Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F87992935
pair_zbl.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Oct 16, 05:05
Size
10 KB
Mime Type
text/x-c
Expires
Fri, Oct 18, 05:05 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
21689675
Attached To
rLAMMPS lammps
pair_zbl.cpp
View Options
/* ----------------------------------------------------------------------
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: Stephen Foiles, Aidan Thompson (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_zbl.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
// From J.F. Zeigler, J. P. Biersack and U. Littmark,
// "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985.
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
using
namespace
PairZBLConstants
;
/* ---------------------------------------------------------------------- */
PairZBL
::
PairZBL
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
PairZBL
::~
PairZBL
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
z
);
memory
->
destroy
(
d1a
);
memory
->
destroy
(
d2a
);
memory
->
destroy
(
d3a
);
memory
->
destroy
(
d4a
);
memory
->
destroy
(
zze
);
memory
->
destroy
(
sw1
);
memory
->
destroy
(
sw2
);
memory
->
destroy
(
sw3
);
memory
->
destroy
(
sw4
);
memory
->
destroy
(
sw5
);
}
}
/* ---------------------------------------------------------------------- */
void
PairZBL
::
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
,
r
,
t
,
fswitch
,
eswitch
;
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
;
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
];
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
<
cut_globalsq
)
{
r
=
sqrt
(
rsq
);
fpair
=
dzbldr
(
r
,
itype
,
jtype
);
if
(
rsq
>
cut_innersq
)
{
t
=
r
-
cut_inner
;
fswitch
=
t
*
t
*
(
sw1
[
itype
][
jtype
]
+
sw2
[
itype
][
jtype
]
*
t
);
fpair
+=
fswitch
;
}
fpair
*=
-
1.0
/
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
)
{
evdwl
=
e_zbl
(
r
,
itype
,
jtype
);
evdwl
+=
sw5
[
itype
][
jtype
];
if
(
rsq
>
cut_innersq
)
{
eswitch
=
t
*
t
*
t
*
(
sw3
[
itype
][
jtype
]
+
sw4
[
itype
][
jtype
]
*
t
);
evdwl
+=
eswitch
;
}
}
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
PairZBL
::
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
(
z
,
n
+
1
,
"pair:z"
);
memory
->
create
(
d1a
,
n
+
1
,
n
+
1
,
"pair:d1a"
);
memory
->
create
(
d2a
,
n
+
1
,
n
+
1
,
"pair:d2a"
);
memory
->
create
(
d3a
,
n
+
1
,
n
+
1
,
"pair:d3a"
);
memory
->
create
(
d4a
,
n
+
1
,
n
+
1
,
"pair:d4a"
);
memory
->
create
(
zze
,
n
+
1
,
n
+
1
,
"pair:zze"
);
memory
->
create
(
sw1
,
n
+
1
,
n
+
1
,
"pair:sw1"
);
memory
->
create
(
sw2
,
n
+
1
,
n
+
1
,
"pair:sw2"
);
memory
->
create
(
sw3
,
n
+
1
,
n
+
1
,
"pair:sw3"
);
memory
->
create
(
sw4
,
n
+
1
,
n
+
1
,
"pair:sw4"
);
memory
->
create
(
sw5
,
n
+
1
,
n
+
1
,
"pair:sw5"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairZBL
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
2
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
cut_inner
=
force
->
numeric
(
FLERR
,
arg
[
0
]);
cut_global
=
force
->
numeric
(
FLERR
,
arg
[
1
]);
if
(
cut_inner
<=
0.0
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
if
(
cut_inner
>
cut_global
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairZBL
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
3
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
;
force
->
bounds
(
arg
[
0
],
atom
->
ntypes
,
ilo
,
ihi
);
int
jlo
,
jhi
;
force
->
bounds
(
arg
[
1
],
atom
->
ntypes
,
jlo
,
jhi
);
double
z_one
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
// Set flag for each i-j pair
// Set z-parameter only for i-i pairs
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
for
(
int
j
=
MAX
(
jlo
,
i
);
j
<=
jhi
;
j
++
)
{
if
(
i
==
j
)
z
[
i
]
=
z_one
;
setflag
[
i
][
j
]
=
1
;
count
++
;
}
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairZBL
::
init_style
()
{
neighbor
->
request
(
this
);
cut_innersq
=
cut_inner
*
cut_inner
;
cut_globalsq
=
cut_global
*
cut_global
;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairZBL
::
init_one
(
int
i
,
int
j
)
{
double
ainv
=
(
pow
(
z
[
i
],
pzbl
)
+
pow
(
z
[
j
],
pzbl
))
/
(
a0
*
force
->
angstrom
);
d1a
[
i
][
j
]
=
d1
*
ainv
;
d2a
[
i
][
j
]
=
d2
*
ainv
;
d3a
[
i
][
j
]
=
d3
*
ainv
;
d4a
[
i
][
j
]
=
d4
*
ainv
;
zze
[
i
][
j
]
=
z
[
i
]
*
z
[
j
]
*
force
->
qqr2e
*
force
->
qelectron
*
force
->
qelectron
;
d1a
[
j
][
i
]
=
d1a
[
i
][
j
];
d2a
[
j
][
i
]
=
d2a
[
i
][
j
];
d3a
[
j
][
i
]
=
d3a
[
i
][
j
];
d4a
[
j
][
i
]
=
d4a
[
i
][
j
];
zze
[
j
][
i
]
=
zze
[
i
][
j
];
// e = t^3 (sw3 + sw4*t) + sw5
// = A/3*t^3 + B/4*t^4 + C
// sw3 = A/3
// sw4 = B/4
// sw5 = C
// dedr = t^2 (sw1 + sw2*t)
// = A*t^2 + B*t^3
// sw1 = A
// sw2 = B
// de2dr2 = 2*A*t + 3*B*t^2
// Require that at t = tc:
// e = -Fc
// dedr = -Fc'
// d2edr2 = -Fc''
// Hence:
// A = (-3Fc' + tc*Fc'')/tc^2
// B = ( 2Fc' - tc*Fc'')/tc^3
// C = -Fc + tc/2*Fc' - tc^2/12*Fc''
double
tc
=
cut_global
-
cut_inner
;
double
fc
=
e_zbl
(
cut_global
,
i
,
j
);
double
fcp
=
dzbldr
(
cut_global
,
i
,
j
);
double
fcpp
=
d2zbldr2
(
cut_global
,
i
,
j
);
double
swa
=
(
-
3.0
*
fcp
+
tc
*
fcpp
)
/
(
tc
*
tc
);
double
swb
=
(
2.0
*
fcp
-
tc
*
fcpp
)
/
(
tc
*
tc
*
tc
);
double
swc
=
-
fc
+
(
tc
/
2.0
)
*
fcp
-
(
tc
*
tc
/
12.0
)
*
fcpp
;
sw1
[
i
][
j
]
=
swa
;
sw2
[
i
][
j
]
=
swb
;
sw3
[
i
][
j
]
=
swa
/
3.0
;
sw4
[
i
][
j
]
=
swb
/
4.0
;
sw5
[
i
][
j
]
=
swc
;
sw1
[
j
][
i
]
=
sw1
[
i
][
j
];
sw2
[
j
][
i
]
=
sw2
[
i
][
j
];
sw3
[
j
][
i
]
=
sw3
[
i
][
j
];
sw4
[
j
][
i
]
=
sw4
[
i
][
j
];
sw5
[
j
][
i
]
=
sw5
[
i
][
j
];
return
cut_global
;
}
/* ---------------------------------------------------------------------- */
double
PairZBL
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
dummy1
,
double
dummy2
,
double
&
fforce
)
{
double
phi
,
r
,
t
,
eswitch
,
fswitch
;
r
=
sqrt
(
rsq
);
fforce
=
dzbldr
(
r
,
itype
,
jtype
);
if
(
rsq
>
cut_innersq
)
{
t
=
r
-
cut_inner
;
fswitch
=
t
*
t
*
(
sw1
[
itype
][
jtype
]
+
sw2
[
itype
][
jtype
]
*
t
);
fforce
+=
fswitch
;
}
fforce
*=
-
1.0
/
r
;
phi
=
e_zbl
(
r
,
itype
,
jtype
);
phi
+=
sw5
[
itype
][
jtype
];
if
(
rsq
>
cut_innersq
)
{
eswitch
=
t
*
t
*
t
*
(
sw3
[
itype
][
jtype
]
+
sw4
[
itype
][
jtype
]
*
t
);
phi
+=
eswitch
;
}
return
phi
;
}
/* ----------------------------------------------------------------------
compute ZBL pair energy
------------------------------------------------------------------------- */
double
PairZBL
::
e_zbl
(
double
r
,
int
i
,
int
j
)
{
double
d1aij
=
d1a
[
i
][
j
];
double
d2aij
=
d2a
[
i
][
j
];
double
d3aij
=
d3a
[
i
][
j
];
double
d4aij
=
d4a
[
i
][
j
];
double
zzeij
=
zze
[
i
][
j
];
double
rinv
=
1.0
/
r
;
double
sum
=
c1
*
exp
(
-
d1aij
*
r
);
sum
+=
c2
*
exp
(
-
d2aij
*
r
);
sum
+=
c3
*
exp
(
-
d3aij
*
r
);
sum
+=
c4
*
exp
(
-
d4aij
*
r
);
double
result
=
zzeij
*
sum
*
rinv
;
return
result
;
};
/* ----------------------------------------------------------------------
compute ZBL first derivative
------------------------------------------------------------------------- */
double
PairZBL
::
dzbldr
(
double
r
,
int
i
,
int
j
)
{
double
d1aij
=
d1a
[
i
][
j
];
double
d2aij
=
d2a
[
i
][
j
];
double
d3aij
=
d3a
[
i
][
j
];
double
d4aij
=
d4a
[
i
][
j
];
double
zzeij
=
zze
[
i
][
j
];
double
rinv
=
1.0
/
r
;
double
e1
=
exp
(
-
d1aij
*
r
);
double
e2
=
exp
(
-
d2aij
*
r
);
double
e3
=
exp
(
-
d3aij
*
r
);
double
e4
=
exp
(
-
d4aij
*
r
);
double
sum
=
c1
*
e1
;
sum
+=
c2
*
e2
;
sum
+=
c3
*
e3
;
sum
+=
c4
*
e4
;
double
sum_p
=
-
c1
*
d1aij
*
e1
;
sum_p
-=
c2
*
d2aij
*
e2
;
sum_p
-=
c3
*
d3aij
*
e3
;
sum_p
-=
c4
*
d4aij
*
e4
;
double
result
=
zzeij
*
(
sum_p
-
sum
*
rinv
)
*
rinv
;
return
result
;
};
/* ----------------------------------------------------------------------
compute ZBL second derivative
------------------------------------------------------------------------- */
double
PairZBL
::
d2zbldr2
(
double
r
,
int
i
,
int
j
)
{
double
d1aij
=
d1a
[
i
][
j
];
double
d2aij
=
d2a
[
i
][
j
];
double
d3aij
=
d3a
[
i
][
j
];
double
d4aij
=
d4a
[
i
][
j
];
double
zzeij
=
zze
[
i
][
j
];
double
rinv
=
1.0
/
r
;
double
e1
=
exp
(
-
d1aij
*
r
);
double
e2
=
exp
(
-
d2aij
*
r
);
double
e3
=
exp
(
-
d3aij
*
r
);
double
e4
=
exp
(
-
d4aij
*
r
);
double
sum
=
c1
*
e1
;
sum
+=
c2
*
e2
;
sum
+=
c3
*
e3
;
sum
+=
c4
*
e4
;
double
sum_p
=
c1
*
e1
*
d1aij
;
sum_p
+=
c2
*
e2
*
d2aij
;
sum_p
+=
c3
*
e3
*
d3aij
;
sum_p
+=
c4
*
e4
*
d4aij
;
double
sum_pp
=
c1
*
e1
*
d1aij
*
d1aij
;
sum_pp
+=
c2
*
e2
*
d2aij
*
d2aij
;
sum_pp
+=
c3
*
e3
*
d3aij
*
d3aij
;
sum_pp
+=
c4
*
e4
*
d4aij
*
d4aij
;
double
result
=
zzeij
*
(
sum_pp
+
2.0
*
sum_p
*
rinv
+
2.0
*
sum
*
rinv
*
rinv
)
*
rinv
;
return
result
;
};
Event Timeline
Log In to Comment