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fix_nve_body.cpp
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Thu, Oct 31, 16:48
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Sat, Nov 2, 16:48 (2 d)
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rLAMMPS lammps
fix_nve_body.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 <stdio.h>
#include <string.h>
#include "fix_nve_body.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_body.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
/* ---------------------------------------------------------------------- */
FixNVEBody
::
FixNVEBody
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
FixNVE
(
lmp
,
narg
,
arg
)
{}
/* ---------------------------------------------------------------------- */
void
FixNVEBody
::
init
()
{
avec
=
(
AtomVecBody
*
)
atom
->
style_match
(
"body"
);
if
(
!
avec
)
error
->
all
(
FLERR
,
"Fix nve/body requires atom style body"
);
// check that all particles are bodies
// no point particles allowed
int
*
body
=
atom
->
body
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
if
(
body
[
i
]
<
0
)
error
->
one
(
FLERR
,
"Fix nve/body requires bodies"
);
FixNVE
::
init
();
}
/* ---------------------------------------------------------------------- */
void
FixNVEBody
::
initial_integrate
(
int
vflag
)
{
double
dtfm
;
double
omega
[
3
];
double
*
quat
,
*
inertia
;
AtomVecBody
::
Bonus
*
bonus
=
avec
->
bonus
;
int
*
body
=
atom
->
body
;
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
**
angmom
=
atom
->
angmom
;
double
**
torque
=
atom
->
torque
;
double
*
rmass
=
atom
->
rmass
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
if
(
igroup
==
atom
->
firstgroup
)
nlocal
=
atom
->
nfirst
;
// set timestep here since dt may have changed or come via rRESPA
dtq
=
0.5
*
dtv
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
dtfm
=
dtf
/
rmass
[
i
];
v
[
i
][
0
]
+=
dtfm
*
f
[
i
][
0
];
v
[
i
][
1
]
+=
dtfm
*
f
[
i
][
1
];
v
[
i
][
2
]
+=
dtfm
*
f
[
i
][
2
];
x
[
i
][
0
]
+=
dtv
*
v
[
i
][
0
];
x
[
i
][
1
]
+=
dtv
*
v
[
i
][
1
];
x
[
i
][
2
]
+=
dtv
*
v
[
i
][
2
];
// update angular momentum by 1/2 step
angmom
[
i
][
0
]
+=
dtf
*
torque
[
i
][
0
];
angmom
[
i
][
1
]
+=
dtf
*
torque
[
i
][
1
];
angmom
[
i
][
2
]
+=
dtf
*
torque
[
i
][
2
];
// 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
inertia
=
bonus
[
body
[
i
]].
inertia
;
quat
=
bonus
[
body
[
i
]].
quat
;
MathExtra
::
mq_to_omega
(
angmom
[
i
],
quat
,
inertia
,
omega
);
MathExtra
::
richardson
(
quat
,
angmom
[
i
],
omega
,
inertia
,
dtq
);
}
}
/* ---------------------------------------------------------------------- */
void
FixNVEBody
::
final_integrate
()
{
double
dtfm
;
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
**
angmom
=
atom
->
angmom
;
double
**
torque
=
atom
->
torque
;
double
*
rmass
=
atom
->
rmass
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
if
(
igroup
==
atom
->
firstgroup
)
nlocal
=
atom
->
nfirst
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
dtfm
=
dtf
/
rmass
[
i
];
v
[
i
][
0
]
+=
dtfm
*
f
[
i
][
0
];
v
[
i
][
1
]
+=
dtfm
*
f
[
i
][
1
];
v
[
i
][
2
]
+=
dtfm
*
f
[
i
][
2
];
angmom
[
i
][
0
]
+=
dtf
*
torque
[
i
][
0
];
angmom
[
i
][
1
]
+=
dtf
*
torque
[
i
][
1
];
angmom
[
i
][
2
]
+=
dtf
*
torque
[
i
][
2
];
}
}
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