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improper_harmonic.cpp
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rLAMMPS lammps
improper_harmonic.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.
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "improper_harmonic.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
ImproperHarmonic
::
ImproperHarmonic
(
LAMMPS
*
lmp
)
:
Improper
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
ImproperHarmonic
::~
ImproperHarmonic
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
k
);
memory
->
destroy
(
chi
);
}
}
/* ---------------------------------------------------------------------- */
void
ImproperHarmonic
::
compute
(
int
eflag
,
int
vflag
)
{
int
i1
,
i2
,
i3
,
i4
,
n
,
type
;
double
vb1x
,
vb1y
,
vb1z
,
vb2x
,
vb2y
,
vb2z
,
vb3x
,
vb3y
,
vb3z
;
double
eimproper
,
f1
[
3
],
f2
[
3
],
f3
[
3
],
f4
[
3
];
double
ss1
,
ss2
,
ss3
,
r1
,
r2
,
r3
,
c0
,
c1
,
c2
,
s1
,
s2
;
double
s12
,
c
,
s
,
domega
,
a
,
a11
,
a22
,
a33
,
a12
,
a13
,
a23
;
double
sx2
,
sy2
,
sz2
;
eimproper
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
**
improperlist
=
neighbor
->
improperlist
;
int
nimproperlist
=
neighbor
->
nimproperlist
;
int
nlocal
=
atom
->
nlocal
;
int
newton_bond
=
force
->
newton_bond
;
for
(
n
=
0
;
n
<
nimproperlist
;
n
++
)
{
i1
=
improperlist
[
n
][
0
];
i2
=
improperlist
[
n
][
1
];
i3
=
improperlist
[
n
][
2
];
i4
=
improperlist
[
n
][
3
];
type
=
improperlist
[
n
][
4
];
// geometry of 4-body
vb1x
=
x
[
i1
][
0
]
-
x
[
i2
][
0
];
vb1y
=
x
[
i1
][
1
]
-
x
[
i2
][
1
];
vb1z
=
x
[
i1
][
2
]
-
x
[
i2
][
2
];
domain
->
minimum_image
(
vb1x
,
vb1y
,
vb1z
);
vb2x
=
x
[
i3
][
0
]
-
x
[
i2
][
0
];
vb2y
=
x
[
i3
][
1
]
-
x
[
i2
][
1
];
vb2z
=
x
[
i3
][
2
]
-
x
[
i2
][
2
];
domain
->
minimum_image
(
vb2x
,
vb2y
,
vb2z
);
vb3x
=
x
[
i4
][
0
]
-
x
[
i3
][
0
];
vb3y
=
x
[
i4
][
1
]
-
x
[
i3
][
1
];
vb3z
=
x
[
i4
][
2
]
-
x
[
i3
][
2
];
domain
->
minimum_image
(
vb3x
,
vb3y
,
vb3z
);
ss1
=
1.0
/
(
vb1x
*
vb1x
+
vb1y
*
vb1y
+
vb1z
*
vb1z
);
ss2
=
1.0
/
(
vb2x
*
vb2x
+
vb2y
*
vb2y
+
vb2z
*
vb2z
);
ss3
=
1.0
/
(
vb3x
*
vb3x
+
vb3y
*
vb3y
+
vb3z
*
vb3z
);
r1
=
sqrt
(
ss1
);
r2
=
sqrt
(
ss2
);
r3
=
sqrt
(
ss3
);
// sin and cos of angle
c0
=
(
vb1x
*
vb3x
+
vb1y
*
vb3y
+
vb1z
*
vb3z
)
*
r1
*
r3
;
c1
=
(
vb1x
*
vb2x
+
vb1y
*
vb2y
+
vb1z
*
vb2z
)
*
r1
*
r2
;
c2
=
-
(
vb3x
*
vb2x
+
vb3y
*
vb2y
+
vb3z
*
vb2z
)
*
r3
*
r2
;
s1
=
1.0
-
c1
*
c1
;
if
(
s1
<
SMALL
)
s1
=
SMALL
;
s1
=
1.0
/
s1
;
s2
=
1.0
-
c2
*
c2
;
if
(
s2
<
SMALL
)
s2
=
SMALL
;
s2
=
1.0
/
s2
;
s12
=
sqrt
(
s1
*
s2
);
c
=
(
c1
*
c2
+
c0
)
*
s12
;
// 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
,
"Improper problem: %d "
BIGINT_FORMAT
" %d %d %d %d"
,
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
;
s
=
sqrt
(
1.0
-
c
*
c
);
if
(
s
<
SMALL
)
s
=
SMALL
;
// force & energy
domega
=
acos
(
c
)
-
chi
[
type
];
a
=
k
[
type
]
*
domega
;
if
(
eflag
)
eimproper
=
a
*
domega
;
a
=
-
a
*
2.0
/
s
;
c
=
c
*
a
;
s12
=
s12
*
a
;
a11
=
c
*
ss1
*
s1
;
a22
=
-
ss2
*
(
2.0
*
c0
*
s12
-
c
*
(
s1
+
s2
));
a33
=
c
*
ss3
*
s2
;
a12
=
-
r1
*
r2
*
(
c1
*
c
*
s1
+
c2
*
s12
);
a13
=
-
r1
*
r3
*
s12
;
a23
=
r2
*
r3
*
(
c2
*
c
*
s2
+
c1
*
s12
);
sx2
=
a22
*
vb2x
+
a23
*
vb3x
+
a12
*
vb1x
;
sy2
=
a22
*
vb2y
+
a23
*
vb3y
+
a12
*
vb1y
;
sz2
=
a22
*
vb2z
+
a23
*
vb3z
+
a12
*
vb1z
;
f1
[
0
]
=
a12
*
vb2x
+
a13
*
vb3x
+
a11
*
vb1x
;
f1
[
1
]
=
a12
*
vb2y
+
a13
*
vb3y
+
a11
*
vb1y
;
f1
[
2
]
=
a12
*
vb2z
+
a13
*
vb3z
+
a11
*
vb1z
;
f2
[
0
]
=
-
sx2
-
f1
[
0
];
f2
[
1
]
=
-
sy2
-
f1
[
1
];
f2
[
2
]
=
-
sz2
-
f1
[
2
];
f4
[
0
]
=
a23
*
vb2x
+
a33
*
vb3x
+
a13
*
vb1x
;
f4
[
1
]
=
a23
*
vb2y
+
a33
*
vb3y
+
a13
*
vb1y
;
f4
[
2
]
=
a23
*
vb2z
+
a33
*
vb3z
+
a13
*
vb1z
;
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
,
eimproper
,
f1
,
f3
,
f4
,
vb1x
,
vb1y
,
vb1z
,
vb2x
,
vb2y
,
vb2z
,
vb3x
,
vb3y
,
vb3z
);
}
}
/* ---------------------------------------------------------------------- */
void
ImproperHarmonic
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
nimpropertypes
;
memory
->
create
(
k
,
n
+
1
,
"improper:k"
);
memory
->
create
(
chi
,
n
+
1
,
"improper:chi"
);
memory
->
create
(
setflag
,
n
+
1
,
"improper:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void
ImproperHarmonic
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
3
)
error
->
all
(
FLERR
,
"Incorrect args for improper coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
;
force
->
bounds
(
arg
[
0
],
atom
->
nimpropertypes
,
ilo
,
ihi
);
double
k_one
=
force
->
numeric
(
arg
[
1
]);
double
chi_one
=
force
->
numeric
(
arg
[
2
]);
// convert chi from degrees to radians
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
k
[
i
]
=
k_one
;
chi
[
i
]
=
chi_one
/
180.0
*
MY_PI
;
setflag
[
i
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for improper coefficients"
);
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void
ImproperHarmonic
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nimpropertypes
,
fp
);
fwrite
(
&
chi
[
1
],
sizeof
(
double
),
atom
->
nimpropertypes
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void
ImproperHarmonic
::
read_restart
(
FILE
*
fp
)
{
allocate
();
if
(
comm
->
me
==
0
)
{
fread
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nimpropertypes
,
fp
);
fread
(
&
chi
[
1
],
sizeof
(
double
),
atom
->
nimpropertypes
,
fp
);
}
MPI_Bcast
(
&
k
[
1
],
atom
->
nimpropertypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
chi
[
1
],
atom
->
nimpropertypes
,
MPI_DOUBLE
,
0
,
world
);
for
(
int
i
=
1
;
i
<=
atom
->
nimpropertypes
;
i
++
)
setflag
[
i
]
=
1
;
}
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