Re: [Ifeffit] Ifeffit Digest, Vol 90, Issue 21

Hi Dominik, I haven't had time to look at your question in detail, but try the link below, and see if you find it helpful: http://cars9.uchicago.edu/ifeffit/Doped --Scott Calvin Sarah Lawrence College On Aug 30, 2010, at 7:43 AM, Jatinkumar Rana wrote:

Dear Dominik,

Thank you so much for your reply. However, i am not able to understand the logic behind removal of following atoms from Feff.inp file as mentioned by you

**In principle, after running ATOMS, you just need to remove atoms from the generated feff.inp file so that the occupancy is correct. I.e., in this case, you need to remove roughly 1/4 of the Fe7, 1/2 of the Cr1, 1/3 of the P61, 2/3 of the P62, and 1/3 of the O614 atoms. Try finding those which are too close to other atoms. The FEFF output might help, so try deleting preferentially those causing FEFF to fail.**

can you please give me the idea behind doing that and is it physically defendable to do such changes ??

Looking forward to your reply..

Best regards, Jatin

On 27.08.2010 14:00, ifeffit-request@millenia.cars.aps.anl.gov wrote:

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Today's Topics:

1. Re: Help with cif file (Dominik Samuelis) 2. catalysis workshop at the karlsruher synchrotron ANKA (Matthias Bauer)

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Message: 1 Date: Fri, 27 Aug 2010 10:09:05 +0200 From: Dominik Samuelis To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Help with cif file Message-ID:<4C7772A1.2000307@fkf.mpg.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Dear Jatin,

in your original cif file, you have site occupancies as low as 0.5 (Cr1 site) and 0.358 (P62). Just setting them to 1 will not help, because ATOMS assumes them to be unity anyway.

For such a complicated unit cell, the typical recipe with using prototypical structures of course does not help, just because there is not a simple prototype structure for arrojadite.

In principle, after running ATOMS, you just need to remove atoms from the generated feff.inp file so that the occupancy is correct. I.e., in this case, you need to remove roughly 1/4 of the Fe7, 1/2 of the Cr1, 1/3 of the P61, 2/3 of the P62, and 1/3 of the O614 atoms. Try finding those which are too close to other atoms. The FEFF output might help, so try deleting preferentially those causing FEFF to fail.

Another solution might be loading the structure's cif file into a structure editor such as DIAMOND. There, you can then check the bond distance histograms and delete atoms accordingly. At the end, just export the data in xyz format and use this as the atom positions list in the feff.inp file.

Regards, Dominik

On 20.08.2010 09:30, Jatinkumar Rana wrote:

...

Dear Dominic, Dear Bruce,

I am also facing the same problem as experienced by Kleper. I am working on the EXAFS analysis of Arrojadite mineral. We have refined the strucutre using neutron diffraction to get crystallographic information which can be fed to ATOMS. The original .cif file contains the fractional occupancy so ATOMS give similar error report as mentioned by Kleper. After reading your post, i changed all site occupancy to 1 and then run ATOMS but still it gives me the error report.

Can anybody tell me, why ATOMS report error ?

I have attached both original .cif file (with fractional occupancy) and modified .cif file (all site occupancy = 1). I have EXAFS spectrum at Fe and Mn K-edge.

Looking forward to your answer.

Thanks a lot in advance...

Best regards, Jatin

On 18.08.2010 19:00, ifeffit-request@millenia.cars.aps.anl.gov wrote:

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Today's Topics:

1. Re: Help with cif file (Dominik Samuelis) 2. Re: Help with cif file (Bruce Ravel)

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Message: 1 Date: Wed, 18 Aug 2010 08:36:03 +0200 From: Dominik Samuelis To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Help with cif file Message-ID:<01A98ED5-00FE-4875-989A-C7663E57BF97@fkf.mpg.de> Content-Type: text/plain; charset=iso-8859-1

Dear Kleper,

even though I haven't tested it in detail, I'm sure the errors come from the fact that ATOMS cannot handle site occupancies other than unity. If you have a look in the cif file, you can see that both W (0.23) and Ti (0.54) have a fractional occupancy:

loop_ _atom_site_label _atom_site_type_symbol _atom_site_symmetry_multiplicity _atom_site_Wyckoff_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy _atom_site_attached_hydrogens _atom_site_calc_flag W1 W4+ 4 e 0. 0. 0.0564(2) 0.23 0 d Ti1 Ti4+ 2 a 0. 0. 0. 0.54 0 d O1 O2- 4 f 0.3007(6) 0.3007(6) 0. 1. 0 d

To get it working, you need to use the prototypical structure (e.g. TiO2) without mixed sites as ATOMS input. In the feff.inp file, you can then change 46 out of 100 Ti atoms to W (5 out of 10 should be ok as well for a smaller cluster). Don't forget to add the appropriate POTENTIALS line for W to the feff.inp. The small shift of the W atoms away from the Ti positions then could be handled by some additional delR parameter for the W paths during fitting.

All the best, Dominik

Am 17.08.2010 um 15:27 schrieb Kleper Rocha:

...

Please,

Could someone help me with the cif file attached, get from the www.crystallographic.net shearch with the terms Ti, W, O. When I try to run the Feff the following message appears.

"Feff 6L.02 WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 1 2 1 0.00000 0.00000 0.00000 2 0.00000 0.00000 -0.16378 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 1 3 1 0.00000 0.00000 0.00000 3 0.00000 0.00000 -0.32756 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 2 3 2 0.00000 0.00000 -0.16378 3 0.00000 0.00000 -0.32756 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 10 11 10 0.00000 0.00000 2.57634 11 0.00000 0.00000 2.74012 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 10 12 10 0.00000 0.00000 2.57634 12 0.00000 0.00000 2.90390 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 11 12 11 0.00000 0.00000 2.74012 12 0.00000 0.00000 2.90390 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 13 14 13 0.00000 0.00000 -2.90390 14 0.00000 0.00000 -3.06768 Run continues... Titanium tungsten oxide (0.54/0.46/2) Ti.54 W.46 O2 O2 Ti0.54 W0.46 Peters, E. Ueber ein niedervalentes Titan-Wolframoxid: Ti0,54 W0,46 O2 Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 free atom potential and density for atom type 3 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 overlapped potential and density for unique potential 3 muffin tin radii and interstitial parameters

This warning indicates a problem in the Atoms list. For some reason you have atoms that are separated by than 0.93 Angstroms (or 1.75 Rydberg).

This may be due to the presence of hydrogen atoms in your feff.inp file, in which case this is an innocuous warning and may be ignored.

However, this may indicate a problem constructing the Atoms list. The most common cause of this problem is a mistake in the crystallographic data used on the Atoms page. You may have incorrect values for lattice constants or angles or incorrect values for site coordinates. You may need a shift vector to move the lattice into its standard setting.

Please be aware that Atoms works with 5 digits of precision. Thus, if you have a site with a coordinate of 1/3, you should use either "1/3" or "0.33333" on the Atoms page. Using insufficient precision, say "0.333" is a common cause of this error message.

Artemis has continued on the possibility that the warning is caused by hydrogen atoms, but be warned that the feff.inp may require your attention."

Thanks in advance.

Kleper de Oliveira Rocha

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