-
Notifications
You must be signed in to change notification settings - Fork 16
/
pre_container.hh
162 lines (152 loc) · 6.25 KB
/
pre_container.hh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
// Voro++, a 3D cell-based Voronoi library
//
// Author : Chris H. Rycroft (LBL / UC Berkeley)
// Email : chr@alum.mit.edu
// Date : August 30th 2011
/** \file pre_container.hh
* \brief Header file for the pre_container and related classes. */
#ifndef VOROPP_PRE_CONTAINER_HH
#define VOROPP_PRE_CONTAINER_HH
#include <cstdio>
#include "c_loops.hh"
#include "container.hh"
namespace voro {
/** \brief A class for storing an arbitrary number of particles, prior to setting
* up a container geometry.
*
* The pre_container_base class can dynamically import and store an arbitrary
* number of particles. Once the particles have been read in, an appropriate
* container class can be set up with the optimal grid size, and the particles
* can be transferred.
*
* The pre_container_base class is not intended for direct use, but forms the
* base of the pre_container and pre_container_poly classes, that add routines
* depending on whether particle radii need to be tracked or not. */
class pre_container_base {
public:
/** The minimum x coordinate of the container. */
const double ax;
/** The maximum x coordinate of the container. */
const double bx;
/** The minimum y coordinate of the container. */
const double ay;
/** The maximum y coordinate of the container. */
const double by;
/** The minimum z coordinate of the container. */
const double az;
/** The maximum z coordinate of the container. */
const double bz;
/** A boolean value that determines if the x coordinate in
* periodic or not. */
const bool xperiodic;
/** A boolean value that determines if the y coordinate in
* periodic or not. */
const bool yperiodic;
/** A boolean value that determines if the z coordinate in
* periodic or not. */
const bool zperiodic;
void guess_optimal(int &nx,int &ny,int &nz);
pre_container_base(double ax_,double bx_,double ay_,double by_,double az_,double bz_,bool xperiodic_,bool yperiodic_,bool zperiodic_,int ps_);
~pre_container_base();
/** Calculates and returns the total number of particles stored
* within the class.
* \return The number of particles. */
inline int total_particles() {
return (end_id-pre_id)*pre_container_chunk_size+(ch_id-*end_id);
}
protected:
/** The number of doubles associated with a single particle
* (three for the standard container, four when radius
* information is stored). */
const int ps;
void new_chunk();
void extend_chunk_index();
/** The size of the chunk index. */
int index_sz;
/** A pointer to the chunk index to store the integer particle
* IDs. */
int **pre_id;
/** A pointer to the last allocated integer ID chunk. */
int **end_id;
/** A pointer to the end of the integer ID chunk index, used to
* determine when the chunk index is full. */
int **l_id;
/** A pointer to the next available slot on the current
* particle ID chunk. */
int *ch_id;
/** A pointer to the end of the current integer chunk. */
int *e_id;
/** A pointer to the chunk index to store the floating point
* information associated with particles. */
double **pre_p;
/** A pointer to the last allocated chunk of floating point
* information. */
double **end_p;
/** A pointer to the next available slot on the current
* floating point chunk. */
double *ch_p;
};
/** \brief A class for storing an arbitrary number of particles without radius
* information, prior to setting up a container geometry.
*
* The pre_container class is an extension of the pre_container_base class for
* cases when no particle radius information is available. */
class pre_container : public pre_container_base {
public:
/** The class constructor sets up the geometry of container,
* initializing the minimum and maximum coordinates in each
* direction.
* \param[in] (ax_,bx_) the minimum and maximum x coordinates.
* \param[in] (ay_,by_) the minimum and maximum y coordinates.
* \param[in] (az_,bz_) the minimum and maximum z coordinates.
* \param[in] (xperiodic_,yperiodic_,zperiodic_ ) flags setting whether the
* container is periodic in
* each coordinate direction. */
pre_container(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
bool xperiodic_,bool yperiodic_,bool zperiodic_)
: pre_container_base(ax_,bx_,ay_,by_,az_,bz_,xperiodic_,yperiodic_,zperiodic_,3) {};
void put(int n,double x,double y,double z);
void import(FILE *fp=stdin);
/** Imports particles from a file.
* \param[in] filename the name of the file to read from. */
inline void import(const char* filename) {
FILE *fp=safe_fopen(filename,"r");
import(fp);
fclose(fp);
}
void setup(container &con);
void setup(particle_order &vo,container &con);
};
/** \brief A class for storing an arbitrary number of particles with radius
* information, prior to setting up a container geometry.
*
* The pre_container_poly class is an extension of the pre_container_base class
* for cases when particle radius information is available. */
class pre_container_poly : public pre_container_base {
public:
/** The class constructor sets up the geometry of container,
* initializing the minimum and maximum coordinates in each
* direction.
* \param[in] (ax_,bx_) the minimum and maximum x coordinates.
* \param[in] (ay_,by_) the minimum and maximum y coordinates.
* \param[in] (az_,bz_) the minimum and maximum z coordinates.
* \param[in] (xperiodic_,yperiodic_,zperiodic_ ) flags setting whether the
* container is periodic in
* each coordinate direction. */
pre_container_poly(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
bool xperiodic_,bool yperiodic_,bool zperiodic_)
: pre_container_base(ax_,bx_,ay_,by_,az_,bz_,xperiodic_,yperiodic_,zperiodic_,4) {};
void put(int n,double x,double y,double z,double r);
void import(FILE *fp=stdin);
/** Imports particles from a file.
* \param[in] filename the name of the file to read from. */
inline void import(const char* filename) {
FILE *fp=safe_fopen(filename,"r");
import(fp);
fclose(fp);
}
void setup(container_poly &con);
void setup(particle_order &vo,container_poly &con);
};
}
#endif