- Ifeffit - millenia.cars.aps.anl.gov

Mehmet Alper Sahiner/FAC/SHU is out of the office.
by Mehmet Sahiner 11 Apr '07

11 Apr '07

I will be out of the office starting 04/09/2007 and will not return until 04/15/2007. I will be at the MRS2007 Meeting in San Francisco between 4/9/07-4/15/07 Alper

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max number of restraints
by Victor.Streltsov＠csiro.au 11 Apr '07

11 Apr '07

Hi, I wonder if there is a way to change a max number of restraints in Artemis or Ifeffit. If you have more than 10 restraints in Artemis (which is possible to input in Artemis without a warning), the Ifeffit gives the following message in "ifeffit interaction buffer": *** feffit:: too many restraints restraint will be ignored: and ignores all restraints after the 10th in the Artemis list. Often, you need more than 10 restraints when fitting data for biological samples (e.g. bond length restraints etc.) Thanks Victor

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setting root for artemis and athena
by Katy Evans 11 Apr '07

11 Apr '07

This may be really simple but I haven't managed to work out how to do it or find it in the instructions. Is there a way to tell Artemis or Athena where to start when you go to open or save a file? If I were to add up the time I spend clicking up through the directories then I suspect I would discover that it would be sufficient for me to learn to play the piano or similar. Maybe. Cheers, Katy katy.evans(a)anu.edu.au RSES, ANU, Mills Rd, ACT 0200 Ph: 02 61254228 Fx: 02 61258253

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Help with MoOx fitting
by g d 05 Apr '07

05 Apr '07

Hi all, Is there anyone having experience with MoOx fitting? The sample I have is MoOx supported on structured silica (most possibly with tetrahedral coordination, because it's R space and EXAFS is very like that of (NH4)2MoO4). The only standard atom.inp files I have are MoO3.inp and MoO2.inp. I didn't get good fitting with these two. Is it better that I use the standard file that corresponding to tetrahedron? If so, could any one share the atom.inp file with me? Thank you so much! Gd _________________________________________________________________ The average US Credit Score is 675. The cost to see yours: $0 by Experian. http://www.freecreditreport.com/pm/default.aspx?sc=660600&bcd=EMAILFOOTERAV…

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DWF's for amorphous InP
by Claudia Schnohr 05 Apr '07

05 Apr '07

Hello everyone. I am a PhD student and I have encountered a problem with analysing the EXAFS of amorphous InP. For amorphous InP the first shell around an In atom is comprised of both P and In atoms. The In leads to a small peak in the R-spectrum that strongly overlaps with the bigger peak due to scattering from P. If I use two different Debye-Waller-factors, one for each scatterer, and let them both float during the fit I get weird values since the coordination numbers for both peaks have to be floated as well. Therefore, some restraint is needed for the DWF's. Is there any correlation between the two DWF's following from theory or experiment that I could use to restrain my fitting parameters ? Are there other possibilities to handle such a situation ? Many thanks in advance for your help, Claudia -- Claudia S. Schnohr Department of Electronic Materials Engineering Research School of Physical Sciences and Engineering The Australian National University Canberra, ACT 0200 AUSTRALIA

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Correlation between SO2 and sigma^2
by Ricardo Faccio 30 Mar '07

30 Mar '07

Hi Bruce and Scott for your valuable comments I am performing refinenments over a serie of cuprates. In this case La2CuO4 should work as a theoretical standard. This is why I wrote to you, but my "interesting" samples don't have much problems. The theoretical standard is the problem! quite crazy! Thanks again I will try Bruce's comments. Best regards Ricardo ------------------------------------------------------------------------- ----- Ing. Quím. Ricardo Faccio Mail: Cryssmat-Lab., Cátedra de Física, DETEMA Facultad de Química, Universidad de la República Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio(a)fq.edu.uy Phone: 598 2 9241860 Int. 109 598 2 9290705 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm

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Fitting EXAFS with out any atomic coordinates?
by Mario Gomez 30 Mar '07

30 Mar '07

Hi Bruce my name is Mario and I was just wondering if your program can fir the EXAFS spectra without any atomic positions. Obviously the answer is no if you use atoms to create the FEFF file but what does one do when we have a semi-crystalline material for which no one has attempted the fractional coordinates. I mean the XRD pattern shows some crystalline but due to the high background I would think it would be very hard to do the Rietveld analysis. So what can one do, can we fit the EXAFS spectra knowing only the chemical composition and perhaps the lattice geometry(orthorhombic or hexagonal)? thanks

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Re: [Ifeffit] Ifeffit Digest, Vol 49, Issue 20
by Ricardo Faccio 29 Mar '07

29 Mar '07

Dear Iffefit users I am performing a refinement for a La2CuO4 in powder. I followed Bruce's course, and I tried determine S02 hopping its correlation with sigma^2. I am attaching a graph of this determination. Please see enclosed the file. My question is: Is common to obtain a S02 of 0.625? and is common to obtain a nearly sigma^2=0? I didn't fit E0, alpha and degeneracy for the first single shell. What is the best strategy to fix this bad result? Thanks in advance Ricardo ------------------------------------------------------------------------- ----- Ing. Quím. Ricardo Faccio Mail: Cryssmat-Lab., Cátedra de Física, DETEMA Facultad de Química, Universidad de la República Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio(a)fq.edu.uy Phone: 598 2 9241860 Int. 109 598 2 9290705 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm

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Re: [Ifeffit] problem with running feff while working your ZnO example file
by Scott Calvin 29 Mar '07

29 Mar '07

Hi Soma, I am cc'ing this to the ifeffit list, as they may have a better answer than I do. The ZnO tutorial does currently have some problems having to do with variable names that became reserved after it was written. Those problems, though, do not cause the symptom you describe. The output of your feff run is "strange"--it claims to have an Rmax of 0, for instance. I'm not sure what could cause that particular problem; hopefully someone else on the list could help you. To start with, information on your operating system, version of Artemis, etc. might be helpful. --Scott Calvin Sarah Lawrence College At 06:29 PM 3/28/2007, soma(a)agni.phys.iit.edu wrote: >Hi Scott > >I work as a beamline scientist at MRCAT, sector 10 in APS where Bruce and >Shelly do their expts and I am trying to learn EXAFS analysis. Bruce >showed me your worked out example on ZnO and I was trying to follow it. > >I followed your notes till where it says to click the button "Run Feff". >When I do that ARtemis palatte gives the following message with red error >message at the end. I have copied that below. When I try putting RMAx 5 >instead of 6, it still keeps on giving the same message. i checked that >nleg was 4 and did not change it. > >I closed all programs in my linux based computer but message keeps on >appearing. Could you please let me know what I should do to proceed. > >Thank you. >Soma > >Soma Chattopadhyay >Beamline Scientist >MRCAT Sector 10 Building 433B >Advanced Photon Source >Argonne National Laboratory >9700 South Cass Avenue, Argonne >IL 60439, USA. >Phone: 1-630 252 0348 >FAX: 1-630 252 0358 >Email: soma(a)agni.phys.iit.edu > >************************************************************************** > >Scott Calvin's ZnO project > 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 > overlapped potential and density for unique potential 0 > overlapped potential and density for unique potential 1 > overlapped potential and density for unique potential 2 > muffin tin radii and interstitial parameters > phase shifts for unique potential 0 > phase shifts for unique potential 1 > phase shifts for unique potential 2 > Preparing plane wave scattering amplitudes... > nncrit in prcrit 9 > Searching for paths... > Rmax 0.0000 keep and heap limits 0.0000000 0.0000000 > Preparing neighbor table > nfound nheap nheapx nsc r > Internal path finder limit exceeded -- path list may be incomplete. > Paths found 0 (nheapx, nbx 1 0) > Eliminating path degeneracies... > Plane wave chi amplitude filter 2.31% > > > Feff's path finder warned of reaching a memory limitation which > caused it not to compute the complete list of paths for your > cluster. There are two ways to avoid this problem when running > Feff. One is to decrease the size of the RMAX parameter in the > Feff input data. The other is to have the Feff calculation not > consider high order multiple scattering paths. Putting "NLEG 4" > in the Feff input data will limit Feff to compute only up to > four-legged (triple scattering) paths. > >**********************************************************************

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Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?
by Scott Calvin 28 Mar '07

28 Mar '07

Hi Mario, There are a couple of different ways to approach the kind of problem you describe, although you must be willing to guess at what the local environment looks like. For example, maybe the chemical composition tells you that you have an iron oxide. At a minimum, you could use Atoms to make a crystal structure for, say, hematite, and then only fit the nearest-neighbor paths, perhaps with an unknown coordination number. This can give you some information. Or, following the same example, maybe you think your material might be like a disordered hematite. Then you could try to fit the hematite structure out for several shells, but with free parameters to account for disorder (e.g. you could include vacancies). The key questions that you should not lose track of: --What would you like to know about your material? --What do you think your material might be like? I think sometimes people forget in particular about the first question. EXAFS doesn't answer generic questions very well ("tell me all about my sample"), but it often answers particular questions quite effectively ("are my iron atoms bonded to oxygen, or sulfur?"). So if you know what your particular questions are you've got a good chance of getting help using Bruce's and Matt's software. --Scott Calvin Sarah Lawrence College At 02:15 PM 3/28/2007, you wrote: >Content-class: urn:content-classes:message >Content-Type: multipart/alternative; > boundary="----_=_NextPart_001_01C77165.0DE07268" > >Hi Bruce my name is Mario and I was just wondering if your program >can fir the EXAFS spectra without any atomic positions. Obviously >the answer is no if you use atoms to create the FEFF file but what >does one do when we have a semi-crystalline material for which no >one has attempted the fractional coordinates. > >I mean the XRD pattern shows some crystalline but due to the high >background I would think it would be very hard to do the Rietveld analysis. > >So what can one do, can we fit the EXAFS spectra knowing only the >chemical composition and perhaps the lattice geometry(orthorhombic >or hexagonal)? > > > >thanks >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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