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npair_skip_size_off2on_oneside.cpp
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Mon, Oct 14, 11:18
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text/x-c
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Wed, Oct 16, 11:18 (1 d, 23 h)
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rLAMMPS lammps
npair_skip_size_off2on_oneside.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_skip_size_off2on_oneside.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "domain.h"
#include "fix_shear_history.h"
#include "my_page.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
NPairSkipSizeOff2onOneside
::
NPairSkipSizeOff2onOneside
(
LAMMPS
*
lmp
)
:
NPair
(
lmp
)
{}
/* ----------------------------------------------------------------------
build skip list for subset of types from parent list
iskip and ijskip flag which atom types and type pairs to skip
parent non-skip list used newton off and was not onesided,
this skip list is newton on and onesided
if list requests it, preserve shear history via fix shear/history
------------------------------------------------------------------------- */
void
NPairSkipSizeOff2onOneside
::
build
(
NeighList
*
list
)
{
int
i
,
j
,
ii
,
jj
,
m
,
n
,
nn
,
itype
,
jnum
,
joriginal
,
flip
,
dnum
,
dnumbytes
,
tmp
;
tagint
jtag
;
int
*
surf
,
*
jlist
;
int
*
npartner
;
tagint
**
partner
;
double
**
shearpartner
;
int
**
firsttouch
;
double
**
firstshear
;
MyPage
<
int
>
*
ipage_touch
;
MyPage
<
double
>
*
dpage_shear
;
NeighList
*
listhistory
;
tagint
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
int
*
ilist
=
list
->
ilist
;
int
*
numneigh
=
list
->
numneigh
;
int
**
firstneigh
=
list
->
firstneigh
;
MyPage
<
int
>
*
ipage
=
list
->
ipage
;
int
*
ilist_skip
=
list
->
listskip
->
ilist
;
int
*
numneigh_skip
=
list
->
listskip
->
numneigh
;
int
**
firstneigh_skip
=
list
->
listskip
->
firstneigh
;
int
inum_skip
=
list
->
listskip
->
inum
;
int
*
iskip
=
list
->
iskip
;
int
**
ijskip
=
list
->
ijskip
;
if
(
domain
->
dimension
==
2
)
surf
=
atom
->
line
;
else
surf
=
atom
->
tri
;
FixShearHistory
*
fix_history
=
(
FixShearHistory
*
)
list
->
fix_history
;
if
(
fix_history
)
{
fix_history
->
nlocal_neigh
=
nlocal
;
fix_history
->
nall_neigh
=
nlocal
+
atom
->
nghost
;
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
();
}
// two loops over parent list required, one to count, one to store
// because onesided constraint means pair I,J may be stored with I or J
// so don't know in advance how much space to alloc for each atom's neighs
// first loop over atoms in other list to count neighbors
// skip I atom entirely if iskip is set for type[I]
// skip I,J pair if ijskip is set for type[I],type[J]
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
numneigh
[
i
]
=
0
;
for
(
ii
=
0
;
ii
<
inum_skip
;
ii
++
)
{
i
=
ilist_skip
[
ii
];
itype
=
type
[
i
];
if
(
iskip
[
itype
])
continue
;
n
=
0
;
// loop over parent non-skip size list
jlist
=
firstneigh_skip
[
i
];
jnum
=
numneigh_skip
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
joriginal
=
jlist
[
jj
];
j
=
joriginal
&
NEIGHMASK
;
if
(
ijskip
[
itype
][
type
[
j
]])
continue
;
// flip I,J if necessary to satisfy onesided constraint
// do not keep if I is now ghost
if
(
surf
[
i
]
>=
0
)
{
if
(
j
>=
nlocal
)
continue
;
tmp
=
i
;
i
=
j
;
j
=
tmp
;
flip
=
1
;
}
else
flip
=
0
;
numneigh
[
i
]
++
;
if
(
flip
)
i
=
j
;
}
}
// allocate all per-atom neigh list chunks, including history
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
numneigh
[
i
]
==
0
)
continue
;
n
=
numneigh
[
i
];
firstneigh
[
i
]
=
ipage
->
get
(
n
);
if
(
ipage
->
status
())
error
->
one
(
FLERR
,
"Neighbor list overflow, boost neigh_modify one"
);
if
(
fix_history
)
{
firsttouch
[
i
]
=
ipage_touch
->
get
(
n
);
firstshear
[
i
]
=
dpage_shear
->
get
(
dnum
*
n
);
}
}
// second loop over atoms in other list to store neighbors
// skip I atom entirely if iskip is set for type[I]
// skip I,J pair if ijskip is set for type[I],type[J]
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
numneigh
[
i
]
=
0
;
for
(
ii
=
0
;
ii
<
inum_skip
;
ii
++
)
{
i
=
ilist_skip
[
ii
];
itype
=
type
[
i
];
if
(
iskip
[
itype
])
continue
;
// loop over parent non-skip size list and optionally its history info
jlist
=
firstneigh_skip
[
i
];
jnum
=
numneigh_skip
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
joriginal
=
jlist
[
jj
];
j
=
joriginal
&
NEIGHMASK
;
if
(
ijskip
[
itype
][
type
[
j
]])
continue
;
// flip I,J if necessary to satisfy onesided constraint
// do not keep if I is now ghost
if
(
surf
[
i
]
>=
0
)
{
if
(
j
>=
nlocal
)
continue
;
tmp
=
i
;
i
=
j
;
j
=
tmp
;
flip
=
1
;
}
else
flip
=
0
;
// store j in neigh list, not joriginal, like other neigh methods
// OK, b/c there is no special list flagging for surfs
firstneigh
[
i
][
numneigh
[
i
]]
=
j
;
// no numeric test for current touch
// just use FSH partner list to infer it
// would require complex calculation for surfs
if
(
fix_history
)
{
jtag
=
tag
[
j
];
n
=
numneigh
[
i
];
nn
=
dnum
*
n
;
for
(
m
=
0
;
m
<
npartner
[
i
];
m
++
)
if
(
partner
[
i
][
m
]
==
jtag
)
break
;
if
(
m
<
npartner
[
i
])
{
firsttouch
[
i
][
n
]
=
1
;
memcpy
(
&
firstshear
[
i
][
nn
],
&
shearpartner
[
i
][
dnum
*
m
],
dnumbytes
);
}
else
{
firsttouch
[
i
][
n
]
=
0
;
memcpy
(
&
firstshear
[
i
][
nn
],
zeroes
,
dnumbytes
);
}
}
numneigh
[
i
]
++
;
if
(
flip
)
i
=
j
;
}
// only add atom I to ilist if it has neighbors
// fix shear/history allows for this in pre_exchange_onesided()
if
(
numneigh
[
i
])
ilist
[
inum
++
]
=
i
;
}
list
->
inum
=
inum
;
}
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