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 georgesterbin...@u.northwestern.edu
To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] more bugs in atoms?
Message-ID: BANLkTi=OH=ncjjmwhke5vlmnteao8k3...@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 = 5.51120b = 5.51120c = 7.79410
alpha = 90.0beta = 90.740gamma = 90.0
core =Co1edge =Krmax = 6.0
!shift 0.25000 0.25000 0.25000
atoms
! elem x y z tag occ.
Fe0.00.00.0 Fe1 1.0
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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