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angle_cosine_shift_exp.cpp
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rLAMMPS lammps
angle_cosine_shift_exp.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: Carsten Svaneborg, science@zqex.dk
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "angle_cosine_shift_exp.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
;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
AngleCosineShiftExp
::
AngleCosineShiftExp
(
LAMMPS
*
lmp
)
:
Angle
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
AngleCosineShiftExp
::~
AngleCosineShiftExp
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
umin
);
memory
->
destroy
(
a
);
memory
->
destroy
(
opt1
);
memory
->
destroy
(
cost
);
memory
->
destroy
(
sint
);
memory
->
destroy
(
theta0
);
memory
->
destroy
(
doExpansion
);
}
}
/* ---------------------------------------------------------------------- */
void
AngleCosineShiftExp
::
compute
(
int
eflag
,
int
vflag
)
{
int
i1
,
i2
,
i3
,
n
,
type
;
double
delx1
,
dely1
,
delz1
,
delx2
,
dely2
,
delz2
;
double
eangle
,
f1
[
3
],
f3
[
3
],
ff
;
double
rsq1
,
rsq2
,
r1
,
r2
,
c
,
s
,
a11
,
a12
,
a22
;
double
exp2
,
aa
,
uumin
,
cccpsss
,
cssmscc
;
eangle
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
**
anglelist
=
neighbor
->
anglelist
;
int
nanglelist
=
neighbor
->
nanglelist
;
int
nlocal
=
atom
->
nlocal
;
int
newton_bond
=
force
->
newton_bond
;
for
(
n
=
0
;
n
<
nanglelist
;
n
++
)
{
i1
=
anglelist
[
n
][
0
];
i2
=
anglelist
[
n
][
1
];
i3
=
anglelist
[
n
][
2
];
type
=
anglelist
[
n
][
3
];
// 1st bond
delx1
=
x
[
i1
][
0
]
-
x
[
i2
][
0
];
dely1
=
x
[
i1
][
1
]
-
x
[
i2
][
1
];
delz1
=
x
[
i1
][
2
]
-
x
[
i2
][
2
];
rsq1
=
delx1
*
delx1
+
dely1
*
dely1
+
delz1
*
delz1
;
r1
=
sqrt
(
rsq1
);
// 2nd bond
delx2
=
x
[
i3
][
0
]
-
x
[
i2
][
0
];
dely2
=
x
[
i3
][
1
]
-
x
[
i2
][
1
];
delz2
=
x
[
i3
][
2
]
-
x
[
i2
][
2
];
rsq2
=
delx2
*
delx2
+
dely2
*
dely2
+
delz2
*
delz2
;
r2
=
sqrt
(
rsq2
);
// c = cosine of angle
c
=
delx1
*
delx2
+
dely1
*
dely2
+
delz1
*
delz2
;
c
/=
r1
*
r2
;
if
(
c
>
1.0
)
c
=
1.0
;
if
(
c
<
-
1.0
)
c
=
-
1.0
;
// C= sine of angle
s
=
sqrt
(
1.0
-
c
*
c
);
if
(
s
<
SMALL
)
s
=
SMALL
;
// force & energy
aa
=
a
[
type
];
uumin
=
umin
[
type
];
cccpsss
=
c
*
cost
[
type
]
+
s
*
sint
[
type
];
cssmscc
=
c
*
sint
[
type
]
-
s
*
cost
[
type
];
if
(
doExpansion
[
type
])
{
// |a|<0.01 so use expansions relative precision <1e-5
// std::cout << "Using expansion\n";
if
(
eflag
)
eangle
=
-
0.125
*
(
1
+
cccpsss
)
*
(
4
+
aa
*
(
cccpsss
-
1
))
*
uumin
;
ff
=
0.25
*
uumin
*
cssmscc
*
(
2
+
aa
*
cccpsss
)
/
s
;
}
else
{
// std::cout << "Not using expansion\n";
exp2
=
exp
(
0.5
*
aa
*
(
1
+
cccpsss
));
if
(
eflag
)
eangle
=
opt1
[
type
]
*
(
1
-
exp2
);
ff
=
0.5
*
a
[
type
]
*
opt1
[
type
]
*
exp2
*
cssmscc
/
s
;
}
a11
=
ff
*
c
/
rsq1
;
a12
=
-
ff
/
(
r1
*
r2
);
a22
=
ff
*
c
/
rsq2
;
f1
[
0
]
=
a11
*
delx1
+
a12
*
delx2
;
f1
[
1
]
=
a11
*
dely1
+
a12
*
dely2
;
f1
[
2
]
=
a11
*
delz1
+
a12
*
delz2
;
f3
[
0
]
=
a22
*
delx2
+
a12
*
delx1
;
f3
[
1
]
=
a22
*
dely2
+
a12
*
dely1
;
f3
[
2
]
=
a22
*
delz2
+
a12
*
delz1
;
// apply force to each of 3 atoms
if
(
newton_bond
||
i1
<
nlocal
)
{
f
[
i1
][
0
]
+=
f1
[
0
];
f
[
i1
][
1
]
+=
f1
[
1
];
f
[
i1
][
2
]
+=
f1
[
2
];
}
if
(
newton_bond
||
i2
<
nlocal
)
{
f
[
i2
][
0
]
-=
f1
[
0
]
+
f3
[
0
];
f
[
i2
][
1
]
-=
f1
[
1
]
+
f3
[
1
];
f
[
i2
][
2
]
-=
f1
[
2
]
+
f3
[
2
];
}
if
(
newton_bond
||
i3
<
nlocal
)
{
f
[
i3
][
0
]
+=
f3
[
0
];
f
[
i3
][
1
]
+=
f3
[
1
];
f
[
i3
][
2
]
+=
f3
[
2
];
}
if
(
evflag
)
ev_tally
(
i1
,
i2
,
i3
,
nlocal
,
newton_bond
,
eangle
,
f1
,
f3
,
delx1
,
dely1
,
delz1
,
delx2
,
dely2
,
delz2
);
}
}
/* ---------------------------------------------------------------------- */
void
AngleCosineShiftExp
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
nangletypes
;
memory
->
create
(
doExpansion
,
n
+
1
,
"angle:doExpansion"
);
memory
->
create
(
umin
,
n
+
1
,
"angle:umin"
);
memory
->
create
(
a
,
n
+
1
,
"angle:a"
);
memory
->
create
(
sint
,
n
+
1
,
"angle:sint"
);
memory
->
create
(
cost
,
n
+
1
,
"angle:cost"
);
memory
->
create
(
opt1
,
n
+
1
,
"angle:opt1"
);
memory
->
create
(
theta0
,
n
+
1
,
"angle:theta0"
);
memory
->
create
(
setflag
,
n
+
1
,
"angle:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void
AngleCosineShiftExp
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
4
)
error
->
all
(
FLERR
,
"Incorrect args for angle coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
;
force
->
bounds
(
arg
[
0
],
atom
->
nangletypes
,
ilo
,
ihi
);
double
umin_
=
force
->
numeric
(
FLERR
,
arg
[
1
]);
double
theta0_
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
double
a_
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
doExpansion
[
i
]
=
(
fabs
(
a_
)
<
0.001
);
umin
[
i
]
=
umin_
;
a
[
i
]
=
a_
;
cost
[
i
]
=
cos
(
theta0_
*
MY_PI
/
180.0
);
sint
[
i
]
=
sin
(
theta0_
*
MY_PI
/
180.0
);
theta0
[
i
]
=
theta0_
*
MY_PI
/
180.0
;
if
(
!
doExpansion
[
i
])
opt1
[
i
]
=
umin_
/
(
exp
(
a_
)
-
1
);
setflag
[
i
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for angle coefficients"
);
}
/* ---------------------------------------------------------------------- */
double
AngleCosineShiftExp
::
equilibrium_angle
(
int
i
)
{
return
theta0
[
i
];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void
AngleCosineShiftExp
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
umin
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
a
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
cost
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
sint
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
theta0
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void
AngleCosineShiftExp
::
read_restart
(
FILE
*
fp
)
{
allocate
();
if
(
comm
->
me
==
0
)
{
fread
(
&
umin
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
a
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
cost
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
sint
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
theta0
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
}
MPI_Bcast
(
&
umin
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
a
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cost
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sint
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
theta0
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
for
(
int
i
=
1
;
i
<=
atom
->
nangletypes
;
i
++
)
{
setflag
[
i
]
=
1
;
doExpansion
[
i
]
=
(
fabs
(
a
[
i
])
<
0.01
);
if
(
!
doExpansion
[
i
])
opt1
[
i
]
=
umin
[
i
]
/
(
exp
(
a
[
i
])
-
1
);
}
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void
AngleCosineShiftExp
::
write_data
(
FILE
*
fp
)
{
for
(
int
i
=
1
;
i
<=
atom
->
nangletypes
;
i
++
)
fprintf
(
fp
,
"%d %g %g %g
\n
"
,
i
,
umin
[
i
],
theta0
[
i
]
/
MY_PI
*
180.0
,
a
[
i
]);
}
/* ---------------------------------------------------------------------- */
double
AngleCosineShiftExp
::
single
(
int
type
,
int
i1
,
int
i2
,
int
i3
)
{
double
**
x
=
atom
->
x
;
double
delx1
=
x
[
i1
][
0
]
-
x
[
i2
][
0
];
double
dely1
=
x
[
i1
][
1
]
-
x
[
i2
][
1
];
double
delz1
=
x
[
i1
][
2
]
-
x
[
i2
][
2
];
domain
->
minimum_image
(
delx1
,
dely1
,
delz1
);
double
r1
=
sqrt
(
delx1
*
delx1
+
dely1
*
dely1
+
delz1
*
delz1
);
double
delx2
=
x
[
i3
][
0
]
-
x
[
i2
][
0
];
double
dely2
=
x
[
i3
][
1
]
-
x
[
i2
][
1
];
double
delz2
=
x
[
i3
][
2
]
-
x
[
i2
][
2
];
domain
->
minimum_image
(
delx2
,
dely2
,
delz2
);
double
r2
=
sqrt
(
delx2
*
delx2
+
dely2
*
dely2
+
delz2
*
delz2
);
double
c
=
delx1
*
delx2
+
dely1
*
dely2
+
delz1
*
delz2
;
c
/=
r1
*
r2
;
if
(
c
>
1.0
)
c
=
1.0
;
if
(
c
<
-
1.0
)
c
=
-
1.0
;
double
s
=
sqrt
(
1.0
-
c
*
c
);
double
cccpsss
=
c
*
cost
[
type
]
+
s
*
sint
[
type
];
if
(
doExpansion
[
type
])
{
return
-
0.125
*
(
1
+
cccpsss
)
*
(
4
+
a
[
type
]
*
(
cccpsss
-
1
))
*
umin
[
type
];
}
else
{
return
opt1
[
type
]
*
(
1
-
exp
(
0.5
*
a
[
type
]
*
(
1
+
cccpsss
)));
}
}
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