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fix_nve_dot.cpp
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rLAMMPS lammps
fix_nve_dot.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: Oliver Henrich (EPCC, University of Edinburgh)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <string.h>
#include "fix_nve_dot.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
using
namespace
MathExtra
;
#define INERTIA 0.2
// moment of inertia prefactor for ellipsoid
/* ---------------------------------------------------------------------- */
FixNVEDot
::
FixNVEDot
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
FixNVE
(
lmp
,
narg
,
arg
)
{}
/* ---------------------------------------------------------------------- */
void
FixNVEDot
::
init
()
{
avec
=
(
AtomVecEllipsoid
*
)
atom
->
style_match
(
"ellipsoid"
);
if
(
!
avec
)
error
->
all
(
FLERR
,
"Compute nve/dot requires atom style ellipsoid"
);
// check that all particles are finite-size ellipsoids
// 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 nve/dot requires extended particles"
);
FixNVE
::
init
();
}
/* ---------------------------------------------------------------------- */
void
FixNVEDot
::
initial_integrate
(
int
vflag
)
{
double
*
shape
,
*
quat
;
double
fquat
[
4
],
conjqm
[
4
],
inertia
[
3
];
AtomVecEllipsoid
::
Bonus
*
bonus
=
avec
->
bonus
;
int
*
ellipsoid
=
atom
->
ellipsoid
;
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
dt
=
update
->
dt
;
dthlf
=
0.5
*
dt
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
dthlfm
=
dthlf
/
rmass
[
i
];
quat
=
bonus
[
ellipsoid
[
i
]].
quat
;
shape
=
bonus
[
ellipsoid
[
i
]].
shape
;
// update momentum by 1/2 step
v
[
i
][
0
]
+=
dthlfm
*
f
[
i
][
0
];
v
[
i
][
1
]
+=
dthlfm
*
f
[
i
][
1
];
v
[
i
][
2
]
+=
dthlfm
*
f
[
i
][
2
];
// update position by full step
x
[
i
][
0
]
+=
dt
*
v
[
i
][
0
];
x
[
i
][
1
]
+=
dt
*
v
[
i
][
1
];
x
[
i
][
2
]
+=
dt
*
v
[
i
][
2
];
// convert angular momentum and torque in space frame into
// quaternion 4-momentum and 1/2 of 4-torque in body frame
vec3_to_vec4
(
quat
,
angmom
[
i
],
conjqm
);
conjqm
[
0
]
*=
2.0
;
conjqm
[
1
]
*=
2.0
;
conjqm
[
2
]
*=
2.0
;
conjqm
[
3
]
*=
2.0
;
vec3_to_vec4
(
quat
,
torque
[
i
],
fquat
);
// update quaternion 4-momentum by 1/2 step
conjqm
[
0
]
+=
dt
*
fquat
[
0
];
conjqm
[
1
]
+=
dt
*
fquat
[
1
];
conjqm
[
2
]
+=
dt
*
fquat
[
2
];
conjqm
[
3
]
+=
dt
*
fquat
[
3
];
// principal moments of inertia
inertia
[
0
]
=
INERTIA
*
rmass
[
i
]
*
(
shape
[
1
]
*
shape
[
1
]
+
shape
[
2
]
*
shape
[
2
]);
inertia
[
1
]
=
INERTIA
*
rmass
[
i
]
*
(
shape
[
0
]
*
shape
[
0
]
+
shape
[
2
]
*
shape
[
2
]);
inertia
[
2
]
=
INERTIA
*
rmass
[
i
]
*
(
shape
[
0
]
*
shape
[
0
]
+
shape
[
1
]
*
shape
[
1
]);
// rotate quaternion and quaternion 4-momentum by full step
no_squish_rotate
(
3
,
conjqm
,
quat
,
inertia
,
dthlf
);
no_squish_rotate
(
2
,
conjqm
,
quat
,
inertia
,
dthlf
);
no_squish_rotate
(
1
,
conjqm
,
quat
,
inertia
,
dt
);
no_squish_rotate
(
2
,
conjqm
,
quat
,
inertia
,
dthlf
);
no_squish_rotate
(
3
,
conjqm
,
quat
,
inertia
,
dthlf
);
qnormalize
(
quat
);
// convert quaternion 4-momentum in body frame back to angular momentum in space frame
vec4_to_vec3
(
quat
,
conjqm
,
angmom
[
i
]);
angmom
[
i
][
0
]
*=
0.5
;
angmom
[
i
][
1
]
*=
0.5
;
angmom
[
i
][
2
]
*=
0.5
;
}
}
/* ---------------------------------------------------------------------- */
void
FixNVEDot
::
final_integrate
()
{
double
*
quat
;
double
fquat
[
4
],
conjqm
[
4
];
double
conjqm_dot_quat
;
AtomVecEllipsoid
::
Bonus
*
bonus
=
avec
->
bonus
;
int
*
ellipsoid
=
atom
->
ellipsoid
;
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
dt
=
update
->
dt
;
dthlf
=
0.5
*
dt
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
dthlfm
=
dthlf
/
rmass
[
i
];
quat
=
bonus
[
ellipsoid
[
i
]].
quat
;
// update momentum
v
[
i
][
0
]
+=
dthlfm
*
f
[
i
][
0
];
v
[
i
][
1
]
+=
dthlfm
*
f
[
i
][
1
];
v
[
i
][
2
]
+=
dthlfm
*
f
[
i
][
2
];
// convert angular momentum and torque in space frame into
// quaternion 4-momentum and 1/2 of 4-torque in body frame
vec3_to_vec4
(
quat
,
angmom
[
i
],
conjqm
);
conjqm
[
0
]
*=
2.0
;
conjqm
[
1
]
*=
2.0
;
conjqm
[
2
]
*=
2.0
;
conjqm
[
3
]
*=
2.0
;
vec3_to_vec4
(
quat
,
torque
[
i
],
fquat
);
// update quaternion 4-momentum by 1/2 step
conjqm
[
0
]
+=
dt
*
fquat
[
0
];
conjqm
[
1
]
+=
dt
*
fquat
[
1
];
conjqm
[
2
]
+=
dt
*
fquat
[
2
];
conjqm
[
3
]
+=
dt
*
fquat
[
3
];
// subtract component parallel to quaternion for improved numerical accuracy
conjqm_dot_quat
=
conjqm
[
0
]
*
quat
[
0
]
+
conjqm
[
1
]
*
quat
[
1
]
+
conjqm
[
2
]
*
quat
[
2
]
+
conjqm
[
3
]
*
quat
[
3
];
conjqm
[
0
]
-=
conjqm_dot_quat
*
quat
[
0
];
conjqm
[
1
]
-=
conjqm_dot_quat
*
quat
[
1
];
conjqm
[
2
]
-=
conjqm_dot_quat
*
quat
[
2
];
conjqm
[
3
]
-=
conjqm_dot_quat
*
quat
[
3
];
// convert quaternion 4-momentum in body frame back to angular momentum in space frame
vec4_to_vec3
(
quat
,
conjqm
,
angmom
[
i
]);
angmom
[
i
][
0
]
*=
0.5
;
angmom
[
i
][
1
]
*=
0.5
;
angmom
[
i
][
2
]
*=
0.5
;
}
}
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