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compute_vcm_chunk.cpp
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Sun, Aug 25, 22:24
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6 KB
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text/x-c
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Tue, Aug 27, 22:24 (1 d, 22 h)
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rLAMMPS lammps
compute_vcm_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_vcm_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
enum
{
ONCE
,
NFREQ
,
EVERY
};
/* ---------------------------------------------------------------------- */
ComputeVCMChunk
::
ComputeVCMChunk
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
4
)
error
->
all
(
FLERR
,
"Illegal compute vcm/chunk command"
);
array_flag
=
1
;
size_array_cols
=
3
;
size_array_rows
=
0
;
size_array_rows_variable
=
1
;
extarray
=
0
;
// ID of compute chunk/atom
int
n
=
strlen
(
arg
[
3
])
+
1
;
idchunk
=
new
char
[
n
];
strcpy
(
idchunk
,
arg
[
3
]);
init
();
// chunk-based data
nchunk
=
1
;
maxchunk
=
0
;
massproc
=
masstotal
=
NULL
;
vcm
=
vcmall
=
NULL
;
allocate
();
firstflag
=
massneed
=
1
;
}
/* ---------------------------------------------------------------------- */
ComputeVCMChunk
::~
ComputeVCMChunk
()
{
delete
[]
idchunk
;
memory
->
destroy
(
massproc
);
memory
->
destroy
(
masstotal
);
memory
->
destroy
(
vcm
);
memory
->
destroy
(
vcmall
);
}
/* ---------------------------------------------------------------------- */
void
ComputeVCMChunk
::
init
()
{
int
icompute
=
modify
->
find_compute
(
idchunk
);
if
(
icompute
<
0
)
error
->
all
(
FLERR
,
"Chunk/atom compute does not exist for compute vcm/chunk"
);
cchunk
=
(
ComputeChunkAtom
*
)
modify
->
compute
[
icompute
];
if
(
strcmp
(
cchunk
->
style
,
"chunk/atom"
)
!=
0
)
error
->
all
(
FLERR
,
"Compute vcm/chunk does not use chunk/atom compute"
);
}
/* ---------------------------------------------------------------------- */
void
ComputeVCMChunk
::
setup
()
{
// one-time calculation of per-chunk mass
// done in setup, so that ComputeChunkAtom::setup() is already called
if
(
firstflag
&&
cchunk
->
idsflag
==
ONCE
)
{
compute_array
();
firstflag
=
massneed
=
0
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputeVCMChunk
::
compute_array
()
{
int
index
;
double
massone
;
invoked_array
=
update
->
ntimestep
;
// compute chunk/atom assigns atoms to chunk IDs
// extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk
=
cchunk
->
setup_chunks
();
cchunk
->
compute_ichunk
();
int
*
ichunk
=
cchunk
->
ichunk
;
if
(
nchunk
>
maxchunk
)
allocate
();
size_array_rows
=
nchunk
;
// zero local per-chunk values
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
vcm
[
i
][
0
]
=
vcm
[
i
][
1
]
=
vcm
[
i
][
2
]
=
0.0
;
if
(
massneed
)
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
massproc
[
i
]
=
0.0
;
// compute VCM for each chunk
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
*
type
=
atom
->
type
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
vcm
[
index
][
0
]
+=
v
[
i
][
0
]
*
massone
;
vcm
[
index
][
1
]
+=
v
[
i
][
1
]
*
massone
;
vcm
[
index
][
2
]
+=
v
[
i
][
2
]
*
massone
;
if
(
massneed
)
massproc
[
index
]
+=
massone
;
}
MPI_Allreduce
(
&
vcm
[
0
][
0
],
&
vcmall
[
0
][
0
],
3
*
nchunk
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
if
(
massneed
)
MPI_Allreduce
(
massproc
,
masstotal
,
nchunk
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
{
vcmall
[
i
][
0
]
/=
masstotal
[
i
];
vcmall
[
i
][
1
]
/=
masstotal
[
i
];
vcmall
[
i
][
2
]
/=
masstotal
[
i
];
}
}
/* ----------------------------------------------------------------------
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
ComputeVCMChunk
::
lock_enable
()
{
cchunk
->
lockcount
++
;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void
ComputeVCMChunk
::
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
ComputeVCMChunk
::
lock_length
()
{
nchunk
=
cchunk
->
setup_chunks
();
return
nchunk
;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void
ComputeVCMChunk
::
lock
(
Fix
*
fixptr
,
bigint
startstep
,
bigint
stopstep
)
{
cchunk
->
lock
(
fixptr
,
startstep
,
stopstep
);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void
ComputeVCMChunk
::
unlock
(
Fix
*
fixptr
)
{
cchunk
->
unlock
(
fixptr
);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void
ComputeVCMChunk
::
allocate
()
{
memory
->
destroy
(
massproc
);
memory
->
destroy
(
masstotal
);
memory
->
destroy
(
vcm
);
memory
->
destroy
(
vcmall
);
maxchunk
=
nchunk
;
memory
->
create
(
massproc
,
maxchunk
,
"vcm/chunk:massproc"
);
memory
->
create
(
masstotal
,
maxchunk
,
"vcm/chunk:masstotal"
);
memory
->
create
(
vcm
,
maxchunk
,
3
,
"vcm/chunk:vcm"
);
memory
->
create
(
vcmall
,
maxchunk
,
3
,
"vcm/chunk:vcmall"
);
array
=
vcmall
;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double
ComputeVCMChunk
::
memory_usage
()
{
double
bytes
=
(
bigint
)
maxchunk
*
2
*
sizeof
(
double
);
bytes
+=
(
bigint
)
maxchunk
*
2
*
3
*
sizeof
(
double
);
return
bytes
;
}
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