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

#include <container_prd.hh>

Inheritance diagram for voro::container_periodic_poly:

Public Member Functions
	container_periodic_poly (double bx_, double bxy_, double by_, double bxz_, double byz_, double bz_, int nx_, int ny_, int nz_, int init_mem_)

void	clear ()

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

void	put (int n, double x, double y, double z, double r, int &ai, int &aj, int &ak)

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_periodic_base
	container_periodic_base (double bx_, double bxy_, double by_, double bxz_, double byz_, double bz_, int nx_, int ny_, int nz_, int init_mem_, int ps)

	~container_periodic_base ()

void	print_all_particles ()

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	create_all_images ()

void	check_compartmentalized ()

Public Member Functions inherited from voro::unitcell
	unitcell (double bx_, double bxy_, double by_, double bxz_, double byz_, double bz_)

void	draw_domain_gnuplot (const char *filename)

void	draw_domain_gnuplot (FILE *fp=stdout)

void	draw_domain_pov (const char *filename)

void	draw_domain_pov (FILE *fp=stdout)

bool	intersects_image (double dx, double dy, double dz, double &vol)

void	images (std::vector< int > &vi, std::vector< double > &vd)

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::radius_poly
	radius_poly ()

Friends
class	voro_compute< container_periodic_poly >

Additional Inherited Members
Data Fields inherited from voro::container_periodic_base
int	ey

int	ez

int	wy

int	wz

int	oy

int	oz

int	oxyz

int **	id

double **	p

int *	co

int *	mem

char *	img

const int	init_mem

const int	ps

Data Fields inherited from voro::unitcell
const double	bx

const double	bxy

const double	by

const double	bxz

const double	byz

const double	bz

voronoicell	unit_voro

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::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_periodic_base
void	add_particle_memory (int i)

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

void	put_locate_block (int &ijk, double &x, double &y, double &z, int &ai, int &aj, int &ak)

void	create_periodic_image (int di, int dj, int dk)

void	create_side_image (int di, int dj, int dk)

void	create_vertical_image (int di, int dj, int dk)

void	put_image (int reg, int fijk, int l, double dx, double dy, double dz)

void	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::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::unitcell
double	max_uv_y

double	max_uv_z

Detailed Description

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

Definition at line 433 of file container_prd.hh.

Constructor & Destructor Documentation

voro::container_periodic_poly::container_periodic_poly	(	double	bx_,
		double	bxy_,
		double	by_,
		double	bxz_,
		double	byz_,
		double	bz_,
		int	nx_,
		int	ny_,
		int	nz_,
		int	init_mem_
	)

The class constructor sets up the geometry of container.

Parameters

[in]	(bx_)	The x coordinate of the first unit vector.
[in]	(bxy_,by_)	The x and y coordinates of the second unit vector.
[in]	(bxz_,byz_,bz_)	The x, y, and z coordinates of the third unit vector.
[in]	(nx_,ny_,nz_)	the number of grid blocks in each of the three coordinate directions.
[in]	init_mem_	the initial memory allocation for each block.

Definition at line 85 of file container_prd.cc.

Member Function Documentation

void voro::container_periodic_poly::clear ( )

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

Definition at line 454 of file container_prd.cc.

void voro::container_periodic_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 510 of file container_prd.cc.

template<class v_cell , class c_loop >

bool voro::container_periodic_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 because it was removed entirely for some reason, then the routine returns false.

Definition at line 608 of file container_prd.hh.

template<class v_cell >

bool voro::container_periodic_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 because it was removed entirely for some reason, then the routine returns false.

Definition at line 620 of file container_prd.hh.

template<class v_cell >

bool voro::container_periodic_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 634 of file container_prd.hh.

template<class c_loop >

void voro::container_periodic_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 527 of file container_prd.hh.

void voro::container_periodic_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 537 of file container_prd.hh.

void voro::container_periodic_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 544 of file container_prd.hh.

template<class c_loop >

void voro::container_periodic_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 554 of file container_prd.hh.

void voro::container_periodic_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 565 of file container_prd.hh.

void voro::container_periodic_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 572 of file container_prd.hh.

template<class c_loop >

void voro::container_periodic_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 475 of file container_prd.hh.

void voro::container_periodic_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 485 of file container_prd.hh.

void voro::container_periodic_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 492 of file container_prd.hh.

template<class c_loop >

void voro::container_periodic_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 501 of file container_prd.hh.

void voro::container_periodic_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 511 of file container_prd.hh.

void voro::container_periodic_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 517 of file container_prd.hh.

bool voro::container_periodic_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 331 of file container_prd.cc.

void voro::container_periodic_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 419 of file container_prd.cc.

void voro::container_periodic_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 432 of file container_prd.cc.

void voro::container_periodic_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 450 of file container_prd.hh.

void voro::container_periodic_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 464 of file container_prd.hh.

template<class c_loop >

void voro::container_periodic_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 583 of file container_prd.hh.

void voro::container_periodic_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 471 of file container_prd.cc.

void voro::container_periodic_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 489 of file container_prd.cc.

void voro::container_periodic_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 105 of file container_prd.cc.

void voro::container_periodic_poly::put	(	int	n,
		double	x,
		double	y,
		double	z,
		double	r,
		int &	ai,
		int &	aj,
		int &	ak
	)

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.
[out]	(ai,aj,ak)	the periodic image displacement that the particle is in, with (0,0,0) corresponding to the primary domain.

Definition at line 135 of file container_prd.cc.

void voro::container_periodic_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 164 of file container_prd.cc.

double voro::container_periodic_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 532 of file container_prd.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