[Ifeffit] more bugs in atoms?

George Sterbinsky GeorgeSterbinsky at u.northwestern.edu
Fri May 27 15:29:06 CDT 2011

Hi Lisa,

The typo in the core atom does not affect the result if run in Artemis. I
think I now have a better grasp of why atoms cannot run my structure
correctly. The standard i2/c setting has a unique axis a, but the structure
in the input file below has a unique axis b. This appears to through atoms
off. If I convert to an I2/a setting, then I get the correct results without
a shift vector.


On Fri, May 27, 2011 at 1:40 PM, Gudrun Lisa Bovenkamp <
bovenkamp at physik.uni-bonn.de> wrote:

> Hi George,
> I cannot understand how you got this atoms.inp file where the core is
> stated to be Co1 and there is only Fe. So, I cannot confirm the crystal
> structure from a database.
> My problem is solved. I understood that the ATOMS program implemented in
> Arthemis and ATOMS 2.5 have some bugs that are corrected in ATOMS 3.0 and
> WebATOMS. When I use those two programs I get a correct crystal structure
> xyz table in feff.inp.
> the only reason that I can think of, why your shifting seem to work better
> is that the atoms.inp file was not representing the correct structure in the
> first place. This can happen when the situation you wnat to describe is not
> the situation that was measured by somebody else. Or there is a mistake in
> the paper.
> Anyway. Thanks for sharing this idea.
> Lisa
>  Date: Thu, 26 May 2011 11:41:08 -0400
>> From: George Sterbinsky <GeorgeSterbinsky at u.northwestern.edu>
>> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>> Subject: Re: [Ifeffit] more bugs in atoms?
>> Message-ID: <BANLkTi=OH=NCJjmwhkE5vLmnTEao8k3avg at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>> 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
>> atoms
>> ! 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?
>> Best,
>> George
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