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manifold_thylakoid.cpp
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Sun, Sep 22, 09:12
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Tue, Sep 24, 09:12 (2 d)
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rLAMMPS lammps
manifold_thylakoid.cpp
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#include "manifold_thylakoid.h"
#include <math.h>
#include "comm.h"
#include "domain.h"
// For some checks regarding the simulation box.
#include "error.h"
#define MANIFOLD_THYLAKOID_DEBUG
using
namespace
LAMMPS_NS
;
using
namespace
user_manifold
;
manifold_thylakoid
::
manifold_thylakoid
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
manifold
(
lmp
)
{
// You can NOT depend on proper construction of the domains in
// the constructor, because the params are set by the function that
// calls the factory-construction method. Instead, the constructing
// fix should call post_param_init();
}
manifold_thylakoid
::~
manifold_thylakoid
()
{
for
(
std
::
size_t
i
=
0
;
i
<
parts
.
size
();
++
i
){
delete
parts
[
i
];
}
}
void
manifold_thylakoid
::
post_param_init
()
{
// Set coefficients:
lT
=
3
;
// Radius of cylinder edges of stacks
LT
=
15
;
// Size of faces of cylinder stacks
pad
=
3
;
// Padding to prevent improper look-ups
wB
=
3.0
;
LB
=
10.0
;
lB
=
3.0
;
wB
=
params
[
0
];
LB
=
params
[
1
];
lB
=
params
[
2
];
if
(
comm
->
me
==
0
){
fprintf
(
screen
,
"My params are now: lT = %f, LT = %f, pad = %f, "
"wB = %f, LB = %f, lB = %f
\n
"
,
lT
,
LT
,
pad
,
wB
,
LB
,
lB
);
fprintf
(
screen
,
"Calling init_domains() from post_param_init().
\n
"
);
}
init_domains
();
checkup
();
}
void
manifold_thylakoid
::
checkup
()
{
if
(
comm
->
me
==
0
){
fprintf
(
screen
,
"This is checkup of thylakoid %p
\n
"
,
this
);
fprintf
(
screen
,
"I have %ld parts. They are:
\n
"
,
parts
.
size
());
for
(
int
i
=
0
;
i
<
parts
.
size
();
++
i
){
fprintf
(
screen
,
"[%f, %f] x [%f, %f] x [%f, %f]
\n
"
,
parts
[
i
]
->
xlo
,
parts
[
i
]
->
xhi
,
parts
[
i
]
->
ylo
,
parts
[
i
]
->
yhi
,
parts
[
i
]
->
zlo
,
parts
[
i
]
->
zhi
);
}
fprintf
(
screen
,
"My params are:
\n
"
);
for
(
int
i
=
0
;
i
<
NPARAMS
;
++
i
){
fprintf
(
screen
,
"%f
\n
"
,
params
[
i
]);
}
}
}
double
manifold_thylakoid
::
g
(
const
double
*
x
)
{
int
err
=
0
;
std
::
size_t
idx
;
thyla_part
*
p
=
get_thyla_part
(
x
,
&
err
,
&
idx
);
if
(
err
){
char
msg
[
2048
];
sprintf
(
msg
,
"Error getting thyla_part for x = (%f, %f, %f)"
,
x
[
0
],
x
[
1
],
x
[
2
]);
error
->
one
(
FLERR
,
msg
);
}
double
con_val
=
p
->
g
(
x
);
if
(
ISFINITE
(
con_val
)
){
return
con_val
;
}
else
{
char
msg
[
2048
];
sprintf
(
msg
,
"Error, thyla_part of type %d returned %f as constraint val!"
,
p
->
type
,
con_val
);
error
->
one
(
FLERR
,
msg
);
return
0
;
}
}
void
manifold_thylakoid
::
n
(
const
double
*
x
,
double
*
n
)
{
int
err
=
0
;
std
::
size_t
idx
;
thyla_part
*
p
=
get_thyla_part
(
x
,
&
err
,
&
idx
);
if
(
err
){
char
msg
[
2048
];
sprintf
(
msg
,
"Error getting thyla_part for x = (%f, %f, %f)"
,
x
[
0
],
x
[
1
],
x
[
2
]);
error
->
one
(
FLERR
,
msg
);
}
p
->
n
(
x
,
n
);
if
(
ISFINITE
(
n
[
0
])
&&
ISFINITE
(
n
[
1
])
&&
ISFINITE
(
n
[
2
])
){
return
;
}
else
{
char
msg
[
2048
];
sprintf
(
msg
,
"Error, thyla_part of type %d returned (%f,%f,%f) as gradient!"
,
p
->
type
,
n
[
0
],
n
[
1
],
n
[
2
]);
error
->
one
(
FLERR
,
msg
);
}
}
thyla_part
*
manifold_thylakoid
::
get_thyla_part
(
const
double
*
x
,
int
*
err_flag
,
std
::
size_t
*
idx
)
{
for
(
std
::
size_t
i
=
0
;
i
<
parts
.
size
();
++
i
){
thyla_part
*
p
=
parts
[
i
];
if
(
is_in_domain
(
p
,
x
)
){
if
(
idx
!=
NULL
)
*
idx
=
i
;
return
p
;
}
}
char
msg
[
2048
];
sprintf
(
msg
,
"Could not find thyla_part for x = (%f,%f,%f)"
,
x
[
0
],
x
[
1
],
x
[
2
]);
error
->
one
(
FLERR
,
msg
);
return
NULL
;
}
void
manifold_thylakoid
::
init_domains
()
{
if
(
wB
+
2
*
lB
>
LT
){
char
msg
[
2048
];
sprintf
(
msg
,
"LT = %f not large enough to accomodate bridge with "
"wB = %f and lB = %f! %f > %f
\n
"
,
LT
,
wB
,
lB
,
wB
+
2
*
lB
,
LT
);
error
->
one
(
FLERR
,
msg
);
}
// Determine some constant coordinates:
x0
=
-
(
0.5
*
LB
+
lB
+
lT
+
LT
+
lT
+
pad
);
y0
=
-
(
0.5
*
LT
+
lT
+
pad
);
z0
=
-
15
;
#ifdef MANIFOLD_THYLAKOID_DEBUG
if
(
comm
->
me
==
0
){
fprintf
(
screen
,
"x0, y0, z0 = %f, %f, %f
\n
"
,
x0
,
y0
,
z0
);
}
#endif
// MANIFOLD_THYLAKOID_DEBUG
#ifndef USE_PHONY_LAMMPS
if
(
x0
<
domain
->
boxlo
[
0
]
){
char
msg
[
2048
];
sprintf
(
msg
,
"Thylakoid expects xlo of at most %f, but found %f"
,
x0
,
domain
->
boxlo
[
0
]);
error
->
one
(
FLERR
,
msg
);
}
if
(
y0
<
domain
->
boxlo
[
1
]
){
char
msg
[
2048
];
sprintf
(
msg
,
"Thylakoid expects ylo of at most %f, but found %f"
,
y0
,
domain
->
boxlo
[
1
]);
error
->
one
(
FLERR
,
msg
);
}
#endif
// Add some padding to prevent improper lookups.
z0
-=
pad
;
x1
=
-
x0
;
y1
=
-
y0
;
z1
=
-
z0
;
Lx
=
x1
-
x0
;
Ly
=
y1
-
y0
;
Lz
=
z1
-
z0
;
#ifndef USE_PHONY_LAMMPS
char
msg
[
2048
];
if
(
x1
>
domain
->
boxhi
[
0
]){
sprintf
(
msg
,
"Expected xhi larger than current box has: %f > %f"
,
x1
,
domain
->
boxhi
[
0
]);
error
->
one
(
FLERR
,
msg
);
}
if
(
y1
>
domain
->
boxhi
[
1
]){
sprintf
(
msg
,
"Expected yhi larger than current box has: %f > %f"
,
y1
,
domain
->
boxhi
[
1
]);
error
->
one
(
FLERR
,
msg
);
}
// if(z1 > domain->boxhi[2]){
// sprintf(msg,"Expected zhi larger than current box has: %f > %f",
// z1, domain->boxhi[2]);
// error->one(FLERR,msg);
// }
#endif
// Create and add the manifold parts to the array.
thyla_part
*
p
;
// Determine coordinates of domain boundaries and centres of "mass":
thyla_part_geom
cllb
,
cllt
,
clrb
,
clrt
;
// Left thylakoid cylinder parts
thyla_part_geom
pll
,
plb
,
plt
,
plr
;
// Left thylakoid plane parts
thyla_part_geom
crlb
,
crlt
,
crrb
,
crrt
;
// Right thylakoid cylinder parts
thyla_part_geom
prl
,
prb
,
prt
,
prr
;
// Right thylakoid plane parts
thyla_part_geom
bl
,
br
,
bc
;
// Bridge left, right connectors and cylinder.
// The bridge is three parts.
// 1. A connector between the right face of the left grana and a cylinder
// 2. A connector between the left face of the right grana and a cylinder
// 3. The aforementioned cylinder.
// 1.:
// Args: pt, X0, R0, R, x0, y0, z0, sign
double
rB
=
0.5
*
wB
;
double
Reff
=
rB
+
lB
;
double
safety_fac
=
1.0
;
bl
.
pt
[
0
]
=
-
0.5
*
LB
;
bl
.
pt
[
1
]
=
0
;
bl
.
pt
[
2
]
=
0
;
bl
.
lo
[
0
]
=
bl
.
pt
[
0
]
-
safety_fac
*
lB
;
bl
.
lo
[
1
]
=
-
(
1.0
+
safety_fac
)
*
Reff
;
bl
.
lo
[
2
]
=
-
(
1.0
+
safety_fac
)
*
Reff
;
bl
.
hi
[
0
]
=
bl
.
pt
[
0
];
bl
.
hi
[
1
]
=
(
1.0
+
safety_fac
)
*
Reff
;
bl
.
hi
[
2
]
=
(
1.0
+
safety_fac
)
*
Reff
;
// double X0, double R0, double R, double s,
#ifdef MANIFOLD_THYLAKOID_DEBUG
if
(
comm
->
me
==
0
){
fprintf
(
screen
,
"x0, r0, R = %f, %f, %f
\n
"
,
bl
.
pt
[
0
],
rB
,
lB
);
}
#endif
// MANIFOLD_THYLAKOID_DEBUG
p
=
make_cyl_to_plane_part
(
bl
.
pt
[
0
],
rB
,
lB
,
-
1
,
bl
.
pt
);
set_domain
(
p
,
bl
.
lo
,
bl
.
hi
);
parts
.
push_back
(
p
);
// 2.:
br
.
pt
[
0
]
=
0.5
*
LB
;
br
.
pt
[
1
]
=
0
;
br
.
pt
[
2
]
=
0
;
br
.
lo
[
0
]
=
br
.
pt
[
0
];
br
.
lo
[
1
]
=
-
(
1.0
+
safety_fac
)
*
Reff
;
br
.
lo
[
2
]
=
-
(
1.0
+
safety_fac
)
*
Reff
;
br
.
hi
[
0
]
=
br
.
pt
[
0
]
+
safety_fac
*
lB
;
br
.
hi
[
1
]
=
(
1.0
+
safety_fac
)
*
Reff
;
br
.
hi
[
2
]
=
(
1.0
+
safety_fac
)
*
Reff
;
// double X0, double R0, double R, double s,
#ifdef MANIFOLD_THYLAKOID_DEBUG
if
(
comm
->
me
==
0
){
fprintf
(
screen
,
"x0, r0, R = %f, %f, %f
\n
"
,
br
.
pt
[
0
],
rB
,
lB
);
}
#endif
// MANIFOLD_THYLAKOID_DEBUG
p
=
make_cyl_to_plane_part
(
br
.
pt
[
0
],
rB
,
lB
,
1
,
br
.
pt
);
set_domain
(
p
,
br
.
lo
,
br
.
hi
);
parts
.
push_back
(
p
);
// 3.:
// Cylinder in between:
bc
.
pt
[
0
]
=
0
;
bc
.
pt
[
1
]
=
0
;
bc
.
pt
[
2
]
=
0
;
bc
.
lo
[
0
]
=
bl
.
pt
[
0
];
bc
.
lo
[
1
]
=
-
Reff
;
bc
.
lo
[
2
]
=
-
Reff
;
bc
.
hi
[
0
]
=
br
.
pt
[
0
];
bc
.
hi
[
1
]
=
Reff
;
bc
.
hi
[
2
]
=
Reff
;
p
=
make_cyl_part
(
0
,
1
,
1
,
bc
.
pt
,
rB
);
set_domain
(
p
,
bc
.
lo
,
bc
.
hi
);
#ifdef MANIFOLD_THYLAKOID_DEBUG
if
(
comm
->
me
==
0
){
fprintf
(
screen
,
"Cylinder lives on [ %f x %f ] x [ %f x %f ] x [ %f x %f]
\n
"
,
bc
.
lo
[
0
],
bc
.
hi
[
0
],
bc
.
lo
[
1
],
bc
.
hi
[
1
],
bc
.
lo
[
2
],
bc
.
hi
[
2
]);
}
#endif
// MANIFOLD_THYLAKOID_DEBUG
parts
.
push_back
(
p
);
// The stack on the left:
cllb
.
lo
[
0
]
=
x0
;
cllb
.
lo
[
1
]
=
y0
;
cllb
.
lo
[
2
]
=
z0
;
cllb
.
pt
[
0
]
=
x0
+
pad
+
lT
;
cllb
.
pt
[
1
]
=
y0
+
pad
+
lT
;
cllb
.
pt
[
2
]
=
0
;
cllb
.
hi
[
0
]
=
cllb
.
pt
[
0
];
cllb
.
hi
[
1
]
=
cllb
.
pt
[
1
];
cllb
.
hi
[
2
]
=
z1
;
p
=
make_cyl_part
(
1
,
1
,
0
,
cllb
.
pt
,
lT
);
set_domain
(
p
,
cllb
.
lo
,
cllb
.
hi
);
parts
.
push_back
(
p
);
// left left top cylinder
cllt
=
cllb
;
cllt
.
lo
[
1
]
=
y1
-
pad
-
lT
;
cllt
.
hi
[
1
]
=
y1
;
cllt
.
pt
[
1
]
=
cllb
.
pt
[
1
]
+
LT
;
p
=
make_cyl_part
(
1
,
1
,
0
,
cllt
.
pt
,
lT
);
set_domain
(
p
,
cllt
.
lo
,
cllt
.
hi
);
parts
.
push_back
(
p
);
// left right bottom cylinder
clrb
=
cllb
;
clrb
.
pt
[
0
]
+=
LT
;
clrb
.
lo
[
0
]
=
clrb
.
pt
[
0
];
clrb
.
hi
[
0
]
=
clrb
.
lo
[
0
]
+
lT
+
lB
;
p
=
make_cyl_part
(
1
,
1
,
0
,
clrb
.
pt
,
lT
);
set_domain
(
p
,
clrb
.
lo
,
clrb
.
hi
);
parts
.
push_back
(
p
);
// left right top cylinder
clrt
=
clrb
;
clrt
.
pt
[
1
]
+=
LT
;
clrt
.
lo
[
1
]
=
y1
-
pad
-
lT
;
clrt
.
hi
[
1
]
=
y1
;
p
=
make_cyl_part
(
1
,
1
,
0
,
clrt
.
pt
,
lT
);
set_domain
(
p
,
clrt
.
lo
,
clrt
.
hi
);
parts
.
push_back
(
p
);
// left left plane
pll
.
pt
[
0
]
=
x0
+
pad
;
pll
.
pt
[
1
]
=
0
;
pll
.
pt
[
2
]
=
0
;
pll
.
lo
[
0
]
=
x0
;
pll
.
lo
[
1
]
=
cllb
.
pt
[
1
];
pll
.
lo
[
2
]
=
z0
;
pll
.
hi
[
0
]
=
pll
.
lo
[
0
]
+
pad
+
lT
;
pll
.
hi
[
1
]
=
pll
.
lo
[
1
]
+
LT
;
pll
.
hi
[
2
]
=
z1
;
p
=
make_plane_part
(
1
,
0
,
0
,
pll
.
pt
);
set_domain
(
p
,
pll
.
lo
,
pll
.
hi
);
parts
.
push_back
(
p
);
// left bottom plane
plb
.
pt
[
0
]
=
x0
+
pad
+
lT
+
0.5
*
LT
;
plb
.
pt
[
1
]
=
y0
+
pad
;
plb
.
pt
[
2
]
=
0
;
plb
.
lo
[
0
]
=
x0
+
pad
+
lT
;
plb
.
lo
[
1
]
=
y0
;
plb
.
lo
[
2
]
=
z0
;
plb
.
hi
[
0
]
=
plb
.
lo
[
0
]
+
LT
;
plb
.
hi
[
1
]
=
plb
.
lo
[
1
]
+
pad
+
lT
;
plb
.
hi
[
2
]
=
z1
;
p
=
make_plane_part
(
0
,
1
,
0
,
plb
.
pt
);
set_domain
(
p
,
plb
.
lo
,
plb
.
hi
);
parts
.
push_back
(
p
);
// left top plane
plt
=
plb
;
plt
.
lo
[
1
]
=
cllb
.
pt
[
1
]
+
LT
;
plt
.
hi
[
1
]
=
y1
;
plt
.
pt
[
1
]
=
y1
-
pad
;
p
=
make_plane_part
(
0
,
1
,
0
,
plt
.
pt
);
set_domain
(
p
,
plt
.
lo
,
plt
.
hi
);
parts
.
push_back
(
p
);
// left right plane
plr
=
pll
;
plr
.
lo
[
0
]
=
bl
.
lo
[
0
]
-
0.5
;
plr
.
lo
[
1
]
=
y0
-
pad
;
plr
.
hi
[
0
]
=
bl
.
lo
[
0
]
+
0.5
;
plr
.
hi
[
1
]
=
y1
+
pad
;
plr
.
pt
[
0
]
=
bl
.
pt
[
0
]
-
lB
;
plr
.
pt
[
1
]
=
0.0
;
plr
.
pt
[
2
]
=
0.0
;
plr
.
hi
[
2
]
=
z1
+
pad
;
plr
.
lo
[
2
]
=
z0
-
pad
;
p
=
make_plane_part
(
1
,
0
,
0
,
plr
.
pt
);
set_domain
(
p
,
plr
.
lo
,
plr
.
hi
);
parts
.
push_back
(
p
);
// Check if this plane lines up with bl:
if
(
fabs
(
plr
.
pt
[
0
]
-
bl
.
pt
[
0
]
+
lB
)
>
1e-8
){
char
msg
[
2048
];
sprintf
(
msg
,
"Origins of plane left right and bridge left misaligned! %f != %f!
\n
"
,
plr
.
pt
[
0
],
bl
.
pt
[
0
]
-
lB
);
error
->
one
(
FLERR
,
msg
);
}
// Now, for the right stack, you can mirror the other...
// To mirror them you need to invert lo[0] and hi[0] and flip their sign.
thyla_part_geom
::
mirror
(
thyla_part_geom
::
DIR_X
,
&
crlb
,
&
cllb
);
p
=
make_cyl_part
(
1
,
1
,
0
,
crlb
.
pt
,
lT
);
set_domain
(
p
,
crlb
.
lo
,
crlb
.
hi
);
parts
.
push_back
(
p
);
thyla_part_geom
::
mirror
(
thyla_part_geom
::
DIR_X
,
&
crlt
,
&
cllt
);
p
=
make_cyl_part
(
1
,
1
,
0
,
crlt
.
pt
,
lT
);
set_domain
(
p
,
crlt
.
lo
,
crlt
.
hi
);
parts
.
push_back
(
p
);
thyla_part_geom
::
mirror
(
thyla_part_geom
::
DIR_X
,
&
crrb
,
&
clrb
);
p
=
make_cyl_part
(
1
,
1
,
0
,
crrb
.
pt
,
lT
);
set_domain
(
p
,
crrb
.
lo
,
crrb
.
hi
);
parts
.
push_back
(
p
);
thyla_part_geom
::
mirror
(
thyla_part_geom
::
DIR_X
,
&
crrt
,
&
clrt
);
p
=
make_cyl_part
(
1
,
1
,
0
,
crrt
.
pt
,
lT
);
set_domain
(
p
,
crrt
.
lo
,
crrt
.
hi
);
parts
.
push_back
(
p
);
thyla_part_geom
::
mirror
(
thyla_part_geom
::
DIR_X
,
&
prl
,
&
pll
);
p
=
make_plane_part
(
1
,
0
,
0
,
prl
.
pt
);
set_domain
(
p
,
prl
.
lo
,
prl
.
hi
);
parts
.
push_back
(
p
);
thyla_part_geom
::
mirror
(
thyla_part_geom
::
DIR_X
,
&
prb
,
&
plb
);
p
=
make_plane_part
(
0
,
1
,
0
,
prb
.
pt
);
set_domain
(
p
,
prb
.
lo
,
prb
.
hi
);
parts
.
push_back
(
p
);
thyla_part_geom
::
mirror
(
thyla_part_geom
::
DIR_X
,
&
prt
,
&
plt
);
p
=
make_plane_part
(
0
,
1
,
0
,
prt
.
pt
);
set_domain
(
p
,
prt
.
lo
,
prt
.
hi
);
parts
.
push_back
(
p
);
// Careful, this one is wrongly named.
thyla_part_geom
::
mirror
(
thyla_part_geom
::
DIR_X
,
&
prr
,
&
plr
);
p
=
make_plane_part
(
1
,
0
,
0
,
prr
.
pt
);
set_domain
(
p
,
prr
.
lo
,
prr
.
hi
);
parts
.
push_back
(
p
);
if
(
fabs
(
prr
.
pt
[
0
]
-
br
.
pt
[
0
]
-
lB
)
>
1e-8
){
char
msg
[
2048
];
sprintf
(
msg
,
"Origins of plane left right and bridge left misaligned! %f != %f!
\n
"
,
prr
.
pt
[
0
],
br
.
pt
[
0
]
+
lB
);
error
->
one
(
FLERR
,
msg
);
}
// For debugging, print the domains and coms:
#ifdef MANIFOLD_THYLAKOID_DEBUG
if
(
comm
->
me
==
0
){
FILE
*
fp_doms
=
fopen
(
"test_doms.dat"
,
"w"
);
FILE
*
fp_coms
=
fopen
(
"test_coms.dat"
,
"w"
);
print_part_data
(
fp_doms
,
fp_coms
);
fclose
(
fp_doms
);
fclose
(
fp_coms
);
}
#endif
// MANIFOLD_THYLAKOID_DEBUG
}
void
manifold_thylakoid
::
set_domain
(
thyla_part
*
p
,
const
std
::
vector
<
double
>
&
lo
,
const
std
::
vector
<
double
>
&
hi
)
{
#ifdef MANIFOLD_THYLAKOID_DEBUG
if
(
comm
->
me
==
0
){
fprintf
(
screen
,
"Adding part with domain [%f, %f] x [%f, %f] x [%f, %f]
\n
"
,
lo
[
0
],
hi
[
0
],
lo
[
1
],
hi
[
1
],
lo
[
2
],
hi
[
2
]
);
}
#endif
// MANIFOLD_THYLAKOID_DEBUG
if
(
lo
[
0
]
>=
hi
[
0
]
){
char
msg
[
2048
];
sprintf
(
msg
,
"xlo >= xhi (%f >= %f)"
,
lo
[
0
],
hi
[
0
]);
error
->
one
(
FLERR
,
msg
);
}
else
if
(
lo
[
1
]
>=
hi
[
1
]
){
char
msg
[
2048
];
sprintf
(
msg
,
"ylo >= yhi (%f >= %f)"
,
lo
[
1
],
hi
[
1
]);
error
->
one
(
FLERR
,
msg
);
}
else
if
(
lo
[
2
]
>=
hi
[
2
]
){
char
msg
[
2048
];
sprintf
(
msg
,
"zlo >= zhi (%f >= %f)"
,
lo
[
2
],
hi
[
2
]);
error
->
one
(
FLERR
,
msg
);
}
p
->
xlo
=
lo
[
0
];
p
->
ylo
=
lo
[
1
];
p
->
zlo
=
lo
[
2
];
p
->
xhi
=
hi
[
0
];
p
->
yhi
=
hi
[
1
];
p
->
zhi
=
hi
[
2
];
}
int
manifold_thylakoid
::
is_in_domain
(
thyla_part
*
part
,
const
double
*
x
)
{
bool
domain_ok
=
(
x
[
0
]
>=
part
->
xlo
)
&&
(
x
[
0
]
<=
part
->
xhi
)
&&
(
x
[
1
]
>=
part
->
ylo
)
&&
(
x
[
1
]
<=
part
->
yhi
)
&&
(
x
[
2
]
>=
part
->
zlo
)
&&
(
x
[
2
]
<=
part
->
zhi
);
if
(
!
domain_ok
)
return
false
;
// From here on out, domain is ok.
if
(
part
->
type
==
thyla_part
::
THYLA_TYPE_CYL_TO_PLANE
){
double
R0
=
part
->
params
[
1
];
double
R
=
part
->
params
[
2
];
double
y
=
x
[
1
];
double
z
=
x
[
2
];
double
dist2
=
y
*
y
+
z
*
z
;
double
RR
=
R0
+
R
;
double
RR2
=
RR
*
RR
;
if
(
dist2
<
RR2
){
return
true
;
}
else
{
// Domain was ok, but radius not.
return
false
;
}
}
else
{
return
true
;
}
}
thyla_part
*
manifold_thylakoid
::
make_plane_part
(
double
a
,
double
b
,
double
c
,
const
std
::
vector
<
double
>
&
pt
)
{
double
args
[
7
];
args
[
0
]
=
a
;
args
[
1
]
=
b
;
args
[
2
]
=
c
;
args
[
3
]
=
pt
[
0
];
args
[
4
]
=
pt
[
1
];
args
[
5
]
=
pt
[
2
];
thyla_part
*
p
=
new
thyla_part
(
thyla_part
::
THYLA_TYPE_PLANE
,
args
,
0
,
0
,
0
,
0
,
0
,
0
);
return
p
;
}
thyla_part
*
manifold_thylakoid
::
make_cyl_part
(
double
a
,
double
b
,
double
c
,
const
std
::
vector
<
double
>
&
pt
,
double
R
)
{
double
args
[
7
];
args
[
0
]
=
a
;
args
[
1
]
=
b
;
args
[
2
]
=
c
;
args
[
3
]
=
pt
[
0
];
args
[
4
]
=
pt
[
1
];
args
[
5
]
=
pt
[
2
];
args
[
6
]
=
R
;
thyla_part
*
p
=
new
thyla_part
(
thyla_part
::
THYLA_TYPE_CYL
,
args
,
0
,
0
,
0
,
0
,
0
,
0
);
return
p
;
}
thyla_part
*
manifold_thylakoid
::
make_sphere_part
(
const
std
::
vector
<
double
>
&
pt
,
double
R
)
{
double
args
[
7
];
args
[
0
]
=
R
;
args
[
1
]
=
pt
[
0
];
args
[
2
]
=
pt
[
1
];
args
[
3
]
=
pt
[
2
];
thyla_part
*
p
=
new
thyla_part
(
thyla_part
::
THYLA_TYPE_SPHERE
,
args
,
0
,
0
,
0
,
0
,
0
,
0
);
return
p
;
}
thyla_part
*
manifold_thylakoid
::
make_cyl_to_plane_part
(
double
X0
,
double
R0
,
double
R
,
double
s
,
const
std
::
vector
<
double
>
&
pt
)
{
double
args
[
7
];
args
[
0
]
=
X0
;
args
[
1
]
=
R0
;
args
[
2
]
=
R
;
args
[
3
]
=
pt
[
0
];
args
[
4
]
=
pt
[
1
];
args
[
5
]
=
pt
[
2
];
args
[
6
]
=
s
;
thyla_part
*
p
=
new
thyla_part
(
thyla_part
::
THYLA_TYPE_CYL_TO_PLANE
,
args
,
0
,
0
,
0
,
0
,
0
,
0
);
return
p
;
}
void
manifold_thylakoid
::
print_part_data
(
FILE
*
fp_doms
,
FILE
*
fp_coms
)
{
for
(
std
::
size_t
i
=
0
;
i
<
parts
.
size
();
++
i
){
thyla_part
*
p
=
parts
[
i
];
fprintf
(
fp_doms
,
"%f %f
\n
"
,
p
->
xlo
,
p
->
ylo
);
fprintf
(
fp_doms
,
"%f %f
\n
"
,
p
->
xlo
,
p
->
yhi
);
fprintf
(
fp_doms
,
"%f %f
\n
"
,
p
->
xhi
,
p
->
yhi
);
fprintf
(
fp_doms
,
"%f %f
\n
"
,
p
->
xhi
,
p
->
ylo
);
fprintf
(
fp_doms
,
"%f %f
\n\n
"
,
p
->
xlo
,
p
->
ylo
);
fprintf
(
fp_coms
,
"%f %f
\n
"
,
p
->
x0
,
p
->
y0
);
}
}
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