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h2.pl
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Created
Thu, Aug 15, 04:42
Size
1 KB
Mime Type
text/x-perl
Expires
Sat, Aug 17, 04:42 (2 d)
Engine
blob
Format
Raw Data
Handle
19888082
Attached To
rLAMMPS lammps
h2.pl
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#!/usr/bin/perl
#
Usage
:
h2
.
pl
<
nx
>
<
ny
>
<
nz
>
<
rs
>
>
data
.
h2
#
#
Generates
rectangular
lattice
of
hydrogen
atoms
,
#
in
each
direction
=
nx
,
#
with
Wigner
radius
rs
.
#
...
#
Shifts
H
atoms
in
alternating
directions
so
they
form
H2
molecule
#
starting
structures
.
$
nx
=
shift
(
@
ARGV
);
$
ny
=
shift
(
@
ARGV
);
$
nz
=
shift
(
@
ARGV
);
$
rs
=
shift
(
@
ARGV
);
$
L
=
1
.
6119919540164693
*
$
rs
;
#
length
of
unit
cell
((
4
/
3
pi
)
^
(
1
/
3
)
$
re
=
1
.
823572
;
#
electron
radius
$
dshift
=
0
.
5
;
$
idx
=
0
;
for
(
$
x
=
0
;
$
x
<
$
nx
;
$
x++
)
{
for
(
$
y
=
0
;
$
y
<
$
ny
;
$
y++
)
{
$
dsign
=
1
;
for
(
$
z
=
0
;
$
z
<
$
nz
;
$
z++
)
{
$
xnuc
[
$
idx
]
=
$
x
*
$
L
+
0
.
5
*
$
L
;
$
ynuc
[
$
idx
]
=
$
y
*
$
L
+
0
.
5
*
$
L
;
$
znuc
[
$
idx
]
=
$
z
*
$
L
+
0
.
5
*
$
L
+
$
dshift
*
$
dsign
;
$
dsign
=
-
$
dsign
;
$
idx++
;
}
}
}
$
numnuc
=
$
idx
;
#
Print
length
of
supercell
printf
(
"Created with h2.pl\n\n"
);
printf
(
"%d atoms\n"
,
$
numnuc
*
2
);
printf
(
"2 atom types\n\n"
);
printf
(
"%f %f xlo xhi\n"
,
0
,
$
L
*
$
nx
);
printf
(
"%f %f ylo yhi\n"
,
0
,
$
L
*
$
ny
);
printf
(
"%f %f zlo zhi\n\n"
,
0
,
$
L
*
$
nz
);
printf
(
"Masses\n\n"
);
printf
(
"1 1.007940\n"
);
printf
(
"2 1.000000\n\n"
);
printf
(
"Atoms\n\n"
);
$
j
=
0
;
#
Print
out
the
nuclei
and
the
core
electrons
for
(
$
i
=
0
;
$
i
<
$
numnuc
;
$
i++
)
{
printf
(
"%i %i %f %i %f %f %f %f\n"
,
$
j+=
1
,
1
,
1
.
0
,
0
,
0
.
0
,
$
xnuc
[
$
i
],
$
ynuc
[
$
i
],
$
znuc
[
$
i
]);
}
$
spin
=
1
;
for
(
$
i
=
0
;
$
i
<
$
numnuc
;
$
i++
)
{
if
(
$
spin
==
1
)
{
$
spin
=
-
1
;}
else
{
$
spin
=
1
;}
printf
(
"%i %i %f %i %f %f %f %f\n"
,
$
j+=
1
,
2
,
0
.
0
,
$
spin
,
$
re
,
$
xnuc
[
$
i
],
$
ynuc
[
$
i
],
$
znuc
[
$
i
]);
}
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