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pair_lj_cut_coul_cut_omp.cpp
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Sat, Sep 14, 16:30
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15 KB
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text/x-c++
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blob
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rLAMMPS lammps
pair_lj_cut_coul_cut_omp.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 "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_lj_cut_coul_cut_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#if defined(_OPENMP)
#include <omp.h>
#endif
using
namespace
LAMMPS_NS
;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
PairLJCutCoulCutOMP
::
PairLJCutCoulCutOMP
(
LAMMPS
*
lmp
)
:
PairOMP
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
PairLJCutCoulCutOMP
::~
PairLJCutCoulCutOMP
()
{
if
(
allocated
)
{
memory
->
destroy_2d_int_array
(
setflag
);
memory
->
destroy_2d_double_array
(
cutsq
);
memory
->
destroy_2d_double_array
(
cut_lj
);
memory
->
destroy_2d_double_array
(
cut_ljsq
);
memory
->
destroy_2d_double_array
(
cut_coul
);
memory
->
destroy_2d_double_array
(
cut_coulsq
);
memory
->
destroy_2d_double_array
(
epsilon
);
memory
->
destroy_2d_double_array
(
sigma
);
memory
->
destroy_2d_double_array
(
lj1
);
memory
->
destroy_2d_double_array
(
lj2
);
memory
->
destroy_2d_double_array
(
lj3
);
memory
->
destroy_2d_double_array
(
lj4
);
memory
->
destroy_2d_double_array
(
offset
);
}
}
/* ---------------------------------------------------------------------- */
void
PairLJCutCoulCutOMP
::
compute
(
int
eflag
,
int
vflag
)
{
if
(
eflag
||
vflag
)
{
ev_setup
(
eflag
,
vflag
);
ev_setup_thr
(
eflag
,
vflag
);
}
else
evflag
=
vflag_fdotr
=
0
;
if
(
evflag
)
{
if
(
eflag
)
{
if
(
force
->
newton_pair
)
return
eval
<
1
,
1
,
1
>
();
else
return
eval
<
1
,
1
,
0
>
();
}
else
{
if
(
force
->
newton_pair
)
return
eval
<
1
,
0
,
1
>
();
else
return
eval
<
1
,
0
,
0
>
();
}
}
else
{
if
(
force
->
newton_pair
)
return
eval
<
0
,
0
,
1
>
();
else
return
eval
<
0
,
0
,
0
>
();
}
}
template
<
int
EVFLAG
,
int
EFLAG
,
int
NEWTON_PAIR
>
void
PairLJCutCoulCutOMP
::
eval
()
{
#if defined(_OPENMP)
#pragma omp parallel default(shared)
#endif
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
,
tid
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
,
fpair
;
double
rsq
,
r2inv
,
r6inv
,
forcecoul
,
forcelj
,
factor_coul
,
factor_lj
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
const
int
nlocal
=
atom
->
nlocal
;
const
int
nall
=
nlocal
+
atom
->
nghost
;
const
int
nthreads
=
comm
->
nthreads
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
double
*
q
=
atom
->
q
;
int
*
type
=
atom
->
type
;
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
double
qqrd2e
=
force
->
qqrd2e
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// loop over neighbors of my atoms
int
iifrom
,
iito
;
f
=
loop_setup_thr
(
f
,
iifrom
,
iito
,
tid
,
inum
,
nall
,
nthreads
);
for
(
ii
=
iifrom
;
ii
<
iito
;
++
ii
)
{
i
=
ilist
[
ii
];
qtmp
=
q
[
i
];
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_coul
=
factor_lj
=
1.0
;
else
{
factor_coul
=
special_coul
[
j
/
nall
];
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
;
if
(
rsq
<
cut_coulsq
[
itype
][
jtype
])
forcecoul
=
qqrd2e
*
qtmp
*
q
[
j
]
*
sqrt
(
r2inv
);
else
forcecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
}
else
forcelj
=
0.0
;
fpair
=
(
factor_coul
*
forcecoul
+
factor_lj
*
forcelj
)
*
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
)
{
if
(
rsq
<
cut_coulsq
[
itype
][
jtype
])
ecoul
=
factor_coul
*
qqrd2e
*
qtmp
*
q
[
j
]
*
sqrt
(
r2inv
);
else
ecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
evdwl
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
])
-
offset
[
itype
][
jtype
];
evdwl
*=
factor_lj
;
}
else
evdwl
=
0.0
;
}
if
(
EVFLAG
)
ev_tally
(
i
,
j
,
nlocal
,
NEWTON_PAIR
,
evdwl
,
ecoul
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
// reduce per thread forces into global force array.
force_reduce_thr
(
atom
->
f
,
nall
,
nthreads
,
tid
);
}
ev_reduce_thr
();
if
(
vflag_fdotr
)
virial_compute
();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairLJCutCoulCutOMP
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ntypes
;
setflag
=
memory
->
create_2d_int_array
(
n
+
1
,
n
+
1
,
"pair:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
for
(
int
j
=
i
;
j
<=
n
;
j
++
)
setflag
[
i
][
j
]
=
0
;
cutsq
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:cutsq"
);
cut_lj
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:cut_lj"
);
cut_ljsq
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:cut_ljsq"
);
cut_coul
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:cut_coul"
);
cut_coulsq
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:cut_coulsq"
);
epsilon
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:epsilon"
);
sigma
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:sigma"
);
lj1
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:lj1"
);
lj2
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:lj2"
);
lj3
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:lj3"
);
lj4
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:lj4"
);
offset
=
memory
->
create_2d_double_array
(
n
+
1
,
n
+
1
,
"pair:offset"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairLJCutCoulCutOMP
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
1
||
narg
>
2
)
error
->
all
(
"Illegal pair_style command"
);
cut_lj_global
=
force
->
numeric
(
arg
[
0
]);
if
(
narg
==
1
)
cut_coul_global
=
cut_lj_global
;
else
cut_coul_global
=
force
->
numeric
(
arg
[
1
]);
// 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_lj
[
i
][
j
]
=
cut_lj_global
;
cut_coul
[
i
][
j
]
=
cut_coul_global
;
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairLJCutCoulCutOMP
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
4
||
narg
>
6
)
error
->
all
(
"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
=
force
->
numeric
(
arg
[
2
]);
double
sigma_one
=
force
->
numeric
(
arg
[
3
]);
double
cut_lj_one
=
cut_lj_global
;
double
cut_coul_one
=
cut_coul_global
;
if
(
narg
>=
5
)
cut_coul_one
=
cut_lj_one
=
force
->
numeric
(
arg
[
4
]);
if
(
narg
==
6
)
cut_coul_one
=
force
->
numeric
(
arg
[
5
]);
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_lj
[
i
][
j
]
=
cut_lj_one
;
cut_coul
[
i
][
j
]
=
cut_coul_one
;
setflag
[
i
][
j
]
=
1
;
count
++
;
}
}
if
(
count
==
0
)
error
->
all
(
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairLJCutCoulCutOMP
::
init_style
()
{
if
(
!
atom
->
q_flag
)
error
->
all
(
"Pair style lj/cut/coul/cut requires atom attribute q"
);
int
irequest
=
neighbor
->
request
(
this
);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairLJCutCoulCutOMP
::
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_lj
[
i
][
j
]
=
mix_distance
(
cut_lj
[
i
][
i
],
cut_lj
[
j
][
j
]);
cut_coul
[
i
][
j
]
=
mix_distance
(
cut_coul
[
i
][
i
],
cut_coul
[
j
][
j
]);
}
double
cut
=
MAX
(
cut_lj
[
i
][
j
],
cut_coul
[
i
][
j
]);
cut_ljsq
[
i
][
j
]
=
cut_lj
[
i
][
j
]
*
cut_lj
[
i
][
j
];
cut_coulsq
[
i
][
j
]
=
cut_coul
[
i
][
j
]
*
cut_coul
[
i
][
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
);
if
(
offset_flag
)
{
double
ratio
=
sigma
[
i
][
j
]
/
cut_lj
[
i
][
j
];
offset
[
i
][
j
]
=
4.0
*
epsilon
[
i
][
j
]
*
(
pow
(
ratio
,
12.0
)
-
pow
(
ratio
,
6.0
));
}
else
offset
[
i
][
j
]
=
0.0
;
cut_ljsq
[
j
][
i
]
=
cut_ljsq
[
i
][
j
];
cut_coulsq
[
j
][
i
]
=
cut_coulsq
[
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
];
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
PI
=
4.0
*
atan
(
1.0
);
double
sig2
=
sigma
[
i
][
j
]
*
sigma
[
i
][
j
];
double
sig6
=
sig2
*
sig2
*
sig2
;
double
rc3
=
cut_lj
[
i
][
j
]
*
cut_lj
[
i
][
j
]
*
cut_lj
[
i
][
j
];
double
rc6
=
rc3
*
rc3
;
double
rc9
=
rc3
*
rc6
;
etail_ij
=
8.0
*
PI
*
all
[
0
]
*
all
[
1
]
*
epsilon
[
i
][
j
]
*
sig6
*
(
sig6
-
3.0
*
rc6
)
/
(
9.0
*
rc9
);
ptail_ij
=
16.0
*
PI
*
all
[
0
]
*
all
[
1
]
*
epsilon
[
i
][
j
]
*
sig6
*
(
2.0
*
sig6
-
3.0
*
rc6
)
/
(
9.0
*
rc9
);
}
return
cut
;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJCutCoulCutOMP
::
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_lj
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut_coul
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairLJCutCoulCutOMP
::
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_lj
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut_coul
[
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_lj
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut_coul
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJCutCoulCutOMP
::
write_restart_settings
(
FILE
*
fp
)
{
fwrite
(
&
cut_lj_global
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut_coul_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
PairLJCutCoulCutOMP
::
read_restart_settings
(
FILE
*
fp
)
{
if
(
comm
->
me
==
0
)
{
fread
(
&
cut_lj_global
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut_coul_global
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
offset_flag
,
sizeof
(
int
),
1
,
fp
);
fread
(
&
mix_flag
,
sizeof
(
int
),
1
,
fp
);
}
MPI_Bcast
(
&
cut_lj_global
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut_coul_global
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
offset_flag
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
mix_flag
,
1
,
MPI_INT
,
0
,
world
);
}
/* ---------------------------------------------------------------------- */
double
PairLJCutCoulCutOMP
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
r2inv
,
r6inv
,
forcecoul
,
forcelj
,
phicoul
,
philj
;
r2inv
=
1.0
/
rsq
;
if
(
rsq
<
cut_coulsq
[
itype
][
jtype
])
forcecoul
=
force
->
qqrd2e
*
atom
->
q
[
i
]
*
atom
->
q
[
j
]
*
sqrt
(
r2inv
);
else
forcecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
}
else
forcelj
=
0.0
;
fforce
=
(
factor_coul
*
forcecoul
+
factor_lj
*
forcelj
)
*
r2inv
;
double
eng
=
0.0
;
if
(
rsq
<
cut_coulsq
[
itype
][
jtype
])
{
phicoul
=
force
->
qqrd2e
*
atom
->
q
[
i
]
*
atom
->
q
[
j
]
*
sqrt
(
r2inv
);
eng
+=
factor_coul
*
phicoul
;
}
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
philj
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
])
-
offset
[
itype
][
jtype
];
eng
+=
factor_lj
*
philj
;
}
return
eng
;
}
/* ---------------------------------------------------------------------- */
double
PairLJCutCoulCutOMP
::
memory_usage
()
{
const
int
n
=
atom
->
ntypes
;
double
bytes
=
PairOMP
::
memory_usage
();
bytes
+=
9
*
((
n
+
1
)
*
(
n
+
1
)
*
sizeof
(
double
)
+
(
n
+
1
)
*
sizeof
(
double
*
));
bytes
+=
1
*
((
n
+
1
)
*
(
n
+
1
)
*
sizeof
(
int
)
+
(
n
+
1
)
*
sizeof
(
int
*
));
return
bytes
;
}
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