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fix_spring_rg.cpp
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Tue, Oct 8, 16:51
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Thu, Oct 10, 16:51 (2 d)
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rLAMMPS lammps
fix_spring_rg.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "fix_spring_rg.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "respa.h"
#include "domain.h"
#include "error.h"
#include "force.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
/* ---------------------------------------------------------------------- */
FixSpringRG
::
FixSpringRG
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
5
)
error
->
all
(
FLERR
,
"Illegal fix spring/rg command"
);
k
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
rg0_flag
=
0
;
if
(
strcmp
(
arg
[
4
],
"NULL"
)
==
0
)
rg0_flag
=
1
;
else
rg0
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
}
/* ---------------------------------------------------------------------- */
int
FixSpringRG
::
setmask
()
{
int
mask
=
0
;
mask
|=
POST_FORCE
;
mask
|=
POST_FORCE_RESPA
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixSpringRG
::
init
()
{
masstotal
=
group
->
mass
(
igroup
);
// if rg0 was specified as NULL, compute current Rg
// only occurs on 1st run
if
(
rg0_flag
)
{
double
xcm
[
3
];
group
->
xcm
(
igroup
,
masstotal
,
xcm
);
rg0
=
group
->
gyration
(
igroup
,
masstotal
,
xcm
);
rg0_flag
=
0
;
}
if
(
strstr
(
update
->
integrate_style
,
"respa"
))
nlevels_respa
=
((
Respa
*
)
update
->
integrate
)
->
nlevels
;
}
/* ---------------------------------------------------------------------- */
void
FixSpringRG
::
setup
(
int
vflag
)
{
if
(
strstr
(
update
->
integrate_style
,
"verlet"
))
post_force
(
vflag
);
else
{
((
Respa
*
)
update
->
integrate
)
->
copy_flevel_f
(
nlevels_respa
-
1
);
post_force_respa
(
vflag
,
nlevels_respa
-
1
,
0
);
((
Respa
*
)
update
->
integrate
)
->
copy_f_flevel
(
nlevels_respa
-
1
);
}
}
/* ---------------------------------------------------------------------- */
void
FixSpringRG
::
post_force
(
int
vflag
)
{
// compute current Rg and center-of-mass
double
xcm
[
3
];
group
->
xcm
(
igroup
,
masstotal
,
xcm
);
double
rg
=
group
->
gyration
(
igroup
,
masstotal
,
xcm
);
// apply restoring force to atoms in group
// f = -k*(r-r0)*mass/masstotal
double
dx
,
dy
,
dz
,
term1
;
double
**
f
=
atom
->
f
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
*
type
=
atom
->
type
;
imageint
*
image
=
atom
->
image
;
double
*
mass
=
atom
->
mass
;
int
nlocal
=
atom
->
nlocal
;
double
massfrac
;
double
unwrap
[
3
];
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
domain
->
unmap
(
x
[
i
],
image
[
i
],
unwrap
);
dx
=
unwrap
[
0
]
-
xcm
[
0
];
dy
=
unwrap
[
1
]
-
xcm
[
1
];
dz
=
unwrap
[
2
]
-
xcm
[
2
];
term1
=
2.0
*
k
*
(
1.0
-
rg0
/
rg
);
massfrac
=
mass
[
type
[
i
]]
/
masstotal
;
f
[
i
][
0
]
-=
term1
*
dx
*
massfrac
;
f
[
i
][
1
]
-=
term1
*
dy
*
massfrac
;
f
[
i
][
2
]
-=
term1
*
dz
*
massfrac
;
}
}
/* ---------------------------------------------------------------------- */
void
FixSpringRG
::
post_force_respa
(
int
vflag
,
int
ilevel
,
int
iloop
)
{
if
(
ilevel
==
nlevels_respa
-
1
)
post_force
(
vflag
);
}
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