Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F79772451
angle_cosine_shift.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Aug 28, 04:11
Size
7 KB
Mime Type
text/x-c
Expires
Fri, Aug 30, 04:11 (2 d)
Engine
blob
Format
Raw Data
Handle
18529713
Attached To
rLAMMPS lammps
angle_cosine_shift.cpp
View Options
/* ----------------------------------------------------------------------
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.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
/* ---------------------------------------------------------------------- */
AngleCosineShift
::
AngleCosineShift
(
LAMMPS
*
lmp
)
:
Angle
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
AngleCosineShift
::~
AngleCosineShift
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
k
);
memory
->
destroy
(
kcost
);
memory
->
destroy
(
ksint
);
memory
->
destroy
(
theta
);
}
}
/* ---------------------------------------------------------------------- */
void
AngleCosineShift
::
compute
(
int
eflag
,
int
vflag
)
{
int
i1
,
i2
,
i3
,
n
,
type
;
double
delx1
,
dely1
,
delz1
,
delx2
,
dely2
,
delz2
;
double
eangle
,
f1
[
3
],
f3
[
3
];
double
rsq1
,
rsq2
,
r1
,
r2
,
c
,
s
,
cps
,
kcos
,
ksin
,
a11
,
a12
,
a22
;
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
];
domain
->
minimum_image
(
delx1
,
dely1
,
delz1
);
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
];
domain
->
minimum_image
(
delx2
,
dely2
,
delz2
);
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
if
(
eflag
)
eangle
=
-
k
[
type
]
-
kcos
*
c
-
ksin
*
s
;
kcos
=
kcost
[
type
];
ksin
=
ksint
[
type
];
cps
=
c
/
s
;
// NOTE absorbed one c
a11
=
(
-
kcos
+
ksin
*
cps
)
*
c
/
rsq1
;
a12
=
(
kcos
-
ksin
*
cps
)
/
(
r1
*
r2
);
a22
=
(
-
kcos
+
ksin
*
cps
)
*
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
AngleCosineShift
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
nangletypes
;
memory
->
create
(
k
,
n
+
1
,
"Angle:k"
);
memory
->
create
(
ksint
,
n
+
1
,
"Angle:ksint"
);
memory
->
create
(
kcost
,
n
+
1
,
"Angle:kcost"
);
memory
->
create
(
theta
,
n
+
1
,
"Angle:theta"
);
memory
->
create
(
setflag
,
n
+
1
,
"Angle:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void
AngleCosineShift
::
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
umin
=
force
->
numeric
(
arg
[
1
]);
double
theta0
=
force
->
numeric
(
arg
[
2
]);
// k=Umin/2
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
k
[
i
]
=
umin
/
2
;
kcost
[
i
]
=
umin
/
2
*
cos
(
theta0
*
3.14159265
/
180
);
ksint
[
i
]
=
umin
/
2
*
sin
(
theta0
*
3.14159265
/
180
);
theta
[
i
]
=
theta0
*
3.14159265
/
180
;
setflag
[
i
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for angle coefficients"
);
}
/* ---------------------------------------------------------------------- */
double
AngleCosineShift
::
equilibrium_angle
(
int
i
)
{
return
theta
[
i
];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void
AngleCosineShift
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
kcost
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
ksint
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
theta
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void
AngleCosineShift
::
read_restart
(
FILE
*
fp
)
{
allocate
();
if
(
comm
->
me
==
0
)
{
fread
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
kcost
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
ksint
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
theta
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
}
MPI_Bcast
(
&
k
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
kcost
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
ksint
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
theta
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
for
(
int
i
=
1
;
i
<=
atom
->
nangletypes
;
i
++
)
setflag
[
i
]
=
1
;
}
/* ---------------------------------------------------------------------- */
double
AngleCosineShift
::
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
);
return
-
k
[
type
]
-
kcost
[
type
]
*
c
-
ksint
[
type
]
*
s
;
}
Event Timeline
Log In to Comment