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rLAMMPS lammps
neigh_gran_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 "group.h"
#include "fix_shear_history.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ----------------------------------------------------------------------
granular 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
Neighbor
::
granular_nsq_no_newton_omp
(
NeighList
*
list
)
{
const
int
nlocal
=
(
includegroup
)
?
atom
->
nfirst
:
atom
->
nlocal
;
const
int
bitmask
=
(
includegroup
)
?
group
->
bitmask
[
includegroup
]
:
0
;
FixShearHistory
*
const
fix_history
=
list
->
fix_history
;
NeighList
*
listgranhistory
=
list
->
listgranhistory
;
NEIGH_OMP_INIT
;
if
(
fix_history
)
if
(
nthreads
>
listgranhistory
->
maxpage
)
listgranhistory
->
add_pages
(
nthreads
-
listgranhistory
->
maxpage
);
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listgranhistory)
#endif
NEIGH_OMP_SETUP
(
nlocal
);
int
i
,
j
,
m
,
n
,
nn
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
double
radi
,
radsum
,
cutsq
;
int
*
neighptr
,
*
touchptr
;
double
*
shearptr
;
int
*
npartner
,
**
partner
;
double
(
**
shearpartner
)[
3
];
int
**
firsttouch
;
double
**
firstshear
;
double
**
x
=
atom
->
x
;
double
*
radius
=
atom
->
radius
;
int
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
*
molecule
=
atom
->
molecule
;
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
int
*
ilist
=
list
->
ilist
;
int
*
numneigh
=
list
->
numneigh
;
int
**
firstneigh
=
list
->
firstneigh
;
if
(
fix_history
)
{
npartner
=
fix_history
->
npartner
;
partner
=
fix_history
->
partner
;
shearpartner
=
fix_history
->
shearpartner
;
firsttouch
=
listgranhistory
->
firstneigh
;
firstshear
=
listgranhistory
->
firstdouble
;
}
int
npage
=
tid
;
int
npnt
=
0
;
for
(
i
=
ifrom
;
i
<
ito
;
i
++
)
{
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if
(
pgsize
-
npnt
<
oneatom
)
{
npnt
=
0
;
npage
+=
nthreads
;
if
(
npage
>=
list
->
maxpage
)
{
list
->
add_pages
(
nthreads
);
if
(
fix_history
)
listgranhistory
->
add_pages
(
nthreads
);
}
}
n
=
nn
=
0
;
neighptr
=
&
(
list
->
pages
[
npage
][
npnt
]);
if
(
fix_history
)
{
touchptr
=
&
(
listgranhistory
->
pages
[
npage
][
npnt
]);
shearptr
=
&
(
listgranhistory
->
dpages
[
npage
][
3
*
npnt
]);
}
}
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
;
shearptr
[
nn
++
]
=
shearpartner
[
i
][
m
][
0
];
shearptr
[
nn
++
]
=
shearpartner
[
i
][
m
][
1
];
shearptr
[
nn
++
]
=
shearpartner
[
i
][
m
][
2
];
}
else
{
touchptr
[
n
]
=
0
;
shearptr
[
nn
++
]
=
0.0
;
shearptr
[
nn
++
]
=
0.0
;
shearptr
[
nn
++
]
=
0.0
;
}
}
else
{
touchptr
[
n
]
=
0
;
shearptr
[
nn
++
]
=
0.0
;
shearptr
[
nn
++
]
=
0.0
;
shearptr
[
nn
++
]
=
0.0
;
}
}
n
++
;
}
}
ilist
[
i
]
=
i
;
firstneigh
[
i
]
=
neighptr
;
numneigh
[
i
]
=
n
;
if
(
fix_history
)
{
firsttouch
[
i
]
=
touchptr
;
firstshear
[
i
]
=
shearptr
;
}
npnt
+=
n
;
if
(
n
>
oneatom
)
error
->
one
(
FLERR
,
"Neighbor list overflow, boost neigh_modify one"
);
}
NEIGH_OMP_CLOSE
;
list
->
inum
=
nlocal
;
}
/* ----------------------------------------------------------------------
granular particles
N^2 / 2 search for neighbor pairs with full Newton's 3rd law
no shear history is allowed for this option
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
Neighbor
::
granular_nsq_newton_omp
(
NeighList
*
list
)
{
const
int
nlocal
=
(
includegroup
)
?
atom
->
nfirst
:
atom
->
nlocal
;
const
int
bitmask
=
(
includegroup
)
?
group
->
bitmask
[
includegroup
]
:
0
;
NEIGH_OMP_INIT
;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
NEIGH_OMP_SETUP
(
nlocal
);
int
i
,
j
,
n
,
itag
,
jtag
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
double
radi
,
radsum
,
cutsq
;
int
*
neighptr
;
double
**
x
=
atom
->
x
;
double
*
radius
=
atom
->
radius
;
int
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
*
molecule
=
atom
->
molecule
;
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
int
*
ilist
=
list
->
ilist
;
int
*
numneigh
=
list
->
numneigh
;
int
**
firstneigh
=
list
->
firstneigh
;
int
npage
=
tid
;
int
npnt
=
0
;
for
(
i
=
ifrom
;
i
<
ito
;
i
++
)
{
#if defined(_OPENMP)
#pragma omp critical
#endif
if
(
pgsize
-
npnt
<
oneatom
)
{
npnt
=
0
;
npage
+=
nthreads
;
if
(
npage
>=
list
->
maxpage
)
list
->
add_pages
(
nthreads
);
}
neighptr
=
&
(
list
->
pages
[
npage
][
npnt
]);
n
=
0
;
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
)
neighptr
[
n
++
]
=
j
;
}
ilist
[
i
]
=
i
;
firstneigh
[
i
]
=
neighptr
;
numneigh
[
i
]
=
n
;
npnt
+=
n
;
if
(
n
>
oneatom
)
error
->
one
(
FLERR
,
"Neighbor list overflow, boost neigh_modify one"
);
}
NEIGH_OMP_CLOSE
;
list
->
inum
=
nlocal
;
}
/* ----------------------------------------------------------------------
granular particles
binned neighbor list construction with partial Newton's 3rd law
shear history must be accounted for when a neighbor pair is added
each owned atom i checks own bin and surrounding bins in non-Newton stencil
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)
------------------------------------------------------------------------- */
void
Neighbor
::
granular_bin_no_newton_omp
(
NeighList
*
list
)
{
// bin local & ghost atoms
bin_atoms
();
const
int
nlocal
=
(
includegroup
)
?
atom
->
nfirst
:
atom
->
nlocal
;
FixShearHistory
*
const
fix_history
=
list
->
fix_history
;
NeighList
*
listgranhistory
=
list
->
listgranhistory
;
NEIGH_OMP_INIT
;
if
(
fix_history
)
if
(
nthreads
>
listgranhistory
->
maxpage
)
listgranhistory
->
add_pages
(
nthreads
-
listgranhistory
->
maxpage
);
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listgranhistory)
#endif
NEIGH_OMP_SETUP
(
nlocal
);
int
i
,
j
,
k
,
m
,
n
,
nn
,
ibin
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
double
radi
,
radsum
,
cutsq
;
int
*
neighptr
,
*
touchptr
;
double
*
shearptr
;
int
*
npartner
,
**
partner
;
double
(
**
shearpartner
)[
3
];
int
**
firsttouch
;
double
**
firstshear
;
// loop over each atom, storing neighbors
double
**
x
=
atom
->
x
;
double
*
radius
=
atom
->
radius
;
int
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
*
molecule
=
atom
->
molecule
;
int
*
ilist
=
list
->
ilist
;
int
*
numneigh
=
list
->
numneigh
;
int
**
firstneigh
=
list
->
firstneigh
;
int
nstencil
=
list
->
nstencil
;
int
*
stencil
=
list
->
stencil
;
if
(
fix_history
)
{
npartner
=
fix_history
->
npartner
;
partner
=
fix_history
->
partner
;
shearpartner
=
fix_history
->
shearpartner
;
firsttouch
=
listgranhistory
->
firstneigh
;
firstshear
=
listgranhistory
->
firstdouble
;
}
int
npage
=
tid
;
int
npnt
=
0
;
for
(
i
=
ifrom
;
i
<
ito
;
i
++
)
{
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if
(
pgsize
-
npnt
<
oneatom
)
{
npnt
=
0
;
npage
+=
nthreads
;
if
(
npage
>=
list
->
maxpage
)
{
list
->
add_pages
(
nthreads
);
if
(
fix_history
)
listgranhistory
->
add_pages
(
nthreads
);
}
}
n
=
nn
=
0
;
neighptr
=
&
(
list
->
pages
[
npage
][
npnt
]);
if
(
fix_history
)
{
touchptr
=
&
(
listgranhistory
->
pages
[
npage
][
npnt
]);
shearptr
=
&
(
listgranhistory
->
dpages
[
npage
][
3
*
npnt
]);
}
}
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
radi
=
radius
[
i
];
ibin
=
coord2bin
(
x
[
i
]);
// loop over all atoms in surrounding bins in stencil including self
// only store pair if i < j
// stores own/own pairs only once
// stores own/ghost pairs on both procs
for
(
k
=
0
;
k
<
nstencil
;
k
++
)
{
for
(
j
=
binhead
[
ibin
+
stencil
[
k
]];
j
>=
0
;
j
=
bins
[
j
])
{
if
(
j
<=
i
)
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
;
shearptr
[
nn
++
]
=
shearpartner
[
i
][
m
][
0
];
shearptr
[
nn
++
]
=
shearpartner
[
i
][
m
][
1
];
shearptr
[
nn
++
]
=
shearpartner
[
i
][
m
][
2
];
}
else
{
touchptr
[
n
]
=
0
;
shearptr
[
nn
++
]
=
0.0
;
shearptr
[
nn
++
]
=
0.0
;
shearptr
[
nn
++
]
=
0.0
;
}
}
else
{
touchptr
[
n
]
=
0
;
shearptr
[
nn
++
]
=
0.0
;
shearptr
[
nn
++
]
=
0.0
;
shearptr
[
nn
++
]
=
0.0
;
}
}
n
++
;
}
}
}
ilist
[
i
]
=
i
;
firstneigh
[
i
]
=
neighptr
;
numneigh
[
i
]
=
n
;
if
(
fix_history
)
{
firsttouch
[
i
]
=
touchptr
;
firstshear
[
i
]
=
shearptr
;
}
npnt
+=
n
;
if
(
n
>
oneatom
)
error
->
one
(
FLERR
,
"Neighbor list overflow, boost neigh_modify one"
);
}
NEIGH_OMP_CLOSE
;
list
->
inum
=
nlocal
;
}
/* ----------------------------------------------------------------------
granular particles
binned neighbor list construction with full Newton's 3rd law
no shear history is allowed for this option
each owned atom i checks its own bin and other bins in Newton stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void
Neighbor
::
granular_bin_newton_omp
(
NeighList
*
list
)
{
// bin local & ghost atoms
bin_atoms
();
const
int
nlocal
=
(
includegroup
)
?
atom
->
nfirst
:
atom
->
nlocal
;
NEIGH_OMP_INIT
;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
NEIGH_OMP_SETUP
(
nlocal
);
int
i
,
j
,
k
,
n
,
ibin
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
double
radi
,
radsum
,
cutsq
;
int
*
neighptr
;
// loop over each atom, storing neighbors
double
**
x
=
atom
->
x
;
double
*
radius
=
atom
->
radius
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
*
molecule
=
atom
->
molecule
;
int
*
ilist
=
list
->
ilist
;
int
*
numneigh
=
list
->
numneigh
;
int
**
firstneigh
=
list
->
firstneigh
;
int
nstencil
=
list
->
nstencil
;
int
*
stencil
=
list
->
stencil
;
int
npage
=
tid
;
int
npnt
=
0
;
for
(
i
=
ifrom
;
i
<
ito
;
i
++
)
{
#if defined(_OPENMP)
#pragma omp critical
#endif
if
(
pgsize
-
npnt
<
oneatom
)
{
npnt
=
0
;
npage
+=
nthreads
;
if
(
npage
>=
list
->
maxpage
)
list
->
add_pages
(
nthreads
);
}
n
=
0
;
neighptr
=
&
(
list
->
pages
[
npage
][
npnt
]);
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
radi
=
radius
[
i
];
// loop over rest of atoms in i's bin, ghosts are at end of linked list
// if j is owned atom, store it, since j is beyond i in linked list
// if j is ghost, only store if j coords are "above and to the right" of i
for
(
j
=
bins
[
i
];
j
>=
0
;
j
=
bins
[
j
])
{
if
(
j
>=
nlocal
)
{
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
)
neighptr
[
n
++
]
=
j
;
}
// loop over all atoms in other bins in stencil, store every pair
ibin
=
coord2bin
(
x
[
i
]);
for
(
k
=
0
;
k
<
nstencil
;
k
++
)
{
for
(
j
=
binhead
[
ibin
+
stencil
[
k
]];
j
>=
0
;
j
=
bins
[
j
])
{
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
;
}
}
ilist
[
i
]
=
i
;
firstneigh
[
i
]
=
neighptr
;
numneigh
[
i
]
=
n
;
npnt
+=
n
;
if
(
n
>
oneatom
)
error
->
one
(
FLERR
,
"Neighbor list overflow, boost neigh_modify one"
);
}
NEIGH_OMP_CLOSE
;
list
->
inum
=
nlocal
;
}
/* ----------------------------------------------------------------------
granular particles
binned neighbor list construction with Newton's 3rd law for triclinic
no shear history is allowed for this option
each owned atom i checks its own bin and other bins in triclinic stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void
Neighbor
::
granular_bin_newton_tri_omp
(
NeighList
*
list
)
{
// bin local & ghost atoms
bin_atoms
();
const
int
nlocal
=
(
includegroup
)
?
atom
->
nfirst
:
atom
->
nlocal
;
NEIGH_OMP_INIT
;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
NEIGH_OMP_SETUP
(
nlocal
);
int
i
,
j
,
k
,
n
,
ibin
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
double
radi
,
radsum
,
cutsq
;
int
*
neighptr
;
// loop over each atom, storing neighbors
double
**
x
=
atom
->
x
;
double
*
radius
=
atom
->
radius
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
*
molecule
=
atom
->
molecule
;
int
*
ilist
=
list
->
ilist
;
int
*
numneigh
=
list
->
numneigh
;
int
**
firstneigh
=
list
->
firstneigh
;
int
nstencil
=
list
->
nstencil
;
int
*
stencil
=
list
->
stencil
;
int
npage
=
tid
;
int
npnt
=
0
;
for
(
i
=
ifrom
;
i
<
ito
;
i
++
)
{
#if defined(_OPENMP)
#pragma omp critical
#endif
if
(
pgsize
-
npnt
<
oneatom
)
{
npnt
=
0
;
npage
+=
nthreads
;
if
(
npage
>=
list
->
maxpage
)
list
->
add_pages
(
nthreads
);
}
n
=
0
;
neighptr
=
&
(
list
->
pages
[
npage
][
npnt
]);
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
radi
=
radius
[
i
];
// loop over all atoms in bins in stencil
// pairs for atoms j "below" i are excluded
// below = lower z or (equal z and lower y) or (equal zy and lower x)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
ibin
=
coord2bin
(
x
[
i
]);
for
(
k
=
0
;
k
<
nstencil
;
k
++
)
{
for
(
j
=
binhead
[
ibin
+
stencil
[
k
]];
j
>=
0
;
j
=
bins
[
j
])
{
if
(
x
[
j
][
2
]
<
ztmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
)
{
if
(
x
[
j
][
1
]
<
ytmp
)
continue
;
if
(
x
[
j
][
1
]
==
ytmp
)
{
if
(
x
[
j
][
0
]
<
xtmp
)
continue
;
if
(
x
[
j
][
0
]
==
xtmp
&&
j
<=
i
)
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
;
}
}
ilist
[
i
]
=
i
;
firstneigh
[
i
]
=
neighptr
;
numneigh
[
i
]
=
n
;
npnt
+=
n
;
if
(
n
>
oneatom
)
error
->
one
(
FLERR
,
"Neighbor list overflow, boost neigh_modify one"
);
}
NEIGH_OMP_CLOSE
;
list
->
inum
=
nlocal
;
}
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