Extension of the container_base class for computing radical Voronoi tessellations. More...

#include <container.hh>

Inheritance diagram for voro::container_poly:

Public Member Functions
	container_poly (double ax_, double bx_, double ay_, double by_, double az_, double bz_, int nx_, int ny_, int nz_, bool xperiodic_, bool yperiodic_, bool zperiodic_, int init_mem)

void	clear ()

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

void	put (particle_order &vo, int n, double x, double y, double z, double r)

void	import (FILE *fp=stdin)

void	import (particle_order &vo, FILE *fp=stdin)

void	import (const char *filename)

void	import (particle_order &vo, const char *filename)

void	compute_all_cells ()

double	sum_cell_volumes ()

template<class c_loop >
void	draw_particles (c_loop &vl, FILE *fp)

void	draw_particles (FILE *fp=stdout)

void	draw_particles (const char *filename)

template<class c_loop >
void	draw_particles_pov (c_loop &vl, FILE *fp)

void	draw_particles_pov (FILE *fp=stdout)

void	draw_particles_pov (const char *filename)

template<class c_loop >
void	draw_cells_gnuplot (c_loop &vl, FILE *fp)

void	draw_cells_gnuplot (FILE *fp=stdout)

void	draw_cells_gnuplot (const char *filename)

template<class c_loop >
void	draw_cells_pov (c_loop &vl, FILE *fp)

void	draw_cells_pov (FILE *fp=stdout)

void	draw_cells_pov (const char *filename)

template<class c_loop >
void	print_custom (c_loop &vl, const char format, FILE fp)

template<class v_cell , class c_loop >
bool	compute_cell (v_cell &c, c_loop &vl)

template<class v_cell >
bool	compute_cell (v_cell &c, int ijk, int q)

template<class v_cell >
bool	compute_ghost_cell (v_cell &c, double x, double y, double z, double r)

void	print_custom (const char format, FILE fp=stdout)

void	print_custom (const char format, const char filename)

bool	find_voronoi_cell (double x, double y, double z, double &rx, double &ry, double &rz, int &pid)

Public Member Functions inherited from voro::container_base
	container_base (double ax_, double bx_, double ay_, double by_, double az_, double bz_, int nx_, int ny_, int nz_, bool xperiodic_, bool yperiodic_, bool zperiodic_, int init_mem, int ps_)

	~container_base ()

bool	point_inside (double x, double y, double z)

void	region_count ()

template<class v_cell >
bool	initialize_voronoicell (v_cell &c, int ijk, int q, int ci, int cj, int ck, int &i, int &j, int &k, double &x, double &y, double &z, int &disp)

void	initialize_search (int ci, int cj, int ck, int ijk, int &i, int &j, int &k, int &disp)

void	frac_pos (double x, double y, double z, double ci, double cj, double ck, double &fx, double &fy, double &fz)

int	region_index (int ci, int cj, int ck, int ei, int ej, int ek, double &qx, double &qy, double &qz, int &disp)

void	draw_domain_gnuplot (FILE *fp=stdout)

void	draw_domain_gnuplot (const char *filename)

void	draw_domain_pov (FILE *fp=stdout)

void	draw_domain_pov (const char *filename)

int	total_particles ()

Public Member Functions inherited from voro::voro_base
bool	contains_neighbor (const char *format)

	voro_base (int nx_, int ny_, int nz_, double boxx_, double boxy_, double boxz_)

Public Member Functions inherited from voro::wall_list
	wall_list ()

	~wall_list ()

void	add_wall (wall *w)

void	add_wall (wall &w)

void	add_wall (wall_list &wl)

bool	point_inside_walls (double x, double y, double z)

template<class c_class >
bool	apply_walls (c_class &c, double x, double y, double z)

void	deallocate ()

Public Member Functions inherited from voro::radius_poly
	radius_poly ()

Friends
class	voro_compute< container_poly >

Additional Inherited Members
Data Fields inherited from voro::container_base
const double	ax

const double	bx

const double	ay

const double	by

const double	az

const double	bz

const bool	xperiodic

const bool	yperiodic

const bool	zperiodic

int **	id

double **	p

int *	co

int *	mem

const int	ps

Data Fields inherited from voro::voro_base
const int	nx

const int	ny

const int	nz

const int	nxy

const int	nxyz

const double	boxx

const double	boxy

const double	boxz

const double	xsp

const double	ysp

const double	zsp

double *	mrad

Data Fields inherited from voro::wall_list
wall **	walls

wall **	wep

Data Fields inherited from voro::radius_poly
double **	ppr

double	max_radius

Static Public Attributes inherited from voro::voro_base
static const unsigned int	wl [wl_seq_length *wl_hgridcu]

Protected Member Functions inherited from voro::container_base
void	add_particle_memory (int i)

bool	put_locate_block (int &ijk, double &x, double &y, double &z)

bool	put_remap (int &ijk, double &x, double &y, double &z)

bool	remap (int &ai, int &aj, int &ak, int &ci, int &cj, int &ck, double &x, double &y, double &z, int &ijk)

Protected Member Functions inherited from voro::voro_base
int	step_int (double a)

int	step_mod (int a, int b)

int	step_div (int a, int b)

Protected Member Functions inherited from voro::wall_list
void	increase_wall_memory ()

Protected Member Functions inherited from voro::radius_poly
void	r_init (int ijk, int s)

void	r_prime (double rv)

bool	r_ctest (double crs, double mrs)

double	r_cutoff (double lrs)

double	r_max_add (double rs)

double	r_current_sub (double rs, int ijk, int q)

double	r_scale (double rs, int ijk, int q)

bool	r_scale_check (double &rs, double mrs, int ijk, int q)

Protected Attributes inherited from voro::wall_list
wall **	wel

int	current_wall_size

Detailed Description

This class is an extension of container_base class that has routines specifically for computing the radical Voronoi tessellation that depends on the particle radii.

Definition at line 507 of file container.hh.

Constructor & Destructor Documentation

voro::container_poly::container_poly	(	double	ax_,
		double	bx_,
		double	ay_,
		double	by_,
		double	az_,
		double	bz_,
		int	nx_,
		int	ny_,
		int	nz_,
		bool	xperiodic_,
		bool	yperiodic_,
		bool	zperiodic_,
		int	init_mem
	)

The class constructor sets up the geometry of container.

Parameters

[in]	(ax_,bx_)	the minimum and maximum x coordinates.
[in]	(ay_,by_)	the minimum and maximum y coordinates.
[in]	(az_,bz_)	the minimum and maximum z coordinates.
[in]	(nx_,ny_,nz_)	the number of grid blocks in each of the three coordinate directions.
[in]	(xperiodic_,yperiodic_,zperiodic_)	flags setting whether the container is periodic in each coordinate direction.
[in]	init_mem	the initial memory allocation for each block.

Definition at line 79 of file container.cc.

Member Function Documentation

void voro::container_poly::clear ( )

Clears a container of particles, also clearing resetting the maximum radius to zero.

Definition at line 390 of file container.cc.

void voro::container_poly::compute_all_cells ( )

Computes all of the Voronoi cells in the container, but does nothing with the output. It is useful for measuring the pure computation time of the Voronoi algorithm, without any additional calculations such as volume evaluation or cell output.

Definition at line 446 of file container.cc.

template<class v_cell , class c_loop >

bool voro::container_poly::compute_cell	(	v_cell &	c,
		c_loop &	vl
	)

inline

Computes the Voronoi cell for a particle currently being referenced by a loop class.

Parameters

[out]	c	a Voronoi cell class in which to store the computed cell.
[in]	vl	the loop class to use.

Returns: True if the cell was computed. If the cell cannot be computed, if it is removed entirely by a wall or boundary condition, then the routine returns false.

Definition at line 681 of file container.hh.

template<class v_cell >

bool voro::container_poly::compute_cell	(	v_cell &	c,
		int	ijk,
		int	q
	)

inline

Computes the Voronoi cell for given particle.

Parameters

[out]	c	a Voronoi cell class in which to store the computed cell.
[in]	ijk	the block that the particle is within.
[in]	q	the index of the particle within the block.

Returns: True if the cell was computed. If the cell cannot be computed, if it is removed entirely by a wall or boundary condition, then the routine returns false.

Definition at line 693 of file container.hh.

template<class v_cell >

bool voro::container_poly::compute_ghost_cell	(	v_cell &	c,
		double	x,
		double	y,
		double	z,
		double	r
	)

inline

Computes the Voronoi cell for a ghost particle at a given location.

Parameters

[out]	c	a Voronoi cell class in which to store the computed cell.
[in]	(x,y,z)	the location of the ghost particle.
[in]	r	the radius of the ghost particle.

Returns: True if the cell was computed. If the cell cannot be computed, if it is removed entirely by a wall or boundary condition, then the routine returns false.

Definition at line 707 of file container.hh.

template<class c_loop >

void voro::container_poly::draw_cells_gnuplot	(	c_loop &	vl,
		FILE *	fp
	)

inline

Computes Voronoi cells and saves the output in gnuplot format.

Parameters

[in]	vl	the loop class to use.
[in]	fp	a file handle to write to.

Definition at line 600 of file container.hh.

void voro::container_poly::draw_cells_gnuplot ( FILE * fp = stdout )

inline

Compute all Voronoi cells and saves the output in gnuplot format.

Parameters

[in] fp a file handle to write to.

Definition at line 610 of file container.hh.

void voro::container_poly::draw_cells_gnuplot ( const char * filename )

inline

Compute all Voronoi cells and saves the output in gnuplot format.

Parameters

[in] filename the name of the file to write to.

Definition at line 617 of file container.hh.

template<class c_loop >

void voro::container_poly::draw_cells_pov	(	c_loop &	vl,
		FILE *	fp
	)

inline

Computes Voronoi cells and saves the output in POV-Ray format.

Parameters

[in]	vl	the loop class to use.
[in]	fp	a file handle to write to.

Definition at line 627 of file container.hh.

void voro::container_poly::draw_cells_pov ( FILE * fp = stdout )

inline

Computes all Voronoi cells and saves the output in POV-Ray format.

Parameters

[in] fp a file handle to write to.

Definition at line 638 of file container.hh.

void voro::container_poly::draw_cells_pov ( const char * filename )

inline

Computes all Voronoi cells and saves the output in POV-Ray format.

Parameters

[in] filename the name of the file to write to.

Definition at line 645 of file container.hh.

template<class c_loop >

void voro::container_poly::draw_particles	(	c_loop &	vl,
		FILE *	fp
	)

inline

Dumps particle IDs, positions and radii to a file.

Parameters

[in]	vl	the loop class to use.
[in]	fp	a file handle to write to.

Definition at line 548 of file container.hh.

void voro::container_poly::draw_particles ( FILE * fp = stdout )

inline

Dumps all of the particle IDs, positions and radii to a file.

Parameters

[in] fp a file handle to write to.

Definition at line 558 of file container.hh.

void voro::container_poly::draw_particles ( const char * filename )

inline

Dumps all of the particle IDs, positions and radii to a file.

Parameters

[in] filename the name of the file to write to.

Definition at line 565 of file container.hh.

template<class c_loop >

void voro::container_poly::draw_particles_pov	(	c_loop &	vl,
		FILE *	fp
	)

inline

Dumps particle positions in POV-Ray format.

Parameters

[in]	vl	the loop class to use.
[in]	fp	a file handle to write to.

Definition at line 574 of file container.hh.

void voro::container_poly::draw_particles_pov ( FILE * fp = stdout )

inline

Dumps all the particle positions in POV-Ray format.

Parameters

[in] fp a file handle to write to.

Definition at line 584 of file container.hh.

void voro::container_poly::draw_particles_pov ( const char * filename )

inline

Dumps all the particle positions in POV-Ray format.

Parameters

[in] filename the name of the file to write to.

Definition at line 590 of file container.hh.

bool voro::container_poly::find_voronoi_cell	(	double	x,
		double	y,
		double	z,
		double &	rx,
		double &	ry,
		double &	rz,
		int &	pid
	)

Takes a vector and finds the particle whose Voronoi cell contains that vector. Additional wall classes are not considered by this routine.

Parameters

[in]	(x,y,z)	the vector to test.
[out]	(rx,ry,rz)	the position of the particle whose Voronoi cell contains the vector. If the container is periodic, this may point to a particle in a periodic image of the primary domain.
[out]	pid	the ID of the particle.

Returns: True if a particle was found. If the container has no particles, then the search will not find a Voronoi cell and false is returned.

Definition at line 272 of file container.cc.

void voro::container_poly::import ( FILE * fp = stdin )

Import a list of particles from an open file stream into the container. Entries of five numbers (Particle ID, x position, y position, z position, radius) are searched for. If the file cannot be successfully read, then the routine causes a fatal error.

Parameters

[in] fp the file handle to read from.

Definition at line 355 of file container.cc.

void voro::container_poly::import	(	particle_order &	vo,
		FILE *	fp = `stdin`
	)

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, radius) are searched for. If the file cannot be successfully read, then the routine causes a fatal error.

Parameters

[in,out]	vo	a reference to an ordering class to use.
[in]	fp	the file handle to read from.

Definition at line 368 of file container.cc.

void voro::container_poly::import ( const char * filename )

inline

Imports a list of particles from an open file stream into the container_poly class. Entries of five numbers (Particle ID, x position, y position, z position, radius) are searched for. If the file cannot be successfully read, then the routine causes a fatal error.

Parameters

[in] filename the name of the file to open and read from.

Definition at line 523 of file container.hh.

void voro::container_poly::import	(	particle_order &	vo,
		const char *	filename
	)

inline

Imports a list of particles from an open file stream into the container_poly class. Entries of five numbers (Particle ID, x position, y position, z position, radius) are searched for. In addition, the order in which particles are read is saved into an ordering class. If the file cannot be successfully read, then the routine causes a fatal error.

Parameters

[in,out]	vo	the ordering class to use.
[in]	filename	the name of the file to open and read from.

Definition at line 537 of file container.hh.

template<class c_loop >

void voro::container_poly::print_custom	(	c_loop &	vl,
		const char *	format,
		FILE *	fp
	)

inline

Computes the Voronoi cells and saves customized information about them.

Parameters

[in]	vl	the loop class to use.
[in]	format	the custom output string to use.
[in]	fp	a file handle to write to.

Definition at line 656 of file container.hh.

void voro::container_poly::print_custom	(	const char *	format,
		FILE *	fp = `stdout`
	)

Computes all the Voronoi cells and saves customized information about them.

Parameters

[in]	format	the custom output string to use.
[in]	fp	a file handle to write to.

Definition at line 407 of file container.cc.

void voro::container_poly::print_custom	(	const char *	format,
		const char *	filename
	)

Computes all the Voronoi cells and saves customized information about them

Parameters

[in]	format	the custom output string to use.
[in]	filename	the name of the file to write to.

Definition at line 425 of file container.cc.

void voro::container_poly::put	(	int	n,
		double	x,
		double	y,
		double	z,
		double	r
	)

Put a particle into the correct region of the container.

Parameters

[in]	n	the numerical ID of the inserted particle.
[in]	(x,y,z)	the position vector of the inserted particle.
[in]	r	the radius of the particle.

Definition at line 100 of file container.cc.

void voro::container_poly::put	(	particle_order &	vo,
		int	n,
		double	x,
		double	y,
		double	z,
		double	r
	)

Put a particle into the correct region of the container, also recording into which region it was stored.

Parameters

[in]	vo	the ordering class in which to record the region.
[in]	n	the numerical ID of the inserted particle.
[in]	(x,y,z)	the position vector of the inserted particle.
[in]	r	the radius of the particle.

Definition at line 131 of file container.cc.

double voro::container_poly::sum_cell_volumes ( )

Calculates all of the Voronoi cells and sums their volumes. In most cases without walls, the sum of the Voronoi cell volumes should equal the volume of the container to numerical precision.

Returns: The sum of all of the computed Voronoi volumes.

Definition at line 468 of file container.cc.

The documentation for this class was generated from the following files:

Public Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation