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data2xmovie.c
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Created
Tue, Sep 3, 08:32
Size
10 KB
Mime Type
text/x-c
Expires
Thu, Sep 5, 08:32 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
14979177
Attached To
rLAMMPS lammps
data2xmovie.c
View Options
/* data2xmovie tool
read LAMMPS data file as input
write a snapshot in XMOVIE format
Syntax: data2xmovie [options] < infile > outfile
Options:
-style atom_style
use the LAMMPS atom style that corresponds to this file
e.g. atomic or bond or angle or full or eam or granular
will be used for reading and writing files
if not specified, atom_style = full
-unmap
unmap all input atom positions using input image flags
image flags must be specified in infile
default is to leave atoms mapped to periodic box
-inbox xlo xhi ylo yhi zlo zhi
use these values for the output bounding box of the system
useful if are unmapping atoms into a larger domain
if not specified use the box bounds read in from infile
*/
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
struct
box
{
double
xlo
,
xhi
,
xsize
;
double
ylo
,
yhi
,
ysize
;
double
zlo
,
zhi
,
zsize
;
};
#define MAXLINE 1000
#define ATOMIC 1
#define BOND 2
#define ANGLE 3
#define FULL 4
#define EAM 5
#define GRANULAR 6
main
(
int
argc
,
char
*
argv
[])
{
char
line
[
1000
];
/* strings for reading/parsing input file */
char
linetoken
[
1000
];
char
*
token
;
/* numbers of various quantities as read in */
int
natoms
,
nbonds
,
nangles
,
ndihedrals
,
nimpropers
;
int
ntypes
,
nbondtypes
,
nangletypes
,
ndihedtypes
,
nimprotypes
;
int
nmolecules
;
/* total # of mols specified by mol tags */
int
atomstyle
;
/* atomstyle for read/write of Atoms */
int
unmap
;
/* 0 = no unmapping, 1 = unmap from input box */
int
outbox
;
/* flag for whether out box is explicitly set */
struct
box
in
,
out
;
/* input/output bounding box */
char
*
gettoken
(
char
*
,
int
);
/* function defs */
void
skipline
(
int
);
/* default input values */
atomstyle
=
0
;
unmap
=
0
;
outbox
=
0
;
/* read input options from command line
should do more error checking for missing args */
int
i
=
1
;
while
(
i
<
argc
)
{
if
(
!
strcmp
(
argv
[
i
],
"-style"
))
{
if
(
strcmp
(
argv
[
i
+
1
],
"atomic"
)
==
0
)
atomstyle
=
ATOMIC
;
else
if
(
strcmp
(
argv
[
i
+
1
],
"bond"
)
==
0
)
atomstyle
=
BOND
;
else
if
(
strcmp
(
argv
[
i
+
1
],
"angle"
)
==
0
)
atomstyle
=
ANGLE
;
else
if
(
strcmp
(
argv
[
i
+
1
],
"full"
)
==
0
)
atomstyle
=
FULL
;
else
if
(
strcmp
(
argv
[
i
+
1
],
"eam"
)
==
0
)
atomstyle
=
EAM
;
else
if
(
strcmp
(
argv
[
i
+
1
],
"granular"
)
==
0
)
atomstyle
=
GRANULAR
;
else
{
fprintf
(
stderr
,
"Error with command-line arg style
\n
"
);
exit
(
1
);
}
i
+=
2
;
}
else
if
(
!
strcmp
(
argv
[
i
],
"-unmap"
))
{
unmap
=
1
;
i
+=
1
;
}
else
if
(
!
strcmp
(
argv
[
i
],
"-inbox"
))
{
outbox
=
1
;
sscanf
(
argv
[
i
+
1
],
"%lg"
,
&
out
.
xlo
);
sscanf
(
argv
[
i
+
2
],
"%lg"
,
&
out
.
xhi
);
sscanf
(
argv
[
i
+
3
],
"%lg"
,
&
out
.
ylo
);
sscanf
(
argv
[
i
+
4
],
"%lg"
,
&
out
.
yhi
);
sscanf
(
argv
[
i
+
5
],
"%lg"
,
&
out
.
zlo
);
sscanf
(
argv
[
i
+
6
],
"%lg"
,
&
out
.
zhi
);
i
+=
7
;
}
else
{
fprintf
(
stderr
,
"Syntax error: data2xmovie [options] < infile > outfile
\n
"
);
exit
(
1
);
}
}
/* error checks */
if
(
atomstyle
==
0
)
{
fprintf
(
stderr
,
"ERROR: must use -style to set atom style
\n
"
);
exit
(
1
);
}
/* defaults */
natoms
=
nbonds
=
nangles
=
ndihedrals
=
nimpropers
=
0
;
ntypes
=
nbondtypes
=
nangletypes
=
ndihedtypes
=
nimprotypes
=
0
;
/* read header */
fgets
(
line
,
MAXLINE
,
stdin
);
while
(
1
)
{
fgets
(
line
,
MAXLINE
,
stdin
);
if
(
strspn
(
line
,
"
\t\n\r
"
)
==
strlen
(
line
))
continue
;
else
if
(
strstr
(
line
,
"atoms"
))
sscanf
(
line
,
"%d"
,
&
natoms
);
else
if
(
strstr
(
line
,
"bonds"
))
sscanf
(
line
,
"%d"
,
&
nbonds
);
else
if
(
strstr
(
line
,
"angles"
))
sscanf
(
line
,
"%d"
,
&
nangles
);
else
if
(
strstr
(
line
,
"dihedrals"
))
sscanf
(
line
,
"%d"
,
&
ndihedrals
);
else
if
(
strstr
(
line
,
"impropers"
))
sscanf
(
line
,
"%d"
,
&
nimpropers
);
else
if
(
strstr
(
line
,
"atom types"
))
sscanf
(
line
,
"%d"
,
&
ntypes
);
else
if
(
strstr
(
line
,
"bond types"
))
sscanf
(
line
,
"%d"
,
&
nbondtypes
);
else
if
(
strstr
(
line
,
"angle types"
))
sscanf
(
line
,
"%d"
,
&
nangletypes
);
else
if
(
strstr
(
line
,
"dihedral types"
))
sscanf
(
line
,
"%d"
,
&
ndihedtypes
);
else
if
(
strstr
(
line
,
"improper types"
))
sscanf
(
line
,
"%d"
,
&
nimprotypes
);
else
if
(
strstr
(
line
,
"xlo xhi"
))
sscanf
(
line
,
"%lg %lg"
,
&
in
.
xlo
,
&
in
.
xhi
);
else
if
(
strstr
(
line
,
"ylo yhi"
))
sscanf
(
line
,
"%lg %lg"
,
&
in
.
ylo
,
&
in
.
yhi
);
else
if
(
strstr
(
line
,
"zlo zhi"
))
sscanf
(
line
,
"%lg %lg"
,
&
in
.
zlo
,
&
in
.
zhi
);
else
break
;
}
/* compute input box size */
in
.
xsize
=
in
.
xhi
-
in
.
xlo
;
in
.
ysize
=
in
.
yhi
-
in
.
ylo
;
in
.
zsize
=
in
.
zhi
-
in
.
zlo
;
/* write XMOVIE header */
printf
(
"ITEM: TIMESTEP
\n
"
);
printf
(
"%d
\n
"
,
0
);
printf
(
"ITEM: NUMBER OF ATOMS
\n
"
);
printf
(
"%d
\n
"
,
natoms
);
printf
(
"ITEM: BOX BOUNDS
\n
"
);
if
(
outbox
)
{
printf
(
"%g %g
\n
"
,
out
.
xlo
,
out
.
xhi
);
printf
(
"%g %g
\n
"
,
out
.
ylo
,
out
.
yhi
);
printf
(
"%g %g
\n
"
,
out
.
zlo
,
out
.
zhi
);
}
else
{
printf
(
"%g %g
\n
"
,
in
.
xlo
,
in
.
xhi
);
printf
(
"%g %g
\n
"
,
in
.
ylo
,
in
.
yhi
);
printf
(
"%g %g
\n
"
,
in
.
zlo
,
in
.
zhi
);
}
/* read identifier strings one by one in free-form part of data file */
token
=
gettoken
(
line
,
1
);
while
(
token
)
{
/* read atoms */
if
(
!
strcmp
(
token
,
"Atoms"
))
{
printf
(
"ITEM: ATOMS
\n
"
);
int
tag
,
type
,
molecule
,
imagex
,
imagey
,
imagez
;
double
x
,
y
,
z
,
radius
,
density
,
q
;
for
(
i
=
0
;
i
<
natoms
;
i
++
)
{
fgets
(
line
,
MAXLINE
,
stdin
);
if
(
unmap
)
{
if
(
atomstyle
==
ATOMIC
)
sscanf
(
line
,
"%d %d %lg %lg %lg %d %d %d"
,
&
tag
,
&
type
,
&
x
,
&
y
,
&
z
,
&
imagex
,
&
imagey
,
&
imagez
);
else
if
(
atomstyle
==
BOND
)
sscanf
(
line
,
"%d %d %d %lg %lg %lg %d %d %d"
,
&
tag
,
&
molecule
,
&
type
,
&
x
,
&
y
,
&
z
,
&
imagex
,
&
imagey
,
&
imagez
);
else
if
(
atomstyle
==
ANGLE
)
sscanf
(
line
,
"%d %d %d %lg %lg %lg %d %d %d"
,
&
tag
,
&
molecule
,
&
type
,
&
x
,
&
y
,
&
z
,
&
imagex
,
&
imagey
,
&
imagez
);
else
if
(
atomstyle
==
FULL
)
sscanf
(
line
,
"%d %d %d %lg %lg %lg %lg %d %d %d"
,
&
tag
,
&
molecule
,
&
type
,
&
q
,
&
x
,
&
y
,
&
z
,
&
imagex
,
&
imagey
,
&
imagez
);
else
if
(
atomstyle
==
EAM
)
sscanf
(
line
,
"%d %d %lg %lg %lg %d %d %d"
,
&
tag
,
&
type
,
&
x
,
&
y
,
&
z
,
&
imagex
,
&
imagey
,
&
imagez
);
else
if
(
atomstyle
==
GRANULAR
)
sscanf
(
line
,
"%d %d %lg %lg %lg %lg %lg %d %d %d"
,
&
tag
,
&
type
,
&
radius
,
&
density
,
&
x
,
&
y
,
&
z
,
&
imagex
,
&
imagey
,
&
imagez
);
}
else
{
if
(
atomstyle
==
ATOMIC
)
sscanf
(
line
,
"%d %d %lg %lg %lg"
,
&
tag
,
&
type
,
&
x
,
&
y
,
&
z
);
else
if
(
atomstyle
==
BOND
)
sscanf
(
line
,
"%d %d %d %lg %lg %lg"
,
&
tag
,
&
molecule
,
&
type
,
&
x
,
&
y
,
&
z
);
else
if
(
atomstyle
==
ANGLE
)
sscanf
(
line
,
"%d %d %d %lg %lg %lg"
,
&
tag
,
&
molecule
,
&
type
,
&
x
,
&
y
,
&
z
);
else
if
(
atomstyle
==
FULL
)
sscanf
(
line
,
"%d %d %d %lg %lg %lg %lg"
,
&
tag
,
&
molecule
,
&
type
,
&
q
,
&
x
,
&
y
,
&
z
);
else
if
(
atomstyle
==
EAM
)
sscanf
(
line
,
"%d %d %lg %lg %lg"
,
&
tag
,
&
type
,
&
x
,
&
y
,
&
z
);
else
if
(
atomstyle
==
GRANULAR
)
sscanf
(
line
,
"%d %d %lg %lg %lg %lg %lg"
,
&
tag
,
&
type
,
&
radius
,
&
density
,
&
x
,
&
y
,
&
z
);
imagez
=
imagey
=
imagex
=
0
;
}
/* unmap atom position if requested */
if
(
unmap
)
{
x
=
x
+
imagex
*
in
.
xsize
;
y
=
y
+
imagey
*
in
.
ysize
;
z
=
z
+
imagez
*
in
.
zsize
;
}
printf
(
"%d %d %g %g %g
\n
"
,
tag
,
type
,
x
,
y
,
z
);
}
}
/* read bonds and replicate */
else
if
(
!
strcmp
(
token
,
"Bonds"
))
{
printf
(
"ITEM: BONDS
\n
"
);
int
n
,
btype
,
bond1
,
bond2
;
for
(
i
=
0
;
i
<
nbonds
;
i
++
)
{
fgets
(
line
,
MAXLINE
,
stdin
);
sscanf
(
line
,
"%d %d %d %d"
,
&
n
,
&
btype
,
&
bond1
,
&
bond2
);
printf
(
"%d %d %d
\n
"
,
btype
,
bond1
,
bond2
);
}
}
/* non-replicated sections - just skip lines */
else
if
(
!
strcmp
(
token
,
"Velocities"
))
skipline
(
natoms
);
else
if
(
!
strcmp
(
token
,
"Angles"
))
skipline
(
nangles
);
else
if
(
!
strcmp
(
token
,
"Dihedrals"
))
skipline
(
ndihedrals
);
else
if
(
!
strcmp
(
token
,
"Impropers"
))
skipline
(
nimpropers
);
else
if
(
!
strcmp
(
token
,
"Masses"
))
skipline
(
ntypes
);
else
if
(
!
strcmp
(
token
,
"Dipoles"
))
skipline
(
ntypes
);
else
if
(
!
strcmp
(
token
,
"Pair Coeffs"
))
skipline
(
ntypes
);
else
if
(
!
strcmp
(
token
,
"Bond Coeffs"
))
skipline
(
nbondtypes
);
else
if
(
!
strcmp
(
token
,
"Angle Coeffs"
))
skipline
(
nangletypes
);
else
if
(
!
strcmp
(
token
,
"Dihedral Coeffs"
))
skipline
(
ndihedtypes
);
else
if
(
!
strcmp
(
token
,
"Improper Coeffs"
))
skipline
(
nimprotypes
);
else
if
(
!
strcmp
(
token
,
"BondBond Coeffs"
))
skipline
(
nangletypes
);
else
if
(
!
strcmp
(
token
,
"BondAngle Coeffs"
))
skipline
(
nangletypes
);
else
if
(
!
strcmp
(
token
,
"MiddleBondTorsion Coeffs"
))
skipline
(
ndihedtypes
);
else
if
(
!
strcmp
(
token
,
"EndBondTorsion Coeffs"
))
skipline
(
ndihedtypes
);
else
if
(
!
strcmp
(
token
,
"AngleTorsion Coeffs"
))
skipline
(
ndihedtypes
);
else
if
(
!
strcmp
(
token
,
"AngleAngleTorsion Coeffs"
))
skipline
(
ndihedtypes
);
else
if
(
!
strcmp
(
token
,
"BondBond13 Coeffs"
))
skipline
(
ndihedtypes
);
else
if
(
!
strcmp
(
token
,
"AngleAngle Coeffs"
))
skipline
(
nimprotypes
);
else
{
fprintf
(
stderr
,
"Error in input data file - unknown identifier %s
\n
"
,
token
);
exit
(
1
);
}
token
=
gettoken
(
line
,
0
);
}
}
/* ------------------------------------------------------------------- */
/* return a LAMMPS keyword from data file
if first is 1, non-blank line with token is in line
else read until find a non-blank line
keyword is all text on line w/out leading & trailing white space
read one additional line after non-blank line (assumed blank)
return ptr to keyword
return NULL if end of file */
char
*
gettoken
(
char
*
line
,
int
first
)
{
char
buffer
[
MAXLINE
];
/* read upto non-blank line plus 1 following line
eof is set to 1 if any read hits end-of-file */
int
eof
=
0
;
if
(
!
first
)
if
(
fgets
(
line
,
MAXLINE
,
stdin
)
==
NULL
)
eof
=
1
;
while
(
eof
==
0
&&
strspn
(
line
,
"
\t\n\r
"
)
==
strlen
(
line
))
if
(
fgets
(
line
,
MAXLINE
,
stdin
)
==
NULL
)
eof
=
1
;
if
(
fgets
(
buffer
,
MAXLINE
,
stdin
)
==
NULL
)
eof
=
1
;
/* if eof, return NULL */
if
(
eof
)
return
NULL
;
/* bracket non-whitespace portion of line */
int
start
=
strspn
(
line
,
"
\t\n\r
"
);
int
stop
=
strlen
(
line
)
-
1
;
while
(
line
[
stop
]
==
' '
||
line
[
stop
]
==
'\t'
||
line
[
stop
]
==
'\n'
||
line
[
stop
]
==
'\r'
)
stop
--
;
line
[
stop
+
1
]
=
'\0'
;
/* return ptr to keyword */
return
&
line
[
start
];
}
/* read n lines and ignore */
void
skipline
(
int
n
)
{
char
line
[
1000
];
while
(
n
)
{
fgets
(
line
,
MAXLINE
,
stdin
);
n
--
;
}
}
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