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pair_lj_sf_dipole_sf.cpp
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rLAMMPS lammps
pair_lj_sf_dipole_sf.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 authors: Mario Orsi (QMUL), m.orsi@qmul.ac.uk
Samuel Genheden (University of Southampton)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "pair_lj_sf_dipole_sf.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
#include "update.h"
#include <string.h>
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
PairLJSFDipoleSF
::
PairLJSFDipoleSF
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
}
/* ---------------------------------------------------------------------- */
PairLJSFDipoleSF
::~
PairLJSFDipoleSF
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
cut_lj
);
memory
->
destroy
(
cut_ljsq
);
memory
->
destroy
(
cut_coul
);
memory
->
destroy
(
cut_coulsq
);
memory
->
destroy
(
epsilon
);
memory
->
destroy
(
sigma
);
memory
->
destroy
(
lj1
);
memory
->
destroy
(
lj2
);
memory
->
destroy
(
lj3
);
memory
->
destroy
(
lj4
);
memory
->
destroy
(
scale
);
}
}
/* ---------------------------------------------------------------------- */
void
PairLJSFDipoleSF
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
ecoul
,
fx
,
fy
,
fz
;
double
rsq
,
rinv
,
r2inv
,
r6inv
,
r3inv
,
r5inv
;
double
forcecoulx
,
forcecouly
,
forcecoulz
,
crossx
,
crossy
,
crossz
;
double
tixcoul
,
tiycoul
,
tizcoul
,
tjxcoul
,
tjycoul
,
tjzcoul
;
double
fq
,
pdotp
,
pidotr
,
pjdotr
,
pre1
,
pre2
,
pre3
,
pre4
;
double
forcelj
,
factor_coul
,
factor_lj
;
double
presf
,
afac
,
bfac
,
pqfac
,
qpfac
,
forceljcut
,
forceljsf
;
double
aforcecoulx
,
aforcecouly
,
aforcecoulz
;
double
bforcecoulx
,
bforcecouly
,
bforcecoulz
;
double
rcutlj2inv
,
rcutcoul2inv
,
rcutlj6inv
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
evdwl
=
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
;
double
**
mu
=
atom
->
mu
;
double
**
torque
=
atom
->
torque
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
// The global scaling parameters aren't used anymore
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
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_lj
=
special_lj
[
sbmask
(
j
)];
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
])
{
r2inv
=
1.0
/
rsq
;
rinv
=
sqrt
(
r2inv
);
// atom can have both a charge and dipole
// i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
forcecoulx
=
forcecouly
=
forcecoulz
=
0.0
;
tixcoul
=
tiycoul
=
tizcoul
=
0.0
;
tjxcoul
=
tjycoul
=
tjzcoul
=
0.0
;
if
(
rsq
<
cut_coulsq
[
itype
][
jtype
])
{
rcutcoul2inv
=
1.0
/
cut_coulsq
[
itype
][
jtype
];
if
(
qtmp
!=
0.0
&&
q
[
j
]
!=
0.0
)
{
pre1
=
qtmp
*
q
[
j
]
*
rinv
*
(
r2inv
-
rcutcoul2inv
);
forcecoulx
+=
pre1
*
delx
;
forcecouly
+=
pre1
*
dely
;
forcecoulz
+=
pre1
*
delz
;
}
if
(
mu
[
i
][
3
]
>
0.0
&&
mu
[
j
][
3
]
>
0.0
)
{
r3inv
=
r2inv
*
rinv
;
r5inv
=
r3inv
*
r2inv
;
pdotp
=
mu
[
i
][
0
]
*
mu
[
j
][
0
]
+
mu
[
i
][
1
]
*
mu
[
j
][
1
]
+
mu
[
i
][
2
]
*
mu
[
j
][
2
];
pidotr
=
mu
[
i
][
0
]
*
delx
+
mu
[
i
][
1
]
*
dely
+
mu
[
i
][
2
]
*
delz
;
pjdotr
=
mu
[
j
][
0
]
*
delx
+
mu
[
j
][
1
]
*
dely
+
mu
[
j
][
2
]
*
delz
;
afac
=
1.0
-
rsq
*
rsq
*
rcutcoul2inv
*
rcutcoul2inv
;
pre1
=
afac
*
(
pdotp
-
3.0
*
r2inv
*
pidotr
*
pjdotr
);
aforcecoulx
=
pre1
*
delx
;
aforcecouly
=
pre1
*
dely
;
aforcecoulz
=
pre1
*
delz
;
bfac
=
1.0
-
4.0
*
rsq
*
sqrt
(
rsq
*
rcutcoul2inv
)
*
rcutcoul2inv
+
3.0
*
rsq
*
rsq
*
rcutcoul2inv
*
rcutcoul2inv
;
presf
=
2.0
*
r2inv
*
pidotr
*
pjdotr
;
bforcecoulx
=
bfac
*
(
pjdotr
*
mu
[
i
][
0
]
+
pidotr
*
mu
[
j
][
0
]
-
presf
*
delx
);
bforcecouly
=
bfac
*
(
pjdotr
*
mu
[
i
][
1
]
+
pidotr
*
mu
[
j
][
1
]
-
presf
*
dely
);
bforcecoulz
=
bfac
*
(
pjdotr
*
mu
[
i
][
2
]
+
pidotr
*
mu
[
j
][
2
]
-
presf
*
delz
);
forcecoulx
+=
3.0
*
r5inv
*
(
aforcecoulx
+
bforcecoulx
);
forcecouly
+=
3.0
*
r5inv
*
(
aforcecouly
+
bforcecouly
);
forcecoulz
+=
3.0
*
r5inv
*
(
aforcecoulz
+
bforcecoulz
);
pre2
=
3.0
*
bfac
*
r5inv
*
pjdotr
;
pre3
=
3.0
*
bfac
*
r5inv
*
pidotr
;
pre4
=
-
bfac
*
r3inv
;
crossx
=
pre4
*
(
mu
[
i
][
1
]
*
mu
[
j
][
2
]
-
mu
[
i
][
2
]
*
mu
[
j
][
1
]);
crossy
=
pre4
*
(
mu
[
i
][
2
]
*
mu
[
j
][
0
]
-
mu
[
i
][
0
]
*
mu
[
j
][
2
]);
crossz
=
pre4
*
(
mu
[
i
][
0
]
*
mu
[
j
][
1
]
-
mu
[
i
][
1
]
*
mu
[
j
][
0
]);
tixcoul
+=
crossx
+
pre2
*
(
mu
[
i
][
1
]
*
delz
-
mu
[
i
][
2
]
*
dely
);
tiycoul
+=
crossy
+
pre2
*
(
mu
[
i
][
2
]
*
delx
-
mu
[
i
][
0
]
*
delz
);
tizcoul
+=
crossz
+
pre2
*
(
mu
[
i
][
0
]
*
dely
-
mu
[
i
][
1
]
*
delx
);
tjxcoul
+=
-
crossx
+
pre3
*
(
mu
[
j
][
1
]
*
delz
-
mu
[
j
][
2
]
*
dely
);
tjycoul
+=
-
crossy
+
pre3
*
(
mu
[
j
][
2
]
*
delx
-
mu
[
j
][
0
]
*
delz
);
tjzcoul
+=
-
crossz
+
pre3
*
(
mu
[
j
][
0
]
*
dely
-
mu
[
j
][
1
]
*
delx
);
}
if
(
mu
[
i
][
3
]
>
0.0
&&
q
[
j
]
!=
0.0
)
{
r3inv
=
r2inv
*
rinv
;
r5inv
=
r3inv
*
r2inv
;
pidotr
=
mu
[
i
][
0
]
*
delx
+
mu
[
i
][
1
]
*
dely
+
mu
[
i
][
2
]
*
delz
;
pre1
=
3.0
*
q
[
j
]
*
r5inv
*
pidotr
*
(
1
-
rsq
*
rcutcoul2inv
);
pqfac
=
1.0
-
3.0
*
rsq
*
rcutcoul2inv
+
2.0
*
rsq
*
sqrt
(
rsq
*
rcutcoul2inv
)
*
rcutcoul2inv
;
pre2
=
q
[
j
]
*
r3inv
*
pqfac
;
forcecoulx
+=
pre2
*
mu
[
i
][
0
]
-
pre1
*
delx
;
forcecouly
+=
pre2
*
mu
[
i
][
1
]
-
pre1
*
dely
;
forcecoulz
+=
pre2
*
mu
[
i
][
2
]
-
pre1
*
delz
;
tixcoul
+=
pre2
*
(
mu
[
i
][
1
]
*
delz
-
mu
[
i
][
2
]
*
dely
);
tiycoul
+=
pre2
*
(
mu
[
i
][
2
]
*
delx
-
mu
[
i
][
0
]
*
delz
);
tizcoul
+=
pre2
*
(
mu
[
i
][
0
]
*
dely
-
mu
[
i
][
1
]
*
delx
);
}
if
(
mu
[
j
][
3
]
>
0.0
&&
qtmp
!=
0.0
)
{
r3inv
=
r2inv
*
rinv
;
r5inv
=
r3inv
*
r2inv
;
pjdotr
=
mu
[
j
][
0
]
*
delx
+
mu
[
j
][
1
]
*
dely
+
mu
[
j
][
2
]
*
delz
;
pre1
=
3.0
*
qtmp
*
r5inv
*
pjdotr
*
(
1
-
rsq
*
rcutcoul2inv
);
qpfac
=
1.0
-
3.0
*
rsq
*
rcutcoul2inv
+
2.0
*
rsq
*
sqrt
(
rsq
*
rcutcoul2inv
)
*
rcutcoul2inv
;
pre2
=
qtmp
*
r3inv
*
qpfac
;
forcecoulx
+=
pre1
*
delx
-
pre2
*
mu
[
j
][
0
];
forcecouly
+=
pre1
*
dely
-
pre2
*
mu
[
j
][
1
];
forcecoulz
+=
pre1
*
delz
-
pre2
*
mu
[
j
][
2
];
tjxcoul
+=
-
pre2
*
(
mu
[
j
][
1
]
*
delz
-
mu
[
j
][
2
]
*
dely
);
tjycoul
+=
-
pre2
*
(
mu
[
j
][
2
]
*
delx
-
mu
[
j
][
0
]
*
delz
);
tjzcoul
+=
-
pre2
*
(
mu
[
j
][
0
]
*
dely
-
mu
[
j
][
1
]
*
delx
);
}
}
// LJ interaction
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forceljcut
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
])
*
r2inv
;
rcutlj2inv
=
1.0
/
cut_ljsq
[
itype
][
jtype
];
rcutlj6inv
=
rcutlj2inv
*
rcutlj2inv
*
rcutlj2inv
;
forceljsf
=
(
lj1
[
itype
][
jtype
]
*
rcutlj6inv
-
lj2
[
itype
][
jtype
])
*
rcutlj6inv
*
rcutlj2inv
;
forcelj
=
factor_lj
*
(
forceljcut
-
forceljsf
);
}
else
forcelj
=
0.0
;
// total force
fq
=
factor_coul
*
qqrd2e
*
scale
[
itype
][
jtype
];
fx
=
fq
*
forcecoulx
+
delx
*
forcelj
;
fy
=
fq
*
forcecouly
+
dely
*
forcelj
;
fz
=
fq
*
forcecoulz
+
delz
*
forcelj
;
// force & torque accumulation
f
[
i
][
0
]
+=
fx
;
f
[
i
][
1
]
+=
fy
;
f
[
i
][
2
]
+=
fz
;
torque
[
i
][
0
]
+=
fq
*
tixcoul
;
torque
[
i
][
1
]
+=
fq
*
tiycoul
;
torque
[
i
][
2
]
+=
fq
*
tizcoul
;
if
(
newton_pair
||
j
<
nlocal
)
{
f
[
j
][
0
]
-=
fx
;
f
[
j
][
1
]
-=
fy
;
f
[
j
][
2
]
-=
fz
;
torque
[
j
][
0
]
+=
fq
*
tjxcoul
;
torque
[
j
][
1
]
+=
fq
*
tjycoul
;
torque
[
j
][
2
]
+=
fq
*
tjzcoul
;
}
if
(
eflag
)
{
if
(
rsq
<
cut_coulsq
[
itype
][
jtype
])
{
ecoul
=
(
1.0
-
sqrt
(
rsq
/
cut_coulsq
[
itype
][
jtype
]));
ecoul
*=
ecoul
;
ecoul
*=
qtmp
*
q
[
j
]
*
rinv
;
if
(
mu
[
i
][
3
]
>
0.0
&&
mu
[
j
][
3
]
>
0.0
)
ecoul
+=
bfac
*
(
r3inv
*
pdotp
-
3.0
*
r5inv
*
pidotr
*
pjdotr
);
if
(
mu
[
i
][
3
]
>
0.0
&&
q
[
j
]
!=
0.0
)
ecoul
+=
-
q
[
j
]
*
r3inv
*
pqfac
*
pidotr
;
if
(
mu
[
j
][
3
]
>
0.0
&&
qtmp
!=
0.0
)
ecoul
+=
qtmp
*
r3inv
*
qpfac
*
pjdotr
;
ecoul
*=
factor_coul
*
qqrd2e
*
scale
[
itype
][
jtype
];
}
else
ecoul
=
0.0
;
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
evdwl
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
])
+
rcutlj6inv
*
(
6
*
lj3
[
itype
][
jtype
]
*
rcutlj6inv
-
3
*
lj4
[
itype
][
jtype
])
*
rsq
*
rcutlj2inv
+
rcutlj6inv
*
(
-
7
*
lj3
[
itype
][
jtype
]
*
rcutlj6inv
+
4
*
lj4
[
itype
][
jtype
]);
evdwl
*=
factor_lj
;
}
else
evdwl
=
0.0
;
}
if
(
evflag
)
ev_tally_xyz
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
ecoul
,
fx
,
fy
,
fz
,
delx
,
dely
,
delz
);
}
}
}
if
(
vflag_fdotr
)
virial_fdotr_compute
();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairLJSFDipoleSF
::
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_lj
,
n
+
1
,
n
+
1
,
"pair:cut_lj"
);
memory
->
create
(
cut_ljsq
,
n
+
1
,
n
+
1
,
"pair:cut_ljsq"
);
memory
->
create
(
cut_coul
,
n
+
1
,
n
+
1
,
"pair:cut_coul"
);
memory
->
create
(
cut_coulsq
,
n
+
1
,
n
+
1
,
"pair:cut_coulsq"
);
memory
->
create
(
epsilon
,
n
+
1
,
n
+
1
,
"pair:epsilon"
);
memory
->
create
(
sigma
,
n
+
1
,
n
+
1
,
"pair:sigma"
);
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"
);
memory
->
create
(
scale
,
n
+
1
,
n
+
1
,
"pair:scale"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairLJSFDipoleSF
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
1
||
narg
>
2
)
error
->
all
(
FLERR
,
"Incorrect args in pair_style command"
);
if
(
strcmp
(
update
->
unit_style
,
"electron"
)
==
0
)
error
->
all
(
FLERR
,
"Cannot (yet) use 'electron' units with dipoles"
);
cut_lj_global
=
force
->
numeric
(
FLERR
,
arg
[
0
]);
if
(
narg
==
1
)
cut_coul_global
=
cut_lj_global
;
else
cut_coul_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
+
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
PairLJSFDipoleSF
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
4
||
narg
>
7
)
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
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
double
sigma_one
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
double
scale_one
=
1.0
;
if
(
narg
>=
5
)
scale_one
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
double
cut_lj_one
=
cut_lj_global
;
double
cut_coul_one
=
cut_coul_global
;
if
(
narg
>=
6
)
cut_coul_one
=
cut_lj_one
=
force
->
numeric
(
FLERR
,
arg
[
5
]);
if
(
narg
==
7
)
cut_coul_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
++
)
{
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
;
scale
[
i
][
j
]
=
scale_one
;
count
++
;
}
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairLJSFDipoleSF
::
init_style
()
{
if
(
!
atom
->
q_flag
||
!
atom
->
mu_flag
||
!
atom
->
torque_flag
)
error
->
all
(
FLERR
,
"Pair dipole/sf requires atom attributes q, mu, torque"
);
neighbor
->
request
(
this
,
instance_me
);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairLJSFDipoleSF
::
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
);
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
];
scale
[
j
][
i
]
=
scale
[
i
][
j
];
return
cut
;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJSFDipoleSF
::
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
);
fwrite
(
&
scale
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairLJSFDipoleSF
::
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
);
fread
(
&
scale
[
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
);
MPI_Bcast
(
&
scale
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairLJSFDipoleSF
::
write_restart_settings
(
FILE
*
fp
)
{
fwrite
(
&
cut_lj_global
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut_coul_global
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
mix_flag
,
sizeof
(
int
),
1
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairLJSFDipoleSF
::
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
(
&
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
(
&
mix_flag
,
1
,
MPI_INT
,
0
,
world
);
}
// PairLJSFDipoleSF: calculation of force is missing (to be implemented)
double
PairLJSFDipoleSF
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
r2inv
,
r6inv
;
double
pdotp
,
pidotr
,
pjdotr
,
pre1
,
delx
,
dely
,
delz
;
double
rinv
,
r3inv
,
r5inv
,
rcutlj2inv
,
rcutcoul2inv
,
rcutlj6inv
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
bfac
,
pqfac
,
qpfac
,
ecoul
,
evdwl
;
double
**
x
=
atom
->
x
;
double
*
q
=
atom
->
q
;
double
**
mu
=
atom
->
mu
;
qtmp
=
q
[
i
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
r2inv
=
1.0
/
rsq
;
rinv
=
sqrt
(
r2inv
);
fforce
=
0.0
;
if
(
rsq
<
cut_coulsq
[
itype
][
jtype
])
{
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
// if (qtmp != 0.0 && q[j] != 0.0) {
// pre1 = qtmp*q[j]*rinv*(r2inv-1.0/cut_coulsq[itype][jtype]);
// forcecoulx += pre1*delx;
// forcecouly += pre1*dely;
// forcecoulz += pre1*delz;
// }
if
(
mu
[
i
][
3
]
>
0.0
&&
mu
[
j
][
3
]
>
0.0
)
{
r3inv
=
r2inv
*
rinv
;
r5inv
=
r3inv
*
r2inv
;
rcutcoul2inv
=
1.0
/
cut_coulsq
[
itype
][
jtype
];
pdotp
=
mu
[
i
][
0
]
*
mu
[
j
][
0
]
+
mu
[
i
][
1
]
*
mu
[
j
][
1
]
+
mu
[
i
][
2
]
*
mu
[
j
][
2
];
pidotr
=
mu
[
i
][
0
]
*
delx
+
mu
[
i
][
1
]
*
dely
+
mu
[
i
][
2
]
*
delz
;
pjdotr
=
mu
[
j
][
0
]
*
delx
+
mu
[
j
][
1
]
*
dely
+
mu
[
j
][
2
]
*
delz
;
bfac
=
1.0
-
4.0
*
rsq
*
sqrt
(
rsq
)
*
rcutcoul2inv
*
sqrt
(
rcutcoul2inv
)
+
3.0
*
rsq
*
rsq
*
rcutcoul2inv
*
rcutcoul2inv
;
}
if
(
mu
[
i
][
3
]
>
0.0
&&
q
[
j
]
!=
0.0
)
{
r3inv
=
r2inv
*
rinv
;
r5inv
=
r3inv
*
r2inv
;
pidotr
=
mu
[
i
][
0
]
*
delx
+
mu
[
i
][
1
]
*
dely
+
mu
[
i
][
2
]
*
delz
;
rcutcoul2inv
=
1.0
/
cut_coulsq
[
itype
][
jtype
];
pqfac
=
1.0
-
3.0
*
rsq
*
rcutcoul2inv
+
2.0
*
rsq
*
sqrt
(
rsq
)
*
rcutcoul2inv
*
sqrt
(
rcutcoul2inv
);
}
if
(
mu
[
j
][
3
]
>
0.0
&&
qtmp
!=
0.0
)
{
r3inv
=
r2inv
*
rinv
;
r5inv
=
r3inv
*
r2inv
;
pjdotr
=
mu
[
j
][
0
]
*
delx
+
mu
[
j
][
1
]
*
dely
+
mu
[
j
][
2
]
*
delz
;
rcutcoul2inv
=
1.0
/
cut_coulsq
[
itype
][
jtype
];
qpfac
=
1.0
-
3.0
*
rsq
*
rcutcoul2inv
+
2.0
*
rsq
*
sqrt
(
rsq
)
*
rcutcoul2inv
*
sqrt
(
rcutcoul2inv
);
}
}
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
r6inv
=
r2inv
*
r2inv
*
r2inv
;
rcutlj2inv
=
1.0
/
cut_ljsq
[
itype
][
jtype
];
rcutlj6inv
=
rcutlj2inv
*
rcutlj2inv
*
rcutlj2inv
;
}
double
eng
=
0.0
;
if
(
rsq
<
cut_coulsq
[
itype
][
jtype
])
{
ecoul
=
(
1.0
-
sqrt
(
rsq
)
/
sqrt
(
cut_coulsq
[
itype
][
jtype
]));
ecoul
*=
ecoul
;
ecoul
*=
qtmp
*
q
[
j
]
*
rinv
;
if
(
mu
[
i
][
3
]
>
0.0
&&
mu
[
j
][
3
]
>
0.0
)
ecoul
+=
bfac
*
(
r3inv
*
pdotp
-
3.0
*
r5inv
*
pidotr
*
pjdotr
);
if
(
mu
[
i
][
3
]
>
0.0
&&
q
[
j
]
!=
0.0
)
ecoul
+=
-
q
[
j
]
*
r3inv
*
pqfac
*
pidotr
;
if
(
mu
[
j
][
3
]
>
0.0
&&
qtmp
!=
0.0
)
ecoul
+=
qtmp
*
r3inv
*
qpfac
*
pjdotr
;
ecoul
*=
factor_coul
*
force
->
qqrd2e
*
scale
[
itype
][
jtype
];
eng
+=
ecoul
;
}
if
(
rsq
<
cut_ljsq
[
itype
][
jtype
])
{
evdwl
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
])
+
rcutlj6inv
*
(
6
*
lj3
[
itype
][
jtype
]
*
rcutlj6inv
-
3
*
lj4
[
itype
][
jtype
])
*
rsq
*
rcutlj2inv
+
rcutlj6inv
*
(
-
7
*
lj3
[
itype
][
jtype
]
*
rcutlj6inv
+
4
*
lj4
[
itype
][
jtype
]);
eng
+=
evdwl
*
factor_lj
;
}
return
eng
;
}
/* ---------------------------------------------------------------------- */
void
*
PairLJSFDipoleSF
::
extract
(
const
char
*
str
,
int
&
dim
)
{
dim
=
2
;
if
(
strcmp
(
str
,
"epsilon"
)
==
0
)
return
(
void
*
)
epsilon
;
if
(
strcmp
(
str
,
"sigma"
)
==
0
)
return
(
void
*
)
sigma
;
if
(
strcmp
(
str
,
"scale"
)
==
0
)
return
(
void
*
)
scale
;
return
NULL
;
}
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