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angle_cosine_delta.cpp
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rLAMMPS lammps
angle_cosine_delta.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), akohlmey at gmail.com
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "angle_cosine_delta.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
AngleCosineDelta
::
AngleCosineDelta
(
LAMMPS
*
lmp
)
:
AngleCosineSquared
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
void
AngleCosineDelta
::
compute
(
int
eflag
,
int
vflag
)
{
int
i1
,
i2
,
i3
,
n
,
type
;
double
delx1
,
dely1
,
delz1
,
delx2
,
dely2
,
delz2
,
theta
,
dtheta
,
dcostheta
,
tk
;
double
eangle
,
f1
[
3
],
f3
[
3
];
double
rsq1
,
rsq2
,
r1
,
r2
,
c
,
a
,
cot
,
a11
,
a12
,
a22
,
b11
,
b12
,
b22
,
c0
,
s0
,
s
;
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
);
// angle (cos and sin)
c
=
delx1
*
delx2
+
dely1
*
dely2
+
delz1
*
delz2
;
c
/=
r1
*
r2
;
if
(
c
>
1.0
)
c
=
1.0
;
if
(
c
<
-
1.0
)
c
=
-
1.0
;
theta
=
acos
(
c
);
s
=
sqrt
(
1.0
-
c
*
c
);
if
(
s
<
SMALL
)
s
=
SMALL
;
s
=
1.0
/
s
;
cot
=
c
/
s
;
// force & energy
dtheta
=
theta
-
theta0
[
type
];
dcostheta
=
cos
(
dtheta
);
tk
=
k
[
type
]
*
(
1.0
-
dcostheta
);
if
(
eflag
)
eangle
=
tk
;
a
=
-
k
[
type
];
// expand dtheta for cos and sin contribution to force
a11
=
a
*
c
/
rsq1
;
a12
=
-
a
/
(
r1
*
r2
);
a22
=
a
*
c
/
rsq2
;
b11
=
-
a
*
c
*
cot
/
rsq1
;
b12
=
a
*
cot
/
(
r1
*
r2
);
b22
=
-
a
*
c
*
cot
/
rsq2
;
c0
=
cos
(
theta0
[
type
]);
s0
=
sin
(
theta0
[
type
]);
f1
[
0
]
=
(
a11
*
delx1
+
a12
*
delx2
)
*
c0
+
(
b11
*
delx1
+
b12
*
delx2
)
*
s0
;
f1
[
1
]
=
(
a11
*
dely1
+
a12
*
dely2
)
*
c0
+
(
b11
*
dely1
+
b12
*
dely2
)
*
s0
;
f1
[
2
]
=
(
a11
*
delz1
+
a12
*
delz2
)
*
c0
+
(
b11
*
delz1
+
b12
*
delz2
)
*
s0
;
f3
[
0
]
=
(
a22
*
delx2
+
a12
*
delx1
)
*
c0
+
(
b22
*
delx2
+
b12
*
delx1
)
*
s0
;
f3
[
1
]
=
(
a22
*
dely2
+
a12
*
dely1
)
*
c0
+
(
b22
*
dely2
+
b12
*
dely1
)
*
s0
;
f3
[
2
]
=
(
a22
*
delz2
+
a12
*
delz1
)
*
c0
+
(
b22
*
delz2
+
b12
*
delz1
)
*
s0
;
// 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
);
}
}
/* ---------------------------------------------------------------------- */
double
AngleCosineDelta
::
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
theta
=
acos
(
c
);
double
dtheta
=
theta
-
theta0
[
type
];
double
dcostheta
=
cos
(
dtheta
);
double
tk
=
k
[
type
]
*
(
1.0
-
dcostheta
);
return
tk
;
}
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