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compute_property_chunk.cpp
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Created
Tue, Jul 23, 01:00
Size
9 KB
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text/x-c
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Thu, Jul 25, 01:00 (1 d, 21 h)
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rLAMMPS lammps
compute_property_chunk.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 "compute_property_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputePropertyChunk
::
ComputePropertyChunk
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
5
)
error
->
all
(
FLERR
,
"Illegal compute property/chunk command"
);
// ID of compute chunk/atom
int
n
=
strlen
(
arg
[
3
])
+
1
;
idchunk
=
new
char
[
n
];
strcpy
(
idchunk
,
arg
[
3
]);
init
();
// parse values
nvalues
=
narg
-
4
;
pack_choice
=
new
FnPtrPack
[
nvalues
];
countflag
=
0
;
int
i
;
for
(
int
iarg
=
4
;
iarg
<
narg
;
iarg
++
)
{
i
=
iarg
-
4
;
if
(
strcmp
(
arg
[
iarg
],
"count"
)
==
0
)
{
pack_choice
[
i
]
=
&
ComputePropertyChunk
::
pack_count
;
countflag
=
1
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"id"
)
==
0
)
{
if
(
!
cchunk
->
compress
)
error
->
all
(
FLERR
,
"Compute chunk/atom stores no IDs for "
"compute property/chunk"
);
pack_choice
[
i
]
=
&
ComputePropertyChunk
::
pack_id
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"coord1"
)
==
0
)
{
if
(
cchunk
->
ncoord
<
1
)
error
->
all
(
FLERR
,
"Compute chunk/atom stores no coord1 for "
"compute property/chunk"
);
pack_choice
[
i
]
=
&
ComputePropertyChunk
::
pack_coord1
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"coord2"
)
==
0
)
{
if
(
cchunk
->
ncoord
<
2
)
error
->
all
(
FLERR
,
"Compute chunk/atom stores no coord2 for "
"compute property/chunk"
);
pack_choice
[
i
]
=
&
ComputePropertyChunk
::
pack_coord2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"coord3"
)
==
0
)
{
if
(
cchunk
->
ncoord
<
3
)
error
->
all
(
FLERR
,
"Compute chunk/atom stores no coord3 for "
"compute property/chunk"
);
pack_choice
[
i
]
=
&
ComputePropertyChunk
::
pack_coord3
;
}
else
error
->
all
(
FLERR
,
"Invalid keyword in compute property/chunk command"
);
}
// initialization
nchunk
=
1
;
maxchunk
=
0
;
vector
=
NULL
;
array
=
NULL
;
count_one
=
count_all
=
NULL
;
allocate
();
if
(
nvalues
==
1
)
{
vector_flag
=
1
;
size_vector
=
0
;
size_vector_variable
=
1
;
extvector
=
0
;
}
else
{
array_flag
=
1
;
size_array_cols
=
nvalues
;
size_array_rows
=
0
;
size_array_rows_variable
=
1
;
extarray
=
0
;
}
}
/* ---------------------------------------------------------------------- */
ComputePropertyChunk
::~
ComputePropertyChunk
()
{
delete
[]
idchunk
;
delete
[]
pack_choice
;
memory
->
destroy
(
vector
);
memory
->
destroy
(
array
);
memory
->
destroy
(
count_one
);
memory
->
destroy
(
count_all
);
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyChunk
::
init
()
{
int
icompute
=
modify
->
find_compute
(
idchunk
);
if
(
icompute
<
0
)
error
->
all
(
FLERR
,
"Chunk/atom compute does not exist for "
"compute property/chunk"
);
cchunk
=
(
ComputeChunkAtom
*
)
modify
->
compute
[
icompute
];
if
(
strcmp
(
cchunk
->
style
,
"chunk/atom"
)
!=
0
)
error
->
all
(
FLERR
,
"Compute property/chunk does not use chunk/atom compute"
);
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyChunk
::
compute_vector
()
{
invoked_vector
=
update
->
ntimestep
;
// compute chunk/atom assigns atoms to chunk IDs
// if need count, extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk
=
cchunk
->
setup_chunks
();
if
(
nchunk
>
maxchunk
)
allocate
();
if
(
nvalues
==
1
)
size_vector
=
nchunk
;
else
size_array_rows
=
nchunk
;
if
(
countflag
)
{
cchunk
->
compute_ichunk
();
ichunk
=
cchunk
->
ichunk
;
}
// fill vector
buf
=
vector
;
(
this
->*
pack_choice
[
0
])(
0
);
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyChunk
::
compute_array
()
{
invoked_array
=
update
->
ntimestep
;
// compute chunk/atom assigns atoms to chunk IDs
// if need count, extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk
=
cchunk
->
setup_chunks
();
if
(
nchunk
>
maxchunk
)
allocate
();
if
(
nvalues
==
1
)
size_vector
=
nchunk
;
else
size_array_rows
=
nchunk
;
if
(
countflag
)
{
cchunk
->
compute_ichunk
();
ichunk
=
cchunk
->
ichunk
;
}
// fill array
if
(
array
)
buf
=
&
array
[
0
][
0
];
for
(
int
n
=
0
;
n
<
nvalues
;
n
++
)
(
this
->*
pack_choice
[
n
])(
n
);
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure vector/array size is locked for Nfreq epoch
by passing lock info along to compute chunk/atom
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
increment lock counter
------------------------------------------------------------------------- */
void
ComputePropertyChunk
::
lock_enable
()
{
cchunk
->
lockcount
++
;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void
ComputePropertyChunk
::
lock_disable
()
{
int
icompute
=
modify
->
find_compute
(
idchunk
);
if
(
icompute
>=
0
)
{
cchunk
=
(
ComputeChunkAtom
*
)
modify
->
compute
[
icompute
];
cchunk
->
lockcount
--
;
}
}
/* ----------------------------------------------------------------------
calculate and return # of chunks = length of vector/array
------------------------------------------------------------------------- */
int
ComputePropertyChunk
::
lock_length
()
{
nchunk
=
cchunk
->
setup_chunks
();
return
nchunk
;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void
ComputePropertyChunk
::
lock
(
Fix
*
fixptr
,
bigint
startstep
,
bigint
stopstep
)
{
cchunk
->
lock
(
fixptr
,
startstep
,
stopstep
);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void
ComputePropertyChunk
::
unlock
(
Fix
*
fixptr
)
{
cchunk
->
unlock
(
fixptr
);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void
ComputePropertyChunk
::
allocate
()
{
memory
->
destroy
(
vector
);
memory
->
destroy
(
array
);
memory
->
destroy
(
count_one
);
memory
->
destroy
(
count_all
);
maxchunk
=
nchunk
;
if
(
nvalues
==
1
)
memory
->
create
(
vector
,
maxchunk
,
"property/chunk:vector"
);
else
memory
->
create
(
array
,
maxchunk
,
nvalues
,
"property/chunk:array"
);
if
(
countflag
)
{
memory
->
create
(
count_one
,
maxchunk
,
"property/chunk:count_one"
);
memory
->
create
(
count_all
,
maxchunk
,
"property/chunk:count_all"
);
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double
ComputePropertyChunk
::
memory_usage
()
{
double
bytes
=
(
bigint
)
nchunk
*
nvalues
*
sizeof
(
double
);
if
(
countflag
)
bytes
+=
(
bigint
)
nchunk
*
2
*
sizeof
(
int
);
return
bytes
;
}
/* ----------------------------------------------------------------------
one method for every keyword compute property/chunk can output
the property is packed into buf starting at n with stride nvalues
customize a new keyword by adding a method
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void
ComputePropertyChunk
::
pack_count
(
int
n
)
{
int
index
;
for
(
int
m
=
0
;
m
<
nchunk
;
m
++
)
count_one
[
m
]
=
0
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
count_one
[
index
]
++
;
}
}
MPI_Allreduce
(
count_one
,
count_all
,
nchunk
,
MPI_INT
,
MPI_SUM
,
world
);
for
(
int
m
=
0
;
m
<
nchunk
;
m
++
)
{
buf
[
n
]
=
count_all
[
m
];
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyChunk
::
pack_id
(
int
n
)
{
int
*
origID
=
cchunk
->
chunkID
;
for
(
int
m
=
0
;
m
<
nchunk
;
m
++
)
{
buf
[
n
]
=
origID
[
m
];
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyChunk
::
pack_coord1
(
int
n
)
{
double
**
coord
=
cchunk
->
coord
;
for
(
int
m
=
0
;
m
<
nchunk
;
m
++
)
{
buf
[
n
]
=
coord
[
m
][
0
];
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyChunk
::
pack_coord2
(
int
n
)
{
double
**
coord
=
cchunk
->
coord
;
for
(
int
m
=
0
;
m
<
nchunk
;
m
++
)
{
buf
[
n
]
=
coord
[
m
][
1
];
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyChunk
::
pack_coord3
(
int
n
)
{
double
**
coord
=
cchunk
->
coord
;
for
(
int
m
=
0
;
m
<
nchunk
;
m
++
)
{
buf
[
n
]
=
coord
[
m
][
2
];
n
+=
nvalues
;
}
}
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