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verlet_intel.cpp
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Sun, Aug 25, 10:25
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Tue, Aug 27, 10:25 (2 d)
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rLAMMPS lammps
verlet_intel.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.
------------------------------------------------------------------------- */
#include "string.h"
#include "verlet_intel.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.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
VerletIntel
::
VerletIntel
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Integrate
(
lmp
,
narg
,
arg
)
{}
/* ----------------------------------------------------------------------
initialization before run
------------------------------------------------------------------------- */
void
VerletIntel
::
init
()
{
Integrate
::
init
();
// warn if no fixes
if
(
modify
->
nfix
==
0
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"No fixes defined, atoms won't move"
);
// virial_style:
// 1 if computed explicitly by pair->compute via sum over pair interactions
// 2 if computed implicitly by pair->virial_fdotr_compute via sum over ghosts
if
(
force
->
newton_pair
)
virial_style
=
2
;
else
virial_style
=
1
;
// setup lists of computes for global and per-atom PE and pressure
ev_setup
();
// detect if fix omp is present for clearing force arrays
int
ifix
=
modify
->
find_fix
(
"package_omp"
);
if
(
ifix
>=
0
)
external_force_clear
=
1
;
if
(
nvlist_atom
)
error
->
all
(
FLERR
,
"Cannot currently get per-atom virials with Intel package."
);
#ifdef _LMP_INTEL_OFFLOAD
ifix
=
modify
->
find_fix
(
"package_intel"
);
if
(
ifix
>=
0
)
fix_intel
=
static_cast
<
FixIntel
*>
(
modify
->
fix
[
ifix
]);
else
fix_intel
=
0
;
#endif
// set flags for what arrays to clear in force_clear()
// need to clear additionals arrays if they exist
torqueflag
=
0
;
if
(
atom
->
torque_flag
)
torqueflag
=
1
;
erforceflag
=
0
;
if
(
atom
->
erforce_flag
)
erforceflag
=
1
;
e_flag
=
0
;
if
(
atom
->
e_flag
)
e_flag
=
1
;
rho_flag
=
0
;
if
(
atom
->
rho_flag
)
rho_flag
=
1
;
// orthogonal vs triclinic simulation box
triclinic
=
domain
->
triclinic
;
}
/* ----------------------------------------------------------------------
setup before run
------------------------------------------------------------------------- */
void
VerletIntel
::
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
);
force_clear
();
modify
->
setup_pre_force
(
vflag
);
if
(
pair_compute_flag
)
force
->
pair
->
compute
(
eflag
,
vflag
);
else
if
(
force
->
pair
)
force
->
pair
->
compute_dummy
(
eflag
,
vflag
);
if
(
atom
->
molecular
)
{
if
(
force
->
bond
)
force
->
bond
->
compute
(
eflag
,
vflag
);
if
(
force
->
angle
)
force
->
angle
->
compute
(
eflag
,
vflag
);
if
(
force
->
dihedral
)
force
->
dihedral
->
compute
(
eflag
,
vflag
);
if
(
force
->
improper
)
force
->
improper
->
compute
(
eflag
,
vflag
);
}
if
(
force
->
kspace
)
{
force
->
kspace
->
setup
();
if
(
kspace_compute_flag
)
force
->
kspace
->
compute
(
eflag
,
vflag
);
else
force
->
kspace
->
compute_dummy
(
eflag
,
vflag
);
}
#ifdef _LMP_INTEL_OFFLOAD
sync_mode
=
0
;
if
(
fix_intel
)
{
if
(
fix_intel
->
offload_balance
()
!=
0.0
)
{
if
(
fix_intel
->
offload_noghost
())
sync_mode
=
2
;
else
sync_mode
=
1
;
}
}
if
(
sync_mode
==
1
)
fix_intel
->
sync_coprocessor
();
#endif
if
(
force
->
newton
)
comm
->
reverse_comm
();
#ifdef _LMP_INTEL_OFFLOAD
if
(
sync_mode
==
2
)
fix_intel
->
sync_coprocessor
();
#endif
modify
->
setup
(
vflag
);
output
->
setup
();
update
->
setupflag
=
0
;
}
/* ----------------------------------------------------------------------
setup without output
flag = 0 = just force calculation
flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */
void
VerletIntel
::
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
);
force_clear
();
modify
->
setup_pre_force
(
vflag
);
if
(
pair_compute_flag
)
force
->
pair
->
compute
(
eflag
,
vflag
);
else
if
(
force
->
pair
)
force
->
pair
->
compute_dummy
(
eflag
,
vflag
);
if
(
atom
->
molecular
)
{
if
(
force
->
bond
)
force
->
bond
->
compute
(
eflag
,
vflag
);
if
(
force
->
angle
)
force
->
angle
->
compute
(
eflag
,
vflag
);
if
(
force
->
dihedral
)
force
->
dihedral
->
compute
(
eflag
,
vflag
);
if
(
force
->
improper
)
force
->
improper
->
compute
(
eflag
,
vflag
);
}
if
(
force
->
kspace
)
{
force
->
kspace
->
setup
();
if
(
kspace_compute_flag
)
force
->
kspace
->
compute
(
eflag
,
vflag
);
else
force
->
kspace
->
compute_dummy
(
eflag
,
vflag
);
}
#ifdef _LMP_INTEL_OFFLOAD
sync_mode
=
0
;
if
(
fix_intel
)
{
if
(
fix_intel
->
offload_balance
()
!=
0.0
)
{
if
(
fix_intel
->
offload_noghost
())
sync_mode
=
2
;
else
sync_mode
=
1
;
}
}
if
(
sync_mode
==
1
)
fix_intel
->
sync_coprocessor
();
#endif
if
(
force
->
newton
)
comm
->
reverse_comm
();
#ifdef _LMP_INTEL_OFFLOAD
if
(
sync_mode
==
2
)
fix_intel
->
sync_coprocessor
();
#endif
modify
->
setup
(
vflag
);
update
->
setupflag
=
0
;
}
/* ----------------------------------------------------------------------
run for N steps
------------------------------------------------------------------------- */
void
VerletIntel
::
run
(
int
n
)
{
bigint
ntimestep
;
int
nflag
,
sortflag
;
int
n_post_integrate
=
modify
->
n_post_integrate
;
int
n_pre_exchange
=
modify
->
n_pre_exchange
;
int
n_pre_neighbor
=
modify
->
n_pre_neighbor
;
int
n_pre_force
=
modify
->
n_pre_force
;
int
n_post_force
=
modify
->
n_post_force
;
int
n_end_of_step
=
modify
->
n_end_of_step
;
if
(
atom
->
sortfreq
>
0
)
sortflag
=
1
;
else
sortflag
=
0
;
for
(
int
i
=
0
;
i
<
n
;
i
++
)
{
ntimestep
=
++
update
->
ntimestep
;
ev_set
(
ntimestep
);
// initial time integration
modify
->
initial_integrate
(
vflag
);
if
(
n_post_integrate
)
modify
->
post_integrate
();
// regular communication vs neighbor list rebuild
nflag
=
neighbor
->
decide
();
if
(
nflag
==
0
)
{
timer
->
stamp
();
comm
->
forward_comm
();
timer
->
stamp
(
TIME_COMM
);
}
else
{
if
(
n_pre_exchange
)
modify
->
pre_exchange
();
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
(
sortflag
&&
ntimestep
>=
atom
->
nextsort
)
atom
->
sort
();
comm
->
borders
();
if
(
triclinic
)
domain
->
lamda2x
(
atom
->
nlocal
+
atom
->
nghost
);
timer
->
stamp
(
TIME_COMM
);
if
(
n_pre_neighbor
)
modify
->
pre_neighbor
();
neighbor
->
build
();
timer
->
stamp
(
TIME_NEIGHBOR
);
}
// force computations
// important for pair to come before bonded contributions
// since some bonded potentials tally pairwise energy/virial
// and Pair:ev_tally() needs to be called before any tallying
force_clear
();
if
(
n_pre_force
)
modify
->
pre_force
(
vflag
);
timer
->
stamp
();
if
(
pair_compute_flag
)
{
force
->
pair
->
compute
(
eflag
,
vflag
);
timer
->
stamp
(
TIME_PAIR
);
}
if
(
atom
->
molecular
)
{
if
(
force
->
bond
)
force
->
bond
->
compute
(
eflag
,
vflag
);
if
(
force
->
angle
)
force
->
angle
->
compute
(
eflag
,
vflag
);
if
(
force
->
dihedral
)
force
->
dihedral
->
compute
(
eflag
,
vflag
);
if
(
force
->
improper
)
force
->
improper
->
compute
(
eflag
,
vflag
);
timer
->
stamp
(
TIME_BOND
);
}
if
(
kspace_compute_flag
)
{
force
->
kspace
->
compute
(
eflag
,
vflag
);
timer
->
stamp
(
TIME_KSPACE
);
}
#ifdef _LMP_INTEL_OFFLOAD
if
(
sync_mode
==
1
)
{
fix_intel
->
sync_coprocessor
();
timer
->
stamp
(
TIME_PAIR
);
}
#endif
// reverse communication of forces
if
(
force
->
newton
)
{
comm
->
reverse_comm
();
timer
->
stamp
(
TIME_COMM
);
}
#ifdef _LMP_INTEL_OFFLOAD
if
(
sync_mode
==
2
)
{
fix_intel
->
sync_coprocessor
();
timer
->
stamp
(
TIME_PAIR
);
}
#endif
// force modifications, final time integration, diagnostics
if
(
n_post_force
)
modify
->
post_force
(
vflag
);
modify
->
final_integrate
();
if
(
n_end_of_step
)
modify
->
end_of_step
();
// all output
if
(
ntimestep
==
output
->
next
)
{
timer
->
stamp
();
output
->
write
(
ntimestep
);
timer
->
stamp
(
TIME_OUTPUT
);
}
}
}
/* ---------------------------------------------------------------------- */
void
VerletIntel
::
cleanup
()
{
modify
->
post_run
();
domain
->
box_too_small_check
();
update
->
update_time
();
}
/* ----------------------------------------------------------------------
clear force on own & ghost atoms
clear other arrays as needed
------------------------------------------------------------------------- */
void
VerletIntel
::
force_clear
()
{
int
i
;
if
(
external_force_clear
)
return
;
// clear force on all particles
// if either newton flag is set, also include ghosts
// when using threads always clear all forces.
if
(
neighbor
->
includegroup
==
0
)
{
int
nall
;
if
(
force
->
newton
)
nall
=
atom
->
nlocal
+
atom
->
nghost
;
else
nall
=
atom
->
nlocal
;
size_t
nbytes
=
sizeof
(
double
)
*
nall
;
if
(
nbytes
)
{
memset
(
&
(
atom
->
f
[
0
][
0
]),
0
,
3
*
nbytes
);
if
(
torqueflag
)
memset
(
&
(
atom
->
torque
[
0
][
0
]),
0
,
3
*
nbytes
);
if
(
erforceflag
)
memset
(
&
(
atom
->
erforce
[
0
]),
0
,
nbytes
);
if
(
e_flag
)
memset
(
&
(
atom
->
de
[
0
]),
0
,
nbytes
);
if
(
rho_flag
)
memset
(
&
(
atom
->
drho
[
0
]),
0
,
nbytes
);
}
// neighbor includegroup flag is set
// clear force only on initial nfirst particles
// if either newton flag is set, also include ghosts
}
else
{
int
nall
=
atom
->
nfirst
;
double
**
f
=
atom
->
f
;
for
(
i
=
0
;
i
<
nall
;
i
++
)
{
f
[
i
][
0
]
=
0.0
;
f
[
i
][
1
]
=
0.0
;
f
[
i
][
2
]
=
0.0
;
}
if
(
torqueflag
)
{
double
**
torque
=
atom
->
torque
;
for
(
i
=
0
;
i
<
nall
;
i
++
)
{
torque
[
i
][
0
]
=
0.0
;
torque
[
i
][
1
]
=
0.0
;
torque
[
i
][
2
]
=
0.0
;
}
}
if
(
erforceflag
)
{
double
*
erforce
=
atom
->
erforce
;
for
(
i
=
0
;
i
<
nall
;
i
++
)
erforce
[
i
]
=
0.0
;
}
if
(
e_flag
)
{
double
*
de
=
atom
->
de
;
for
(
i
=
0
;
i
<
nall
;
i
++
)
de
[
i
]
=
0.0
;
}
if
(
rho_flag
)
{
double
*
drho
=
atom
->
drho
;
for
(
i
=
0
;
i
<
nall
;
i
++
)
drho
[
i
]
=
0.0
;
}
if
(
force
->
newton
)
{
nall
=
atom
->
nlocal
+
atom
->
nghost
;
for
(
i
=
atom
->
nlocal
;
i
<
nall
;
i
++
)
{
f
[
i
][
0
]
=
0.0
;
f
[
i
][
1
]
=
0.0
;
f
[
i
][
2
]
=
0.0
;
}
if
(
torqueflag
)
{
double
**
torque
=
atom
->
torque
;
for
(
i
=
atom
->
nlocal
;
i
<
nall
;
i
++
)
{
torque
[
i
][
0
]
=
0.0
;
torque
[
i
][
1
]
=
0.0
;
torque
[
i
][
2
]
=
0.0
;
}
}
if
(
erforceflag
)
{
double
*
erforce
=
atom
->
erforce
;
for
(
i
=
atom
->
nlocal
;
i
<
nall
;
i
++
)
erforce
[
i
]
=
0.0
;
}
if
(
e_flag
)
{
double
*
de
=
atom
->
de
;
for
(
i
=
0
;
i
<
nall
;
i
++
)
de
[
i
]
=
0.0
;
}
if
(
rho_flag
)
{
double
*
drho
=
atom
->
drho
;
for
(
i
=
0
;
i
<
nall
;
i
++
)
drho
[
i
]
=
0.0
;
}
}
}
}
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