Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F79341239
compute_vcm_chunk.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sun, Aug 25, 22:24
Size
6 KB
Mime Type
text/x-c
Expires
Tue, Aug 27, 22:24 (2 d)
Engine
blob
Format
Raw Data
Handle
20175777
Attached To
rLAMMPS lammps
compute_vcm_chunk.cpp
View Options
/* ----------------------------------------------------------------------
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
;
}
Event Timeline
Log In to Comment