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dumper_lammps.cc
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Mon, Sep 9, 04:25
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rLIBMULTISCALE LibMultiScale
dumper_lammps.cc
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/**
* @file dumper_lammps.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date Tue Aug 12 14:38:53 2014
*
* @brief This dumper allows to generate lammps text files
*
* @section LICENSE
*
* Copyright INRIA and CEA
*
* The LibMultiScale is a C++ parallel framework for the multiscale
* coupling methods dedicated to material simulations. This framework
* provides an API which makes it possible to program coupled simulations
* and integration of already existing codes.
*
* This Project was initiated in a collaboration between INRIA Futurs Bordeaux
* within ScAlApplix team and CEA/DPTA Ile de France.
* The project is now continued at the Ecole Polytechnique Fédérale de Lausanne
* within the LSMS/ENAC laboratory.
*
* This software is governed by the CeCILL-C license under French law and
* abiding by the rules of distribution of free software. You can use,
* modify and/ or redistribute the software under the terms of the CeCILL-C
* license as circulated by CEA, CNRS and INRIA at the following URL
* "http://www.cecill.info".
*
* As a counterpart to the access to the source code and rights to copy,
* modify and redistribute granted by the license, users are provided only
* with a limited warranty and the software's author, the holder of the
* economic rights, and the successive licensors have only limited
* liability.
*
* In this respect, the user's attention is drawn to the risks associated
* with loading, using, modifying and/or developing or reproducing the
* software by the user in light of its specific status of free software,
* that may mean that it is complicated to manipulate, and that also
* therefore means that it is reserved for developers and experienced
* professionals having in-depth computer knowledge. Users are therefore
* encouraged to load and test the software's suitability as regards their
* requirements in conditions enabling the security of their systems and/or
* data to be ensured and, more generally, to use and operate it in the
* same conditions as regards security.
*
* The fact that you are presently reading this means that you have had
* knowledge of the CeCILL-C license and that you accept its terms.
*
*/
#include "lm_common.hh"
#include "dumper_lammps.hh"
#include "lib_md.hh"
#include "lib_continuum.hh"
#include "lib_dd.hh"
#include "compute_extract.hh"
#include <iomanip>
#include "ref_point_data.hh"
#include "communicator.hh"
#include <fstream>
/* -------------------------------------------------------------------------- */
__BEGIN_LIBMULTISCALE__
template
<
typename
Cont
>
void
DumperLammps
<
Cont
>::
dump
(
Cont
&
cont
){
static
const
UInt
Dim
=
Cont
::
Dim
;
//get the parallel context
Communicator
&
comm
=
Communicator
::
getCommunicator
();
CommGroup
group
=
cont
.
getCommGroup
();
UInt
my_rank
=
comm
.
groupRank
(
lm_my_proc_id
,
group
);
UInt
nb_procs
=
comm
.
getNBprocsOnGroup
(
group
);
LM_ASSERT
(
nb_procs
==
1
,
"DumperLammps is not yet parallel"
);
//prepare to retreive data from all other processors
ComputeExtract
<
Cont
>
positions
(
"ComputeExtract:"
+
this
->
getID
(),
Dim
);
positions
.
setParam
(
"FIELD"
,
_position
);
positions
.
build
(
cont
);
ComputeExtract
<
Cont
>
velocities
(
"ComputeExtract:"
+
this
->
getID
(),
Dim
);
velocities
.
setParam
(
"FIELD"
,
_velocity
);
velocities
.
build
(
cont
);
UInt
nb_atoms
=
positions
.
getTotalNbData
()
/
Dim
;
std
::
ofstream
file
;
//open the file and write the headers
if
(
my_rank
==
0
){
std
::
stringstream
sstr
;
sstr
<<
this
->
getBaseName
()
<<
"_"
<<
current_step
<<
".lammps"
;
file
.
open
(
sstr
.
str
().
c_str
());
if
(
!
file
.
is_open
())
LM_FATAL
(
"could not open file "
<<
sstr
.
str
());
file
<<
"LAMMPS data file
\n\n\n
"
;
file
<<
nb_atoms
<<
" atoms
\n\n
"
;
UInt
ntypes
=
geometries_for_types
.
size
();
if
(
ntypes
==
0
)
++
ntypes
;
file
<<
ntypes
<<
" atom types
\n\n
"
;
const
Quantity
<
Length
,
3
>
&
xmin
=
cont
.
getBoundingBox
().
getXmin
();
const
Quantity
<
Length
,
3
>
&
xmax
=
cont
.
getBoundingBox
().
getXmax
();
for
(
UInt
i
=
0
;
i
<
3
;
++
i
)
{
file
<<
std
::
scientific
<<
std
::
setprecision
(
15
)
<<
xmin
[
i
]
<<
" "
<<
xmax
[
i
]
<<
" "
;
if
(
i
==
0
)
file
<<
"xlo xhi
\n
"
;
if
(
i
==
1
)
file
<<
"ylo yhi
\n
"
;
if
(
i
==
2
)
file
<<
"zlo zhi
\n
"
;
}
file
<<
"Masses
\n\n
"
;
file
<<
"1 "
<<
std
::
scientific
<<
std
::
setprecision
(
15
)
<<
cont
.
get
(
0
).
mass
()
<<
"
\n\n
"
;
file
<<
"Atoms
\n\n
"
;
}
UInt
index_atom
=
1
;
for
(
UInt
p
=
0
;
p
<
nb_procs
;
++
p
)
{
std
::
vector
<
Real
>
&
data1
=
positions
.
gatherData
(
p
);
if
(
my_rank
==
0
){
for
(
UInt
j
=
0
;
j
<
data1
.
size
()
/
Dim
;
++
j
,
++
index_atom
){
Real
X
[
3
]
=
{
0.
,
0.
,
0.
};
for
(
UInt
i
=
0
;
i
<
Dim
;
++
i
)
X
[
i
]
=
data1
[
j
*
Dim
+
i
];
UInt
type
=
1
;
for
(
UInt
g
=
0
;
g
<
geometries_for_types
.
size
();
++
g
){
Geometry
*
geom
=
geometries_for_types
[
g
];
if
(
geom
->
contains
<
Dim
>
(
X
))
type
=
g
+
1
;
}
file
<<
index_atom
<<
" "
<<
type
<<
" "
<<
X
[
0
]
<<
" "
<<
X
[
1
]
<<
" "
<<
X
[
2
]
<<
std
::
endl
;
}
}
}
index_atom
=
1
;
for
(
UInt
p
=
0
;
p
<
nb_procs
;
++
p
)
{
std
::
vector
<
Real
>
&
data2
=
velocities
.
gatherData
(
p
);
if
(
my_rank
==
0
){
file
<<
"Velocities"
<<
std
::
endl
;
file
<<
" "
<<
std
::
endl
;
for
(
UInt
j
=
0
;
j
<
data2
.
size
()
/
Dim
;
++
j
,
++
index_atom
){
Real
X
[
3
]
=
{
0.
,
0.
,
0.
};
for
(
UInt
i
=
0
;
i
<
Dim
;
++
i
)
X
[
i
]
=
data2
[
j
*
Dim
+
i
];
file
<<
index_atom
<<
" "
<<
X
[
0
]
<<
" "
<<
X
[
1
]
<<
" "
<<
X
[
2
]
<<
std
::
endl
;
}
}
}
file
.
close
();
}
/* -------------------------------------------------------------------------- */
/* LMDESC LAMMPS
This dumper ouputs LAMMPS text files
*/
/* LMHERITANCE dumper */
/* LMEXAMPLE DUMPER lmp LAMMPS INPUT md FREQ 100 PREFIX ./ */
template
<
typename
Cont
>
void
DumperLammps
<
Cont
>::
declareParams
(){
Dumper
<
Cont
>::
declareParams
();
// Till commented this, since the variable is not used. In any case, the current position is dumped, never the initial
//this->parseKeyword("MODE",mode);
// parseCumulativeKeyword("ADDTYPE",ParserGeometry,geometries_for_types);
// if ("ADDTYPE" == key){
// GeomID geom;
// Parser::parseGeometry(geom,line);
// geometries_for_types.push_back(GeometryManager::getManager().getGeometry(geom));
// return true;
// }
}
/* -------------------------------------------------------------------------- */
DECLARE_DUMPER_REF
(
DumperLammps
,
LIST_ATOM_MODEL
)
DECLARE_DUMPER_REF
(
DumperLammps
,
LIST_CONTINUUM_MODEL
)
DECLARE_DUMPER_REF
(
DumperLammps
,
LIST_DD_MODEL
)
DECLARE_DUMPER_REFPOINT
(
DumperLammps
)
DECLARE_DUMPER_GENERIC_MESH
(
DumperLammps
)
__END_LIBMULTISCALE__
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