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fix_reaxc_species_kokkos.cpp
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Sat, Jul 6, 01:38
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rLAMMPS lammps
fix_reaxc_species_kokkos.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: Stan Moore (Sandia)
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <math.h>
#include "atom.h"
#include <string.h>
#include "fix_ave_atom.h"
#include "fix_reaxc_species_kokkos.h"
#include "domain.h"
#include "update.h"
#include "pair_reax_c_kokkos.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "comm.h"
#include "force.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
#include "reaxc_list.h"
#include "atom_masks.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
/* ---------------------------------------------------------------------- */
FixReaxCSpeciesKokkos
::
FixReaxCSpeciesKokkos
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
FixReaxCSpecies
(
lmp
,
narg
,
arg
)
{
kokkosable
=
1
;
atomKK
=
(
AtomKokkos
*
)
atom
;
// NOTE: Could improve performance if a Kokkos version of ComputeSpecAtom is added
datamask_read
=
X_MASK
|
V_MASK
|
Q_MASK
|
MASK_MASK
;
datamask_modify
=
EMPTY_MASK
;
}
/* ---------------------------------------------------------------------- */
FixReaxCSpeciesKokkos
::~
FixReaxCSpeciesKokkos
()
{
}
/* ---------------------------------------------------------------------- */
void
FixReaxCSpeciesKokkos
::
init
()
{
Pair
*
pair_kk
=
force
->
pair_match
(
"reax/c/kk"
,
1
);
if
(
pair_kk
==
NULL
)
error
->
all
(
FLERR
,
"Cannot use fix reax/c/species/kk without "
"pair_style reax/c/kk"
);
FixReaxCSpecies
::
init
();
}
/* ---------------------------------------------------------------------- */
void
FixReaxCSpeciesKokkos
::
FindMolecule
()
{
int
i
,
j
,
ii
,
jj
,
inum
,
itype
,
jtype
,
loop
,
looptot
;
int
change
,
done
,
anychange
;
int
*
mask
=
atom
->
mask
;
double
bo_tmp
,
bo_cut
;
double
**
spec_atom
=
f_SPECBOND
->
array_atom
;
inum
=
reaxc
->
list
->
inum
;
typename
ArrayTypes
<
LMPHostType
>::
t_int_1d
ilist
;
if
(
reaxc
->
execution_space
==
Host
)
{
NeighListKokkos
<
LMPHostType
>*
k_list
=
static_cast
<
NeighListKokkos
<
LMPHostType
>*>
(
reaxc
->
list
);
k_list
->
k_ilist
.
sync
<
LMPHostType
>
();
ilist
=
k_list
->
k_ilist
.
h_view
;
}
else
{
NeighListKokkos
<
LMPDeviceType
>*
k_list
=
static_cast
<
NeighListKokkos
<
LMPDeviceType
>*>
(
reaxc
->
list
);
k_list
->
k_ilist
.
sync
<
LMPHostType
>
();
ilist
=
k_list
->
k_ilist
.
h_view
;
}
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
mask
[
i
]
&
groupbit
)
{
clusterID
[
i
]
=
atom
->
tag
[
i
];
x0
[
i
].
x
=
spec_atom
[
i
][
1
];
x0
[
i
].
y
=
spec_atom
[
i
][
2
];
x0
[
i
].
z
=
spec_atom
[
i
][
3
];
}
else
clusterID
[
i
]
=
0.0
;
}
loop
=
0
;
while
(
1
)
{
comm
->
forward_comm_fix
(
this
);
loop
++
;
change
=
0
;
while
(
1
)
{
done
=
1
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
!
(
mask
[
i
]
&
groupbit
))
continue
;
itype
=
atom
->
type
[
i
];
for
(
jj
=
0
;
jj
<
MAXSPECBOND
;
jj
++
)
{
j
=
reaxc
->
tmpid
[
i
][
jj
];
if
(
j
<
i
)
continue
;
if
(
!
(
mask
[
j
]
&
groupbit
))
continue
;
if
(
clusterID
[
i
]
==
clusterID
[
j
]
&&
PBCconnected
[
i
]
==
PBCconnected
[
j
]
&&
x0
[
i
].
x
==
x0
[
j
].
x
&&
x0
[
i
].
y
==
x0
[
j
].
y
&&
x0
[
i
].
z
==
x0
[
j
].
z
)
continue
;
jtype
=
atom
->
type
[
j
];
bo_cut
=
BOCut
[
itype
][
jtype
];
bo_tmp
=
spec_atom
[
i
][
jj
+
7
];
if
(
bo_tmp
>
bo_cut
)
{
clusterID
[
i
]
=
clusterID
[
j
]
=
MIN
(
clusterID
[
i
],
clusterID
[
j
]);
PBCconnected
[
i
]
=
PBCconnected
[
j
]
=
MAX
(
PBCconnected
[
i
],
PBCconnected
[
j
]);
x0
[
i
]
=
x0
[
j
]
=
chAnchor
(
x0
[
i
],
x0
[
j
]);
if
((
fabs
(
spec_atom
[
i
][
1
]
-
spec_atom
[
j
][
1
])
>
reaxc
->
control
->
bond_cut
)
||
(
fabs
(
spec_atom
[
i
][
2
]
-
spec_atom
[
j
][
2
])
>
reaxc
->
control
->
bond_cut
)
||
(
fabs
(
spec_atom
[
i
][
3
]
-
spec_atom
[
j
][
3
])
>
reaxc
->
control
->
bond_cut
))
PBCconnected
[
i
]
=
PBCconnected
[
j
]
=
1
;
done
=
0
;
}
}
}
if
(
!
done
)
change
=
1
;
if
(
done
)
break
;
}
MPI_Allreduce
(
&
change
,
&
anychange
,
1
,
MPI_INT
,
MPI_MAX
,
world
);
if
(
!
anychange
)
break
;
MPI_Allreduce
(
&
loop
,
&
looptot
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
if
(
looptot
>=
400
*
nprocs
)
break
;
}
}
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