java.lang.Object
- gov.nih.mipav.model.structures.Voro.voro_base_unitcell

Direct Known Subclasses:

Voro.container_periodic_base

Enclosing class:

Voro
```
class Voro.voro_base_unitcell
extends java.lang.Object
```

Field Summary

Fields
Modifier and Type	Field	Description
`double`	`boxx`	The size of a computational block in the x direction.
`double`	`boxy`	The size of a computational block in the y direction.
`double`	`boxz`	The size of a computational block in the z direction.
`double`	`bx`	The x coordinate of the first vector defining the periodic domain.
`double`	`bxy`	The x coordinate of the second vector defining the periodic domain.
`double`	`bxz`	The x coordinate of the third vector defining the periodic domain.
`double`	`by`	The y coordinate of the second vector defining the periodic domain.
`double`	`byz`	The y coordinate of the third vector defining the periodic domain.
`double`	`bz`	The z coordinate of the third vector defining the periodic domain.
`protected double`	`max_uv_y`	The maximum y-coordinate that could possibly cut the computed unit Voronoi cell.
`protected double`	`max_uv_z`	The maximum z-coordinate that could possibly cut the computed unit Voronoi cell.
`double[]`	`mrad`	An array to hold the minimum distances associated with the worklists.
`int`	`nx`	The number of blocks in the x direction.
`int`	`nxy`	A finalant, set to the value of nx multiplied by ny, which is used in the routines that step through blocks in sequence.
`int`	`nxyz`	A finalant, set to the value of nxnynz, which is used in the routines that step through blocks in sequence.
`int`	`ny`	The number of blocks in the y direction.
`int`	`nz`	The number of blocks in the z direction.
`Voro.voronoicell`	`unit_voro`	The computed unit Voronoi cell corresponding the given 3D non-rectangular periodic domain geometry.
`double`	`xsp`	The inverse box length in the x direction.
`double`	`ysp`	The inverse box length in the y direction.
`double`	`zsp`	The inverse box length in the z direction.

Constructor Summary

Constructors
Constructor	Description
`voro_base_unitcell(double bx_, double bxy_, double by_, double bxz_, double byz_, double bz_)`	Initializes the unit cell class for a particular non-orthogonal periodic geometry, corresponding to a parallelepiped with sides given by three vectors.
`voro_base_unitcell(double bx_, double bxy_, double by_, double bxz_, double byz_, double bz_, int nx_, int ny_, int nz_, double boxx_, double boxy_, double boxz_)`
`voro_base_unitcell(int nx_, int ny_, int nz_, double boxx_, double boxy_, double boxz_)`	This function is called during container finalruction.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`(package private) void`	`compute_minimum(double[] minr, double xlo, double xhi, double ylo, double yhi, double zlo, double zhi, int ti, int tj, int tk)`	Computes the minimum distance from a subregion to a given block.
`(package private) boolean`	`contains_neighbor(byte[] format)`	Checks to see whether "%n" appears in a format sequence to determine whether neighbor information is required or not.
`(package private) boolean`	`contains_neighbor(char[] format)`
`void`	`draw_domain_gnuplot(java.io.RandomAccessFile fp)`	Draws the periodic domain in gnuplot format.
`void`	`draw_domain_gnuplot(java.lang.String filename)`	Draws an outline of the domain in Gnuplot format.
`void`	`draw_domain_pov(java.io.RandomAccessFile fp)`	Draws the periodic domain in POV-Ray format.
`void`	`draw_domain_pov(java.lang.String filename)`
`void`	`images(java.util.Vector<java.lang.Integer> vi, java.util.Vector<java.lang.Double> vd)`	Computes a list of periodic domain images that intersect the unit Voronoi cell.
`boolean`	`intersects_image(double dx, double dy, double dz, double[] vol)`	Calculates whether the unit Voronoi cell intersects a given periodic image of the domain.
`protected int`	`step_div(int a, int b)`	A custom Double division function that returns consistent stepping for negative numbers.
`protected int`	`step_int(double a)`	A custom int function that returns consistent stepping for negative numbers, so that (-1.5, -0.5, 0.5, 1.5) maps to (-2,-1,0,1).
`protected int`	`step_mod(int a, int b)`	A custom modulo function that returns consistent stepping for negative numbers.
`private void`	`unit_voro_apply(int i, int j, int k)`	Applies a pair of opposing plane cuts from a periodic image point to the unit Voronoi cell.
`private boolean`	`unit_voro_intersect(int l)`	Tests to see if a shell of periodic images could possibly cut the periodic unit cell.
`private boolean`	`unit_voro_test(int i, int j, int k)`	Tests to see if a plane cut from a particular periodic image will cut th unit Voronoi cell.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - nx
```
public int nx
```
    The number of blocks in the x direction.
  - ny
```
public int ny
```
    The number of blocks in the y direction.
  - nz
```
public int nz
```
    The number of blocks in the z direction.
  - nxy
```
public int nxy
```
    A finalant, set to the value of nx multiplied by ny, which is used in the routines that step through blocks in sequence.
  - nxyz
```
public int nxyz
```
    A finalant, set to the value of nx*ny*nz, which is used in the routines that step through blocks in sequence.
  - boxx
```
public double boxx
```
    The size of a computational block in the x direction.
  - boxy
```
public double boxy
```
    The size of a computational block in the y direction.
  - boxz
```
public double boxz
```
    The size of a computational block in the z direction.
  - xsp
```
public double xsp
```
    The inverse box length in the x direction.
  - ysp
```
public double ysp
```
    The inverse box length in the y direction.
  - zsp
```
public double zsp
```
    The inverse box length in the z direction.
  - mrad
```
public double[] mrad
```
    An array to hold the minimum distances associated with the worklists. This array is initialized during container finalruction, by the initialize_radii() routine.
  - bx
```
public double bx
```
    The x coordinate of the first vector defining the periodic domain.
  - bxy
```
public double bxy
```
    The x coordinate of the second vector defining the periodic domain.
  - by
```
public double by
```
    The y coordinate of the second vector defining the periodic domain.
  - bxz
```
public double bxz
```
    The x coordinate of the third vector defining the periodic domain.
  - byz
```
public double byz
```
    The y coordinate of the third vector defining the periodic domain.
  - bz
```
public double bz
```
    The z coordinate of the third vector defining the periodic domain.
  - unit_voro
```
public Voro.voronoicell unit_voro
```
    The computed unit Voronoi cell corresponding the given 3D non-rectangular periodic domain geometry.
  - max_uv_y
```
protected double max_uv_y
```
    The maximum y-coordinate that could possibly cut the computed unit Voronoi cell.
  - max_uv_z
```
protected double max_uv_z
```
    The maximum z-coordinate that could possibly cut the computed unit Voronoi cell.
- Constructor Detail
  - voro_base_unitcell
```
public voro_base_unitcell(int nx_,
                          int ny_,
                          int nz_,
                          double boxx_,
                          double boxy_,
                          double boxz_)
```
    This function is called during container finalruction. The routine scans all of the worklists in the wl[] array. For a given worklist of blocks labeled \f$w_1\f$ to \f$w_n\f$, it computes a sequence \f$r_0\f$ to \f$r_n\f$ so that $r_i$ is the minimum distance to all the blocks \f$w_{j}\f$ where \f$j>i\f$ and all blocks outside the worklist. The values of \f$r_n\f$ is calculated first, as the minimum distance to any block in the shell surrounding the worklist. The \f$r_i\f$ are then computed in reverse order by considering the distance to \f$w_{i+1}\f$.
  - voro_base_unitcell
```
public voro_base_unitcell(double bx_,
                          double bxy_,
                          double by_,
                          double bxz_,
                          double byz_,
                          double bz_)
```
    Initializes the unit cell class for a particular non-orthogonal periodic geometry, corresponding to a parallelepiped with sides given by three vectors. The class constructs the unit Voronoi cell corresponding to this geometry. \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.
  - voro_base_unitcell
```
public voro_base_unitcell(double bx_,
                          double bxy_,
                          double by_,
                          double bxz_,
                          double byz_,
                          double bz_,
                          int nx_,
                          int ny_,
                          int nz_,
                          double boxx_,
                          double boxy_,
                          double boxz_)
```
- Method Detail
  - step_int
```
protected int step_int(double a)
```
    A custom int function that returns consistent stepping for negative numbers, so that (-1.5, -0.5, 0.5, 1.5) maps to (-2,-1,0,1). \param[in] a the number to consider. \return The value of the custom int operation.
  - step_mod
```
protected int step_mod(int a,
                       int b)
```
    A custom modulo function that returns consistent stepping for negative numbers. For example, (-2,-1,0,1,2) step_mod 2 is (0,1,0,1,0). \param[in] (a,b) the input Doubles. \return The value of a modulo b, consistent for negative numbers.
  - step_div
```
protected int step_div(int a,
                       int b)
```
    A custom Double division function that returns consistent stepping for negative numbers. For example, (-2,-1,0,1,2) step_div 2 is (-1,-1,0,0,1). \param[in] (a,b) the input Doubles. \return The value of a div b, consistent for negative numbers.
  - compute_minimum
```
void compute_minimum(double[] minr,
                     double xlo,
                     double xhi,
                     double ylo,
                     double yhi,
                     double zlo,
                     double zhi,
                     int ti,
                     int tj,
                     int tk)
```
    Computes the minimum distance from a subregion to a given block. If this distance is smaller than the value of minr, then it passes \param[in,out] minr a pointer to the current minimum distance. If the distance computed in this function is smaller, then this distance is set to the new one. \param[out] (xlo,ylo,zlo) the lower coordinates of the subregion being considered. \param[out] (xhi,yhi,zhi) the upper coordinates of the subregion being considered. \param[in] (ti,tj,tk) the coordinates of the block.
  - contains_neighbor
```
boolean contains_neighbor(byte[] format)
```
    Checks to see whether "%n" appears in a format sequence to determine whether neighbor information is required or not. \param[in] format the format string to check. \return True if a "%n" is found, false otherwise.
  - contains_neighbor
```
boolean contains_neighbor(char[] format)
```
  - draw_domain_gnuplot
```
public void draw_domain_gnuplot(java.lang.String filename)
```
    Draws an outline of the domain in Gnuplot format. \param[in] filename the filename to write to.
  - draw_domain_gnuplot
```
public void draw_domain_gnuplot(java.io.RandomAccessFile fp)
```
    Draws the periodic domain in gnuplot format. \param[in] fp the file handle to write to.
  - draw_domain_pov
```
public void draw_domain_pov(java.lang.String filename)
```
  - draw_domain_pov
```
public void draw_domain_pov(java.io.RandomAccessFile fp)
```
    Draws the periodic domain in POV-Ray format. \param[in] fp the file handle to write to.
  - intersects_image
```
public boolean intersects_image(double dx,
                                double dy,
                                double dz,
                                double[] vol)
```
    Calculates whether the unit Voronoi cell intersects a given periodic image of the domain. \param[in] (dx,dy,dz) the displacement of the periodic image. \param[out] vol the proportion of the unit cell volume within this image, only computed in the case that the two intersect. \return True if they intersect, false otherwise.
  - images
```
public void images(java.util.Vector<java.lang.Integer> vi,
                   java.util.Vector<java.lang.Double> vd)
```
    Computes a list of periodic domain images that intersect the unit Voronoi cell. \param[out] vi a vector containing triplets (i,j,k) corresponding to domain images that intersect the unit Voronoi cell, when it is centered in the middle of the primary domain. \param[out] vd a vector containing the fraction of the Voronoi cell volume within each corresponding image listed in vi.
  - unit_voro_apply
```
private void unit_voro_apply(int i,
                             int j,
                             int k)
```
    Applies a pair of opposing plane cuts from a periodic image point to the unit Voronoi cell. \param[in] (i,j,k) the index of the periodic image to consider.
  - unit_voro_intersect
```
private boolean unit_voro_intersect(int l)
```
    Tests to see if a shell of periodic images could possibly cut the periodic unit cell. \param[in] l the index of the shell to consider. \return True if a point in the shell cuts the cell, false otherwise.
  - unit_voro_test
```
private boolean unit_voro_test(int i,
                               int j,
                               int k)
```
    Tests to see if a plane cut from a particular periodic image will cut th unit Voronoi cell. \param[in] (i,j,k) the index of the periodic image to consider. \return True if the image cuts the cell, false otherwise.

Class Voro.voro_base_unitcell

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

nx

ny

nz

nxy

nxyz

boxx

boxy

boxz

xsp

ysp

zsp

mrad

bx

bxy

by

bxz

byz

bz

unit_voro

max_uv_y

max_uv_z

Constructor Detail

voro_base_unitcell

voro_base_unitcell

voro_base_unitcell

Method Detail

step_int

step_mod

step_div

compute_minimum

contains_neighbor

contains_neighbor

draw_domain_gnuplot

draw_domain_gnuplot

draw_domain_pov

draw_domain_pov

intersects_image

images

unit_voro_apply

unit_voro_intersect

unit_voro_test