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rLAMMPS lammps
pair_thole.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_thole.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "fix.h"
#include "fix_store.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
PairThole
::
PairThole
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
fix_drude
=
NULL
;
}
/* ---------------------------------------------------------------------- */
PairThole
::~
PairThole
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
polar
);
memory
->
destroy
(
thole
);
memory
->
destroy
(
ascreen
);
memory
->
destroy
(
cut
);
memory
->
destroy
(
scale
);
}
}
/* ---------------------------------------------------------------------- */
void
PairThole
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
double
qi
,
qj
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
ecoul
,
fpair
;
double
r
,
rsq
,
r2inv
,
rinv
,
factor_coul
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
factor_f
,
factor_e
;
int
di
,
dj
;
double
dcoul
,
asr
,
exp_asr
;
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
;
int
*
drudetype
=
fix_drude
->
drudetype
;
tagint
*
drudeid
=
fix_drude
->
drudeid
;
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
];
// only on core-drude pair
if
(
drudetype
[
type
[
i
]]
==
NOPOL_TYPE
)
continue
;
di
=
domain
->
closest_image
(
i
,
atom
->
map
(
drudeid
[
i
]));
// get dq of the core via the drude charge
if
(
drudetype
[
type
[
i
]]
==
DRUDE_TYPE
)
qi
=
q
[
i
];
else
qi
=
-
q
[
di
];
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
;
// only on core-drude pair, but not into the same pair
if
(
drudetype
[
type
[
j
]]
==
NOPOL_TYPE
||
j
==
di
)
continue
;
// get dq of the core via the drude charge
if
(
drudetype
[
type
[
j
]]
==
DRUDE_TYPE
)
qj
=
q
[
j
];
else
{
dj
=
domain
->
closest_image
(
j
,
atom
->
map
(
drudeid
[
j
]));
qj
=
-
q
[
dj
];
}
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
);
r
=
sqrt
(
rsq
);
asr
=
ascreen
[
itype
][
jtype
]
*
r
;
exp_asr
=
exp
(
-
asr
);
dcoul
=
qqrd2e
*
qi
*
qj
*
scale
[
itype
][
jtype
]
*
rinv
;
factor_f
=
0.5
*
(
2.
+
(
exp_asr
*
(
-
2.
-
asr
*
(
2.
+
asr
))))
-
factor_coul
;
if
(
eflag
)
factor_e
=
0.5
*
(
2.
-
(
exp_asr
*
(
2.
+
asr
)))
-
factor_coul
;
fpair
=
factor_f
*
dcoul
*
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
)
ecoul
=
factor_e
*
dcoul
;
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
PairThole
::
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
(
scale
,
n
+
1
,
n
+
1
,
"pair:scale"
);
memory
->
create
(
ascreen
,
n
+
1
,
n
+
1
,
"pair:ascreen"
);
memory
->
create
(
thole
,
n
+
1
,
n
+
1
,
"pair:thole"
);
memory
->
create
(
polar
,
n
+
1
,
n
+
1
,
"pair:polar"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairThole
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
2
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
thole_global
=
force
->
numeric
(
FLERR
,
arg
[
0
]);
cut_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
])
{
thole
[
i
][
j
]
=
thole_global
;
cut
[
i
][
j
]
=
cut_global
;
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairThole
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
3
||
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
polar_one
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
double
thole_one
=
thole_global
;
double
cut_one
=
cut_global
;
if
(
narg
>=
4
)
thole_one
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
if
(
narg
==
5
)
cut_one
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
for
(
int
j
=
MAX
(
jlo
,
i
);
j
<=
jhi
;
j
++
)
{
polar
[
i
][
j
]
=
polar_one
;
thole
[
i
][
j
]
=
thole_one
;
ascreen
[
i
][
j
]
=
thole
[
i
][
j
]
/
pow
(
polar
[
i
][
j
],
1.
/
3.
);
cut
[
i
][
j
]
=
cut_one
;
scale
[
i
][
j
]
=
1.0
;
setflag
[
i
][
j
]
=
1
;
count
++
;
}
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairThole
::
init_style
()
{
if
(
!
atom
->
q_flag
)
error
->
all
(
FLERR
,
"Pair style thole requires atom attribute q"
);
int
ifix
;
for
(
ifix
=
0
;
ifix
<
modify
->
nfix
;
ifix
++
)
if
(
strcmp
(
modify
->
fix
[
ifix
]
->
style
,
"drude"
)
==
0
)
break
;
if
(
ifix
==
modify
->
nfix
)
error
->
all
(
FLERR
,
"Pair thole requires fix drude"
);
fix_drude
=
(
FixDrude
*
)
modify
->
fix
[
ifix
];
neighbor
->
request
(
this
,
instance_me
);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairThole
::
init_one
(
int
i
,
int
j
)
{
if
(
setflag
[
i
][
j
]
==
0
)
cut
[
i
][
j
]
=
mix_distance
(
cut
[
i
][
i
],
cut
[
j
][
j
]);
polar
[
j
][
i
]
=
polar
[
i
][
j
];
thole
[
j
][
i
]
=
thole
[
i
][
j
];
ascreen
[
j
][
i
]
=
ascreen
[
i
][
j
];
scale
[
j
][
i
]
=
scale
[
i
][
j
];
return
cut
[
i
][
j
];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairThole
::
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
(
&
polar
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
thole
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairThole
::
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
(
&
polar
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
thole
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
ascreen
[
i
][
j
]
=
thole
[
i
][
j
]
/
pow
(
polar
[
i
][
j
],
1.
/
3.
);
}
MPI_Bcast
(
&
polar
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
thole
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
ascreen
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairThole
::
write_restart_settings
(
FILE
*
fp
)
{
fwrite
(
&
thole_global
,
sizeof
(
double
),
1
,
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
PairThole
::
read_restart_settings
(
FILE
*
fp
)
{
if
(
comm
->
me
==
0
)
{
fread
(
&
thole_global
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut_global
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
offset_flag
,
sizeof
(
int
),
1
,
fp
);
fread
(
&
mix_flag
,
sizeof
(
int
),
1
,
fp
);
}
MPI_Bcast
(
&
thole_global
,
1
,
MPI_DOUBLE
,
0
,
world
);
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
PairThole
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
r2inv
,
rinv
,
r
,
phicoul
;
double
qi
,
qj
,
factor_f
,
factor_e
,
dcoul
,
asr
,
exp_asr
;
int
di
,
dj
;
int
*
drudetype
=
fix_drude
->
drudetype
;
tagint
*
drudeid
=
fix_drude
->
drudeid
;
int
*
type
=
atom
->
type
;
// only on core-drude pair, but not on the same pair
if
(
drudetype
[
type
[
i
]]
==
NOPOL_TYPE
||
drudetype
[
type
[
j
]]
==
NOPOL_TYPE
||
j
==
i
)
return
0.0
;
// get dq of the core via the drude charge
if
(
drudetype
[
type
[
i
]]
==
DRUDE_TYPE
)
qi
=
atom
->
q
[
i
];
else
{
di
=
domain
->
closest_image
(
i
,
atom
->
map
(
drudeid
[
i
]));
qi
=
-
atom
->
q
[
di
];
}
if
(
drudetype
[
type
[
j
]]
==
DRUDE_TYPE
)
qj
=
atom
->
q
[
j
];
else
{
dj
=
domain
->
closest_image
(
j
,
atom
->
map
(
drudeid
[
j
]));
qj
=
-
atom
->
q
[
dj
];
}
r2inv
=
1.0
/
rsq
;
fforce
=
phicoul
=
0.0
;
if
(
rsq
<
cutsq
[
itype
][
jtype
])
{
rinv
=
sqrt
(
r2inv
);
r
=
sqrt
(
rsq
);
asr
=
ascreen
[
itype
][
jtype
]
*
r
;
exp_asr
=
exp
(
-
asr
);
dcoul
=
force
->
qqrd2e
*
qi
*
qj
*
scale
[
itype
][
jtype
]
*
rinv
;
factor_f
=
0.5
*
(
2.
+
(
exp_asr
*
(
-
2.
-
asr
*
(
2.
+
asr
))))
-
factor_coul
;
fforce
=
factor_f
*
dcoul
*
r2inv
;
factor_e
=
0.5
*
(
2.
-
(
exp_asr
*
(
2.
+
asr
)))
-
factor_coul
;
phicoul
=
factor_e
*
dcoul
;
}
return
phicoul
;
}
/* ---------------------------------------------------------------------- */
void
*
PairThole
::
extract
(
const
char
*
str
,
int
&
dim
)
{
dim
=
4
;
if
(
strcmp
(
str
,
"scale"
)
==
0
)
return
(
void
*
)
scale
;
if
(
strcmp
(
str
,
"polar"
)
==
0
)
return
(
void
*
)
polar
;
if
(
strcmp
(
str
,
"thole"
)
==
0
)
return
(
void
*
)
thole
;
if
(
strcmp
(
str
,
"ascreen"
)
==
0
)
return
(
void
*
)
ascreen
;
return
NULL
;
}
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