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container.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.hh
* \brief Header file for the container_base and related classes. */
#ifndef VOROPP_CONTAINER_HH
#define VOROPP_CONTAINER_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 "rad_option.hh"
namespace
voro
{
/** \brief Pure virtual class from which wall objects are derived.
*
* This is a pure virtual class for a generic wall object. A wall object
* can be specified by deriving a new class from this and specifying the
* functions.*/
class
wall
{
public
:
virtual
~
wall
()
{}
/** A pure virtual function for testing whether a point is
* inside the wall object. */
virtual
bool
point_inside
(
double
x
,
double
y
,
double
z
)
=
0
;
/** A pure virtual function for cutting a cell without
* neighbor-tracking with a wall. */
virtual
bool
cut_cell
(
voronoicell
&
c
,
double
x
,
double
y
,
double
z
)
=
0
;
/** A pure virtual function for cutting a cell with
* neighbor-tracking enabled with a wall. */
virtual
bool
cut_cell
(
voronoicell_neighbor
&
c
,
double
x
,
double
y
,
double
z
)
=
0
;
};
/** \brief A class for storing a list of pointers to walls.
*
* This class stores a list of pointers to wall classes. It contains several
* simple routines that make use of the wall classes (such as telling whether a
* given position is inside all of the walls or not). It can be used by itself,
* but also forms part of container_base, for associating walls with this
* class. */
class
wall_list
{
public
:
/** An array holding pointers to wall objects. */
wall
**
walls
;
/** A pointer to the next free position to add a wall pointer.
*/
wall
**
wep
;
wall_list
();
~
wall_list
();
/** Adds a wall to the list.
* \param[in] w the wall to add. */
inline
void
add_wall
(
wall
*
w
)
{
if
(
wep
==
wel
)
increase_wall_memory
();
*
(
wep
++
)
=
w
;
}
/** Adds a wall to the list.
* \param[in] w a reference to the wall to add. */
inline
void
add_wall
(
wall
&
w
)
{
add_wall
(
&
w
);}
void
add_wall
(
wall_list
&
wl
);
/** Determines whether a given position is inside all of the
* walls on the list.
* \param[in] (x,y,z) the position to test.
* \return True if it is inside, false if it is outside. */
inline
bool
point_inside_walls
(
double
x
,
double
y
,
double
z
)
{
for
(
wall
**
wp
=
walls
;
wp
<
wep
;
wp
++
)
if
(
!
((
*
wp
)
->
point_inside
(
x
,
y
,
z
)))
return
false
;
return
true
;
}
/** Cuts a Voronoi cell by all of the walls currently on
* the list.
* \param[in] c a reference to the Voronoi cell class.
* \param[in] (x,y,z) the position of the cell.
* \return True if the cell still exists, false if the cell is
* deleted. */
template
<
class
c_class
>
bool
apply_walls
(
c_class
&
c
,
double
x
,
double
y
,
double
z
)
{
for
(
wall
**
wp
=
walls
;
wp
<
wep
;
wp
++
)
if
(
!
((
*
wp
)
->
cut_cell
(
c
,
x
,
y
,
z
)))
return
false
;
return
true
;
}
void
deallocate
();
protected
:
void
increase_wall_memory
();
/** A pointer to the limit of the walls array, used to
* determine when array is full. */
wall
**
wel
;
/** The current amount of memory allocated for walls. */
int
current_wall_size
;
};
/** \brief Class for representing a particle system in a three-dimensional
* rectangular box.
*
* This class represents a system of particles in a three-dimensional
* rectangular box. Any combination of non-periodic and periodic coordinates
* can be used in the three coordinate directions. The class is not intended
* for direct use, but instead forms the base of the container and
* container_poly classes that add specialized routines for computing the
* regular and radical Voronoi tessellations respectively. It contains routines
* that are commonly between these two classes, such as those for drawing the
* domain, and placing particles within the internal data structure.
*
* The class is derived from the wall_list class, which encapsulates routines
* for associating walls with the container, and the voro_base class, which
* encapsulates routines about the underlying computational grid. */
class
container_base
:
public
voro_base
,
public
wall_list
{
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
;
/** 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
;
/** 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_base
(
double
ax_
,
double
bx_
,
double
ay_
,
double
by_
,
double
az_
,
double
bz_
,
int
nx_
,
int
ny_
,
int
nz_
,
bool
xperiodic_
,
bool
yperiodic_
,
bool
zperiodic_
,
int
init_mem
,
int
ps_
);
~
container_base
();
bool
point_inside
(
double
x
,
double
y
,
double
z
);
void
region_count
();
/** 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 fill the
* entire container. For non-periodic coordinates, this is set
* by the position of the walls. For periodic coordinates, the
* space is equally divided in either direction from the
* particle's initial position. Plane cuts made by any walls
* that have been added are then applied to the cell.
* \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
)
{
double
x1
,
x2
,
y1
,
y2
,
z1
,
z2
,
*
pp
=
p
[
ijk
]
+
ps
*
q
;
x
=*
(
pp
++
);
y
=*
(
pp
++
);
z
=*
pp
;
if
(
xperiodic
)
{
x1
=-
(
x2
=
0.5
*
(
bx
-
ax
));
i
=
nx
;}
else
{
x1
=
ax
-
x
;
x2
=
bx
-
x
;
i
=
ci
;}
if
(
yperiodic
)
{
y1
=-
(
y2
=
0.5
*
(
by
-
ay
));
j
=
ny
;}
else
{
y1
=
ay
-
y
;
y2
=
by
-
y
;
j
=
cj
;}
if
(
zperiodic
)
{
z1
=-
(
z2
=
0.5
*
(
bz
-
az
));
k
=
nz
;}
else
{
z1
=
az
-
z
;
z2
=
bz
-
z
;
k
=
ck
;}
c
.
init
(
x1
,
x2
,
y1
,
y2
,
z1
,
z2
);
if
(
!
apply_walls
(
c
,
x
,
y
,
z
))
return
false
;
disp
=
ijk
-
i
-
nx
*
(
j
+
ny
*
k
);
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. */
inline
void
initialize_search
(
int
ci
,
int
cj
,
int
ck
,
int
ijk
,
int
&
i
,
int
&
j
,
int
&
k
,
int
&
disp
)
{
i
=
xperiodic
?
nx:
ci
;
j
=
yperiodic
?
ny:
cj
;
k
=
zperiodic
?
nz:
ck
;
disp
=
ijk
-
i
-
nx
*
(
j
+
ny
*
k
);
}
/** 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
-
ax
-
boxx
*
ci
;
fy
=
y
-
ay
-
boxy
*
cj
;
fz
=
z
-
az
-
boxz
*
ck
;
}
/** 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.
* \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
)
{
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
;}
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
;}
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
;}
return
disp
+
ei
+
nx
*
(
ej
+
ny
*
ek
);
}
void
draw_domain_gnuplot
(
FILE
*
fp
=
stdout
);
/** Draws an outline of the domain in Gnuplot format.
* \param[in] filename the filename to write to. */
inline
void
draw_domain_gnuplot
(
const
char
*
filename
)
{
FILE
*
fp
=
safe_fopen
(
filename
,
"w"
);
draw_domain_gnuplot
(
fp
);
fclose
(
fp
);
}
void
draw_domain_pov
(
FILE
*
fp
=
stdout
);
/** Draws an outline of the domain in Gnuplot format.
* \param[in] filename the filename to write to. */
inline
void
draw_domain_pov
(
const
char
*
filename
)
{
FILE
*
fp
=
safe_fopen
(
filename
,
"w"
);
draw_domain_pov
(
fp
);
fclose
(
fp
);
}
/** Sums up the total number of stored particles.
* \return The number of particles. */
inline
int
total_particles
()
{
int
tp
=*
co
;
for
(
int
*
cop
=
co
+
1
;
cop
<
co
+
nxyz
;
cop
++
)
tp
+=*
cop
;
return
tp
;
}
protected
:
void
add_particle_memory
(
int
i
);
inline
bool
put_locate_block
(
int
&
ijk
,
double
&
x
,
double
&
y
,
double
&
z
);
inline
bool
put_remap
(
int
&
ijk
,
double
&
x
,
double
&
y
,
double
&
z
);
inline
bool
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_base class for computing regular Voronoi
* tessellations.
*
* This class is an extension of the container_base class that has routines
* specifically for computing the regular Voronoi tessellation with no
* dependence on particle radii. */
class
container
:
public
container_base
,
public
radius_mono
{
public
:
container
(
double
ax_
,
double
bx_
,
double
ay_
,
double
by_
,
double
az_
,
double
bz_
,
int
nx_
,
int
ny_
,
int
nz_
,
bool
xperiodic_
,
bool
yperiodic_
,
bool
zperiodic_
,
int
init_mem
);
void
clear
();
void
put
(
int
n
,
double
x
,
double
y
,
double
z
);
void
put
(
particle_order
&
vo
,
int
n
,
double
x
,
double
y
,
double
z
);
void
import
(
FILE
*
fp
=
stdin
);
void
import
(
particle_order
&
vo
,
FILE
*
fp
=
stdin
);
/** 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
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
\n
sphere{<%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
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
vl
(
*
this
);
draw_cells_gnuplot
(
vl
,
fp
);
}
/** Computes 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
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, if it is removed entirely by a wall or boundary
* condition, 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, if it is removed entirely by a wall or boundary
* condition, then the routine returns false. */
template
<
class
v_cell
>
inline
bool
compute_cell
(
v_cell
&
c
,
int
ijk
,
int
q
)
{
int
k
=
ijk
/
nxy
,
ijkt
=
ijk
-
nxy
*
k
,
j
=
ijkt
/
nx
,
i
=
ijkt
-
j
*
nx
;
return
vc
.
compute_cell
(
c
,
ijk
,
q
,
i
,
j
,
k
);
}
private
:
voro_compute
<
container
>
vc
;
friend
class
voro_compute
<
container
>
;
};
/** \brief Extension of the container_base class for computing radical Voronoi
* tessellations.
*
* This class is an extension of container_base class that has routines
* specifically for computing the radical Voronoi tessellation that depends on
* the particle radii. */
class
container_poly
:
public
container_base
,
public
radius_poly
{
public
:
container_poly
(
double
ax_
,
double
bx_
,
double
ay_
,
double
by_
,
double
az_
,
double
bz_
,
int
nx_
,
int
ny_
,
int
nz_
,
bool
xperiodic_
,
bool
yperiodic_
,
bool
zperiodic_
,
int
init_mem
);
void
clear
();
void
put
(
int
n
,
double
x
,
double
y
,
double
z
,
double
r
);
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
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
\n
sphere{<%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
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
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
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, if it is removed entirely by a wall or boundary
* condition, 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, if it is removed entirely by a wall or boundary
* condition, then the routine returns false. */
template
<
class
v_cell
>
inline
bool
compute_cell
(
v_cell
&
c
,
int
ijk
,
int
q
)
{
int
k
=
ijk
/
nxy
,
ijkt
=
ijk
-
nxy
*
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_poly
>
vc
;
friend
class
voro_compute
<
container_poly
>
;
};
}
#endif
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