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compute_group_group.cpp
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Mon, Sep 30, 23:18
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5 KB
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Wed, Oct 2, 23:18 (1 d, 21 h)
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rLAMMPS lammps
compute_group_group.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: Naveen Michaud-Agrawal (Johns Hopkins U)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "string.h"
#include "compute_group_group.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "neigh_list.h"
#include "group.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputeGroupGroup
::
ComputeGroupGroup
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
4
)
error
->
all
(
"Illegal compute group/group command"
);
scalar_flag
=
vector_flag
=
1
;
size_vector
=
3
;
extscalar
=
1
;
extvector
=
1
;
int
n
=
strlen
(
arg
[
3
])
+
1
;
group2
=
new
char
[
n
];
strcpy
(
group2
,
arg
[
3
]);
jgroup
=
group
->
find
(
group2
);
if
(
jgroup
==
-
1
)
error
->
all
(
"Compute group/group group ID does not exist"
);
jgroupbit
=
group
->
bitmask
[
jgroup
];
vector
=
new
double
[
3
];
}
/* ---------------------------------------------------------------------- */
ComputeGroupGroup
::~
ComputeGroupGroup
()
{
delete
[]
group2
;
delete
[]
vector
;
}
/* ---------------------------------------------------------------------- */
void
ComputeGroupGroup
::
init
()
{
if
(
force
->
pair
==
NULL
)
error
->
all
(
"No pair style defined for compute group/group"
);
// if non-hybrid, then error if single_enable = 0
// if hybrid, let hybrid determine if sub-style sets single_enable = 0
if
(
force
->
pair_match
(
"hybrid"
,
0
)
==
NULL
&&
force
->
pair
->
single_enable
==
0
)
error
->
all
(
"Pair style does not support compute group/group"
);
pair
=
force
->
pair
;
cutsq
=
force
->
pair
->
cutsq
;
// recheck that group 2 has not been deleted
jgroup
=
group
->
find
(
group2
);
if
(
jgroup
==
-
1
)
error
->
all
(
"Compute group/group group ID does not exist"
);
jgroupbit
=
group
->
bitmask
[
jgroup
];
// need an occasional half neighbor list
int
irequest
=
neighbor
->
request
((
void
*
)
this
);
neighbor
->
requests
[
irequest
]
->
pair
=
0
;
neighbor
->
requests
[
irequest
]
->
compute
=
1
;
neighbor
->
requests
[
irequest
]
->
occasional
=
1
;
}
/* ---------------------------------------------------------------------- */
void
ComputeGroupGroup
::
init_list
(
int
id
,
NeighList
*
ptr
)
{
list
=
ptr
;
}
/* ---------------------------------------------------------------------- */
double
ComputeGroupGroup
::
compute_scalar
()
{
invoked_scalar
=
invoked_vector
=
update
->
ntimestep
;
interact
();
return
scalar
;
}
/* ---------------------------------------------------------------------- */
void
ComputeGroupGroup
::
compute_vector
()
{
invoked_scalar
=
invoked_vector
=
update
->
ntimestep
;
interact
();
}
/* ---------------------------------------------------------------------- */
void
ComputeGroupGroup
::
interact
()
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
;
double
rsq
,
eng
,
fpair
,
factor_coul
,
factor_lj
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
nall
=
nlocal
+
atom
->
nghost
;
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
int
newton_pair
=
force
->
newton_pair
;
// invoke half neighbor list (will copy or build if necessary)
neighbor
->
build_one
(
list
->
index
);
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// loop over neighbors of my atoms
// skip if I,J are not in 2 groups
double
one
[
4
],
all
[
4
];
one
[
0
]
=
one
[
1
]
=
one
[
2
]
=
one
[
3
]
=
0.0
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
mask
[
i
]
&
groupbit
)
othergroupbit
=
jgroupbit
;
else
if
(
mask
[
i
]
&
jgroupbit
)
othergroupbit
=
groupbit
;
else
continue
;
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
];
if
(
j
<
nall
)
factor_coul
=
factor_lj
=
1.0
;
else
{
factor_coul
=
special_coul
[
j
/
nall
];
factor_lj
=
special_lj
[
j
/
nall
];
j
%=
nall
;
}
if
(
!
(
mask
[
j
]
&
othergroupbit
))
continue
;
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
])
{
eng
=
pair
->
single
(
i
,
j
,
itype
,
jtype
,
rsq
,
factor_coul
,
factor_lj
,
fpair
);
// energy only computed once so tally full amount
// force tally is jgroup acting on igroup
if
(
newton_pair
||
j
<
nlocal
)
{
one
[
0
]
+=
eng
;
if
(
othergroupbit
==
jgroupbit
)
{
one
[
1
]
+=
delx
*
fpair
;
one
[
2
]
+=
dely
*
fpair
;
one
[
3
]
+=
delz
*
fpair
;
}
if
(
othergroupbit
==
groupbit
)
{
one
[
1
]
-=
delx
*
fpair
;
one
[
2
]
-=
dely
*
fpair
;
one
[
3
]
-=
delz
*
fpair
;
}
// energy computed twice so tally half amount
// only tally force if I own igroup atom
}
else
{
one
[
0
]
+=
0.5
*
eng
;
if
(
othergroupbit
==
jgroupbit
)
{
one
[
1
]
+=
delx
*
fpair
;
one
[
2
]
+=
dely
*
fpair
;
one
[
3
]
+=
delz
*
fpair
;
}
}
}
}
}
MPI_Allreduce
(
one
,
all
,
4
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
scalar
=
all
[
0
];
vector
[
0
]
=
all
[
1
];
vector
[
1
]
=
all
[
2
];
vector
[
2
]
=
all
[
3
];
}
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