Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F85131099
fix_wiggle.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Thu, Sep 26, 23:56
Size
4 KB
Mime Type
text/x-c
Expires
Sat, Sep 28, 23:56 (2 d)
Engine
blob
Format
Raw Data
Handle
21132863
Attached To
rLAMMPS lammps
fix_wiggle.cpp
View Options
/* ----------------------------------------------------------------------
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
;
}
Event Timeline
Log In to Comment