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fix_nh_body.cpp
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Wed, Aug 28, 01:34
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rLAMMPS lammps
fix_nh_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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
based on FixNHAsphere
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include "math_extra.h"
#include "fix_nh_body.h"
#include "atom.h"
#include "atom_vec_body.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
/* ---------------------------------------------------------------------- */
FixNHBody
::
FixNHBody
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
FixNH
(
lmp
,
narg
,
arg
)
{
}
/* ---------------------------------------------------------------------- */
void
FixNHBody
::
init
()
{
avec
=
(
AtomVecBody
*
)
atom
->
style_match
(
"body"
);
if
(
!
avec
)
error
->
all
(
FLERR
,
"Compute nvt/nph/npt body requires atom style body"
);
// check that all particles are finite-size
// no point particles allowed, spherical is OK
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 nvt/nph/npt body requires bodies"
);
FixNH
::
init
();
}
/* ----------------------------------------------------------------------
perform half-step update of angular momentum
-----------------------------------------------------------------------*/
void
FixNHBody
::
nve_v
()
{
// standard nve_v velocity update
FixNH
::
nve_v
();
double
**
angmom
=
atom
->
angmom
;
double
**
torque
=
atom
->
torque
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
if
(
igroup
==
atom
->
firstgroup
)
nlocal
=
atom
->
nfirst
;
// update angular momentum by 1/2 step for all particles
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
angmom
[
i
][
0
]
+=
dtf
*
torque
[
i
][
0
];
angmom
[
i
][
1
]
+=
dtf
*
torque
[
i
][
1
];
angmom
[
i
][
2
]
+=
dtf
*
torque
[
i
][
2
];
}
}
}
/* ----------------------------------------------------------------------
perform full-step update of orientation
-----------------------------------------------------------------------*/
void
FixNHBody
::
nve_x
()
{
double
omega
[
3
];
double
*
quat
,
*
inertia
;
// standard nve_x position update
FixNH
::
nve_x
();
AtomVecBody
::
Bonus
*
bonus
=
avec
->
bonus
;
int
*
body
=
atom
->
body
;
double
**
angmom
=
atom
->
angmom
;
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
;
// update quaternion a full step via Richardson iteration
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
// 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
);
}
}
/* ----------------------------------------------------------------------
perform half-step temperature scaling of angular momentum
-----------------------------------------------------------------------*/
void
FixNHBody
::
nh_v_temp
()
{
// standard nh_v_temp scaling
FixNH
::
nh_v_temp
();
double
**
angmom
=
atom
->
angmom
;
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
)
{
angmom
[
i
][
0
]
*=
factor_eta
;
angmom
[
i
][
1
]
*=
factor_eta
;
angmom
[
i
][
2
]
*=
factor_eta
;
}
}
}
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