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fix_nh_sphere_omp.cpp
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Fri, Sep 6, 13:16
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rLAMMPS lammps
fix_nh_sphere_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 <math.h>
#include "fix_nh_sphere_omp.h"
#include "atom.h"
#include "atom_vec.h"
#include "compute.h"
#include "group.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
enum
{
NOBIAS
,
BIAS
};
#define INERTIA 0.4
// moment of inertia prefactor for sphere
typedef
struct
{
double
x
,
y
,
z
;
}
dbl3_t
;
/* ---------------------------------------------------------------------- */
FixNHSphereOMP
::
FixNHSphereOMP
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
FixNHOMP
(
lmp
,
narg
,
arg
)
{
if
(
!
atom
->
sphere_flag
)
error
->
all
(
FLERR
,
"Fix nvt/nph/npt sphere requires atom style sphere"
);
}
/* ---------------------------------------------------------------------- */
void
FixNHSphereOMP
::
init
()
{
// check that all particles are finite-size
// no point particles allowed
double
*
radius
=
atom
->
radius
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
if
(
radius
[
i
]
==
0.0
)
error
->
one
(
FLERR
,
"Fix nvt/sphere requires extended particles"
);
FixNHOMP
::
init
();
}
/* ----------------------------------------------------------------------
perform half-step update of rotational and COM velocities
-----------------------------------------------------------------------*/
void
FixNHSphereOMP
::
nve_v
()
{
dbl3_t
*
_noalias
const
v
=
(
dbl3_t
*
)
atom
->
v
[
0
];
dbl3_t
*
_noalias
const
omega
=
(
dbl3_t
*
)
atom
->
omega
[
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
radius
=
atom
->
radius
;
const
double
*
_noalias
const
rmass
=
atom
->
rmass
;
const
int
*
_noalias
const
mask
=
atom
->
mask
;
// set timestep here since dt may have changed or come via rRESPA
const
double
dtfrotate
=
dtf
/
INERTIA
;
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.
// update omega for all particles
// d_omega/dt = torque / inertia
// 4 cases depending on radius vs shape and rmass vs mass
#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
;
const
double
dtirotate
=
dtfrotate
/
(
radius
[
i
]
*
radius
[
i
]
*
rmass
[
i
]);
omega
[
i
].
x
+=
dtirotate
*
torque
[
i
].
x
;
omega
[
i
].
y
+=
dtirotate
*
torque
[
i
].
y
;
omega
[
i
].
z
+=
dtirotate
*
torque
[
i
].
z
;
}
}
}
/* ----------------------------------------------------------------------
perform half-step scaling of rotatonal velocities
-----------------------------------------------------------------------*/
void
FixNHSphereOMP
::
nh_v_temp
()
{
dbl3_t
*
_noalias
const
v
=
(
dbl3_t
*
)
atom
->
v
[
0
];
dbl3_t
*
_noalias
const
omega
=
(
dbl3_t
*
)
atom
->
omega
[
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
;
omega
[
i
].
x
*=
factor_eta
;
omega
[
i
].
y
*=
factor_eta
;
omega
[
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
);
omega
[
i
].
x
*=
factor_eta
;
omega
[
i
].
y
*=
factor_eta
;
omega
[
i
].
z
*=
factor_eta
;
}
}
}
}
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