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dump_atom.cpp
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Wed, Sep 4, 22:56
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14 KB
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text/x-c
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Fri, Sep 6, 22:56 (2 d)
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blob
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20484405
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rLAMMPS lammps
dump_atom.cpp
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/* ----------------------------------------------------------------------
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
;
}
}
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