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Sat, Oct 19, 17:39
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text/x-c
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Mon, Oct 21, 17:39 (2 d)
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rLAMMPS lammps
binary2txt.cpp
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/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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.
------------------------------------------------------------------------ */
// Convert one or more LAMMPS binary dump files to ASCII text files
//
// this serial code must be compiled on a platform that can read the binary
// dump files since binary formats are not compatible across all platforms
//
// Syntax: binary2txt file1 file2 ...
// Creates: file1.txt file2.txt ...
#include <stdio.h>
#include <string.h>
// these must match settings in src/lmptype.h which builds LAMMPS with
// -DLAMMPS_SMALLBIG (the default), -DLAMMPS_BIGBIG, or -DLAMMPS_SMALLSMALL
// you can edit the tools/Makefile to enforce the same setting
// for the build of binary2txt, e.g.
// g++ -g -DLAMMPS_BIGBIG binarytxt.o -o binary2txt
// again -DLAMMPS_SMALLBIG is the default
#include "stdint.h"
#define __STDC_FORMAT_MACROS
#include "inttypes.h"
#ifndef PRId64
#define PRId64 "ld"
#endif
#if !defined(LAMMPS_SMALLSMALL) && !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
#define LAMMPS_SMALLBIG
#endif
#if defined(LAMMPS_SMALLBIG)
typedef
int
tagint
;
typedef
int64_t
bigint
;
#define BIGINT_FORMAT "%" PRId64
#elif defined(LAMMPS_SMALLSMALL)
typedef
int
tagint
;
typedef
int
bigint
;
#define BIGINT_FORMAT "%d"
#else
/* LAMMPS_BIGBIG */
typedef
int64_t
tagint
;
typedef
int64_t
bigint
;
#define BIGINT_FORMAT "%" PRId64
#endif
int
main
(
int
narg
,
char
**
arg
)
{
int
i
,
j
,
k
,
m
,
n
;
bigint
ntimestep
,
natoms
;
int
size_one
,
nchunk
,
triclinic
;
double
xlo
,
xhi
,
ylo
,
yhi
,
zlo
,
zhi
,
xy
,
xz
,
yz
;
int
boundary
[
3
][
2
];
char
boundstr
[
9
];
int
maxbuf
=
0
;
double
*
buf
=
NULL
;
if
(
narg
==
1
)
{
printf
(
"Syntax: binary2txt file1 file2 ...
\n
"
);
return
1
;
}
// loop over files
for
(
int
iarg
=
1
;
iarg
<
narg
;
iarg
++
)
{
printf
(
"%s:"
,
arg
[
iarg
]);
fflush
(
stdout
);
FILE
*
fp
=
fopen
(
arg
[
iarg
],
"rb"
);
if
(
!
fp
)
{
printf
(
"ERROR: Could not open %s
\n
"
,
arg
[
iarg
]);
return
1
;
}
n
=
strlen
(
arg
[
iarg
])
+
1
+
4
;
char
*
filetxt
=
new
char
[
n
];
strcpy
(
filetxt
,
arg
[
iarg
]);
strcat
(
filetxt
,
".txt"
);
FILE
*
fptxt
=
fopen
(
filetxt
,
"w"
);
delete
[]
filetxt
;
// loop over snapshots in file
while
(
1
)
{
fread
(
&
ntimestep
,
sizeof
(
bigint
),
1
,
fp
);
// detect end-of-file
if
(
feof
(
fp
))
{
fclose
(
fp
);
fclose
(
fptxt
);
break
;
}
fread
(
&
natoms
,
sizeof
(
bigint
),
1
,
fp
);
fread
(
&
triclinic
,
sizeof
(
int
),
1
,
fp
);
fread
(
&
boundary
[
0
][
0
],
6
*
sizeof
(
int
),
1
,
fp
);
fread
(
&
xlo
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
xhi
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
ylo
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
yhi
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
zlo
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
zhi
,
sizeof
(
double
),
1
,
fp
);
if
(
triclinic
)
{
fread
(
&
xy
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
xz
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
yz
,
sizeof
(
double
),
1
,
fp
);
}
fread
(
&
size_one
,
sizeof
(
int
),
1
,
fp
);
fread
(
&
nchunk
,
sizeof
(
int
),
1
,
fp
);
fprintf
(
fptxt
,
"ITEM: TIMESTEP
\n
"
);
fprintf
(
fptxt
,
BIGINT_FORMAT
"
\n
"
,
ntimestep
);
fprintf
(
fptxt
,
"ITEM: NUMBER OF ATOMS
\n
"
);
fprintf
(
fptxt
,
BIGINT_FORMAT
"
\n
"
,
natoms
);
m
=
0
;
for
(
int
idim
=
0
;
idim
<
3
;
idim
++
)
{
for
(
int
iside
=
0
;
iside
<
2
;
iside
++
)
{
if
(
boundary
[
idim
][
iside
]
==
0
)
boundstr
[
m
++
]
=
'p'
;
else
if
(
boundary
[
idim
][
iside
]
==
1
)
boundstr
[
m
++
]
=
'f'
;
else
if
(
boundary
[
idim
][
iside
]
==
2
)
boundstr
[
m
++
]
=
's'
;
else
if
(
boundary
[
idim
][
iside
]
==
3
)
boundstr
[
m
++
]
=
'm'
;
}
boundstr
[
m
++
]
=
' '
;
}
boundstr
[
8
]
=
'\0'
;
if
(
!
triclinic
)
{
fprintf
(
fptxt
,
"ITEM: BOX BOUNDS %s
\n
"
,
boundstr
);
fprintf
(
fptxt
,
"%g %g
\n
"
,
xlo
,
xhi
);
fprintf
(
fptxt
,
"%g %g
\n
"
,
ylo
,
yhi
);
fprintf
(
fptxt
,
"%g %g
\n
"
,
zlo
,
zhi
);
}
else
{
fprintf
(
fptxt
,
"ITEM: BOX BOUNDS %s xy xz yz
\n
"
,
boundstr
);
fprintf
(
fptxt
,
"%g %g %g
\n
"
,
xlo
,
xhi
,
xy
);
fprintf
(
fptxt
,
"%g %g %g
\n
"
,
ylo
,
yhi
,
xz
);
fprintf
(
fptxt
,
"%g %g %g
\n
"
,
zlo
,
zhi
,
yz
);
}
fprintf
(
fptxt
,
"ITEM: ATOMS
\n
"
);
// loop over processor chunks in file
for
(
i
=
0
;
i
<
nchunk
;
i
++
)
{
fread
(
&
n
,
sizeof
(
int
),
1
,
fp
);
// extend buffer to fit chunk size
if
(
n
>
maxbuf
)
{
if
(
buf
)
delete
[]
buf
;
buf
=
new
double
[
n
];
maxbuf
=
n
;
}
// read chunk and write as size_one values per line
fread
(
buf
,
sizeof
(
double
),
n
,
fp
);
n
/=
size_one
;
m
=
0
;
for
(
j
=
0
;
j
<
n
;
j
++
)
{
for
(
k
=
0
;
k
<
size_one
;
k
++
)
fprintf
(
fptxt
,
"%g "
,
buf
[
m
++
]);
fprintf
(
fptxt
,
"
\n
"
);
}
}
printf
(
" "
BIGINT_FORMAT
,
ntimestep
);
fflush
(
stdout
);
}
printf
(
"
\n
"
);
}
if
(
buf
)
delete
[]
buf
;
return
0
;
}
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