1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
|
#!/usr/bin/perl -w
## This is a simple example of the use of the Xtal.pm module.
##
## Given this information about a crystal, rhombohedral AgNO3
##
## title = silver nitrate
## space = r 3 c
## a = 6.342
## alpha = 47.8167
## atoms
## Ag 0.25000 0.25000 0.25000 Ag1 (2b)
## N 0.00000 0.00000 0.00000 N1 (2a)
## O 0.25000 -0.25000 0.00000 O1 (6e)
##
## this example will write the contents of the unit cell in cartesian
## coordinates to standard output. I chose a rhombohedral cell for
## this example because the volume and metric tensor are non-trivial
## but still easy to calculate by hand.
use Xray::Xtal;
## create a new cell and set its attributes
$cell = Xray::Xtal::Cell -> new()
-> make(Space_group => "r 3 c", A => 6.342, Alpha => 47.8167);
## (you could also say Space_group => 161 or Space_group => "c_3v^6")
## (you could also use the hexagonal setting, although the cartesian
## coordinates would come out differently)
## some work space
@sites = ();
$n = 0;
## create the sites and define their attributes
$sites[$n++] = Xray::Xtal::Site -> new()
-> make(Element=>"Ag", X=>0.25, Y=>0.25, Z=>0.25);
$sites[$n++] = Xray::Xtal::Site -> new()
-> make(Element=>"N", X=>0, Y=>0, Z=>0 );
$sites[$n++] = Xray::Xtal::Site -> new()
-> make(Element=>"O", X=>0.25, Y=>-0.25, Z=>0 );
## now fill out the contents of the unit cell. this line demonstartes
## the relationship between the Cell and Site objects
$cell -> populate(\@sites);
## the populate method fills up the contents attribute of the cell
## with the complete description of the unit cell (assuming, of
## course, that all the sites were defined)
($contents) = $cell -> attributes("Contents");
@list = @$contents; # the notation gets hairy, this helps
## $contents is an anonymous array which we want to access in list
## context. Each element of that array is itself an anonymous array
## describing a position in the unit cell. The first three elements
## of the position description are the fractional x, y, and z
## coordinates of that position. The last element is a *reference* to
## the site that generated that position. This leads to a lot of
## notation...
## note that all of the positions in the unit cell have been
## canonicalized to the first octant (well, actually to the first
## octant in fractional coordinates. this example just happens to
## also be in the first octant in Cartesian coordinates.)
print <<EOH
From this description of a unit cell in crystallographic notation:
title = silver nitrate
space = r 3 c
a = 6.342
alpha = 47.8167
atoms
Ag 0.25000 0.25000 0.25000 Ag1 (2b)
N 0.00000 0.00000 0.00000 N1 (2a)
O 0.25000 -0.25000 0.00000 O1 (6e)
We get this description in Cartesian coordinates:
EOH
;
while (@list) {
$this = shift(@list);
($x, $y, $z) = $cell -> metric($$this[0], $$this[1], $$this[2]);
($elem) = $ {$$this[3]} -> attributes("Element");
printf " %-2s\t%8.5f\t%8.5f\t%8.5f$/", $elem, $x, $y, $z;
};
## all done!
|
