[Ifeffit] Error in paths with ifeffit

[Bruce Ravel]

On Thursday 16 July 2009 04:42:41 pm you wrote:
> When I try to obtain the path with the attached
> cif file, I find distance As_O(8) = 2.142 A, this
> is uncorrect, because there is no oxygen atom at that distance.
> What is going on?

Hi Elsa,

For some reason, Artemis does the wrong thing with the setting of the
space group.  According to your CIF file, the proper setting of the
space group is P 21/n.  For some reason, when Artemis reads that CIF
file, it uses P 21/c as the space group symbol.  That is strange
behavior -- I will have to investigate what is going on.

The work-around on the Atoms page in Artemis is to change the space
group to "P 21/n" before running feff.  If you are using Atoms at the
command line, you will have to tell Atoms to write out an atoms.inp
file, edit that, then run feff.  That's all a bit irritating, but it
is at least workable. 

When I ran your cif file after specifying "P 21/n" on the Atoms page,
I got this for the first several neighbors:

    0.00000    0.00000    0.00000  0 As1             0.00000
   -0.46784   -0.12630    1.58774  4 O3_1            1.66004
   -0.88804   -0.96644   -1.02986  4 O1_1            1.66830
    1.65544   -0.19677   -0.19615  4 O2_1            1.67859
   -0.36279    1.66519   -0.35929  4 O4_1            1.74171
   -0.22909    1.88872   -1.29544  1 H1_1            2.30172
    2.26346    1.49452    0.40642  1 H13_1           2.74263
    2.03956   -2.01248    0.21917  1 H10_1           2.87366
    1.14080   -0.11749    2.64281  1 H8_1            2.88092
    2.08625   -0.17254   -2.02856  1 H5_1            2.91501
   -2.72907   -0.44011   -1.05767  1 H9_1            2.95976

That looks more like what you were expecting....

B


PS: The proper address for the mailing list is
ifeffit at millenia.cars.aps.anl.gov rather than ifeffit-owner at ...  Mail
to ifeffit-owner goes just to Matt and I rather than to the whole
list.


-- 

 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/