Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F80965197
bond_fene_expand.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, Sep 3, 12:26
Size
8 KB
Mime Type
text/x-c
Expires
Thu, Sep 5, 12:26 (2 d)
Engine
blob
Format
Raw Data
Handle
20027351
Attached To
rLAMMPS lammps
bond_fene_expand.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.
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "bond_fene_expand.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
BondFENEExpand
::
BondFENEExpand
(
LAMMPS
*
lmp
)
:
Bond
(
lmp
)
{
TWO_1_3
=
pow
(
2.0
,(
1.0
/
3.0
));
}
/* ---------------------------------------------------------------------- */
BondFENEExpand
::~
BondFENEExpand
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
k
);
memory
->
destroy
(
r0
);
memory
->
destroy
(
epsilon
);
memory
->
destroy
(
sigma
);
memory
->
destroy
(
shift
);
}
}
/* ---------------------------------------------------------------------- */
void
BondFENEExpand
::
compute
(
int
eflag
,
int
vflag
)
{
int
i1
,
i2
,
n
,
type
;
double
delx
,
dely
,
delz
,
ebond
,
fbond
;
double
rsq
,
r0sq
,
rlogarg
,
sr2
,
sr6
;
double
r
,
rshift
,
rshiftsq
;
ebond
=
sr6
=
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
];
// force from log term
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
r
=
sqrt
(
rsq
);
rshift
=
r
-
shift
[
type
];
rshiftsq
=
rshift
*
rshift
;
r0sq
=
r0
[
type
]
*
r0
[
type
];
rlogarg
=
1.0
-
rshiftsq
/
r0sq
;
// if r -> r0, then rlogarg < 0.0 which is an error
// issue a warning and reset rlogarg = epsilon
// if r > 2*r0 something serious is wrong, abort
if
(
rlogarg
<
0.1
)
{
char
str
[
128
];
sprintf
(
str
,
"FENE bond too long: "
BIGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
" %g"
,
update
->
ntimestep
,
atom
->
tag
[
i1
],
atom
->
tag
[
i2
],
sqrt
(
rsq
));
error
->
warning
(
FLERR
,
str
,
0
);
if
(
rlogarg
<=
-
3.0
)
error
->
one
(
FLERR
,
"Bad FENE bond"
);
rlogarg
=
0.1
;
}
fbond
=
-
k
[
type
]
*
rshift
/
rlogarg
/
r
;
// force from LJ term
if
(
rshiftsq
<
TWO_1_3
*
sigma
[
type
]
*
sigma
[
type
])
{
sr2
=
sigma
[
type
]
*
sigma
[
type
]
/
rshiftsq
;
sr6
=
sr2
*
sr2
*
sr2
;
fbond
+=
48.0
*
epsilon
[
type
]
*
sr6
*
(
sr6
-
0.5
)
/
rshift
/
r
;
}
// energy
if
(
eflag
)
{
ebond
=
-
0.5
*
k
[
type
]
*
r0sq
*
log
(
rlogarg
);
if
(
rshiftsq
<
TWO_1_3
*
sigma
[
type
]
*
sigma
[
type
])
ebond
+=
4.0
*
epsilon
[
type
]
*
sr6
*
(
sr6
-
1.0
)
+
epsilon
[
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
BondFENEExpand
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
nbondtypes
;
memory
->
create
(
k
,
n
+
1
,
"bond:k"
);
memory
->
create
(
r0
,
n
+
1
,
"bond:r0"
);
memory
->
create
(
epsilon
,
n
+
1
,
"bond:epsilon"
);
memory
->
create
(
sigma
,
n
+
1
,
"bond:sigma"
);
memory
->
create
(
shift
,
n
+
1
,
"bond:shift"
);
memory
->
create
(
setflag
,
n
+
1
,
"bond:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void
BondFENEExpand
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
6
)
error
->
all
(
FLERR
,
"Incorrect args for bond coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
;
force
->
bounds
(
arg
[
0
],
atom
->
nbondtypes
,
ilo
,
ihi
);
double
k_one
=
force
->
numeric
(
FLERR
,
arg
[
1
]);
double
r0_one
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
double
epsilon_one
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
double
sigma_one
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
double
shift_one
=
force
->
numeric
(
FLERR
,
arg
[
5
]);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
k
[
i
]
=
k_one
;
r0
[
i
]
=
r0_one
;
epsilon
[
i
]
=
epsilon_one
;
sigma
[
i
]
=
sigma_one
;
shift
[
i
]
=
shift_one
;
setflag
[
i
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for bond coefficients"
);
}
/* ----------------------------------------------------------------------
check if special_bond settings are valid
------------------------------------------------------------------------- */
void
BondFENEExpand
::
init_style
()
{
// special bonds should be 0 1 1
if
(
force
->
special_lj
[
1
]
!=
0.0
||
force
->
special_lj
[
2
]
!=
1.0
||
force
->
special_lj
[
3
]
!=
1.0
)
{
if
(
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"Use special bonds = 0,1,1 with bond style fene/expand"
);
}
}
/* ---------------------------------------------------------------------- */
double
BondFENEExpand
::
equilibrium_distance
(
int
i
)
{
return
0.97
*
sigma
[
i
]
+
shift
[
i
];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
BondFENEExpand
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
k
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fwrite
(
&
r0
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fwrite
(
&
epsilon
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fwrite
(
&
sigma
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fwrite
(
&
shift
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
BondFENEExpand
::
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
(
&
epsilon
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fread
(
&
sigma
[
1
],
sizeof
(
double
),
atom
->
nbondtypes
,
fp
);
fread
(
&
shift
[
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
(
&
epsilon
[
1
],
atom
->
nbondtypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sigma
[
1
],
atom
->
nbondtypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
shift
[
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
BondFENEExpand
::
write_data
(
FILE
*
fp
)
{
for
(
int
i
=
1
;
i
<=
atom
->
nbondtypes
;
i
++
)
fprintf
(
fp
,
"%d %g %g %g %g %g
\n
"
,
i
,
k
[
i
],
r0
[
i
],
epsilon
[
i
],
sigma
[
i
],
shift
[
i
]);
}
/* ---------------------------------------------------------------------- */
double
BondFENEExpand
::
single
(
int
type
,
double
rsq
,
int
i
,
int
j
,
double
&
fforce
)
{
double
r
=
sqrt
(
rsq
);
double
rshift
=
r
-
shift
[
type
];
double
rshiftsq
=
rshift
*
rshift
;
double
r0sq
=
r0
[
type
]
*
r0
[
type
];
double
rlogarg
=
1.0
-
rshiftsq
/
r0sq
;
// if r -> r0, then rlogarg < 0.0 which is an error
// issue a warning and reset rlogarg = epsilon
// if r > 2*r0 something serious is wrong, abort
if
(
rlogarg
<
0.1
)
{
char
str
[
128
];
sprintf
(
str
,
"FENE bond too long: "
BIGINT_FORMAT
" %g"
,
update
->
ntimestep
,
sqrt
(
rsq
));
error
->
warning
(
FLERR
,
str
,
0
);
if
(
rlogarg
<=
-
3.0
)
error
->
one
(
FLERR
,
"Bad FENE bond"
);
rlogarg
=
0.1
;
}
double
eng
=
-
0.5
*
k
[
type
]
*
r0sq
*
log
(
rlogarg
);
fforce
=
-
k
[
type
]
*
rshift
/
rlogarg
/
r
;
if
(
rshiftsq
<
TWO_1_3
*
sigma
[
type
]
*
sigma
[
type
])
{
double
sr2
,
sr6
;
sr2
=
sigma
[
type
]
*
sigma
[
type
]
/
rshiftsq
;
sr6
=
sr2
*
sr2
*
sr2
;
eng
+=
4.0
*
epsilon
[
type
]
*
sr6
*
(
sr6
-
1.0
)
+
epsilon
[
type
];
fforce
+=
48.0
*
epsilon
[
type
]
*
sr6
*
(
sr6
-
0.5
)
/
rshift
/
r
;
}
return
eng
;
}
Event Timeline
Log In to Comment