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compute_pair_local.cpp
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Created
Mon, Jul 8, 11:08
Size
6 KB
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text/x-c
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Wed, Jul 10, 11:08 (1 d, 23 h)
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rLAMMPS lammps
compute_pair_local.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 "math.h"
#include "string.h"
#include "compute_pair_local.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "neigh_list.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
ComputePairLocal
::
ComputePairLocal
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
4
)
error
->
all
(
"Illegal compute pair/local command"
);
local_flag
=
1
;
nvalues
=
narg
-
3
;
if
(
nvalues
==
1
)
size_local_cols
=
0
;
else
size_local_cols
=
nvalues
;
dflag
=
eflag
=
fflag
=
-
1
;
nvalues
=
0
;
int
i
;
for
(
int
iarg
=
3
;
iarg
<
narg
;
iarg
++
)
{
i
=
iarg
-
3
;
if
(
strcmp
(
arg
[
iarg
],
"dist"
)
==
0
)
dflag
=
nvalues
++
;
else
if
(
strcmp
(
arg
[
iarg
],
"eng"
)
==
0
)
eflag
=
nvalues
++
;
else
if
(
strcmp
(
arg
[
iarg
],
"force"
)
==
0
)
fflag
=
nvalues
++
;
else
error
->
all
(
"Invalid keyword in compute pair/local command"
);
}
nmax
=
0
;
vector
=
NULL
;
array
=
NULL
;
}
/* ---------------------------------------------------------------------- */
ComputePairLocal
::~
ComputePairLocal
()
{
memory
->
sfree
(
vector
);
memory
->
destroy_2d_double_array
(
array
);
}
/* ---------------------------------------------------------------------- */
void
ComputePairLocal
::
init
()
{
if
(
force
->
pair
==
NULL
)
error
->
all
(
"No pair style is defined for compute pair/local"
);
if
(
force
->
pair
->
single_enable
==
0
)
error
->
all
(
"Pair style does not support compute pair/local"
);
// need an occasional half neighbor list
int
irequest
=
neighbor
->
request
((
void
*
)
this
);
neighbor
->
requests
[
irequest
]
->
pair
=
0
;
neighbor
->
requests
[
irequest
]
->
compute
=
1
;
neighbor
->
requests
[
irequest
]
->
occasional
=
1
;
}
/* ---------------------------------------------------------------------- */
void
ComputePairLocal
::
init_list
(
int
id
,
NeighList
*
ptr
)
{
list
=
ptr
;
}
/* ---------------------------------------------------------------------- */
void
ComputePairLocal
::
compute_local
()
{
invoked_local
=
update
->
ntimestep
;
// count local entries and compute pair info
ncount
=
compute_pairs
(
0
);
if
(
ncount
>
nmax
)
reallocate
(
ncount
);
size_local_rows
=
ncount
;
ncount
=
compute_pairs
(
1
);
}
/* ----------------------------------------------------------------------
count pairs and compute pair info on this proc
only count pair once if newton_pair is off
both atom I,J must be in group
if flag is set, compute requested info about pair
------------------------------------------------------------------------- */
int
ComputePairLocal
::
compute_pairs
(
int
flag
)
{
int
i
,
j
,
m
,
n
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
;
double
rsq
,
eng
,
fpair
,
factor_coul
,
factor_lj
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
*
dbuf
,
*
ebuf
,
*
fbuf
;
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
nall
=
nlocal
+
atom
->
nghost
;
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
int
newton_pair
=
force
->
newton_pair
;
// invoke half neighbor list (will copy or build if necessary)
if
(
flag
==
0
)
neighbor
->
build_one
(
list
->
index
);
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// loop over neighbors of my atoms
// skip if I or J are not in group
if
(
flag
)
{
if
(
nvalues
==
1
)
{
if
(
dflag
>=
0
)
dbuf
=
vector
;
if
(
eflag
>=
0
)
ebuf
=
vector
;
if
(
fflag
>=
0
)
fbuf
=
vector
;
}
else
{
if
(
dflag
>=
0
)
dbuf
=
&
array
[
0
][
dflag
];
if
(
eflag
>=
0
)
ebuf
=
&
array
[
0
][
eflag
];
if
(
fflag
>=
0
)
fbuf
=
&
array
[
0
][
fflag
];
}
}
Pair
*
pair
=
force
->
pair
;
double
**
cutsq
=
force
->
pair
->
cutsq
;
m
=
n
=
0
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
!
(
mask
[
i
]
&
groupbit
))
continue
;
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
itype
=
type
[
i
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
if
(
j
<
nall
)
factor_coul
=
factor_lj
=
1.0
;
else
{
factor_coul
=
special_coul
[
j
/
nall
];
factor_lj
=
special_lj
[
j
/
nall
];
j
%=
nall
;
}
if
(
!
(
mask
[
j
]
&
groupbit
))
continue
;
if
(
newton_pair
==
0
&&
j
>=
nlocal
)
continue
;
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
jtype
=
type
[
j
];
if
(
rsq
>=
cutsq
[
itype
][
jtype
])
continue
;
if
(
flag
)
{
if
(
dflag
>=
0
)
dbuf
[
n
]
=
sqrt
(
rsq
);
if
(
eflag
>=
0
||
fflag
>=
0
)
{
eng
=
pair
->
single
(
i
,
j
,
itype
,
jtype
,
rsq
,
factor_coul
,
factor_lj
,
fpair
);
if
(
eflag
>=
0
)
ebuf
[
n
]
=
eng
;
if
(
fflag
>=
0
)
fbuf
[
n
]
=
sqrt
(
rsq
)
*
fpair
;
}
n
+=
nvalues
;
}
m
++
;
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
ComputePairLocal
::
reallocate
(
int
n
)
{
// grow vector or array and indices array
while
(
nmax
<
n
)
nmax
+=
DELTA
;
if
(
nvalues
==
1
)
{
memory
->
sfree
(
vector
);
vector
=
(
double
*
)
memory
->
smalloc
(
nmax
*
sizeof
(
double
),
"pair/local:vector"
);
vector_local
=
vector
;
}
else
{
memory
->
destroy_2d_double_array
(
array
);
array
=
memory
->
create_2d_double_array
(
nmax
,
nvalues
,
"pair/local:array"
);
array_local
=
array
;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double
ComputePairLocal
::
memory_usage
()
{
double
bytes
=
nmax
*
nvalues
*
sizeof
(
double
);
return
bytes
;
}
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