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pair_lj_smooth_linear.cpp
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Sat, Oct 5, 11:01
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text/x-c
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Mon, Oct 7, 11:01 (2 d)
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rLAMMPS lammps
pair_lj_smooth_linear.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: Jonathan Zimmerman (Sandia)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_lj_smooth_linear.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
PairLJSmoothLinear
::
PairLJSmoothLinear
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
PairLJSmoothLinear
::~
PairLJSmoothLinear
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
cut
);
memory
->
destroy
(
epsilon
);
memory
->
destroy
(
sigma
);
memory
->
destroy
(
ljcut
);
memory
->
destroy
(
dljcut
);
memory
->
destroy
(
lj1
);
memory
->
destroy
(
lj2
);
memory
->
destroy
(
lj3
);
memory
->
destroy
(
lj4
);
}
}
/* ---------------------------------------------------------------------- */
void
PairLJSmoothLinear
::
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
,
r6inv
,
forcelj
,
factor_lj
;
double
r
,
rinv
;
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
;
int
nall
=
nlocal
+
atom
->
nghost
;
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
];
if
(
j
<
nall
)
factor_lj
=
1.0
;
else
{
factor_lj
=
special_lj
[
j
/
nall
];
j
%=
nall
;
}
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
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
rinv
=
sqrt
(
r2inv
);
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
forcelj
=
rinv
*
forcelj
-
dljcut
[
itype
][
jtype
];
fpair
=
factor_lj
*
forcelj
*
rinv
;
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
)
{
r
=
sqrt
(
rsq
);
evdwl
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
]);
evdwl
=
evdwl
-
ljcut
[
itype
][
jtype
]
+
(
r
-
cut
[
itype
][
jtype
])
*
dljcut
[
itype
][
jtype
];
}
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
PairLJSmoothLinear
::
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
(
cut
,
n
+
1
,
n
+
1
,
"pair:cut"
);
memory
->
create
(
epsilon
,
n
+
1
,
n
+
1
,
"pair:epsilon"
);
memory
->
create
(
sigma
,
n
+
1
,
n
+
1
,
"pair:sigma"
);
memory
->
create
(
ljcut
,
n
+
1
,
n
+
1
,
"pair:ljcut"
);
memory
->
create
(
dljcut
,
n
+
1
,
n
+
1
,
"pair:dljcut"
);
memory
->
create
(
lj1
,
n
+
1
,
n
+
1
,
"pair:lj1"
);
memory
->
create
(
lj2
,
n
+
1
,
n
+
1
,
"pair:lj2"
);
memory
->
create
(
lj3
,
n
+
1
,
n
+
1
,
"pair:lj3"
);
memory
->
create
(
lj4
,
n
+
1
,
n
+
1
,
"pair:lj4"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairLJSmoothLinear
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
1
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
cut_global
=
atof
(
arg
[
0
]);
// reset cutoffs that have been explicitly set
if
(
allocated
)
{
int
i
,
j
;
for
(
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
j
=
i
+
1
;
j
<=
atom
->
ntypes
;
j
++
)
if
(
setflag
[
i
][
j
])
{
cut
[
i
][
j
]
=
cut_global
;
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairLJSmoothLinear
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
4
&&
narg
!=
5
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
,
jlo
,
jhi
;
force
->
bounds
(
arg
[
0
],
atom
->
ntypes
,
ilo
,
ihi
);
force
->
bounds
(
arg
[
1
],
atom
->
ntypes
,
jlo
,
jhi
);
double
epsilon_one
=
atof
(
arg
[
2
]);
double
sigma_one
=
atof
(
arg
[
3
]);
double
cut_one
=
cut_global
;
if
(
narg
==
5
)
{
cut_one
=
atof
(
arg
[
4
]);
}
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
for
(
int
j
=
MAX
(
jlo
,
i
);
j
<=
jhi
;
j
++
)
{
epsilon
[
i
][
j
]
=
epsilon_one
;
sigma
[
i
][
j
]
=
sigma_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
PairLJSmoothLinear
::
init_one
(
int
i
,
int
j
)
{
if
(
setflag
[
i
][
j
]
==
0
)
{
epsilon
[
i
][
j
]
=
mix_energy
(
epsilon
[
i
][
i
],
epsilon
[
j
][
j
],
sigma
[
i
][
i
],
sigma
[
j
][
j
]);
sigma
[
i
][
j
]
=
mix_distance
(
sigma
[
i
][
i
],
sigma
[
j
][
j
]);
cut
[
i
][
j
]
=
mix_distance
(
cut
[
i
][
i
],
cut
[
j
][
j
]);
}
lj1
[
i
][
j
]
=
48.0
*
epsilon
[
i
][
j
]
*
pow
(
sigma
[
i
][
j
],
12.0
);
lj2
[
i
][
j
]
=
24.0
*
epsilon
[
i
][
j
]
*
pow
(
sigma
[
i
][
j
],
6.0
);
lj3
[
i
][
j
]
=
4.0
*
epsilon
[
i
][
j
]
*
pow
(
sigma
[
i
][
j
],
12.0
);
lj4
[
i
][
j
]
=
4.0
*
epsilon
[
i
][
j
]
*
pow
(
sigma
[
i
][
j
],
6.0
);
double
cut6inv
=
pow
(
cut
[
i
][
j
],
-
6.0
);
double
cutinv
=
1.0
/
cut
[
i
][
j
];
ljcut
[
i
][
j
]
=
cut6inv
*
(
lj3
[
i
][
j
]
*
cut6inv
-
lj4
[
i
][
j
]);
dljcut
[
i
][
j
]
=
cutinv
*
cut6inv
*
(
lj1
[
i
][
j
]
*
cut6inv
-
lj2
[
i
][
j
]);
lj1
[
j
][
i
]
=
lj1
[
i
][
j
];
lj2
[
j
][
i
]
=
lj2
[
i
][
j
];
lj3
[
j
][
i
]
=
lj3
[
i
][
j
];
lj4
[
j
][
i
]
=
lj4
[
i
][
j
];
ljcut
[
j
][
i
]
=
ljcut
[
i
][
j
];
dljcut
[
j
][
i
]
=
dljcut
[
i
][
j
];
return
cut
[
i
][
j
];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJSmoothLinear
::
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
(
&
epsilon
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
sigma
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairLJSmoothLinear
::
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
(
&
epsilon
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
sigma
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
MPI_Bcast
(
&
epsilon
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sigma
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJSmoothLinear
::
write_restart_settings
(
FILE
*
fp
)
{
fwrite
(
&
cut_global
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
mix_flag
,
sizeof
(
int
),
1
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairLJSmoothLinear
::
read_restart_settings
(
FILE
*
fp
)
{
int
me
=
comm
->
me
;
if
(
me
==
0
)
{
fread
(
&
cut_global
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
mix_flag
,
sizeof
(
int
),
1
,
fp
);
}
MPI_Bcast
(
&
cut_global
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
mix_flag
,
1
,
MPI_INT
,
0
,
world
);
}
/* ---------------------------------------------------------------------- */
double
PairLJSmoothLinear
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
r2inv
,
r6inv
,
forcelj
,
philj
,
r
,
rinv
;
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
rinv
=
sqrt
(
r2inv
);
r
=
sqrt
(
rsq
);
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
forcelj
=
rinv
*
forcelj
-
dljcut
[
itype
][
jtype
];
fforce
=
factor_lj
*
forcelj
*
rinv
;
philj
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
]);
philj
=
philj
-
ljcut
[
itype
][
jtype
]
+
(
r
-
cut
[
itype
][
jtype
])
*
dljcut
[
itype
][
jtype
];
return
factor_lj
*
philj
;
}
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