Object methods

Manually inputing crystal data

Starting with this atoms.inp file

title YBCO: Y Ba2 Cu3 O7 
space P M M M 
rmax=5.2              a 3.823   b 3.886 c 11.681
core=cu2
atom
! At.type   x        y       z      tag
   Y       0.5      0.5     0.5   
   Ba      0.5      0.5     0.184
   Cu      0        0       0        cu1
   Cu      0        0       0.356    cu2
   O       0        0.5     0        o1
   O       0        0       0.158    o2
   O       0        0.5     0.379    o3
   O       0.5      0       0.377    o4

you can manually load up the attributes of the Atoms object. This is what the ATOMS interface in ARTEMIS does. A straight-forward, brute-force approach is shown in this example:

#!/usr/bin/perl
use Demeter;

my $atoms = Demeter::Atoms->new();
$atoms -> set(a=>3.823, b=>3.886, c=>11.681);
$atoms -> space('P M M M');
## add each site
$atoms -> push_sites( join("|", 'Y',  0.5, 0.5, 0.5,   'y'  ) );
$atoms -> push_sites( join("|", 'Ba', 0.5, 0.5, 0.184, 'ba' ) );
$atoms -> push_sites( join("|", 'Cu', 0.0, 0.0, 0.0,   'cu1') );
$atoms -> push_sites( join("|", 'Cu', 0.0, 0.0, 0.356, 'cu2') );
$atoms -> push_sites( join("|", 'O',  0.0, 0.5, 0.0,   'o1' ) );
$atoms -> push_sites( join("|", 'O',  0.0, 0.0, 0.158, 'o2' ) );
$atoms -> push_sites( join("|", 'O',  0.0, 0.5, 0.379, 'o3' ) );
$atoms -> push_sites( join("|", 'O',  0.5, 0.0, 0.377, 'o4' ) );
$atoms -> core('cu2');
$atoms -> set(rpath=>5.2, rmax => 8);
print $atoms->Write("feff6");

Once all the data is set, simply call the Write method and the object will take care of populating the cell and explanding the cluster.

Note the odd syntax in lines 8 through 15 for loading the sites attribute. The elements of that array are strings of vertical-bar-separated values of element symbol, fractional x coordinate, fractional y coordinate, fractional z coordinate, and tag. Note that the tag has a limit of 10 characters.

At line 16, the central atom is chosen by specifying a valid tag as the value of the core attribute.

Other methods

Absorption calculations: xsec, deltamu density mcmaster i0 selfsig selfamp netsig

Mentions cluster and nclus attributes