.
    double
    bz
    The maximum z coordinate of the container.
    protected int
    ch_id
    A pointer to the next available slot on the current particle ID chunk.
    protected int
    ch_p
    A pointer to the next available slot on the current floating point chunk.
    protected int
    e_id
    A pointer to the end of the current integer chunk.
    protected int
    end_id_outer_index
    A pointer to the last allocated integer ID chunk.
    protected int
    end_p_outer_index
    A pointer to the last allocated chunk of floating point information.
    protected int
    index_sz
    The size of the chunk index.
    protected int
    l_id
    A pointer to the end of the integer ID chunk index, used to determine when the chunk index is full.
    protected int[][]
    pre_id
    A pointer to the chunk index to store the integer particle IDs.
    protected double[][]
    pre_p
    A pointer to the chunk index to store the floating point information associated with particles.
    protected int
    ps
    The number of doubles associated with a single particle (three for the standard container, four when radius information is stored).
    boolean
    xperiodic
    A boolean value that determines if the x coordinate in periodic or not.
    boolean
    yperiodic
    A boolean value that determines if the y coordinate in periodic or not.
    boolean
    zperiodic
    A boolean value that determines if the z coordinate in periodic or not.

  • Constructor Summary

    Constructors
    Constructor
    Description
    pre_container_base(double ax_, double bx_, double ay_, double by_, double az_, double bz_, boolean xperiodic_, boolean yperiodic_, boolean zperiodic_, int ps_)
    The class constructor sets up the geometry of container, initializing the minimum and maximum coordinates in each direction.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    delete()
    The destructor frees the dynamically allocated memory.
    protected void
    extend_chunk_index()
    Extends the index of chunks.
    void
    guess_optimal(int[] nx, int[] ny, int[] nz)
    Makes a guess at the optimal grid of blocks to use, computing in a way that \param[out] (nx,ny,nz) the number of blocks to use.
    protected void
    new_chunk()
    Allocates a new chunk of memory for storing particles.
    int
    total_particles()
    Calculates and returns the total number of particles stored within the class.

    Methods inherited from class java.lang.Object

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

  • Field Details

    • ax

      public double ax
      The minimum x coordinate of the container.

    • bx

      public double bx
      The maximum x coordinate of the container.

    • ay

      public double ay
      The minimum y coordinate of the container.

    • by

      public double by
      The maximum y coordinate of the container.

    • az

      public double az
      The minimum z coordinate of the container.

    • bz

      public double bz
      The maximum z coordinate of the container.

    • xperiodic

      public boolean xperiodic
      A boolean value that determines if the x coordinate in periodic or not.

    • yperiodic

      public boolean yperiodic
      A boolean value that determines if the y coordinate in periodic or not.

    • zperiodic

      public boolean zperiodic
      A boolean value that determines if the z coordinate in periodic or not.

    • ps

      protected int ps
      The number of doubles associated with a single particle (three for the standard container, four when radius information is stored).

    • index_sz

      protected int index_sz
      The size of the chunk index.

    • pre_id

      protected int[][] pre_id
      A pointer to the chunk index to store the integer particle IDs.

    • end_id_outer_index

      protected int end_id_outer_index
      A pointer to the last allocated integer ID chunk.

    • l_id

      protected int l_id
      A pointer to the end of the integer ID chunk index, used to determine when the chunk index is full.

    • ch_id

      protected int ch_id
      A pointer to the next available slot on the current particle ID chunk.

    • e_id

      protected int e_id
      A pointer to the end of the current integer chunk.

    • pre_p

      protected double[][] pre_p
      A pointer to the chunk index to store the floating point information associated with particles.

    • end_p_outer_index

      protected int end_p_outer_index
      A pointer to the last allocated chunk of floating point information.

    • ch_p

      protected int ch_p
      A pointer to the next available slot on the current floating point chunk.

  • Constructor Details

    • pre_container_base

      public pre_container_base(double ax_, double bx_, double ay_, double by_, double az_, double bz_, boolean xperiodic_, boolean yperiodic_, boolean zperiodic_, int ps_)
      The class constructor sets up the geometry of container, initializing the minimum and maximum coordinates in each direction. It allocates an initial chunk into which to store particle information. \param[in] (ax_,bx_) the minimum and maximum x coordinates. \param[in] (ay_,by_) the minimum and maximum y coordinates. \param[in] (az_,bz_) the minimum and maximum z coordinates. \param[in] (xperiodic_,yperiodic_,zperiodic_ ) flags setting whether the container is periodic in each coordinate direction. \param[in] ps_ the number of floating point entries to store for each particle.

  • Method Details

    • guess_optimal

      public void guess_optimal(int[] nx, int[] ny, int[] nz)
      Makes a guess at the optimal grid of blocks to use, computing in a way that \param[out] (nx,ny,nz) the number of blocks to use.

    • delete

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

    • total_particles

      public int total_particles()
      Calculates and returns the total number of particles stored within the class. \return The number of particles.

    • new_chunk

      protected void new_chunk()
      Allocates a new chunk of memory for storing particles.

    • extend_chunk_index

      protected void extend_chunk_index()
      Extends the index of chunks.