Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F80897016
dump_cfg_gz.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, Sep 3, 03:37
Size
4 KB
Mime Type
text/x-c
Expires
Thu, Sep 5, 03:37 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
20401928
Attached To
rLAMMPS lammps
dump_cfg_gz.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 "dump_cfg_gz.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "update.h"
#include <string.h>
using
namespace
LAMMPS_NS
;
#define UNWRAPEXPAND 10.0
DumpCFGGZ
::
DumpCFGGZ
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
DumpCFG
(
lmp
,
narg
,
arg
)
{
gzFp
=
NULL
;
if
(
!
compressed
)
error
->
all
(
FLERR
,
"Dump cfg/gz only writes compressed files"
);
}
/* ---------------------------------------------------------------------- */
DumpCFGGZ
::~
DumpCFGGZ
()
{
if
(
gzFp
)
gzclose
(
gzFp
);
gzFp
=
NULL
;
fp
=
NULL
;
}
/* ----------------------------------------------------------------------
generic opening of a dump file
ASCII or binary or gzipped
some derived classes override this function
------------------------------------------------------------------------- */
void
DumpCFGGZ
::
openfile
()
{
// single file, already opened, so just return
if
(
singlefile_opened
)
return
;
if
(
multifile
==
0
)
singlefile_opened
=
1
;
// if one file per timestep, replace '*' with current timestep
char
*
filecurrent
=
filename
;
if
(
multiproc
)
filecurrent
=
multiname
;
if
(
multifile
)
{
char
*
filestar
=
filecurrent
;
filecurrent
=
new
char
[
strlen
(
filestar
)
+
16
];
char
*
ptr
=
strchr
(
filestar
,
'*'
);
*
ptr
=
'\0'
;
if
(
padflag
==
0
)
sprintf
(
filecurrent
,
"%s"
BIGINT_FORMAT
"%s"
,
filestar
,
update
->
ntimestep
,
ptr
+
1
);
else
{
char
bif
[
8
],
pad
[
16
];
strcpy
(
bif
,
BIGINT_FORMAT
);
sprintf
(
pad
,
"%%s%%0%d%s%%s"
,
padflag
,
&
bif
[
1
]);
sprintf
(
filecurrent
,
pad
,
filestar
,
update
->
ntimestep
,
ptr
+
1
);
}
*
ptr
=
'*'
;
}
// each proc with filewriter = 1 opens a file
if
(
filewriter
)
{
if
(
append_flag
)
{
gzFp
=
gzopen
(
filecurrent
,
"ab9"
);
}
else
{
gzFp
=
gzopen
(
filecurrent
,
"wb9"
);
}
if
(
gzFp
==
NULL
)
error
->
one
(
FLERR
,
"Cannot open dump file"
);
}
else
gzFp
=
NULL
;
// delete string with timestep replaced
if
(
multifile
)
delete
[]
filecurrent
;
}
/* ---------------------------------------------------------------------- */
void
DumpCFGGZ
::
write_header
(
bigint
n
)
{
// set scale factor used by AtomEye for CFG viz
// default = 1.0
// for peridynamics, set to pre-computed PD scale factor
// so PD particles mimic C atoms
// for unwrapped coords, set to UNWRAPEXPAND (10.0)
// so molecules are not split across periodic box boundaries
double
scale
=
1.0
;
if
(
atom
->
peri_flag
)
scale
=
atom
->
pdscale
;
else
if
(
unwrapflag
==
1
)
scale
=
UNWRAPEXPAND
;
char
str
[
64
];
sprintf
(
str
,
"Number of particles = %s
\n
"
,
BIGINT_FORMAT
);
gzprintf
(
gzFp
,
str
,
n
);
gzprintf
(
gzFp
,
"A = %g Angstrom (basic length-scale)
\n
"
,
scale
);
gzprintf
(
gzFp
,
"H0(1,1) = %g A
\n
"
,
domain
->
xprd
);
gzprintf
(
gzFp
,
"H0(1,2) = 0 A
\n
"
);
gzprintf
(
gzFp
,
"H0(1,3) = 0 A
\n
"
);
gzprintf
(
gzFp
,
"H0(2,1) = %g A
\n
"
,
domain
->
xy
);
gzprintf
(
gzFp
,
"H0(2,2) = %g A
\n
"
,
domain
->
yprd
);
gzprintf
(
gzFp
,
"H0(2,3) = 0 A
\n
"
);
gzprintf
(
gzFp
,
"H0(3,1) = %g A
\n
"
,
domain
->
xz
);
gzprintf
(
gzFp
,
"H0(3,2) = %g A
\n
"
,
domain
->
yz
);
gzprintf
(
gzFp
,
"H0(3,3) = %g A
\n
"
,
domain
->
zprd
);
gzprintf
(
gzFp
,
".NO_VELOCITY.
\n
"
);
gzprintf
(
gzFp
,
"entry_count = %d
\n
"
,
nfield
-
2
);
for
(
int
i
=
0
;
i
<
nfield
-
5
;
i
++
)
gzprintf
(
gzFp
,
"auxiliary[%d] = %s
\n
"
,
i
,
auxname
[
i
]);
}
/* ---------------------------------------------------------------------- */
void
DumpCFGGZ
::
write_data
(
int
n
,
double
*
mybuf
)
{
gzwrite
(
gzFp
,
mybuf
,
sizeof
(
char
)
*
n
);
}
/* ---------------------------------------------------------------------- */
void
DumpCFGGZ
::
write
()
{
DumpCFG
::
write
();
if
(
filewriter
)
{
if
(
multifile
)
{
gzclose
(
gzFp
);
gzFp
=
NULL
;
}
else
{
if
(
flush_flag
)
gzflush
(
gzFp
,
Z_SYNC_FLUSH
);
}
}
}
Event Timeline
Log In to Comment