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fix_nh_asphere_omp.cpp
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rLAMMPS lammps
fix_nh_asphere_omp.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: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "math_extra.h"
#include "fix_nh_asphere_omp.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "compute.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
enum
{
NOBIAS
,
BIAS
};
typedef
struct
{
double
x
,
y
,
z
;
}
dbl3_t
;
#if defined(__GNUC__)
#define _noalias __restrict
#else
#define _noalias
#endif
/* ---------------------------------------------------------------------- */
FixNHAsphereOMP
::
FixNHAsphereOMP
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
FixNHOMP
(
lmp
,
narg
,
arg
)
{
}
/* ---------------------------------------------------------------------- */
void
FixNHAsphereOMP
::
init
()
{
avec
=
(
AtomVecEllipsoid
*
)
atom
->
style_match
(
"ellipsoid"
);
if
(
!
avec
)
error
->
all
(
FLERR
,
"Compute nvt/nph/npt asphere requires atom style ellipsoid"
);
// 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
(
FLERR
,
"Fix nvt/nph/npt asphere requires extended particles"
);
FixNHOMP
::
init
();
}
/* ----------------------------------------------------------------------
perform half-step update of angular momentum and COM velocity
-----------------------------------------------------------------------*/
void
FixNHAsphereOMP
::
nve_v
()
{
dbl3_t
*
_noalias
const
v
=
(
dbl3_t
*
)
atom
->
v
[
0
];
dbl3_t
*
_noalias
const
angmom
=
(
dbl3_t
*
)
atom
->
angmom
[
0
];
const
dbl3_t
*
_noalias
const
f
=
(
dbl3_t
*
)
atom
->
f
[
0
];
const
dbl3_t
*
_noalias
const
torque
=
(
dbl3_t
*
)
atom
->
torque
[
0
];
const
double
*
_noalias
const
rmass
=
atom
->
rmass
;
const
int
*
_noalias
const
mask
=
atom
->
mask
;
const
int
nlocal
=
(
igroup
==
atom
->
firstgroup
)
?
atom
->
nfirst
:
atom
->
nlocal
;
int
i
;
// standard nve_v velocity update. for efficiency the loop is
// merged with FixNHOMP instead of calling it for the COM update.
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
const
double
dtfm
=
dtf
/
rmass
[
i
];
v
[
i
].
x
+=
dtfm
*
f
[
i
].
x
;
v
[
i
].
y
+=
dtfm
*
f
[
i
].
y
;
v
[
i
].
z
+=
dtfm
*
f
[
i
].
z
;
angmom
[
i
].
x
+=
dtf
*
torque
[
i
].
x
;
angmom
[
i
].
y
+=
dtf
*
torque
[
i
].
y
;
angmom
[
i
].
z
+=
dtf
*
torque
[
i
].
z
;
}
}
}
/* ----------------------------------------------------------------------
perform full-step update of position and orientation
-----------------------------------------------------------------------*/
void
FixNHAsphereOMP
::
nve_x
()
{
dbl3_t
*
_noalias
const
x
=
(
dbl3_t
*
)
atom
->
x
[
0
];
const
dbl3_t
*
_noalias
const
v
=
(
dbl3_t
*
)
atom
->
v
[
0
];
dbl3_t
*
_noalias
const
angmom
=
(
dbl3_t
*
)
atom
->
angmom
[
0
];
const
double
*
_noalias
const
rmass
=
atom
->
rmass
;
const
int
*
_noalias
const
mask
=
atom
->
mask
;
AtomVecEllipsoid
::
Bonus
*
_noalias
const
bonus
=
avec
->
bonus
;
const
int
*
_noalias
const
ellipsoid
=
atom
->
ellipsoid
;
const
int
nlocal
=
(
igroup
==
atom
->
firstgroup
)
?
atom
->
nfirst
:
atom
->
nlocal
;
int
i
;
// set timestep here since dt may have changed or come via rRESPA
dtq
=
0.5
*
dtv
;
// standard nve_x position update and
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion
// principal moments of inertia
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
double
omega
[
3
],
inertia
[
3
];
x
[
i
].
x
+=
dtv
*
v
[
i
].
x
;
x
[
i
].
y
+=
dtv
*
v
[
i
].
y
;
x
[
i
].
z
+=
dtv
*
v
[
i
].
z
;
// principal moments of inertia
const
double
*
const
shape
=
bonus
[
ellipsoid
[
i
]].
shape
;
double
*
const
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
].
x
,
quat
,
inertia
,
omega
);
MathExtra
::
richardson
(
quat
,
&
angmom
[
i
].
x
,
omega
,
inertia
,
dtq
);
}
}
/* ----------------------------------------------------------------------
perform half-step temperature scaling of angular momentum
-----------------------------------------------------------------------*/
void
FixNHAsphereOMP
::
nh_v_temp
()
{
dbl3_t
*
_noalias
const
v
=
(
dbl3_t
*
)
atom
->
v
[
0
];
dbl3_t
*
_noalias
const
angmom
=
(
dbl3_t
*
)
atom
->
angmom
[
0
];
const
int
*
_noalias
const
mask
=
atom
->
mask
;
const
int
nlocal
=
(
igroup
==
atom
->
firstgroup
)
?
atom
->
nfirst
:
atom
->
nlocal
;
int
i
;
if
(
which
==
NOBIAS
)
{
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
v
[
i
].
x
*=
factor_eta
;
v
[
i
].
y
*=
factor_eta
;
v
[
i
].
z
*=
factor_eta
;
angmom
[
i
].
x
*=
factor_eta
;
angmom
[
i
].
y
*=
factor_eta
;
angmom
[
i
].
z
*=
factor_eta
;
}
}
}
else
if
(
which
==
BIAS
)
{
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
double
buf
[
3
];
if
(
mask
[
i
]
&
groupbit
)
{
temperature
->
remove_bias
(
i
,
&
v
[
i
].
x
);
v
[
i
].
x
*=
factor_eta
;
v
[
i
].
y
*=
factor_eta
;
v
[
i
].
z
*=
factor_eta
;
temperature
->
restore_bias
(
i
,
&
v
[
i
].
x
);
angmom
[
i
].
x
*=
factor_eta
;
angmom
[
i
].
y
*=
factor_eta
;
angmom
[
i
].
z
*=
factor_eta
;
}
}
}
}
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