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compute_cluster_atom.cpp
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Tue, Sep 3, 20:51
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Thu, Sep 5, 20:51 (2 d)
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rLAMMPS lammps
compute_cluster_atom.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 <string.h>
#include <stdlib.h>
#include "compute_cluster_atom.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "group.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputeClusterAtom
::
ComputeClusterAtom
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
),
clusterID
(
NULL
)
{
if
(
narg
!=
4
)
error
->
all
(
FLERR
,
"Illegal compute cluster/atom command"
);
double
cutoff
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
cutsq
=
cutoff
*
cutoff
;
peratom_flag
=
1
;
size_peratom_cols
=
0
;
comm_forward
=
1
;
nmax
=
0
;
}
/* ---------------------------------------------------------------------- */
ComputeClusterAtom
::~
ComputeClusterAtom
()
{
memory
->
destroy
(
clusterID
);
}
/* ---------------------------------------------------------------------- */
void
ComputeClusterAtom
::
init
()
{
if
(
atom
->
tag_enable
==
0
)
error
->
all
(
FLERR
,
"Cannot use compute cluster/atom unless atoms have IDs"
);
if
(
force
->
pair
==
NULL
)
error
->
all
(
FLERR
,
"Compute cluster/atom requires a pair style be defined"
);
if
(
sqrt
(
cutsq
)
>
force
->
pair
->
cutforce
)
error
->
all
(
FLERR
,
"Compute cluster/atom cutoff is longer than pairwise cutoff"
);
// need an occasional full neighbor list
// full required so that pair of atoms on 2 procs both set their clusterID
int
irequest
=
neighbor
->
request
(
this
,
instance_me
);
neighbor
->
requests
[
irequest
]
->
pair
=
0
;
neighbor
->
requests
[
irequest
]
->
compute
=
1
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
full
=
1
;
neighbor
->
requests
[
irequest
]
->
occasional
=
1
;
int
count
=
0
;
for
(
int
i
=
0
;
i
<
modify
->
ncompute
;
i
++
)
if
(
strcmp
(
modify
->
compute
[
i
]
->
style
,
"cluster/atom"
)
==
0
)
count
++
;
if
(
count
>
1
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"More than one compute cluster/atom"
);
}
/* ---------------------------------------------------------------------- */
void
ComputeClusterAtom
::
init_list
(
int
id
,
NeighList
*
ptr
)
{
list
=
ptr
;
}
/* ---------------------------------------------------------------------- */
void
ComputeClusterAtom
::
compute_peratom
()
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
invoked_peratom
=
update
->
ntimestep
;
// grow clusterID array if necessary
if
(
atom
->
nmax
>
nmax
)
{
memory
->
destroy
(
clusterID
);
nmax
=
atom
->
nmax
;
memory
->
create
(
clusterID
,
nmax
,
"cluster/atom:clusterID"
);
vector_atom
=
clusterID
;
}
// invoke full neighbor list (will copy or build if necessary)
neighbor
->
build_one
(
list
);
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// if group is dynamic, insure ghost atom masks are current
if
(
group
->
dynamic
[
igroup
])
{
commflag
=
0
;
comm
->
forward_comm_compute
(
this
);
}
// every atom starts in its own cluster, with clusterID = atomID
tagint
*
tag
=
atom
->
tag
;
int
*
mask
=
atom
->
mask
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
mask
[
i
]
&
groupbit
)
clusterID
[
i
]
=
tag
[
i
];
else
clusterID
[
i
]
=
0
;
}
// loop until no more changes on any proc:
// acquire clusterIDs of ghost atoms
// loop over my atoms, checking distance to neighbors
// if both atoms are in cluster, assign lowest clusterID to both
// iterate until no changes in my atoms
// then check if any proc made changes
commflag
=
1
;
double
**
x
=
atom
->
x
;
int
change
,
done
,
anychange
;
while
(
1
)
{
comm
->
forward_comm_compute
(
this
);
change
=
0
;
while
(
1
)
{
done
=
1
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
!
(
mask
[
i
]
&
groupbit
))
continue
;
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
if
(
!
(
mask
[
j
]
&
groupbit
))
continue
;
if
(
clusterID
[
i
]
==
clusterID
[
j
])
continue
;
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
if
(
rsq
<
cutsq
)
{
clusterID
[
i
]
=
clusterID
[
j
]
=
MIN
(
clusterID
[
i
],
clusterID
[
j
]);
done
=
0
;
}
}
}
if
(
!
done
)
change
=
1
;
if
(
done
)
break
;
}
// stop if all procs are done
MPI_Allreduce
(
&
change
,
&
anychange
,
1
,
MPI_INT
,
MPI_MAX
,
world
);
if
(
!
anychange
)
break
;
}
}
/* ---------------------------------------------------------------------- */
int
ComputeClusterAtom
::
pack_forward_comm
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
m
=
0
;
if
(
commflag
)
{
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
clusterID
[
j
];
}
}
else
{
int
*
mask
=
atom
->
mask
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
ComputeClusterAtom
::
unpack_forward_comm
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
if
(
commflag
)
for
(
i
=
first
;
i
<
last
;
i
++
)
clusterID
[
i
]
=
buf
[
m
++
];
else
{
int
*
mask
=
atom
->
mask
;
for
(
i
=
first
;
i
<
last
;
i
++
)
mask
[
i
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double
ComputeClusterAtom
::
memory_usage
()
{
double
bytes
=
nmax
*
sizeof
(
double
);
return
bytes
;
}
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