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angle_dipole.cpp
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rLAMMPS lammps
angle_dipole.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 authors: Mario Orsi & Wei Ding (QMUL), m.orsi@qmul.ac.uk
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "angle_dipole.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
/* ---------------------------------------------------------------------- */
AngleDipole
::
AngleDipole
(
LAMMPS
*
lmp
)
:
Angle
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
AngleDipole
::~
AngleDipole
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
k
);
memory
->
destroy
(
gamma0
);
}
}
/* ---------------------------------------------------------------------- */
void
AngleDipole
::
compute
(
int
eflag
,
int
vflag
)
{
int
iRef
,
iDip
,
iDummy
,
n
,
type
;
double
delx
,
dely
,
delz
;
double
eangle
,
tangle
,
fi
[
3
],
fj
[
3
];
double
r
,
cosGamma
,
deltaGamma
,
kdg
,
rmu
;
eangle
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
0
;
double
**
x
=
atom
->
x
;
// position vector
double
**
mu
=
atom
->
mu
;
// point-dipole components and moment magnitude
double
**
torque
=
atom
->
torque
;
int
**
anglelist
=
neighbor
->
anglelist
;
int
nanglelist
=
neighbor
->
nanglelist
;
int
nlocal
=
atom
->
nlocal
;
int
newton_bond
=
force
->
newton_bond
;
double
**
f
=
atom
->
f
;
double
delTx
,
delTy
,
delTz
;
double
fx
,
fy
,
fz
,
fmod
,
fmod_sqrtff
;
if
(
!
newton_bond
)
error
->
all
(
FLERR
,
"'newton' flag for bonded interactions must be 'on'"
);
for
(
n
=
0
;
n
<
nanglelist
;
n
++
)
{
iDip
=
anglelist
[
n
][
0
];
// dipole whose orientation is to be restrained
iRef
=
anglelist
[
n
][
1
];
// reference atom toward which dipole will point
iDummy
=
anglelist
[
n
][
2
];
// dummy atom - irrelevant to the interaction
type
=
anglelist
[
n
][
3
];
delx
=
x
[
iRef
][
0
]
-
x
[
iDip
][
0
];
dely
=
x
[
iRef
][
1
]
-
x
[
iDip
][
1
];
delz
=
x
[
iRef
][
2
]
-
x
[
iDip
][
2
];
r
=
sqrt
(
delx
*
delx
+
dely
*
dely
+
delz
*
delz
);
rmu
=
r
*
mu
[
iDip
][
3
];
cosGamma
=
(
mu
[
iDip
][
0
]
*
delx
+
mu
[
iDip
][
1
]
*
dely
+
mu
[
iDip
][
2
]
*
delz
)
/
rmu
;
deltaGamma
=
cosGamma
-
cos
(
gamma0
[
type
]);
kdg
=
k
[
type
]
*
deltaGamma
;
if
(
eflag
)
eangle
=
kdg
*
deltaGamma
;
// energy
tangle
=
2.0
*
kdg
/
rmu
;
delTx
=
tangle
*
(
dely
*
mu
[
iDip
][
2
]
-
delz
*
mu
[
iDip
][
1
]);
delTy
=
tangle
*
(
delz
*
mu
[
iDip
][
0
]
-
delx
*
mu
[
iDip
][
2
]);
delTz
=
tangle
*
(
delx
*
mu
[
iDip
][
1
]
-
dely
*
mu
[
iDip
][
0
]);
torque
[
iDip
][
0
]
+=
delTx
;
torque
[
iDip
][
1
]
+=
delTy
;
torque
[
iDip
][
2
]
+=
delTz
;
// Force couple that counterbalances dipolar torque
fx
=
dely
*
delTz
-
delz
*
delTy
;
// direction (fi): - r x (-T)
fy
=
delz
*
delTx
-
delx
*
delTz
;
fz
=
delx
*
delTy
-
dely
*
delTx
;
fmod
=
sqrt
(
delTx
*
delTx
+
delTy
*
delTy
+
delTz
*
delTz
)
/
r
;
// magnitude
fmod_sqrtff
=
fmod
/
sqrt
(
fx
*
fx
+
fy
*
fy
+
fz
*
fz
);
fi
[
0
]
=
fx
*
fmod_sqrtff
;
fi
[
1
]
=
fy
*
fmod_sqrtff
;
fi
[
2
]
=
fz
*
fmod_sqrtff
;
fj
[
0
]
=
-
fi
[
0
];
fj
[
1
]
=
-
fi
[
1
];
fj
[
2
]
=
-
fi
[
2
];
f
[
iDip
][
0
]
+=
fj
[
0
];
f
[
iDip
][
1
]
+=
fj
[
1
];
f
[
iDip
][
2
]
+=
fj
[
2
];
f
[
iRef
][
0
]
+=
fi
[
0
];
f
[
iRef
][
1
]
+=
fi
[
1
];
f
[
iRef
][
2
]
+=
fi
[
2
];
if
(
evflag
)
// virial = rij.fi = 0 (fj = -fi & fk = 0)
ev_tally
(
iRef
,
iDip
,
iDummy
,
nlocal
,
newton_bond
,
eangle
,
fj
,
fi
,
0.0
,
0.0
,
0.0
,
0.0
,
0.0
,
0.0
);
}
}
/* ---------------------------------------------------------------------- */
void
AngleDipole
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
nangletypes
;
memory
->
create
(
k
,
n
+
1
,
"angle:k"
);
memory
->
create
(
gamma0
,
n
+
1
,
"angle:gamma0"
);
memory
->
create
(
setflag
,
n
+
1
,
"angle:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void
AngleDipole
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
3
)
error
->
all
(
FLERR
,
"Incorrect args for angle coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
;
force
->
bounds
(
arg
[
0
],
atom
->
nangletypes
,
ilo
,
ihi
);
double
k_one
=
force
->
numeric
(
FLERR
,
arg
[
1
]);
double
gamma0_one
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
// convert gamma0 from degrees to radians
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
k
[
i
]
=
k_one
;
gamma0
[
i
]
=
gamma0_one
/
180.0
*
MY_PI
;
setflag
[
i
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for angle coefficients"
);
}
/* ----------------------------------------------------------------------
used by SHAKE
------------------------------------------------------------------------- */
double
AngleDipole
::
equilibrium_angle
(
int
i
)
{
return
gamma0
[
i
];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void
AngleDipole
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
gamma0
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void
AngleDipole
::
read_restart
(
FILE
*
fp
)
{
allocate
();
if
(
comm
->
me
==
0
)
{
fread
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
gamma0
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
}
MPI_Bcast
(
&
k
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
gamma0
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
for
(
int
i
=
1
;
i
<=
atom
->
nangletypes
;
i
++
)
setflag
[
i
]
=
1
;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void
AngleDipole
::
write_data
(
FILE
*
fp
)
{
for
(
int
i
=
1
;
i
<=
atom
->
nangletypes
;
i
++
)
fprintf
(
fp
,
"%d %g %g
\n
"
,
i
,
k
[
i
],
gamma0
[
i
]);
}
/* ----------------------------------------------------------------------
used by ComputeAngleLocal
------------------------------------------------------------------------- */
double
AngleDipole
::
single
(
int
type
,
int
iRef
,
int
iDip
,
int
iDummy
)
{
double
**
x
=
atom
->
x
;
// position vector
double
**
mu
=
atom
->
mu
;
// point-dipole components and moment magnitude
double
delx
=
x
[
iRef
][
0
]
-
x
[
iDip
][
0
];
double
dely
=
x
[
iRef
][
1
]
-
x
[
iDip
][
1
];
double
delz
=
x
[
iRef
][
2
]
-
x
[
iDip
][
2
];
domain
->
minimum_image
(
delx
,
dely
,
delz
);
double
r
=
sqrt
(
delx
*
delx
+
dely
*
dely
+
delz
*
delz
);
double
rmu
=
r
*
mu
[
iDip
][
3
];
double
cosGamma
=
(
mu
[
iDip
][
0
]
*
delx
+
mu
[
iDip
][
1
]
*
dely
+
mu
[
iDip
][
2
]
*
delz
)
/
rmu
;
double
deltaGamma
=
cosGamma
-
cos
(
gamma0
[
type
]);
double
kdg
=
k
[
type
]
*
deltaGamma
;
return
kdg
*
deltaGamma
;
// energy
}
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