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.
George On Fri, May 27, 2011 at 1:40 PM, Gudrun Lisa Bovenkamp < bovenk...@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 <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 = 5.51120 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 >> >> >> _______________________________________________ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >
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