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reader_native.cpp
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Sat, Jul 13, 18:38
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10 KB
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Mon, Jul 15, 18:38 (1 d, 21 h)
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rLAMMPS lammps
reader_native.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 <stdlib.h>
#include "reader_native.h"
#include "atom.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define MAXLINE 1024
// max line length in dump file
// also in read_dump.cpp
enum
{
ID
,
TYPE
,
X
,
Y
,
Z
,
VX
,
VY
,
VZ
,
Q
,
IX
,
IY
,
IZ
,
FX
,
FY
,
FZ
};
enum
{
UNSET
,
NOSCALE_NOWRAP
,
NOSCALE_WRAP
,
SCALE_NOWRAP
,
SCALE_WRAP
};
/* ---------------------------------------------------------------------- */
ReaderNative
::
ReaderNative
(
LAMMPS
*
lmp
)
:
Reader
(
lmp
)
{
line
=
new
char
[
MAXLINE
];
words
=
NULL
;
fieldindex
=
NULL
;
}
/* ---------------------------------------------------------------------- */
ReaderNative
::~
ReaderNative
()
{
delete
[]
line
;
delete
[]
words
;
memory
->
destroy
(
fieldindex
);
}
/* ----------------------------------------------------------------------
read and return time stamp from dump file
if first read reaches end-of-file, return 1 so caller can open next file
only called by proc 0
------------------------------------------------------------------------- */
int
ReaderNative
::
read_time
(
bigint
&
ntimestep
)
{
char
*
eof
=
fgets
(
line
,
MAXLINE
,
fp
);
if
(
eof
==
NULL
)
return
1
;
if
(
strstr
(
line
,
"ITEM: TIMESTEP"
)
!=
line
)
error
->
one
(
FLERR
,
"Dump file is incorrectly formatted"
);
read_lines
(
1
);
sscanf
(
line
,
BIGINT_FORMAT
,
&
ntimestep
);
return
0
;
}
/* ----------------------------------------------------------------------
skip snapshot from timestamp onward
only called by proc 0
------------------------------------------------------------------------- */
void
ReaderNative
::
skip
()
{
read_lines
(
2
);
bigint
natoms
;
sscanf
(
line
,
BIGINT_FORMAT
,
&
natoms
);
read_lines
(
5
);
// invoke read_lines() in chunks no larger than MAXSMALLINT
int
nchunk
;
bigint
nremain
=
natoms
;
while
(
nremain
)
{
nchunk
=
MIN
(
nremain
,
MAXSMALLINT
);
read_lines
(
nchunk
);
nremain
-=
nchunk
;
}
}
/* ----------------------------------------------------------------------
read remaining header info:
return natoms
box bounds, triclinic (inferred), fieldflag (1 if any fields not found),
xyz flags = UNSET (not a requested field), SCALE/WRAP as in enum
if fieldflag set:
match Nfield fields to per-atom column labels
allocate and set fieldindex = which column each field maps to
fieldtype = X,VX,IZ etc
fieldlabel = user-specified label or NULL if use fieldtype default
xyz flags = scaleflag+wrapflag if has fieldlabel name,
else set by x,xs,xu,xsu
only called by proc 0
------------------------------------------------------------------------- */
bigint
ReaderNative
::
read_header
(
double
box
[
3
][
3
],
int
&
triclinic
,
int
fieldinfo
,
int
nfield
,
int
*
fieldtype
,
char
**
fieldlabel
,
int
scaleflag
,
int
wrapflag
,
int
&
fieldflag
,
int
&
xflag
,
int
&
yflag
,
int
&
zflag
)
{
bigint
natoms
;
read_lines
(
2
);
sscanf
(
line
,
BIGINT_FORMAT
,
&
natoms
);
triclinic
=
0
;
box
[
0
][
2
]
=
box
[
1
][
2
]
=
box
[
2
][
2
]
=
0.0
;
read_lines
(
1
);
if
(
line
[
strlen
(
"ITEM: BOX BOUNDS "
)]
==
'x'
)
triclinic
=
1
;
read_lines
(
1
);
if
(
!
triclinic
)
sscanf
(
line
,
"%lg %lg"
,
&
box
[
0
][
0
],
&
box
[
0
][
1
]);
else
sscanf
(
line
,
"%lg %lg %lg"
,
&
box
[
0
][
0
],
&
box
[
0
][
1
],
&
box
[
0
][
2
]);
read_lines
(
1
);
if
(
!
triclinic
)
sscanf
(
line
,
"%lg %lg"
,
&
box
[
1
][
0
],
&
box
[
1
][
1
]);
else
sscanf
(
line
,
"%lg %lg %lg"
,
&
box
[
1
][
0
],
&
box
[
1
][
1
],
&
box
[
1
][
2
]);
read_lines
(
1
);
if
(
!
triclinic
)
sscanf
(
line
,
"%lg %lg"
,
&
box
[
2
][
0
],
&
box
[
2
][
1
]);
else
sscanf
(
line
,
"%lg %lg %lg"
,
&
box
[
2
][
0
],
&
box
[
2
][
1
],
&
box
[
2
][
2
]);
read_lines
(
1
);
// if no field info requested, just return
if
(
!
fieldinfo
)
return
natoms
;
// exatract column labels and match to requested fields
char
*
labelline
=
&
line
[
strlen
(
"ITEM: ATOMS "
)];
nwords
=
atom
->
count_words
(
labelline
);
char
**
labels
=
new
char
*
[
nwords
];
labels
[
0
]
=
strtok
(
labelline
,
"
\t\n\r\f
"
);
if
(
labels
[
0
]
==
NULL
)
{
delete
[]
labels
;
return
1
;
}
for
(
int
m
=
1
;
m
<
nwords
;
m
++
)
{
labels
[
m
]
=
strtok
(
NULL
,
"
\t\n\r\f
"
);
if
(
labels
[
m
]
==
NULL
)
{
delete
[]
labels
;
return
1
;
}
}
// match each field with a column of per-atom data
// if fieldlabel set, match with explicit column
// else infer one or more column matches from fieldtype
// xyz flag set by scaleflag + wrapflag (if fieldlabel set) or column label
memory
->
create
(
fieldindex
,
nfield
,
"read_dump:fieldindex"
);
int
s_index
,
u_index
,
su_index
;
xflag
=
UNSET
;
yflag
=
UNSET
;
zflag
=
UNSET
;
for
(
int
i
=
0
;
i
<
nfield
;
i
++
)
{
if
(
fieldlabel
[
i
])
{
fieldindex
[
i
]
=
find_label
(
fieldlabel
[
i
],
nwords
,
labels
);
if
(
fieldtype
[
i
]
==
X
)
xflag
=
2
*
scaleflag
+
wrapflag
+
1
;
else
if
(
fieldtype
[
i
]
==
Y
)
yflag
=
2
*
scaleflag
+
wrapflag
+
1
;
else
if
(
fieldtype
[
i
]
==
Z
)
zflag
=
2
*
scaleflag
+
wrapflag
+
1
;
}
else
if
(
fieldtype
[
i
]
==
ID
)
fieldindex
[
i
]
=
find_label
(
"id"
,
nwords
,
labels
);
else
if
(
fieldtype
[
i
]
==
TYPE
)
fieldindex
[
i
]
=
find_label
(
"type"
,
nwords
,
labels
);
else
if
(
fieldtype
[
i
]
==
X
)
{
fieldindex
[
i
]
=
find_label
(
"x"
,
nwords
,
labels
);
xflag
=
NOSCALE_WRAP
;
if
(
fieldindex
[
i
]
<
0
)
{
fieldindex
[
i
]
=
nwords
;
s_index
=
find_label
(
"xs"
,
nwords
,
labels
);
u_index
=
find_label
(
"xu"
,
nwords
,
labels
);
su_index
=
find_label
(
"xsu"
,
nwords
,
labels
);
if
(
s_index
>=
0
&&
s_index
<
fieldindex
[
i
])
{
fieldindex
[
i
]
=
s_index
;
xflag
=
SCALE_WRAP
;
}
if
(
u_index
>=
0
&&
u_index
<
fieldindex
[
i
])
{
fieldindex
[
i
]
=
u_index
;
xflag
=
NOSCALE_NOWRAP
;
}
if
(
su_index
>=
0
&&
su_index
<
fieldindex
[
i
])
{
fieldindex
[
i
]
=
su_index
;
xflag
=
SCALE_NOWRAP
;
}
}
if
(
fieldindex
[
i
]
==
nwords
)
fieldindex
[
i
]
=
-
1
;
}
else
if
(
fieldtype
[
i
]
==
Y
)
{
fieldindex
[
i
]
=
find_label
(
"y"
,
nwords
,
labels
);
yflag
=
NOSCALE_WRAP
;
if
(
fieldindex
[
i
]
<
0
)
{
fieldindex
[
i
]
=
nwords
;
s_index
=
find_label
(
"ys"
,
nwords
,
labels
);
u_index
=
find_label
(
"yu"
,
nwords
,
labels
);
su_index
=
find_label
(
"ysu"
,
nwords
,
labels
);
if
(
s_index
>=
0
&&
s_index
<
fieldindex
[
i
])
{
fieldindex
[
i
]
=
s_index
;
yflag
=
SCALE_WRAP
;
}
if
(
u_index
>=
0
&&
u_index
<
fieldindex
[
i
])
{
fieldindex
[
i
]
=
u_index
;
yflag
=
NOSCALE_NOWRAP
;
}
if
(
su_index
>=
0
&&
su_index
<
fieldindex
[
i
])
{
fieldindex
[
i
]
=
su_index
;
yflag
=
SCALE_NOWRAP
;
}
}
if
(
fieldindex
[
i
]
==
nwords
)
fieldindex
[
i
]
=
-
1
;
}
else
if
(
fieldtype
[
i
]
==
Z
)
{
fieldindex
[
i
]
=
find_label
(
"z"
,
nwords
,
labels
);
zflag
=
NOSCALE_WRAP
;
if
(
fieldindex
[
i
]
<
0
)
{
fieldindex
[
i
]
=
nwords
;
s_index
=
find_label
(
"zs"
,
nwords
,
labels
);
u_index
=
find_label
(
"zu"
,
nwords
,
labels
);
su_index
=
find_label
(
"zsu"
,
nwords
,
labels
);
if
(
s_index
>=
0
&&
s_index
<
fieldindex
[
i
])
{
fieldindex
[
i
]
=
s_index
;
zflag
=
SCALE_WRAP
;
}
if
(
u_index
>=
0
&&
u_index
<
fieldindex
[
i
])
{
fieldindex
[
i
]
=
u_index
;
zflag
=
NOSCALE_NOWRAP
;
}
if
(
su_index
>=
0
&&
su_index
<
fieldindex
[
i
])
{
fieldindex
[
i
]
=
su_index
;
zflag
=
SCALE_NOWRAP
;
}
}
if
(
fieldindex
[
i
]
==
nwords
)
fieldindex
[
i
]
=
-
1
;
}
else
if
(
fieldtype
[
i
]
==
VX
)
fieldindex
[
i
]
=
find_label
(
"vx"
,
nwords
,
labels
);
else
if
(
fieldtype
[
i
]
==
VY
)
fieldindex
[
i
]
=
find_label
(
"vy"
,
nwords
,
labels
);
else
if
(
fieldtype
[
i
]
==
VZ
)
fieldindex
[
i
]
=
find_label
(
"vz"
,
nwords
,
labels
);
else
if
(
fieldtype
[
i
]
==
FX
)
fieldindex
[
i
]
=
find_label
(
"fx"
,
nwords
,
labels
);
else
if
(
fieldtype
[
i
]
==
FY
)
fieldindex
[
i
]
=
find_label
(
"fy"
,
nwords
,
labels
);
else
if
(
fieldtype
[
i
]
==
FZ
)
fieldindex
[
i
]
=
find_label
(
"fz"
,
nwords
,
labels
);
else
if
(
fieldtype
[
i
]
==
Q
)
fieldindex
[
i
]
=
find_label
(
"q"
,
nwords
,
labels
);
else
if
(
fieldtype
[
i
]
==
IX
)
fieldindex
[
i
]
=
find_label
(
"ix"
,
nwords
,
labels
);
else
if
(
fieldtype
[
i
]
==
IY
)
fieldindex
[
i
]
=
find_label
(
"iy"
,
nwords
,
labels
);
else
if
(
fieldtype
[
i
]
==
IZ
)
fieldindex
[
i
]
=
find_label
(
"iz"
,
nwords
,
labels
);
}
delete
[]
labels
;
// set fieldflag = -1 if any unfound fields
fieldflag
=
0
;
for
(
int
i
=
0
;
i
<
nfield
;
i
++
)
if
(
fieldindex
[
i
]
<
0
)
fieldflag
=
-
1
;
// create internal vector of word ptrs for future parsing of per-atom lines
words
=
new
char
*
[
nwords
];
return
natoms
;
}
/* ----------------------------------------------------------------------
read N atom lines from dump file
stores appropriate values in fields array
return 0 if success, 1 if error
only called by proc 0
------------------------------------------------------------------------- */
void
ReaderNative
::
read_atoms
(
int
n
,
int
nfield
,
double
**
fields
)
{
int
i
,
m
;
char
*
eof
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
eof
=
fgets
(
line
,
MAXLINE
,
fp
);
if
(
eof
==
NULL
)
error
->
one
(
FLERR
,
"Unexpected end of dump file"
);
// tokenize the line
words
[
0
]
=
strtok
(
line
,
"
\t\n\r\f
"
);
for
(
m
=
1
;
m
<
nwords
;
m
++
)
words
[
m
]
=
strtok
(
NULL
,
"
\t\n\r\f
"
);
// convert selected fields to floats
for
(
m
=
0
;
m
<
nfield
;
m
++
)
fields
[
i
][
m
]
=
atof
(
words
[
fieldindex
[
m
]]);
}
}
/* ----------------------------------------------------------------------
match label to any of N labels
return index of match or -1 if no match
------------------------------------------------------------------------- */
int
ReaderNative
::
find_label
(
const
char
*
label
,
int
n
,
char
**
labels
)
{
for
(
int
i
=
0
;
i
<
n
;
i
++
)
if
(
strcmp
(
label
,
labels
[
i
])
==
0
)
return
i
;
return
-
1
;
}
/* ----------------------------------------------------------------------
read N lines from dump file
only last one is saved in line
only called by proc 0
------------------------------------------------------------------------- */
void
ReaderNative
::
read_lines
(
int
n
)
{
char
*
eof
=
NULL
;
if
(
n
<=
0
)
return
;
for
(
int
i
=
0
;
i
<
n
;
i
++
)
eof
=
fgets
(
line
,
MAXLINE
,
fp
);
if
(
eof
==
NULL
)
error
->
one
(
FLERR
,
"Unexpected end of dump file"
);
}
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