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voro::container Class Reference

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

`#include <container.hh>`

Inheritance diagram for voro::container:

## Public Member Functions
| container (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)
void | put (particle_order &vo, int n, double x, double y, double z)
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)
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)
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)
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 ()

## Friends
class | voro_compute< container >

## 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
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_mono
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 the container_base class that has routines specifically for computing the regular Voronoi tessellation with no dependence on particle radii.

Definition at line 285 of file container.hh.

## Constructor & Destructor Documentation

voro::container::container | ( | 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 64 of file container.cc.

## Member Function Documentation

void voro::container::clear | ( |  | ) |

Clears a container of particles.

Definition at line 384 of file container.cc.

void voro::container::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 435 of file container.cc.

template<class v_cell , class c_loop >

bool voro::container::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 460 of file container.hh.

template<class v_cell >

bool voro::container::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 472 of file container.hh.

template<class v_cell >

bool voro::container::compute_ghost_cell | ( | v_cell & | c,
|  | double | x,
|  | double | y,
|  | double | z
| ) |  |
| 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.

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 485 of file container.hh.

template<class c_loop >

void voro::container::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 376 of file container.hh.

void voro::container::draw_cells_gnuplot | ( | FILE * | fp = `stdout` | ) |
| inline

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

Parameters

  [in] | fp | a file handle to write to.

Definition at line 386 of file container.hh.

void voro::container::draw_cells_gnuplot | ( | const char * | filename | ) |
| inline

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

Parameters

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

Definition at line 393 of file container.hh.

template<class c_loop >

void voro::container::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 403 of file container.hh.

void voro::container::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 414 of file container.hh.

void voro::container::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 421 of file container.hh.

template<class c_loop >

void voro::container::draw_particles | ( | c_loop & | vl,
|  | FILE * | fp
| ) |  |
| inline

Dumps particle IDs and positions to a file.

Parameters

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

Definition at line 326 of file container.hh.

void voro::container::draw_particles | ( | FILE * | fp = `stdout` | ) |
| inline

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

Parameters

  [in] | fp | a file handle to write to.

Definition at line 335 of file container.hh.

void voro::container::draw_particles | ( | const char * | filename | ) |
| inline

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

Parameters

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

Definition at line 341 of file container.hh.

template<class c_loop >

void voro::container::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 350 of file container.hh.

void voro::container::draw_particles_pov | ( | FILE * | fp = `stdout` | ) |
| inline

Dumps all particle positions in POV-Ray format.

Parameters

  [in] | fp | a file handle to write to.

Definition at line 360 of file container.hh.

void voro::container::draw_particles_pov | ( | const char * | filename | ) |
| inline

Dumps all particle positions in POV-Ray format.

Parameters

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

Definition at line 366 of file container.hh.

bool voro::container::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. This is equivalent to finding the particle which is nearest to the 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 234 of file container.cc.

void voro::container::import | ( | FILE * | fp = `stdin` | ) |

Import a list of particles from an open file stream into the container. Entries of four numbers (Particle ID, x position, y position, z position) 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 330 of file container.cc.

void voro::container::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) 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 343 of file container.cc.

void voro::container::import | ( | const char * | filename | ) |
| inline

Imports a list of particles from an open file stream into the container. Entries of four numbers (Particle ID, x position, y position, z position) 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 301 of file container.hh.

void voro::container::import | ( | particle_order & | vo,
|  | const char * | filename
| ) |  |
| inline

Imports a list of particles from an open file stream into the container. Entries of four numbers (Particle ID, x position, y position, z position) 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 315 of file container.hh.

template<class c_loop >

void voro::container::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 432 of file container.hh.

void voro::container::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 398 of file container.cc.

void voro::container::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 415 of file container.cc.

void voro::container::put | ( | int | n,
|  | double | x,
|  | double | y,
|  | double | z
| ) |  |

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.

Definition at line 87 of file container.cc.

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

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.

Definition at line 115 of file container.cc.

double voro::container::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 456 of file container.cc.

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

- container.hh
- container.cc