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bond_fene_expand.cpp
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Mon, Oct 7, 16:39
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Wed, Oct 9, 16:39 (1 d, 23 h)
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rLAMMPS lammps
bond_fene_expand.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 <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
;
}
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