[Ifeffit] Ifeffit Digest, Vol 166, Issue 12

Bruce Ravel bravel at bnl.gov
Wed Dec 21 14:58:26 CST 2016

On 12/21/2016 02:50 PM, Robert Gordon wrote:
> So, for all but tetragonal, the orientation of the cluster can be
> identified with the
> orientation of the crystal axes. Does it not seem more logical to
> preserve the
> apparent orientation with respect to the crystal axes so that, when
> (issues in FEFF6 aside), confusion is less-likely?

Hmm ... I think I understand your point.

I think you may be ascribing too much agency and intelligence to the the 
Atoms algorithm.  The way Atoms works these days is to use this 
tabulation of chapter 7 of volume A of the International Tables:


It selects the symmetry operations appropriate to the specified space 
group and applies them to the list of unique coordinates.  In the case 
of a space group with multiple settings, it uses some heuristics to try 
to guess the correct setting.  (That's what things like "b_unique" and 
so on are all about.  Those heuristics often fail.)  It expands out a 
unit cell and weeds through the unit cell to identify duplicates (i.e. 
high symmetry positions that repeatedly generate the same location when 
the symmetry operations are applied).  It then stacks up enough unit 
cells to contain the cluster, then translates fractional coordinates to 
Cartesian coordinates.

At no point in that operation does the program make any decisions on the 
basis of the definitions of the Cartesian axes.

None of this is a value judgment on what you have said or on Raj's 
original question -- I'm simply explaining how the program works.  There 
just isn't an obvious mechanism in the code to let the user orient the 
cluster in a certain way.  That's an interesting idea, but not something 
available at this time.

To use Feff's polarization, you have to choose a polarization vector 
appropriate to the cluster as written.  Or, I suppose, write your own 
tool to rotate the cluster to a more convenient orientation.


  Bruce Ravel  ------------------------------------ bravel at bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 743, Room 114
  Upton NY, 11973

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/

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