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pair_coul_diel.cpp
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rLAMMPS lammps
pair_coul_diel.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributiong authors: Arben Jusufi, Axel Kohlmeyer (Temple U.)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_coul_diel.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
PairCoulDiel
::
PairCoulDiel
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
PairCoulDiel
::~
PairCoulDiel
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
sigmae
);
memory
->
destroy
(
rme
);
memory
->
destroy
(
offset
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
cut
);
allocated
=
0
;
}
}
/* ---------------------------------------------------------------------- */
void
PairCoulDiel
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
ecoul
,
fpair
;
double
rsq
,
r
,
rarg
,
th
,
depsdr
,
epsr
,
forcecoul
,
factor_coul
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
ecoul
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
double
*
q
=
atom
->
q
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
double
*
special_coul
=
force
->
special_coul
;
int
newton_pair
=
force
->
newton_pair
;
double
qqrd2e
=
force
->
qqrd2e
;
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
];
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
];
factor_coul
=
special_coul
[
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
])
{
r
=
sqrt
(
rsq
);
rarg
=
(
r
-
rme
[
itype
][
jtype
])
/
sigmae
[
itype
][
jtype
];
th
=
tanh
(
rarg
);
epsr
=
a_eps
+
b_eps
*
th
;
depsdr
=
b_eps
*
(
1.0
-
th
*
th
)
/
sigmae
[
itype
][
jtype
];
forcecoul
=
qqrd2e
*
qtmp
*
q
[
j
]
*
((
eps_s
*
(
epsr
+
r
*
depsdr
)
/
epsr
/
epsr
)
-
1.
)
/
rsq
;
fpair
=
factor_coul
*
forcecoul
/
r
;
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
)
{
ecoul
=
(
qqrd2e
*
qtmp
*
q
[
j
]
*
((
eps_s
/
epsr
)
-
1.
)
/
r
)
-
offset
[
itype
][
jtype
];
ecoul
*=
factor_coul
;
}
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
0.0
,
ecoul
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
if
(
vflag_fdotr
)
virial_fdotr_compute
();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairCoulDiel
::
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
(
sigmae
,
n
+
1
,
n
+
1
,
"pair:sigmae"
);
memory
->
create
(
rme
,
n
+
1
,
n
+
1
,
"pair:rme"
);
memory
->
create
(
offset
,
n
+
1
,
n
+
1
,
"pair:offset"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairCoulDiel
::
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
+
1
;
j
<=
atom
->
ntypes
;
j
++
)
if
(
setflag
[
i
][
j
])
cut
[
i
][
j
]
=
cut_global
;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairCoulDiel
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
5
||
narg
>
6
)
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
);
eps_s
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
double
rme_one
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
double
sigmae_one
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
double
cut_one
=
cut_global
;
if
(
narg
==
6
)
cut_one
=
force
->
numeric
(
FLERR
,
arg
[
5
]);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
for
(
int
j
=
MAX
(
jlo
,
i
);
j
<=
jhi
;
j
++
)
{
sigmae
[
i
][
j
]
=
sigmae_one
;
rme
[
i
][
j
]
=
rme_one
;
cut
[
i
][
j
]
=
cut_one
;
setflag
[
i
][
j
]
=
1
;
count
++
;
}
}
a_eps
=
0.5
*
(
5.2
+
eps_s
);
b_eps
=
0.5
*
(
eps_s
-
5.2
);
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairCoulDiel
::
init_style
()
{
if
(
!
atom
->
q_flag
)
error
->
all
(
FLERR
,
"Pair style coul/diel requires atom attribute q"
);
neighbor
->
request
(
this
,
instance_me
);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairCoulDiel
::
init_one
(
int
i
,
int
j
)
{
if
(
setflag
[
i
][
j
]
==
0
)
{
error
->
all
(
FLERR
,
"for pair style coul/diel, parameters need to be set explicitly for all pairs."
);
}
double
*
q
=
atom
->
q
;
double
qqrd2e
=
force
->
qqrd2e
;
if
(
offset_flag
)
{
double
rarg
=
(
cut
[
i
][
j
]
-
rme
[
i
][
j
])
/
sigmae
[
i
][
j
];
double
epsr
=
a_eps
+
b_eps
*
tanh
(
rarg
);
offset
[
i
][
j
]
=
qqrd2e
*
q
[
i
]
*
q
[
j
]
*
((
eps_s
/
epsr
)
-
1.
)
/
cut
[
i
][
j
];
}
else
offset
[
i
][
j
]
=
0.0
;
sigmae
[
j
][
i
]
=
sigmae
[
i
][
j
];
rme
[
j
][
i
]
=
rme
[
i
][
j
];
offset
[
j
][
i
]
=
offset
[
i
][
j
];
cut
[
j
][
i
]
=
cut
[
i
][
j
];
return
cut
[
i
][
j
];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairCoulDiel
::
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
(
&
rme
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
sigmae
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairCoulDiel
::
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
(
setflag
[
i
][
j
])
{
if
(
me
==
0
)
{
fread
(
&
rme
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
sigmae
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
MPI_Bcast
(
&
rme
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sigmae
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairCoulDiel
::
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
);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairCoulDiel
::
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
);
}
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
);
}
/* ---------------------------------------------------------------------- */
double
PairCoulDiel
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
r
,
rarg
,
forcedielec
,
phidielec
;
double
th
,
epsr
,
depsdr
;
double
*
q
=
atom
->
q
;
double
qqrd2e
=
force
->
qqrd2e
;
r
=
sqrt
(
rsq
);
rarg
=
(
r
-
rme
[
itype
][
jtype
])
/
sigmae
[
itype
][
jtype
];
th
=
tanh
(
rarg
);
epsr
=
a_eps
+
b_eps
*
th
;
depsdr
=
b_eps
*
(
1.
-
th
*
th
)
/
sigmae
[
itype
][
jtype
];
forcedielec
=
qqrd2e
*
q
[
i
]
*
q
[
j
]
*
((
eps_s
*
(
epsr
+
r
*
depsdr
)
/
epsr
/
epsr
)
-
1.
)
/
rsq
;
fforce
=
factor_coul
*
forcedielec
/
r
;
phidielec
=
(
qqrd2e
*
q
[
i
]
*
q
[
j
]
*
((
eps_s
/
epsr
)
-
1.
)
/
r
)
-
offset
[
itype
][
jtype
];
return
factor_coul
*
phidielec
;
}
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