Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F70112802
pair_yukawa.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
Fri, Jul 5, 08:14
Size
9 KB
Mime Type
text/x-c
Expires
Sun, Jul 7, 08:14 (2 d)
Engine
blob
Format
Raw Data
Handle
18792399
Attached To
rLAMMPS lammps
pair_yukawa.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 "pair_yukawa.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
PairYukawa
::
PairYukawa
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
writedata
=
1
;
}
/* ---------------------------------------------------------------------- */
PairYukawa
::~
PairYukawa
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
rad
);
memory
->
destroy
(
cut
);
memory
->
destroy
(
a
);
memory
->
destroy
(
offset
);
}
}
/* ---------------------------------------------------------------------- */
void
PairYukawa
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
fpair
;
double
rsq
,
r2inv
,
r
,
rinv
,
screening
,
forceyukawa
,
factor
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
evdwl
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
double
*
special_lj
=
force
->
special_lj
;
int
newton_pair
=
force
->
newton_pair
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// loop over neighbors of my atoms
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
itype
=
type
[
i
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
factor
=
special_lj
[
sbmask
(
j
)];
j
&=
NEIGHMASK
;
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
jtype
=
type
[
j
];
if
(
rsq
<
cutsq
[
itype
][
jtype
])
{
r2inv
=
1.0
/
rsq
;
r
=
sqrt
(
rsq
);
rinv
=
1.0
/
r
;
screening
=
exp
(
-
kappa
*
r
);
forceyukawa
=
a
[
itype
][
jtype
]
*
screening
*
(
kappa
+
rinv
);
fpair
=
factor
*
forceyukawa
*
r2inv
;
f
[
i
][
0
]
+=
delx
*
fpair
;
f
[
i
][
1
]
+=
dely
*
fpair
;
f
[
i
][
2
]
+=
delz
*
fpair
;
if
(
newton_pair
||
j
<
nlocal
)
{
f
[
j
][
0
]
-=
delx
*
fpair
;
f
[
j
][
1
]
-=
dely
*
fpair
;
f
[
j
][
2
]
-=
delz
*
fpair
;
}
if
(
eflag
)
{
evdwl
=
a
[
itype
][
jtype
]
*
screening
*
rinv
-
offset
[
itype
][
jtype
];
evdwl
*=
factor
;
}
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
0.0
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
if
(
vflag_fdotr
)
virial_fdotr_compute
();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairYukawa
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ntypes
;
memory
->
create
(
setflag
,
n
+
1
,
n
+
1
,
"pair:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
for
(
int
j
=
i
;
j
<=
n
;
j
++
)
setflag
[
i
][
j
]
=
0
;
memory
->
create
(
cutsq
,
n
+
1
,
n
+
1
,
"pair:cutsq"
);
memory
->
create
(
rad
,
n
+
1
,
"pair:rad"
);
memory
->
create
(
cut
,
n
+
1
,
n
+
1
,
"pair:cut"
);
memory
->
create
(
a
,
n
+
1
,
n
+
1
,
"pair:a"
);
memory
->
create
(
offset
,
n
+
1
,
n
+
1
,
"pair:offset"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairYukawa
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
2
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
kappa
=
force
->
numeric
(
FLERR
,
arg
[
0
]);
cut_global
=
force
->
numeric
(
FLERR
,
arg
[
1
]);
// reset cutoffs that have been explicitly set
if
(
allocated
)
{
int
i
,
j
;
for
(
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
j
=
i
;
j
<=
atom
->
ntypes
;
j
++
)
if
(
setflag
[
i
][
j
])
cut
[
i
][
j
]
=
cut_global
;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairYukawa
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
3
||
narg
>
4
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
,
jlo
,
jhi
;
force
->
bounds
(
FLERR
,
arg
[
0
],
atom
->
ntypes
,
ilo
,
ihi
);
force
->
bounds
(
FLERR
,
arg
[
1
],
atom
->
ntypes
,
jlo
,
jhi
);
double
a_one
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
double
cut_one
=
cut_global
;
if
(
narg
==
4
)
cut_one
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
for
(
int
j
=
MAX
(
jlo
,
i
);
j
<=
jhi
;
j
++
)
{
a
[
i
][
j
]
=
a_one
;
cut
[
i
][
j
]
=
cut_one
;
setflag
[
i
][
j
]
=
1
;
count
++
;
}
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairYukawa
::
init_one
(
int
i
,
int
j
)
{
if
(
setflag
[
i
][
j
]
==
0
)
{
a
[
i
][
j
]
=
mix_energy
(
a
[
i
][
i
],
a
[
j
][
j
],
1.0
,
1.0
);
cut
[
i
][
j
]
=
mix_distance
(
cut
[
i
][
i
],
cut
[
j
][
j
]);
}
if
(
offset_flag
&&
(
cut
[
i
][
j
]
>
0.0
))
{
double
screening
=
exp
(
-
kappa
*
cut
[
i
][
j
]);
offset
[
i
][
j
]
=
a
[
i
][
j
]
*
screening
/
cut
[
i
][
j
];
}
else
offset
[
i
][
j
]
=
0.0
;
a
[
j
][
i
]
=
a
[
i
][
j
];
offset
[
j
][
i
]
=
offset
[
i
][
j
];
return
cut
[
i
][
j
];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairYukawa
::
write_restart
(
FILE
*
fp
)
{
write_restart_settings
(
fp
);
int
i
,
j
;
for
(
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
j
=
i
;
j
<=
atom
->
ntypes
;
j
++
)
{
fwrite
(
&
setflag
[
i
][
j
],
sizeof
(
int
),
1
,
fp
);
if
(
setflag
[
i
][
j
])
{
fwrite
(
&
a
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairYukawa
::
read_restart
(
FILE
*
fp
)
{
read_restart_settings
(
fp
);
allocate
();
int
i
,
j
;
int
me
=
comm
->
me
;
for
(
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
j
=
i
;
j
<=
atom
->
ntypes
;
j
++
)
{
if
(
me
==
0
)
fread
(
&
setflag
[
i
][
j
],
sizeof
(
int
),
1
,
fp
);
MPI_Bcast
(
&
setflag
[
i
][
j
],
1
,
MPI_INT
,
0
,
world
);
if
(
setflag
[
i
][
j
])
{
if
(
me
==
0
)
{
fread
(
&
a
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
MPI_Bcast
(
&
a
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairYukawa
::
write_restart_settings
(
FILE
*
fp
)
{
fwrite
(
&
kappa
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut_global
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
offset_flag
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
mix_flag
,
sizeof
(
int
),
1
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairYukawa
::
read_restart_settings
(
FILE
*
fp
)
{
if
(
comm
->
me
==
0
)
{
fread
(
&
kappa
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut_global
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
offset_flag
,
sizeof
(
int
),
1
,
fp
);
fread
(
&
mix_flag
,
sizeof
(
int
),
1
,
fp
);
}
MPI_Bcast
(
&
kappa
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut_global
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
offset_flag
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
mix_flag
,
1
,
MPI_INT
,
0
,
world
);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void
PairYukawa
::
write_data
(
FILE
*
fp
)
{
for
(
int
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
fprintf
(
fp
,
"%d %g
\n
"
,
i
,
a
[
i
][
i
]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void
PairYukawa
::
write_data_all
(
FILE
*
fp
)
{
for
(
int
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
int
j
=
i
;
j
<=
atom
->
ntypes
;
j
++
)
fprintf
(
fp
,
"%d %d %g %g
\n
"
,
i
,
j
,
a
[
i
][
j
],
cut
[
i
][
j
]);
}
/* ---------------------------------------------------------------------- */
double
PairYukawa
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
r2inv
,
r
,
rinv
,
screening
,
forceyukawa
,
phi
;
r2inv
=
1.0
/
rsq
;
r
=
sqrt
(
rsq
);
rinv
=
1.0
/
r
;
screening
=
exp
(
-
kappa
*
r
);
forceyukawa
=
a
[
itype
][
jtype
]
*
screening
*
(
kappa
+
rinv
);
fforce
=
factor_lj
*
forceyukawa
*
r2inv
;
phi
=
a
[
itype
][
jtype
]
*
screening
*
rinv
-
offset
[
itype
][
jtype
];
return
factor_lj
*
phi
;
}
Event Timeline
Log In to Comment