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dumper_lammps.cc
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Sat, Aug 31, 06:58
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Mon, Sep 2, 06:58 (1 d, 21 h)
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rAKA akantu
dumper_lammps.cc
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/**
* @file dumper_lammps.cc
*
* @author Till Junge <till.junge@epfl.ch>
*
* @date creation: Thu Nov 25 2010
* @date last modification: Mon Jun 10 2013
*
* @brief implementation of lammps dumper
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <sstream>
#include "iohelper_common.hh"
#include "dumper_lammps.hh"
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
/// remark #981: operands are evaluated in unspecified order
#pragma warning ( disable : 981 )
#endif
//defined(__INTEL_COMPILER)
__BEGIN_IOHELPER__
template
<
LammpsAtomStyle
style
>
DumperLammps
<
style
>::
DumperLammps
(
Real
*
bounds
,
const
std
::
string
&
prefix
)
:
Dumper
(
prefix
),
bounds
(
bounds
)
{
this
->
registerDumpOptions
(
"lammps"
,
""
,
""
,
_df_proc_id
);
}
/* -------------------------------------------------------------------------- */
template
<
LammpsAtomStyle
style
>
void
DumperLammps
<
style
>::
dump
(
const
std
::
string
&
current_name
,
const
UInt
count
)
{
Dumper
::
dump
(
current_name
,
count
);
std
::
string
filename
=
this
->
getAbsoluteFilePath
(
this
->
getBaseName
(),
"lammps"
);
std
::
ios_base
::
openmode
mode
=
std
::
fstream
::
in
|
std
::
fstream
::
out
|
std
::
fstream
::
trunc
;
this
->
lammps_dump_file
.
open
(
filename
.
c_str
(),
mode
);
this
->
dumpHead
(
this
->
bounds
);
this
->
dumpAdd
();
this
->
dumpFinalize
();
this
->
incDumpStep
();
}
/* -------------------------------------------------------------------------- */
template
<
LammpsAtomStyle
style
>
void
DumperLammps
<
style
>::
dumpHead
(
Real
*
bounds
)
{
this
->
curr_nb_atom
=
0
;
if
(
!
this
->
lammps_dump_file
.
good
())
{
std
::
cerr
<<
"hach"
<<
std
::
endl
;
if
(
this
->
lammps_dump_file
.
rdstate
()
&
std
::
fstream
::
eofbit
)
std
::
cerr
<<
" 1 "
<<
std
::
endl
;
if
(
this
->
lammps_dump_file
.
rdstate
()
&
std
::
fstream
::
failbit
)
std
::
cerr
<<
" 2 "
<<
std
::
endl
;
if
(
this
->
lammps_dump_file
.
rdstate
()
&
std
::
fstream
::
badbit
)
std
::
cerr
<<
" 3 "
<<
std
::
endl
;
if
(
this
->
lammps_dump_file
.
rdstate
()
&
std
::
fstream
::
goodbit
)
std
::
cerr
<<
" 4 "
<<
std
::
endl
;
exit
(
-
1
);
}
this
->
lammps_dump_file
<<
"LAMMPS data file"
<<
std
::
endl
<<
std
::
endl
<<
std
::
endl
;
this
->
nb_atom_position
=
lammps_dump_file
.
tellp
();
//dump whitespaces to later fill in nb_atoms
this
->
lammps_dump_file
<<
" "
<<
std
::
endl
;
this
->
lammps_dump_file
<<
"0 bonds"
<<
std
::
endl
<<
"1 atom types"
<<
std
::
endl
<<
"0 bond types"
<<
std
::
endl
;
if
(
bounds
!=
NULL
)
{
this
->
lammps_dump_file
<<
std
::
endl
;
this
->
lammps_dump_file
<<
bounds
[
0
]
<<
" "
<<
bounds
[
1
]
<<
" xlo xhi"
<<
std
::
endl
;
this
->
lammps_dump_file
<<
bounds
[
2
]
<<
" "
<<
bounds
[
3
]
<<
" ylo yhi"
<<
std
::
endl
;
this
->
lammps_dump_file
<<
bounds
[
4
]
<<
" "
<<
bounds
[
5
]
<<
" zlo zhi"
<<
std
::
endl
;
this
->
lammps_dump_file
<<
std
::
endl
;
}
this
->
lammps_dump_file
<<
"Atoms"
<<
std
::
endl
<<
std
::
endl
;
this
->
lammps_dump_file
.
setf
(
std
::
ios
::
scientific
,
std
::
ios
::
floatfield
);
this
->
lammps_dump_file
.
precision
(
16
);
}
/* -------------------------------------------------------------------------- */
template
<
LammpsAtomStyle
style
>
void
DumperLammps
<
style
>::
dumpAdd
(
int
_grain_id
)
{
this
->
grain_id
=
_grain_id
;
per_node_data
[
std
::
string
(
"positions"
)]
->
accept
(
*
this
);
// ContainerArray<Real> cont(_points,_dimension,_nb);
// Field<ContainerArray<Real> > field(cont,"temporary");
// // set temporary values
// field.accept(*this);//this brings me to visit
}
/* -------------------------------------------------------------------------- */
template
<
LammpsAtomStyle
style
>
void
DumperLammps
<
style
>::
dumpFinalize
(){
this
->
lammps_dump_file
.
seekp
(
this
->
nb_atom_position
);
this
->
lammps_dump_file
<<
curr_nb_atom
<<
" atoms"
;
this
->
lammps_dump_file
.
close
();
}
/* -------------------------------------------------------------------------- */
template
class
DumperLammps
<
atomic
>
;
template
class
DumperLammps
<
bond
>
;
__END_IOHELPER__
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