[Ifeffit] Quick question about atoms.exe and .cif files

Bruce Ravel bravel at bnl.gov
Tue Aug 26 08:05:31 CDT 2008

On Tuesday 26 August 2008 01:44:03 you wrote:
> Hi Bruce,
>      I have atoms running well, but whenever I input a simple diamond
> structure .cif file (like the attached silicon.cif file), I get the wrong
> structure.  I've tried everything that I could think of, but it doesn't
> work.  I'm not sure if it is something I'm doing wrong, or something
> intrinsic in the .cif file.  I'm currently running the command line program
> with the command "atoms.exe -u -o "silicon.inf" "Silicon.cif"", with the
> files being appropriately loaded.  If you get the chance could you tell me
> if it is an easy problem that I can quickly fix (and the solution), or if
> it is something more in depth: I'd appreciate it.
> Zak

I am forwarding this question to the Ifeffit mailing list.  This is
the sort of question for which that forum was created.  Please make
use of it.

As the warning message says, "F d -3 m" is one of those space groups
in the International Tables that offers two choices for the position
of the origin.  There is no way to correct that from the command line,
so your two options are:

  1. Use Artemis to generate your unit cell file and apply the shift
     vector given in the warning message


  2. Edit the cif file to put the Si atom at (1/8,1/8,1/8)


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

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 My homepage:    http://xafs.org/BruceRavel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

-------------- next part --------------
_chemical_name 'Silicon'
'Wyckoff R W G'
_journal_name_full "Crystal Structures"
_journal_volume 1 
_journal_year 1963
_journal_page_first 7
_journal_page_last 83
 Second edition. Interscience Publishers, New York, New York
 Sample at T = 300 K
_chemical_formula_sum 'Si'
_cell_length_a 5.43070
_cell_length_b 5.43070
_cell_length_c 5.43070
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 160.165
_symmetry_space_group_name_H-M 'F d 3 m'
Si   0.00000   0.00000   0.00000

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