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pair_tersoff_mod_omp.cpp
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Fri, Sep 6, 08:24
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6 KB
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text/x-c++
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Sun, Sep 8, 08:24 (2 d)
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blob
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20569485
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rLAMMPS lammps
pair_tersoff_mod_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_tersoff_mod_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "suffix.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
PairTersoffMODOMP
::
PairTersoffMODOMP
(
LAMMPS
*
lmp
)
:
PairTersoffMOD
(
lmp
),
ThrOMP
(
lmp
,
THR_PAIR
)
{
suffix_flag
|=
Suffix
::
OMP
;
respa_enable
=
0
;
}
/* ---------------------------------------------------------------------- */
void
PairTersoffMODOMP
::
compute
(
int
eflag
,
int
vflag
)
{
if
(
eflag
||
vflag
)
{
ev_setup
(
eflag
,
vflag
);
}
else
evflag
=
vflag_fdotr
=
vflag_atom
=
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(none) shared(eflag,vflag)
#endif
{
int
ifrom
,
ito
,
tid
;
loop_setup_thr
(
ifrom
,
ito
,
tid
,
inum
,
nthreads
);
ThrData
*
thr
=
fix
->
get_thr
(
tid
);
ev_setup_thr
(
eflag
,
vflag
,
nall
,
eatom
,
vatom
,
thr
);
if
(
evflag
)
{
if
(
eflag
)
{
if
(
vflag_atom
)
eval
<
1
,
1
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
1
,
1
,
0
>
(
ifrom
,
ito
,
thr
);
}
else
{
if
(
vflag_atom
)
eval
<
1
,
0
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
1
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
}
}
else
eval
<
0
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
reduce_thr
(
this
,
eflag
,
vflag
,
thr
);
}
// end of omp parallel region
}
template
<
int
EVFLAG
,
int
EFLAG
,
int
VFLAG_ATOM
>
void
PairTersoffMODOMP
::
eval
(
int
iifrom
,
int
iito
,
ThrData
*
const
thr
)
{
int
i
,
j
,
k
,
ii
,
jj
,
kk
,
jnum
;
tagint
itag
,
jtag
;
int
itype
,
jtype
,
ktype
,
iparam_ij
,
iparam_ijk
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
fpair
;
double
rsq
,
rsq1
,
rsq2
;
double
delr1
[
3
],
delr2
[
3
],
fi
[
3
],
fj
[
3
],
fk
[
3
];
double
zeta_ij
,
prefactor
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
evdwl
=
0.0
;
const
dbl3_t
*
_noalias
const
x
=
(
dbl3_t
*
)
atom
->
x
[
0
];
dbl3_t
*
_noalias
const
f
=
(
dbl3_t
*
)
thr
->
get_f
()[
0
];
const
tagint
*
_noalias
const
tag
=
atom
->
tag
;
const
int
*
_noalias
const
type
=
atom
->
type
;
const
int
nlocal
=
atom
->
nlocal
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
double
fxtmp
,
fytmp
,
fztmp
;
// loop over full neighbor list of my atoms
for
(
ii
=
iifrom
;
ii
<
iito
;
++
ii
)
{
i
=
ilist
[
ii
];
itag
=
tag
[
i
];
itype
=
map
[
type
[
i
]];
xtmp
=
x
[
i
].
x
;
ytmp
=
x
[
i
].
y
;
ztmp
=
x
[
i
].
z
;
fxtmp
=
fytmp
=
fztmp
=
0.0
;
// two-body interactions, skip half of them
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
jtag
=
tag
[
j
];
if
(
itag
>
jtag
)
{
if
((
itag
+
jtag
)
%
2
==
0
)
continue
;
}
else
if
(
itag
<
jtag
)
{
if
((
itag
+
jtag
)
%
2
==
1
)
continue
;
}
else
{
if
(
x
[
j
].
z
<
ztmp
)
continue
;
if
(
x
[
j
].
z
==
ztmp
&&
x
[
j
].
y
<
ytmp
)
continue
;
if
(
x
[
j
].
z
==
ztmp
&&
x
[
j
].
y
==
ytmp
&&
x
[
j
].
x
<
xtmp
)
continue
;
}
jtype
=
map
[
type
[
j
]];
delx
=
xtmp
-
x
[
j
].
x
;
dely
=
ytmp
-
x
[
j
].
y
;
delz
=
ztmp
-
x
[
j
].
z
;
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
iparam_ij
=
elem2param
[
itype
][
jtype
][
jtype
];
if
(
rsq
>
params
[
iparam_ij
].
cutsq
)
continue
;
repulsive
(
&
params
[
iparam_ij
],
rsq
,
fpair
,
EFLAG
,
evdwl
);
fxtmp
+=
delx
*
fpair
;
fytmp
+=
dely
*
fpair
;
fztmp
+=
delz
*
fpair
;
f
[
j
].
x
-=
delx
*
fpair
;
f
[
j
].
y
-=
dely
*
fpair
;
f
[
j
].
z
-=
delz
*
fpair
;
if
(
EVFLAG
)
ev_tally_thr
(
this
,
i
,
j
,
nlocal
,
/* newton_pair */
1
,
evdwl
,
0.0
,
fpair
,
delx
,
dely
,
delz
,
thr
);
}
// three-body interactions
// skip immediately if I-J is not within cutoff
double
fjxtmp
,
fjytmp
,
fjztmp
;
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
jtype
=
map
[
type
[
j
]];
iparam_ij
=
elem2param
[
itype
][
jtype
][
jtype
];
delr1
[
0
]
=
x
[
j
].
x
-
xtmp
;
delr1
[
1
]
=
x
[
j
].
y
-
ytmp
;
delr1
[
2
]
=
x
[
j
].
z
-
ztmp
;
rsq1
=
delr1
[
0
]
*
delr1
[
0
]
+
delr1
[
1
]
*
delr1
[
1
]
+
delr1
[
2
]
*
delr1
[
2
];
if
(
rsq1
>
params
[
iparam_ij
].
cutsq
)
continue
;
// accumulate bondorder zeta for each i-j interaction via loop over k
fjxtmp
=
fjytmp
=
fjztmp
=
0.0
;
zeta_ij
=
0.0
;
for
(
kk
=
0
;
kk
<
jnum
;
kk
++
)
{
if
(
jj
==
kk
)
continue
;
k
=
jlist
[
kk
];
k
&=
NEIGHMASK
;
ktype
=
map
[
type
[
k
]];
iparam_ijk
=
elem2param
[
itype
][
jtype
][
ktype
];
delr2
[
0
]
=
x
[
k
].
x
-
xtmp
;
delr2
[
1
]
=
x
[
k
].
y
-
ytmp
;
delr2
[
2
]
=
x
[
k
].
z
-
ztmp
;
rsq2
=
delr2
[
0
]
*
delr2
[
0
]
+
delr2
[
1
]
*
delr2
[
1
]
+
delr2
[
2
]
*
delr2
[
2
];
if
(
rsq2
>
params
[
iparam_ijk
].
cutsq
)
continue
;
zeta_ij
+=
zeta
(
&
params
[
iparam_ijk
],
rsq1
,
rsq2
,
delr1
,
delr2
);
}
// pairwise force due to zeta
force_zeta
(
&
params
[
iparam_ij
],
rsq1
,
zeta_ij
,
fpair
,
prefactor
,
EFLAG
,
evdwl
);
fxtmp
+=
delr1
[
0
]
*
fpair
;
fytmp
+=
delr1
[
1
]
*
fpair
;
fztmp
+=
delr1
[
2
]
*
fpair
;
fjxtmp
-=
delr1
[
0
]
*
fpair
;
fjytmp
-=
delr1
[
1
]
*
fpair
;
fjztmp
-=
delr1
[
2
]
*
fpair
;
if
(
EVFLAG
)
ev_tally_thr
(
this
,
i
,
j
,
nlocal
,
/* newton_pair */
1
,
evdwl
,
0.0
,
-
fpair
,
-
delr1
[
0
],
-
delr1
[
1
],
-
delr1
[
2
],
thr
);
// attractive term via loop over k
for
(
kk
=
0
;
kk
<
jnum
;
kk
++
)
{
if
(
jj
==
kk
)
continue
;
k
=
jlist
[
kk
];
k
&=
NEIGHMASK
;
ktype
=
map
[
type
[
k
]];
iparam_ijk
=
elem2param
[
itype
][
jtype
][
ktype
];
delr2
[
0
]
=
x
[
k
].
x
-
xtmp
;
delr2
[
1
]
=
x
[
k
].
y
-
ytmp
;
delr2
[
2
]
=
x
[
k
].
z
-
ztmp
;
rsq2
=
delr2
[
0
]
*
delr2
[
0
]
+
delr2
[
1
]
*
delr2
[
1
]
+
delr2
[
2
]
*
delr2
[
2
];
if
(
rsq2
>
params
[
iparam_ijk
].
cutsq
)
continue
;
attractive
(
&
params
[
iparam_ijk
],
prefactor
,
rsq1
,
rsq2
,
delr1
,
delr2
,
fi
,
fj
,
fk
);
fxtmp
+=
fi
[
0
];
fytmp
+=
fi
[
1
];
fztmp
+=
fi
[
2
];
fjxtmp
+=
fj
[
0
];
fjytmp
+=
fj
[
1
];
fjztmp
+=
fj
[
2
];
f
[
k
].
x
+=
fk
[
0
];
f
[
k
].
y
+=
fk
[
1
];
f
[
k
].
z
+=
fk
[
2
];
if
(
VFLAG_ATOM
)
v_tally3_thr
(
i
,
j
,
k
,
fj
,
fk
,
delr1
,
delr2
,
thr
);
}
f
[
j
].
x
+=
fjxtmp
;
f
[
j
].
y
+=
fjytmp
;
f
[
j
].
z
+=
fjztmp
;
}
f
[
i
].
x
+=
fxtmp
;
f
[
i
].
y
+=
fytmp
;
f
[
i
].
z
+=
fztmp
;
}
}
/* ---------------------------------------------------------------------- */
double
PairTersoffMODOMP
::
memory_usage
()
{
double
bytes
=
memory_usage_thr
();
bytes
+=
PairTersoffMOD
::
memory_usage
();
return
bytes
;
}
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