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fix_nve_asphere_noforce.cpp
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Sat, Oct 19, 18:50
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rLAMMPS lammps
fix_nve_asphere_noforce.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_nve_asphere_noforce.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "group.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
/* ---------------------------------------------------------------------- */
FixNVEAsphereNoforce
::
FixNVEAsphereNoforce
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
FixNVENoforce
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
3
)
error
->
all
(
FLERR
,
"Illegal fix nve/asphere/noforce command"
);
time_integrate
=
1
;
}
/* ---------------------------------------------------------------------- */
void
FixNVEAsphereNoforce
::
init
()
{
// error check
avec
=
(
AtomVecEllipsoid
*
)
atom
->
style_match
(
"ellipsoid"
);
if
(
!
atom
->
ellipsoid_flag
)
error
->
all
(
FLERR
,
"Fix nve/asphere/noforce requires atom style ellipsoid"
);
FixNVENoforce
::
init
();
dtq
=
0.5
*
dtv
;
// check that all particles are finite-size ellipsoids
// no point particles allowed, spherical is OK
int
*
ellipsoid
=
atom
->
ellipsoid
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
if
(
ellipsoid
[
i
]
<
0
)
error
->
one
(
FLERR
,
"Fix nve/asphere/noforce requires extended particles"
);
}
/* ---------------------------------------------------------------------- */
void
FixNVEAsphereNoforce
::
initial_integrate
(
int
vflag
)
{
AtomVecEllipsoid
::
Bonus
*
bonus
;
if
(
avec
)
bonus
=
avec
->
bonus
;
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
**
angmom
=
atom
->
angmom
;
double
*
rmass
=
atom
->
rmass
;
int
*
ellipsoid
=
atom
->
ellipsoid
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
if
(
igroup
==
atom
->
firstgroup
)
nlocal
=
atom
->
nfirst
;
double
*
shape
,
*
quat
;
double
inertia
[
3
],
omega
[
3
];
// update positions and quaternions for all particles
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
x
[
i
][
0
]
+=
dtv
*
v
[
i
][
0
];
x
[
i
][
1
]
+=
dtv
*
v
[
i
][
1
];
x
[
i
][
2
]
+=
dtv
*
v
[
i
][
2
];
// principal moments of inertia
shape
=
bonus
[
ellipsoid
[
i
]].
shape
;
quat
=
bonus
[
ellipsoid
[
i
]].
quat
;
inertia
[
0
]
=
rmass
[
i
]
*
(
shape
[
1
]
*
shape
[
1
]
+
shape
[
2
]
*
shape
[
2
])
/
5.0
;
inertia
[
1
]
=
rmass
[
i
]
*
(
shape
[
0
]
*
shape
[
0
]
+
shape
[
2
]
*
shape
[
2
])
/
5.0
;
inertia
[
2
]
=
rmass
[
i
]
*
(
shape
[
0
]
*
shape
[
0
]
+
shape
[
1
]
*
shape
[
1
])
/
5.0
;
// compute omega at 1/2 step from angmom at 1/2 step and current q
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion
MathExtra
::
mq_to_omega
(
angmom
[
i
],
quat
,
inertia
,
omega
);
MathExtra
::
richardson
(
quat
,
angmom
[
i
],
omega
,
inertia
,
dtq
);
}
}
}
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