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compute_body_local.cpp
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Mon, Oct 14, 19:52
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6 KB
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text/x-c
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Wed, Oct 16, 19:52 (2 d)
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rLAMMPS lammps
compute_body_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_body_local.h"
#include "atom.h"
#include "atom_vec_body.h"
#include "body.h"
#include "update.h"
#include "domain.h"
#include "force.h"
#include "bond.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define DELTA 10000
enum
{
ID
,
TYPE
,
INDEX
};
/* ---------------------------------------------------------------------- */
ComputeBodyLocal
::
ComputeBodyLocal
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
4
)
error
->
all
(
FLERR
,
"Illegal compute body/local command"
);
local_flag
=
1
;
nvalues
=
narg
-
3
;
if
(
nvalues
==
1
)
size_local_cols
=
0
;
else
size_local_cols
=
nvalues
;
which
=
new
int
[
nvalues
];
index
=
new
int
[
nvalues
];
nvalues
=
0
;
for
(
int
iarg
=
3
;
iarg
<
narg
;
iarg
++
)
{
if
(
strcmp
(
arg
[
iarg
],
"id"
)
==
0
)
which
[
nvalues
++
]
=
ID
;
else
if
(
strcmp
(
arg
[
iarg
],
"type"
)
==
0
)
which
[
nvalues
++
]
=
TYPE
;
else
{
which
[
nvalues
]
=
INDEX
;
index
[
nvalues
]
=
force
->
inumeric
(
FLERR
,
arg
[
iarg
])
-
1
;
nvalues
++
;
}
}
avec
=
(
AtomVecBody
*
)
atom
->
style_match
(
"body"
);
if
(
!
avec
)
error
->
all
(
FLERR
,
"Compute body/local requires atom style body"
);
bptr
=
avec
->
bptr
;
int
indexmax
=
bptr
->
noutcol
();
for
(
int
i
=
0
;
i
<
nvalues
;
i
++
)
{
if
(
which
[
i
]
==
INDEX
&&
(
index
[
i
]
<
0
||
index
[
i
]
>=
indexmax
))
error
->
all
(
FLERR
,
"Invalid index in compute body/local command"
);
}
nmax
=
0
;
vector
=
NULL
;
array
=
NULL
;
}
/* ---------------------------------------------------------------------- */
ComputeBodyLocal
::~
ComputeBodyLocal
()
{
delete
[]
which
;
delete
[]
index
;
memory
->
destroy
(
vector
);
memory
->
destroy
(
array
);
}
/* ---------------------------------------------------------------------- */
void
ComputeBodyLocal
::
init
()
{
// if non-body particles in group insure only indices 1,2,3 are used
int
nonbody
=
0
;
int
*
mask
=
atom
->
mask
;
int
*
body
=
atom
->
body
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
if
(
body
[
i
]
<
0
)
nonbody
=
1
;
int
flag
;
MPI_Allreduce
(
&
nonbody
,
&
flag
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
if
(
flag
)
{
for
(
int
i
=
0
;
i
<
nvalues
;
i
++
)
if
(
which
[
i
]
==
INDEX
&&
index
[
i
]
>
2
)
error
->
all
(
FLERR
,
"Invalid index for non-body particles "
"in compute body/local command"
);
}
// do initial memory allocation so that memory_usage() is correct
int
ncount
=
compute_body
(
0
);
if
(
ncount
>
nmax
)
reallocate
(
ncount
);
size_local_rows
=
ncount
;
}
/* ---------------------------------------------------------------------- */
void
ComputeBodyLocal
::
compute_local
()
{
invoked_local
=
update
->
ntimestep
;
// count local entries and compute body info
int
ncount
=
compute_body
(
0
);
if
(
ncount
>
nmax
)
reallocate
(
ncount
);
size_local_rows
=
ncount
;
ncount
=
compute_body
(
1
);
}
/* ----------------------------------------------------------------------
count body info and compute body info on this proc
flag = 0, only count
flag = 1, also compute
------------------------------------------------------------------------- */
int
ComputeBodyLocal
::
compute_body
(
int
flag
)
{
// perform count
int
*
mask
=
atom
->
mask
;
int
*
body
=
atom
->
body
;
int
nlocal
=
atom
->
nlocal
;
int
ncount
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
if
(
body
[
i
]
<
0
)
ncount
++
;
else
ncount
+=
bptr
->
noutrow
(
body
[
i
]);
}
if
(
flag
==
0
)
return
ncount
;
// perform computation and fill output vector/array
int
m
,
n
,
ibonus
;
double
*
values
=
new
double
[
bptr
->
noutcol
()];
double
**
x
=
atom
->
x
;
tagint
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
ncount
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
if
(
body
[
i
]
<
0
)
{
if
(
nvalues
==
1
)
{
if
(
which
[
0
]
==
ID
)
vector
[
ncount
]
=
tag
[
i
];
else
if
(
which
[
0
]
==
TYPE
)
vector
[
ncount
]
=
type
[
i
];
else
vector
[
ncount
]
=
x
[
i
][
index
[
0
]];
}
else
{
for
(
m
=
0
;
m
<
nvalues
;
m
++
)
{
if
(
which
[
m
]
==
ID
)
array
[
ncount
][
m
]
=
tag
[
i
];
else
if
(
which
[
m
]
==
TYPE
)
array
[
ncount
][
m
]
=
type
[
i
];
else
array
[
ncount
][
m
]
=
x
[
i
][
index
[
m
]];
}
}
ncount
++
;
}
else
{
ibonus
=
body
[
i
];
n
=
bptr
->
noutrow
(
ibonus
);
for
(
int
j
=
0
;
j
<
n
;
j
++
)
{
bptr
->
output
(
ibonus
,
j
,
values
);
if
(
nvalues
==
1
)
{
if
(
which
[
0
]
==
ID
)
vector
[
ncount
]
=
tag
[
i
];
else
if
(
which
[
0
]
==
TYPE
)
vector
[
ncount
]
=
type
[
i
];
else
vector
[
ncount
]
=
values
[
index
[
0
]];
}
else
{
for
(
m
=
0
;
m
<
nvalues
;
m
++
)
{
if
(
which
[
m
]
==
ID
)
array
[
ncount
][
m
]
=
tag
[
i
];
else
if
(
which
[
m
]
==
TYPE
)
array
[
ncount
][
m
]
=
type
[
i
];
else
array
[
ncount
][
m
]
=
values
[
index
[
m
]];
}
}
ncount
++
;
}
}
}
}
delete
[]
values
;
return
ncount
;
}
/* ---------------------------------------------------------------------- */
void
ComputeBodyLocal
::
reallocate
(
int
n
)
{
// grow vector or array and indices array
while
(
nmax
<
n
)
nmax
+=
DELTA
;
if
(
nvalues
==
1
)
{
memory
->
destroy
(
vector
);
memory
->
create
(
vector
,
nmax
,
"body/local:vector"
);
vector_local
=
vector
;
}
else
{
memory
->
destroy
(
array
);
memory
->
create
(
array
,
nmax
,
nvalues
,
"body/local:array"
);
array_local
=
array
;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double
ComputeBodyLocal
::
memory_usage
()
{
double
bytes
=
nmax
*
nvalues
*
sizeof
(
double
);
return
bytes
;
}
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