cell.hh

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// Voro++, a 3D cell-based Voronoi library
//
// Author   : Chris H. Rycroft (LBL / UC Berkeley)
// Email    : [email protected]
// Date     : August 30th 2011

/** \file cell.hh
 * \brief Header file for the voronoicell and related classes. */

#ifndef VOROPP_CELL_HH
#define VOROPP_CELL_HH

#include <vector>

#include "config.hh"
#include "common.hh"

namespace voro {

/** \brief A class representing a single Voronoi cell.
 *
 * This class represents a single Voronoi cell, as a collection of vertices
 * that are connected by edges. The class contains routines for initializing
 * the Voronoi cell to be simple shapes such as a box, tetrahedron, or octahedron.
 * It the contains routines for recomputing the cell based on cutting it
 * by a plane, which forms the key routine for the Voronoi cell computation.
 * It contains numerous routine for computing statistics about the Voronoi cell,
 * and it can output the cell in several formats.
 *
 * This class is not intended for direct use, but forms the base of the
 * voronoicell and voronoicell_neighbor classes, which extend it based on
 * whether neighboring particle ID information needs to be tracked. */
class voronoicell_base {
        public:
                /** This holds the current size of the arrays ed and nu, which
                 * hold the vertex information. If more vertices are created
                 * than can fit in this array, then it is dynamically extended
                 * using the add_memory_vertices routine. */
                int current_vertices;
                /** This holds the current maximum allowed order of a vertex,
                 * which sets the size of the mem, mep, and mec arrays. If a
                 * vertex is created with more vertices than this, the arrays
                 * are dynamically extended using the add_memory_vorder routine.
                 */
                int current_vertex_order;
                /** This sets the size of the main delete stack. */
                int current_delete_size;
                /** This sets the size of the auxiliary delete stack. */
                int current_delete2_size;
                /** This sets the total number of vertices in the current cell.
                 */
                int p;
                /** This is the index of particular point in the cell, which is
                 * used to start the tracing routines for plane intersection
                 * and cutting. These routines will work starting from any
                 * point, but it's often most efficient to start from the last
                 * point considered, since in many cases, the cell construction
                 * algorithm may consider many planes with similar vectors
                 * concurrently. */
                int up;
                /** This is a two dimensional array that holds information
                 * about the edge connections of the vertices that make up the
                 * cell. The two dimensional array is not allocated in the
                 * usual method. To account for the fact the different vertices
                 * have different orders, and thus require different amounts of
                 * storage, the elements of ed[i] point to one-dimensional
                 * arrays in the mep[] array of different sizes.
                 *
                 * More specifically, if vertex i has order m, then ed[i]
                 * points to a one-dimensional array in mep[m] that has 2*m+1
                 * entries. The first m elements hold the neighboring edges, so
                 * that the jth edge of vertex i is held in ed[i][j]. The next
                 * m elements hold a table of relations which is redundant but
                 * helps speed up the computation. It satisfies the relation
                 * ed[ed[i][j]][ed[i][m+j]]=i. The final entry holds a back
                 * pointer, so that ed[i+2*m]=i. The back pointers are used
                 * when rearranging the memory. */
                int **ed;
                /** This array holds the order of the vertices in the Voronoi
                 * cell. This array is dynamically allocated, with its current
                 * size held by current_vertices. */
                int *nu;
                /** This in an array with size 3*current_vertices for holding
                 * the positions of the vertices. */
                double *pts;
                voronoicell_base();
                ~voronoicell_base();
                void init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax);
                void init_octahedron_base(double l);
                void init_tetrahedron_base(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3);
                void translate(double x,double y,double z);
                void draw_pov(double x,double y,double z,FILE *fp=stdout);
                /** Outputs the cell in POV-Ray format, using cylinders for edges
                 * and spheres for vertices, to a given file.
                 * \param[in] (x,y,z) a displacement to add to the cell's
                 *                    position.
                 * \param[in] filename the name of the file to write to. */
                inline void draw_pov(double x,double y,double z,const char *filename) {
                        FILE *fp=safe_fopen(filename,"w");
                        draw_pov(x,y,z,fp);
                        fclose(fp);
                };
                void draw_pov_mesh(double x,double y,double z,FILE *fp=stdout);
                /** Outputs the cell in POV-Ray format as a mesh2 object to a
                 * given file.
                 * \param[in] (x,y,z) a displacement to add to the cell's
                 *                    position.
                 * \param[in] filename the name of the file to write to. */
                inline void draw_pov_mesh(double x,double y,double z,const char *filename) {
                        FILE *fp=safe_fopen(filename,"w");
                        draw_pov_mesh(x,y,z,fp);
                        fclose(fp);
                }
                void draw_gnuplot(double x,double y,double z,FILE *fp=stdout);
                /** Outputs the cell in Gnuplot format a given file.
                 * \param[in] (x,y,z) a displacement to add to the cell's
                 *                    position.
                 * \param[in] filename the name of the file to write to. */
                inline void draw_gnuplot(double x,double y,double z,const char *filename) {
                        FILE *fp=safe_fopen(filename,"w");
                        draw_gnuplot(x,y,z,fp);
                        fclose(fp);
                }
                double volume();
                double max_radius_squared();
                double total_edge_distance();
                double surface_area();
                void centroid(double &cx,double &cy,double &cz);
                int number_of_faces();
                int number_of_edges();
                void vertex_orders(std::vector<int> &v);
                void output_vertex_orders(FILE *fp=stdout);
                void vertices(std::vector<double> &v);
                void output_vertices(FILE *fp=stdout);
                void vertices(double x,double y,double z,std::vector<double> &v);
                void output_vertices(double x,double y,double z,FILE *fp=stdout);
                void face_areas(std::vector<double> &v);
                /** Outputs the areas of the faces.
                 * \param[in] fp the file handle to write to. */
                inline void output_face_areas(FILE *fp=stdout) {
                        std::vector<double> v;face_areas(v);
                        voro_print_vector(v,fp);
                }
                void face_orders(std::vector<int> &v);
                /** Outputs a list of the number of sides of each face.
                 * \param[in] fp the file handle to write to. */
                inline void output_face_orders(FILE *fp=stdout) {
                        std::vector<int> v;face_orders(v);
                        voro_print_vector(v,fp);
                }
                void face_freq_table(std::vector<int> &v);
                /** Outputs a */
                inline void output_face_freq_table(FILE *fp=stdout) {
                        std::vector<int> v;face_freq_table(v);
                        voro_print_vector(v,fp);
                }
                void face_vertices(std::vector<int> &v);
                /** Outputs the */
                inline void output_face_vertices(FILE *fp=stdout) {
                        std::vector<int> v;face_vertices(v);
                        voro_print_face_vertices(v,fp);
                }
                void face_perimeters(std::vector<double> &v);
                /** Outputs a list of the perimeters of each face.
                 * \param[in] fp the file handle to write to. */
                inline void output_face_perimeters(FILE *fp=stdout) {
                        std::vector<double> v;face_perimeters(v);
                        voro_print_vector(v,fp);
                }
                void normals(std::vector<double> &v);
                /** Outputs a list of the perimeters of each face.
                 * \param[in] fp the file handle to write to. */
                inline void output_normals(FILE *fp=stdout) {
                        std::vector<double> v;normals(v);
                        voro_print_positions(v,fp);
                }
                /** Outputs a custom string of information about the Voronoi
                 * cell to a file. It assumes the cell is at (0,0,0) and has a
                 * the default_radius associated with it.
                 * \param[in] format the custom format string to use.
                 * \param[in] fp the file handle to write to. */
                inline void output_custom(const char *format,FILE *fp=stdout) {output_custom(format,0,0,0,0,default_radius,fp);}
                void output_custom(const char *format,int i,double x,double y,double z,double r,FILE *fp=stdout);
                template<class vc_class>
                bool nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id);
                bool plane_intersects(double x,double y,double z,double rsq);
                bool plane_intersects_guess(double x,double y,double z,double rsq);
                void construct_relations();
                void check_relations();
                void check_duplicates();
                void print_edges();
                /** Returns a list of IDs of neighboring particles
                 * corresponding to each face.
                 * \param[out] v a reference to a vector in which to return the
                 *               results. If no neighbor information is
                 *               available, a blank vector is returned. */
                virtual void neighbors(std::vector<int> &v) {v.clear();}
                /** This is a virtual function that is overridden by a routine
                 * to print a list of IDs of neighboring particles
                 * corresponding to each face. By default, when no neighbor
                 * information is available, the routine does nothing.
                 * \param[in] fp the file handle to write to. */
                virtual void output_neighbors(FILE *fp=stdout) {}
                /** This a virtual function that is overridden by a routine to
                 * print the neighboring particle IDs for a given vertex. By
                 * default, when no neighbor information is available, the
                 * routine does nothing.
                 * \param[in] i the vertex to consider. */
                virtual void print_edges_neighbors(int i) {};
                /** This is a simple inline function for picking out the index
                 * of the next edge counterclockwise at the current vertex.
                 * \param[in] a the index of an edge of the current vertex.
                 * \param[in] p the number of the vertex.
                 * \return 0 if a=nu[p]-1, or a+1 otherwise. */
                inline int cycle_up(int a,int p) {return a==nu[p]-1?0:a+1;}
                /** This is a simple inline function for picking out the index
                 * of the next edge clockwise from the current vertex.
                 * \param[in] a the index of an edge of the current vertex.
                 * \param[in] p the number of the vertex.
                 * \return nu[p]-1 if a=0, or a-1 otherwise. */
                inline int cycle_down(int a,int p) {return a==0?nu[p]-1:a-1;}
        protected:
                /** This a one dimensional array that holds the current sizes
                 * of the memory allocations for them mep array.*/
                int *mem;
                /** This is a one dimensional array that holds the current
                 * number of vertices of order p that are stored in the mep[p]
                 * array. */
                int *mec;
                /** This is a two dimensional array for holding the information
                 * about the edges of the Voronoi cell. mep[p] is a
                 * one-dimensional array for holding the edge information about
                 * all vertices of order p, with each vertex holding 2*p+1
                 * integers of information. The total number of vertices held
                 * on mep[p] is stored in mem[p]. If the space runs out, the
                 * code allocates more using the add_memory() routine. */
                int **mep;
                inline void reset_edges();
                template<class vc_class>
                void check_memory_for_copy(vc_class &vc,voronoicell_base* vb);
                void copy(voronoicell_base* vb);
        private:
                /** This is the delete stack, used to store the vertices which
                 * are going to be deleted during the plane cutting procedure.
                 */
                int *ds,*stacke;
                /** This is the auxiliary delete stack, which has size set by
                 * current_delete2_size. */
                int *ds2,*stacke2;
                /** This stores the current memory allocation for the marginal
                 * cases. */
                int current_marginal;
                /** This stores the total number of marginal points which are
                 * currently in the buffer. */
                int n_marg;
                /** This array contains a list of the marginal points, and also
                 * the outcomes of the marginal tests. */
                int *marg;
                /** The x coordinate of the normal vector to the test plane. */
                double px;
                /** The y coordinate of the normal vector to the test plane. */
                double py;
                /** The z coordinate of the normal vector to the test plane. */
                double pz;
                /** The magnitude of the normal vector to the test plane. */
                double prsq;
                template<class vc_class>
                void add_memory(vc_class &vc,int i,int *stackp2);
                template<class vc_class>
                void add_memory_vertices(vc_class &vc);
                template<class vc_class>
                void add_memory_vorder(vc_class &vc);
                void add_memory_ds(int *&stackp);
                void add_memory_ds2(int *&stackp2);
                template<class vc_class>
                inline bool collapse_order1(vc_class &vc);
                template<class vc_class>
                inline bool collapse_order2(vc_class &vc);
                template<class vc_class>
                inline bool delete_connection(vc_class &vc,int j,int k,bool hand);
                template<class vc_class>
                inline bool search_for_outside_edge(vc_class &vc,int &up);
                template<class vc_class>
                inline void add_to_stack(vc_class &vc,int lp,int *&stackp2);
                inline bool plane_intersects_track(double x,double y,double z,double rs,double g);
                inline void normals_search(std::vector<double> &v,int i,int j,int k);
                inline bool search_edge(int l,int &m,int &k);
                inline int m_test(int n,double &ans);
                int check_marginal(int n,double &ans);
                friend class voronoicell;
                friend class voronoicell_neighbor;
};

/** \brief Extension of the voronoicell_base class to represent a Voronoi
 * cell without neighbor information.
 *
 * This class is an extension of the voronoicell_base class, in cases when
 * is not necessary to track the IDs of neighboring particles associated
 * with each face of the Voronoi cell. */
class voronoicell : public voronoicell_base {
        public:
                using voronoicell_base::nplane;
                /** Copies the information from another voronoicell class into
                 * this class, extending memory allocation if necessary.
                 * \param[in] c the class to copy. */
                inline void operator=(voronoicell &c) {
                        voronoicell_base* vb((voronoicell_base*) &c);
                        check_memory_for_copy(*this,vb);copy(vb);
                }
                /** Cuts a Voronoi cell using by the plane corresponding to the
                 * perpendicular bisector of a particle.
                 * \param[in] (x,y,z) the position of the particle.
                 * \param[in] rsq the modulus squared of the vector.
                 * \param[in] p_id the plane ID, ignored for this case where no
                 *                 neighbor tracking is enabled.
                 * \return False if the plane cut deleted the cell entirely,
                 *         true otherwise. */
                inline bool nplane(double x,double y,double z,double rsq,int p_id) {
                        return nplane(*this,x,y,z,rsq,0);
                }
                /** Cuts a Voronoi cell using by the plane corresponding to the
                 * perpendicular bisector of a particle.
                 * \param[in] (x,y,z) the position of the particle.
                 * \param[in] p_id the plane ID, ignored for this case where no
                 *                 neighbor tracking is enabled.
                 * \return False if the plane cut deleted the cell entirely,
                 *         true otherwise. */
                inline bool nplane(double x,double y,double z,int p_id) {
                        double rsq=x*x+y*y+z*z;
                        return nplane(*this,x,y,z,rsq,0);
                }
                /** Cuts a Voronoi cell using by the plane corresponding to the
                 * perpendicular bisector of a particle.
                 * \param[in] (x,y,z) the position of the particle.
                 * \param[in] rsq the modulus squared of the vector.
                 * \return False if the plane cut deleted the cell entirely,
                 *         true otherwise. */
                inline bool plane(double x,double y,double z,double rsq) {
                        return nplane(*this,x,y,z,rsq,0);
                }
                /** Cuts a Voronoi cell using by the plane corresponding to the
                 * perpendicular bisector of a particle.
                 * \param[in] (x,y,z) the position of the particle.
                 * \return False if the plane cut deleted the cell entirely,
                 *         true otherwise. */
                inline bool plane(double x,double y,double z) {
                        double rsq=x*x+y*y+z*z;
                        return nplane(*this,x,y,z,rsq,0);
                }
                /** Initializes the Voronoi cell to be rectangular box with the
                 * given dimensions.
                 * \param[in] (xmin,xmax) the minimum and maximum x coordinates.
                 * \param[in] (ymin,ymax) the minimum and maximum y coordinates.
                 * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */
                inline void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) {
                        init_base(xmin,xmax,ymin,ymax,zmin,zmax);
                }
                /** Initializes the cell to be an octahedron with vertices at
                 * (l,0,0), (-l,0,0), (0,l,0), (0,-l,0), (0,0,l), and (0,0,-l).
                 * \param[in] l a parameter setting the size of the octahedron.
                 */
                inline void init_octahedron(double l) {
                        init_octahedron_base(l);
                }
                /** Initializes the cell to be a tetrahedron.
                 * \param[in] (x0,y0,z0) the coordinates of the first vertex.
                 * \param[in] (x1,y1,z1) the coordinates of the second vertex.
                 * \param[in] (x2,y2,z2) the coordinates of the third vertex.
                 * \param[in] (x3,y3,z3) the coordinates of the fourth vertex.
                 */
                inline void init_tetrahedron(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3) {
                        init_tetrahedron_base(x0,y0,z0,x1,y1,z1,x2,y2,z2,x3,y3,z3);
                }
        private:
                inline void n_allocate(int i,int m) {};
                inline void n_add_memory_vertices(int i) {};
                inline void n_add_memory_vorder(int i) {};
                inline void n_set_pointer(int p,int n) {};
                inline void n_copy(int a,int b,int c,int d) {};
                inline void n_set(int a,int b,int c) {};
                inline void n_set_aux1(int k) {};
                inline void n_copy_aux1(int a,int b) {};
                inline void n_copy_aux1_shift(int a,int b) {};
                inline void n_set_aux2_copy(int a,int b) {};
                inline void n_copy_pointer(int a,int b) {};
                inline void n_set_to_aux1(int j) {};
                inline void n_set_to_aux2(int j) {};
                inline void n_allocate_aux1(int i) {};
                inline void n_switch_to_aux1(int i) {};
                inline void n_copy_to_aux1(int i,int m) {};
                inline void n_set_to_aux1_offset(int k,int m) {};
                inline void n_neighbors(std::vector<int> &v) {v.clear();};
                friend class voronoicell_base;
};

/** \brief Extension of the voronoicell_base class to represent a Voronoi cell
 * with neighbor information.
 *
 * This class is an extension of the voronoicell_base class, in cases when the
 * IDs of neighboring particles associated with each face of the Voronoi cell.
 * It contains additional data structures mne and ne for storing this
 * information. */
class voronoicell_neighbor : public voronoicell_base {
        public:
                using voronoicell_base::nplane;
                /** This two dimensional array holds the neighbor information
                 * associated with each vertex. mne[p] is a one dimensional
                 * array which holds all of the neighbor information for
                 * vertices of order p. */
                int **mne;
                /** This is a two dimensional array that holds the neighbor
                 * information associated with each vertex. ne[i] points to a
                 * one-dimensional array in mne[nu[i]]. ne[i][j] holds the
                 * neighbor information associated with the jth edge of vertex
                 * i. It is set to the ID number of the plane that made the
                 * face that is clockwise from the jth edge. */
                int **ne;
                voronoicell_neighbor();
                ~voronoicell_neighbor();
                void operator=(voronoicell &c);
                void operator=(voronoicell_neighbor &c);
                /** Cuts the Voronoi cell by a particle whose center is at a
                 * separation of (x,y,z) from the cell center. The value of rsq
                 * should be initially set to \f$x^2+y^2+z^2\f$.
                 * \param[in] (x,y,z) the normal vector to the plane.
                 * \param[in] rsq the distance along this vector of the plane.
                 * \param[in] p_id the plane ID (for neighbor tracking only).
                 * \return False if the plane cut deleted the cell entirely,
                 * true otherwise. */
                inline bool nplane(double x,double y,double z,double rsq,int p_id) {
                        return nplane(*this,x,y,z,rsq,p_id);
                }
                /** This routine calculates the modulus squared of the vector
                 * before passing it to the main nplane() routine with full
                 * arguments.
                 * \param[in] (x,y,z) the vector to cut the cell by.
                 * \param[in] p_id the plane ID (for neighbor tracking only).
                 * \return False if the plane cut deleted the cell entirely,
                 *         true otherwise. */
                inline bool nplane(double x,double y,double z,int p_id) {
                        double rsq=x*x+y*y+z*z;
                        return nplane(*this,x,y,z,rsq,p_id);
                }
                /** This version of the plane routine just makes up the plane
                 * ID to be zero. It will only be referenced if neighbor
                 * tracking is enabled.
                 * \param[in] (x,y,z) the vector to cut the cell by.
                 * \param[in] rsq the modulus squared of the vector.
                 * \return False if the plane cut deleted the cell entirely,
                 *         true otherwise. */
                inline bool plane(double x,double y,double z,double rsq) {
                        return nplane(*this,x,y,z,rsq,0);
                }
                /** Cuts a Voronoi cell using the influence of a particle at
                 * (x,y,z), first calculating the modulus squared of this
                 * vector before passing it to the main nplane() routine. Zero
                 * is supplied as the plane ID, which will be ignored unless
                 * neighbor tracking is enabled.
                 * \param[in] (x,y,z) the vector to cut the cell by.
                 * \return False if the plane cut deleted the cell entirely,
                 *         true otherwise. */
                inline bool plane(double x,double y,double z) {
                        double rsq=x*x+y*y+z*z;
                        return nplane(*this,x,y,z,rsq,0);
                }
                void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax);
                void init_octahedron(double l);
                void init_tetrahedron(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3);
                void check_facets();
                virtual void neighbors(std::vector<int> &v);
                virtual void print_edges_neighbors(int i);
                virtual void output_neighbors(FILE *fp=stdout) {
                        std::vector<int> v;neighbors(v);
                        voro_print_vector(v,fp);
                }
        private:
                int *paux1;
                int *paux2;
                inline void n_allocate(int i,int m) {mne[i]=new int[m*i];}
                inline void n_add_memory_vertices(int i) {
                        int **pp=new int*[i];
                        for(int j=0;j<current_vertices;j++) pp[j]=ne[j];
                        delete [] ne;ne=pp;
                }
                inline void n_add_memory_vorder(int i) {
                        int **p2=new int*[i];
                        for(int j=0;j<current_vertex_order;j++) p2[j]=mne[j];
                        delete [] mne;mne=p2;
                }
                inline void n_set_pointer(int p,int n) {
                        ne[p]=mne[n]+n*mec[n];
                }
                inline void n_copy(int a,int b,int c,int d) {ne[a][b]=ne[c][d];}
                inline void n_set(int a,int b,int c) {ne[a][b]=c;}
                inline void n_set_aux1(int k) {paux1=mne[k]+k*mec[k];}
                inline void n_copy_aux1(int a,int b) {paux1[b]=ne[a][b];}
                inline void n_copy_aux1_shift(int a,int b) {paux1[b]=ne[a][b+1];}
                inline void n_set_aux2_copy(int a,int b) {
                        paux2=mne[b]+b*mec[b];
                        for(int i=0;i<b;i++) ne[a][i]=paux2[i];
                }
                inline void n_copy_pointer(int a,int b) {ne[a]=ne[b];}
                inline void n_set_to_aux1(int j) {ne[j]=paux1;}
                inline void n_set_to_aux2(int j) {ne[j]=paux2;}
                inline void n_allocate_aux1(int i) {paux1=new int[i*mem[i]];}
                inline void n_switch_to_aux1(int i) {delete [] mne[i];mne[i]=paux1;}
                inline void n_copy_to_aux1(int i,int m) {paux1[m]=mne[i][m];}
                inline void n_set_to_aux1_offset(int k,int m) {ne[k]=paux1+m;}
                friend class voronoicell_base;
};

}

#endif