Package gov.nih.mipav.model.structures

Class Voro.pre_container

java.lang.Object

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

gov.nih.mipav.model.structures.Voro.pre_container

Enclosing class:

Voro

class Voro.pre_container
extends Voro.pre_container_base

\brief A class for storing an arbitrary number of particles without radius information, prior to setting up a container geometry. The pre_container class is an extension of the pre_container_base class for cases when no 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(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 into the container.
void	importList(java.lang.String filename)	Imports particles from a file.
void	put(int n, double x, double y, double z)	Stores a particle ID and position, allocating a new memory chunk if necessary.
void	setup(Voro.container_radius_mono con)	Transfers the particles stored within the class to a container class.
void	setup(Voro.particle_order vo, Voro.container_radius_mono con)	Transfers the particles stored within the class to a container 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

public pre_container(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)

Stores a particle ID and position, allocating a new memory chunk if necessary. For coordinate directions in which the container is not periodic, the routine checks to make sure that the particle is within the container bounds. If the particle is out of bounds, it is not stored. \param[in] n the numerical ID of the inserted particle. \param[in] (x,y,z) the position vector of the inserted particle.

importList

public void importList(java.io.File fp)

Import a list of particles from an open file stream into the container. 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_radius_mono con)

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

setup

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

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