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npair_half_size_nsq_newtoff.cpp
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Thu, Sep 12, 04:29
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rLAMMPS lammps
npair_half_size_nsq_newtoff.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_newtoff.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "group.h"
#include "molecule.h"
#include "domain.h"
#include "fix_shear_history.h"
#include "my_page.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
NPairHalfSizeNsqNewtoff
::
NPairHalfSizeNsqNewtoff
(
LAMMPS
*
lmp
)
:
NPair
(
lmp
)
{}
/* ----------------------------------------------------------------------
size particles
N^2 / 2 search for neighbor pairs with partial 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
pair added if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */
void
NPairHalfSizeNsqNewtoff
::
build
(
NeighList
*
list
)
{
int
i
,
j
,
m
,
n
,
nn
,
bitmask
,
dnum
,
dnumbytes
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
double
radi
,
radsum
,
cutsq
;
int
*
neighptr
,
*
touchptr
;
double
*
shearptr
;
int
*
npartner
;
tagint
**
partner
;
double
**
shearpartner
;
int
**
firsttouch
;
double
**
firstshear
;
MyPage
<
int
>
*
ipage_touch
;
MyPage
<
double
>
*
dpage_shear
;
NeighList
*
listhistory
;
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
nlocal
=
atom
->
nlocal
;
int
nall
=
nlocal
+
atom
->
nghost
;
if
(
includegroup
)
{
nlocal
=
atom
->
nfirst
;
bitmask
=
group
->
bitmask
[
includegroup
];
}
int
*
ilist
=
list
->
ilist
;
int
*
numneigh
=
list
->
numneigh
;
int
**
firstneigh
=
list
->
firstneigh
;
MyPage
<
int
>
*
ipage
=
list
->
ipage
;
FixShearHistory
*
fix_history
=
(
FixShearHistory
*
)
list
->
fix_history
;
if
(
fix_history
)
{
fix_history
->
nlocal_neigh
=
nlocal
;
fix_history
->
nall_neigh
=
nall
;
npartner
=
fix_history
->
npartner
;
partner
=
fix_history
->
partner
;
shearpartner
=
fix_history
->
shearpartner
;
listhistory
=
list
->
listhistory
;
firsttouch
=
listhistory
->
firstneigh
;
firstshear
=
listhistory
->
firstdouble
;
ipage_touch
=
listhistory
->
ipage
;
dpage_shear
=
listhistory
->
dpage
;
dnum
=
listhistory
->
dnum
;
dnumbytes
=
dnum
*
sizeof
(
double
);
}
int
inum
=
0
;
ipage
->
reset
();
if
(
fix_history
)
{
ipage_touch
->
reset
();
dpage_shear
->
reset
();
}
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
n
=
0
;
neighptr
=
ipage
->
vget
();
if
(
fix_history
)
{
nn
=
0
;
touchptr
=
ipage_touch
->
vget
();
shearptr
=
dpage_shear
->
vget
();
}
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
(
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
)
{
neighptr
[
n
]
=
j
;
if
(
fix_history
)
{
if
(
rsq
<
radsum
*
radsum
)
{
for
(
m
=
0
;
m
<
npartner
[
i
];
m
++
)
if
(
partner
[
i
][
m
]
==
tag
[
j
])
break
;
if
(
m
<
npartner
[
i
])
{
touchptr
[
n
]
=
1
;
memcpy
(
&
shearptr
[
nn
],
&
shearpartner
[
i
][
dnum
*
m
],
dnumbytes
);
nn
+=
dnum
;
}
else
{
touchptr
[
n
]
=
0
;
memcpy
(
&
shearptr
[
nn
],
zeroes
,
dnumbytes
);
nn
+=
dnum
;
}
}
else
{
touchptr
[
n
]
=
0
;
memcpy
(
&
shearptr
[
nn
],
zeroes
,
dnumbytes
);
nn
+=
dnum
;
}
}
n
++
;
}
}
ilist
[
inum
++
]
=
i
;
firstneigh
[
i
]
=
neighptr
;
numneigh
[
i
]
=
n
;
ipage
->
vgot
(
n
);
if
(
ipage
->
status
())
error
->
one
(
FLERR
,
"Neighbor list overflow, boost neigh_modify one"
);
if
(
fix_history
)
{
firsttouch
[
i
]
=
touchptr
;
firstshear
[
i
]
=
shearptr
;
ipage_touch
->
vgot
(
n
);
dpage_shear
->
vgot
(
nn
);
}
}
list
->
inum
=
inum
;
}
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