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reader_xyz.cpp
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Created
Thu, Oct 10, 03:21
Size
6 KB
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text/x-c
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Sat, Oct 12, 03:21 (1 d, 22 h)
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21486462
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rLAMMPS lammps
reader_xyz.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: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include "reader_xyz.h"
#include "atom.h"
#include "memory.h"
#include "error.h"
#include "force.h"
using
namespace
LAMMPS_NS
;
#define MAXLINE 1024
// max line length in dump file
enum
{
ID
,
TYPE
,
X
,
Y
,
Z
};
/* ---------------------------------------------------------------------- */
ReaderXYZ
::
ReaderXYZ
(
LAMMPS
*
lmp
)
:
Reader
(
lmp
)
{
line
=
new
char
[
MAXLINE
];
fieldindex
=
NULL
;
nstep
=
0
;
}
/* ---------------------------------------------------------------------- */
ReaderXYZ
::~
ReaderXYZ
()
{
delete
[]
line
;
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
ReaderXYZ
::
read_time
(
bigint
&
ntimestep
)
{
char
*
eof
=
fgets
(
line
,
MAXLINE
,
fp
);
if
(
eof
==
NULL
)
return
1
;
// first line has to have the number of atoms
// truncate the string to the first whitespace,
// so force->bnumeric() does not hiccup
for
(
int
i
=
0
;
(
i
<
MAXLINE
)
&&
(
eof
[
i
]
!=
'\0'
);
++
i
)
{
if
(
eof
[
i
]
==
'\n'
||
eof
[
i
]
==
'\r'
||
eof
[
i
]
==
' '
||
eof
[
i
]
==
'\t'
)
{
eof
[
i
]
=
'\0'
;
break
;
}
}
natoms
=
force
->
bnumeric
(
FLERR
,
line
);
if
(
natoms
<
1
)
error
->
one
(
FLERR
,
"Dump file is incorrectly formatted"
);
// skip over comment/title line
read_lines
(
1
);
// fake time step numbers
ntimestep
=
nstep
;
// count this frame
++
nstep
;
return
0
;
}
/* ----------------------------------------------------------------------
skip snapshot from timestamp onward
only called by proc 0
------------------------------------------------------------------------- */
void
ReaderXYZ
::
skip
()
{
// 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 = from input scaleflag & wrapflag
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 flag = scaledflag if has fieldlabel name, else set by x,xs,xu,xsu
only called by proc 0
------------------------------------------------------------------------- */
bigint
ReaderXYZ
::
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
)
{
nid
=
0
;
// signal that we have no box info at all
triclinic
=
-
1
;
// if no field info requested, just return
if
(
!
fieldinfo
)
return
natoms
;
memory
->
create
(
fieldindex
,
nfield
,
"read_dump:fieldindex"
);
// for xyz we know nothing about the style of coordinates,
// so caller has to set the proper flags
xflag
=
2
*
scaleflag
+
wrapflag
+
1
;
yflag
=
2
*
scaleflag
+
wrapflag
+
1
;
zflag
=
2
*
scaleflag
+
wrapflag
+
1
;
// copy fieldtype list for supported fields
fieldflag
=
0
;
for
(
int
i
=
0
;
i
<
nfield
;
i
++
)
{
if
(
(
fieldtype
[
i
]
==
X
)
||
(
fieldtype
[
i
]
==
Y
)
||
(
fieldtype
[
i
]
==
Z
)
||
(
fieldtype
[
i
]
==
ID
)
||
(
fieldtype
[
i
]
==
TYPE
)
)
{
fieldindex
[
i
]
=
fieldtype
[
i
];
}
else
{
fieldflag
=
1
;
}
}
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
ReaderXYZ
::
read_atoms
(
int
n
,
int
nfield
,
double
**
fields
)
{
int
i
,
m
;
char
*
eof
;
int
mytype
;
double
myx
,
myy
,
myz
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
eof
=
fgets
(
line
,
MAXLINE
,
fp
);
if
(
eof
==
NULL
)
error
->
one
(
FLERR
,
"Unexpected end of dump file"
);
++
nid
;
sscanf
(
line
,
"%*s%lg%lg%lg"
,
&
myx
,
&
myy
,
&
myz
);
// XXX: we could insert an element2type translation here
// XXX: for now we flag unrecognized types as type 0,
// XXX: which should trigger an error, if LAMMPS uses it.
mytype
=
atoi
(
line
);
for
(
m
=
0
;
m
<
nfield
;
m
++
)
{
switch
(
fieldindex
[
m
])
{
case
X:
fields
[
i
][
m
]
=
myx
;
break
;
case
Y:
fields
[
i
][
m
]
=
myy
;
break
;
case
Z:
fields
[
i
][
m
]
=
myz
;
break
;
case
ID:
fields
[
i
][
m
]
=
nid
;
break
;
case
TYPE:
fields
[
i
][
m
]
=
mytype
;
break
;
}
}
}
}
/* ----------------------------------------------------------------------
read N lines from dump file
only last one is saved in line
only called by proc 0
------------------------------------------------------------------------- */
void
ReaderXYZ
::
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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