[Ifeffit] more bugs in atoms?

Kropf, Arthur Jeremy kropf at anl.gov
Thu May 26 11:46:18 CDT 2011

One way to assure that the paths aren't assumed to be degenerate would
be to use a different potential index for the different Fe sites.  This
could be useful if the Fe sites are actually different.  If they are the
same, you can treat them as separate paths when you fit by copying the
path and setting the degeneracy however you like along with whatever
fitting variables the paths require.


	From: ifeffit-bounces at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of George
	Sent: Thursday, May 26, 2011 10:41 AM
	To: XAFS Analysis using Ifeffit
	Subject: Re: [Ifeffit] more bugs in atoms?
	Hi Lisa,
	Let me just mention one situation I have encountered using
atoms, and how I resolved it. I am not sure if this is the result of a
bug or not, but perhaps you can try applying the approach I took to your
own situation and see if it can resolve your problem.
	The issue I encountered was running atoms for a monoclinic I2/c
structure, space group 15.
	Here is the atoms input file: 
	! This atoms input file was generated by Artemis 0.8.014
	! Atoms written by and copyright (c) Bruce Ravel, 1998-2001
	title = ...
	space = i 2/c 1 1
	a =      5.51120    b =      5.51120    c =      7.79410
	alpha =     90.0    beta =     90.740    gamma =     90.0
	core =    Co1    edge =    K    rmax =      6.0
	!shift   0.25000   0.25000   0.25000
	! elem   x          y          z     tag           occ.
	  Fe    0.00000    0.00000    0.00000  Fe1           1.00000
	If one calculates the Fe-Fe distance between the atom at (0,0,0)
and the atom at (0, 0, 0.5), from application of the (x, -y, -z+0.5)
lattice translation, one finds a Fe-Fe distance of 3.9705. However, if
one runs the above atoms input file, this Fe-Fe distance is not found.
Instead, a shift vector of (0.25, 0.25, 0.25) is needed to get the
correct Fe-Fe distance. Note, the i2/c space group is listed with only
one origin in the international tables. I determined the necessary shift
vector from trail and error. It is still unclear to me why it was
necessary to include a shift vector. So the best suggestion I have is
that you can try including different shift vectors in your own atoms.inp
file and see if you can get agreement with the crystallography program
that way. Since, as I said, it isn't clear to me why this fixed my
problem, its hard to say if this is the same issue you are having, but
it may be worth a try.
	It may also be worth while to calculate some atomic distances
from the lattice positions given in the international tables, and see if
atoms or the crystallography program is giving you the same thing.
	Finally, let me add on another question for the list here since
it is somewhat related. When one runs the above atoms.inp file with the
(0.25, 0.25, 0.25) shift vector one finds four Fe1_1 atoms at 3.9701 and
two Fe_2 atoms at 3.9705. When one then runs Feff, it combines these
into a single Fe1_1 scattering path with N=6. Is there a command can be
placed in the Feff input file to tell Feff not to combine identical
paths like this?
	On Fri, May 13, 2011 at 5:00 PM, Gudrun Lisa Bovenkamp
<bovenkamp at physik.uni-bonn.de> wrote:

		Hi George,
		thanks for responding. I sure imported the same
structural information into atoms and the crystal structure program.

			Hi Lisa,
			I'm not very familiar with PbSO4, so I'm not
sure if I can help, but your
			email immediately brought some questions to
			First, did you import the same information into
atoms and the crystal
			structure program? The way you worded your
message made me think that the
			crystal structure program already "knew" the
structure of PbSO4, in which
			case perhaps it is using a structure that is
slightly different from the one
			you import into atoms.
			Second, what is the source of the structure data
you are feeding into atoms?
			In my experience, errors and inconsistencies in
the reporting of structure
			data in the literature can lead to unusual
results in atoms.

		Ifeffit mailing list
		Ifeffit at millenia.cars.aps.anl.gov

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