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domain_lammps_dynamic.cc
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rLIBMULTISCALE LibMultiScale
domain_lammps_dynamic.cc
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/**
* @file domain_lammps_dynamic.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Jaehyun Cho <jaehyun.cho@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
*
* @date Tue Jan 21 09:03:57 2014
*
* @brief This is the generic LAMMPS model capable of explicit dynamics
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#define TIMER
//#define CHECK_STABILITY
#define VMAX 1e-2
/* -------------------------------------------------------------------------- */
#include "lm_common.hh"
#include "lammps_common.hh"
#include "domain_lammps_dynamic.hh"
#include "import_lammps.hh"
#include "trace_atom.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
// LAMMPS include files
#include "integrate.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "input.h"
#include "change_box.h"
/* -------------------------------------------------------------------------- */
__BEGIN_LIBMULTISCALE__
template
<
UInt
Dim
>
void
DomainLammpsDynamic
<
Dim
>::
init
(){
this
->
update
->
whichflag
=
1
;
LAMMPS_NS
::
LAMMPS
::
init
();
this
->
update
->
integrate
->
setup
();
this
->
initDOFs
();
this
->
atoms
.
getRefManager
().
setState
(
true
);
}
/* -------------------------------------------------------------------------- */
template
<
UInt
Dim
>
DomainLammpsDynamic
<
Dim
>::
DomainLammpsDynamic
(
DomainID
ID
,
CommGroup
GID
)
:
DomainLammps
<
Dim
>
(
ID
,
GID
)
{
}
/* -------------------------------------------------------------------------- */
template
<
UInt
Dim
>
void
DomainLammpsDynamic
<
Dim
>::
performStep1
(){
DomainLammps
<
Dim
>::
performStep1
();
VIEW_ATOM
(
RefLammps
<
Dim
>
);
STARTTIMER
(
"AtomStepPosition"
);
this
->
update
->
ntimestep
++
;
//this->update->eflag_global++; //to print out thermo values
//this->update->vflag_global++; //to print out thermo values
this
->
update
->
integrate
->
ev_set
(
this
->
update
->
ntimestep
);
this
->
modify
->
initial_integrate
(
0
);
this
->
echangeAtomes
();
STOPTIMER
(
"AtomStepPosition"
);
VIEW_ATOM
(
RefLammps
<
Dim
>
);
#ifdef CHECK_STABILITY
UInt
nlocal
=
atom
->
nlocal
;
UInt
nb_colded
=
0
;
for
(
UInt
i
=
0
;
i
<
nlocal
;
++
i
){
Real
vx
=
atom
->
v
[
i
][
0
];
Real
vy
=
atom
->
v
[
i
][
1
];
Real
vz
=
atom
->
v
[
i
][
2
];
Real
v2
=
vx
*
vx
+
vy
*
vy
+
vz
*
vz
;
if
(
v2
>
VMAX
*
VMAX
){
++
nb_colded
;
Real
vnew
=
VMAX
/
sqrt
(
v2
);
atom
->
v
[
i
][
0
]
*=
vnew
;
atom
->
v
[
i
][
1
]
*=
vnew
;
atom
->
v
[
i
][
2
]
*=
vnew
;
// atom->f[i][0] = 0;
// atom->f[i][1] = 0;
// atom->f[i][2] = 0;
}
}
// if (nb_colded) DUMP("simulation getting unstable, colding it artificially (nb_colded = " << nb_colded << ")",DBG_MESSAGE);
#endif
this
->
atoms
.
incRelease
();
}
/* -------------------------------------------------------------------------- */
template
<
UInt
Dim
>
void
DomainLammpsDynamic
<
Dim
>::
performStep3
(){
VIEW_ATOM
(
RefLammps
<
Dim
>
);
DUMP
(
"AtomStepVelocities x "
<<
this
->
atom
->
x
,
DBG_INFO
);
STARTTIMER
(
"AtomStepVelocities"
);
this
->
modify
->
final_integrate
();
if
(
this
->
modify
->
n_end_of_step
)
this
->
modify
->
end_of_step
();
if
(
LAMMPS_NS
::
LAMMPS
::
output
->
next
==
this
->
update
->
ntimestep
)
{
this
->
timer
->
stamp
();
LAMMPS_NS
::
LAMMPS
::
output
->
write
(
this
->
update
->
ntimestep
);
this
->
timer
->
stamp
(
TIME_OUTPUT
);
}
STOPTIMER
(
"AtomStepVelocities"
);
VIEW_ATOM
(
RefLammps
<
Dim
>
);
this
->
atoms
.
incRelease
();
}
/* -------------------------------------------------------------------------- */
template
<
UInt
Dim
>
void
DomainLammpsDynamic
<
Dim
>::
performStep2
(){
if
(
!
Communicator
::
getCommunicator
().
amIinGroup
(
this
->
getGroupID
()))
return
;
VIEW_ATOM
(
RefLammps
<
Dim
>
);
STARTTIMER
(
"AtomStepForces"
);
UInt
eflag
,
vflag
;
eflag
=
this
->
update
->
integrate
->
eflag
;
vflag
=
this
->
update
->
integrate
->
vflag
;
this
->
force_clear
(
vflag
);
if
(
this
->
modify
->
n_pre_force
)
this
->
modify
->
pre_force
(
vflag
);
this
->
timer
->
stamp
();
if
(
this
->
atom
->
molecular
)
{
if
(
this
->
force
->
bond
)
this
->
force
->
bond
->
compute
(
eflag
,
vflag
);
if
(
this
->
force
->
angle
)
this
->
force
->
angle
->
compute
(
eflag
,
vflag
);
if
(
this
->
force
->
dihedral
)
this
->
force
->
dihedral
->
compute
(
eflag
,
vflag
);
if
(
this
->
force
->
improper
)
this
->
force
->
improper
->
compute
(
eflag
,
vflag
);
this
->
timer
->
stamp
(
TIME_BOND
);
}
if
(
this
->
force
->
pair
)
{
this
->
force
->
pair
->
compute
(
eflag
,
vflag
);
this
->
timer
->
stamp
(
TIME_PAIR
);
}
if
(
this
->
force
->
kspace
)
{
this
->
force
->
kspace
->
compute
(
eflag
,
vflag
);
this
->
timer
->
stamp
(
TIME_KSPACE
);
}
if
(
this
->
force
->
newton
)
{
this
->
comm
->
reverse_comm
();
this
->
timer
->
stamp
(
TIME_COMM
);
}
if
(
this
->
modify
->
n_post_force
)
this
->
modify
->
post_force
(
vflag
);
STOPTIMER
(
"AtomStepForces"
);
VIEW_ATOM
(
RefLammps
<
Dim
>
);
this
->
atoms
.
incRelease
();
}
/* -------------------------------------------------------------------------- */
template
class
DomainLammpsDynamic
<
2
>
;
template
class
DomainLammpsDynamic
<
3
>
;
__END_LIBMULTISCALE__
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