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nbin_ssa.cpp
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rLAMMPS lammps
nbin_ssa.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 authors:
James Larentzos (ARL) and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */
#include "nbin_ssa.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
NBinSSA
::
NBinSSA
(
LAMMPS
*
lmp
)
:
NBinStandard
(
lmp
)
{
for
(
int
i
=
0
;
i
<
8
;
i
++
)
{
gairhead_ssa
[
i
]
=
-
1
;
}
}
NBinSSA
::~
NBinSSA
()
{
}
/* ----------------------------------------------------------------------
bin owned and ghost atoms for the Shardlow Splitting Algorithm (SSA)
local atoms are in distinct bins (binhead[]) from the ghosts
ghost atoms are "binned" in gairhead_ssa[] instead
ghosts which are not in an Active Interaction Region (AIR) are skipped
------------------------------------------------------------------------- */
void
NBinSSA
::
bin_atoms
()
{
int
i
,
ibin
;
int
nlocal
=
atom
->
nlocal
;
int
nall
=
nlocal
+
atom
->
nghost
;
if
(
includegroup
)
nlocal
=
atom
->
nfirst
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
xbin
,
ybin
,
zbin
;
last_bin
=
update
->
ntimestep
;
bboxlo_
[
0
]
=
bboxlo
[
0
];
bboxlo_
[
1
]
=
bboxlo
[
1
];
bboxlo_
[
2
]
=
bboxlo
[
2
];
bboxhi_
[
0
]
=
bboxhi
[
0
];
bboxhi_
[
1
]
=
bboxhi
[
1
];
bboxhi_
[
2
]
=
bboxhi
[
2
];
for
(
i
=
0
;
i
<
8
;
i
++
)
{
gairhead_ssa
[
i
]
=
-
1
;
}
for
(
i
=
0
;
i
<
mbins
;
i
++
)
{
binhead
[
i
]
=
-
1
;
}
// bin in reverse order so linked list will be in forward order
if
(
includegroup
)
{
int
bitmask
=
group
->
bitmask
[
includegroup
];
int
nowned
=
atom
->
nlocal
;
// NOTE: nlocal was set to atom->nfirst above
for
(
i
=
nall
-
1
;
i
>=
nowned
;
i
--
)
{
ibin
=
coord2ssaAIR
(
x
[
i
]);
if
(
ibin
<
1
)
continue
;
// skip ghost atoms not in AIR
if
(
mask
[
i
]
&
bitmask
)
{
bins
[
i
]
=
gairhead_ssa
[
ibin
];
gairhead_ssa
[
ibin
]
=
i
;
}
}
}
else
{
for
(
i
=
nall
-
1
;
i
>=
nlocal
;
i
--
)
{
ibin
=
coord2ssaAIR
(
x
[
i
]);
if
(
ibin
<
1
)
continue
;
// skip ghost atoms not in AIR
bins
[
i
]
=
gairhead_ssa
[
ibin
];
gairhead_ssa
[
ibin
]
=
i
;
}
}
for
(
i
=
nlocal
-
1
;
i
>=
0
;
i
--
)
{
ibin
=
coord2bin
(
x
[
i
][
0
],
x
[
i
][
1
],
x
[
i
][
2
],
xbin
,
ybin
,
zbin
);
// Find the bounding box of the local atoms in the bins
if
(
xbin
<
lbinxlo
)
lbinxlo
=
xbin
;
if
(
xbin
>=
lbinxhi
)
lbinxhi
=
xbin
+
1
;
if
(
ybin
<
lbinylo
)
lbinylo
=
ybin
;
if
(
ybin
>=
lbinyhi
)
lbinyhi
=
ybin
+
1
;
if
(
zbin
<
lbinzlo
)
lbinzlo
=
zbin
;
if
(
zbin
>=
lbinzhi
)
lbinzhi
=
zbin
+
1
;
bins
[
i
]
=
binhead
[
ibin
];
binhead
[
ibin
]
=
i
;
}
}
/* ---------------------------------------------------------------------- */
void
NBinSSA
::
bin_atoms_setup
(
int
nall
)
{
NBinStandard
::
bin_atoms_setup
(
nall
);
// Setup the parent class's data too
// Clear the local bin extent bounding box.
lbinxlo
=
mbinx
-
1
;
// Safe to = stencil->sx + 1
lbinylo
=
mbiny
-
1
;
// Safe to = stencil->sy + 1
lbinzlo
=
mbinz
-
1
;
// Safe to = stencil->sz + 1
lbinxhi
=
0
;
// Safe to = mbinx - stencil->sx - 1
lbinyhi
=
0
;
// Safe to = mbiny - stencil->sy - 1
lbinzhi
=
0
;
// Safe to = mbinz - stencil->sz - 1
}
/* ---------------------------------------------------------------------- */
bigint
NBinSSA
::
memory_usage
()
{
bigint
bytes
=
NBinStandard
::
memory_usage
();
// Count the parent's usage too
return
bytes
;
}
/* ----------------------------------------------------------------------
convert atom coords into the ssa active interaction region number
------------------------------------------------------------------------- */
int
NBinSSA
::
coord2ssaAIR
(
const
double
*
x
)
{
int
ix
,
iy
,
iz
;
ix
=
iy
=
iz
=
0
;
if
(
x
[
2
]
<
domain
->
sublo
[
2
])
iz
=
-
1
;
if
(
x
[
2
]
>=
domain
->
subhi
[
2
])
iz
=
1
;
if
(
x
[
1
]
<
domain
->
sublo
[
1
])
iy
=
-
1
;
if
(
x
[
1
]
>=
domain
->
subhi
[
1
])
iy
=
1
;
if
(
x
[
0
]
<
domain
->
sublo
[
0
])
ix
=
-
1
;
if
(
x
[
0
]
>=
domain
->
subhi
[
0
])
ix
=
1
;
if
(
iz
<
0
){
return
-
1
;
}
else
if
(
iz
==
0
){
if
(
iy
<
0
)
return
-
1
;
// bottom left/middle/right
if
(
(
iy
==
0
)
&&
(
ix
<
0
)
)
return
-
1
;
// left atoms
if
(
(
iy
==
0
)
&&
(
ix
==
0
)
)
return
0
;
// Locally owned atoms
if
(
(
iy
==
0
)
&&
(
ix
>
0
)
)
return
2
;
// Right atoms
if
(
(
iy
>
0
)
&&
(
ix
==
0
)
)
return
1
;
// Top-middle atoms
if
(
(
iy
>
0
)
&&
(
ix
!=
0
)
)
return
3
;
// Top-right and top-left atoms
}
else
{
// iz > 0
if
((
ix
==
0
)
&&
(
iy
==
0
))
return
4
;
// Back atoms
if
((
ix
==
0
)
&&
(
iy
!=
0
))
return
5
;
// Top-back and bottom-back atoms
if
((
ix
!=
0
)
&&
(
iy
==
0
))
return
6
;
// Left-back and right-back atoms
if
((
ix
!=
0
)
&&
(
iy
!=
0
))
return
7
;
// Back corner atoms
}
return
-
2
;
}
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