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fix_wiggle.cpp
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Created
Fri, Aug 16, 19:00
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4 KB
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text/x-c
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Sun, Aug 18, 19:00 (2 d)
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blob
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rLAMMPS lammps
fix_wiggle.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 "stdlib.h"
#include "fix_wiggle.h"
#include "atom.h"
#include "update.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
FixWiggle
::
FixWiggle
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
6
)
error
->
all
(
"Illegal fix wiggle command"
);
// parse command-line args
if
(
strcmp
(
arg
[
3
],
"x"
)
==
0
)
axis
=
0
;
else
if
(
strcmp
(
arg
[
3
],
"y"
)
==
0
)
axis
=
1
;
else
if
(
strcmp
(
arg
[
3
],
"z"
)
==
0
)
axis
=
2
;
else
error
->
all
(
"Illegal fix wiggle command"
);
amplitude
=
atof
(
arg
[
4
]);
period
=
atof
(
arg
[
5
]);
// perform initial allocation of atom-based array
// register with Atom class
original
=
NULL
;
grow_arrays
(
atom
->
nmax
);
atom
->
add_callback
(
0
);
// oscillation parameters
double
PI
=
4.0
*
atan
(
1.0
);
omega
=
2.0
*
PI
/
period
;
time_origin
=
update
->
ntimestep
;
// original = initial atom coord in wiggled direction
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
original
[
i
]
=
x
[
i
][
axis
];
else
original
[
i
]
=
0.0
;
}
/* ---------------------------------------------------------------------- */
FixWiggle
::~
FixWiggle
()
{
// unregister callbacks to this fix from Atom class
atom
->
delete_callback
(
id
,
0
);
// delete locally stored array
memory
->
sfree
(
original
);
}
/* ---------------------------------------------------------------------- */
int
FixWiggle
::
setmask
()
{
int
mask
=
0
;
mask
|=
POST_FORCE
;
mask
|=
POST_FORCE_RESPA
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixWiggle
::
init
()
{
dt
=
update
->
dt
;
if
(
strcmp
(
update
->
integrate_style
,
"respa"
)
==
0
)
nlevels_respa
=
((
Respa
*
)
update
->
integrate
)
->
nlevels
;
}
/* ---------------------------------------------------------------------- */
void
FixWiggle
::
post_force
(
int
vflag
)
{
double
arg
=
omega
*
(
update
->
ntimestep
-
time_origin
)
*
dt
;
double
cosine
=
cos
(
arg
);
double
sine
=
sin
(
arg
);
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
x
[
i
][
axis
]
=
original
[
i
]
+
amplitude
-
amplitude
*
cosine
;
v
[
i
][
axis
]
=
dt
*
amplitude
*
omega
*
sine
;
f
[
i
][
axis
]
=
0.0
;
}
}
}
/* ---------------------------------------------------------------------- */
void
FixWiggle
::
post_force_respa
(
int
vflag
,
int
ilevel
,
int
iloop
)
{
if
(
ilevel
==
nlevels_respa
-
1
)
post_force
(
vflag
);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
int
FixWiggle
::
memory_usage
()
{
int
bytes
=
atom
->
nmax
*
sizeof
(
double
);
return
bytes
;
}
/* ----------------------------------------------------------------------
allocate local atom-based array
------------------------------------------------------------------------- */
void
FixWiggle
::
grow_arrays
(
int
nmax
)
{
original
=
(
double
*
)
memory
->
srealloc
(
original
,
nmax
*
sizeof
(
double
),
"wiggle:original"
);
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void
FixWiggle
::
copy_arrays
(
int
i
,
int
j
)
{
original
[
j
]
=
original
[
i
];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int
FixWiggle
::
pack_exchange
(
int
i
,
double
*
buf
)
{
buf
[
0
]
=
original
[
i
];
return
1
;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int
FixWiggle
::
unpack_exchange
(
int
nlocal
,
double
*
buf
)
{
original
[
nlocal
]
=
buf
[
0
];
return
1
;
}
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