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dump_bond.cpp
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Created
Wed, Sep 11, 02:28
Size
3 KB
Mime Type
text/x-c
Expires
Fri, Sep 13, 02:28 (1 d, 23 h)
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blob
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Raw Data
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20692137
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rLAMMPS lammps
dump_bond.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 "string.h"
#include "dump_bond.h"
#include "atom.h"
#include "domain.h"
#include "update.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
DumpBond
::
DumpBond
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Dump
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
5
)
error
->
all
(
"Illegal dump bond command"
);
if
(
atom
->
molecular
==
0
)
error
->
all
(
"Cannot use dump bond with non-molecular system"
);
size_one
=
3
;
char
*
str
=
(
char
*
)
"%d %d %d %d"
;
int
n
=
strlen
(
str
)
+
1
;
format_default
=
new
char
[
n
];
strcpy
(
format_default
,
str
);
// one-time file open
if
(
multifile
==
0
)
openfile
();
}
/* ---------------------------------------------------------------------- */
void
DumpBond
::
init
()
{
delete
[]
format
;
char
*
str
;
if
(
format_user
)
str
=
format_user
;
else
str
=
format_default
;
int
n
=
strlen
(
str
)
+
2
;
format
=
new
char
[
n
];
strcpy
(
format
,
str
);
strcat
(
format
,
"
\n
"
);
}
/* ---------------------------------------------------------------------- */
void
DumpBond
::
write_header
(
int
ndump
)
{
fprintf
(
fp
,
"ITEM: TIMESTEP
\n
"
);
fprintf
(
fp
,
"%d
\n
"
,
update
->
ntimestep
);
fprintf
(
fp
,
"ITEM: NUMBER OF BONDS
\n
"
);
fprintf
(
fp
,
"%d
\n
"
,
ndump
);
fprintf
(
fp
,
"ITEM: BONDS
\n
"
);
}
/* ---------------------------------------------------------------------- */
int
DumpBond
::
count
()
{
index
=
0
;
int
*
num_bond
=
atom
->
num_bond
;
int
**
bond_type
=
atom
->
bond_type
;
int
**
bond_atom
=
atom
->
bond_atom
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
i
,
j
,
k
;
int
m
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
!
(
mask
[
i
]
&
groupbit
))
continue
;
for
(
j
=
0
;
j
<
num_bond
[
i
];
j
++
)
{
k
=
atom
->
map
(
bond_atom
[
i
][
j
]);
if
(
k
>=
0
&&
!
(
mask
[
k
]
&
groupbit
))
continue
;
if
(
bond_type
[
i
][
j
]
==
0
)
continue
;
m
++
;
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
DumpBond
::
pack
()
{
int
*
num_bond
=
atom
->
num_bond
;
int
**
bond_type
=
atom
->
bond_type
;
int
**
bond_atom
=
atom
->
bond_atom
;
int
*
tag
=
atom
->
tag
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
i
,
j
,
k
,
type
,
iatom
;
int
m
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
!
(
mask
[
i
]
&
groupbit
))
continue
;
for
(
j
=
0
;
j
<
num_bond
[
i
];
j
++
)
{
iatom
=
bond_atom
[
i
][
j
];
k
=
atom
->
map
(
iatom
);
if
(
k
>=
0
&&
!
(
mask
[
k
]
&
groupbit
))
continue
;
type
=
bond_type
[
i
][
j
];
if
(
type
==
0
)
continue
;
buf
[
m
++
]
=
type
;
buf
[
m
++
]
=
tag
[
i
];
buf
[
m
++
]
=
iatom
;
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
DumpBond
::
write_data
(
int
n
,
double
*
buf
)
{
int
m
=
0
;
for
(
int
i
=
0
;
i
<
n
;
i
++
)
{
index
++
;
fprintf
(
fp
,
format
,
index
,
static_cast
<
int
>
(
buf
[
m
]),
static_cast
<
int
>
(
buf
[
m
+
1
]),
static_cast
<
int
>
(
buf
[
m
+
2
]));
m
+=
size_one
;
}
}
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