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compute_vacf.cpp
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Sat, Jul 20, 21:11
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Mon, Jul 22, 21:11 (1 d, 23 h)
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rLAMMPS lammps
compute_vacf.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 ret
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_vacf.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "modify.h"
#include "fix_store.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputeVACF
::
ComputeVACF
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
3
)
error
->
all
(
FLERR
,
"Illegal compute vacf command"
);
vector_flag
=
1
;
size_vector
=
4
;
extvector
=
0
;
// create a new fix STORE style
// id = compute-ID + COMPUTE_STORE, fix group = compute group
int
n
=
strlen
(
id
)
+
strlen
(
"_COMPUTE_STORE"
)
+
1
;
id_fix
=
new
char
[
n
];
strcpy
(
id_fix
,
id
);
strcat
(
id_fix
,
"_COMPUTE_STORE"
);
char
**
newarg
=
new
char
*
[
5
];
newarg
[
0
]
=
id_fix
;
newarg
[
1
]
=
group
->
names
[
igroup
];
newarg
[
2
]
=
(
char
*
)
"STORE"
;
newarg
[
3
]
=
(
char
*
)
"1"
;
newarg
[
4
]
=
(
char
*
)
"3"
;
modify
->
add_fix
(
5
,
newarg
);
fix
=
(
FixStore
*
)
modify
->
fix
[
modify
->
nfix
-
1
];
delete
[]
newarg
;
// store current velocities in fix store array
// skip if reset from restart file
if
(
fix
->
restart_reset
)
fix
->
restart_reset
=
0
;
else
{
double
**
voriginal
=
fix
->
astore
;
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
voriginal
[
i
][
0
]
=
v
[
i
][
0
];
voriginal
[
i
][
1
]
=
v
[
i
][
1
];
voriginal
[
i
][
2
]
=
v
[
i
][
2
];
}
else
voriginal
[
i
][
0
]
=
voriginal
[
i
][
1
]
=
voriginal
[
i
][
2
]
=
0.0
;
}
// displacement vector
vector
=
new
double
[
4
];
}
/* ---------------------------------------------------------------------- */
ComputeVACF
::~
ComputeVACF
()
{
// check nfix in case all fixes have already been deleted
if
(
modify
->
nfix
)
modify
->
delete_fix
(
id_fix
);
delete
[]
id_fix
;
delete
[]
vector
;
}
/* ---------------------------------------------------------------------- */
void
ComputeVACF
::
init
()
{
// set fix which stores original atom velocities
int
ifix
=
modify
->
find_fix
(
id_fix
);
if
(
ifix
<
0
)
error
->
all
(
FLERR
,
"Could not find compute vacf fix ID"
);
fix
=
(
FixStore
*
)
modify
->
fix
[
ifix
];
// nvacf = # of atoms in group
nvacf
=
group
->
count
(
igroup
);
}
/* ---------------------------------------------------------------------- */
void
ComputeVACF
::
compute_vector
()
{
invoked_vector
=
update
->
ntimestep
;
double
**
voriginal
=
fix
->
astore
;
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
vxsq
,
vysq
,
vzsq
;
double
vacf
[
4
];
vacf
[
0
]
=
vacf
[
1
]
=
vacf
[
2
]
=
vacf
[
3
]
=
0.0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
vxsq
=
v
[
i
][
0
]
*
voriginal
[
i
][
0
];
vysq
=
v
[
i
][
1
]
*
voriginal
[
i
][
1
];
vzsq
=
v
[
i
][
2
]
*
voriginal
[
i
][
2
];
vacf
[
0
]
+=
vxsq
;
vacf
[
1
]
+=
vysq
;
vacf
[
2
]
+=
vzsq
;
vacf
[
3
]
+=
vxsq
+
vysq
+
vzsq
;
}
MPI_Allreduce
(
vacf
,
vector
,
4
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
if
(
nvacf
)
{
vector
[
0
]
/=
nvacf
;
vector
[
1
]
/=
nvacf
;
vector
[
2
]
/=
nvacf
;
vector
[
3
]
/=
nvacf
;
}
}
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