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 java.lang.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

All Methods Instance Methods Concrete Methods
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 Detail
  - 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 Detail
  - 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 Detail
  - 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.

Class Voro.pre_container_base

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

ax

bx

ay

by

az

bz

xperiodic

yperiodic

zperiodic

ps

index_sz

pre_id

end_id_outer_index

l_id

ch_id

e_id

pre_p

end_p_outer_index

ch_p

Constructor Detail

pre_container_base

Method Detail

guess_optimal

delete

total_particles

new_chunk

extend_chunk_index