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respa_omp.cpp
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Tue, Aug 27, 04:59
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Thu, Aug 29, 04:59 (1 d, 23 h)
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20203962
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rLAMMPS lammps
respa_omp.cpp
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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#include "respa_omp.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "atom.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "output.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "fix_respa.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
#if defined(_OPENMP)
#include <omp.h>
#endif
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
RespaOMP
::
RespaOMP
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Respa
(
lmp
,
narg
,
arg
),
ThrOMP
(
lmp
,
THR_INTGR
)
{
}
/* ----------------------------------------------------------------------
initialization before run
------------------------------------------------------------------------- */
void
RespaOMP
::
init
()
{
Respa
::
init
();
if
(
atom
->
torque
)
error
->
all
(
FLERR
,
"Extended particles are not supported by respa/omp
\n
"
);
}
/* ----------------------------------------------------------------------
setup before run
------------------------------------------------------------------------- */
void
RespaOMP
::
setup
()
{
if
(
comm
->
me
==
0
&&
screen
)
fprintf
(
screen
,
"Setting up run ...
\n
"
);
update
->
setupflag
=
1
;
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
atom
->
setup
();
modify
->
setup_pre_exchange
();
if
(
triclinic
)
domain
->
x2lamda
(
atom
->
nlocal
);
domain
->
pbc
();
domain
->
reset_box
();
comm
->
setup
();
if
(
neighbor
->
style
)
neighbor
->
setup_bins
();
comm
->
exchange
();
if
(
atom
->
sortfreq
>
0
)
atom
->
sort
();
comm
->
borders
();
if
(
triclinic
)
domain
->
lamda2x
(
atom
->
nlocal
+
atom
->
nghost
);
domain
->
image_check
();
domain
->
box_too_small_check
();
modify
->
setup_pre_neighbor
();
neighbor
->
build
();
neighbor
->
ncalls
=
0
;
// compute all forces
ev_set
(
update
->
ntimestep
);
for
(
int
ilevel
=
0
;
ilevel
<
nlevels
;
ilevel
++
)
{
force_clear
(
newton
[
ilevel
]);
modify
->
setup_pre_force_respa
(
vflag
,
ilevel
);
if
(
level_bond
==
ilevel
&&
force
->
bond
)
force
->
bond
->
compute
(
eflag
,
vflag
);
if
(
level_angle
==
ilevel
&&
force
->
angle
)
force
->
angle
->
compute
(
eflag
,
vflag
);
if
(
level_dihedral
==
ilevel
&&
force
->
dihedral
)
force
->
dihedral
->
compute
(
eflag
,
vflag
);
if
(
level_improper
==
ilevel
&&
force
->
improper
)
force
->
improper
->
compute
(
eflag
,
vflag
);
if
(
level_pair
==
ilevel
&&
pair_compute_flag
)
force
->
pair
->
compute
(
eflag
,
vflag
);
if
(
level_inner
==
ilevel
&&
pair_compute_flag
)
force
->
pair
->
compute_inner
();
if
(
level_middle
==
ilevel
&&
pair_compute_flag
)
force
->
pair
->
compute_middle
();
if
(
level_outer
==
ilevel
&&
pair_compute_flag
)
force
->
pair
->
compute_outer
(
eflag
,
vflag
);
if
(
level_kspace
==
ilevel
&&
force
->
kspace
)
{
force
->
kspace
->
setup
();
if
(
kspace_compute_flag
)
force
->
kspace
->
compute
(
eflag
,
vflag
);
}
// reduce forces from per-thread arrays, if needed
if
(
!
fix
->
get_reduced
())
{
const
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
const
int
nthreads
=
comm
->
nthreads
;
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
{
#if defined(_OPENMP)
int
tid
=
omp_get_thread_num
();
#else
int
tid
=
0
;
#endif
data_reduce_thr
(
atom
->
f
[
0
],
nall
,
nthreads
,
3
,
tid
);
}
fix
->
did_reduce
();
}
if
(
newton
[
ilevel
])
comm
->
reverse_comm
();
copy_f_flevel
(
ilevel
);
}
modify
->
setup
(
vflag
);
sum_flevel_f
();
output
->
setup
();
update
->
setupflag
=
0
;
}
/* ----------------------------------------------------------------------
setup without output
flag = 0 = just force calculation
flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */
void
RespaOMP
::
setup_minimal
(
int
flag
)
{
update
->
setupflag
=
1
;
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if
(
flag
)
{
modify
->
setup_pre_exchange
();
if
(
triclinic
)
domain
->
x2lamda
(
atom
->
nlocal
);
domain
->
pbc
();
domain
->
reset_box
();
comm
->
setup
();
if
(
neighbor
->
style
)
neighbor
->
setup_bins
();
comm
->
exchange
();
comm
->
borders
();
if
(
triclinic
)
domain
->
lamda2x
(
atom
->
nlocal
+
atom
->
nghost
);
domain
->
image_check
();
domain
->
box_too_small_check
();
modify
->
setup_pre_neighbor
();
neighbor
->
build
();
neighbor
->
ncalls
=
0
;
}
// compute all forces
ev_set
(
update
->
ntimestep
);
for
(
int
ilevel
=
0
;
ilevel
<
nlevels
;
ilevel
++
)
{
force_clear
(
newton
[
ilevel
]);
modify
->
setup_pre_force_respa
(
vflag
,
ilevel
);
if
(
level_bond
==
ilevel
&&
force
->
bond
)
force
->
bond
->
compute
(
eflag
,
vflag
);
if
(
level_angle
==
ilevel
&&
force
->
angle
)
force
->
angle
->
compute
(
eflag
,
vflag
);
if
(
level_dihedral
==
ilevel
&&
force
->
dihedral
)
force
->
dihedral
->
compute
(
eflag
,
vflag
);
if
(
level_improper
==
ilevel
&&
force
->
improper
)
force
->
improper
->
compute
(
eflag
,
vflag
);
if
(
level_pair
==
ilevel
&&
pair_compute_flag
)
force
->
pair
->
compute
(
eflag
,
vflag
);
if
(
level_inner
==
ilevel
&&
pair_compute_flag
)
force
->
pair
->
compute_inner
();
if
(
level_middle
==
ilevel
&&
pair_compute_flag
)
force
->
pair
->
compute_middle
();
if
(
level_outer
==
ilevel
&&
pair_compute_flag
)
force
->
pair
->
compute_outer
(
eflag
,
vflag
);
if
(
level_kspace
==
ilevel
&&
force
->
kspace
)
{
force
->
kspace
->
setup
();
if
(
kspace_compute_flag
)
force
->
kspace
->
compute
(
eflag
,
vflag
);
}
// reduce forces from per-thread arrays, if needed
if
(
!
fix
->
get_reduced
())
{
const
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
const
int
nthreads
=
comm
->
nthreads
;
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
{
#if defined(_OPENMP)
int
tid
=
omp_get_thread_num
();
#else
int
tid
=
0
;
#endif
data_reduce_thr
(
atom
->
f
[
0
],
nall
,
nthreads
,
3
,
tid
);
}
fix
->
did_reduce
();
}
if
(
newton
[
ilevel
])
comm
->
reverse_comm
();
copy_f_flevel
(
ilevel
);
}
modify
->
setup
(
vflag
);
sum_flevel_f
();
update
->
setupflag
=
0
;
}
/* ---------------------------------------------------------------------- */
void
RespaOMP
::
recurse
(
int
ilevel
)
{
copy_flevel_f
(
ilevel
);
for
(
int
iloop
=
0
;
iloop
<
loop
[
ilevel
];
iloop
++
)
{
timer
->
stamp
();
modify
->
initial_integrate_respa
(
vflag
,
ilevel
,
iloop
);
if
(
modify
->
n_post_integrate_respa
)
modify
->
post_integrate_respa
(
ilevel
,
iloop
);
timer
->
stamp
(
Timer
::
MODIFY
);
if
(
ilevel
)
recurse
(
ilevel
-
1
);
// at outermost level, check on rebuilding neighbor list
// at innermost level, communicate
// at middle levels, do nothing
if
(
ilevel
==
nlevels
-
1
)
{
int
nflag
=
neighbor
->
decide
();
if
(
nflag
)
{
if
(
modify
->
n_pre_exchange
)
{
timer
->
stamp
();
modify
->
pre_exchange
();
timer
->
stamp
(
Timer
::
MODIFY
);
}
if
(
triclinic
)
domain
->
x2lamda
(
atom
->
nlocal
);
domain
->
pbc
();
if
(
domain
->
box_change
)
{
domain
->
reset_box
();
comm
->
setup
();
if
(
neighbor
->
style
)
neighbor
->
setup_bins
();
}
timer
->
stamp
();
comm
->
exchange
();
if
(
atom
->
sortfreq
>
0
&&
update
->
ntimestep
>=
atom
->
nextsort
)
atom
->
sort
();
comm
->
borders
();
timer
->
stamp
(
Timer
::
COMM
);
if
(
triclinic
)
domain
->
lamda2x
(
atom
->
nlocal
+
atom
->
nghost
);
if
(
modify
->
n_pre_neighbor
)
{
timer
->
stamp
();
modify
->
pre_neighbor
();
timer
->
stamp
(
Timer
::
MODIFY
);
}
neighbor
->
build
();
timer
->
stamp
(
Timer
::
NEIGHBOR
);
}
}
else
if
(
ilevel
==
0
)
{
timer
->
stamp
();
comm
->
forward_comm
();
timer
->
stamp
(
Timer
::
COMM
);
}
force_clear
(
newton
[
ilevel
]);
if
(
modify
->
n_pre_force_respa
)
{
timer
->
stamp
();
modify
->
pre_force_respa
(
vflag
,
ilevel
,
iloop
);
timer
->
stamp
(
Timer
::
MODIFY
);
}
timer
->
stamp
();
if
(
level_bond
==
ilevel
&&
force
->
bond
)
{
force
->
bond
->
compute
(
eflag
,
vflag
);
timer
->
stamp
(
Timer
::
BOND
);
}
if
(
level_angle
==
ilevel
&&
force
->
angle
)
{
force
->
angle
->
compute
(
eflag
,
vflag
);
timer
->
stamp
(
Timer
::
BOND
);
}
if
(
level_dihedral
==
ilevel
&&
force
->
dihedral
)
{
force
->
dihedral
->
compute
(
eflag
,
vflag
);
timer
->
stamp
(
Timer
::
BOND
);
}
if
(
level_improper
==
ilevel
&&
force
->
improper
)
{
force
->
improper
->
compute
(
eflag
,
vflag
);
timer
->
stamp
(
Timer
::
BOND
);
}
if
(
level_pair
==
ilevel
&&
pair_compute_flag
)
{
force
->
pair
->
compute
(
eflag
,
vflag
);
timer
->
stamp
(
Timer
::
PAIR
);
}
if
(
level_inner
==
ilevel
&&
pair_compute_flag
)
{
force
->
pair
->
compute_inner
();
timer
->
stamp
(
Timer
::
PAIR
);
}
if
(
level_middle
==
ilevel
&&
pair_compute_flag
)
{
force
->
pair
->
compute_middle
();
timer
->
stamp
(
Timer
::
PAIR
);
}
if
(
level_outer
==
ilevel
&&
pair_compute_flag
)
{
force
->
pair
->
compute_outer
(
eflag
,
vflag
);
timer
->
stamp
(
Timer
::
PAIR
);
}
if
(
level_kspace
==
ilevel
&&
kspace_compute_flag
)
{
force
->
kspace
->
compute
(
eflag
,
vflag
);
timer
->
stamp
(
Timer
::
KSPACE
);
}
// reduce forces from per-thread arrays, if needed
if
(
!
fix
->
get_reduced
())
{
const
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
const
int
nthreads
=
comm
->
nthreads
;
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
{
#if defined(_OPENMP)
int
tid
=
omp_get_thread_num
();
#else
int
tid
=
0
;
#endif
data_reduce_thr
(
atom
->
f
[
0
],
nall
,
nthreads
,
3
,
tid
);
}
fix
->
did_reduce
();
}
if
(
newton
[
ilevel
])
{
comm
->
reverse_comm
();
timer
->
stamp
(
Timer
::
COMM
);
}
timer
->
stamp
();
if
(
modify
->
n_post_force_respa
)
modify
->
post_force_respa
(
vflag
,
ilevel
,
iloop
);
modify
->
final_integrate_respa
(
ilevel
,
iloop
);
timer
->
stamp
(
Timer
::
MODIFY
);
}
copy_f_flevel
(
ilevel
);
}
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