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francois |
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// Voro++, a 3D cell-based Voronoi library |
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// |
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// Author : Chris H. Rycroft (LBL / UC Berkeley) |
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// Email : chr@alum.mit.edu |
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// Date : August 30th 2011 |
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/** \file container.hh |
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* \brief Header file for the container_base and related classes. */ |
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#ifndef VOROPP_CONTAINER_HH |
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#define VOROPP_CONTAINER_HH |
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#include <cstdio> |
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#include <vector> |
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#include "config.hh" |
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#include "common.hh" |
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#include "v_base.hh" |
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#include "cell.hh" |
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#include "c_loops.hh" |
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#include "v_compute.hh" |
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#include "rad_option.hh" |
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namespace voro { |
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/** \brief Pure virtual class from which wall objects are derived. |
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* |
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* This is a pure virtual class for a generic wall object. A wall object |
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* can be specified by deriving a new class from this and specifying the |
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* functions.*/ |
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class wall { |
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public: |
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virtual ~wall() {} |
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/** A pure virtual function for testing whether a point is |
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* inside the wall object. */ |
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virtual bool point_inside(double x,double y,double z) = 0; |
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/** A pure virtual function for cutting a cell without |
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* neighbor-tracking with a wall. */ |
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virtual bool cut_cell(voronoicell &c,double x,double y,double z) = 0; |
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/** A pure virtual function for cutting a cell with |
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* neighbor-tracking enabled with a wall. */ |
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virtual bool cut_cell(voronoicell_neighbor &c,double x,double y,double z) = 0; |
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}; |
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/** \brief A class for storing a list of pointers to walls. |
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* |
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* This class stores a list of pointers to wall classes. It contains several |
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* simple routines that make use of the wall classes (such as telling whether a |
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* given position is inside all of the walls or not). It can be used by itself, |
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* but also forms part of container_base, for associating walls with this |
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* class. */ |
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class wall_list { |
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public: |
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/** An array holding pointers to wall objects. */ |
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wall **walls; |
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/** A pointer to the next free position to add a wall pointer. |
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*/ |
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wall **wep; |
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wall_list(); |
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~wall_list(); |
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/** Adds a wall to the list. |
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* \param[in] w the wall to add. */ |
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inline void add_wall(wall *w) { |
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if(wep==wel) increase_wall_memory(); |
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*(wep++)=w; |
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} |
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/** Adds a wall to the list. |
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* \param[in] w a reference to the wall to add. */ |
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inline void add_wall(wall &w) {add_wall(&w);} |
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void add_wall(wall_list &wl); |
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/** Determines whether a given position is inside all of the |
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* walls on the list. |
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* \param[in] (x,y,z) the position to test. |
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* \return True if it is inside, false if it is outside. */ |
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inline bool point_inside_walls(double x,double y,double z) { |
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for(wall **wp=walls;wp<wep;wp++) if(!((*wp)->point_inside(x,y,z))) return false; |
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return true; |
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} |
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/** Cuts a Voronoi cell by all of the walls currently on |
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* the list. |
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* \param[in] c a reference to the Voronoi cell class. |
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* \param[in] (x,y,z) the position of the cell. |
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* \return True if the cell still exists, false if the cell is |
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* deleted. */ |
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template<class c_class> |
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bool apply_walls(c_class &c,double x,double y,double z) { |
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for(wall **wp=walls;wp<wep;wp++) if(!((*wp)->cut_cell(c,x,y,z))) return false; |
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return true; |
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} |
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void deallocate(); |
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protected: |
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void increase_wall_memory(); |
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/** A pointer to the limit of the walls array, used to |
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* determine when array is full. */ |
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wall **wel; |
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/** The current amount of memory allocated for walls. */ |
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int current_wall_size; |
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}; |
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/** \brief Class for representing a particle system in a three-dimensional |
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* rectangular box. |
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* |
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* This class represents a system of particles in a three-dimensional |
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* rectangular box. Any combination of non-periodic and periodic coordinates |
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* can be used in the three coordinate directions. The class is not intended |
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* for direct use, but instead forms the base of the container and |
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* container_poly classes that add specialized routines for computing the |
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* regular and radical Voronoi tessellations respectively. It contains routines |
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* that are commonly between these two classes, such as those for drawing the |
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* domain, and placing particles within the internal data structure. |
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* |
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* The class is derived from the wall_list class, which encapsulates routines |
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* for associating walls with the container, and the voro_base class, which |
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* encapsulates routines about the underlying computational grid. */ |
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class container_base : public voro_base, public wall_list { |
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public: |
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/** The minimum x coordinate of the container. */ |
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const double ax; |
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/** The maximum x coordinate of the container. */ |
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const double bx; |
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/** The minimum y coordinate of the container. */ |
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const double ay; |
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/** The maximum y coordinate of the container. */ |
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const double by; |
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/** The minimum z coordinate of the container. */ |
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const double az; |
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/** The maximum z coordinate of the container. */ |
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const double bz; |
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/** A boolean value that determines if the x coordinate in |
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* periodic or not. */ |
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const bool xperiodic; |
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/** A boolean value that determines if the y coordinate in |
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* periodic or not. */ |
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const bool yperiodic; |
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/** A boolean value that determines if the z coordinate in |
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* periodic or not. */ |
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const bool zperiodic; |
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/** This array holds the numerical IDs of each particle in each |
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* computational box. */ |
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int **id; |
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/** A two dimensional array holding particle positions. For the |
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* derived container_poly class, this also holds particle |
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* radii. */ |
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double **p; |
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/** This array holds the number of particles within each |
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* computational box of the container. */ |
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int *co; |
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/** This array holds the maximum amount of particle memory for |
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* each computational box of the container. If the number of |
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* particles in a particular box ever approaches this limit, |
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* more is allocated using the add_particle_memory() function. |
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*/ |
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int *mem; |
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/** The amount of memory in the array structure for each |
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* particle. This is set to 3 when the basic class is |
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* initialized, so that the array holds (x,y,z) positions. If |
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* the container class is initialized as part of the derived |
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* class container_poly, then this is set to 4, to also hold |
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* the particle radii. */ |
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const int ps; |
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container_base(double ax_,double bx_,double ay_,double by_,double az_,double bz_, |
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int nx_,int ny_,int nz_,bool xperiodic_,bool yperiodic_,bool zperiodic_, |
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int init_mem,int ps_); |
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~container_base(); |
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bool point_inside(double x,double y,double z); |
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void region_count(); |
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/** Initializes the Voronoi cell prior to a compute_cell |
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* operation for a specific particle being carried out by a |
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* voro_compute class. The cell is initialized to fill the |
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* entire container. For non-periodic coordinates, this is set |
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* by the position of the walls. For periodic coordinates, the |
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* space is equally divided in either direction from the |
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* particle's initial position. Plane cuts made by any walls |
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* that have been added are then applied to the cell. |
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* \param[in,out] c a reference to a voronoicell object. |
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* \param[in] ijk the block that the particle is within. |
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* \param[in] q the index of the particle within its block. |
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* \param[in] (ci,cj,ck) the coordinates of the block in the |
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* container coordinate system. |
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* \param[out] (i,j,k) the coordinates of the test block |
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* relative to the voro_compute |
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* coordinate system. |
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* \param[out] (x,y,z) the position of the particle. |
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* \param[out] disp a block displacement used internally by the |
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* compute_cell routine. |
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* \return False if the plane cuts applied by walls completely |
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* removed the cell, true otherwise. */ |
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template<class v_cell> |
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inline bool initialize_voronoicell(v_cell &c,int ijk,int q,int ci,int cj,int ck, |
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int &i,int &j,int &k,double &x,double &y,double &z,int &disp) { |
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double x1,x2,y1,y2,z1,z2,*pp=p[ijk]+ps*q; |
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x=*(pp++);y=*(pp++);z=*pp; |
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if(xperiodic) {x1=-(x2=0.5*(bx-ax));i=nx;} else {x1=ax-x;x2=bx-x;i=ci;} |
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if(yperiodic) {y1=-(y2=0.5*(by-ay));j=ny;} else {y1=ay-y;y2=by-y;j=cj;} |
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if(zperiodic) {z1=-(z2=0.5*(bz-az));k=nz;} else {z1=az-z;z2=bz-z;k=ck;} |
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c.init(x1,x2,y1,y2,z1,z2); |
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if(!apply_walls(c,x,y,z)) return false; |
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disp=ijk-i-nx*(j+ny*k); |
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return true; |
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} |
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/** Initializes parameters for a find_voronoi_cell call within |
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* the voro_compute template. |
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* \param[in] (ci,cj,ck) the coordinates of the test block in |
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* the container coordinate system. |
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* \param[in] ijk the index of the test block |
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* \param[out] (i,j,k) the coordinates of the test block |
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* relative to the voro_compute |
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* coordinate system. |
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* \param[out] disp a block displacement used internally by the |
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* find_voronoi_cell routine. */ |
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inline void initialize_search(int ci,int cj,int ck,int ijk,int &i,int &j,int &k,int &disp) { |
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i=xperiodic?nx:ci; |
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j=yperiodic?ny:cj; |
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k=zperiodic?nz:ck; |
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disp=ijk-i-nx*(j+ny*k); |
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} |
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/** Returns the position of a particle currently being computed |
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* relative to the computational block that it is within. It is |
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* used to select the optimal worklist entry to use. |
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* \param[in] (x,y,z) the position of the particle. |
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* \param[in] (ci,cj,ck) the block that the particle is within. |
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* \param[out] (fx,fy,fz) the position relative to the block. |
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*/ |
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inline void frac_pos(double x,double y,double z,double ci,double cj,double ck, |
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double &fx,double &fy,double &fz) { |
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fx=x-ax-boxx*ci; |
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fy=y-ay-boxy*cj; |
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fz=z-az-boxz*ck; |
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} |
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/** Calculates the index of block in the container structure |
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* corresponding to given coordinates. |
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* \param[in] (ci,cj,ck) the coordinates of the original block |
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* in the current computation, relative |
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* to the container coordinate system. |
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* \param[in] (ei,ej,ek) the displacement of the current block |
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* from the original block. |
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* \param[in,out] (qx,qy,qz) the periodic displacement that |
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* must be added to the particles |
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* within the computed block. |
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* \param[in] disp a block displacement used internally by the |
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* find_voronoi_cell and compute_cell routines. |
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* \return The block index. */ |
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inline int region_index(int ci,int cj,int ck,int ei,int ej,int ek,double &qx,double &qy,double &qz,int &disp) { |
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if(xperiodic) {if(ci+ei<nx) {ei+=nx;qx=-(bx-ax);} else if(ci+ei>=(nx<<1)) {ei-=nx;qx=bx-ax;} else qx=0;} |
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if(yperiodic) {if(cj+ej<ny) {ej+=ny;qy=-(by-ay);} else if(cj+ej>=(ny<<1)) {ej-=ny;qy=by-ay;} else qy=0;} |
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if(zperiodic) {if(ck+ek<nz) {ek+=nz;qz=-(bz-az);} else if(ck+ek>=(nz<<1)) {ek-=nz;qz=bz-az;} else qz=0;} |
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return disp+ei+nx*(ej+ny*ek); |
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} |
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void draw_domain_gnuplot(FILE *fp=stdout); |
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/** Draws an outline of the domain in Gnuplot format. |
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* \param[in] filename the filename to write to. */ |
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inline void draw_domain_gnuplot(const char* filename) { |
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FILE *fp=safe_fopen(filename,"w"); |
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draw_domain_gnuplot(fp); |
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fclose(fp); |
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} |
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void draw_domain_pov(FILE *fp=stdout); |
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/** Draws an outline of the domain in Gnuplot format. |
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* \param[in] filename the filename to write to. */ |
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inline void draw_domain_pov(const char* filename) { |
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FILE *fp=safe_fopen(filename,"w"); |
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draw_domain_pov(fp); |
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fclose(fp); |
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} |
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/** Sums up the total number of stored particles. |
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* \return The number of particles. */ |
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inline int total_particles() { |
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int tp=*co; |
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for(int *cop=co+1;cop<co+nxyz;cop++) tp+=*cop; |
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return tp; |
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} |
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protected: |
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void add_particle_memory(int i); |
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bool put_locate_block(int &ijk,double &x,double &y,double &z); |
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inline bool put_remap(int &ijk,double &x,double &y,double &z); |
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inline bool remap(int &ai,int &aj,int &ak,int &ci,int &cj,int &ck,double &x,double &y,double &z,int &ijk); |
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}; |
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/** \brief Extension of the container_base class for computing regular Voronoi |
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* tessellations. |
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* |
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* This class is an extension of the container_base class that has routines |
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* specifically for computing the regular Voronoi tessellation with no |
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* dependence on particle radii. */ |
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class container : public container_base, public radius_mono { |
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public: |
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container(double ax_,double bx_,double ay_,double by_,double az_,double bz_, |
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int nx_,int ny_,int nz_,bool xperiodic_,bool yperiodic_,bool zperiodic_,int init_mem); |
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void clear(); |
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void put(int n,double x,double y,double z); |
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void put(particle_order &vo,int n,double x,double y,double z); |
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void import(FILE *fp=stdin); |
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void import(particle_order &vo,FILE *fp=stdin); |
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/** Imports a list of particles from an open file stream into |
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* the container. Entries of four numbers (Particle ID, x |
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* position, y position, z position) are searched for. If the |
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* file cannot be successfully read, then the routine causes a |
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* fatal error. |
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* \param[in] filename the name of the file to open and read |
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* from. */ |
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inline void import(const char* filename) { |
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FILE *fp=safe_fopen(filename,"r"); |
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import(fp); |
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fclose(fp); |
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} |
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/** Imports a list of particles from an open file stream into |
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* the container. Entries of four numbers (Particle ID, x |
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* position, y position, z position) are searched for. In |
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* addition, the order in which particles are read is saved |
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* into an ordering class. If the file cannot be successfully |
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* read, then the routine causes a fatal error. |
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* \param[in,out] vo the ordering class to use. |
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* \param[in] filename the name of the file to open and read |
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* from. */ |
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inline void import(particle_order &vo,const char* filename) { |
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FILE *fp=safe_fopen(filename,"r"); |
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import(vo,fp); |
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fclose(fp); |
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} |
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void compute_all_cells(); |
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double sum_cell_volumes(); |
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|
|
/** Dumps particle IDs and positions to a file. |
| 323 |
|
|
* \param[in] vl the loop class to use. |
| 324 |
|
|
* \param[in] fp a file handle to write to. */ |
| 325 |
|
|
template<class c_loop> |
| 326 |
|
|
void draw_particles(c_loop &vl,FILE *fp) { |
| 327 |
|
|
double *pp; |
| 328 |
|
|
if(vl.start()) do { |
| 329 |
|
|
pp=p[vl.ijk]+3*vl.q; |
| 330 |
|
|
fprintf(fp,"%d %g %g %g\n",id[vl.ijk][vl.q],*pp,pp[1],pp[2]); |
| 331 |
|
|
} while(vl.inc()); |
| 332 |
|
|
} |
| 333 |
|
|
/** Dumps all of the particle IDs and positions to a file. |
| 334 |
|
|
* \param[in] fp a file handle to write to. */ |
| 335 |
|
|
inline void draw_particles(FILE *fp=stdout) { |
| 336 |
|
|
c_loop_all vl(*this); |
| 337 |
|
|
draw_particles(vl,fp); |
| 338 |
|
|
} |
| 339 |
|
|
/** Dumps all of the particle IDs and positions to a file. |
| 340 |
|
|
* \param[in] filename the name of the file to write to. */ |
| 341 |
|
|
inline void draw_particles(const char *filename) { |
| 342 |
|
|
FILE *fp=safe_fopen(filename,"w"); |
| 343 |
|
|
draw_particles(fp); |
| 344 |
|
|
fclose(fp); |
| 345 |
|
|
} |
| 346 |
|
|
/** Dumps particle positions in POV-Ray format. |
| 347 |
|
|
* \param[in] vl the loop class to use. |
| 348 |
|
|
* \param[in] fp a file handle to write to. */ |
| 349 |
|
|
template<class c_loop> |
| 350 |
|
|
void draw_particles_pov(c_loop &vl,FILE *fp) { |
| 351 |
|
|
double *pp; |
| 352 |
|
|
if(vl.start()) do { |
| 353 |
|
|
pp=p[vl.ijk]+3*vl.q; |
| 354 |
|
|
fprintf(fp,"// id %d\nsphere{<%g,%g,%g>,s}\n", |
| 355 |
|
|
id[vl.ijk][vl.q],*pp,pp[1],pp[2]); |
| 356 |
|
|
} while(vl.inc()); |
| 357 |
|
|
} |
| 358 |
|
|
/** Dumps all particle positions in POV-Ray format. |
| 359 |
|
|
* \param[in] fp a file handle to write to. */ |
| 360 |
|
|
inline void draw_particles_pov(FILE *fp=stdout) { |
| 361 |
|
|
c_loop_all vl(*this); |
| 362 |
|
|
draw_particles_pov(vl,fp); |
| 363 |
|
|
} |
| 364 |
|
|
/** Dumps all particle positions in POV-Ray format. |
| 365 |
|
|
* \param[in] filename the name of the file to write to. */ |
| 366 |
|
|
inline void draw_particles_pov(const char *filename) { |
| 367 |
|
|
FILE *fp=safe_fopen(filename,"w"); |
| 368 |
|
|
draw_particles_pov(fp); |
| 369 |
|
|
fclose(fp); |
| 370 |
|
|
} |
| 371 |
|
|
/** Computes Voronoi cells and saves the output in gnuplot |
| 372 |
|
|
* format. |
| 373 |
|
|
* \param[in] vl the loop class to use. |
| 374 |
|
|
* \param[in] fp a file handle to write to. */ |
| 375 |
|
|
template<class c_loop> |
| 376 |
|
|
void draw_cells_gnuplot(c_loop &vl,FILE *fp) { |
| 377 |
|
|
voronoicell c;double *pp; |
| 378 |
|
|
if(vl.start()) do if(compute_cell(c,vl)) { |
| 379 |
|
|
pp=p[vl.ijk]+ps*vl.q; |
| 380 |
|
|
c.draw_gnuplot(*pp,pp[1],pp[2],fp); |
| 381 |
|
|
} while(vl.inc()); |
| 382 |
|
|
} |
| 383 |
|
|
/** Computes all Voronoi cells and saves the output in gnuplot |
| 384 |
|
|
* format. |
| 385 |
|
|
* \param[in] fp a file handle to write to. */ |
| 386 |
|
|
inline void draw_cells_gnuplot(FILE *fp=stdout) { |
| 387 |
|
|
c_loop_all vl(*this); |
| 388 |
|
|
draw_cells_gnuplot(vl,fp); |
| 389 |
|
|
} |
| 390 |
|
|
/** Computes all Voronoi cells and saves the output in gnuplot |
| 391 |
|
|
* format. |
| 392 |
|
|
* \param[in] filename the name of the file to write to. */ |
| 393 |
|
|
inline void draw_cells_gnuplot(const char *filename) { |
| 394 |
|
|
FILE *fp=safe_fopen(filename,"w"); |
| 395 |
|
|
draw_cells_gnuplot(fp); |
| 396 |
|
|
fclose(fp); |
| 397 |
|
|
} |
| 398 |
|
|
/** Computes Voronoi cells and saves the output in POV-Ray |
| 399 |
|
|
* format. |
| 400 |
|
|
* \param[in] vl the loop class to use. |
| 401 |
|
|
* \param[in] fp a file handle to write to. */ |
| 402 |
|
|
template<class c_loop> |
| 403 |
|
|
void draw_cells_pov(c_loop &vl,FILE *fp) { |
| 404 |
|
|
voronoicell c;double *pp; |
| 405 |
|
|
if(vl.start()) do if(compute_cell(c,vl)) { |
| 406 |
|
|
fprintf(fp,"// cell %d\n",id[vl.ijk][vl.q]); |
| 407 |
|
|
pp=p[vl.ijk]+ps*vl.q; |
| 408 |
|
|
c.draw_pov(*pp,pp[1],pp[2],fp); |
| 409 |
|
|
} while(vl.inc()); |
| 410 |
|
|
} |
| 411 |
|
|
/** Computes all Voronoi cells and saves the output in POV-Ray |
| 412 |
|
|
* format. |
| 413 |
|
|
* \param[in] fp a file handle to write to. */ |
| 414 |
|
|
inline void draw_cells_pov(FILE *fp=stdout) { |
| 415 |
|
|
c_loop_all vl(*this); |
| 416 |
|
|
draw_cells_pov(vl,fp); |
| 417 |
|
|
} |
| 418 |
|
|
/** Computes all Voronoi cells and saves the output in POV-Ray |
| 419 |
|
|
* format. |
| 420 |
|
|
* \param[in] filename the name of the file to write to. */ |
| 421 |
|
|
inline void draw_cells_pov(const char *filename) { |
| 422 |
|
|
FILE *fp=safe_fopen(filename,"w"); |
| 423 |
|
|
draw_cells_pov(fp); |
| 424 |
|
|
fclose(fp); |
| 425 |
|
|
} |
| 426 |
|
|
/** Computes the Voronoi cells and saves customized information |
| 427 |
|
|
* about them. |
| 428 |
|
|
* \param[in] vl the loop class to use. |
| 429 |
|
|
* \param[in] format the custom output string to use. |
| 430 |
|
|
* \param[in] fp a file handle to write to. */ |
| 431 |
|
|
template<class c_loop> |
| 432 |
|
|
void print_custom(c_loop &vl,const char *format,FILE *fp) { |
| 433 |
|
|
int ijk,q;double *pp; |
| 434 |
|
|
if(contains_neighbor(format)) { |
| 435 |
|
|
voronoicell_neighbor c; |
| 436 |
|
|
if(vl.start()) do if(compute_cell(c,vl)) { |
| 437 |
|
|
ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q; |
| 438 |
|
|
c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],default_radius,fp); |
| 439 |
|
|
} while(vl.inc()); |
| 440 |
|
|
} else { |
| 441 |
|
|
voronoicell c; |
| 442 |
|
|
if(vl.start()) do if(compute_cell(c,vl)) { |
| 443 |
|
|
ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q; |
| 444 |
|
|
c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],default_radius,fp); |
| 445 |
|
|
} while(vl.inc()); |
| 446 |
|
|
} |
| 447 |
|
|
} |
| 448 |
|
|
void print_custom(const char *format,FILE *fp=stdout); |
| 449 |
|
|
void print_custom(const char *format,const char *filename); |
| 450 |
|
|
bool find_voronoi_cell(double x,double y,double z,double &rx,double &ry,double &rz,int &pid); |
| 451 |
|
|
/** Computes the Voronoi cell for a particle currently being |
| 452 |
|
|
* referenced by a loop class. |
| 453 |
|
|
* \param[out] c a Voronoi cell class in which to store the |
| 454 |
|
|
* computed cell. |
| 455 |
|
|
* \param[in] vl the loop class to use. |
| 456 |
|
|
* \return True if the cell was computed. If the cell cannot be |
| 457 |
|
|
* computed, if it is removed entirely by a wall or boundary |
| 458 |
|
|
* condition, then the routine returns false. */ |
| 459 |
|
|
template<class v_cell,class c_loop> |
| 460 |
|
|
inline bool compute_cell(v_cell &c,c_loop &vl) { |
| 461 |
|
|
return vc.compute_cell(c,vl.ijk,vl.q,vl.i,vl.j,vl.k); |
| 462 |
|
|
} |
| 463 |
|
|
/** Computes the Voronoi cell for given particle. |
| 464 |
|
|
* \param[out] c a Voronoi cell class in which to store the |
| 465 |
|
|
* computed cell. |
| 466 |
|
|
* \param[in] ijk the block that the particle is within. |
| 467 |
|
|
* \param[in] q the index of the particle within the block. |
| 468 |
|
|
* \return True if the cell was computed. If the cell cannot be |
| 469 |
|
|
* computed, if it is removed entirely by a wall or boundary |
| 470 |
|
|
* condition, then the routine returns false. */ |
| 471 |
|
|
template<class v_cell> |
| 472 |
|
|
inline bool compute_cell(v_cell &c,int ijk,int q) { |
| 473 |
|
|
int k=ijk/nxy,ijkt=ijk-nxy*k,j=ijkt/nx,i=ijkt-j*nx; |
| 474 |
|
|
return vc.compute_cell(c,ijk,q,i,j,k); |
| 475 |
|
|
} |
| 476 |
|
|
/** Computes the Voronoi cell for a ghost particle at a given |
| 477 |
|
|
* location. |
| 478 |
|
|
* \param[out] c a Voronoi cell class in which to store the |
| 479 |
|
|
* computed cell. |
| 480 |
|
|
* \param[in] (x,y,z) the location of the ghost particle. |
| 481 |
|
|
* \return True if the cell was computed. If the cell cannot be |
| 482 |
|
|
* computed, if it is removed entirely by a wall or boundary |
| 483 |
|
|
* condition, then the routine returns false. */ |
| 484 |
|
|
template<class v_cell> |
| 485 |
|
|
inline bool compute_ghost_cell(v_cell &c,double x,double y,double z) { |
| 486 |
|
|
int ijk; |
| 487 |
|
|
if(put_locate_block(ijk,x,y,z)) { |
| 488 |
|
|
double *pp=p[ijk]+3*co[ijk]++; |
| 489 |
|
|
*(pp++)=x;*(pp++)=y;*pp=z; |
| 490 |
|
|
bool q=compute_cell(c,ijk,co[ijk]-1); |
| 491 |
|
|
co[ijk]--; |
| 492 |
|
|
return q; |
| 493 |
|
|
} |
| 494 |
|
|
return false; |
| 495 |
|
|
} |
| 496 |
|
|
private: |
| 497 |
|
|
voro_compute<container> vc; |
| 498 |
|
|
friend class voro_compute<container>; |
| 499 |
|
|
}; |
| 500 |
|
|
|
| 501 |
|
|
/** \brief Extension of the container_base class for computing radical Voronoi |
| 502 |
|
|
* tessellations. |
| 503 |
|
|
* |
| 504 |
|
|
* This class is an extension of container_base class that has routines |
| 505 |
|
|
* specifically for computing the radical Voronoi tessellation that depends on |
| 506 |
|
|
* the particle radii. */ |
| 507 |
|
|
class container_poly : public container_base, public radius_poly { |
| 508 |
|
|
public: |
| 509 |
|
|
container_poly(double ax_,double bx_,double ay_,double by_,double az_,double bz_, |
| 510 |
|
|
int nx_,int ny_,int nz_,bool xperiodic_,bool yperiodic_,bool zperiodic_,int init_mem); |
| 511 |
|
|
void clear(); |
| 512 |
|
|
void put(int n,double x,double y,double z,double r); |
| 513 |
|
|
void put(particle_order &vo,int n,double x,double y,double z,double r); |
| 514 |
|
|
void import(FILE *fp=stdin); |
| 515 |
|
|
void import(particle_order &vo,FILE *fp=stdin); |
| 516 |
|
|
/** Imports a list of particles from an open file stream into |
| 517 |
|
|
* the container_poly class. Entries of five numbers (Particle |
| 518 |
|
|
* ID, x position, y position, z position, radius) are searched |
| 519 |
|
|
* for. If the file cannot be successfully read, then the |
| 520 |
|
|
* routine causes a fatal error. |
| 521 |
|
|
* \param[in] filename the name of the file to open and read |
| 522 |
|
|
* from. */ |
| 523 |
|
|
inline void import(const char* filename) { |
| 524 |
|
|
FILE *fp=safe_fopen(filename,"r"); |
| 525 |
|
|
import(fp); |
| 526 |
|
|
fclose(fp); |
| 527 |
|
|
} |
| 528 |
|
|
/** Imports a list of particles from an open file stream into |
| 529 |
|
|
* the container_poly class. Entries of five numbers (Particle |
| 530 |
|
|
* ID, x position, y position, z position, radius) are searched |
| 531 |
|
|
* for. In addition, the order in which particles are read is |
| 532 |
|
|
* saved into an ordering class. If the file cannot be |
| 533 |
|
|
* successfully read, then the routine causes a fatal error. |
| 534 |
|
|
* \param[in,out] vo the ordering class to use. |
| 535 |
|
|
* \param[in] filename the name of the file to open and read |
| 536 |
|
|
* from. */ |
| 537 |
|
|
inline void import(particle_order &vo,const char* filename) { |
| 538 |
|
|
FILE *fp=safe_fopen(filename,"r"); |
| 539 |
|
|
import(vo,fp); |
| 540 |
|
|
fclose(fp); |
| 541 |
|
|
} |
| 542 |
|
|
void compute_all_cells(); |
| 543 |
|
|
double sum_cell_volumes(); |
| 544 |
|
|
/** Dumps particle IDs, positions and radii to a file. |
| 545 |
|
|
* \param[in] vl the loop class to use. |
| 546 |
|
|
* \param[in] fp a file handle to write to. */ |
| 547 |
|
|
template<class c_loop> |
| 548 |
|
|
void draw_particles(c_loop &vl,FILE *fp) { |
| 549 |
|
|
double *pp; |
| 550 |
|
|
if(vl.start()) do { |
| 551 |
|
|
pp=p[vl.ijk]+4*vl.q; |
| 552 |
|
|
fprintf(fp,"%d %g %g %g %g\n",id[vl.ijk][vl.q],*pp,pp[1],pp[2],pp[3]); |
| 553 |
|
|
} while(vl.inc()); |
| 554 |
|
|
} |
| 555 |
|
|
/** Dumps all of the particle IDs, positions and radii to a |
| 556 |
|
|
* file. |
| 557 |
|
|
* \param[in] fp a file handle to write to. */ |
| 558 |
|
|
inline void draw_particles(FILE *fp=stdout) { |
| 559 |
|
|
c_loop_all vl(*this); |
| 560 |
|
|
draw_particles(vl,fp); |
| 561 |
|
|
} |
| 562 |
|
|
/** Dumps all of the particle IDs, positions and radii to a |
| 563 |
|
|
* file. |
| 564 |
|
|
* \param[in] filename the name of the file to write to. */ |
| 565 |
|
|
inline void draw_particles(const char *filename) { |
| 566 |
|
|
FILE *fp=safe_fopen(filename,"w"); |
| 567 |
|
|
draw_particles(fp); |
| 568 |
|
|
fclose(fp); |
| 569 |
|
|
} |
| 570 |
|
|
/** Dumps particle positions in POV-Ray format. |
| 571 |
|
|
* \param[in] vl the loop class to use. |
| 572 |
|
|
* \param[in] fp a file handle to write to. */ |
| 573 |
|
|
template<class c_loop> |
| 574 |
|
|
void draw_particles_pov(c_loop &vl,FILE *fp) { |
| 575 |
|
|
double *pp; |
| 576 |
|
|
if(vl.start()) do { |
| 577 |
|
|
pp=p[vl.ijk]+4*vl.q; |
| 578 |
|
|
fprintf(fp,"// id %d\nsphere{<%g,%g,%g>,%g}\n", |
| 579 |
|
|
id[vl.ijk][vl.q],*pp,pp[1],pp[2],pp[3]); |
| 580 |
|
|
} while(vl.inc()); |
| 581 |
|
|
} |
| 582 |
|
|
/** Dumps all the particle positions in POV-Ray format. |
| 583 |
|
|
* \param[in] fp a file handle to write to. */ |
| 584 |
|
|
inline void draw_particles_pov(FILE *fp=stdout) { |
| 585 |
|
|
c_loop_all vl(*this); |
| 586 |
|
|
draw_particles_pov(vl,fp); |
| 587 |
|
|
} |
| 588 |
|
|
/** Dumps all the particle positions in POV-Ray format. |
| 589 |
|
|
* \param[in] filename the name of the file to write to. */ |
| 590 |
|
|
inline void draw_particles_pov(const char *filename) { |
| 591 |
|
|
FILE *fp=safe_fopen(filename,"w"); |
| 592 |
|
|
draw_particles_pov(fp); |
| 593 |
|
|
fclose(fp); |
| 594 |
|
|
} |
| 595 |
|
|
/** Computes Voronoi cells and saves the output in gnuplot |
| 596 |
|
|
* format. |
| 597 |
|
|
* \param[in] vl the loop class to use. |
| 598 |
|
|
* \param[in] fp a file handle to write to. */ |
| 599 |
|
|
template<class c_loop> |
| 600 |
|
|
void draw_cells_gnuplot(c_loop &vl,FILE *fp) { |
| 601 |
|
|
voronoicell c;double *pp; |
| 602 |
|
|
if(vl.start()) do if(compute_cell(c,vl)) { |
| 603 |
|
|
pp=p[vl.ijk]+ps*vl.q; |
| 604 |
|
|
c.draw_gnuplot(*pp,pp[1],pp[2],fp); |
| 605 |
|
|
} while(vl.inc()); |
| 606 |
|
|
} |
| 607 |
|
|
/** Compute all Voronoi cells and saves the output in gnuplot |
| 608 |
|
|
* format. |
| 609 |
|
|
* \param[in] fp a file handle to write to. */ |
| 610 |
|
|
inline void draw_cells_gnuplot(FILE *fp=stdout) { |
| 611 |
|
|
c_loop_all vl(*this); |
| 612 |
|
|
draw_cells_gnuplot(vl,fp); |
| 613 |
|
|
} |
| 614 |
|
|
/** Compute all Voronoi cells and saves the output in gnuplot |
| 615 |
|
|
* format. |
| 616 |
|
|
* \param[in] filename the name of the file to write to. */ |
| 617 |
|
|
inline void draw_cells_gnuplot(const char *filename) { |
| 618 |
|
|
FILE *fp=safe_fopen(filename,"w"); |
| 619 |
|
|
draw_cells_gnuplot(fp); |
| 620 |
|
|
fclose(fp); |
| 621 |
|
|
} |
| 622 |
|
|
/** Computes Voronoi cells and saves the output in POV-Ray |
| 623 |
|
|
* format. |
| 624 |
|
|
* \param[in] vl the loop class to use. |
| 625 |
|
|
* \param[in] fp a file handle to write to. */ |
| 626 |
|
|
template<class c_loop> |
| 627 |
|
|
void draw_cells_pov(c_loop &vl,FILE *fp) { |
| 628 |
|
|
voronoicell c;double *pp; |
| 629 |
|
|
if(vl.start()) do if(compute_cell(c,vl)) { |
| 630 |
|
|
fprintf(fp,"// cell %d\n",id[vl.ijk][vl.q]); |
| 631 |
|
|
pp=p[vl.ijk]+ps*vl.q; |
| 632 |
|
|
c.draw_pov(*pp,pp[1],pp[2],fp); |
| 633 |
|
|
} while(vl.inc()); |
| 634 |
|
|
} |
| 635 |
|
|
/** Computes all Voronoi cells and saves the output in POV-Ray |
| 636 |
|
|
* format. |
| 637 |
|
|
* \param[in] fp a file handle to write to. */ |
| 638 |
|
|
inline void draw_cells_pov(FILE *fp=stdout) { |
| 639 |
|
|
c_loop_all vl(*this); |
| 640 |
|
|
draw_cells_pov(vl,fp); |
| 641 |
|
|
} |
| 642 |
|
|
/** Computes all Voronoi cells and saves the output in POV-Ray |
| 643 |
|
|
* format. |
| 644 |
|
|
* \param[in] filename the name of the file to write to. */ |
| 645 |
|
|
inline void draw_cells_pov(const char *filename) { |
| 646 |
|
|
FILE *fp=safe_fopen(filename,"w"); |
| 647 |
|
|
draw_cells_pov(fp); |
| 648 |
|
|
fclose(fp); |
| 649 |
|
|
} |
| 650 |
|
|
/** Computes the Voronoi cells and saves customized information |
| 651 |
|
|
* about them. |
| 652 |
|
|
* \param[in] vl the loop class to use. |
| 653 |
|
|
* \param[in] format the custom output string to use. |
| 654 |
|
|
* \param[in] fp a file handle to write to. */ |
| 655 |
|
|
template<class c_loop> |
| 656 |
|
|
void print_custom(c_loop &vl,const char *format,FILE *fp) { |
| 657 |
|
|
int ijk,q;double *pp; |
| 658 |
|
|
if(contains_neighbor(format)) { |
| 659 |
|
|
voronoicell_neighbor c; |
| 660 |
|
|
if(vl.start()) do if(compute_cell(c,vl)) { |
| 661 |
|
|
ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q; |
| 662 |
|
|
c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],pp[3],fp); |
| 663 |
|
|
} while(vl.inc()); |
| 664 |
|
|
} else { |
| 665 |
|
|
voronoicell c; |
| 666 |
|
|
if(vl.start()) do if(compute_cell(c,vl)) { |
| 667 |
|
|
ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q; |
| 668 |
|
|
c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],pp[3],fp); |
| 669 |
|
|
} while(vl.inc()); |
| 670 |
|
|
} |
| 671 |
|
|
} |
| 672 |
|
|
/** Computes the Voronoi cell for a particle currently being |
| 673 |
|
|
* referenced by a loop class. |
| 674 |
|
|
* \param[out] c a Voronoi cell class in which to store the |
| 675 |
|
|
* computed cell. |
| 676 |
|
|
* \param[in] vl the loop class to use. |
| 677 |
|
|
* \return True if the cell was computed. If the cell cannot be |
| 678 |
|
|
* computed, if it is removed entirely by a wall or boundary |
| 679 |
|
|
* condition, then the routine returns false. */ |
| 680 |
|
|
template<class v_cell,class c_loop> |
| 681 |
|
|
inline bool compute_cell(v_cell &c,c_loop &vl) { |
| 682 |
|
|
return vc.compute_cell(c,vl.ijk,vl.q,vl.i,vl.j,vl.k); |
| 683 |
|
|
} |
| 684 |
|
|
/** Computes the Voronoi cell for given particle. |
| 685 |
|
|
* \param[out] c a Voronoi cell class in which to store the |
| 686 |
|
|
* computed cell. |
| 687 |
|
|
* \param[in] ijk the block that the particle is within. |
| 688 |
|
|
* \param[in] q the index of the particle within the block. |
| 689 |
|
|
* \return True if the cell was computed. If the cell cannot be |
| 690 |
|
|
* computed, if it is removed entirely by a wall or boundary |
| 691 |
|
|
* condition, then the routine returns false. */ |
| 692 |
|
|
template<class v_cell> |
| 693 |
|
|
inline bool compute_cell(v_cell &c,int ijk,int q) { |
| 694 |
|
|
int k=ijk/nxy,ijkt=ijk-nxy*k,j=ijkt/nx,i=ijkt-j*nx; |
| 695 |
|
|
return vc.compute_cell(c,ijk,q,i,j,k); |
| 696 |
|
|
} |
| 697 |
|
|
/** Computes the Voronoi cell for a ghost particle at a given |
| 698 |
|
|
* location. |
| 699 |
|
|
* \param[out] c a Voronoi cell class in which to store the |
| 700 |
|
|
* computed cell. |
| 701 |
|
|
* \param[in] (x,y,z) the location of the ghost particle. |
| 702 |
|
|
* \param[in] r the radius of the ghost particle. |
| 703 |
|
|
* \return True if the cell was computed. If the cell cannot be |
| 704 |
|
|
* computed, if it is removed entirely by a wall or boundary |
| 705 |
|
|
* condition, then the routine returns false. */ |
| 706 |
|
|
template<class v_cell> |
| 707 |
|
|
inline bool compute_ghost_cell(v_cell &c,double x,double y,double z,double r) { |
| 708 |
|
|
int ijk; |
| 709 |
|
|
if(put_locate_block(ijk,x,y,z)) { |
| 710 |
|
|
double *pp=p[ijk]+4*co[ijk]++,tm=max_radius; |
| 711 |
|
|
*(pp++)=x;*(pp++)=y;*(pp++)=z;*pp=r; |
| 712 |
|
|
if(r>max_radius) max_radius=r; |
| 713 |
|
|
bool q=compute_cell(c,ijk,co[ijk]-1); |
| 714 |
|
|
co[ijk]--;max_radius=tm; |
| 715 |
|
|
return q; |
| 716 |
|
|
} |
| 717 |
|
|
return false; |
| 718 |
|
|
} |
| 719 |
|
|
void print_custom(const char *format,FILE *fp=stdout); |
| 720 |
|
|
void print_custom(const char *format,const char *filename); |
| 721 |
|
|
bool find_voronoi_cell(double x,double y,double z,double &rx,double &ry,double &rz,int &pid); |
| 722 |
|
|
private: |
| 723 |
|
|
voro_compute<container_poly> vc; |
| 724 |
|
|
friend class voro_compute<container_poly>; |
| 725 |
|
|
}; |
| 726 |
|
|
|
| 727 |
|
|
} |
| 728 |
|
|
|
| 729 |
|
|
#endif |
