Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F65900477
atom_vec_granular.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
Thu, Jun 6, 23:25
Size
19 KB
Mime Type
text/x-c
Expires
Sat, Jun 8, 23:25 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
18116525
Attached To
rLAMMPS lammps
atom_vec_granular.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 "math.h"
#include "stdlib.h"
#include "atom_vec_granular.h"
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "force.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecGranular
::
AtomVecGranular
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
AtomVec
(
lmp
,
narg
,
arg
)
{
comm_x_only
=
comm_f_only
=
0
;
ghost_velocity
=
1
;
size_comm
=
9
;
size_reverse
=
6
;
size_border
=
14
;
size_data_atom
=
7
;
size_data_vel
=
7
;
xcol_data
=
5
;
atom
->
radius_flag
=
atom
->
density_flag
=
atom
->
rmass_flag
=
1
;
atom
->
omega_flag
=
atom
->
torque_flag
=
1
;
PI
=
4.0
*
atan
(
1.0
);
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void
AtomVecGranular
::
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"
);
radius
=
atom
->
radius
=
(
double
*
)
memory
->
srealloc
(
atom
->
radius
,
nmax
*
sizeof
(
double
),
"atom:radius"
);
density
=
atom
->
density
=
(
double
*
)
memory
->
srealloc
(
atom
->
density
,
nmax
*
sizeof
(
double
),
"atom:density"
);
rmass
=
atom
->
rmass
=
(
double
*
)
memory
->
srealloc
(
atom
->
rmass
,
nmax
*
sizeof
(
double
),
"atom:rmass"
);
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
AtomVecGranular
::
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
];
radius
[
j
]
=
radius
[
i
];
density
[
j
]
=
density
[
i
];
rmass
[
j
]
=
rmass
[
i
];
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
AtomVecGranular
::
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
AtomVecGranular
::
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
AtomVecGranular
::
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
AtomVecGranular
::
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
AtomVecGranular
::
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
AtomVecGranular
::
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
AtomVecGranular
::
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
AtomVecGranular
::
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
AtomVecGranular
::
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
++
]
=
radius
[
j
];
buf
[
m
++
]
=
rmass
[
j
];
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
++
]
=
radius
[
j
];
buf
[
m
++
]
=
rmass
[
j
];
buf
[
m
++
]
=
omega
[
j
][
0
];
buf
[
m
++
]
=
omega
[
j
][
1
];
buf
[
m
++
]
=
omega
[
j
][
2
];
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecGranular
::
pack_border_one
(
int
i
,
double
*
buf
)
{
buf
[
0
]
=
v
[
i
][
0
];
buf
[
1
]
=
v
[
i
][
1
];
buf
[
2
]
=
v
[
i
][
2
];
buf
[
3
]
=
radius
[
i
];
buf
[
4
]
=
rmass
[
i
];
buf
[
5
]
=
omega
[
i
][
0
];
buf
[
6
]
=
omega
[
i
][
1
];
buf
[
7
]
=
omega
[
i
][
2
];
return
8
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecGranular
::
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
++
];
radius
[
i
]
=
buf
[
m
++
];
rmass
[
i
]
=
buf
[
m
++
];
omega
[
i
][
0
]
=
buf
[
m
++
];
omega
[
i
][
1
]
=
buf
[
m
++
];
omega
[
i
][
2
]
=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecGranular
::
unpack_border_one
(
int
i
,
double
*
buf
)
{
v
[
i
][
0
]
=
buf
[
0
];
v
[
i
][
1
]
=
buf
[
1
];
v
[
i
][
2
]
=
buf
[
2
];
radius
[
i
]
=
buf
[
3
];
rmass
[
i
]
=
buf
[
4
];
omega
[
i
][
0
]
=
buf
[
5
];
omega
[
i
][
1
]
=
buf
[
6
];
omega
[
i
][
2
]
=
buf
[
7
];
return
8
;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int
AtomVecGranular
::
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
++
]
=
radius
[
i
];
buf
[
m
++
]
=
density
[
i
];
buf
[
m
++
]
=
rmass
[
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
AtomVecGranular
::
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
++
]);
radius
[
nlocal
]
=
buf
[
m
++
];
density
[
nlocal
]
=
buf
[
m
++
];
rmass
[
nlocal
]
=
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
AtomVecGranular
::
size_restart
()
{
int
i
;
int
nlocal
=
atom
->
nlocal
;
int
n
=
16
*
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
AtomVecGranular
::
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
++
]
=
radius
[
i
];
buf
[
m
++
]
=
density
[
i
];
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
AtomVecGranular
::
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
++
];
radius
[
nlocal
]
=
buf
[
m
++
];
density
[
nlocal
]
=
buf
[
m
++
];
if
(
radius
[
nlocal
]
==
0.0
)
rmass
[
nlocal
]
=
density
[
nlocal
];
else
rmass
[
nlocal
]
=
4.0
*
PI
/
3.0
*
radius
[
nlocal
]
*
radius
[
nlocal
]
*
radius
[
nlocal
]
*
density
[
nlocal
];
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
AtomVecGranular
::
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
;
radius
[
nlocal
]
=
0.5
;
density
[
nlocal
]
=
1.0
;
rmass
[
nlocal
]
=
4.0
*
PI
/
3.0
*
radius
[
nlocal
]
*
radius
[
nlocal
]
*
radius
[
nlocal
]
*
density
[
nlocal
];
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
AtomVecGranular
::
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"
);
radius
[
nlocal
]
=
0.5
*
atof
(
values
[
2
]);
if
(
radius
[
nlocal
]
<
0.0
)
error
->
one
(
"Invalid radius in Atoms section of data file"
);
density
[
nlocal
]
=
atof
(
values
[
3
]);
if
(
density
[
nlocal
]
<=
0.0
)
error
->
one
(
"Invalid density in Atoms section of data file"
);
if
(
radius
[
nlocal
]
==
0.0
)
rmass
[
nlocal
]
=
density
[
nlocal
];
else
rmass
[
nlocal
]
=
4.0
*
PI
/
3.0
*
radius
[
nlocal
]
*
radius
[
nlocal
]
*
radius
[
nlocal
]
*
density
[
nlocal
];
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
AtomVecGranular
::
data_atom_hybrid
(
int
nlocal
,
char
**
values
)
{
radius
[
nlocal
]
=
0.5
*
atof
(
values
[
0
]);
if
(
radius
[
nlocal
]
<
0.0
)
error
->
one
(
"Invalid radius in Atoms section of data file"
);
density
[
nlocal
]
=
atof
(
values
[
1
]);
if
(
density
[
nlocal
]
<=
0.0
)
error
->
one
(
"Invalid density in Atoms section of data file"
);
if
(
radius
[
nlocal
]
==
0.0
)
rmass
[
nlocal
]
=
density
[
nlocal
];
else
rmass
[
nlocal
]
=
4.0
*
PI
/
3.0
*
radius
[
nlocal
]
*
radius
[
nlocal
]
*
radius
[
nlocal
]
*
density
[
nlocal
];
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
2
;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void
AtomVecGranular
::
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
AtomVecGranular
::
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
AtomVecGranular
::
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
(
"radius"
))
bytes
+=
nmax
*
sizeof
(
double
);
if
(
atom
->
memcheck
(
"density"
))
bytes
+=
nmax
*
sizeof
(
double
);
if
(
atom
->
memcheck
(
"rmass"
))
bytes
+=
nmax
*
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