4.1. Crystal data

The crystal cell data – including lattice constants and angles, the space group symbol, and the elements of the shift vector – are placed in text boxes for easy editing. The coordinates of the unique sites are listed in the grid at the bottom of the window. The absorber is chosen by clicking one of the boxes on the Core column.

Remember that FEFF considers numbers with 5 digits of precision after the decimal point. 0.333 is not the same thing as 0.33333. You may, however, enter things like 1/3 and avoid the precision issue entirely.

As a new feature compared to earlier versions of ATOMS, there are two radial distances. The cluster size determines the extent of the cluster expanded into the feff.inp. This should usually be set to something rather large, 9 Å is often a good default. This probably (but not always!) assures that the cluster in the feff.inp file is adequately large to include all unique potentials and has all atom types sufficiently well bounded that the muffin tin potentials are likely to be be computed reasonably well.

The second distance will set the value of RMAX in the feff.inp file. In general, you do not want this to be much larger than the extent of the data you intend to analyze. 5 Å or 6 Å is usually the largest sensible value for longest path. The reason for this is that the pathfinder part of FEFF has been rewritten for this version of ARTEMIS. While the new pathfinder implementation offers a number of useful new features, it is substantially slower than FEFF's native pathfinder. In any case, there is no benefit to computing paths that you will never use in your fit.

The absorption edge for the calculation is chosen from the menu to the left of the lattice constant area. This is usually determined from the input data, but may need to be explicitly selected. If not specified in the atoms.inp file, the edge will be set to K for element lighter than Ce (Z=58), and to L_III for heavier elements.

The style menu is another new feature in this version of ATOMS. It is used to set how the list of unique potentials is determined from the elements in the atoms list. The choices are

elements

Each unique element species is assigned a potential number.

tags

Each unique tag is assigned a potential number.

sites

Each crystallographic site is assigned a potential number.

Remember that FEFF only allows for 7 unique potentials other than the absorber. The tags and sites options can often result in more than 7 potnatials, which will result in an unrunnable feff.inp file. Specifying unique potentials by tags is a good way of differentiating between dissimilar atoms of the same species. For example, in an oxygenyl species, it is often useful to give the axial oxygen atoms a different potential from the remaining oxygens by using the tags option.

Here is an example of an atoms.inp file for sodium uranyl acetate, which contains two very short axial oxygen atoms double bonded to the uranium atoms at about 1.8 Å and a number of equatorial oxygen atoms at a much longer distance. The axial and equatorial oxygen positions are distinguished by their tags and will given separate unique potentials when using the tags style.

title        Templeton et al.
title        Redetermination and Absolute configuration of Sodium Uranyl(VI) triacetate.
title        Acta Cryst 1985 C41 1439-1441
space = P 21 3
a =   10.6890        b =      10.6890        c =      10.6890
alpha =       90.0   beta =   90.0   gamma =  90.0
core =       U       edge =  L3
atoms
! elem   x          y          z       tag        occ
  U     0.42940    0.42940    0.42940  U             1.00000
  Na    0.82860    0.82860    0.82860  Na            1.00000
  O     0.33430    0.33430    0.33430  Oax           1.00000
  O     0.52420    0.52420    0.52420  Oax           1.00000
  O     0.38340    0.29450    0.61100  Oeq           1.00000
  O     0.54640    0.24430    0.50070  Oeq           1.00000
  C     0.47860    0.22600    0.59500  C             1.00000
  C     0.50880    0.12400    0.68620  C             1.00000

The assignment of potential indeces is explained in detail and with examples in a later chapter.

4.1.1. Polarization

A FEFF calculation considering linear polarization can be triggered by setting one or more non-zero values for the polarization vector.

This vector sets the value of the POLARIZATION keyword in the resulting feff.inp. The value written in the feff.inp file is the value that will be used in the pathfinder and when computing the path contributions. That is, if you edit the POLARIZATION in the feff.inp file, the edited value will take precedence over the value specified here.

Caution

FEFF's ELLIPTICITY keyword is not supported at this time. That means the trick of modeling “polarization in the plane” is not yet supported by ARTEMIS.

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