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neigh_list.cpp
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Created
Mon, Aug 19, 11:10
Size
7 KB
Mime Type
text/x-c
Expires
Wed, Aug 21, 11:10 (2 d)
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blob
Format
Raw Data
Handle
20016670
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rLAMMPS lammps
neigh_list.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 "neigh_list.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define PGDELTA 1
enum
{
NSQ
,
BIN
,
MULTI
};
// also in neighbor.cpp
/* ---------------------------------------------------------------------- */
NeighList
::
NeighList
(
LAMMPS
*
lmp
,
int
size
)
:
Pointers
(
lmp
)
{
maxlocal
=
0
;
pgsize
=
size
;
ilist
=
NULL
;
numneigh
=
NULL
;
firstneigh
=
NULL
;
firstdouble
=
NULL
;
maxpage
=
0
;
pages
=
NULL
;
dpages
=
NULL
;
dnum
=
0
;
skip
=
0
;
iskip
=
NULL
;
ijskip
=
NULL
;
listgranhistory
=
NULL
;
fix_history
=
NULL
;
respamiddle
=
0
;
listinner
=
NULL
;
listmiddle
=
NULL
;
listfull
=
NULL
;
listcopy
=
NULL
;
listskip
=
NULL
;
maxstencil
=
0
;
stencil
=
NULL
;
maxstencil_multi
=
0
;
nstencil_multi
=
NULL
;
stencil_multi
=
NULL
;
distsq_multi
=
NULL
;
}
/* ---------------------------------------------------------------------- */
NeighList
::~
NeighList
()
{
if
(
!
listcopy
)
{
memory
->
sfree
(
ilist
);
memory
->
sfree
(
numneigh
);
memory
->
sfree
(
firstneigh
);
memory
->
sfree
(
firstdouble
);
for
(
int
i
=
0
;
i
<
maxpage
;
i
++
)
memory
->
sfree
(
pages
[
i
]);
memory
->
sfree
(
pages
);
if
(
dnum
)
{
for
(
int
i
=
0
;
i
<
maxpage
;
i
++
)
memory
->
sfree
(
dpages
[
i
]);
memory
->
sfree
(
dpages
);
}
}
if
(
maxstencil
)
memory
->
sfree
(
stencil
);
if
(
maxstencil_multi
)
{
for
(
int
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
{
memory
->
sfree
(
stencil_multi
[
i
]);
memory
->
sfree
(
distsq_multi
[
i
]);
}
delete
[]
nstencil_multi
;
delete
[]
stencil_multi
;
delete
[]
distsq_multi
;
}
}
/* ----------------------------------------------------------------------
grow atom arrays to allow for nmax atoms
triggered by more atoms on a processor
------------------------------------------------------------------------- */
void
NeighList
::
grow
(
int
nmax
)
{
// skip if grow not needed (don't think this should happen)
if
(
nmax
<=
maxlocal
)
return
;
maxlocal
=
nmax
;
memory
->
sfree
(
ilist
);
memory
->
sfree
(
numneigh
);
memory
->
sfree
(
firstneigh
);
ilist
=
(
int
*
)
memory
->
smalloc
(
maxlocal
*
sizeof
(
int
),
"neighlist:ilist"
);
numneigh
=
(
int
*
)
memory
->
smalloc
(
maxlocal
*
sizeof
(
int
),
"neighlist:numneigh"
);
firstneigh
=
(
int
**
)
memory
->
smalloc
(
maxlocal
*
sizeof
(
int
*
),
"neighlist:firstneigh"
);
if
(
dnum
)
firstdouble
=
(
double
**
)
memory
->
smalloc
(
maxlocal
*
sizeof
(
double
*
),
"neighlist:firstdouble"
);
}
/* ----------------------------------------------------------------------
insure stencils are large enough for smax bins
style = BIN or MULTI
------------------------------------------------------------------------- */
void
NeighList
::
stencil_allocate
(
int
smax
,
int
style
)
{
int
i
;
if
(
style
==
BIN
)
{
if
(
smax
>
maxstencil
)
{
maxstencil
=
smax
;
memory
->
sfree
(
stencil
);
stencil
=
(
int
*
)
memory
->
smalloc
(
smax
*
sizeof
(
int
),
"neighlist:stencil"
);
}
}
else
{
int
n
=
atom
->
ntypes
;
if
(
maxstencil_multi
==
0
)
{
nstencil_multi
=
new
int
[
n
+
1
];
stencil_multi
=
new
int
*
[
n
+
1
];
distsq_multi
=
new
double
*
[
n
+
1
];
for
(
i
=
1
;
i
<=
n
;
i
++
)
{
nstencil_multi
[
i
]
=
0
;
stencil_multi
[
i
]
=
NULL
;
distsq_multi
[
i
]
=
NULL
;
}
}
if
(
smax
>
maxstencil_multi
)
{
maxstencil_multi
=
smax
;
for
(
i
=
1
;
i
<=
n
;
i
++
)
{
memory
->
sfree
(
stencil_multi
[
i
]);
memory
->
sfree
(
distsq_multi
[
i
]);
stencil_multi
[
i
]
=
(
int
*
)
memory
->
smalloc
(
smax
*
sizeof
(
int
),
"neighlist:stencil_multi"
);
distsq_multi
[
i
]
=
(
double
*
)
memory
->
smalloc
(
smax
*
sizeof
(
double
),
"neighlist:distsq_multi"
);
}
}
}
}
/* ----------------------------------------------------------------------
add PGDELTA pages to neighbor list
------------------------------------------------------------------------- */
int
**
NeighList
::
add_pages
()
{
int
npage
=
maxpage
;
maxpage
+=
PGDELTA
;
pages
=
(
int
**
)
memory
->
srealloc
(
pages
,
maxpage
*
sizeof
(
int
*
),
"neighlist:pages"
);
for
(
int
i
=
npage
;
i
<
maxpage
;
i
++
)
pages
[
i
]
=
(
int
*
)
memory
->
smalloc
(
pgsize
*
sizeof
(
int
),
"neighlist:pages[i]"
);
if
(
dnum
)
{
dpages
=
(
double
**
)
memory
->
srealloc
(
dpages
,
maxpage
*
sizeof
(
double
*
),
"neighlist:dpages"
);
for
(
int
i
=
npage
;
i
<
maxpage
;
i
++
)
dpages
[
i
]
=
(
double
*
)
memory
->
smalloc
(
dnum
*
pgsize
*
sizeof
(
double
),
"neighlist:dpages[i]"
);
}
return
pages
;
}
/* ----------------------------------------------------------------------
print attributes of this list and associated request
------------------------------------------------------------------------- */
void
NeighList
::
print_attributes
()
{
if
(
comm
->
me
!=
0
)
return
;
NeighRequest
*
rq
=
neighbor
->
requests
[
index
];
printf
(
"Neighbor list/request %d:
\n
"
,
index
);
printf
(
" %d = build flag
\n
"
,
buildflag
);
printf
(
" %d = grow flag
\n
"
,
growflag
);
printf
(
" %d = stencil flag
\n
"
,
stencilflag
);
printf
(
"
\n
"
);
printf
(
" %d = pair
\n
"
,
rq
->
pair
);
printf
(
" %d = fix
\n
"
,
rq
->
fix
);
printf
(
" %d = compute
\n
"
,
rq
->
compute
);
printf
(
" %d = command
\n
"
,
rq
->
command
);
printf
(
"
\n
"
);
printf
(
" %d = half
\n
"
,
rq
->
half
);
printf
(
" %d = full
\n
"
,
rq
->
full
);
printf
(
" %d = gran
\n
"
,
rq
->
gran
);
printf
(
" %d = granhistory
\n
"
,
rq
->
granhistory
);
printf
(
" %d = respainner
\n
"
,
rq
->
respainner
);
printf
(
" %d = respamiddle
\n
"
,
rq
->
respamiddle
);
printf
(
" %d = respaouter
\n
"
,
rq
->
respaouter
);
printf
(
" %d = half_from_full
\n
"
,
rq
->
half_from_full
);
printf
(
"
\n
"
);
printf
(
" %d = occasional
\n
"
,
rq
->
occasional
);
printf
(
" %d = dnum
\n
"
,
rq
->
dnum
);
printf
(
" %d = copy
\n
"
,
rq
->
copy
);
printf
(
" %d = skip
\n
"
,
rq
->
skip
);
printf
(
" %d = otherlist
\n
"
,
rq
->
otherlist
);
printf
(
" %p = listskip
\n
"
,
listskip
);
printf
(
"
\n
"
);
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
if growflag = 0, maxlocal & maxpage will also be 0
if stencilflag = 0, maxstencil * maxstencil_multi will also be 0
------------------------------------------------------------------------- */
double
NeighList
::
memory_usage
()
{
double
bytes
=
0.0
;
bytes
+=
2
*
maxlocal
*
sizeof
(
int
);
bytes
+=
maxlocal
*
sizeof
(
int
*
);
bytes
+=
maxpage
*
pgsize
*
sizeof
(
int
);
if
(
dnum
)
{
bytes
+=
maxlocal
*
sizeof
(
double
*
);
bytes
+=
dnum
*
maxpage
*
pgsize
*
sizeof
(
double
);
}
if
(
maxstencil
)
bytes
+=
maxstencil
*
sizeof
(
int
);
if
(
maxstencil_multi
)
{
bytes
+=
atom
->
ntypes
*
maxstencil_multi
*
sizeof
(
int
);
bytes
+=
atom
->
ntypes
*
maxstencil_multi
*
sizeof
(
double
);
}
return
bytes
;
}
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