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pair_gran_hooke_omp.cpp
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Tue, Jul 23, 00:28
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text/x-c++
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Thu, Jul 25, 00:28 (2 d)
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rLAMMPS lammps
pair_gran_hooke_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
This software is distributed under the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "math.h"
#include "pair_gran_hooke_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
PairGranHookeOMP
::
PairGranHookeOMP
(
LAMMPS
*
lmp
)
:
PairGranHooke
(
lmp
),
ThrOMP
(
lmp
,
PAIR
)
{
respa_enable
=
0
;
}
/* ---------------------------------------------------------------------- */
void
PairGranHookeOMP
::
compute
(
int
eflag
,
int
vflag
)
{
if
(
eflag
||
vflag
)
{
ev_setup
(
eflag
,
vflag
);
ev_setup_thr
(
this
);
}
else
evflag
=
vflag_fdotr
=
0
;
const
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
const
int
nthreads
=
comm
->
nthreads
;
const
int
inum
=
list
->
inum
;
#if defined(_OPENMP)
#pragma omp parallel default(shared)
#endif
{
int
ifrom
,
ito
,
tid
;
double
**
f
,
**
torque
;
f
=
loop_setup_thr
(
atom
->
f
,
ifrom
,
ito
,
tid
,
inum
,
nall
,
nthreads
);
torque
=
atom
->
torque
+
tid
*
nall
;
if
(
evflag
)
if
(
force
->
newton_pair
)
eval
<
1
,
1
>
(
f
,
torque
,
ifrom
,
ito
,
tid
);
else
eval
<
1
,
0
>
(
f
,
torque
,
ifrom
,
ito
,
tid
);
else
if
(
force
->
newton_pair
)
eval
<
0
,
1
>
(
f
,
torque
,
ifrom
,
ito
,
tid
);
else
eval
<
0
,
0
>
(
f
,
torque
,
ifrom
,
ito
,
tid
);
// reduce per thread forces and torque into global arrays.
data_reduce_thr
(
&
(
atom
->
f
[
0
][
0
]),
nall
,
nthreads
,
3
,
tid
);
data_reduce_thr
(
&
(
atom
->
torque
[
0
][
0
]),
nall
,
nthreads
,
3
,
tid
);
}
// end of omp parallel region
// reduce per thread energy and virial, if requested.
if
(
evflag
)
ev_reduce_thr
(
this
);
}
template
<
int
EVFLAG
,
int
NEWTON_PAIR
>
void
PairGranHookeOMP
::
eval
(
double
**
f
,
double
**
torque
,
int
iifrom
,
int
iito
,
int
tid
)
{
int
i
,
j
,
ii
,
jj
,
jnum
,
itype
,
jtype
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
fx
,
fy
,
fz
;
double
radi
,
radj
,
radsum
,
rsq
,
r
,
rinv
,
rsqinv
;
double
vr1
,
vr2
,
vr3
,
vnnr
,
vn1
,
vn2
,
vn3
,
vt1
,
vt2
,
vt3
;
double
wr1
,
wr2
,
wr3
;
double
vtr1
,
vtr2
,
vtr3
,
vrel
;
double
meff
,
damp
,
ccel
,
tor1
,
tor2
,
tor3
;
double
fn
,
fs
,
ft
,
fs1
,
fs2
,
fs3
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
**
omega
=
atom
->
omega
;
double
*
radius
=
atom
->
radius
;
double
*
rmass
=
atom
->
rmass
;
double
*
mass
=
atom
->
mass
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
fxtmp
,
fytmp
,
fztmp
;
double
t1tmp
,
t2tmp
,
t3tmp
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// loop over neighbors of my atoms
for
(
ii
=
iifrom
;
ii
<
iito
;
++
ii
)
{
i
=
ilist
[
ii
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
radi
=
radius
[
i
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
fxtmp
=
fytmp
=
fztmp
=
t1tmp
=
t2tmp
=
t3tmp
=
0.0
;
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
radj
=
radius
[
j
];
radsum
=
radi
+
radj
;
if
(
rsq
<
radsum
*
radsum
)
{
r
=
sqrt
(
rsq
);
rinv
=
1.0
/
r
;
rsqinv
=
1.0
/
rsq
;
// relative translational velocity
vr1
=
v
[
i
][
0
]
-
v
[
j
][
0
];
vr2
=
v
[
i
][
1
]
-
v
[
j
][
1
];
vr3
=
v
[
i
][
2
]
-
v
[
j
][
2
];
// normal component
vnnr
=
vr1
*
delx
+
vr2
*
dely
+
vr3
*
delz
;
vn1
=
delx
*
vnnr
*
rsqinv
;
vn2
=
dely
*
vnnr
*
rsqinv
;
vn3
=
delz
*
vnnr
*
rsqinv
;
// tangential component
vt1
=
vr1
-
vn1
;
vt2
=
vr2
-
vn2
;
vt3
=
vr3
-
vn3
;
// relative rotational velocity
wr1
=
(
radi
*
omega
[
i
][
0
]
+
radj
*
omega
[
j
][
0
])
*
rinv
;
wr2
=
(
radi
*
omega
[
i
][
1
]
+
radj
*
omega
[
j
][
1
])
*
rinv
;
wr3
=
(
radi
*
omega
[
i
][
2
]
+
radj
*
omega
[
j
][
2
])
*
rinv
;
// normal forces = Hookian contact + normal velocity damping
if
(
rmass
)
{
meff
=
rmass
[
i
]
*
rmass
[
j
]
/
(
rmass
[
i
]
+
rmass
[
j
]);
if
(
mask
[
i
]
&
freeze_group_bit
)
meff
=
rmass
[
j
];
if
(
mask
[
j
]
&
freeze_group_bit
)
meff
=
rmass
[
i
];
}
else
{
itype
=
type
[
i
];
jtype
=
type
[
j
];
meff
=
mass
[
itype
]
*
mass
[
jtype
]
/
(
mass
[
itype
]
+
mass
[
jtype
]);
if
(
mask
[
i
]
&
freeze_group_bit
)
meff
=
mass
[
jtype
];
if
(
mask
[
j
]
&
freeze_group_bit
)
meff
=
mass
[
itype
];
}
damp
=
meff
*
gamman
*
vnnr
*
rsqinv
;
ccel
=
kn
*
(
radsum
-
r
)
*
rinv
-
damp
;
// relative velocities
vtr1
=
vt1
-
(
delz
*
wr2
-
dely
*
wr3
);
vtr2
=
vt2
-
(
delx
*
wr3
-
delz
*
wr1
);
vtr3
=
vt3
-
(
dely
*
wr1
-
delx
*
wr2
);
vrel
=
vtr1
*
vtr1
+
vtr2
*
vtr2
+
vtr3
*
vtr3
;
vrel
=
sqrt
(
vrel
);
// force normalization
fn
=
xmu
*
fabs
(
ccel
*
r
);
fs
=
meff
*
gammat
*
vrel
;
if
(
vrel
!=
0.0
)
ft
=
MIN
(
fn
,
fs
)
/
vrel
;
else
ft
=
0.0
;
// tangential force due to tangential velocity damping
fs1
=
-
ft
*
vtr1
;
fs2
=
-
ft
*
vtr2
;
fs3
=
-
ft
*
vtr3
;
// forces & torques
fx
=
delx
*
ccel
+
fs1
;
fy
=
dely
*
ccel
+
fs2
;
fz
=
delz
*
ccel
+
fs3
;
fxtmp
+=
fx
;
fytmp
+=
fy
;
fztmp
+=
fz
;
tor1
=
rinv
*
(
dely
*
fs3
-
delz
*
fs2
);
tor2
=
rinv
*
(
delz
*
fs1
-
delx
*
fs3
);
tor3
=
rinv
*
(
delx
*
fs2
-
dely
*
fs1
);
t1tmp
-=
radi
*
tor1
;
t2tmp
-=
radi
*
tor2
;
t3tmp
-=
radi
*
tor3
;
if
(
NEWTON_PAIR
||
j
<
nlocal
)
{
f
[
j
][
0
]
-=
fx
;
f
[
j
][
1
]
-=
fy
;
f
[
j
][
2
]
-=
fz
;
torque
[
j
][
0
]
-=
radj
*
tor1
;
torque
[
j
][
1
]
-=
radj
*
tor2
;
torque
[
j
][
2
]
-=
radj
*
tor3
;
}
if
(
EVFLAG
)
ev_tally_xyz_thr
(
this
,
i
,
j
,
nlocal
,
NEWTON_PAIR
,
0.0
,
0.0
,
fx
,
fy
,
fz
,
delx
,
dely
,
delz
,
tid
);
}
}
f
[
i
][
0
]
+=
fxtmp
;
f
[
i
][
1
]
+=
fytmp
;
f
[
i
][
2
]
+=
fztmp
;
torque
[
i
][
0
]
+=
t1tmp
;
torque
[
i
][
1
]
+=
t2tmp
;
torque
[
i
][
2
]
+=
t3tmp
;
}
}
/* ---------------------------------------------------------------------- */
double
PairGranHookeOMP
::
memory_usage
()
{
double
bytes
=
memory_usage_thr
();
bytes
+=
PairGranHooke
::
memory_usage
();
return
bytes
;
}
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