6. Atoms

6.1. Input crystal data

The attributes of the Atoms object can be populated in one of three ways, by reading an atoms.inp file, by reading a CIF file, or by setting the attributes programmatically.

The format of the atoms.inp file is documented elsewhere. Importing data from one is as simple as specifying the file when the Atoms object is created. In this example, an atoms.inp file is imported and an input file for FEFF6 is written to standard output.

#!/usr/bin/perl
use Demeter;

my $atoms = Demeter::Atoms->new(file => "ybco.inp");
print $atoms->Write("feff6");

The command-line ATOMS program that comes with DEMETER is longer than 5 lines, but does not really do much beyond this example.

Importing crystal data from a CIF file is no more difficult, however you need to explicitly tell the Atoms object that the input data is in CIF format. The Atoms object assumes that the value of the file attribute points at an atoms.inp file, so the cif attribute must be used to specify a CIF file.

#!/usr/bin/perl
use Demeter;

my $atoms = Demeter::Atoms->new(cif => "Fe2N_ICSD.cif");
print $atoms->Write("feff6");

The STAR::Parser module is used to interpret the CIF file. This is a quirky bit of code and my understanding of it is not so deep. There are probably examples of CIF files that do not get imported properly, but it seems to work in most cases. You should consider a valid CIF file that cannot be imported by DEMETER to be a reportable DEMETER bug.

CIF files can contain more than one structure. By default, DEMETER will import the first structure contained in the CIF file. To specify another structure, use the record attribute. Note that the counting is zero based, so this example is importing the second record in the CIF file. In a GUI like ARTEMIS, it is probably wise to let the user count from 1 and to do the translation behind the scenes.

#!/usr/bin/perl
use Demeter;

my $atoms = Demeter::Atoms->new(cif => "AuCl.cif", record=>1);
print $atoms->Write("feff6");

The Artemis document offers more discussion of the content of the atoms.inp file.

6.2. Object methods

6.2.1. 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 (awkward, perhaps, but that's how it works) 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.

6.3. Other methods

Todo

• Absorption calculations: xsec, deltamu density mcmaster i0 selfsig selfamp netsig
• Mentions cluster and nclus attributes

6.4. Output

Output from the Atoms object is handled by the Write method. Note that this is capitalized to avoid any possible confusion (by perl or by a syntax highlighting text editor) with perl's write function, as shown in this example:

#!/usr/bin/perl
use Demeter;

my $atoms = Demeter::Atoms->new(file => "ybco.inp");
print $atoms->Write("feff6");

There are several output targets, which are formatted using templates from the Atoms template set. The output targets, i.e. the arguments of the Write method, that come with DEMETER are:

feff6

Input file for FEFF6.

feff7

Input file for FEFF7 (which is not really very different from the FEFF6 input file).

feff8

Input file for FEFF8.

atoms

Input file for ATOMS. This used as the save-file target for a GUI.

p1

Input file for ATOMS using the P 1 spacegroup and the fully populated unit cell. Here's an example:

title = YBCO: Y Ba2 Cu3 O7
space = P M M M
a     =   3.82300    b    =   3.88600    c     =  11.68100
alpha =  90.00000    beta =  90.00000    gamma =  90.00000
rmax  =   5.20000    core  = cu2
shift =
atoms
# el.     x           y           z        tag
  Y      0.50000     0.50000     0.50000   Y
  Ba     0.50000     0.50000     0.18400   Ba
  Ba     0.50000     0.50000     0.81600   Ba
  Cu     0.00000     0.00000     0.00000   cu1
  Cu     0.00000     0.00000     0.35600   cu2
  Cu     0.00000     0.00000     0.64400   cu2
  O      0.00000     0.50000     0.00000   o1
  O      0.00000     0.00000     0.15800   o2
  O      0.00000     0.00000     0.84200   o2
  O      0.00000     0.50000     0.37900   o3
  O      0.00000     0.50000     0.62100   o3
  O      0.50000     0.00000     0.37700   o4
  O      0.50000     0.00000     0.62300   o4

absorption

A file containing several interesting calculations using tables of absorption coefficients. Here's an example:

## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
##  total mu*x=1:  8.160 microns,  unit edge step:  23.243 microns
##  specific gravity:  6.375
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
##  normalization correction:     0.00046 ang^2
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--

spacegroup

A file containing a description of the space group. Here's an example:

# title = YBCO: Y Ba2 Cu3 O7
# space = P M M M
# a     =   3.82300    b    =   3.88600    c     =  11.68100
# alpha =  90.00000    beta =  90.00000    gamma =  90.00000
# rmax  =   5.20000    core  = cu2
# shift =
# atoms
# # el.     x           y           z        tag
#   Y      0.50000     0.50000     0.50000   Y
#   Ba     0.50000     0.50000     0.18400   Ba
#   Cu     0.00000     0.00000     0.00000   cu1
#   Cu     0.00000     0.00000     0.35600   cu2
#   O      0.00000     0.50000     0.00000   o1
#   O      0.00000     0.00000     0.15800   o2
#   O      0.00000     0.50000     0.37900   o3
#   O      0.50000     0.00000     0.37700   o4

Spacegroup P M M M (#47)

  Schoenflies: D_2h^1
  Full symbol: p 2/m 2/m 2/m
  New symbol :
  Thirtyfive :
  Nicknames  :

  Common shift vector:


  Bravais translations:

  8 positions:
       x         y         z
      -x        -y         z
      -x         y        -z
       x        -y        -z
      -x        -y        -z
       x         y        -z
       x        -y         z
      -x         y         z

xyz and alchemy

These are two common formats for molecule visualization software.

overfull

This is an xyz file containing the contents of the fully decorated unit cell, also including atoms that are near to all the corners, edges, and walls. This helps to make a figure like this of a well-decorated unit cell:

The ♦Atoms→overfull_margin parameter is used to set what is meant by “near” the remaining corners, edges, and walls.

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