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rLIBMULTISCALE LibMultiScale
import_lammps.hh
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/**
* @file import_lammps.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date Mon Oct 28 19:23:14 2013
*
* @brief The programming hooks to let LM be aware of processor migrations
*
* @section LICENSE
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* LibMultiScale 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.
*
* LibMultiScale 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 LibMultiScale. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __LIBMULTISCALE_IMPORT_LAMMPS_HH__
#define __LIBMULTISCALE_IMPORT_LAMMPS_HH__
/* -------------------------------------------------------------------------- */
#include "reference_manager_lammps.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_LIBMULTISCALE__
/* -------------------------------------------------------------------------- */
class
ImportLammpsInterface
{
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public
:
template
<
UInt
Dim
>
static
void
createImportLammps
(
ReferenceManagerLammps
<
Dim
>
&
ref_manager
);
static
ImportLammpsInterface
&
getImport
(){
if
(
import
==
NULL
)
LM_FATAL
(
"function createImportLammps was not previously called"
);
return
*
import
;
};
static
void
setGeom
(
Geometry
*
g
,
UInt
itype
=
0
){
import
->
geom
[
itype
]
=
g
;
};
Geometry
&
getGeom
(
UInt
itype
=
0
){
if
(
import
->
geom
.
count
(
itype
)
==
0
)
return
*
import
->
geom
[
0
];
else
return
*
import
->
geom
[
itype
];
};
virtual
void
init
(
LAMMPS_NS
::
Domain
&
domain
,
LAMMPS_NS
::
Atom
&
atom
,
LAMMPS_NS
::
Comm
&
comm
,
MPI_Comm
&
world
,
int
me
,
int
nprocs
)
=
0
;
virtual
void
moveAtom
(
UInt
i
,
UInt
j
)
=
0
;
virtual
void
atomCommunications
()
=
0
;
virtual
void
updateRefSubSets
()
=
0
;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private
:
std
::
map
<
UInt
,
Geometry
*>
geom
;
static
ImportLammpsInterface
*
import
;
};
/* -------------------------------------------------------------------------- */
template
<
UInt
Dim
>
class
ImportLammps
:
public
ImportLammpsInterface
{
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
class
Tensor
{
public
:
void
resize
(
int
nb
[
3
]){
// DUMP("resize " << nb[0] << " " << nb[1] << " " << nb[2],DBG_MESSAGE);
array
.
resize
(
nb
[
0
]
*
nb
[
1
]
*
nb
[
2
]);
for
(
UInt
i
=
0
;
i
<
3
;
++
i
)
sizes
[
i
]
=
nb
[
i
];
};
int
&
operator
[](
int
index
[
3
]){
// DUMP("access " << index[0] << " " << index[1] << " " << index[2],DBG_MESSAGE);
// for (UInt i = 0; i < sizes[0]*sizes[1]*sizes[2]; ++i) {
// DUMP("val[" << i << "] = " << array[i],DBG_MESSAGE);
// }
return
array
[
index
[
0
]
+
index
[
1
]
*
sizes
[
0
]
+
index
[
2
]
*
sizes
[
0
]
*
sizes
[
1
]];
};
private
:
std
::
vector
<
int
>
array
;
UInt
sizes
[
3
];
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public
:
ImportLammps
(
ReferenceManagerLammps
<
Dim
>
&
r
)
:
ref_manager
(
r
){};
virtual
~
ImportLammps
(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public
:
void
init
(
LAMMPS_NS
::
Domain
&
domain
,
LAMMPS_NS
::
Atom
&
atom
,
LAMMPS_NS
::
Comm
&
comm
,
MPI_Comm
&
world
,
int
me
,
int
nprocs
);
void
setPeriodic
(
int
per
[
3
]){
for
(
UInt
i
=
0
;
i
<
3
;
++
i
)
periodic
[
i
]
=
per
[
i
];
};
void
setPeriodic
(
int
perx
,
int
pery
,
int
perz
){
periodic
[
0
]
=
perx
;
periodic
[
1
]
=
pery
;
periodic
[
2
]
=
perz
;
};
inline
void
registerSend
(
UInt
at
,
UInt
toProc
);
void
registerSends
();
void
atomCommunications
();
void
atomCommunication
();
void
setupTopology
();
int
getProcNumber
(
int
index
[
3
],
int
offset
[
3
]);
void
checkConsistency
();
void
unPackAtoms
(
UInt
procDe
);
void
acceptAtom
(
UInt
i
,
UInt
fromProc
){
ref_manager
.
acceptAtom
(
i
,
fromProc
);};
void
sendAtom
(
UInt
i
,
UInt
toProc
){
ref_manager
.
sendAtom
(
i
,
toProc
);};
void
moveAtom
(
UInt
i
,
UInt
j
){
ref_manager
.
moveAtom
(
i
,
j
);};
void
updateRefSubSets
(){
ref_manager
.
updateRefSubSets
();};
private
:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public
:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private
:
int
periodic
[
3
];
Real
*
Xlo
;
Real
*
Xhi
;
int
comProcs
[
26
];
std
::
vector
<
std
::
vector
<
Real
>
>
buf_send
;
std
::
vector
<
std
::
vector
<
Real
>
>
buf_recv
;
std
::
vector
<
UInt
>
proc_comm
;
UInt
packSize
;
int
nbrProc
[
3
];
Tensor
proc_matrix
;
ReferenceManagerLammps
<
Dim
>
&
ref_manager
;
int
me
;
MPI_Comm
world
;
int
nprocs
;
int
old_nlocal
;
LAMMPS_NS
::
Atom
*
atom
;
LAMMPS_NS
::
Domain
*
domain
;
LAMMPS_NS
::
Comm
*
comm
;
};
/* -------------------------------------------------------------------------- */
template
<
UInt
Dim
>
void
ImportLammpsInterface
::
createImportLammps
(
ReferenceManagerLammps
<
Dim
>
&
ref_manager
){
import
=
new
ImportLammps
<
Dim
>
(
ref_manager
);
}
/* -------------------------------------------------------------------------- */
__END_LIBMULTISCALE__
#endif
/* __LIBMULTISCALE_IMPORT_LAMMPS_HH__ */
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