Package gov.nih.mipav.model.structures

Class Voro.pre_container_poly

java.lang.Object

gov.nih.mipav.model.structures.Voro.pre_container_base

gov.nih.mipav.model.structures.Voro.pre_container_poly

Enclosing class:

Voro

class Voro.pre_container_poly
extends Voro.pre_container_base

\brief A class for storing an arbitrary number of particles with radius information, prior to setting up a container geometry. The pre_container_poly class is an extension of the pre_container_base class for cases when particle radius information is available.

Field Summary

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

ax, ay, az, bx, by, bz, ch_id, ch_p, e_id, end_id_outer_index, end_p_outer_index, index_sz, l_id, pre_id, pre_p, ps, xperiodic, yperiodic, zperiodic

Constructor Summary

Constructors

Constructor	Description
pre_container_poly(double ax_, double bx_, double ay_, double by_, double az_, double bz_, boolean xperiodic_, boolean yperiodic_, boolean zperiodic_)	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	importList(java.io.File fp)	Import a list of particles from an open file stream, also storing the order of that the particles are read.
void	importList(java.lang.String filename)	Imports particles from a file.
void	put(int n, double x, double y, double z, double r)	Stores a particle ID and position, allocating a new memory chunk if necessary.
void	setup(Voro.container_poly_radius_poly con)	Transfers the particles stored within the class to a container_poly class.
void	setup(Voro.particle_order vo, Voro.container_poly_radius_poly con)	Transfers the particles stored within the class to a container_poly class, also recording the order in which particles were stored.

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

delete, extend_chunk_index, guess_optimal, new_chunk, total_particles

Methods inherited from class java.lang.Object

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

Constructor Detail

pre_container_poly

public pre_container_poly(double ax_,
                          double bx_,
                          double ay_,
                          double by_,
                          double az_,
                          double bz_,
                          boolean xperiodic_,
                          boolean yperiodic_,
                          boolean zperiodic_)

The class constructor sets up the geometry of container, initializing the minimum and maximum coordinates in each direction. \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.

Method Detail

put

public void put(int n,
                double x,
                double y,
                double z,
                double r)

Stores a particle ID and position, allocating a new memory chunk if necessary. \param[in] n the numerical ID of the inserted particle. \param[in] (x,y,z) the position vector of the inserted particle. \param[in] r the radius of the particle.

importList

public void importList(java.io.File fp)

Import a list of particles from an open file stream, also storing the order of that the particles are read. Entries of four numbers (Particle ID, x position, y position, z position) are searched for. If the file cannot be successfully read, then the routine causes a fatal error. \param[in] fp the file handle to read from.

importList

public void importList(java.lang.String filename)

Imports particles from a file. \param[in] filename the name of the file to read from.

setup

public void setup(Voro.container_poly_radius_poly con)

Transfers the particles stored within the class to a container_poly class. \param[in] con the container_poly class to transfer to.

setup

public void setup(Voro.particle_order vo,
                  Voro.container_poly_radius_poly con)

Transfers the particles stored within the class to a container_poly class, also recording the order in which particles were stored. \param[in] vo the ordering class to use. \param[in] con the container_poly class to transfer to.