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rLAMMPS lammps
angle_class2.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: Eric Simon (Cray)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "angle_class2.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
/* ---------------------------------------------------------------------- */
AngleClass2
::
AngleClass2
(
LAMMPS
*
lmp
)
:
Angle
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
AngleClass2
::~
AngleClass2
()
{
if
(
allocated
)
{
memory
->
sfree
(
setflag
);
memory
->
sfree
(
setflag_a
);
memory
->
sfree
(
setflag_bb
);
memory
->
sfree
(
setflag_ba
);
memory
->
sfree
(
theta0
);
memory
->
sfree
(
k2
);
memory
->
sfree
(
k3
);
memory
->
sfree
(
k4
);
memory
->
sfree
(
bb_k
);
memory
->
sfree
(
bb_r1
);
memory
->
sfree
(
bb_r2
);
memory
->
sfree
(
ba_k1
);
memory
->
sfree
(
ba_k2
);
memory
->
sfree
(
ba_r1
);
memory
->
sfree
(
ba_r2
);
}
}
/* ---------------------------------------------------------------------- */
void
AngleClass2
::
compute
(
int
eflag
,
int
vflag
)
{
int
i1
,
i2
,
i3
,
n
,
type
,
factor
;
double
delx1
,
dely1
,
delz1
,
delx2
,
dely2
,
delz2
,
rfactor
;
double
dtheta
,
dtheta2
,
dtheta3
,
dtheta4
,
de_angle
;
double
dr1
,
dr2
,
tk1
,
tk2
,
aa1
,
aa2
,
aa11
,
aa12
,
aa21
,
aa22
;
double
rsq1
,
rsq2
,
r1
,
r2
,
c
,
s
,
a
,
a11
,
a12
,
a22
,
b1
,
b2
,
vx1
,
vx2
,
vy1
,
vy2
,
vz1
,
vz2
;
double
vx11
,
vx12
,
vy11
,
vy12
,
vz11
,
vz12
,
vx21
,
vx22
,
vy21
,
vy22
,
vz21
,
vz22
;
energy
=
0.0
;
if
(
vflag
)
for
(
n
=
0
;
n
<
6
;
n
++
)
virial
[
n
]
=
0.0
;
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
];
if
(
newton_bond
)
factor
=
3
;
else
{
factor
=
0
;
if
(
i1
<
nlocal
)
factor
++
;
if
(
i2
<
nlocal
)
factor
++
;
if
(
i3
<
nlocal
)
factor
++
;
}
rfactor
=
factor
/
3.0
;
// 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
);
// 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
;
// force & energy for angle term
dtheta
=
acos
(
c
)
-
theta0
[
type
];
dtheta2
=
dtheta
*
dtheta
;
dtheta3
=
dtheta2
*
dtheta
;
dtheta4
=
dtheta3
*
dtheta
;
de_angle
=
2.0
*
k2
[
type
]
*
dtheta
+
3.0
*
k3
[
type
]
*
dtheta2
+
4.0
*
k4
[
type
]
*
dtheta3
;
a
=
de_angle
*
s
;
a11
=
a
*
c
/
rsq1
;
a12
=
-
a
/
(
r1
*
r2
);
a22
=
a
*
c
/
rsq2
;
vx1
=
a11
*
delx1
+
a12
*
delx2
;
vy1
=
a11
*
dely1
+
a12
*
dely2
;
vz1
=
a11
*
delz1
+
a12
*
delz2
;
vx2
=
a22
*
delx2
+
a12
*
delx1
;
vy2
=
a22
*
dely2
+
a12
*
dely1
;
vz2
=
a22
*
delz2
+
a12
*
delz1
;
if
(
eflag
)
energy
+=
rfactor
*
(
k2
[
type
]
*
dtheta2
+
k3
[
type
]
*
dtheta3
+
k4
[
type
]
*
dtheta4
);
// force & energy for bond-bond term
dr1
=
r1
-
bb_r1
[
type
];
dr2
=
r2
-
bb_r2
[
type
];
tk1
=
bb_k
[
type
]
*
dr1
;
tk2
=
bb_k
[
type
]
*
dr2
;
vx1
+=
delx1
*
tk2
/
r1
;
vy1
+=
dely1
*
tk2
/
r1
;
vz1
+=
delz1
*
tk2
/
r1
;
vx2
+=
delx2
*
tk1
/
r2
;
vy2
+=
dely2
*
tk1
/
r2
;
vz2
+=
delz2
*
tk1
/
r2
;
if
(
eflag
)
energy
+=
rfactor
*
bb_k
[
type
]
*
dr1
*
dr2
;
// force & energy for bond-angle term
aa1
=
s
*
dr1
*
ba_k1
[
type
];
aa2
=
s
*
dr2
*
ba_k2
[
type
];
aa11
=
aa1
*
c
/
rsq1
;
aa12
=
-
aa1
/
(
r1
*
r2
);
aa21
=
aa2
*
c
/
rsq1
;
aa22
=
-
aa2
/
(
r1
*
r2
);
vx11
=
(
aa11
*
delx1
)
+
(
aa12
*
delx2
);
vx12
=
(
aa21
*
delx1
)
+
(
aa22
*
delx2
);
vy11
=
(
aa11
*
dely1
)
+
(
aa12
*
dely2
);
vy12
=
(
aa21
*
dely1
)
+
(
aa22
*
dely2
);
vz11
=
(
aa11
*
delz1
)
+
(
aa12
*
delz2
);
vz12
=
(
aa21
*
delz1
)
+
(
aa22
*
delz2
);
aa11
=
aa1
*
c
/
rsq2
;
aa21
=
aa2
*
c
/
rsq2
;
vx21
=
(
aa11
*
delx2
)
+
(
aa12
*
delx1
);
vx22
=
(
aa21
*
delx2
)
+
(
aa22
*
delx1
);
vy21
=
(
aa11
*
dely2
)
+
(
aa12
*
dely1
);
vy22
=
(
aa21
*
dely2
)
+
(
aa22
*
dely1
);
vz21
=
(
aa11
*
delz2
)
+
(
aa12
*
delz1
);
vz22
=
(
aa21
*
delz2
)
+
(
aa22
*
delz1
);
b1
=
ba_k1
[
type
]
*
dtheta
/
r1
;
b2
=
ba_k2
[
type
]
*
dtheta
/
r2
;
vx1
+=
vx11
+
b1
*
delx1
+
vx12
;
vy1
+=
vy11
+
b1
*
dely1
+
vy12
;
vz1
+=
vz11
+
b1
*
delz1
+
vz12
;
vx2
+=
vx21
+
b2
*
delx2
+
vx22
;
vy2
+=
vy21
+
b2
*
dely2
+
vy22
;
vz2
+=
vz21
+
b2
*
delz2
+
vz22
;
if
(
eflag
)
energy
+=
rfactor
*
((
ba_k1
[
type
]
*
dr1
*
dtheta
)
+
(
ba_k2
[
type
]
*
dr2
*
dtheta
));
// apply force to each of 3 atoms
if
(
newton_bond
||
i1
<
nlocal
)
{
f
[
i1
][
0
]
-=
vx1
;
f
[
i1
][
1
]
-=
vy1
;
f
[
i1
][
2
]
-=
vz1
;
}
if
(
newton_bond
||
i2
<
nlocal
)
{
f
[
i2
][
0
]
+=
vx1
+
vx2
;
f
[
i2
][
1
]
+=
vy1
+
vy2
;
f
[
i2
][
2
]
+=
vz1
+
vz2
;
}
if
(
newton_bond
||
i3
<
nlocal
)
{
f
[
i3
][
0
]
-=
vx2
;
f
[
i3
][
1
]
-=
vy2
;
f
[
i3
][
2
]
-=
vz2
;
}
// virial contribution
if
(
vflag
)
{
virial
[
0
]
-=
rfactor
*
(
delx1
*
vx1
+
delx2
*
vx2
);
virial
[
1
]
-=
rfactor
*
(
dely1
*
vy1
+
dely2
*
vy2
);
virial
[
2
]
-=
rfactor
*
(
delz1
*
vz1
+
delz2
*
vz2
);
virial
[
3
]
-=
rfactor
*
(
delx1
*
vy1
+
delx2
*
vy2
);
virial
[
4
]
-=
rfactor
*
(
delx1
*
vz1
+
delx2
*
vz2
);
virial
[
5
]
-=
rfactor
*
(
dely1
*
vz1
+
dely2
*
vz2
);
}
}
}
/* ---------------------------------------------------------------------- */
void
AngleClass2
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
nangletypes
;
theta0
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"angle:theta0"
);
k2
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"angle:k2"
);
k3
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"angle:k3"
);
k4
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"angle:k4"
);
bb_k
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"angle:bb_k"
);
bb_r1
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"angle:bb_r1"
);
bb_r2
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"angle:bb_r2"
);
ba_k1
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"angle:ba_k1"
);
ba_k2
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"angle:ba_k2"
);
ba_r1
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"angle:ba_r1"
);
ba_r2
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"angle:ba_r2"
);
setflag
=
(
int
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
int
),
"angle:setflag"
);
setflag_a
=
(
int
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
int
),
"angle:setflag_a"
);
setflag_bb
=
(
int
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
int
),
"angle:setflag_bb"
);
setflag_ba
=
(
int
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
int
),
"angle:setflag_ba"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
setflag_a
[
i
]
=
setflag_bb
[
i
]
=
setflag_ba
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
which = 0 -> Angle coeffs
which = 1 -> BondBond coeffs
which = 2 -> BondAngle coeffs
------------------------------------------------------------------------- */
void
AngleClass2
::
coeff
(
int
which
,
int
narg
,
char
**
arg
)
{
if
(
which
<
0
||
which
>
2
)
error
->
all
(
"Invalid coeffs for this angle style"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
;
force
->
bounds
(
arg
[
0
],
atom
->
nangletypes
,
ilo
,
ihi
);
int
count
=
0
;
if
(
which
==
0
)
{
if
(
narg
!=
5
)
error
->
all
(
"Incorrect args for angle coefficients"
);
double
theta0_one
=
atof
(
arg
[
1
]);
double
k2_one
=
atof
(
arg
[
2
]);
double
k3_one
=
atof
(
arg
[
3
]);
double
k4_one
=
atof
(
arg
[
4
]);
// convert theta0 from degrees to radians
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
theta0
[
i
]
=
theta0_one
/
180.0
*
PI
;
k2
[
i
]
=
k2_one
;
k3
[
i
]
=
k3_one
;
k4
[
i
]
=
k4_one
;
setflag_a
[
i
]
=
1
;
count
++
;
}
}
if
(
which
==
1
)
{
if
(
narg
!=
4
)
error
->
all
(
"Incorrect args for angle coefficients"
);
double
bb_k_one
=
atof
(
arg
[
1
]);
double
bb_r1_one
=
atof
(
arg
[
2
]);
double
bb_r2_one
=
atof
(
arg
[
3
]);
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
bb_k
[
i
]
=
bb_k_one
;
bb_r1
[
i
]
=
bb_r1_one
;
bb_r2
[
i
]
=
bb_r2_one
;
setflag_bb
[
i
]
=
1
;
count
++
;
}
}
if
(
which
==
2
)
{
if
(
narg
!=
5
)
error
->
all
(
"Incorrect args for angle coefficients"
);
double
ba_k1_one
=
atof
(
arg
[
1
]);
double
ba_k2_one
=
atof
(
arg
[
2
]);
double
ba_r1_one
=
atof
(
arg
[
3
]);
double
ba_r2_one
=
atof
(
arg
[
4
]);
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
ba_k1
[
i
]
=
ba_k1_one
;
ba_k2
[
i
]
=
ba_k2_one
;
ba_r1
[
i
]
=
ba_r1_one
;
ba_r2
[
i
]
=
ba_r2_one
;
setflag_ba
[
i
]
=
1
;
count
++
;
}
}
if
(
count
==
0
)
error
->
all
(
"Incorrect args for angle coefficients"
);
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
if
(
setflag_a
[
i
]
==
1
&&
setflag_bb
[
i
]
==
1
&&
setflag_ba
[
i
]
==
1
)
setflag
[
i
]
=
1
;
}
/* ---------------------------------------------------------------------- */
double
AngleClass2
::
equilibrium_angle
(
int
i
)
{
return
theta0
[
i
];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void
AngleClass2
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
theta0
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
k2
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
k3
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
k4
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
bb_k
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
bb_r1
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
bb_r2
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
ba_k1
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
ba_k2
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
ba_r1
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fwrite
(
&
ba_r2
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void
AngleClass2
::
read_restart
(
FILE
*
fp
)
{
allocate
();
if
(
comm
->
me
==
0
)
{
fread
(
&
theta0
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
k2
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
k3
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
k4
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
bb_k
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
bb_r1
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
bb_r2
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
ba_k1
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
ba_k2
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
ba_r1
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
fread
(
&
ba_r2
[
1
],
sizeof
(
double
),
atom
->
nangletypes
,
fp
);
}
MPI_Bcast
(
&
theta0
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
k2
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
k3
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
k4
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
bb_k
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
bb_r1
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
bb_r2
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
ba_k1
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
ba_k2
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
ba_r1
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
ba_r2
[
1
],
atom
->
nangletypes
,
MPI_DOUBLE
,
0
,
world
);
for
(
int
i
=
1
;
i
<=
atom
->
nangletypes
;
i
++
)
setflag
[
i
]
=
1
;
}
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