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compute_property_molecule.cpp
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Mon, Sep 30, 13:04
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Wed, Oct 2, 13:04 (2 d)
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rLAMMPS lammps
compute_property_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 "string.h"
#include "compute_property_molecule.h"
#include "atom.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputePropertyMolecule
::
ComputePropertyMolecule
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
4
)
error
->
all
(
FLERR
,
"Illegal compute property/molecule command"
);
if
(
atom
->
molecular
==
0
)
error
->
all
(
FLERR
,
"Compute property/molecule requires molecular atom style"
);
nvalues
=
narg
-
3
;
pack_choice
=
new
FnPtrPack
[
nvalues
];
int
i
;
for
(
int
iarg
=
3
;
iarg
<
narg
;
iarg
++
)
{
i
=
iarg
-
3
;
if
(
strcmp
(
arg
[
iarg
],
"mol"
)
==
0
)
pack_choice
[
i
]
=
&
ComputePropertyMolecule
::
pack_mol
;
else
if
(
strcmp
(
arg
[
iarg
],
"count"
)
==
0
)
pack_choice
[
i
]
=
&
ComputePropertyMolecule
::
pack_count
;
else
error
->
all
(
FLERR
,
"Invalid keyword in compute property/molecule command"
);
}
// setup molecule-based data
nmolecules
=
molecules_in_group
(
idlo
,
idhi
);
vector
=
NULL
;
array
=
NULL
;
if
(
nvalues
==
1
)
{
memory
->
create
(
vector
,
nmolecules
,
"property/molecule:vector"
);
vector_flag
=
1
;
size_vector
=
nmolecules
;
extvector
=
0
;
}
else
{
memory
->
create
(
array
,
nmolecules
,
nvalues
,
"property/molecule:array"
);
array_flag
=
1
;
size_array_rows
=
nmolecules
;
size_array_cols
=
nvalues
;
extarray
=
0
;
}
// fill vector or array with molecule values
if
(
nvalues
==
1
)
{
buf
=
vector
;
(
this
->*
pack_choice
[
0
])(
0
);
}
else
{
if
(
array
)
buf
=
&
array
[
0
][
0
];
for
(
int
n
=
0
;
n
<
nvalues
;
n
++
)
(
this
->*
pack_choice
[
n
])(
n
);
}
}
/* ---------------------------------------------------------------------- */
ComputePropertyMolecule
::~
ComputePropertyMolecule
()
{
delete
[]
pack_choice
;
memory
->
destroy
(
vector
);
memory
->
destroy
(
array
);
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyMolecule
::
init
()
{
int
ntmp
=
molecules_in_group
(
idlo
,
idhi
);
if
(
ntmp
!=
nmolecules
)
error
->
all
(
FLERR
,
"Molecule count changed in compute property/molecule"
);
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyMolecule
::
compute_vector
()
{
invoked_vector
=
update
->
ntimestep
;
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyMolecule
::
compute_array
()
{
invoked_array
=
update
->
ntimestep
;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double
ComputePropertyMolecule
::
memory_usage
()
{
double
bytes
=
(
bigint
)
nmolecules
*
nvalues
*
sizeof
(
double
);
if
(
molmap
)
bytes
+=
(
idhi
-
idlo
+
1
)
*
sizeof
(
int
);
return
bytes
;
}
/* ----------------------------------------------------------------------
one method for every keyword compute property/molecule can output
the atom property is packed into buf starting at n with stride nvalues
customize a new keyword by adding a method
------------------------------------------------------------------------- */
void
ComputePropertyMolecule
::
pack_mol
(
int
n
)
{
for
(
tagint
m
=
idlo
;
m
<=
idhi
;
m
++
)
if
(
molmap
==
NULL
||
molmap
[
m
-
idlo
]
>=
0
)
{
buf
[
n
]
=
m
;
n
+=
nvalues
;
}
}
/* ---------------------------------------------------------------------- */
void
ComputePropertyMolecule
::
pack_count
(
int
n
)
{
int
i
,
m
;
tagint
imol
;
int
*
count_one
=
new
int
[
nmolecules
];
for
(
m
=
0
;
m
<
nmolecules
;
m
++
)
count_one
[
m
]
=
0
;
tagint
*
molecule
=
atom
->
molecule
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
imol
=
molecule
[
i
];
if
(
molmap
)
imol
=
molmap
[
imol
-
idlo
];
else
imol
--
;
count_one
[
imol
]
++
;
}
int
*
count_all
=
new
int
[
nmolecules
];
MPI_Allreduce
(
count_one
,
count_all
,
nmolecules
,
MPI_INT
,
MPI_SUM
,
world
);
for
(
m
=
0
;
m
<
nmolecules
;
m
++
)
if
(
molmap
==
NULL
||
molmap
[
m
]
>=
0
)
{
buf
[
n
]
=
count_all
[
m
];
n
+=
nvalues
;
}
delete
[]
count_one
;
delete
[]
count_all
;
}
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