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pair_tri_lj_omp.cpp
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rLAMMPS lammps
pair_tri_lj_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 author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "math.h"
#include "pair_tri_lj_omp.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_tri.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include <string.h>
#include "suffix.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
PairTriLJOMP
::
PairTriLJOMP
(
LAMMPS
*
lmp
)
:
PairTriLJ
(
lmp
),
ThrOMP
(
lmp
,
THR_PAIR
)
{
suffix_flag
|=
Suffix
::
OMP
;
respa_enable
=
0
;
}
/* ---------------------------------------------------------------------- */
void
PairTriLJOMP
::
compute
(
int
eflag
,
int
vflag
)
{
if
(
eflag
||
vflag
)
{
ev_setup
(
eflag
,
vflag
);
}
else
evflag
=
vflag_fdotr
=
0
;
const
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
const
int
nthreads
=
comm
->
nthreads
;
const
int
inum
=
list
->
inum
;
const
int
*
const
tri
=
atom
->
tri
;
const
int
*
const
type
=
atom
->
type
;
AtomVecTri
::
Bonus
*
const
bonus
=
avec
->
bonus
;
// grow discrete list if necessary and initialize
if
(
nall
>
nmax
)
{
nmax
=
nall
;
memory
->
destroy
(
dnum
);
memory
->
destroy
(
dfirst
);
memory
->
create
(
dnum
,
nall
,
"pair:dnum"
);
memory
->
create
(
dfirst
,
nall
,
"pair:dfirst"
);
}
memset
(
dnum
,
0
,
nall
*
sizeof
(
int
));
ndiscrete
=
0
;
// need to discretize the system ahead of time
// until we find a good way to multi-thread it.
for
(
int
i
=
0
;
i
<
nall
;
++
i
)
{
double
dc1
[
3
],
dc2
[
3
],
dc3
[
3
],
p
[
3
][
3
];
if
(
tri
[
i
]
>=
0
)
{
if
(
dnum
[
i
]
==
0
)
{
MathExtra
::
quat_to_mat
(
bonus
[
tri
[
i
]].
quat
,
p
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c1
,
dc1
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c2
,
dc2
);
MathExtra
::
matvec
(
p
,
bonus
[
tri
[
i
]].
c3
,
dc3
);
dfirst
[
i
]
=
ndiscrete
;
discretize
(
i
,
sigma
[
type
[
i
]][
type
[
i
]],
dc1
,
dc2
,
dc3
);
dnum
[
i
]
=
ndiscrete
-
dfirst
[
i
];
}
}
}
#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
(
force
->
newton_pair
)
eval
<
1
,
1
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
1
,
1
,
0
>
(
ifrom
,
ito
,
thr
);
}
else
{
if
(
force
->
newton_pair
)
eval
<
1
,
0
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
1
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
}
}
else
{
if
(
force
->
newton_pair
)
eval
<
0
,
0
,
1
>
(
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
NEWTON_PAIR
>
void
PairTriLJOMP
::
eval
(
int
iifrom
,
int
iito
,
ThrData
*
const
thr
)
{
int
i
,
j
,
ii
,
jj
,
jnum
,
itype
,
jtype
;
int
ni
,
nj
,
npi
,
npj
,
ifirst
,
jfirst
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
fpair
;
double
rsq
,
r2inv
,
r6inv
,
term1
,
term2
,
sig
,
sig3
,
forcelj
;
double
dxi
,
dxj
,
dyi
,
dyj
,
dzi
,
dzj
;
double
xi
[
3
],
xj
[
3
],
fi
[
3
],
fj
[
3
],
ti
[
3
],
tj
[
3
];
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
const
double
*
const
*
const
x
=
atom
->
x
;
double
*
const
*
const
f
=
thr
->
get_f
();
double
*
const
*
const
torque
=
thr
->
get_torque
();
const
int
*
const
tri
=
atom
->
tri
;
const
int
*
const
type
=
atom
->
type
;
const
int
nlocal
=
atom
->
nlocal
;
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
];
itype
=
type
[
i
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
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
;
jtype
=
type
[
j
];
if
(
rsq
>=
cutsq
[
itype
][
jtype
])
continue
;
// tri/tri interactions = NxN particles
// c1,c2,c3 = corner pts of triangle I or J
evdwl
=
0.0
;
if
(
tri
[
i
]
>=
0
&&
tri
[
j
]
>=
0
)
{
npi
=
dnum
[
i
];
ifirst
=
dfirst
[
i
];
npj
=
dnum
[
j
];
jfirst
=
dfirst
[
j
];
fi
[
0
]
=
fi
[
1
]
=
fi
[
2
]
=
fj
[
0
]
=
fj
[
1
]
=
fj
[
2
]
=
0.0
;
ti
[
0
]
=
ti
[
1
]
=
ti
[
2
]
=
tj
[
0
]
=
tj
[
1
]
=
tj
[
2
]
=
0.0
;
for
(
ni
=
0
;
ni
<
npi
;
ni
++
)
{
dxi
=
discrete
[
ifirst
+
ni
].
dx
;
dyi
=
discrete
[
ifirst
+
ni
].
dy
;
dzi
=
discrete
[
ifirst
+
ni
].
dz
;
for
(
nj
=
0
;
nj
<
npj
;
nj
++
)
{
dxj
=
discrete
[
jfirst
+
nj
].
dx
;
dyj
=
discrete
[
jfirst
+
nj
].
dy
;
dzj
=
discrete
[
jfirst
+
nj
].
dz
;
xi
[
0
]
=
x
[
i
][
0
]
+
dxi
;
xi
[
1
]
=
x
[
i
][
1
]
+
dyi
;
xi
[
2
]
=
x
[
i
][
2
]
+
dzi
;
xj
[
0
]
=
x
[
j
][
0
]
+
dxj
;
xj
[
1
]
=
x
[
j
][
1
]
+
dyj
;
xj
[
2
]
=
x
[
j
][
2
]
+
dzj
;
delx
=
xi
[
0
]
-
xj
[
0
];
dely
=
xi
[
1
]
-
xj
[
1
];
delz
=
xi
[
2
]
-
xj
[
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
sig
=
0.5
*
(
discrete
[
ifirst
+
ni
].
sigma
+
discrete
[
jfirst
+
nj
].
sigma
);
sig3
=
sig
*
sig
*
sig
;
term2
=
24.0
*
epsilon
[
itype
][
jtype
]
*
sig3
*
sig3
;
term1
=
2.0
*
term2
*
sig3
*
sig3
;
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
term1
*
r6inv
-
term2
);
fpair
=
forcelj
*
r2inv
;
if
(
EFLAG
)
evdwl
+=
r6inv
*
(
term1
/
12.0
*
r6inv
-
term2
/
6.0
);
fi
[
0
]
+=
delx
*
fpair
;
fi
[
1
]
+=
dely
*
fpair
;
fi
[
2
]
+=
delz
*
fpair
;
ti
[
0
]
+=
fpair
*
(
dyi
*
delz
-
dzi
*
dely
);
ti
[
1
]
+=
fpair
*
(
dzi
*
delx
-
dxi
*
delz
);
ti
[
2
]
+=
fpair
*
(
dxi
*
dely
-
dyi
*
delx
);
if
(
NEWTON_PAIR
||
j
<
nlocal
)
{
fj
[
0
]
-=
delx
*
fpair
;
fj
[
1
]
-=
dely
*
fpair
;
fj
[
2
]
-=
delz
*
fpair
;
tj
[
0
]
-=
fpair
*
(
dyj
*
delz
-
dzj
*
dely
);
tj
[
1
]
-=
fpair
*
(
dzj
*
delx
-
dxj
*
delz
);
tj
[
2
]
-=
fpair
*
(
dxj
*
dely
-
dyj
*
delx
);
}
}
}
f
[
i
][
0
]
+=
fi
[
0
];
f
[
i
][
1
]
+=
fi
[
1
];
f
[
i
][
2
]
+=
fi
[
2
];
f
[
j
][
0
]
+=
fj
[
0
];
f
[
j
][
1
]
+=
fj
[
1
];
f
[
j
][
2
]
+=
fj
[
2
];
torque
[
i
][
0
]
+=
ti
[
0
];
torque
[
i
][
1
]
+=
ti
[
1
];
torque
[
i
][
2
]
+=
ti
[
2
];
torque
[
j
][
0
]
+=
tj
[
0
];
torque
[
j
][
1
]
+=
tj
[
1
];
torque
[
j
][
2
]
+=
tj
[
2
];
// tri/particle interaction = Nx1 particles
// c1,c2,c3 = corner pts of triangle I
}
else
if
(
tri
[
i
]
>=
0
)
{
npi
=
dnum
[
i
];
ifirst
=
dfirst
[
i
];
fi
[
0
]
=
fi
[
1
]
=
fi
[
2
]
=
fj
[
0
]
=
fj
[
1
]
=
fj
[
2
]
=
0.0
;
ti
[
0
]
=
ti
[
1
]
=
ti
[
2
]
=
tj
[
0
]
=
tj
[
1
]
=
tj
[
2
]
=
0.0
;
for
(
ni
=
0
;
ni
<
npi
;
ni
++
)
{
dxi
=
discrete
[
ifirst
+
ni
].
dx
;
dyi
=
discrete
[
ifirst
+
ni
].
dy
;
dzi
=
discrete
[
ifirst
+
ni
].
dz
;
xi
[
0
]
=
x
[
i
][
0
]
+
dxi
;
xi
[
1
]
=
x
[
i
][
1
]
+
dyi
;
xi
[
2
]
=
x
[
i
][
2
]
+
dzi
;
xj
[
0
]
=
x
[
j
][
0
];
xj
[
1
]
=
x
[
j
][
1
];
xj
[
2
]
=
x
[
j
][
2
];
delx
=
xi
[
0
]
-
xj
[
0
];
dely
=
xi
[
1
]
-
xj
[
1
];
delz
=
xi
[
2
]
-
xj
[
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
sig
=
0.5
*
(
discrete
[
ifirst
+
ni
].
sigma
+
sigma
[
jtype
][
jtype
]);
sig3
=
sig
*
sig
*
sig
;
term2
=
24.0
*
epsilon
[
itype
][
jtype
]
*
sig3
*
sig3
;
term1
=
2.0
*
term2
*
sig3
*
sig3
;
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
term1
*
r6inv
-
term2
);
fpair
=
forcelj
*
r2inv
;
if
(
EFLAG
)
evdwl
+=
r6inv
*
(
term1
/
12.0
*
r6inv
-
term2
/
6.0
);
fi
[
0
]
+=
delx
*
fpair
;
fi
[
1
]
+=
dely
*
fpair
;
fi
[
2
]
+=
delz
*
fpair
;
ti
[
0
]
+=
fpair
*
(
dyi
*
delz
-
dzi
*
dely
);
ti
[
1
]
+=
fpair
*
(
dzi
*
delx
-
dxi
*
delz
);
ti
[
2
]
+=
fpair
*
(
dxi
*
dely
-
dyi
*
delx
);
if
(
NEWTON_PAIR
||
j
<
nlocal
)
{
fj
[
0
]
-=
delx
*
fpair
;
fj
[
1
]
-=
dely
*
fpair
;
fj
[
2
]
-=
delz
*
fpair
;
tj
[
0
]
-=
fpair
*
(
dyj
*
delz
-
dzj
*
dely
);
tj
[
1
]
-=
fpair
*
(
dzj
*
delx
-
dxj
*
delz
);
tj
[
2
]
-=
fpair
*
(
dxj
*
dely
-
dyj
*
delx
);
}
}
f
[
i
][
0
]
+=
fi
[
0
];
f
[
i
][
1
]
+=
fi
[
1
];
f
[
i
][
2
]
+=
fi
[
2
];
f
[
j
][
0
]
+=
fj
[
0
];
f
[
j
][
1
]
+=
fj
[
1
];
f
[
j
][
2
]
+=
fj
[
2
];
torque
[
i
][
0
]
+=
ti
[
0
];
torque
[
i
][
1
]
+=
ti
[
1
];
torque
[
i
][
2
]
+=
ti
[
2
];
torque
[
j
][
0
]
+=
tj
[
0
];
torque
[
j
][
1
]
+=
tj
[
1
];
torque
[
j
][
2
]
+=
tj
[
2
];
// particle/tri interaction = Nx1 particles
// c1,c2,c3 = corner pts of triangle J
}
else
if
(
tri
[
j
]
>=
0
)
{
npj
=
dnum
[
j
];
jfirst
=
dfirst
[
j
];
fi
[
0
]
=
fi
[
1
]
=
fi
[
2
]
=
fj
[
0
]
=
fj
[
1
]
=
fj
[
2
]
=
0.0
;
ti
[
0
]
=
ti
[
1
]
=
ti
[
2
]
=
tj
[
0
]
=
tj
[
1
]
=
tj
[
2
]
=
0.0
;
for
(
nj
=
0
;
nj
<
npj
;
nj
++
)
{
dxj
=
discrete
[
jfirst
+
nj
].
dx
;
dyj
=
discrete
[
jfirst
+
nj
].
dy
;
dzj
=
discrete
[
jfirst
+
nj
].
dz
;
xi
[
0
]
=
x
[
i
][
0
];
xi
[
1
]
=
x
[
i
][
1
];
xi
[
2
]
=
x
[
i
][
2
];
xj
[
0
]
=
x
[
j
][
0
]
+
dxj
;
xj
[
1
]
=
x
[
j
][
1
]
+
dyj
;
xj
[
2
]
=
x
[
j
][
2
]
+
dzj
;
delx
=
xi
[
0
]
-
xj
[
0
];
dely
=
xi
[
1
]
-
xj
[
1
];
delz
=
xi
[
2
]
-
xj
[
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
sig
=
0.5
*
(
sigma
[
itype
][
itype
]
+
discrete
[
jfirst
+
nj
].
sigma
);
sig3
=
sig
*
sig
*
sig
;
term2
=
24.0
*
epsilon
[
itype
][
jtype
]
*
sig3
*
sig3
;
term1
=
2.0
*
term2
*
sig3
*
sig3
;
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
term1
*
r6inv
-
term2
);
fpair
=
forcelj
*
r2inv
;
if
(
EFLAG
)
evdwl
+=
r6inv
*
(
term1
/
12.0
*
r6inv
-
term2
/
6.0
);
if
(
EFLAG
)
evdwl
+=
r6inv
*
(
term1
/
12.0
*
r6inv
-
term2
/
6.0
);
fi
[
0
]
+=
delx
*
fpair
;
fi
[
1
]
+=
dely
*
fpair
;
fi
[
2
]
+=
delz
*
fpair
;
ti
[
0
]
+=
fpair
*
(
dyi
*
delz
-
dzi
*
dely
);
ti
[
1
]
+=
fpair
*
(
dzi
*
delx
-
dxi
*
delz
);
ti
[
2
]
+=
fpair
*
(
dxi
*
dely
-
dyi
*
delx
);
if
(
NEWTON_PAIR
||
j
<
nlocal
)
{
fj
[
0
]
-=
delx
*
fpair
;
fj
[
1
]
-=
dely
*
fpair
;
fj
[
2
]
-=
delz
*
fpair
;
tj
[
0
]
-=
fpair
*
(
dyj
*
delz
-
dzj
*
dely
);
tj
[
1
]
-=
fpair
*
(
dzj
*
delx
-
dxj
*
delz
);
tj
[
2
]
-=
fpair
*
(
dxj
*
dely
-
dyj
*
delx
);
}
}
f
[
i
][
0
]
+=
fi
[
0
];
f
[
i
][
1
]
+=
fi
[
1
];
f
[
i
][
2
]
+=
fi
[
2
];
f
[
j
][
0
]
+=
fj
[
0
];
f
[
j
][
1
]
+=
fj
[
1
];
f
[
j
][
2
]
+=
fj
[
2
];
torque
[
i
][
0
]
+=
ti
[
0
];
torque
[
i
][
1
]
+=
ti
[
1
];
torque
[
i
][
2
]
+=
ti
[
2
];
torque
[
j
][
0
]
+=
tj
[
0
];
torque
[
j
][
1
]
+=
tj
[
1
];
torque
[
j
][
2
]
+=
tj
[
2
];
// particle/particle interaction = 1x1 particles
}
else
{
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
fpair
=
forcelj
*
r2inv
;
if
(
EFLAG
)
evdwl
+=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
]);
f
[
i
][
0
]
+=
delx
*
fpair
;
f
[
i
][
1
]
+=
dely
*
fpair
;
f
[
i
][
2
]
+=
delz
*
fpair
;
if
(
NEWTON_PAIR
||
j
<
nlocal
)
{
f
[
j
][
0
]
-=
delx
*
fpair
;
f
[
j
][
1
]
-=
dely
*
fpair
;
f
[
j
][
2
]
-=
delz
*
fpair
;
}
}
if
(
EVFLAG
)
ev_tally_thr
(
this
,
i
,
j
,
nlocal
,
NEWTON_PAIR
,
evdwl
,
0.0
,
fpair
,
delx
,
dely
,
delz
,
thr
);
}
}
}
/* ---------------------------------------------------------------------- */
double
PairTriLJOMP
::
memory_usage
()
{
double
bytes
=
memory_usage_thr
();
bytes
+=
PairTriLJ
::
memory_usage
();
return
bytes
;
}
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