Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F79694090
bond_harmonic_shift.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Tue, Aug 27, 19:05
Size
5 KB
Mime Type
text/x-c
Expires
Thu, Aug 29, 19:05 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
20188893
Attached To
rLAMMPS lammps
bond_harmonic_shift.cpp
View Options
/* ----------------------------------------------------------------------
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
];
domain
->
minimum_image
(
delx
,
dely
,
delz
);
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
(
arg
[
1
]);
// energy at minimum
double
r0_one
=
force
->
numeric
(
arg
[
2
]);
// position of minimum
double
r1_one
=
force
->
numeric
(
arg
[
3
]);
// position where energy = 0
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
;
}
/* ---------------------------------------------------------------------- */
double
BondHarmonicShift
::
single
(
int
type
,
double
rsq
,
int
i
,
int
j
)
{
double
r
=
sqrt
(
rsq
);
double
dr
=
r
-
r0
[
type
];
double
dr2
=
r0
[
type
]
-
r1
[
type
];
return
k
[
type
]
*
(
dr
*
dr
-
dr2
*
dr2
);
}
Event Timeline
Log In to Comment