Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F86816995
dump_atom.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
Tue, Oct 8, 19:08
Size
14 KB
Mime Type
text/x-c
Expires
Thu, Oct 10, 19:08 (1 d, 21 h)
Engine
blob
Format
Raw Data
Handle
21486486
Attached To
rLAMMPS lammps
dump_atom.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 "string.h"
#include "dump_atom.h"
#include "domain.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define ONELINE 256
#define DELTA 1048576
/* ---------------------------------------------------------------------- */
DumpAtom
::
DumpAtom
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Dump
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
5
)
error
->
all
(
FLERR
,
"Illegal dump atom command"
);
scale_flag
=
1
;
image_flag
=
0
;
buffer_allow
=
1
;
buffer_flag
=
1
;
format_default
=
NULL
;
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
init_style
()
{
if
(
image_flag
==
0
)
size_one
=
5
;
else
size_one
=
8
;
// default format depends on image flags
delete
[]
format
;
if
(
format_user
)
{
int
n
=
strlen
(
format_user
)
+
2
;
format
=
new
char
[
n
];
strcpy
(
format
,
format_user
);
strcat
(
format
,
"
\n
"
);
}
else
{
char
*
str
;
if
(
image_flag
==
0
)
str
=
(
char
*
)
"%d %d %g %g %g"
;
else
str
=
(
char
*
)
"%d %d %g %g %g %d %d %d"
;
int
n
=
strlen
(
str
)
+
2
;
format
=
new
char
[
n
];
strcpy
(
format
,
str
);
strcat
(
format
,
"
\n
"
);
}
// setup boundary string
domain
->
boundary_string
(
boundstr
);
// setup column string
if
(
scale_flag
==
0
&&
image_flag
==
0
)
columns
=
(
char
*
)
"id type x y z"
;
else
if
(
scale_flag
==
0
&&
image_flag
==
1
)
columns
=
(
char
*
)
"id type x y z ix iy iz"
;
else
if
(
scale_flag
==
1
&&
image_flag
==
0
)
columns
=
(
char
*
)
"id type xs ys zs"
;
else
if
(
scale_flag
==
1
&&
image_flag
==
1
)
columns
=
(
char
*
)
"id type xs ys zs ix iy iz"
;
// setup function ptrs
if
(
binary
&&
domain
->
triclinic
==
0
)
header_choice
=
&
DumpAtom
::
header_binary
;
else
if
(
binary
&&
domain
->
triclinic
==
1
)
header_choice
=
&
DumpAtom
::
header_binary_triclinic
;
else
if
(
!
binary
&&
domain
->
triclinic
==
0
)
header_choice
=
&
DumpAtom
::
header_item
;
else
if
(
!
binary
&&
domain
->
triclinic
==
1
)
header_choice
=
&
DumpAtom
::
header_item_triclinic
;
if
(
scale_flag
==
1
&&
image_flag
==
0
&&
domain
->
triclinic
==
0
)
pack_choice
=
&
DumpAtom
::
pack_scale_noimage
;
else
if
(
scale_flag
==
1
&&
image_flag
==
1
&&
domain
->
triclinic
==
0
)
pack_choice
=
&
DumpAtom
::
pack_scale_image
;
else
if
(
scale_flag
==
1
&&
image_flag
==
0
&&
domain
->
triclinic
==
1
)
pack_choice
=
&
DumpAtom
::
pack_scale_noimage_triclinic
;
else
if
(
scale_flag
==
1
&&
image_flag
==
1
&&
domain
->
triclinic
==
1
)
pack_choice
=
&
DumpAtom
::
pack_scale_image_triclinic
;
else
if
(
scale_flag
==
0
&&
image_flag
==
0
)
pack_choice
=
&
DumpAtom
::
pack_noscale_noimage
;
else
if
(
scale_flag
==
0
&&
image_flag
==
1
)
pack_choice
=
&
DumpAtom
::
pack_noscale_image
;
if
(
image_flag
==
0
)
convert_choice
=
&
DumpAtom
::
convert_noimage
;
else
convert_choice
=
&
DumpAtom
::
convert_image
;
if
(
binary
)
write_choice
=
&
DumpAtom
::
write_binary
;
else
if
(
buffer_flag
==
1
)
write_choice
=
&
DumpAtom
::
write_string
;
else
if
(
image_flag
==
0
)
write_choice
=
&
DumpAtom
::
write_lines_noimage
;
else
if
(
image_flag
==
1
)
write_choice
=
&
DumpAtom
::
write_lines_image
;
// open single file, one time only
if
(
multifile
==
0
)
openfile
();
}
/* ---------------------------------------------------------------------- */
int
DumpAtom
::
modify_param
(
int
narg
,
char
**
arg
)
{
if
(
strcmp
(
arg
[
0
],
"scale"
)
==
0
)
{
if
(
narg
<
2
)
error
->
all
(
FLERR
,
"Illegal dump_modify command"
);
if
(
strcmp
(
arg
[
1
],
"yes"
)
==
0
)
scale_flag
=
1
;
else
if
(
strcmp
(
arg
[
1
],
"no"
)
==
0
)
scale_flag
=
0
;
else
error
->
all
(
FLERR
,
"Illegal dump_modify command"
);
return
2
;
}
else
if
(
strcmp
(
arg
[
0
],
"image"
)
==
0
)
{
if
(
narg
<
2
)
error
->
all
(
FLERR
,
"Illegal dump_modify command"
);
if
(
strcmp
(
arg
[
1
],
"yes"
)
==
0
)
image_flag
=
1
;
else
if
(
strcmp
(
arg
[
1
],
"no"
)
==
0
)
image_flag
=
0
;
else
error
->
all
(
FLERR
,
"Illegal dump_modify command"
);
return
2
;
}
return
0
;
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
write_header
(
bigint
ndump
)
{
if
(
multiproc
)
(
this
->*
header_choice
)(
ndump
);
else
if
(
me
==
0
)
(
this
->*
header_choice
)(
ndump
);
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
pack
(
int
*
ids
)
{
(
this
->*
pack_choice
)(
ids
);
}
/* ---------------------------------------------------------------------- */
int
DumpAtom
::
convert_string
(
int
n
,
double
*
mybuf
)
{
return
(
this
->*
convert_choice
)(
n
,
mybuf
);
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
write_data
(
int
n
,
double
*
mybuf
)
{
(
this
->*
write_choice
)(
n
,
mybuf
);
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
header_binary
(
bigint
ndump
)
{
fwrite
(
&
update
->
ntimestep
,
sizeof
(
bigint
),
1
,
fp
);
fwrite
(
&
ndump
,
sizeof
(
bigint
),
1
,
fp
);
fwrite
(
&
domain
->
triclinic
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
domain
->
boundary
[
0
][
0
],
6
*
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
boxxlo
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
boxxhi
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
boxylo
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
boxyhi
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
boxzlo
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
boxzhi
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
size_one
,
sizeof
(
int
),
1
,
fp
);
if
(
multiproc
)
fwrite
(
&
nclusterprocs
,
sizeof
(
int
),
1
,
fp
);
else
fwrite
(
&
nprocs
,
sizeof
(
int
),
1
,
fp
);
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
header_binary_triclinic
(
bigint
ndump
)
{
fwrite
(
&
update
->
ntimestep
,
sizeof
(
bigint
),
1
,
fp
);
fwrite
(
&
ndump
,
sizeof
(
bigint
),
1
,
fp
);
fwrite
(
&
domain
->
triclinic
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
domain
->
boundary
[
0
][
0
],
6
*
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
boxxlo
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
boxxhi
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
boxylo
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
boxyhi
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
boxzlo
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
boxzhi
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
boxxy
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
boxxz
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
boxyz
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
size_one
,
sizeof
(
int
),
1
,
fp
);
if
(
multiproc
)
fwrite
(
&
nclusterprocs
,
sizeof
(
int
),
1
,
fp
);
else
fwrite
(
&
nprocs
,
sizeof
(
int
),
1
,
fp
);
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
header_item
(
bigint
ndump
)
{
fprintf
(
fp
,
"ITEM: TIMESTEP
\n
"
);
fprintf
(
fp
,
BIGINT_FORMAT
"
\n
"
,
update
->
ntimestep
);
fprintf
(
fp
,
"ITEM: NUMBER OF ATOMS
\n
"
);
fprintf
(
fp
,
BIGINT_FORMAT
"
\n
"
,
ndump
);
fprintf
(
fp
,
"ITEM: BOX BOUNDS %s
\n
"
,
boundstr
);
fprintf
(
fp
,
"%g %g
\n
"
,
boxxlo
,
boxxhi
);
fprintf
(
fp
,
"%g %g
\n
"
,
boxylo
,
boxyhi
);
fprintf
(
fp
,
"%g %g
\n
"
,
boxzlo
,
boxzhi
);
fprintf
(
fp
,
"ITEM: ATOMS %s
\n
"
,
columns
);
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
header_item_triclinic
(
bigint
ndump
)
{
fprintf
(
fp
,
"ITEM: TIMESTEP
\n
"
);
fprintf
(
fp
,
BIGINT_FORMAT
"
\n
"
,
update
->
ntimestep
);
fprintf
(
fp
,
"ITEM: NUMBER OF ATOMS
\n
"
);
fprintf
(
fp
,
BIGINT_FORMAT
"
\n
"
,
ndump
);
fprintf
(
fp
,
"ITEM: BOX BOUNDS xy xz yz %s
\n
"
,
boundstr
);
fprintf
(
fp
,
"%g %g %g
\n
"
,
boxxlo
,
boxxhi
,
boxxy
);
fprintf
(
fp
,
"%g %g %g
\n
"
,
boxylo
,
boxyhi
,
boxxz
);
fprintf
(
fp
,
"%g %g %g
\n
"
,
boxzlo
,
boxzhi
,
boxyz
);
fprintf
(
fp
,
"ITEM: ATOMS %s
\n
"
,
columns
);
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
pack_scale_image
(
int
*
ids
)
{
int
m
,
n
;
int
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
imageint
*
image
=
atom
->
image
;
int
*
mask
=
atom
->
mask
;
double
**
x
=
atom
->
x
;
int
nlocal
=
atom
->
nlocal
;
double
invxprd
=
1.0
/
domain
->
xprd
;
double
invyprd
=
1.0
/
domain
->
yprd
;
double
invzprd
=
1.0
/
domain
->
zprd
;
m
=
n
=
00
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
buf
[
m
++
]
=
tag
[
i
];
buf
[
m
++
]
=
type
[
i
];
buf
[
m
++
]
=
(
x
[
i
][
0
]
-
boxxlo
)
*
invxprd
;
buf
[
m
++
]
=
(
x
[
i
][
1
]
-
boxylo
)
*
invyprd
;
buf
[
m
++
]
=
(
x
[
i
][
2
]
-
boxzlo
)
*
invzprd
;
buf
[
m
++
]
=
(
image
[
i
]
&
IMGMASK
)
-
IMGMAX
;
buf
[
m
++
]
=
(
image
[
i
]
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
;
buf
[
m
++
]
=
(
image
[
i
]
>>
IMG2BITS
)
-
IMGMAX
;
if
(
ids
)
ids
[
n
++
]
=
tag
[
i
];
}
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
pack_scale_noimage
(
int
*
ids
)
{
int
m
,
n
;
int
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
double
**
x
=
atom
->
x
;
int
nlocal
=
atom
->
nlocal
;
double
invxprd
=
1.0
/
domain
->
xprd
;
double
invyprd
=
1.0
/
domain
->
yprd
;
double
invzprd
=
1.0
/
domain
->
zprd
;
m
=
n
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
buf
[
m
++
]
=
tag
[
i
];
buf
[
m
++
]
=
type
[
i
];
buf
[
m
++
]
=
(
x
[
i
][
0
]
-
boxxlo
)
*
invxprd
;
buf
[
m
++
]
=
(
x
[
i
][
1
]
-
boxylo
)
*
invyprd
;
buf
[
m
++
]
=
(
x
[
i
][
2
]
-
boxzlo
)
*
invzprd
;
if
(
ids
)
ids
[
n
++
]
=
tag
[
i
];
}
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
pack_scale_image_triclinic
(
int
*
ids
)
{
int
m
,
n
;
int
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
imageint
*
image
=
atom
->
image
;
int
*
mask
=
atom
->
mask
;
double
**
x
=
atom
->
x
;
int
nlocal
=
atom
->
nlocal
;
double
lamda
[
3
];
m
=
n
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
buf
[
m
++
]
=
tag
[
i
];
buf
[
m
++
]
=
type
[
i
];
domain
->
x2lamda
(
x
[
i
],
lamda
);
buf
[
m
++
]
=
lamda
[
0
];
buf
[
m
++
]
=
lamda
[
1
];
buf
[
m
++
]
=
lamda
[
2
];
buf
[
m
++
]
=
(
image
[
i
]
&
IMGMASK
)
-
IMGMAX
;
buf
[
m
++
]
=
(
image
[
i
]
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
;
buf
[
m
++
]
=
(
image
[
i
]
>>
IMG2BITS
)
-
IMGMAX
;
if
(
ids
)
ids
[
n
++
]
=
tag
[
i
];
}
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
pack_scale_noimage_triclinic
(
int
*
ids
)
{
int
m
,
n
;
int
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
double
**
x
=
atom
->
x
;
int
nlocal
=
atom
->
nlocal
;
double
lamda
[
3
];
m
=
n
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
buf
[
m
++
]
=
tag
[
i
];
buf
[
m
++
]
=
type
[
i
];
domain
->
x2lamda
(
x
[
i
],
lamda
);
buf
[
m
++
]
=
lamda
[
0
];
buf
[
m
++
]
=
lamda
[
1
];
buf
[
m
++
]
=
lamda
[
2
];
if
(
ids
)
ids
[
n
++
]
=
tag
[
i
];
}
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
pack_noscale_image
(
int
*
ids
)
{
int
m
,
n
;
int
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
imageint
*
image
=
atom
->
image
;
int
*
mask
=
atom
->
mask
;
double
**
x
=
atom
->
x
;
int
nlocal
=
atom
->
nlocal
;
m
=
n
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
buf
[
m
++
]
=
tag
[
i
];
buf
[
m
++
]
=
type
[
i
];
buf
[
m
++
]
=
x
[
i
][
0
];
buf
[
m
++
]
=
x
[
i
][
1
];
buf
[
m
++
]
=
x
[
i
][
2
];
buf
[
m
++
]
=
(
image
[
i
]
&
IMGMASK
)
-
IMGMAX
;
buf
[
m
++
]
=
(
image
[
i
]
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
;
buf
[
m
++
]
=
(
image
[
i
]
>>
IMG2BITS
)
-
IMGMAX
;
if
(
ids
)
ids
[
n
++
]
=
tag
[
i
];
}
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
pack_noscale_noimage
(
int
*
ids
)
{
int
m
,
n
;
int
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
double
**
x
=
atom
->
x
;
int
nlocal
=
atom
->
nlocal
;
m
=
n
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
buf
[
m
++
]
=
tag
[
i
];
buf
[
m
++
]
=
type
[
i
];
buf
[
m
++
]
=
x
[
i
][
0
];
buf
[
m
++
]
=
x
[
i
][
1
];
buf
[
m
++
]
=
x
[
i
][
2
];
if
(
ids
)
ids
[
n
++
]
=
tag
[
i
];
}
}
/* ----------------------------------------------------------------------
convert mybuf of doubles to one big formatted string in sbuf
return -1 if strlen exceeds an int, since used as arg in MPI calls in Dump
------------------------------------------------------------------------- */
int
DumpAtom
::
convert_image
(
int
n
,
double
*
mybuf
)
{
int
offset
=
0
;
int
m
=
0
;
for
(
int
i
=
0
;
i
<
n
;
i
++
)
{
if
(
offset
+
ONELINE
>
maxsbuf
)
{
if
((
bigint
)
maxsbuf
+
DELTA
>
MAXSMALLINT
)
return
-
1
;
maxsbuf
+=
DELTA
;
memory
->
grow
(
sbuf
,
maxsbuf
,
"dump:sbuf"
);
}
offset
+=
sprintf
(
&
sbuf
[
offset
],
format
,
static_cast
<
int
>
(
mybuf
[
m
]),
static_cast
<
int
>
(
mybuf
[
m
+
1
]),
mybuf
[
m
+
2
],
mybuf
[
m
+
3
],
mybuf
[
m
+
4
],
static_cast
<
int
>
(
mybuf
[
m
+
5
]),
static_cast
<
int
>
(
mybuf
[
m
+
6
]),
static_cast
<
int
>
(
mybuf
[
m
+
7
]));
m
+=
size_one
;
}
return
offset
;
}
/* ---------------------------------------------------------------------- */
int
DumpAtom
::
convert_noimage
(
int
n
,
double
*
mybuf
)
{
int
offset
=
0
;
int
m
=
0
;
for
(
int
i
=
0
;
i
<
n
;
i
++
)
{
if
(
offset
+
ONELINE
>
maxsbuf
)
{
if
((
bigint
)
maxsbuf
+
DELTA
>
MAXSMALLINT
)
return
-
1
;
maxsbuf
+=
DELTA
;
memory
->
grow
(
sbuf
,
maxsbuf
,
"dump:sbuf"
);
}
offset
+=
sprintf
(
&
sbuf
[
offset
],
format
,
static_cast
<
int
>
(
mybuf
[
m
]),
static_cast
<
int
>
(
mybuf
[
m
+
1
]),
mybuf
[
m
+
2
],
mybuf
[
m
+
3
],
mybuf
[
m
+
4
]);
m
+=
size_one
;
}
return
offset
;
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
write_binary
(
int
n
,
double
*
mybuf
)
{
n
*=
size_one
;
fwrite
(
&
n
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
mybuf
,
sizeof
(
double
),
n
,
fp
);
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
write_string
(
int
n
,
double
*
mybuf
)
{
fwrite
(
mybuf
,
sizeof
(
char
),
n
,
fp
);
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
write_lines_image
(
int
n
,
double
*
mybuf
)
{
int
m
=
0
;
for
(
int
i
=
0
;
i
<
n
;
i
++
)
{
fprintf
(
fp
,
format
,
static_cast
<
int
>
(
mybuf
[
m
]),
static_cast
<
int
>
(
mybuf
[
m
+
1
]),
mybuf
[
m
+
2
],
mybuf
[
m
+
3
],
mybuf
[
m
+
4
],
static_cast
<
int
>
(
mybuf
[
m
+
5
]),
static_cast
<
int
>
(
mybuf
[
m
+
6
]),
static_cast
<
int
>
(
mybuf
[
m
+
7
]));
m
+=
size_one
;
}
}
/* ---------------------------------------------------------------------- */
void
DumpAtom
::
write_lines_noimage
(
int
n
,
double
*
mybuf
)
{
int
m
=
0
;
for
(
int
i
=
0
;
i
<
n
;
i
++
)
{
fprintf
(
fp
,
format
,
static_cast
<
int
>
(
mybuf
[
m
]),
static_cast
<
int
>
(
mybuf
[
m
+
1
]),
mybuf
[
m
+
2
],
mybuf
[
m
+
3
],
mybuf
[
m
+
4
]);
m
+=
size_one
;
}
}
Event Timeline
Log In to Comment