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fix_reaxc_bonds.cpp
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Sat, Aug 17, 00:55
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9 KB
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text/x-c
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Mon, Aug 19, 00:55 (2 d)
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blob
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Raw Data
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19941681
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rLAMMPS lammps
fix_reaxc_bonds.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: Ray Shan (Sandia, tnshan@sandia.gov)
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include "fix_ave_atom.h"
#include "fix_reaxc_bonds.h"
#include "atom.h"
#include "update.h"
#include "pair_reaxc.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 "reaxc_types.h"
#include "reaxc_defs.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
/* ---------------------------------------------------------------------- */
FixReaxCBonds
::
FixReaxCBonds
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
5
)
error
->
all
(
FLERR
,
"Illegal fix reax/c/bonds command"
);
MPI_Comm_rank
(
world
,
&
me
);
MPI_Comm_size
(
world
,
&
nprocs
);
ntypes
=
atom
->
ntypes
;
nmax
=
atom
->
nmax
;
nevery
=
force
->
inumeric
(
FLERR
,
arg
[
3
]);
if
(
nevery
<=
0
)
error
->
all
(
FLERR
,
"Illegal fix reax/c/bonds command"
);
if
(
me
==
0
)
{
char
*
suffix
=
strrchr
(
arg
[
4
],
'.'
);
if
(
suffix
&&
strcmp
(
suffix
,
".gz"
)
==
0
)
{
#ifdef LAMMPS_GZIP
char
gzip
[
128
];
sprintf
(
gzip
,
"gzip -6 > %s"
,
arg
[
4
]);
#ifdef _WIN32
fp
=
_popen
(
gzip
,
"wb"
);
#else
fp
=
popen
(
gzip
,
"w"
);
#endif
#else
error
->
one
(
FLERR
,
"Cannot open gzipped file"
);
#endif
}
else
fp
=
fopen
(
arg
[
4
],
"w"
);
if
(
fp
==
NULL
)
{
char
str
[
128
];
sprintf
(
str
,
"Cannot open fix reax/c/bonds file %s"
,
arg
[
4
]);
error
->
one
(
FLERR
,
str
);
}
}
if
(
atom
->
tag_consecutive
()
==
0
)
error
->
all
(
FLERR
,
"Atom IDs must be consecutive for fix reax/c bonds"
);
abo
=
NULL
;
neighid
=
NULL
;
numneigh
=
NULL
;
allocate
();
}
/* ---------------------------------------------------------------------- */
FixReaxCBonds
::~
FixReaxCBonds
()
{
MPI_Comm_rank
(
world
,
&
me
);
destroy
();
if
(
me
==
0
)
fclose
(
fp
);
}
/* ---------------------------------------------------------------------- */
int
FixReaxCBonds
::
setmask
()
{
int
mask
=
0
;
mask
|=
END_OF_STEP
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixReaxCBonds
::
setup
(
int
vflag
)
{
end_of_step
();
}
/* ---------------------------------------------------------------------- */
void
FixReaxCBonds
::
init
()
{
reaxc
=
(
PairReaxC
*
)
force
->
pair_match
(
"reax/c"
,
0
);
if
(
reaxc
==
NULL
)
error
->
all
(
FLERR
,
"Cannot use fix reax/c/bonds without "
"pair_style reax/c, reax/c/kk, or reax/c/omp"
);
}
/* ---------------------------------------------------------------------- */
void
FixReaxCBonds
::
end_of_step
()
{
Output_ReaxC_Bonds
(
update
->
ntimestep
,
fp
);
if
(
me
==
0
)
fflush
(
fp
);
}
/* ---------------------------------------------------------------------- */
void
FixReaxCBonds
::
Output_ReaxC_Bonds
(
bigint
ntimestep
,
FILE
*
fp
)
{
int
i
,
j
;
int
nbuf
,
nbuf_local
;
int
nlocal_max
,
numbonds
,
numbonds_max
;
double
*
buf
;
int
nlocal
=
atom
->
nlocal
;
int
nlocal_tot
=
static_cast
<
int
>
(
atom
->
natoms
);
if
(
atom
->
nmax
>
nmax
)
{
destroy
();
nmax
=
atom
->
nmax
;
allocate
();
}
for
(
i
=
0
;
i
<
nmax
;
i
++
)
{
numneigh
[
i
]
=
0
;
for
(
j
=
0
;
j
<
MAXREAXBOND
;
j
++
)
{
neighid
[
i
][
j
]
=
0
;
abo
[
i
][
j
]
=
0.0
;
}
}
numbonds
=
0
;
FindBond
(
lists
,
numbonds
);
// allocate a temporary buffer for the snapshot info
MPI_Allreduce
(
&
numbonds
,
&
numbonds_max
,
1
,
MPI_INT
,
MPI_MAX
,
world
);
MPI_Allreduce
(
&
nlocal
,
&
nlocal_max
,
1
,
MPI_INT
,
MPI_MAX
,
world
);
nbuf
=
1
+
(
numbonds_max
*
2
+
10
)
*
nlocal_max
;
memory
->
create
(
buf
,
nbuf
,
"reax/c/bonds:buf"
);
for
(
i
=
0
;
i
<
nbuf
;
i
++
)
buf
[
i
]
=
0.0
;
// Pass information to buffer
PassBuffer
(
buf
,
nbuf_local
);
// Receive information from buffer for output
RecvBuffer
(
buf
,
nbuf
,
nbuf_local
,
nlocal_tot
,
numbonds_max
);
memory
->
destroy
(
buf
);
}
/* ---------------------------------------------------------------------- */
void
FixReaxCBonds
::
FindBond
(
struct
_reax_list
*
lists
,
int
&
numbonds
)
{
int
*
ilist
,
i
,
ii
,
inum
;
int
j
,
pj
,
nj
;
tagint
jtag
;
double
bo_tmp
,
bo_cut
;
inum
=
reaxc
->
list
->
inum
;
ilist
=
reaxc
->
list
->
ilist
;
bond_data
*
bo_ij
;
bo_cut
=
reaxc
->
control
->
bg_cut
;
tagint
*
tag
=
atom
->
tag
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
nj
=
0
;
for
(
pj
=
Start_Index
(
i
,
reaxc
->
lists
);
pj
<
End_Index
(
i
,
reaxc
->
lists
);
++
pj
)
{
bo_ij
=
&
(
reaxc
->
lists
->
select
.
bond_list
[
pj
]
);
j
=
bo_ij
->
nbr
;
jtag
=
tag
[
j
];
bo_tmp
=
bo_ij
->
bo_data
.
BO
;
if
(
bo_tmp
>
bo_cut
)
{
neighid
[
i
][
nj
]
=
jtag
;
abo
[
i
][
nj
]
=
bo_tmp
;
nj
++
;
}
}
numneigh
[
i
]
=
nj
;
if
(
nj
>
numbonds
)
numbonds
=
nj
;
}
}
/* ---------------------------------------------------------------------- */
void
FixReaxCBonds
::
PassBuffer
(
double
*
buf
,
int
&
nbuf_local
)
{
int
i
,
j
,
k
,
numbonds
;
int
nlocal
=
atom
->
nlocal
;
j
=
2
;
buf
[
0
]
=
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
buf
[
j
-
1
]
=
atom
->
tag
[
i
];
buf
[
j
+
0
]
=
atom
->
type
[
i
];
buf
[
j
+
1
]
=
reaxc
->
workspace
->
total_bond_order
[
i
];
buf
[
j
+
2
]
=
reaxc
->
workspace
->
nlp
[
i
];
buf
[
j
+
3
]
=
atom
->
q
[
i
];
buf
[
j
+
4
]
=
numneigh
[
i
];
numbonds
=
nint
(
buf
[
j
+
4
]);
for
(
k
=
5
;
k
<
5
+
numbonds
;
k
++
)
{
buf
[
j
+
k
]
=
neighid
[
i
][
k
-
5
];
}
j
+=
(
5
+
numbonds
);
if
(
atom
->
molecule
==
NULL
)
buf
[
j
]
=
0.0
;
else
buf
[
j
]
=
atom
->
molecule
[
i
];
j
++
;
for
(
k
=
0
;
k
<
numbonds
;
k
++
)
{
buf
[
j
+
k
]
=
abo
[
i
][
k
];
}
j
+=
(
1
+
numbonds
);
}
nbuf_local
=
j
-
1
;
}
/* ---------------------------------------------------------------------- */
void
FixReaxCBonds
::
RecvBuffer
(
double
*
buf
,
int
nbuf
,
int
nbuf_local
,
int
natoms
,
int
maxnum
)
{
int
i
,
j
,
k
,
itype
;
int
inode
,
nlocal_tmp
,
numbonds
;
tagint
itag
,
jtag
;
int
nlocal
=
atom
->
nlocal
;
bigint
ntimestep
=
update
->
ntimestep
;
double
sbotmp
,
nlptmp
,
avqtmp
,
abotmp
;
double
cutof3
=
reaxc
->
control
->
bg_cut
;
MPI_Request
irequest
,
irequest2
;
if
(
me
==
0
){
fprintf
(
fp
,
"# Timestep "
BIGINT_FORMAT
"
\n
"
,
ntimestep
);
fprintf
(
fp
,
"#
\n
"
);
fprintf
(
fp
,
"# Number of particles %d
\n
"
,
natoms
);
fprintf
(
fp
,
"#
\n
"
);
fprintf
(
fp
,
"# Max number of bonds per atom %d with "
"coarse bond order cutoff %5.3f
\n
"
,
maxnum
,
cutof3
);
fprintf
(
fp
,
"# Particle connection table and bond orders
\n
"
);
fprintf
(
fp
,
"# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q
\n
"
);
}
j
=
2
;
if
(
me
==
0
)
{
for
(
inode
=
0
;
inode
<
nprocs
;
inode
++
)
{
if
(
inode
==
0
)
{
nlocal_tmp
=
nlocal
;
}
else
{
MPI_Irecv
(
&
buf
[
0
],
nbuf
,
MPI_DOUBLE
,
inode
,
0
,
world
,
&
irequest
);
MPI_Wait
(
&
irequest
,
MPI_STATUS_IGNORE
);
nlocal_tmp
=
nint
(
buf
[
0
]);
}
j
=
2
;
for
(
i
=
0
;
i
<
nlocal_tmp
;
i
++
)
{
itag
=
static_cast
<
tagint
>
(
buf
[
j
-
1
]);
itype
=
nint
(
buf
[
j
+
0
]);
sbotmp
=
buf
[
j
+
1
];
nlptmp
=
buf
[
j
+
2
];
avqtmp
=
buf
[
j
+
3
];
numbonds
=
nint
(
buf
[
j
+
4
]);
fprintf
(
fp
,
" "
TAGINT_FORMAT
" %d %d"
,
itag
,
itype
,
numbonds
);
for
(
k
=
5
;
k
<
5
+
numbonds
;
k
++
)
{
jtag
=
static_cast
<
tagint
>
(
buf
[
j
+
k
]);
fprintf
(
fp
,
" "
TAGINT_FORMAT
,
jtag
);
}
j
+=
(
5
+
numbonds
);
fprintf
(
fp
,
" "
TAGINT_FORMAT
,
static_cast
<
tagint
>
(
buf
[
j
]));
j
++
;
for
(
k
=
0
;
k
<
numbonds
;
k
++
)
{
abotmp
=
buf
[
j
+
k
];
fprintf
(
fp
,
"%14.3f"
,
abotmp
);
}
j
+=
(
1
+
numbonds
);
fprintf
(
fp
,
"%14.3f%14.3f%14.3f
\n
"
,
sbotmp
,
nlptmp
,
avqtmp
);
}
}
}
else
{
MPI_Isend
(
&
buf
[
0
],
nbuf_local
,
MPI_DOUBLE
,
0
,
0
,
world
,
&
irequest2
);
MPI_Wait
(
&
irequest2
,
MPI_STATUS_IGNORE
);
}
if
(
me
==
0
)
fprintf
(
fp
,
"#
\n
"
);
}
/* ---------------------------------------------------------------------- */
int
FixReaxCBonds
::
nint
(
const
double
&
r
)
{
int
i
=
0
;
if
(
r
>
0.0
)
i
=
static_cast
<
int
>
(
r
+
0.5
);
else
if
(
r
<
0.0
)
i
=
static_cast
<
int
>
(
r
-
0.5
);
return
i
;
}
/* ---------------------------------------------------------------------- */
void
FixReaxCBonds
::
destroy
()
{
memory
->
destroy
(
abo
);
memory
->
destroy
(
neighid
);
memory
->
destroy
(
numneigh
);
}
/* ---------------------------------------------------------------------- */
void
FixReaxCBonds
::
allocate
()
{
memory
->
create
(
abo
,
nmax
,
MAXREAXBOND
,
"reax/c/bonds:abo"
);
memory
->
create
(
neighid
,
nmax
,
MAXREAXBOND
,
"reax/c/bonds:neighid"
);
memory
->
create
(
numneigh
,
nmax
,
"reax/c/bonds:numneigh"
);
}
/* ---------------------------------------------------------------------- */
double
FixReaxCBonds
::
memory_usage
()
{
double
bytes
;
bytes
=
3.0
*
nmax
*
sizeof
(
double
);
bytes
+=
nmax
*
sizeof
(
int
);
bytes
+=
1.0
*
nmax
*
MAXREAXBOND
*
sizeof
(
double
);
bytes
+=
1.0
*
nmax
*
MAXREAXBOND
*
sizeof
(
int
);
return
bytes
;
}
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