Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F81105991
pair_gauss_cut.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, Sep 4, 05:49
Size
10 KB
Mime Type
text/x-c
Expires
Fri, Sep 6, 05:49 (2 d)
Engine
blob
Format
Raw Data
Handle
18323485
Attached To
rLAMMPS lammps
pair_gauss_cut.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: Arben Jusufi, Axel Kohlmeyer (Temple U.)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_gauss_cut.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "update.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "math_const.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
/* ---------------------------------------------------------------------- */
PairGaussCut
::
PairGaussCut
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
respa_enable
=
0
;
}
/* ---------------------------------------------------------------------- */
PairGaussCut
::~
PairGaussCut
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
cut
);
memory
->
destroy
(
hgauss
);
memory
->
destroy
(
sigmah
);
memory
->
destroy
(
rmh
);
memory
->
destroy
(
pgauss
);
memory
->
destroy
(
offset
);
}
}
/* ---------------------------------------------------------------------- */
void
PairGaussCut
::
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
,
rexp
,
ugauss
,
factor_lj
;
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
;
double
*
special_lj
=
force
->
special_lj
;
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
];
factor_lj
=
special_lj
[
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
);
rexp
=
(
r
-
rmh
[
itype
][
jtype
])
/
sigmah
[
itype
][
jtype
];
ugauss
=
pgauss
[
itype
][
jtype
]
*
exp
(
-
0.5
*
rexp
*
rexp
);
fpair
=
factor_lj
*
rexp
/
r
*
ugauss
/
sigmah
[
itype
][
jtype
];
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
=
ugauss
-
offset
[
itype
][
jtype
];
evdwl
*=
factor_lj
;
}
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
PairGaussCut
::
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
(
hgauss
,
n
+
1
,
n
+
1
,
"pair:hgauss"
);
memory
->
create
(
sigmah
,
n
+
1
,
n
+
1
,
"pair:sigmah"
);
memory
->
create
(
rmh
,
n
+
1
,
n
+
1
,
"pair:rmh"
);
memory
->
create
(
pgauss
,
n
+
1
,
n
+
1
,
"pair:pgauss"
);
memory
->
create
(
offset
,
n
+
1
,
n
+
1
,
"pair:offset"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairGaussCut
::
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
PairGaussCut
::
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
);
double
hgauss_one
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
double
rmh_one
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
double
sigmah_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
++
)
{
hgauss
[
i
][
j
]
=
hgauss_one
;
sigmah
[
i
][
j
]
=
sigmah_one
;
rmh
[
i
][
j
]
=
rmh_one
;
cut
[
i
][
j
]
=
cut_one
;
setflag
[
i
][
j
]
=
1
;
count
++
;
}
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairGaussCut
::
init_one
(
int
i
,
int
j
)
{
if
(
setflag
[
i
][
j
]
==
0
)
error
->
all
(
FLERR
,
"All pair coeffs are not set"
);
pgauss
[
i
][
j
]
=
hgauss
[
i
][
j
]
/
sqrt
(
MY_2PI
)
/
sigmah
[
i
][
j
];
if
(
offset_flag
)
{
double
rexp
=
(
cut
[
i
][
j
]
-
rmh
[
i
][
j
])
/
sigmah
[
i
][
j
];
offset
[
i
][
j
]
=
pgauss
[
i
][
j
]
*
exp
(
-
0.5
*
rexp
*
rexp
);
}
else
offset
[
i
][
j
]
=
0.0
;
hgauss
[
j
][
i
]
=
hgauss
[
i
][
j
];
sigmah
[
j
][
i
]
=
sigmah
[
i
][
j
];
rmh
[
j
][
i
]
=
rmh
[
i
][
j
];
pgauss
[
j
][
i
]
=
pgauss
[
i
][
j
];
offset
[
j
][
i
]
=
offset
[
i
][
j
];
cut
[
j
][
i
]
=
cut
[
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
);
}
return
cut
[
i
][
j
];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairGaussCut
::
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
(
&
hgauss
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
rmh
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
sigmah
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
cut
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairGaussCut
::
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
(
&
hgauss
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
rmh
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
sigmah
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
fread
(
&
cut
[
i
][
j
],
sizeof
(
double
),
1
,
fp
);
}
MPI_Bcast
(
&
hgauss
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rmh
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sigmah
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cut
[
i
][
j
],
1
,
MPI_DOUBLE
,
0
,
world
);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairGaussCut
::
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
PairGaussCut
::
read_restart_settings
(
FILE
*
fp
)
{
int
me
=
comm
->
me
;
if
(
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
PairGaussCut
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
r
,
rexp
,
ugauss
,
phigauss
;
r
=
sqrt
(
rsq
);
rexp
=
(
r
-
rmh
[
itype
][
jtype
])
/
sigmah
[
itype
][
jtype
];
ugauss
=
pgauss
[
itype
][
jtype
]
*
exp
(
-
0.5
*
rexp
*
rexp
);
fforce
=
factor_lj
*
rexp
/
r
*
ugauss
/
sigmah
[
itype
][
jtype
];
phigauss
=
ugauss
-
offset
[
itype
][
jtype
];
return
factor_lj
*
phigauss
;
}
/* ---------------------------------------------------------------------- */
double
PairGaussCut
::
memory_usage
()
{
const
int
n
=
atom
->
ntypes
;
double
bytes
=
Pair
::
memory_usage
();
bytes
+=
7
*
((
n
+
1
)
*
(
n
+
1
)
*
sizeof
(
double
)
+
(
n
+
1
)
*
sizeof
(
double
*
));
bytes
+=
1
*
((
n
+
1
)
*
(
n
+
1
)
*
sizeof
(
int
)
+
(
n
+
1
)
*
sizeof
(
int
*
));
return
bytes
;
}
Event Timeline
Log In to Comment