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fix_reax_c.cpp
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Wed, Jul 3, 18:37
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Fri, Jul 5, 18:37 (2 d)
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rLAMMPS lammps
fix_reax_c.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: Hasan Metin Aktulga, Purdue University
(now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov)
Please cite the related publication:
H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
"Parallel Reactive Molecular Dynamics: Numerical Methods and
Algorithmic Techniques", Parallel Computing, in press.
------------------------------------------------------------------------- */
#include "fix_reax_c.h"
#include "atom.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
#define MAX_REAX_BONDS 30
#define MIN_REAX_BONDS 15
#define MIN_REAX_HBONDS 25
/* ---------------------------------------------------------------------- */
FixReaxC
::
FixReaxC
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
// perform initial allocation of atom-based arrays
// register with atom class
num_bonds
=
NULL
;
num_hbonds
=
NULL
;
grow_arrays
(
atom
->
nmax
);
atom
->
add_callback
(
0
);
// initialize arrays to MIN so atom migration is OK the 1st time
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
num_bonds
[
i
]
=
num_hbonds
[
i
]
=
MIN_REAX_BONDS
;
// set comm sizes needed by this fix
comm_forward
=
1
;
}
/* ---------------------------------------------------------------------- */
FixReaxC
::~
FixReaxC
()
{
// unregister this fix so atom class doesn't invoke it any more
atom
->
delete_callback
(
id
,
0
);
// delete locally stored arrays
memory
->
destroy
(
num_bonds
);
memory
->
destroy
(
num_hbonds
);
}
/* ---------------------------------------------------------------------- */
int
FixReaxC
::
setmask
()
{
int
mask
=
0
;
return
mask
;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double
FixReaxC
::
memory_usage
()
{
int
nmax
=
atom
->
nmax
;
double
bytes
=
nmax
*
2
*
sizeof
(
int
);
return
bytes
;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void
FixReaxC
::
grow_arrays
(
int
nmax
)
{
memory
->
grow
(
num_bonds
,
nmax
,
"reaxc:num_bonds"
);
memory
->
grow
(
num_hbonds
,
nmax
,
"reaxc:num_hbonds"
);
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void
FixReaxC
::
copy_arrays
(
int
i
,
int
j
,
int
delflag
)
{
num_bonds
[
j
]
=
num_bonds
[
i
];
num_hbonds
[
j
]
=
num_hbonds
[
i
];
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int
FixReaxC
::
pack_exchange
(
int
i
,
double
*
buf
)
{
buf
[
0
]
=
num_bonds
[
i
];
buf
[
1
]
=
num_hbonds
[
i
];
return
2
;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int
FixReaxC
::
unpack_exchange
(
int
nlocal
,
double
*
buf
)
{
num_bonds
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
0
]);
num_hbonds
[
nlocal
]
=
static_cast
<
int
>
(
buf
[
1
]);
return
2
;
}
/* ---------------------------------------------------------------------- */
int
FixReaxC
::
pack_forward_comm
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
num_bonds
[
j
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
FixReaxC
::
unpack_forward_comm
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
num_bonds
[
i
]
=
static_cast
<
int
>
(
buf
[
m
++
]);
}
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