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pair_python.cpp
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Created
Sat, Jun 8, 09:42
Size
5 KB
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text/x-c
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Mon, Jun 10, 09:42 (1 d, 23 h)
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rLAMMPS lammps
pair_python.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 author: Axel Kohlmeyer and Richard Berger (Temple U)
------------------------------------------------------------------------- */
#include <Python.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_python.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "neigh_list.h"
#include "python.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
PairPython
::
PairPython
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
respa_enable
=
0
;
single_enable
=
0
;
writedata
=
0
;
restartinfo
=
0
;
one_coeff
=
1
;
reinitflag
=
0
;
python
->
init
();
}
/* ---------------------------------------------------------------------- */
PairPython
::~
PairPython
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
}
}
/* ---------------------------------------------------------------------- */
void
PairPython
::
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
,
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
])
{
const
double
r
=
sqrt
(
rsq
);
printf
(
"compute f at r=%g for types %d,%d with factor %g
\n
"
,
r
,
itype
,
jtype
,
factor_lj
);
fpair
=
0.0
;
fpair
*=
factor_lj
;
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
)
{
printf
(
"compute e at r=%g for types %d,%d with factor %g
\n
"
,
r
,
itype
,
jtype
,
factor_lj
);
evdwl
=
0.0
;
evdwl
*=
factor_lj
;
}
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
0.0
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairPython
::
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"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairPython
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
1
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
cut_global
=
force
->
numeric
(
FLERR
,
arg
[
0
]);
}
/* ----------------------------------------------------------------------
set coeffs for all type pairs
------------------------------------------------------------------------- */
void
PairPython
::
coeff
(
int
narg
,
char
**
arg
)
{
const
int
ntypes
=
atom
->
ntypes
;
if
(
narg
!=
3
+
ntypes
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
if
(
!
allocated
)
allocate
();
// make sure I,J args are * *
if
(
strcmp
(
arg
[
0
],
"*"
)
!=
0
||
strcmp
(
arg
[
1
],
"*"
)
!=
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
// check if potential python file exists
FILE
*
fp
=
fopen
(
arg
[
2
],
"r"
);
if
(
fp
==
NULL
)
error
->
all
(
FLERR
,
"Cannot open python pair potential class file"
);
PyGILState_STATE
gstate
=
PyGILState_Ensure
();
PyObject
*
pModule
=
PyImport_AddModule
(
"__main__"
);
if
(
!
pModule
)
error
->
all
(
FLERR
,
"Could not initialize embedded Python"
);
int
err
=
PyRun_SimpleFile
(
fp
,
arg
[
2
]);
if
(
err
)
error
->
all
(
FLERR
,
"Loading python pair style class failure"
);
fclose
(
fp
);
PyObject
*
py_pair_instance
=
PyObject_GetAttrString
(
pModule
,
"lammps_pair_style"
);
if
(
!
py_pair_instance
)
{
PyGILState_Release
(
gstate
);
error
->
all
(
FLERR
,
"Could not find 'lammps_pair_style instance'"
);
}
for
(
int
i
=
1
;
i
<=
ntypes
;
i
++
)
{
for
(
int
j
=
i
;
j
<=
ntypes
;
j
++
)
{
if
(
strcmp
(
arg
[
2
+
i
],
"NULL"
)
!=
0
)
{
setflag
[
i
][
j
]
=
1
;
cutsq
[
i
][
j
]
=
cut_global
*
cut_global
;
}
}
}
PyGILState_Release
(
gstate
);
}
/* ---------------------------------------------------------------------- */
double
PairPython
::
init_one
(
int
,
int
)
{
return
cut_global
;
}
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