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voro::container_periodic_poly Class Reference

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]ca Voronoi cell class in which to store the computed cell.
[in]vlthe 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]ca Voronoi cell class in which to store the computed cell.
[in]ijkthe block that the particle is within.
[in]qthe 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]ca Voronoi cell class in which to store the computed cell.
[in](x,y,z)the location of the ghost particle.
[in]rthe 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]vlthe loop class to use.
[in]fpa 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]fpa 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]filenamethe 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]vlthe loop class to use.
[in]fpa 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]fpa 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]filenamethe 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]vlthe loop class to use.
[in]fpa 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]fpa 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]filenamethe 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]vlthe loop class to use.
[in]fpa 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]fpa 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]filenamethe 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]pidthe 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]fpthe 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]voa reference to an ordering class to use.
[in]fpthe 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]filenamethe 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]vothe ordering class to use.
[in]filenamethe 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]vlthe loop class to use.
[in]formatthe custom output string to use.
[in]fpa 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]formatthe custom output string to use.
[in]fpa 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]formatthe custom output string to use.
[in]filenamethe 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]nthe numerical ID of the inserted particle.
[in](x,y,z)the position vector of the inserted particle.
[in]rthe 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]nthe numerical ID of the inserted particle.
[in](x,y,z)the position vector of the inserted particle.
[in]rthe 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]vothe ordering class in which to record the region.
[in]nthe numerical ID of the inserted particle.
[in](x,y,z)the position vector of the inserted particle.
[in]rthe 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: