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rLAMMPS lammps
neigh_full.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 "neigh_list.h"
#include "atom.h"
#include "domain.h"
#include "my_page.h"
#include "group.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ----------------------------------------------------------------------
N^2 search for all neighbors
every neighbor pair appears in list of both atoms i and j
------------------------------------------------------------------------- */
void
Neighbor
::
full_nsq
(
NeighList
*
list
)
{
int
i
,
j
,
n
,
itype
,
jtype
,
which
,
bitmask
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
int
*
neighptr
;
int
**
special
=
atom
->
special
;
int
**
nspecial
=
atom
->
nspecial
;
int
*
tag
=
atom
->
tag
;
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
*
molecule
=
atom
->
molecule
;
int
nlocal
=
atom
->
nlocal
;
int
nall
=
nlocal
+
atom
->
nghost
;
int
molecular
=
atom
->
molecular
;
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
;
int
inum
=
0
;
ipage
->
reset
();
// loop over owned atoms, storing neighbors
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
n
=
0
;
neighptr
=
ipage
->
vget
();
itype
=
type
[
i
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
// loop over all atoms, owned and ghost
// skip i = j
for
(
j
=
0
;
j
<
nall
;
j
++
)
{
if
(
includegroup
&&
!
(
mask
[
j
]
&
bitmask
))
continue
;
if
(
i
==
j
)
continue
;
jtype
=
type
[
j
];
if
(
exclude
&&
exclusion
(
i
,
j
,
itype
,
jtype
,
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
;
if
(
rsq
<=
cutneighsq
[
itype
][
jtype
])
{
if
(
molecular
)
{
which
=
find_special
(
special
[
i
],
nspecial
[
i
],
tag
[
j
]);
if
(
which
==
0
)
neighptr
[
n
++
]
=
j
;
else
if
(
domain
->
minimum_image_check
(
delx
,
dely
,
delz
))
neighptr
[
n
++
]
=
j
;
else
if
(
which
>
0
)
neighptr
[
n
++
]
=
j
^
(
which
<<
SBBITS
);
}
else
neighptr
[
n
++
]
=
j
;
}
}
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"
);
}
list
->
inum
=
inum
;
list
->
gnum
=
0
;
}
/* ----------------------------------------------------------------------
N^2 search for all neighbors
include neighbors of ghost atoms, but no "special neighbors" for ghosts
every neighbor pair appears in list of both atoms i and j
------------------------------------------------------------------------- */
void
Neighbor
::
full_nsq_ghost
(
NeighList
*
list
)
{
int
i
,
j
,
n
,
itype
,
jtype
,
which
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
int
*
neighptr
;
int
**
special
=
atom
->
special
;
int
**
nspecial
=
atom
->
nspecial
;
int
*
tag
=
atom
->
tag
;
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
*
molecule
=
atom
->
molecule
;
int
nlocal
=
atom
->
nlocal
;
int
nall
=
nlocal
+
atom
->
nghost
;
int
molecular
=
atom
->
molecular
;
int
*
ilist
=
list
->
ilist
;
int
*
numneigh
=
list
->
numneigh
;
int
**
firstneigh
=
list
->
firstneigh
;
MyPage
<
int
>
*
ipage
=
list
->
ipage
;
int
inum
=
0
;
ipage
->
reset
();
// loop over owned & ghost atoms, storing neighbors
for
(
i
=
0
;
i
<
nall
;
i
++
)
{
n
=
0
;
neighptr
=
ipage
->
vget
();
itype
=
type
[
i
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
// loop over all atoms, owned and ghost
// skip i = j
// no molecular test when i = ghost atom
if
(
i
<
nlocal
)
{
for
(
j
=
0
;
j
<
nall
;
j
++
)
{
if
(
i
==
j
)
continue
;
jtype
=
type
[
j
];
if
(
exclude
&&
exclusion
(
i
,
j
,
itype
,
jtype
,
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
;
if
(
rsq
<=
cutneighsq
[
itype
][
jtype
])
{
if
(
molecular
)
{
which
=
find_special
(
special
[
i
],
nspecial
[
i
],
tag
[
j
]);
if
(
which
==
0
)
neighptr
[
n
++
]
=
j
;
else
if
(
domain
->
minimum_image_check
(
delx
,
dely
,
delz
))
neighptr
[
n
++
]
=
j
;
else
if
(
which
>
0
)
neighptr
[
n
++
]
=
j
^
(
which
<<
SBBITS
);
}
else
neighptr
[
n
++
]
=
j
;
}
}
}
else
{
for
(
j
=
0
;
j
<
nall
;
j
++
)
{
if
(
i
==
j
)
continue
;
jtype
=
type
[
j
];
if
(
exclude
&&
exclusion
(
i
,
j
,
itype
,
jtype
,
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
;
if
(
rsq
<=
cutneighghostsq
[
itype
][
jtype
])
neighptr
[
n
++
]
=
j
;
}
}
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"
);
}
list
->
inum
=
atom
->
nlocal
;
list
->
gnum
=
inum
-
atom
->
nlocal
;
}
/* ----------------------------------------------------------------------
binned neighbor list construction for all neighbors
every neighbor pair appears in list of both atoms i and j
------------------------------------------------------------------------- */
void
Neighbor
::
full_bin
(
NeighList
*
list
)
{
int
i
,
j
,
k
,
n
,
itype
,
jtype
,
ibin
,
which
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
int
*
neighptr
;
// bin owned & ghost atoms
bin_atoms
();
int
**
special
=
atom
->
special
;
int
**
nspecial
=
atom
->
nspecial
;
int
*
tag
=
atom
->
tag
;
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
*
molecule
=
atom
->
molecule
;
int
nlocal
=
atom
->
nlocal
;
int
molecular
=
atom
->
molecular
;
if
(
includegroup
)
nlocal
=
atom
->
nfirst
;
int
*
ilist
=
list
->
ilist
;
int
*
numneigh
=
list
->
numneigh
;
int
**
firstneigh
=
list
->
firstneigh
;
int
nstencil
=
list
->
nstencil
;
int
*
stencil
=
list
->
stencil
;
MyPage
<
int
>
*
ipage
=
list
->
ipage
;
int
inum
=
0
;
ipage
->
reset
();
// loop over owned atoms, storing neighbors
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
n
=
0
;
neighptr
=
ipage
->
vget
();
itype
=
type
[
i
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
// loop over all atoms in surrounding bins in stencil including self
// skip i = j
ibin
=
coord2bin
(
x
[
i
]);
for
(
k
=
0
;
k
<
nstencil
;
k
++
)
{
for
(
j
=
binhead
[
ibin
+
stencil
[
k
]];
j
>=
0
;
j
=
bins
[
j
])
{
if
(
i
==
j
)
continue
;
jtype
=
type
[
j
];
if
(
exclude
&&
exclusion
(
i
,
j
,
itype
,
jtype
,
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
;
if
(
rsq
<=
cutneighsq
[
itype
][
jtype
])
{
if
(
molecular
)
{
which
=
find_special
(
special
[
i
],
nspecial
[
i
],
tag
[
j
]);
if
(
which
==
0
)
neighptr
[
n
++
]
=
j
;
else
if
(
domain
->
minimum_image_check
(
delx
,
dely
,
delz
))
neighptr
[
n
++
]
=
j
;
else
if
(
which
>
0
)
neighptr
[
n
++
]
=
j
^
(
which
<<
SBBITS
);
}
else
neighptr
[
n
++
]
=
j
;
}
}
}
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"
);
}
list
->
inum
=
inum
;
list
->
gnum
=
0
;
}
/* ----------------------------------------------------------------------
binned neighbor list construction for all neighbors
include neighbors of ghost atoms, but no "special neighbors" for ghosts
every neighbor pair appears in list of both atoms i and j
------------------------------------------------------------------------- */
void
Neighbor
::
full_bin_ghost
(
NeighList
*
list
)
{
int
i
,
j
,
k
,
n
,
itype
,
jtype
,
ibin
,
which
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
int
xbin
,
ybin
,
zbin
,
xbin2
,
ybin2
,
zbin2
;
int
*
neighptr
;
// bin owned & ghost atoms
bin_atoms
();
int
**
special
=
atom
->
special
;
int
**
nspecial
=
atom
->
nspecial
;
int
*
tag
=
atom
->
tag
;
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
*
molecule
=
atom
->
molecule
;
int
nlocal
=
atom
->
nlocal
;
int
nall
=
nlocal
+
atom
->
nghost
;
int
molecular
=
atom
->
molecular
;
int
*
ilist
=
list
->
ilist
;
int
*
numneigh
=
list
->
numneigh
;
int
**
firstneigh
=
list
->
firstneigh
;
int
nstencil
=
list
->
nstencil
;
int
*
stencil
=
list
->
stencil
;
int
**
stencilxyz
=
list
->
stencilxyz
;
MyPage
<
int
>
*
ipage
=
list
->
ipage
;
int
inum
=
0
;
ipage
->
reset
();
// loop over owned & ghost atoms, storing neighbors
for
(
i
=
0
;
i
<
nall
;
i
++
)
{
n
=
0
;
neighptr
=
ipage
->
vget
();
itype
=
type
[
i
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
// loop over all atoms in surrounding bins in stencil including self
// when i is a ghost atom, must check if stencil bin is out of bounds
// skip i = j
// no molecular test when i = ghost atom
if
(
i
<
nlocal
)
{
ibin
=
coord2bin
(
x
[
i
]);
for
(
k
=
0
;
k
<
nstencil
;
k
++
)
{
for
(
j
=
binhead
[
ibin
+
stencil
[
k
]];
j
>=
0
;
j
=
bins
[
j
])
{
if
(
i
==
j
)
continue
;
jtype
=
type
[
j
];
if
(
exclude
&&
exclusion
(
i
,
j
,
itype
,
jtype
,
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
;
if
(
rsq
<=
cutneighsq
[
itype
][
jtype
])
{
if
(
molecular
)
{
which
=
find_special
(
special
[
i
],
nspecial
[
i
],
tag
[
j
]);
if
(
which
==
0
)
neighptr
[
n
++
]
=
j
;
else
if
(
domain
->
minimum_image_check
(
delx
,
dely
,
delz
))
neighptr
[
n
++
]
=
j
;
else
if
(
which
>
0
)
neighptr
[
n
++
]
=
j
^
(
which
<<
SBBITS
);
}
else
neighptr
[
n
++
]
=
j
;
}
}
}
}
else
{
ibin
=
coord2bin
(
x
[
i
],
xbin
,
ybin
,
zbin
);
for
(
k
=
0
;
k
<
nstencil
;
k
++
)
{
xbin2
=
xbin
+
stencilxyz
[
k
][
0
];
ybin2
=
ybin
+
stencilxyz
[
k
][
1
];
zbin2
=
zbin
+
stencilxyz
[
k
][
2
];
if
(
xbin2
<
0
||
xbin2
>=
mbinx
||
ybin2
<
0
||
ybin2
>=
mbiny
||
zbin2
<
0
||
zbin2
>=
mbinz
)
continue
;
for
(
j
=
binhead
[
ibin
+
stencil
[
k
]];
j
>=
0
;
j
=
bins
[
j
])
{
if
(
i
==
j
)
continue
;
jtype
=
type
[
j
];
if
(
exclude
&&
exclusion
(
i
,
j
,
itype
,
jtype
,
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
;
if
(
rsq
<=
cutneighghostsq
[
itype
][
jtype
])
neighptr
[
n
++
]
=
j
;
}
}
}
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"
);
}
list
->
inum
=
atom
->
nlocal
;
list
->
gnum
=
inum
-
atom
->
nlocal
;
}
/* ----------------------------------------------------------------------
binned neighbor list construction for all neighbors
multi-type stencil is itype dependent and is distance checked
every neighbor pair appears in list of both atoms i and j
------------------------------------------------------------------------- */
void
Neighbor
::
full_multi
(
NeighList
*
list
)
{
int
i
,
j
,
k
,
n
,
itype
,
jtype
,
ibin
,
which
,
ns
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
int
*
neighptr
,
*
s
;
double
*
cutsq
,
*
distsq
;
// bin local & ghost atoms
bin_atoms
();
// loop over each atom, storing neighbors
int
**
special
=
atom
->
special
;
int
**
nspecial
=
atom
->
nspecial
;
int
*
tag
=
atom
->
tag
;
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
*
molecule
=
atom
->
molecule
;
int
nlocal
=
atom
->
nlocal
;
int
molecular
=
atom
->
molecular
;
if
(
includegroup
)
nlocal
=
atom
->
nfirst
;
int
*
ilist
=
list
->
ilist
;
int
*
numneigh
=
list
->
numneigh
;
int
**
firstneigh
=
list
->
firstneigh
;
int
*
nstencil_multi
=
list
->
nstencil_multi
;
int
**
stencil_multi
=
list
->
stencil_multi
;
double
**
distsq_multi
=
list
->
distsq_multi
;
MyPage
<
int
>
*
ipage
=
list
->
ipage
;
int
inum
=
0
;
ipage
->
reset
();
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
n
=
0
;
neighptr
=
ipage
->
vget
();
itype
=
type
[
i
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
// loop over all atoms in other bins in stencil, including self
// skip if i,j neighbor cutoff is less than bin distance
// skip i = j
ibin
=
coord2bin
(
x
[
i
]);
s
=
stencil_multi
[
itype
];
distsq
=
distsq_multi
[
itype
];
cutsq
=
cutneighsq
[
itype
];
ns
=
nstencil_multi
[
itype
];
for
(
k
=
0
;
k
<
ns
;
k
++
)
{
for
(
j
=
binhead
[
ibin
+
s
[
k
]];
j
>=
0
;
j
=
bins
[
j
])
{
jtype
=
type
[
j
];
if
(
cutsq
[
jtype
]
<
distsq
[
k
])
continue
;
if
(
i
==
j
)
continue
;
if
(
exclude
&&
exclusion
(
i
,
j
,
itype
,
jtype
,
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
;
if
(
rsq
<=
cutneighsq
[
itype
][
jtype
])
{
if
(
molecular
)
{
which
=
find_special
(
special
[
i
],
nspecial
[
i
],
tag
[
j
]);
if
(
which
==
0
)
neighptr
[
n
++
]
=
j
;
else
if
(
domain
->
minimum_image_check
(
delx
,
dely
,
delz
))
neighptr
[
n
++
]
=
j
;
else
if
(
which
>
0
)
neighptr
[
n
++
]
=
j
^
(
which
<<
SBBITS
);
}
else
neighptr
[
n
++
]
=
j
;
}
}
}
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"
);
}
list
->
inum
=
inum
;
list
->
gnum
=
0
;
}
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