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bond_harmonic_shift.cpp
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rLAMMPS lammps
bond_harmonic_shift.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: Carsten Svaneborg, science@zqex.dk
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "bond_harmonic_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
;
/* ---------------------------------------------------------------------- */
BondHarmonicShift
::
BondHarmonicShift
(
LAMMPS
*
lmp
)
:
Bond
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
BondHarmonicShift
::~
BondHarmonicShift
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
k
);
memory
->
destroy
(
r0
);
memory
->
destroy
(
r1
);
}
}
/* ---------------------------------------------------------------------- */
void
BondHarmonicShift
::
compute
(
int
eflag
,
int
vflag
)
{
int
i1
,
i2
,
n
,
type
;
double
delx
,
dely
,
delz
,
ebond
,
fbond
;
double
rsq
,
r
,
dr
,
rk
;
ebond
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
**
bondlist
=
neighbor
->
bondlist
;
int
nbondlist
=
neighbor
->
nbondlist
;
int
nlocal
=
atom
->
nlocal
;
int
newton_bond
=
force
->
newton_bond
;
for
(
n
=
0
;
n
<
nbondlist
;
n
++
)
{
i1
=
bondlist
[
n
][
0
];
i2
=
bondlist
[
n
][
1
];
type
=
bondlist
[
n
][
2
];
delx
=
x
[
i1
][
0
]
-
x
[
i2
][
0
];
dely
=
x
[
i1
][
1
]
-
x
[
i2
][
1
];
delz
=
x
[
i1
][
2
]
-
x
[
i2
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
r
=
sqrt
(
rsq
);
dr
=
r
-
r0
[
type
];
rk
=
k
[
type
]
*
dr
;
// force & energy
if
(
r
>
0.0
)
fbond
=
-
2.0
*
rk
/
r
;
else
fbond
=
0.0
;
if
(
eflag
)
ebond
=
k
[
type
]
*
(
dr
*
dr
-
(
r0
[
type
]
-
r1
[
type
])
*
(
r0
[
type
]
-
r1
[
type
])
);
// apply force to each of 2 atoms
if
(
newton_bond
||
i1
<
nlocal
)
{
f
[
i1
][
0
]
+=
delx
*
fbond
;
f
[
i1
][
1
]
+=
dely
*
fbond
;
f
[
i1
][
2
]
+=
delz
*
fbond
;
}
if
(
newton_bond
||
i2
<
nlocal
)
{
f
[
i2
][
0
]
-=
delx
*
fbond
;
f
[
i2
][
1
]
-=
dely
*
fbond
;
f
[
i2
][
2
]
-=
delz
*
fbond
;
}
if
(
evflag
)
ev_tally
(
i1
,
i2
,
nlocal
,
newton_bond
,
ebond
,
fbond
,
delx
,
dely
,
delz
);
}
}
/* ---------------------------------------------------------------------- */
void
BondHarmonicShift
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
nbondtypes
;
memory
->
create
(
k
,
n
+
1
,
"bond:k"
);
memory
->
create
(
r0
,
n
+
1
,
"bond:r0"
);
memory
->
create
(
r1
,
n
+
1
,
"bond:r1"
);
memory
->
create
(
setflag
,
n
+
1
,
"bond:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void
BondHarmonicShift
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
4
)
error
->
all
(
FLERR
,
"Incorrect args for bond coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
;
force
->
bounds
(
arg
[
0
],
atom
->
nbondtypes
,
ilo
,
ihi
);
double
Umin
=
force
->
numeric
(
FLERR
,
arg
[
1
]);
// energy at minimum
double
r0_one
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
// position of minimum
double
r1_one
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
// position where energy = 0
if
(
r0_one
==
r1_one
)
error
->
all
(
FLERR
,
"Bond harmonic/shift r0 and r1 must be different"
);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
k
[
i
]
=
Umin
/
((
r0_one
-
r1_one
)
*
(
r0_one
-
r1_one
));
r0
[
i
]
=
r0_one
;
r1
[
i
]
=
r1_one
;
setflag
[
i
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for bond coefficients"
);
}
/* ----------------------------------------------------------------------
return an equilbrium bond length
------------------------------------------------------------------------- */
double
BondHarmonicShift
::
equilibrium_distance
(
int
i
)
{
return
r0
[
i
];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void
BondHarmonicShift
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fwrite
(
&
r0
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fwrite
(
&
r1
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void
BondHarmonicShift
::
read_restart
(
FILE
*
fp
)
{
allocate
();
if
(
comm
->
me
==
0
)
{
fread
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fread
(
&
r0
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fread
(
&
r1
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
}
MPI_Bcast
(
&
k
[
1
],
atom
->
nbondtypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
r0
[
1
],
atom
->
nbondtypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
r1
[
1
],
atom
->
nbondtypes
,
MPI_DOUBLE
,
0
,
world
);
for
(
int
i
=
1
;
i
<=
atom
->
nbondtypes
;
i
++
)
setflag
[
i
]
=
1
;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void
BondHarmonicShift
::
write_data
(
FILE
*
fp
)
{
for
(
int
i
=
1
;
i
<=
atom
->
nbondtypes
;
i
++
)
{
double
d2
=
(
r0
[
i
]
-
r1
[
i
])
*
(
r0
[
i
]
-
r1
[
i
]);
fprintf
(
fp
,
"%d %g %g %g
\n
"
,
i
,
k
[
i
]
*
d2
,
r0
[
i
],
r1
[
i
]);
}
}
/* ---------------------------------------------------------------------- */
double
BondHarmonicShift
::
single
(
int
type
,
double
rsq
,
int
i
,
int
j
,
double
&
fforce
)
{
double
r
=
sqrt
(
rsq
);
double
dr
=
r
-
r0
[
type
];
double
dr2
=
r0
[
type
]
-
r1
[
type
];
fforce
=
-
2.0
*
k
[
type
]
*
dr
/
r
;
return
k
[
type
]
*
(
dr
*
dr
-
dr2
*
dr2
);
}
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