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rLAMMPS lammps
dihedral_quadratic.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: Loukas D. Peristeras (Scienomics SARL)
[ based on dihedral_helix.cpp Paul Crozier (SNL) ]
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "dihedral_quadratic.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define TOLERANCE 0.05
#define SMALL 0.001
#define SMALLER 0.00001
/* ---------------------------------------------------------------------- */
DihedralQuadratic
::
DihedralQuadratic
(
LAMMPS
*
lmp
)
:
Dihedral
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
DihedralQuadratic
::~
DihedralQuadratic
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
k
);
memory
->
destroy
(
phi0
);
}
}
/* ---------------------------------------------------------------------- */
void
DihedralQuadratic
::
compute
(
int
eflag
,
int
vflag
)
{
int
i1
,
i2
,
i3
,
i4
,
n
,
type
;
double
vb1x
,
vb1y
,
vb1z
,
vb2x
,
vb2y
,
vb2z
,
vb3x
,
vb3y
,
vb3z
,
vb2xm
,
vb2ym
,
vb2zm
;
double
edihedral
,
f1
[
3
],
f2
[
3
],
f3
[
3
],
f4
[
3
];
double
sb1
,
sb2
,
sb3
,
rb1
,
rb3
,
c0
,
b1mag2
,
b1mag
,
b2mag2
;
double
b2mag
,
b3mag2
,
b3mag
,
ctmp
,
r12c1
,
c1mag
,
r12c2
;
double
c2mag
,
sc1
,
sc2
,
s1
,
s12
,
c
,
p
,
pd
,
a
,
a11
,
a22
;
double
a33
,
a12
,
a13
,
a23
,
sx2
,
sy2
,
sz2
;
double
s2
,
cx
,
cy
,
cz
,
cmag
,
dx
,
phi
,
si
,
sin2
;
edihedral
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
**
dihedrallist
=
neighbor
->
dihedrallist
;
int
ndihedrallist
=
neighbor
->
ndihedrallist
;
int
nlocal
=
atom
->
nlocal
;
int
newton_bond
=
force
->
newton_bond
;
for
(
n
=
0
;
n
<
ndihedrallist
;
n
++
)
{
i1
=
dihedrallist
[
n
][
0
];
i2
=
dihedrallist
[
n
][
1
];
i3
=
dihedrallist
[
n
][
2
];
i4
=
dihedrallist
[
n
][
3
];
type
=
dihedrallist
[
n
][
4
];
// 1st bond
vb1x
=
x
[
i1
][
0
]
-
x
[
i2
][
0
];
vb1y
=
x
[
i1
][
1
]
-
x
[
i2
][
1
];
vb1z
=
x
[
i1
][
2
]
-
x
[
i2
][
2
];
// 2nd bond
vb2x
=
x
[
i3
][
0
]
-
x
[
i2
][
0
];
vb2y
=
x
[
i3
][
1
]
-
x
[
i2
][
1
];
vb2z
=
x
[
i3
][
2
]
-
x
[
i2
][
2
];
vb2xm
=
-
vb2x
;
vb2ym
=
-
vb2y
;
vb2zm
=
-
vb2z
;
// 3rd bond
vb3x
=
x
[
i4
][
0
]
-
x
[
i3
][
0
];
vb3y
=
x
[
i4
][
1
]
-
x
[
i3
][
1
];
vb3z
=
x
[
i4
][
2
]
-
x
[
i3
][
2
];
// c0 calculation
sb1
=
1.0
/
(
vb1x
*
vb1x
+
vb1y
*
vb1y
+
vb1z
*
vb1z
);
sb2
=
1.0
/
(
vb2x
*
vb2x
+
vb2y
*
vb2y
+
vb2z
*
vb2z
);
sb3
=
1.0
/
(
vb3x
*
vb3x
+
vb3y
*
vb3y
+
vb3z
*
vb3z
);
rb1
=
sqrt
(
sb1
);
rb3
=
sqrt
(
sb3
);
c0
=
(
vb1x
*
vb3x
+
vb1y
*
vb3y
+
vb1z
*
vb3z
)
*
rb1
*
rb3
;
// 1st and 2nd angle
b1mag2
=
vb1x
*
vb1x
+
vb1y
*
vb1y
+
vb1z
*
vb1z
;
b1mag
=
sqrt
(
b1mag2
);
b2mag2
=
vb2x
*
vb2x
+
vb2y
*
vb2y
+
vb2z
*
vb2z
;
b2mag
=
sqrt
(
b2mag2
);
b3mag2
=
vb3x
*
vb3x
+
vb3y
*
vb3y
+
vb3z
*
vb3z
;
b3mag
=
sqrt
(
b3mag2
);
ctmp
=
vb1x
*
vb2x
+
vb1y
*
vb2y
+
vb1z
*
vb2z
;
r12c1
=
1.0
/
(
b1mag
*
b2mag
);
c1mag
=
ctmp
*
r12c1
;
ctmp
=
vb2xm
*
vb3x
+
vb2ym
*
vb3y
+
vb2zm
*
vb3z
;
r12c2
=
1.0
/
(
b2mag
*
b3mag
);
c2mag
=
ctmp
*
r12c2
;
// cos and sin of 2 angles and final c
sin2
=
MAX
(
1.0
-
c1mag
*
c1mag
,
0.0
);
sc1
=
sqrt
(
sin2
);
if
(
sc1
<
SMALL
)
sc1
=
SMALL
;
sc1
=
1.0
/
sc1
;
sin2
=
MAX
(
1.0
-
c2mag
*
c2mag
,
0.0
);
sc2
=
sqrt
(
sin2
);
if
(
sc2
<
SMALL
)
sc2
=
SMALL
;
sc2
=
1.0
/
sc2
;
s1
=
sc1
*
sc1
;
s2
=
sc2
*
sc2
;
s12
=
sc1
*
sc2
;
c
=
(
c0
+
c1mag
*
c2mag
)
*
s12
;
cx
=
vb1y
*
vb2z
-
vb1z
*
vb2y
;
cy
=
vb1z
*
vb2x
-
vb1x
*
vb2z
;
cz
=
vb1x
*
vb2y
-
vb1y
*
vb2x
;
cmag
=
sqrt
(
cx
*
cx
+
cy
*
cy
+
cz
*
cz
);
dx
=
(
cx
*
vb3x
+
cy
*
vb3y
+
cz
*
vb3z
)
/
cmag
/
b3mag
;
// error check
if
(
c
>
1.0
+
TOLERANCE
||
c
<
(
-
1.0
-
TOLERANCE
))
{
int
me
;
MPI_Comm_rank
(
world
,
&
me
);
if
(
screen
)
{
char
str
[
128
];
sprintf
(
str
,
"Dihedral problem: %d "
BIGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
,
me
,
update
->
ntimestep
,
atom
->
tag
[
i1
],
atom
->
tag
[
i2
],
atom
->
tag
[
i3
],
atom
->
tag
[
i4
]);
error
->
warning
(
FLERR
,
str
,
0
);
fprintf
(
screen
,
" 1st atom: %d %g %g %g
\n
"
,
me
,
x
[
i1
][
0
],
x
[
i1
][
1
],
x
[
i1
][
2
]);
fprintf
(
screen
,
" 2nd atom: %d %g %g %g
\n
"
,
me
,
x
[
i2
][
0
],
x
[
i2
][
1
],
x
[
i2
][
2
]);
fprintf
(
screen
,
" 3rd atom: %d %g %g %g
\n
"
,
me
,
x
[
i3
][
0
],
x
[
i3
][
1
],
x
[
i3
][
2
]);
fprintf
(
screen
,
" 4th atom: %d %g %g %g
\n
"
,
me
,
x
[
i4
][
0
],
x
[
i4
][
1
],
x
[
i4
][
2
]);
}
}
if
(
c
>
1.0
)
c
=
1.0
;
if
(
c
<
-
1.0
)
c
=
-
1.0
;
// force & energy
// p = k ( phi- phi0)^2
// pd = dp/dc
phi
=
acos
(
c
);
if
(
dx
<
0.0
)
phi
*=
-
1.0
;
si
=
sin
(
phi
);
double
dphi
=
phi
-
phi0
[
type
];
p
=
k
[
type
]
*
dphi
;
if
(
fabs
(
si
)
<
SMALLER
)
{
pd
=
-
2.0
*
k
[
type
];
}
else
{
pd
=
-
2.0
*
p
/
si
;
}
p
=
p
*
dphi
;
if
(
eflag
)
edihedral
=
p
;
a
=
pd
;
c
=
c
*
a
;
s12
=
s12
*
a
;
a11
=
c
*
sb1
*
s1
;
a22
=
-
sb2
*
(
2.0
*
c0
*
s12
-
c
*
(
s1
+
s2
));
a33
=
c
*
sb3
*
s2
;
a12
=
-
r12c1
*
(
c1mag
*
c
*
s1
+
c2mag
*
s12
);
a13
=
-
rb1
*
rb3
*
s12
;
a23
=
r12c2
*
(
c2mag
*
c
*
s2
+
c1mag
*
s12
);
sx2
=
a12
*
vb1x
+
a22
*
vb2x
+
a23
*
vb3x
;
sy2
=
a12
*
vb1y
+
a22
*
vb2y
+
a23
*
vb3y
;
sz2
=
a12
*
vb1z
+
a22
*
vb2z
+
a23
*
vb3z
;
f1
[
0
]
=
a11
*
vb1x
+
a12
*
vb2x
+
a13
*
vb3x
;
f1
[
1
]
=
a11
*
vb1y
+
a12
*
vb2y
+
a13
*
vb3y
;
f1
[
2
]
=
a11
*
vb1z
+
a12
*
vb2z
+
a13
*
vb3z
;
f2
[
0
]
=
-
sx2
-
f1
[
0
];
f2
[
1
]
=
-
sy2
-
f1
[
1
];
f2
[
2
]
=
-
sz2
-
f1
[
2
];
f4
[
0
]
=
a13
*
vb1x
+
a23
*
vb2x
+
a33
*
vb3x
;
f4
[
1
]
=
a13
*
vb1y
+
a23
*
vb2y
+
a33
*
vb3y
;
f4
[
2
]
=
a13
*
vb1z
+
a23
*
vb2z
+
a33
*
vb3z
;
f3
[
0
]
=
sx2
-
f4
[
0
];
f3
[
1
]
=
sy2
-
f4
[
1
];
f3
[
2
]
=
sz2
-
f4
[
2
];
// apply force to each of 4 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
]
+=
f2
[
0
];
f
[
i2
][
1
]
+=
f2
[
1
];
f
[
i2
][
2
]
+=
f2
[
2
];
}
if
(
newton_bond
||
i3
<
nlocal
)
{
f
[
i3
][
0
]
+=
f3
[
0
];
f
[
i3
][
1
]
+=
f3
[
1
];
f
[
i3
][
2
]
+=
f3
[
2
];
}
if
(
newton_bond
||
i4
<
nlocal
)
{
f
[
i4
][
0
]
+=
f4
[
0
];
f
[
i4
][
1
]
+=
f4
[
1
];
f
[
i4
][
2
]
+=
f4
[
2
];
}
if
(
evflag
)
ev_tally
(
i1
,
i2
,
i3
,
i4
,
nlocal
,
newton_bond
,
edihedral
,
f1
,
f3
,
f4
,
vb1x
,
vb1y
,
vb1z
,
vb2x
,
vb2y
,
vb2z
,
vb3x
,
vb3y
,
vb3z
);
}
}
/* ---------------------------------------------------------------------- */
void
DihedralQuadratic
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ndihedraltypes
;
memory
->
create
(
k
,
n
+
1
,
"dihedral:k"
);
memory
->
create
(
phi0
,
n
+
1
,
"dihedral:phi0"
);
memory
->
create
(
setflag
,
n
+
1
,
"dihedral:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void
DihedralQuadratic
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
3
)
error
->
all
(
FLERR
,
"Incorrect args for dihedral coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
;
force
->
bounds
(
arg
[
0
],
atom
->
ndihedraltypes
,
ilo
,
ihi
);
double
k_one
=
force
->
numeric
(
FLERR
,
arg
[
1
]);
double
phi0_one
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
// require k >= 0
if
(
k_one
<
0.0
)
error
->
all
(
FLERR
,
"Incorrect coefficient arg for dihedral coefficients"
);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
k
[
i
]
=
k_one
;
phi0
[
i
]
=
phi0_one
;
setflag
[
i
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for dihedral coefficients"
);
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void
DihedralQuadratic
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
k
[
1
],
sizeof
(
double
),
atom
->
ndihedraltypes
,
fp
);
fwrite
(
&
phi0
[
1
],
sizeof
(
double
),
atom
->
ndihedraltypes
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void
DihedralQuadratic
::
read_restart
(
FILE
*
fp
)
{
allocate
();
if
(
comm
->
me
==
0
)
{
fread
(
&
k
[
1
],
sizeof
(
double
),
atom
->
ndihedraltypes
,
fp
);
fread
(
&
phi0
[
1
],
sizeof
(
int
),
atom
->
ndihedraltypes
,
fp
);
}
MPI_Bcast
(
&
k
[
1
],
atom
->
ndihedraltypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
phi0
[
1
],
atom
->
ndihedraltypes
,
MPI_DOUBLE
,
0
,
world
);
for
(
int
i
=
1
;
i
<=
atom
->
ndihedraltypes
;
i
++
)
setflag
[
i
]
=
1
;
}
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