Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F85136448
atom_vec_colloid.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Fri, Sep 27, 00:51
Size
16 KB
Mime Type
text/x-c
Expires
Sun, Sep 29, 00:51 (2 d)
Engine
blob
Format
Raw Data
Handle
21133503
Attached To
rLAMMPS lammps
atom_vec_colloid.cpp
View Options
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "atom_vec_colloid.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecColloid
::
AtomVecColloid
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
AtomVec
(
lmp
,
narg
,
arg
)
{
mass_type
=
1
;
shape_type
=
1
;
comm_x_only
=
comm_f_only
=
0
;
ghost_velocity
=
1
;
size_comm
=
9
;
size_reverse
=
6
;
size_border
=
12
;
size_data_atom
=
5
;
size_data_vel
=
7
;
xcol_data
=
3
;
atom
->
omega_flag
=
atom
->
torque_flag
=
1
;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void
AtomVecColloid
::
grow
(
int
n
)
{
if
(
n
==
0
)
nmax
+=
DELTA
;
else
nmax
=
n
;
atom
->
nmax
=
nmax
;
tag
=
atom
->
tag
=
(
int
*
)
memory
->
srealloc
(
atom
->
tag
,
nmax
*
sizeof
(
int
),
"atom:tag"
);
type
=
atom
->
type
=
(
int
*
)
memory
->
srealloc
(
atom
->
type
,
nmax
*
sizeof
(
int
),
"atom:type"
);
mask
=
atom
->
mask
=
(
int
*
)
memory
->
srealloc
(
atom
->
mask
,
nmax
*
sizeof
(
int
),
"atom:mask"
);
image
=
atom
->
image
=
(
int
*
)
memory
->
srealloc
(
atom
->
image
,
nmax
*
sizeof
(
int
),
"atom:image"
);
x
=
atom
->
x
=
memory
->
grow_2d_double_array
(
atom
->
x
,
nmax
,
3
,
"atom:x"
);
v
=
atom
->
v
=
memory
->
grow_2d_double_array
(
atom
->
v
,
nmax
,
3
,
"atom:v"
);
f
=
atom
->
f
=
memory
->
grow_2d_double_array
(
atom
->
f
,
nmax
,
3
,
"atom:f"
);
omega
=
atom
->
omega
=
memory
->
grow_2d_double_array
(
atom
->
omega
,
nmax
,
3
,
"atom:omega"
);
torque
=
atom
->
torque
=
memory
->
grow_2d_double_array
(
atom
->
torque
,
nmax
,
3
,
"atom:torque"
);
if
(
atom
->
nextra_grow
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_grow
;
iextra
++
)
modify
->
fix
[
atom
->
extra_grow
[
iextra
]]
->
grow_arrays
(
nmax
);
}
/* ---------------------------------------------------------------------- */
void
AtomVecColloid
::
copy
(
int
i
,
int
j
)
{
tag
[
j
]
=
tag
[
i
];
type
[
j
]
=
type
[
i
];
mask
[
j
]
=
mask
[
i
];
image
[
j
]
=
image
[
i
];
x
[
j
][
0
]
=
x
[
i
][
0
];
x
[
j
][
1
]
=
x
[
i
][
1
];
x
[
j
][
2
]
=
x
[
i
][
2
];
v
[
j
][
0
]
=
v
[
i
][
0
];
v
[
j
][
1
]
=
v
[
i
][
1
];
v
[
j
][
2
]
=
v
[
i
][
2
];
omega
[
j
][
0
]
=
omega
[
i
][
0
];
omega
[
j
][
1
]
=
omega
[
i
][
1
];
omega
[
j
][
2
]
=
omega
[
i
][
2
];
if
(
atom
->
nextra_grow
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_grow
;
iextra
++
)
modify
->
fix
[
atom
->
extra_grow
[
iextra
]]
->
copy_arrays
(
i
,
j
);
}
/* ---------------------------------------------------------------------- */
int
AtomVecColloid
::
pack_comm
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
double
dx
,
dy
,
dz
;
m
=
0
;
if
(
pbc_flag
==
0
)
{
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
];
buf
[
m
++
]
=
x
[
j
][
1
];
buf
[
m
++
]
=
x
[
j
][
2
];
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
buf
[
m
++
]
=
omega
[
j
][
0
];
buf
[
m
++
]
=
omega
[
j
][
1
];
buf
[
m
++
]
=
omega
[
j
][
2
];
}
}
else
{
if
(
domain
->
triclinic
==
0
)
{
dx
=
pbc
[
0
]
*
domain
->
xprd
;
dy
=
pbc
[
1
]
*
domain
->
yprd
;
dz
=
pbc
[
2
]
*
domain
->
zprd
;
}
else
{
dx
=
pbc
[
0
]
*
domain
->
xprd
+
pbc
[
5
]
*
domain
->
xy
+
pbc
[
4
]
*
domain
->
xz
;
dy
=
pbc
[
1
]
*
domain
->
yprd
+
pbc
[
3
]
*
domain
->
yz
;
dz
=
pbc
[
2
]
*
domain
->
zprd
;
}
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
buf
[
m
++
]
=
omega
[
j
][
0
];
buf
[
m
++
]
=
omega
[
j
][
1
];
buf
[
m
++
]
=
omega
[
j
][
2
];
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecColloid
::
pack_comm_one
(
int
i
,
double
*
buf
)
{
buf
[
0
]
=
v
[
i
][
0
];
buf
[
1
]
=
v
[
i
][
1
];
buf
[
2
]
=
v
[
i
][
2
];
buf
[
3
]
=
omega
[
i
][
0
];
buf
[
4
]
=
omega
[
i
][
1
];
buf
[
5
]
=
omega
[
i
][
2
];
return
6
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecColloid
::
unpack_comm
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
x
[
i
][
0
]
=
buf
[
m
++
];
x
[
i
][
1
]
=
buf
[
m
++
];
x
[
i
][
2
]
=
buf
[
m
++
];
v
[
i
][
0
]
=
buf
[
m
++
];
v
[
i
][
1
]
=
buf
[
m
++
];
v
[
i
][
2
]
=
buf
[
m
++
];
omega
[
i
][
0
]
=
buf
[
m
++
];
omega
[
i
][
1
]
=
buf
[
m
++
];
omega
[
i
][
2
]
=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecColloid
::
unpack_comm_one
(
int
i
,
double
*
buf
)
{
v
[
i
][
0
]
=
buf
[
0
];
v
[
i
][
1
]
=
buf
[
1
];
v
[
i
][
2
]
=
buf
[
2
];
omega
[
i
][
0
]
=
buf
[
3
];
omega
[
i
][
1
]
=
buf
[
4
];
omega
[
i
][
2
]
=
buf
[
5
];
return
6
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecColloid
::
pack_reverse
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
buf
[
m
++
]
=
f
[
i
][
0
];
buf
[
m
++
]
=
f
[
i
][
1
];
buf
[
m
++
]
=
f
[
i
][
2
];
buf
[
m
++
]
=
torque
[
i
][
0
];
buf
[
m
++
]
=
torque
[
i
][
1
];
buf
[
m
++
]
=
torque
[
i
][
2
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecColloid
::
pack_reverse_one
(
int
i
,
double
*
buf
)
{
buf
[
0
]
=
torque
[
i
][
0
];
buf
[
1
]
=
torque
[
i
][
1
];
buf
[
2
]
=
torque
[
i
][
2
];
return
3
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecColloid
::
unpack_reverse
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
f
[
j
][
0
]
+=
buf
[
m
++
];
f
[
j
][
1
]
+=
buf
[
m
++
];
f
[
j
][
2
]
+=
buf
[
m
++
];
torque
[
j
][
0
]
+=
buf
[
m
++
];
torque
[
j
][
1
]
+=
buf
[
m
++
];
torque
[
j
][
2
]
+=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecColloid
::
unpack_reverse_one
(
int
i
,
double
*
buf
)
{
torque
[
i
][
0
]
+=
buf
[
0
];
torque
[
i
][
1
]
+=
buf
[
1
];
torque
[
i
][
2
]
+=
buf
[
2
];
return
3
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecColloid
::
pack_border
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
double
dx
,
dy
,
dz
;
m
=
0
;
if
(
pbc_flag
==
0
)
{
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
];
buf
[
m
++
]
=
x
[
j
][
1
];
buf
[
m
++
]
=
x
[
j
][
2
];
buf
[
m
++
]
=
tag
[
j
];
buf
[
m
++
]
=
type
[
j
];
buf
[
m
++
]
=
mask
[
j
];
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
buf
[
m
++
]
=
omega
[
j
][
0
];
buf
[
m
++
]
=
omega
[
j
][
1
];
buf
[
m
++
]
=
omega
[
j
][
2
];
}
}
else
{
if
(
domain
->
triclinic
==
0
)
{
dx
=
pbc
[
0
]
*
domain
->
xprd
;
dy
=
pbc
[
1
]
*
domain
->
yprd
;
dz
=
pbc
[
2
]
*
domain
->
zprd
;
}
else
{
dx
=
pbc
[
0
];
dy
=
pbc
[
1
];
dz
=
pbc
[
2
];
}
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
buf
[
m
++
]
=
tag
[
j
];
buf
[
m
++
]
=
type
[
j
];
buf
[
m
++
]
=
mask
[
j
];
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
buf
[
m
++
]
=
omega
[
j
][
0
];
buf
[
m
++
]
=
omega
[
j
][
1
];
buf
[
m
++
]
=
omega
[
j
][
2
];
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecColloid
::
pack_border_one
(
int
i
,
double
*
buf
)
{
buf
[
0
]
=
v
[
i
][
0
];
buf
[
1
]
=
v
[
i
][
1
];
buf
[
2
]
=
v
[
i
][
2
];
buf
[
3
]
=
omega
[
i
][
0
];
buf
[
4
]
=
omega
[
i
][
1
];
buf
[
5
]
=
omega
[
i
][
2
];
return
6
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecColloid
::
unpack_border
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
if
(
i
==
nmax
)
grow
(
0
);
x
[
i
][
0
]
=
buf
[
m
++
];
x
[
i
][
1
]
=
buf
[
m
++
];
x
[
i
][
2
]
=
buf
[
m
++
];
tag
[
i
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
type
[
i
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
mask
[
i
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
v
[
i
][
0
]
=
buf
[
m
++
];
v
[
i
][
1
]
=
buf
[
m
++
];
v
[
i
][
2
]
=
buf
[
m
++
];
omega
[
i
][
0
]
=
buf
[
m
++
];
omega
[
i
][
1
]
=
buf
[
m
++
];
omega
[
i
][
2
]
=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecColloid
::
unpack_border_one
(
int
i
,
double
*
buf
)
{
v
[
i
][
0
]
=
buf
[
0
];
v
[
i
][
1
]
=
buf
[
1
];
v
[
i
][
2
]
=
buf
[
2
];
omega
[
i
][
0
]
=
buf
[
3
];
omega
[
i
][
1
]
=
buf
[
4
];
omega
[
i
][
2
]
=
buf
[
5
];
return
6
;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int
AtomVecColloid
::
pack_exchange
(
int
i
,
double
*
buf
)
{
int
m
=
1
;
buf
[
m
++
]
=
x
[
i
][
0
];
buf
[
m
++
]
=
x
[
i
][
1
];
buf
[
m
++
]
=
x
[
i
][
2
];
buf
[
m
++
]
=
v
[
i
][
0
];
buf
[
m
++
]
=
v
[
i
][
1
];
buf
[
m
++
]
=
v
[
i
][
2
];
buf
[
m
++
]
=
tag
[
i
];
buf
[
m
++
]
=
type
[
i
];
buf
[
m
++
]
=
mask
[
i
];
buf
[
m
++
]
=
image
[
i
];
buf
[
m
++
]
=
omega
[
i
][
0
];
buf
[
m
++
]
=
omega
[
i
][
1
];
buf
[
m
++
]
=
omega
[
i
][
2
];
if
(
atom
->
nextra_grow
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_grow
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_grow
[
iextra
]]
->
pack_exchange
(
i
,
&
buf
[
m
]);
buf
[
0
]
=
m
;
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecColloid
::
unpack_exchange
(
double
*
buf
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
grow
(
0
);
int
m
=
1
;
x
[
nlocal
][
0
]
=
buf
[
m
++
];
x
[
nlocal
][
1
]
=
buf
[
m
++
];
x
[
nlocal
][
2
]
=
buf
[
m
++
];
v
[
nlocal
][
0
]
=
buf
[
m
++
];
v
[
nlocal
][
1
]
=
buf
[
m
++
];
v
[
nlocal
][
2
]
=
buf
[
m
++
];
tag
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
type
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
mask
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
image
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
omega
[
nlocal
][
0
]
=
buf
[
m
++
];
omega
[
nlocal
][
1
]
=
buf
[
m
++
];
omega
[
nlocal
][
2
]
=
buf
[
m
++
];
if
(
atom
->
nextra_grow
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_grow
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_grow
[
iextra
]]
->
unpack_exchange
(
nlocal
,
&
buf
[
m
]);
atom
->
nlocal
++
;
return
m
;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int
AtomVecColloid
::
size_restart
()
{
int
i
;
int
nlocal
=
atom
->
nlocal
;
int
n
=
14
*
nlocal
;
if
(
atom
->
nextra_restart
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_restart
;
iextra
++
)
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
n
+=
modify
->
fix
[
atom
->
extra_restart
[
iextra
]]
->
size_restart
(
i
);
return
n
;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int
AtomVecColloid
::
pack_restart
(
int
i
,
double
*
buf
)
{
int
m
=
1
;
buf
[
m
++
]
=
x
[
i
][
0
];
buf
[
m
++
]
=
x
[
i
][
1
];
buf
[
m
++
]
=
x
[
i
][
2
];
buf
[
m
++
]
=
tag
[
i
];
buf
[
m
++
]
=
type
[
i
];
buf
[
m
++
]
=
mask
[
i
];
buf
[
m
++
]
=
image
[
i
];
buf
[
m
++
]
=
v
[
i
][
0
];
buf
[
m
++
]
=
v
[
i
][
1
];
buf
[
m
++
]
=
v
[
i
][
2
];
buf
[
m
++
]
=
omega
[
i
][
0
];
buf
[
m
++
]
=
omega
[
i
][
1
];
buf
[
m
++
]
=
omega
[
i
][
2
];
if
(
atom
->
nextra_restart
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_restart
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_restart
[
iextra
]]
->
pack_restart
(
i
,
&
buf
[
m
]);
buf
[
0
]
=
m
;
return
m
;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int
AtomVecColloid
::
unpack_restart
(
double
*
buf
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
{
grow
(
0
);
if
(
atom
->
nextra_store
)
atom
->
extra
=
memory
->
grow_2d_double_array
(
atom
->
extra
,
nmax
,
atom
->
nextra_store
,
"atom:extra"
);
}
int
m
=
1
;
x
[
nlocal
][
0
]
=
buf
[
m
++
];
x
[
nlocal
][
1
]
=
buf
[
m
++
];
x
[
nlocal
][
2
]
=
buf
[
m
++
];
tag
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
type
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
mask
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
image
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
v
[
nlocal
][
0
]
=
buf
[
m
++
];
v
[
nlocal
][
1
]
=
buf
[
m
++
];
v
[
nlocal
][
2
]
=
buf
[
m
++
];
omega
[
nlocal
][
0
]
=
buf
[
m
++
];
omega
[
nlocal
][
1
]
=
buf
[
m
++
];
omega
[
nlocal
][
2
]
=
buf
[
m
++
];
double
**
extra
=
atom
->
extra
;
if
(
atom
->
nextra_store
)
{
int
size
=
static_cast
<
int
>
(
buf
[
0
])
-
m
;
for
(
int
i
=
0
;
i
<
size
;
i
++
)
extra
[
nlocal
][
i
]
=
buf
[
m
++
];
}
atom
->
nlocal
++
;
return
m
;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void
AtomVecColloid
::
create_atom
(
int
itype
,
double
*
coord
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
grow
(
0
);
tag
[
nlocal
]
=
0
;
type
[
nlocal
]
=
itype
;
x
[
nlocal
][
0
]
=
coord
[
0
];
x
[
nlocal
][
1
]
=
coord
[
1
];
x
[
nlocal
][
2
]
=
coord
[
2
];
mask
[
nlocal
]
=
1
;
image
[
nlocal
]
=
(
512
<<
20
)
|
(
512
<<
10
)
|
512
;
v
[
nlocal
][
0
]
=
0.0
;
v
[
nlocal
][
1
]
=
0.0
;
v
[
nlocal
][
2
]
=
0.0
;
omega
[
nlocal
][
0
]
=
0.0
;
omega
[
nlocal
][
1
]
=
0.0
;
omega
[
nlocal
][
2
]
=
0.0
;
atom
->
nlocal
++
;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void
AtomVecColloid
::
data_atom
(
double
*
coord
,
int
imagetmp
,
char
**
values
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
grow
(
0
);
tag
[
nlocal
]
=
atoi
(
values
[
0
]);
if
(
tag
[
nlocal
]
<=
0
)
error
->
one
(
"Invalid atom ID in Atoms section of data file"
);
type
[
nlocal
]
=
atoi
(
values
[
1
]);
if
(
type
[
nlocal
]
<=
0
||
type
[
nlocal
]
>
atom
->
ntypes
)
error
->
one
(
"Invalid atom type in Atoms section of data file"
);
x
[
nlocal
][
0
]
=
coord
[
0
];
x
[
nlocal
][
1
]
=
coord
[
1
];
x
[
nlocal
][
2
]
=
coord
[
2
];
image
[
nlocal
]
=
imagetmp
;
mask
[
nlocal
]
=
1
;
v
[
nlocal
][
0
]
=
0.0
;
v
[
nlocal
][
1
]
=
0.0
;
v
[
nlocal
][
2
]
=
0.0
;
omega
[
nlocal
][
0
]
=
0.0
;
omega
[
nlocal
][
1
]
=
0.0
;
omega
[
nlocal
][
2
]
=
0.0
;
atom
->
nlocal
++
;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int
AtomVecColloid
::
data_atom_hybrid
(
int
nlocal
,
char
**
values
)
{
v
[
nlocal
][
0
]
=
0.0
;
v
[
nlocal
][
1
]
=
0.0
;
v
[
nlocal
][
2
]
=
0.0
;
omega
[
nlocal
][
0
]
=
0.0
;
omega
[
nlocal
][
1
]
=
0.0
;
omega
[
nlocal
][
2
]
=
0.0
;
return
0
;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void
AtomVecColloid
::
data_vel
(
int
m
,
char
**
values
)
{
v
[
m
][
0
]
=
atof
(
values
[
0
]);
v
[
m
][
1
]
=
atof
(
values
[
1
]);
v
[
m
][
2
]
=
atof
(
values
[
2
]);
omega
[
m
][
0
]
=
atof
(
values
[
3
]);
omega
[
m
][
1
]
=
atof
(
values
[
4
]);
omega
[
m
][
2
]
=
atof
(
values
[
5
]);
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
int
AtomVecColloid
::
data_vel_hybrid
(
int
m
,
char
**
values
)
{
omega
[
m
][
0
]
=
atof
(
values
[
0
]);
omega
[
m
][
1
]
=
atof
(
values
[
1
]);
omega
[
m
][
2
]
=
atof
(
values
[
2
]);
return
3
;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double
AtomVecColloid
::
memory_usage
()
{
double
bytes
=
0.0
;
if
(
atom
->
memcheck
(
"tag"
))
bytes
+=
nmax
*
sizeof
(
int
);
if
(
atom
->
memcheck
(
"type"
))
bytes
+=
nmax
*
sizeof
(
int
);
if
(
atom
->
memcheck
(
"mask"
))
bytes
+=
nmax
*
sizeof
(
int
);
if
(
atom
->
memcheck
(
"image"
))
bytes
+=
nmax
*
sizeof
(
int
);
if
(
atom
->
memcheck
(
"x"
))
bytes
+=
nmax
*
3
*
sizeof
(
double
);
if
(
atom
->
memcheck
(
"v"
))
bytes
+=
nmax
*
3
*
sizeof
(
double
);
if
(
atom
->
memcheck
(
"f"
))
bytes
+=
nmax
*
3
*
sizeof
(
double
);
if
(
atom
->
memcheck
(
"omega"
))
bytes
+=
nmax
*
3
*
sizeof
(
double
);
if
(
atom
->
memcheck
(
"torque"
))
bytes
+=
nmax
*
3
*
sizeof
(
double
);
return
bytes
;
}
Event Timeline
Log In to Comment