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compute_gyration_molecule.cpp
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rLAMMPS lammps
compute_gyration_molecule.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 "compute_gyration_molecule.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputeGyrationMolecule
::
ComputeGyrationMolecule
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
3
)
error
->
all
(
"Illegal compute gyration/molecule command"
);
if
(
atom
->
molecular
==
0
)
error
->
all
(
"Compute gyration/molecule requires molecular atom style"
);
vector_flag
=
1
;
extvector
=
0
;
// setup molecule-based data
nmolecules
=
molecules_in_group
(
idlo
,
idhi
);
size_vector
=
nmolecules
;
massproc
=
(
double
*
)
memory
->
smalloc
(
nmolecules
*
sizeof
(
double
),
"gyration/molecule:massproc"
);
masstotal
=
(
double
*
)
memory
->
smalloc
(
nmolecules
*
sizeof
(
double
),
"gyration/molecule:masstotal"
);
com
=
memory
->
create_2d_double_array
(
nmolecules
,
3
,
"gyration/molecule:com"
);
comall
=
memory
->
create_2d_double_array
(
nmolecules
,
3
,
"gyration/molecule:comall"
);
rg
=
(
double
*
)
memory
->
smalloc
(
nmolecules
*
sizeof
(
double
),
"gyration/molecule:rg"
);
rgall
=
(
double
*
)
memory
->
smalloc
(
nmolecules
*
sizeof
(
double
),
"gyration/molecule:rgall"
);
vector
=
rgall
;
// compute masstotal for each molecule
int
*
mask
=
atom
->
mask
;
int
*
molecule
=
atom
->
molecule
;
int
*
type
=
atom
->
type
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
nlocal
=
atom
->
nlocal
;
int
i
,
imol
;
double
massone
;
for
(
i
=
0
;
i
<
nmolecules
;
i
++
)
massproc
[
i
]
=
0.0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
imol
=
molecule
[
i
];
if
(
molmap
)
imol
=
molmap
[
imol
-
idlo
];
else
imol
--
;
massproc
[
imol
]
+=
massone
;
}
MPI_Allreduce
(
massproc
,
masstotal
,
nmolecules
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
}
/* ---------------------------------------------------------------------- */
ComputeGyrationMolecule
::~
ComputeGyrationMolecule
()
{
memory
->
sfree
(
massproc
);
memory
->
sfree
(
masstotal
);
memory
->
destroy_2d_double_array
(
com
);
memory
->
destroy_2d_double_array
(
comall
);
memory
->
sfree
(
rg
);
memory
->
sfree
(
rgall
);
}
/* ---------------------------------------------------------------------- */
void
ComputeGyrationMolecule
::
init
()
{
int
ntmp
=
molecules_in_group
(
idlo
,
idhi
);
if
(
ntmp
!=
nmolecules
)
error
->
all
(
"Molecule count changed in compute gyration/molecule"
);
}
/* ---------------------------------------------------------------------- */
void
ComputeGyrationMolecule
::
compute_vector
()
{
int
i
,
imol
;
double
xbox
,
ybox
,
zbox
,
dx
,
dy
,
dz
;
double
massone
;
invoked_array
=
update
->
ntimestep
;
for
(
i
=
0
;
i
<
nmolecules
;
i
++
)
com
[
i
][
0
]
=
com
[
i
][
1
]
=
com
[
i
][
2
]
=
0.0
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
*
molecule
=
atom
->
molecule
;
int
*
type
=
atom
->
type
;
int
*
image
=
atom
->
image
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
nlocal
=
atom
->
nlocal
;
double
xprd
=
domain
->
xprd
;
double
yprd
=
domain
->
yprd
;
double
zprd
=
domain
->
zprd
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
xbox
=
(
image
[
i
]
&
1023
)
-
512
;
ybox
=
(
image
[
i
]
>>
10
&
1023
)
-
512
;
zbox
=
(
image
[
i
]
>>
20
)
-
512
;
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
imol
=
molecule
[
i
];
if
(
molmap
)
imol
=
molmap
[
imol
-
idlo
];
else
imol
--
;
com
[
imol
][
0
]
+=
(
x
[
i
][
0
]
+
xbox
*
xprd
)
*
massone
;
com
[
imol
][
1
]
+=
(
x
[
i
][
1
]
+
ybox
*
yprd
)
*
massone
;
com
[
imol
][
2
]
+=
(
x
[
i
][
2
]
+
zbox
*
zprd
)
*
massone
;
}
MPI_Allreduce
(
&
com
[
0
][
0
],
&
comall
[
0
][
0
],
3
*
nmolecules
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
for
(
i
=
0
;
i
<
nmolecules
;
i
++
)
{
comall
[
i
][
0
]
/=
masstotal
[
i
];
comall
[
i
][
1
]
/=
masstotal
[
i
];
comall
[
i
][
2
]
/=
masstotal
[
i
];
}
for
(
i
=
0
;
i
<
nmolecules
;
i
++
)
rg
[
i
]
=
0.0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
xbox
=
(
image
[
i
]
&
1023
)
-
512
;
ybox
=
(
image
[
i
]
>>
10
&
1023
)
-
512
;
zbox
=
(
image
[
i
]
>>
20
)
-
512
;
imol
=
molecule
[
i
];
if
(
molmap
)
imol
=
molmap
[
imol
-
idlo
];
else
imol
--
;
dx
=
(
x
[
i
][
0
]
+
xbox
*
xprd
)
-
comall
[
imol
][
0
];
dy
=
(
x
[
i
][
1
]
+
ybox
*
yprd
)
-
comall
[
imol
][
1
];
dz
=
(
x
[
i
][
2
]
+
zbox
*
zprd
)
-
comall
[
imol
][
2
];
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
rg
[
imol
]
+=
(
dx
*
dx
+
dy
*
dy
+
dz
*
dz
)
*
massone
;
}
MPI_Allreduce
(
rg
,
rgall
,
nmolecules
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
for
(
i
=
0
;
i
<
nmolecules
;
i
++
)
rgall
[
i
]
=
sqrt
(
rgall
[
i
]
/
masstotal
[
i
]);
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double
ComputeGyrationMolecule
::
memory_usage
()
{
double
bytes
=
4
*
nmolecules
*
sizeof
(
double
);
if
(
molmap
)
bytes
+=
(
idhi
-
idlo
+
1
)
*
sizeof
(
int
);
bytes
+=
2
*
nmolecules
*
3
*
sizeof
(
double
);
return
bytes
;
}
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