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npair_half_size_nsq_newton_omp.cpp
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Sun, Jun 2, 09:09
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rLAMMPS lammps
npair_half_size_nsq_newton_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 <string.h>
#include "npair_half_size_nsq_newton_omp.h"
#include "npair_omp.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "group.h"
#include "my_page.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
NPairHalfSizeNsqNewtonOmp
::
NPairHalfSizeNsqNewtonOmp
(
LAMMPS
*
lmp
)
:
NPair
(
lmp
)
{}
/* ----------------------------------------------------------------------
size particles
N^2 / 2 search for neighbor pairs with full Newton's 3rd law
shear history must be accounted for when a neighbor pair is added
pair added to list if atoms i and j are both owned and i < j
if j is ghost only me or other proc adds pair
decision based on itag,jtag tests
------------------------------------------------------------------------- */
void
NPairHalfSizeNsqNewtonOmp
::
build
(
NeighList
*
list
)
{
const
int
nlocal
=
(
includegroup
)
?
atom
->
nfirst
:
atom
->
nlocal
;
const
int
bitmask
=
(
includegroup
)
?
group
->
bitmask
[
includegroup
]
:
0
;;
const
int
history
=
list
->
history
;
const
int
mask_history
=
3
<<
SBBITS
;
NPAIR_OMP_INIT
;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
NPAIR_OMP_SETUP
(
nlocal
);
int
i
,
j
,
m
,
n
,
nn
,
itag
,
jtag
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
double
radi
,
radsum
,
cutsq
;
int
*
neighptr
;
double
**
x
=
atom
->
x
;
double
*
radius
=
atom
->
radius
;
tagint
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
tagint
*
molecule
=
atom
->
molecule
;
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
int
*
ilist
=
list
->
ilist
;
int
*
numneigh
=
list
->
numneigh
;
int
**
firstneigh
=
list
->
firstneigh
;
// each thread has its own page allocator
MyPage
<
int
>
&
ipage
=
list
->
ipage
[
tid
];
ipage
.
reset
();
for
(
i
=
ifrom
;
i
<
ito
;
i
++
)
{
n
=
0
;
neighptr
=
ipage
.
vget
();
itag
=
tag
[
i
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
radi
=
radius
[
i
];
// loop over remaining atoms, owned and ghost
for
(
j
=
i
+
1
;
j
<
nall
;
j
++
)
{
if
(
includegroup
&&
!
(
mask
[
j
]
&
bitmask
))
continue
;
if
(
j
>=
nlocal
)
{
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
][
2
]
<
ztmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
)
{
if
(
x
[
j
][
1
]
<
ytmp
)
continue
;
if
(
x
[
j
][
1
]
==
ytmp
&&
x
[
j
][
0
]
<
xtmp
)
continue
;
}
}
}
if
(
exclude
&&
exclusion
(
i
,
j
,
type
[
i
],
type
[
j
],
mask
,
molecule
))
continue
;
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
radsum
=
radi
+
radius
[
j
];
cutsq
=
(
radsum
+
skin
)
*
(
radsum
+
skin
);
if
(
rsq
<=
cutsq
)
{
if
(
history
&&
rsq
<
radsum
*
radsum
)
neighptr
[
n
++
]
=
j
^
mask_history
;
else
neighptr
[
n
++
]
=
j
;
}
}
ilist
[
i
]
=
i
;
firstneigh
[
i
]
=
neighptr
;
numneigh
[
i
]
=
n
;
ipage
.
vgot
(
n
);
if
(
ipage
.
status
())
error
->
one
(
FLERR
,
"Neighbor list overflow, boost neigh_modify one"
);
}
NPAIR_OMP_CLOSE
;
list
->
inum
=
nlocal
;
}
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