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pair_nm_cut.cpp
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rLAMMPS lammps
pair_nm_cut.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: Julien Devemy (ICCF)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_nm_cut.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
/* ---------------------------------------------------------------------- */
PairNMCut
::
PairNMCut
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
writedata
=
1
;
}
/* ---------------------------------------------------------------------- */
PairNMCut
::~
PairNMCut
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
cut
);
memory
->
destroy
(
e0
);
memory
->
destroy
(
r0
);
memory
->
destroy
(
nn
);
memory
->
destroy
(
mm
);
memory
->
destroy
(
nm
);
memory
->
destroy
(
e0nm
);
memory
->
destroy
(
r0n
);
memory
->
destroy
(
r0m
);
memory
->
destroy
(
offset
);
}
}
/* ---------------------------------------------------------------------- */
void
PairNMCut
::
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
,
factor_lj
;
double
r
,
forcenm
,
rminv
,
rninv
;
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_lj
=
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
);
rminv
=
pow
(
r2inv
,
mm
[
itype
][
jtype
]
/
2.0
);
rninv
=
pow
(
r2inv
,
nn
[
itype
][
jtype
]
/
2.0
);
forcenm
=
e0nm
[
itype
][
jtype
]
*
nm
[
itype
][
jtype
]
*
(
r0n
[
itype
][
jtype
]
/
pow
(
r
,
nn
[
itype
][
jtype
])
-
r0m
[
itype
][
jtype
]
/
pow
(
r
,
mm
[
itype
][
jtype
]));
fpair
=
factor_lj
*
forcenm
*
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
=
e0nm
[
itype
][
jtype
]
*
(
mm
[
itype
][
jtype
]
*
r0n
[
itype
][
jtype
]
*
rninv
-
nn
[
itype
][
jtype
]
*
r0m
[
itype
][
jtype
]
*
rminv
)
-
offset
[
itype
][
jtype
];
evdwl
*=
factor_lj
;
}
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
PairNMCut
::
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
(
e0
,
n
+
1
,
n
+
1
,
"pair:e0"
);
memory
->
create
(
r0
,
n
+
1
,
n
+
1
,
"pair:r0"
);
memory
->
create
(
nn
,
n
+
1
,
n
+
1
,
"pair:nn"
);
memory
->
create
(
mm
,
n
+
1
,
n
+
1
,
"pair:mm"
);
memory
->
create
(
nm
,
n
+
1
,
n
+
1
,
"pair:nm"
);
memory
->
create
(
e0nm
,
n
+
1
,
n
+
1
,
"pair:e0nm"
);
memory
->
create
(
r0n
,
n
+
1
,
n
+
1
,
"pair:r0n"
);
memory
->
create
(
r0m
,
n
+
1
,
n
+
1
,
"pair:r0m"
);
memory
->
create
(
offset
,
n
+
1
,
n
+
1
,
"pair:offset"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairNMCut
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
1
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
cut_global
=
force
->
numeric
(
FLERR
,
arg
[
0
]);
// 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
PairNMCut
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
6
||
narg
>
7
)
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
e0_one
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
double
r0_one
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
double
nn_one
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
double
mm_one
=
force
->
numeric
(
FLERR
,
arg
[
5
]);
double
cut_one
=
cut_global
;
if
(
narg
==
7
)
cut_one
=
force
->
numeric
(
FLERR
,
arg
[
6
]);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
for
(
int
j
=
MAX
(
jlo
,
i
);
j
<=
jhi
;
j
++
)
{
e0
[
i
][
j
]
=
e0_one
;
r0
[
i
][
j
]
=
r0_one
;
nn
[
i
][
j
]
=
nn_one
;
mm
[
i
][
j
]
=
mm_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
PairNMCut
::
init_one
(
int
i
,
int
j
)
{
if
(
setflag
[
i
][
j
]
==
0
)
error
->
all
(
FLERR
,
"All pair coeffs are not set"
);
nm
[
i
][
j
]
=
nn
[
i
][
j
]
*
mm
[
i
][
j
];
e0nm
[
i
][
j
]
=
e0
[
i
][
j
]
/
(
nn
[
i
][
j
]
-
mm
[
i
][
j
]);
r0n
[
i
][
j
]
=
pow
(
r0
[
i
][
j
],
nn
[
i
][
j
]);
r0m
[
i
][
j
]
=
pow
(
r0
[
i
][
j
],
mm
[
i
][
j
]);
if
(
offset_flag
&&
(
cut
[
i
][
j
]
>
0.0
))
{
offset
[
i
][
j
]
=
e0nm
[
i
][
j
]
*
((
mm
[
i
][
j
]
*
r0n
[
i
][
j
]
/
pow
(
cut
[
i
][
j
],
nn
[
i
][
j
]))
-
(
nn
[
i
][
j
]
*
r0m
[
i
][
j
]
/
pow
(
cut
[
i
][
j
],
mm
[
i
][
j
])));
}
else
offset
[
i
][
j
]
=
0.0
;
e0
[
j
][
i
]
=
e0
[
i
][
j
];
nn
[
j
][
i
]
=
nn
[
i
][
j
];
mm
[
j
][
i
]
=
mm
[
i
][
j
];
nm
[
j
][
i
]
=
nm
[
i
][
j
];
r0
[
j
][
i
]
=
r0
[
i
][
j
];
e0nm
[
j
][
i
]
=
e0nm
[
i
][
j
];
r0n
[
j
][
i
]
=
r0n
[
i
][
j
];
r0m
[
j
][
i
]
=
r0m
[
i
][
j
];
offset
[
j
][
i
]
=
offset
[
i
][
j
];
// compute I,J contribution to long-range tail correction
// count total # of atoms of type I and J via Allreduce
if
(
tail_flag
)
{
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
double
count
[
2
],
all
[
2
];
count
[
0
]
=
count
[
1
]
=
0.0
;
for
(
int
k
=
0
;
k
<
nlocal
;
k
++
)
{
if
(
type
[
k
]
==
i
)
count
[
0
]
+=
1.0
;
if
(
type
[
k
]
==
j
)
count
[
1
]
+=
1.0
;
}
MPI_Allreduce
(
count
,
all
,
2
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
double
rr1
=
mm
[
i
][
j
]
*
(
nn
[
i
][
j
]
-
1
)
*
pow
(
r0
[
i
][
j
],
nn
[
i
][
j
]);
double
rr2
=
nn
[
i
][
j
]
*
(
mm
[
i
][
j
]
-
1
)
*
pow
(
r0
[
i
][
j
],
mm
[
i
][
j
]);
double
p1
=
1
-
nn
[
i
][
j
];
double
p2
=
1
-
mm
[
i
][
j
];
double
rrr1
=
pow
(
r0
[
i
][
j
],
nn
[
i
][
j
])
*
(
1
-
nn
[
i
][
j
]);
double
rrr2
=
pow
(
r0
[
i
][
j
],
mm
[
i
][
j
])
*
(
1
-
mm
[
i
][
j
]);
etail_ij
=
2.0
*
MY_PI
*
all
[
0
]
*
all
[
1
]
*
e0nm
[
i
][
j
]
*
(
rr1
*
pow
(
cut
[
i
][
j
],
p1
)
-
rr2
*
pow
(
cut
[
i
][
j
],
p2
));
ptail_ij
=
2.0
*
MY_PI
*
all
[
0
]
*
all
[
1
]
*
e0nm
[
i
][
j
]
*
nn
[
i
][
j
]
*
mm
[
i
][
j
]
*
(
rrr1
*
pow
(
cut
[
i
][
j
],
p1
)
-
rrr2
*
pow
(
cut
[
i
][
j
],
p2
));
}
return
cut
[
i
][
j
];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairNMCut
::
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
(
&
e0
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
r0
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
nn
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
mm
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairNMCut
::
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
(
&
e0
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
r0
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
nn
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
mm
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
MPI_Bcast
(
&
e0
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
r0
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
nn
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
mm
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairNMCut
::
write_restart_settings
(
FILE
*
fp
)
{
fwrite
(
&
cut_global
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
offset_flag
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
mix_flag
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
tail_flag
,
sizeof
(
int
),
1
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairNMCut
::
read_restart_settings
(
FILE
*
fp
)
{
if
(
comm
->
me
==
0
)
{
fread
(
&
cut_global
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
offset_flag
,
sizeof
(
int
),
1
,
fp
);
fread
(
&
mix_flag
,
sizeof
(
int
),
1
,
fp
);
fread
(
&
tail_flag
,
sizeof
(
int
),
1
,
fp
);
}
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
);
MPI_Bcast
(
&
tail_flag
,
1
,
MPI_INT
,
0
,
world
);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void
PairNMCut
::
write_data
(
FILE
*
fp
)
{
for
(
int
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
fprintf
(
fp
,
"%d %g %g %g %g
\n
"
,
i
,
e0
[
i
][
i
],
r0
[
i
][
i
],
nn
[
i
][
i
],
mm
[
i
][
i
]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void
PairNMCut
::
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 %g %g %g
\n
"
,
i
,
j
,
e0
[
i
][
j
],
r0
[
i
][
j
],
nn
[
i
][
j
],
mm
[
i
][
j
],
cut
[
i
][
j
]);
}
/* ---------------------------------------------------------------------- */
double
PairNMCut
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
r2inv
,
r
,
forcenm
,
phinm
;
r2inv
=
1.0
/
rsq
;
r
=
sqrt
(
rsq
);
forcenm
=
e0nm
[
itype
][
jtype
]
*
nm
[
itype
][
jtype
]
*
(
r0n
[
itype
][
jtype
]
/
pow
(
r
,
nn
[
itype
][
jtype
])
-
r0m
[
itype
][
jtype
]
/
pow
(
r
,
mm
[
itype
][
jtype
]));
fforce
=
factor_lj
*
forcenm
*
r2inv
;
phinm
=
e0nm
[
itype
][
jtype
]
*
(
mm
[
itype
][
jtype
]
*
r0n
[
itype
][
jtype
]
/
pow
(
r
,
nn
[
itype
][
jtype
])
-
nn
[
itype
][
jtype
]
*
r0m
[
itype
][
jtype
]
/
pow
(
r
,
mm
[
itype
][
jtype
]))
-
offset
[
itype
][
jtype
];
return
factor_lj
*
phinm
;
}
/* ---------------------------------------------------------------------- */
void
*
PairNMCut
::
extract
(
const
char
*
str
,
int
&
dim
)
{
dim
=
2
;
if
(
strcmp
(
str
,
"e0"
)
==
0
)
return
(
void
*
)
e0
;
if
(
strcmp
(
str
,
"r0"
)
==
0
)
return
(
void
*
)
r0
;
if
(
strcmp
(
str
,
"nn"
)
==
0
)
return
(
void
*
)
nn
;
if
(
strcmp
(
str
,
"mm"
)
==
0
)
return
(
void
*
)
mm
;
return
NULL
;
}
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