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neigh_derive_omp.cpp
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Sun, Sep 15, 08:16
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text/x-c
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Tue, Sep 17, 08:16 (1 d, 21 h)
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rLAMMPS lammps
neigh_derive_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.
------------------------------------------------------------------------- */
#include "neighbor.h"
#include "neighbor_omp.h"
#include "neigh_list.h"
#include "atom.h"
#include "comm.h"
#include "my_page.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ----------------------------------------------------------------------
build half list from full list
pair stored once if i,j are both owned and i < j
pair stored by me if j is ghost (also stored by proc owning j)
works if full list is a skip list
------------------------------------------------------------------------- */
void
Neighbor
::
half_from_full_no_newton_omp
(
NeighList
*
list
)
{
const
int
inum_full
=
list
->
listfull
->
inum
;
NEIGH_OMP_INIT
;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
NEIGH_OMP_SETUP
(
inum_full
);
int
i
,
j
,
ii
,
jj
,
n
,
jnum
,
joriginal
;
int
*
neighptr
,
*
jlist
;
int
*
ilist
=
list
->
ilist
;
int
*
numneigh
=
list
->
numneigh
;
int
**
firstneigh
=
list
->
firstneigh
;
int
*
ilist_full
=
list
->
listfull
->
ilist
;
int
*
numneigh_full
=
list
->
listfull
->
numneigh
;
int
**
firstneigh_full
=
list
->
listfull
->
firstneigh
;
// each thread has its own page allocator
MyPage
<
int
>
&
ipage
=
list
->
ipage
[
tid
];
ipage
.
reset
();
// loop over atoms in full list
for
(
ii
=
ifrom
;
ii
<
ito
;
ii
++
)
{
n
=
0
;
neighptr
=
ipage
.
vget
();
// loop over parent full list
i
=
ilist_full
[
ii
];
jlist
=
firstneigh_full
[
i
];
jnum
=
numneigh_full
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
joriginal
=
jlist
[
jj
];
j
=
joriginal
&
NEIGHMASK
;
if
(
j
>
i
)
neighptr
[
n
++
]
=
joriginal
;
}
ilist
[
ii
]
=
i
;
firstneigh
[
i
]
=
neighptr
;
numneigh
[
i
]
=
n
;
ipage
.
vgot
(
n
);
if
(
ipage
.
status
())
error
->
one
(
FLERR
,
"Neighbor list overflow, boost neigh_modify one"
);
}
NEIGH_OMP_CLOSE
;
list
->
inum
=
inum_full
;
}
/* ----------------------------------------------------------------------
build half list from full list
pair stored once if i,j are both owned and i < j
if j is ghost, only store if j coords are "above and to the right" of i
works if full list is a skip list
------------------------------------------------------------------------- */
void
Neighbor
::
half_from_full_newton_omp
(
NeighList
*
list
)
{
const
int
inum_full
=
list
->
listfull
->
inum
;
NEIGH_OMP_INIT
;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
NEIGH_OMP_SETUP
(
inum_full
);
int
i
,
j
,
ii
,
jj
,
n
,
jnum
,
joriginal
;
int
*
neighptr
,
*
jlist
;
double
xtmp
,
ytmp
,
ztmp
;
double
**
x
=
atom
->
x
;
int
nlocal
=
atom
->
nlocal
;
int
*
ilist
=
list
->
ilist
;
int
*
numneigh
=
list
->
numneigh
;
int
**
firstneigh
=
list
->
firstneigh
;
int
*
ilist_full
=
list
->
listfull
->
ilist
;
int
*
numneigh_full
=
list
->
listfull
->
numneigh
;
int
**
firstneigh_full
=
list
->
listfull
->
firstneigh
;
// each thread has its own page allocator
MyPage
<
int
>
&
ipage
=
list
->
ipage
[
tid
];
ipage
.
reset
();
// loop over parent full list
for
(
ii
=
ifrom
;
ii
<
ito
;
ii
++
)
{
n
=
0
;
neighptr
=
ipage
.
vget
();
i
=
ilist_full
[
ii
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
// loop over full neighbor list
jlist
=
firstneigh_full
[
i
];
jnum
=
numneigh_full
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
joriginal
=
jlist
[
jj
];
j
=
joriginal
&
NEIGHMASK
;
if
(
j
<
nlocal
)
{
if
(
i
>
j
)
continue
;
}
else
{
if
(
x
[
j
][
2
]
<
ztmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
)
{
if
(
x
[
j
][
1
]
<
ytmp
)
continue
;
if
(
x
[
j
][
1
]
==
ytmp
&&
x
[
j
][
0
]
<
xtmp
)
continue
;
}
}
neighptr
[
n
++
]
=
joriginal
;
}
ilist
[
ii
]
=
i
;
firstneigh
[
i
]
=
neighptr
;
numneigh
[
i
]
=
n
;
ipage
.
vgot
(
n
);
if
(
ipage
.
status
())
error
->
one
(
FLERR
,
"Neighbor list overflow, boost neigh_modify one"
);
}
NEIGH_OMP_CLOSE
;
list
->
inum
=
inum_full
;
}
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