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rLAMMPS lammps
angle_charmm.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: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "angle_charmm.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
/* ---------------------------------------------------------------------- */
AngleCharmm
::
AngleCharmm
(
LAMMPS
*
lmp
)
:
Angle
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
AngleCharmm
::~
AngleCharmm
()
{
if
(
allocated
&&
!
copymode
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
k
);
memory
->
destroy
(
theta0
);
memory
->
destroy
(
k_ub
);
memory
->
destroy
(
r_ub
);
}
}
/* ---------------------------------------------------------------------- */
void
AngleCharmm
::
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
dtheta
,
tk
;
double
rsq1
,
rsq2
,
r1
,
r2
,
c
,
s
,
a
,
a11
,
a12
,
a22
;
double
delxUB
,
delyUB
,
delzUB
,
rsqUB
,
rUB
,
dr
,
rk
,
forceUB
;
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
);
// Urey-Bradley bond
delxUB
=
x
[
i3
][
0
]
-
x
[
i1
][
0
];
delyUB
=
x
[
i3
][
1
]
-
x
[
i1
][
1
];
delzUB
=
x
[
i3
][
2
]
-
x
[
i1
][
2
];
rsqUB
=
delxUB
*
delxUB
+
delyUB
*
delyUB
+
delzUB
*
delzUB
;
rUB
=
sqrt
(
rsqUB
);
// Urey-Bradley force & energy
dr
=
rUB
-
r_ub
[
type
];
rk
=
k_ub
[
type
]
*
dr
;
if
(
rUB
>
0.0
)
forceUB
=
-
2.0
*
rk
/
rUB
;
else
forceUB
=
0.0
;
if
(
eflag
)
eangle
=
rk
*
dr
;
// 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
;
s
=
sqrt
(
1.0
-
c
*
c
);
if
(
s
<
SMALL
)
s
=
SMALL
;
s
=
1.0
/
s
;
// harmonic force & energy
dtheta
=
acos
(
c
)
-
theta0
[
type
];
tk
=
k
[
type
]
*
dtheta
;
if
(
eflag
)
eangle
+=
tk
*
dtheta
;
a
=
-
2.0
*
tk
*
s
;
a11
=
a
*
c
/
rsq1
;
a12
=
-
a
/
(
r1
*
r2
);
a22
=
a
*
c
/
rsq2
;
f1
[
0
]
=
a11
*
delx1
+
a12
*
delx2
-
delxUB
*
forceUB
;
f1
[
1
]
=
a11
*
dely1
+
a12
*
dely2
-
delyUB
*
forceUB
;
f1
[
2
]
=
a11
*
delz1
+
a12
*
delz2
-
delzUB
*
forceUB
;
f3
[
0
]
=
a22
*
delx2
+
a12
*
delx1
+
delxUB
*
forceUB
;
f3
[
1
]
=
a22
*
dely2
+
a12
*
dely1
+
delyUB
*
forceUB
;
f3
[
2
]
=
a22
*
delz2
+
a12
*
delz1
+
delzUB
*
forceUB
;
// 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
AngleCharmm
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
nangletypes
;
memory
->
create
(
k
,
n
+
1
,
"angle:k"
);
memory
->
create
(
theta0
,
n
+
1
,
"angle:theta0"
);
memory
->
create
(
k_ub
,
n
+
1
,
"angle:k_ub"
);
memory
->
create
(
r_ub
,
n
+
1
,
"angle:r_ub"
);
memory
->
create
(
setflag
,
n
+
1
,
"angle:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void
AngleCharmm
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
5
)
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
theta0_one
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
double
k_ub_one
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
double
r_ub_one
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
// convert theta0 from degrees to radians
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
k
[
i
]
=
k_one
;
theta0
[
i
]
=
theta0_one
/
180.0
*
MY_PI
;
k_ub
[
i
]
=
k_ub_one
;
r_ub
[
i
]
=
r_ub_one
;
setflag
[
i
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for angle coefficients"
);
}
/* ---------------------------------------------------------------------- */
double
AngleCharmm
::
equilibrium_angle
(
int
i
)
{
return
theta0
[
i
];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void
AngleCharmm
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
theta0
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
k_ub
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
r_ub
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void
AngleCharmm
::
read_restart
(
FILE
*
fp
)
{
allocate
();
if
(
comm
->
me
==
0
)
{
fread
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
theta0
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
k_ub
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
r_ub
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
}
MPI_Bcast
(
&
k
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
theta0
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
k_ub
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
r_ub
[
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
AngleCharmm
::
write_data
(
FILE
*
fp
)
{
for
(
int
i
=
1
;
i
<=
atom
->
nangletypes
;
i
++
)
fprintf
(
fp
,
"%d %g %g %g %g
\n
"
,
i
,
k
[
i
],
theta0
[
i
]
/
MY_PI
*
180.0
,
k_ub
[
i
],
r_ub
[
i
]);
}
/* ---------------------------------------------------------------------- */
double
AngleCharmm
::
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
delxUB
=
x
[
i3
][
0
]
-
x
[
i1
][
0
];
double
delyUB
=
x
[
i3
][
1
]
-
x
[
i1
][
1
];
double
delzUB
=
x
[
i3
][
2
]
-
x
[
i1
][
2
];
domain
->
minimum_image
(
delxUB
,
delyUB
,
delzUB
);
double
rUB
=
sqrt
(
delxUB
*
delxUB
+
delyUB
*
delyUB
+
delzUB
*
delzUB
);
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
dtheta
=
acos
(
c
)
-
theta0
[
type
];
double
tk
=
k
[
type
]
*
dtheta
;
double
dr
=
rUB
-
r_ub
[
type
];
double
rk
=
k_ub
[
type
]
*
dr
;
return
(
tk
*
dtheta
+
rk
*
dr
);
}
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