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compute_gyration_chunk.cpp
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rLAMMPS lammps
compute_gyration_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 <math.h>
#include <string.h>
#include "compute_gyration_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
;
/* ---------------------------------------------------------------------- */
ComputeGyrationChunk
::
ComputeGyrationChunk
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
),
idchunk
(
NULL
),
massproc
(
NULL
),
masstotal
(
NULL
),
com
(
NULL
),
comall
(
NULL
),
rg
(
NULL
),
rgall
(
NULL
),
rgt
(
NULL
),
rgtall
(
NULL
)
{
if
(
narg
<
4
)
error
->
all
(
FLERR
,
"Illegal compute gyration/chunk command"
);
// ID of compute chunk/atom
int
n
=
strlen
(
arg
[
3
])
+
1
;
idchunk
=
new
char
[
n
];
strcpy
(
idchunk
,
arg
[
3
]);
init
();
// optional args
tensor
=
0
;
int
iarg
=
4
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"tensor"
)
==
0
)
{
tensor
=
1
;
iarg
++
;
}
else
error
->
all
(
FLERR
,
"Illegal compute gyration/chunk command"
);
}
if
(
tensor
)
{
array_flag
=
1
;
size_array_cols
=
6
;
size_array_rows
=
0
;
size_array_rows_variable
=
1
;
extarray
=
0
;
}
else
{
vector_flag
=
1
;
size_vector
=
0
;
size_vector_variable
=
1
;
extvector
=
0
;
}
// chunk-based data
nchunk
=
1
;
maxchunk
=
0
;
allocate
();
}
/* ---------------------------------------------------------------------- */
ComputeGyrationChunk
::~
ComputeGyrationChunk
()
{
delete
[]
idchunk
;
memory
->
destroy
(
massproc
);
memory
->
destroy
(
masstotal
);
memory
->
destroy
(
com
);
memory
->
destroy
(
comall
);
memory
->
destroy
(
rg
);
memory
->
destroy
(
rgall
);
memory
->
destroy
(
rgt
);
memory
->
destroy
(
rgtall
);
}
/* ---------------------------------------------------------------------- */
void
ComputeGyrationChunk
::
init
()
{
int
icompute
=
modify
->
find_compute
(
idchunk
);
if
(
icompute
<
0
)
error
->
all
(
FLERR
,
"Chunk/atom compute does not exist for "
"compute gyration/chunk"
);
cchunk
=
(
ComputeChunkAtom
*
)
modify
->
compute
[
icompute
];
if
(
strcmp
(
cchunk
->
style
,
"chunk/atom"
)
!=
0
)
error
->
all
(
FLERR
,
"Compute gyration/chunk does not use chunk/atom compute"
);
}
/* ---------------------------------------------------------------------- */
void
ComputeGyrationChunk
::
compute_vector
()
{
int
i
,
index
;
double
dx
,
dy
,
dz
,
massone
;
double
unwrap
[
3
];
invoked_array
=
update
->
ntimestep
;
com_chunk
();
int
*
ichunk
=
cchunk
->
ichunk
;
for
(
i
=
0
;
i
<
nchunk
;
i
++
)
rg
[
i
]
=
0.0
;
// compute Rg for each chunk
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
*
type
=
atom
->
type
;
imageint
*
image
=
atom
->
image
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
domain
->
unmap
(
x
[
i
],
image
[
i
],
unwrap
);
dx
=
unwrap
[
0
]
-
comall
[
index
][
0
];
dy
=
unwrap
[
1
]
-
comall
[
index
][
1
];
dz
=
unwrap
[
2
]
-
comall
[
index
][
2
];
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
rg
[
index
]
+=
(
dx
*
dx
+
dy
*
dy
+
dz
*
dz
)
*
massone
;
}
MPI_Allreduce
(
rg
,
rgall
,
nchunk
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
if
(
masstotal
[
i
]
>
0.0
)
rgall
[
i
]
=
sqrt
(
rgall
[
i
]
/
masstotal
[
i
]);
}
/* ---------------------------------------------------------------------- */
void
ComputeGyrationChunk
::
compute_array
()
{
int
i
,
j
,
index
;
double
dx
,
dy
,
dz
,
massone
;
double
unwrap
[
3
];
invoked_array
=
update
->
ntimestep
;
com_chunk
();
int
*
ichunk
=
cchunk
->
ichunk
;
for
(
i
=
0
;
i
<
nchunk
;
i
++
)
for
(
j
=
0
;
j
<
6
;
j
++
)
rgt
[
i
][
j
]
=
0.0
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
*
type
=
atom
->
type
;
imageint
*
image
=
atom
->
image
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
domain
->
unmap
(
x
[
i
],
image
[
i
],
unwrap
);
dx
=
unwrap
[
0
]
-
comall
[
index
][
0
];
dy
=
unwrap
[
1
]
-
comall
[
index
][
1
];
dz
=
unwrap
[
2
]
-
comall
[
index
][
2
];
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
rgt
[
index
][
0
]
+=
dx
*
dx
*
massone
;
rgt
[
index
][
1
]
+=
dy
*
dy
*
massone
;
rgt
[
index
][
2
]
+=
dz
*
dz
*
massone
;
rgt
[
index
][
3
]
+=
dx
*
dy
*
massone
;
rgt
[
index
][
4
]
+=
dx
*
dz
*
massone
;
rgt
[
index
][
5
]
+=
dy
*
dz
*
massone
;
}
if
(
nchunk
)
MPI_Allreduce
(
&
rgt
[
0
][
0
],
&
rgtall
[
0
][
0
],
nchunk
*
6
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
for
(
i
=
0
;
i
<
nchunk
;
i
++
)
{
if
(
masstotal
[
i
]
>
0.0
)
{
for
(
j
=
0
;
j
<
6
;
j
++
)
rgtall
[
i
][
j
]
=
rgtall
[
i
][
j
]
/
masstotal
[
i
];
}
}
}
/* ----------------------------------------------------------------------
calculate per-chunk COM, used by both scalar and tensor
------------------------------------------------------------------------- */
void
ComputeGyrationChunk
::
com_chunk
()
{
int
index
;
double
massone
;
double
unwrap
[
3
];
// 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
();
if
(
tensor
)
size_array_rows
=
nchunk
;
else
size_vector
=
nchunk
;
// zero local per-chunk values
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
{
massproc
[
i
]
=
0.0
;
com
[
i
][
0
]
=
com
[
i
][
1
]
=
com
[
i
][
2
]
=
0.0
;
}
// compute COM for each chunk
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
*
type
=
atom
->
type
;
imageint
*
image
=
atom
->
image
;
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
]];
domain
->
unmap
(
x
[
i
],
image
[
i
],
unwrap
);
massproc
[
index
]
+=
massone
;
com
[
index
][
0
]
+=
unwrap
[
0
]
*
massone
;
com
[
index
][
1
]
+=
unwrap
[
1
]
*
massone
;
com
[
index
][
2
]
+=
unwrap
[
2
]
*
massone
;
}
MPI_Allreduce
(
massproc
,
masstotal
,
nchunk
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
MPI_Allreduce
(
&
com
[
0
][
0
],
&
comall
[
0
][
0
],
3
*
nchunk
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
{
if
(
masstotal
[
i
]
>
0.0
)
{
comall
[
i
][
0
]
/=
masstotal
[
i
];
comall
[
i
][
1
]
/=
masstotal
[
i
];
comall
[
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
ComputeGyrationChunk
::
lock_enable
()
{
cchunk
->
lockcount
++
;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void
ComputeGyrationChunk
::
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
ComputeGyrationChunk
::
lock_length
()
{
nchunk
=
cchunk
->
setup_chunks
();
return
nchunk
;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void
ComputeGyrationChunk
::
lock
(
Fix
*
fixptr
,
bigint
startstep
,
bigint
stopstep
)
{
cchunk
->
lock
(
fixptr
,
startstep
,
stopstep
);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void
ComputeGyrationChunk
::
unlock
(
Fix
*
fixptr
)
{
cchunk
->
unlock
(
fixptr
);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void
ComputeGyrationChunk
::
allocate
()
{
memory
->
destroy
(
massproc
);
memory
->
destroy
(
masstotal
);
memory
->
destroy
(
com
);
memory
->
destroy
(
comall
);
memory
->
destroy
(
rg
);
memory
->
destroy
(
rgall
);
memory
->
destroy
(
rgt
);
memory
->
destroy
(
rgtall
);
maxchunk
=
nchunk
;
memory
->
create
(
massproc
,
maxchunk
,
"gyration/chunk:massproc"
);
memory
->
create
(
masstotal
,
maxchunk
,
"gyration/chunk:masstotal"
);
memory
->
create
(
com
,
maxchunk
,
3
,
"gyration/chunk:com"
);
memory
->
create
(
comall
,
maxchunk
,
3
,
"gyration/chunk:comall"
);
if
(
tensor
)
{
memory
->
create
(
rgt
,
maxchunk
,
6
,
"gyration/chunk:rgt"
);
memory
->
create
(
rgtall
,
maxchunk
,
6
,
"gyration/chunk:rgtall"
);
array
=
rgtall
;
}
else
{
memory
->
create
(
rg
,
maxchunk
,
"gyration/chunk:rg"
);
memory
->
create
(
rgall
,
maxchunk
,
"gyration/chunk:rgall"
);
vector
=
rgall
;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double
ComputeGyrationChunk
::
memory_usage
()
{
double
bytes
=
(
bigint
)
maxchunk
*
2
*
sizeof
(
double
);
bytes
+=
(
bigint
)
maxchunk
*
2
*
3
*
sizeof
(
double
);
if
(
tensor
)
bytes
+=
(
bigint
)
maxchunk
*
2
*
6
*
sizeof
(
double
);
else
bytes
+=
(
bigint
)
maxchunk
*
2
*
sizeof
(
double
);
return
bytes
;
}
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