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fix_nh_asphere.cpp
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Fri, Sep 6, 22:03
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rLAMMPS lammps
fix_nh_asphere.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: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "math_extra.h"
#include "fix_nh_asphere.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
FixNHAsphere
::
FixNHAsphere
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
FixNH
(
lmp
,
narg
,
arg
)
{
avec
=
(
AtomVecEllipsoid
*
)
atom
->
style_match
(
"ellipsoid"
);
if
(
!
avec
)
error
->
all
(
"Compute nvt/nph/npt asphere requires atom style ellipsoid"
);
}
/* ---------------------------------------------------------------------- */
void
FixNHAsphere
::
init
()
{
// check that all particles are finite-size
// 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
(
"Fix nvt/nph/npt asphere requires extended particles"
);
FixNH
::
init
();
}
/* ----------------------------------------------------------------------
Richardson iteration to update quaternion accurately
------------------------------------------------------------------------- */
void
FixNHAsphere
::
richardson
(
double
*
q
,
double
*
m
,
double
*
moments
)
{
// compute omega at 1/2 step from m at 1/2 step and q at 0
double
w
[
3
];
omega_from_mq
(
q
,
m
,
moments
,
w
);
// full update from dq/dt = 1/2 w q
double
wq
[
4
];
MathExtra
::
multiply_vec_quat
(
w
,
q
,
wq
);
double
qfull
[
4
];
qfull
[
0
]
=
q
[
0
]
+
dtq
*
wq
[
0
];
qfull
[
1
]
=
q
[
1
]
+
dtq
*
wq
[
1
];
qfull
[
2
]
=
q
[
2
]
+
dtq
*
wq
[
2
];
qfull
[
3
]
=
q
[
3
]
+
dtq
*
wq
[
3
];
MathExtra
::
normalize4
(
qfull
);
// 1st half of update from dq/dt = 1/2 w q
double
qhalf
[
4
];
qhalf
[
0
]
=
q
[
0
]
+
0.5
*
dtq
*
wq
[
0
];
qhalf
[
1
]
=
q
[
1
]
+
0.5
*
dtq
*
wq
[
1
];
qhalf
[
2
]
=
q
[
2
]
+
0.5
*
dtq
*
wq
[
2
];
qhalf
[
3
]
=
q
[
3
]
+
0.5
*
dtq
*
wq
[
3
];
MathExtra
::
normalize4
(
qhalf
);
// re-compute omega at 1/2 step from m at 1/2 step and q at 1/2 step
// recompute wq
omega_from_mq
(
qhalf
,
m
,
moments
,
w
);
MathExtra
::
multiply_vec_quat
(
w
,
qhalf
,
wq
);
// 2nd half of update from dq/dt = 1/2 w q
qhalf
[
0
]
+=
0.5
*
dtq
*
wq
[
0
];
qhalf
[
1
]
+=
0.5
*
dtq
*
wq
[
1
];
qhalf
[
2
]
+=
0.5
*
dtq
*
wq
[
2
];
qhalf
[
3
]
+=
0.5
*
dtq
*
wq
[
3
];
MathExtra
::
normalize4
(
qhalf
);
// corrected Richardson update
q
[
0
]
=
2.0
*
qhalf
[
0
]
-
qfull
[
0
];
q
[
1
]
=
2.0
*
qhalf
[
1
]
-
qfull
[
1
];
q
[
2
]
=
2.0
*
qhalf
[
2
]
-
qfull
[
2
];
q
[
3
]
=
2.0
*
qhalf
[
3
]
-
qfull
[
3
];
MathExtra
::
normalize4
(
q
);
}
/* ----------------------------------------------------------------------
compute omega from angular momentum
w = omega = angular velocity in space frame
wbody = angular velocity in body frame
project space-frame angular momentum onto body axes
and divide by principal moments
------------------------------------------------------------------------- */
void
FixNHAsphere
::
omega_from_mq
(
double
*
q
,
double
*
m
,
double
*
inertia
,
double
*
w
)
{
double
rot
[
3
][
3
];
MathExtra
::
quat_to_mat
(
q
,
rot
);
double
wbody
[
3
];
MathExtra
::
transpose_times_column3
(
rot
,
m
,
wbody
);
wbody
[
0
]
/=
inertia
[
0
];
wbody
[
1
]
/=
inertia
[
1
];
wbody
[
2
]
/=
inertia
[
2
];
MathExtra
::
times_column3
(
rot
,
wbody
,
w
);
}
/* ----------------------------------------------------------------------
perform half-step update of angular momentum
-----------------------------------------------------------------------*/
void
FixNHAsphere
::
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
FixNHAsphere
::
nve_x
()
{
// standard nve_x position update
FixNH
::
nve_x
();
AtomVecEllipsoid
::
Bonus
*
bonus
=
avec
->
bonus
;
int
*
ellipsoid
=
atom
->
ellipsoid
;
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
// returns new normalized quaternion
// principal moments of inertia
double
*
shape
,
*
quat
;
double
inertia
[
3
];
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
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
;
richardson
(
quat
,
angmom
[
i
],
inertia
);
}
}
/* ----------------------------------------------------------------------
perform half-step temperature scaling of angular momentum
-----------------------------------------------------------------------*/
void
FixNHAsphere
::
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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