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container_prd.hh
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// Voro++, a 3D cell-based Voronoi library
//
// Author : Chris H. Rycroft (LBL / UC Berkeley)
// Email : chr@alum.mit.edu
// Date : August 30th 2011
/** \file container_prd.hh
* \brief Header file for the container_periodic_base and related classes. */
#ifndef VOROPP_CONTAINER_PRD_HH
#define VOROPP_CONTAINER_PRD_HH
#include <cstdio>
#include <vector>
#include "config.hh"
#include "common.hh"
#include "v_base.hh"
#include "cell.hh"
#include "c_loops.hh"
#include "v_compute.hh"
#include "unitcell.hh"
#include "rad_option.hh"
namespace voro {
/** \brief Class for representing a particle system in a 3D periodic
* non-orthogonal periodic domain.
*
* This class represents a particle system in a three-dimensional
* non-orthogonal periodic domain. The domain is defined by three periodicity
* vectors (bx,0,0), (bxy,by,0), and (bxz,byz,bz) that represent a
* parallelepiped. Internally, the class stores particles in the box 0<x<bx,
* 0<y<by, 0<z<bz, and constructs periodic images of particles that displaced
* by the three periodicity vectors when they are necessary for the
* computation. The internal memory structure for this class is significantly
* different from the container_base class in order to handle the dynamic
* construction of these periodic images.
*
* The class is derived from the unitcell class, which encapsulates information
* about the domain geometry, and the voro_base class, which encapsulates
* information about the underlying computational grid. */
class container_periodic_base : public unitcell, public voro_base {
public:
/** The lower y index (inclusive) of the primary domain within
* the block structure. */
int ey;
/** The lower z index (inclusive) of the primary domain within
* the block structure. */
int ez;
/** The upper y index (exclusive) of the primary domain within
* the block structure. */
int wy;
/** The upper z index (exclusive) of the primary domain within
* the block structure. */
int wz;
/** The total size of the block structure (including images) in
* the y direction. */
int oy;
/** The total size of the block structure (including images) in
* the z direction. */
int oz;
/** The total number of blocks. */
int oxyz;
/** This array holds the numerical IDs of each particle in each
* computational box. */
int **id;
/** A two dimensional array holding particle positions. For the
* derived container_poly class, this also holds particle
* radii. */
double **p;
/** This array holds the number of particles within each
* computational box of the container. */
int *co;
/** This array holds the maximum amount of particle memory for
* each computational box of the container. If the number of
* particles in a particular box ever approaches this limit,
* more is allocated using the add_particle_memory() function.
*/
int *mem;
/** An array holding information about periodic image
* construction at a given location. */
char *img;
/** The initial amount of memory to allocate for particles
* for each block. */
const int init_mem;
/** The amount of memory in the array structure for each
* particle. This is set to 3 when the basic class is
* initialized, so that the array holds (x,y,z) positions. If
* the container class is initialized as part of the derived
* class container_poly, then this is set to 4, to also hold
* the particle radii. */
const int ps;
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();
/** Prints all particles in the container, including those that
* have been constructed in image blocks. */
inline void print_all_particles() {
int ijk,q;
for(ijk=0;ijk<oxyz;ijk++) for(q=0;q<co[ijk];q++)
printf("%d %g %g %g\n",id[ijk][q],p[ijk][ps*q],p[ijk][ps*q+1],p[ijk][ps*q+2]);
}
void region_count();
/** Initializes the Voronoi cell prior to a compute_cell
* operation for a specific particle being carried out by a
* voro_compute class. The cell is initialized to be the
* pre-computed unit Voronoi cell based on planes formed by
* periodic images of the particle.
* \param[in,out] c a reference to a voronoicell object.
* \param[in] ijk the block that the particle is within.
* \param[in] q the index of the particle within its block.
* \param[in] (ci,cj,ck) the coordinates of the block in the
* container coordinate system.
* \param[out] (i,j,k) the coordinates of the test block
* relative to the voro_compute
* coordinate system.
* \param[out] (x,y,z) the position of the particle.
* \param[out] disp a block displacement used internally by the
* compute_cell routine.
* \return False if the plane cuts applied by walls completely
* removed the cell, true otherwise. */
template<class v_cell>
inline 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) {
c=unit_voro;
double *pp=p[ijk]+ps*q;
x=*(pp++);y=*(pp++);z=*pp;
i=nx;j=ey;k=ez;
return true;
}
/** Initializes parameters for a find_voronoi_cell call within
* the voro_compute template.
* \param[in] (ci,cj,ck) the coordinates of the test block in
* the container coordinate system.
* \param[in] ijk the index of the test block
* \param[out] (i,j,k) the coordinates of the test block
* relative to the voro_compute
* coordinate system.
* \param[out] disp a block displacement used internally by the
* find_voronoi_cell routine (but not needed
* in this instance.) */
inline void initialize_search(int ci,int cj,int ck,int ijk,int &i,int &j,int &k,int &disp) {
i=nx;j=ey;k=ez;
}
/** Returns the position of a particle currently being computed
* relative to the computational block that it is within. It is
* used to select the optimal worklist entry to use.
* \param[in] (x,y,z) the position of the particle.
* \param[in] (ci,cj,ck) the block that the particle is within.
* \param[out] (fx,fy,fz) the position relative to the block.
*/
inline void frac_pos(double x,double y,double z,double ci,double cj,double ck,double &fx,double &fy,double &fz) {
fx=x-boxx*ci;
fy=y-boxy*(cj-ey);
fz=z-boxz*(ck-ez);
}
/** Calculates the index of block in the container structure
* corresponding to given coordinates.
* \param[in] (ci,cj,ck) the coordinates of the original block
* in the current computation, relative
* to the container coordinate system.
* \param[in] (ei,ej,ek) the displacement of the current block
* from the original block.
* \param[in,out] (qx,qy,qz) the periodic displacement that
* must be added to the particles
* within the computed block.
* \param[in] disp a block displacement used internally by the
* find_voronoi_cell and compute_cell routines
* (but not needed in this instance.)
* \return The block index. */
inline int region_index(int ci,int cj,int ck,int ei,int ej,int ek,double &qx,double &qy,double &qz,int &disp) {
int qi=ci+(ei-nx),qj=cj+(ej-ey),qk=ck+(ek-ez);
int iv(step_div(qi,nx));if(iv!=0) {qx=iv*bx;qi-=nx*iv;} else qx=0;
create_periodic_image(qi,qj,qk);
return qi+nx*(qj+oy*qk);
}
void create_all_images();
void check_compartmentalized();
protected:
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);
/** Creates particles within an image block by copying them
* from the primary domain and shifting them. If the given
* block is aligned with the primary domain in the z-direction,
* the routine calls the simpler create_side_image routine
* where the image block may comprise of particles from up to
* two primary blocks. Otherwise is calls the more complex
* create_vertical_image where the image block may comprise of
* particles from up to four primary blocks.
* \param[in] (di,dj,dk) the coordinates of the image block to
* create. */
inline void create_periodic_image(int di,int dj,int dk) {
if(di<0||di>=nx||dj<0||dj>=oy||dk<0||dk>=oz)
voro_fatal_error("Constructing periodic image for nonexistent point",VOROPP_INTERNAL_ERROR);
if(dk>=ez&&dk<wz) {
if(dj<ey||dj>=wy) create_side_image(di,dj,dk);
} else create_vertical_image(di,dj,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);
inline void remap(int &ai,int &aj,int &ak,int &ci,int &cj,int &ck,double &x,double &y,double &z,int &ijk);
};
/** \brief Extension of the container_periodic_base class for computing regular
* Voronoi tessellations.
*
* This class is an extension of the container_periodic_base that has routines
* specifically for computing the regular Voronoi tessellation with no
* dependence on particle radii. */
class container_periodic : public container_periodic_base, public radius_mono {
public:
container_periodic(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);
void put(int n,double x,double y,double z,int &ai,int &aj,int &ak);
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);
/** 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.
* \param[in] filename the name of the file to open and read
* from. */
inline void import(const char* filename) {
FILE *fp=safe_fopen(filename,"r");
import(fp);
fclose(fp);
}
/** 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.
* \param[in,out] vo the ordering class to use.
* \param[in] filename the name of the file to open and read
* from. */
inline void import(particle_order &vo,const char* filename) {
FILE *fp=safe_fopen(filename,"r");
import(vo,fp);
fclose(fp);
}
void compute_all_cells();
double sum_cell_volumes();
/** Dumps particle IDs and positions to a file.
* \param[in] vl the loop class to use.
* \param[in] fp a file handle to write to. */
template<class c_loop>
void draw_particles(c_loop &vl,FILE *fp) {
double *pp;
if(vl.start()) do {
pp=p[vl.ijk]+3*vl.q;
fprintf(fp,"%d %g %g %g\n",id[vl.ijk][vl.q],*pp,pp[1],pp[2]);
} while(vl.inc());
}
/** Dumps all of the particle IDs and positions to a file.
* \param[in] fp a file handle to write to. */
inline void draw_particles(FILE *fp=stdout) {
c_loop_all_periodic vl(*this);
draw_particles(vl,fp);
}
/** Dumps all of the particle IDs and positions to a file.
* \param[in] filename the name of the file to write to. */
inline void draw_particles(const char *filename) {
FILE *fp=safe_fopen(filename,"w");
draw_particles(fp);
fclose(fp);
}
/** Dumps particle positions in POV-Ray format.
* \param[in] vl the loop class to use.
* \param[in] fp a file handle to write to. */
template<class c_loop>
void draw_particles_pov(c_loop &vl,FILE *fp) {
double *pp;
if(vl.start()) do {
pp=p[vl.ijk]+3*vl.q;
fprintf(fp,"// id %d\nsphere{<%g,%g,%g>,s}\n",
id[vl.ijk][vl.q],*pp,pp[1],pp[2]);
} while(vl.inc());
}
/** Dumps all particle positions in POV-Ray format.
* \param[in] fp a file handle to write to. */
inline void draw_particles_pov(FILE *fp=stdout) {
c_loop_all_periodic vl(*this);
draw_particles_pov(vl,fp);
}
/** Dumps all particle positions in POV-Ray format.
* \param[in] filename the name of the file to write to. */
inline void draw_particles_pov(const char *filename) {
FILE *fp=safe_fopen(filename,"w");
draw_particles_pov(fp);
fclose(fp);
}
/** Computes Voronoi cells and saves the output in gnuplot
* format.
* \param[in] vl the loop class to use.
* \param[in] fp a file handle to write to. */
template<class c_loop>
void draw_cells_gnuplot(c_loop &vl,FILE *fp) {
voronoicell c;double *pp;
if(vl.start()) do if(compute_cell(c,vl)) {
pp=p[vl.ijk]+ps*vl.q;
c.draw_gnuplot(*pp,pp[1],pp[2],fp);
} while(vl.inc());
}
/** Computes all Voronoi cells and saves the output in gnuplot
* format.
* \param[in] fp a file handle to write to. */
inline void draw_cells_gnuplot(FILE *fp=stdout) {
c_loop_all_periodic vl(*this);
draw_cells_gnuplot(vl,fp);
}
/** Compute all Voronoi cells and saves the output in gnuplot
* format.
* \param[in] filename the name of the file to write to. */
inline void draw_cells_gnuplot(const char *filename) {
FILE *fp=safe_fopen(filename,"w");
draw_cells_gnuplot(fp);
fclose(fp);
}
/** Computes Voronoi cells and saves the output in POV-Ray
* format.
* \param[in] vl the loop class to use.
* \param[in] fp a file handle to write to. */
template<class c_loop>
void draw_cells_pov(c_loop &vl,FILE *fp) {
voronoicell c;double *pp;
if(vl.start()) do if(compute_cell(c,vl)) {
fprintf(fp,"// cell %d\n",id[vl.ijk][vl.q]);
pp=p[vl.ijk]+ps*vl.q;
c.draw_pov(*pp,pp[1],pp[2],fp);
} while(vl.inc());
}
/** Computes all Voronoi cells and saves the output in POV-Ray
* format.
* \param[in] fp a file handle to write to. */
inline void draw_cells_pov(FILE *fp=stdout) {
c_loop_all_periodic vl(*this);
draw_cells_pov(vl,fp);
}
/** Computes all Voronoi cells and saves the output in POV-Ray
* format.
* \param[in] filename the name of the file to write to. */
inline void draw_cells_pov(const char *filename) {
FILE *fp=safe_fopen(filename,"w");
draw_cells_pov(fp);
fclose(fp);
}
/** Computes the Voronoi cells and saves customized information
* about them.
* \param[in] vl the loop class to use.
* \param[in] format the custom output string to use.
* \param[in] fp a file handle to write to. */
template<class c_loop>
void print_custom(c_loop &vl,const char *format,FILE *fp) {
int ijk,q;double *pp;
if(contains_neighbor(format)) {
voronoicell_neighbor c;
if(vl.start()) do if(compute_cell(c,vl)) {
ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],default_radius,fp);
} while(vl.inc());
} else {
voronoicell c;
if(vl.start()) do if(compute_cell(c,vl)) {
ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],default_radius,fp);
} while(vl.inc());
}
}
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);
/** Computes the Voronoi cell for a particle currently being
* referenced by a loop class.
* \param[out] c a Voronoi cell class in which to store the
* computed cell.
* \param[in] vl the loop class to use.
* \return 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. */
template<class v_cell,class c_loop>
inline bool compute_cell(v_cell &c,c_loop &vl) {
return vc.compute_cell(c,vl.ijk,vl.q,vl.i,vl.j,vl.k);
}
/** Computes the Voronoi cell for given particle.
* \param[out] c a Voronoi cell class in which to store the
* computed cell.
* \param[in] ijk the block that the particle is within.
* \param[in] q the index of the particle within the block.
* \return 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. */
template<class v_cell>
inline bool compute_cell(v_cell &c,int ijk,int q) {
int k(ijk/(nx*oy)),ijkt(ijk-(nx*oy)*k),j(ijkt/nx),i(ijkt-j*nx);
return vc.compute_cell(c,ijk,q,i,j,k);
}
private:
voro_compute<container_periodic> vc;
friend class voro_compute<container_periodic>;
};
/** \brief Extension of the container_periodic_base class for computing radical
* Voronoi tessellations.
*
* 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. */
class container_periodic_poly : public container_periodic_base, public radius_poly {
public:
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);
/** 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.
* \param[in] filename the name of the file to open and read
* from. */
inline void import(const char* filename) {
FILE *fp=safe_fopen(filename,"r");
import(fp);
fclose(fp);
}
/** 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.
* \param[in,out] vo the ordering class to use.
* \param[in] filename the name of the file to open and read
* from. */
inline void import(particle_order &vo,const char* filename) {
FILE *fp=safe_fopen(filename,"r");
import(vo,fp);
fclose(fp);
}
void compute_all_cells();
double sum_cell_volumes();
/** Dumps particle IDs, positions and radii to a file.
* \param[in] vl the loop class to use.
* \param[in] fp a file handle to write to. */
template<class c_loop>
void draw_particles(c_loop &vl,FILE *fp) {
double *pp;
if(vl.start()) do {
pp=p[vl.ijk]+4*vl.q;
fprintf(fp,"%d %g %g %g %g\n",id[vl.ijk][vl.q],*pp,pp[1],pp[2],pp[3]);
} while(vl.inc());
}
/** Dumps all of the particle IDs, positions and radii to a
* file.
* \param[in] fp a file handle to write to. */
inline void draw_particles(FILE *fp=stdout) {
c_loop_all_periodic vl(*this);
draw_particles(vl,fp);
}
/** Dumps all of the particle IDs, positions and radii to a
* file.
* \param[in] filename the name of the file to write to. */
inline void draw_particles(const char *filename) {
FILE *fp=safe_fopen(filename,"w");
draw_particles(fp);
fclose(fp);
}
/** Dumps particle positions in POV-Ray format.
* \param[in] vl the loop class to use.
* \param[in] fp a file handle to write to. */
template<class c_loop>
void draw_particles_pov(c_loop &vl,FILE *fp) {
double *pp;
if(vl.start()) do {
pp=p[vl.ijk]+4*vl.q;
fprintf(fp,"// id %d\nsphere{<%g,%g,%g>,%g}\n",
id[vl.ijk][vl.q],*pp,pp[1],pp[2],pp[3]);
} while(vl.inc());
}
/** Dumps all the particle positions in POV-Ray format.
* \param[in] fp a file handle to write to. */
inline void draw_particles_pov(FILE *fp=stdout) {
c_loop_all_periodic vl(*this);
draw_particles_pov(vl,fp);
}
/** Dumps all the particle positions in POV-Ray format.
* \param[in] filename the name of the file to write to. */
inline void draw_particles_pov(const char *filename) {
FILE *fp(safe_fopen(filename,"w"));
draw_particles_pov(fp);
fclose(fp);
}
/** Computes Voronoi cells and saves the output in gnuplot
* format.
* \param[in] vl the loop class to use.
* \param[in] fp a file handle to write to. */
template<class c_loop>
void draw_cells_gnuplot(c_loop &vl,FILE *fp) {
voronoicell c;double *pp;
if(vl.start()) do if(compute_cell(c,vl)) {
pp=p[vl.ijk]+ps*vl.q;
c.draw_gnuplot(*pp,pp[1],pp[2],fp);
} while(vl.inc());
}
/** Compute all Voronoi cells and saves the output in gnuplot
* format.
* \param[in] fp a file handle to write to. */
inline void draw_cells_gnuplot(FILE *fp=stdout) {
c_loop_all_periodic vl(*this);
draw_cells_gnuplot(vl,fp);
}
/** Compute all Voronoi cells and saves the output in gnuplot
* format.
* \param[in] filename the name of the file to write to. */
inline void draw_cells_gnuplot(const char *filename) {
FILE *fp(safe_fopen(filename,"w"));
draw_cells_gnuplot(fp);
fclose(fp);
}
/** Computes Voronoi cells and saves the output in POV-Ray
* format.
* \param[in] vl the loop class to use.
* \param[in] fp a file handle to write to. */
template<class c_loop>
void draw_cells_pov(c_loop &vl,FILE *fp) {
voronoicell c;double *pp;
if(vl.start()) do if(compute_cell(c,vl)) {
fprintf(fp,"// cell %d\n",id[vl.ijk][vl.q]);
pp=p[vl.ijk]+ps*vl.q;
c.draw_pov(*pp,pp[1],pp[2],fp);
} while(vl.inc());
}
/** Computes all Voronoi cells and saves the output in POV-Ray
* format.
* \param[in] fp a file handle to write to. */
inline void draw_cells_pov(FILE *fp=stdout) {
c_loop_all_periodic vl(*this);
draw_cells_pov(vl,fp);
}
/** Computes all Voronoi cells and saves the output in POV-Ray
* format.
* \param[in] filename the name of the file to write to. */
inline void draw_cells_pov(const char *filename) {
FILE *fp(safe_fopen(filename,"w"));
draw_cells_pov(fp);
fclose(fp);
}
/** Computes the Voronoi cells and saves customized information
* about them.
* \param[in] vl the loop class to use.
* \param[in] format the custom output string to use.
* \param[in] fp a file handle to write to. */
template<class c_loop>
void print_custom(c_loop &vl,const char *format,FILE *fp) {
int ijk,q;double *pp;
if(contains_neighbor(format)) {
voronoicell_neighbor c;
if(vl.start()) do if(compute_cell(c,vl)) {
ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],pp[3],fp);
} while(vl.inc());
} else {
voronoicell c;
if(vl.start()) do if(compute_cell(c,vl)) {
ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],pp[3],fp);
} while(vl.inc());
}
}
/** Computes the Voronoi cell for a particle currently being
* referenced by a loop class.
* \param[out] c a Voronoi cell class in which to store the
* computed cell.
* \param[in] vl the loop class to use.
* \return 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. */
template<class v_cell,class c_loop>
inline bool compute_cell(v_cell &c,c_loop &vl) {
return vc.compute_cell(c,vl.ijk,vl.q,vl.i,vl.j,vl.k);
}
/** Computes the Voronoi cell for given particle.
* \param[out] c a Voronoi cell class in which to store the
* computed cell.
* \param[in] ijk the block that the particle is within.
* \param[in] q the index of the particle within the block.
* \return 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. */
template<class v_cell>
inline bool compute_cell(v_cell &c,int ijk,int q) {
int k(ijk/(nx*oy)),ijkt(ijk-(nx*oy)*k),j(ijkt/nx),i(ijkt-j*nx);
return vc.compute_cell(c,ijk,q,i,j,k);
}
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);
private:
voro_compute<container_periodic_poly> vc;
friend class voro_compute<container_periodic_poly>;
};
}
#endif

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