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

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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[howto] configurational average in EXAFS with FEFF
by Mauro Rovezzi 28 Mar '07

28 Mar '07

Dear all, I would like your point of view on how to approach configurational average in EXAFS analysis with FEFF (let's not consider GNXAS for the moment). In particular, I'm trying to combine ab-initio DFT numerical simulations with EXAFS for doped semiconductors where in the minimized cluster there are N absorbing atoms. Usually I don't use the CFAVERAGE card because fractional degeneracies are not taken into account and, to have a qualitative analysis, I calculate an "extended"-XANES (up to 8.0 A^-1) for each cluster - where each absorbing atom is shifted to (0,0,0) - and then I average over all single-cluster signals. Well, at this point my question is: how to proceed in the quantitative analysis with Ifeffit? In fact, considering only single-scattering expansion for all the clusters the result could be seen as a radial distribution for each scattering pair where the integral gives the coordination number and the FWHM a structural Debye-Waller factor. How to combine these informations? Thanks for the answers, Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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the ifeffit wiki
by Bruce Ravel 26 Mar '07

26 Mar '07

Hi everyone, I just finished cleaning some really distasteful vandalism off of the Ifefift wiki. Several pages had been edited to add dozens of links to pages that have .... ummmm .... very little to do with XAS. Such vandalism is unwelcome on the ifeffit wiki and is most certainly not what Matt and I intended when we started it. I check for this sort of thing fairly often, but much of the latest crop of vandalism had been there for 24 hours without my noticing. If you ever see content on a wiki page that is clearly the work of a wiki vandal, feel free to clean it up or to drop me a private email and I will do so. In any event, please do not be mad at those of us who administer the wiki. We really intend the ifeffit wiki to be a place where you can bring your children to learn about XAS ;-) B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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in situ liquid cell
by Renato Canha Ambrosio 26 Mar '07

26 Mar '07

Dear Colleagues, I need to perform XAFS measurements microemulsions (liquid). As I do not have a liquid cell for the in situ XAFS measurements, I would like to know more about liquid cells. Could anyone shoot its cell and send me the photo? I am designing a cell where you optimize the edge jump by modifying the optical path. Thank you very much for your kind attention Renato Canha Ambrosio ---------- Original Message ----------- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Thu, 22 Mar 2007 17:45:00 -0500 Subject: Ifeffit Digest, Vol 49, Issue 14 > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > Today's Topics: > > 1. Re: EXAFS reference materials (Frenkel, Anatoly) > 2. Re: EXAFS reference materials (Scott Calvin) > 3. Re: EXAFS reference materials (Frenkel, Anatoly) > 4. Some more questions (Shantanu Behera) > 5. Re: Some more questions (Bruce Ravel) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 22 Mar 2007 15:28:55 -0400 > From: "Frenkel, Anatoly" <frenkel(a)bnl.gov> > Subject: Re: [Ifeffit] EXAFS reference materials > To: <rh2rr(a)virginia.edu> > Cc: Ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <0D9ED6BC247DA847A3855B6726D6E34421854C(a)exchangemb1.bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Ruoshuang, > > I am cc'ing this email to IFEFFIT mailing list. There are several > reasons (I am listing just a few) you should measure a reference > sample simultaneously with unknown materials. > > 1) to align the unknown sample scans prior to merging. If those data > are noisy, reference sample can be used for the alignment. In > addition, if you want to compare samples before and after some > changes that may affect their energy positions (e.g., oxidation, > reduction, doping, metal-insulator transition, etc.) you want to > align all of their references to reliably analyze these changes. > > For this purpose, it does not matter whether you use a metal or a > metal oxide or any other standard with the same resonant element. > > 2) to find S02 value. It is usually the same in most samples which > have the same resonant element. > > For this purpose, what matters the most is whether you can reliably > find S02 from your standard (and then impose it on your unknown > sample). Thus, some exotic reference which may still be good for 1) > may not be as good for 2) since it may be difficult to refine its > structure and get precise value for S02. The metals would be the > best, but if you have other materials with "open lattices", e.g., > fcc, rock salt, etc., with well defined first shell that you can > fit with the miniumum parameters, they will all work fine. > > 3) to use as a model for your analysis. > > If you analyze an alloy, as in your case, you want to compare EXAFS > results in your alloys against those in relevant pure compounds. For > binary alloys, the best reference will be a pure metal, for ternary - > an intermetallic compound, etc. An oxide would not be so useful for > modeling. For that reason, people often measure more than one > reference, as per 1),2) and 3). > > Hope it helps, > > Anatoly > > ________________________________ > > From: rh2rr(a)virginia.edu [mailto:rh2rr@virginia.edu] > Sent: Thu 3/22/2007 2:54 PM > To: Frenkel, Anatoly > Subject: EXAFS reference materials > > Dear Dr. Frenkel, > > I'll do EXAFS on metallic glass but I am not sure about the reference > materials. [...] > We are trying to study structural relaxation of metallic glass by > EXAFS. My samples are Al-TM-RE (TM=Fe,Co,Ni, RE=Gd,Ce,Y). Because Ce > and Y are easily oxidized in air, some people suggest use cerium > oxide and yttrium oxide as reference materials. My question is: when > I do EXAFS measurement and data analysis, is METAL necessary for > reference materials, or METAL OXIDE is fine as reference? > > Your kind help would be greatly appreciated. > > Ruoshuang Huang > > ------------------- > Ruoshuang Huang > Research Associate > Materials Science and Engineering > University of Virginia > Phone: 434-982-0238 > Fax: 434-982-5799 > > ------------------------------ > > Message: 2 > Date: Thu, 22 Mar 2007 15:48:31 -0400 > From: Scott Calvin <SCalvin(a)slc.edu> > Subject: Re: [Ifeffit] EXAFS reference materials > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <0JFB006RXLO7QHX0(a)mta3.srv.hcvlny.cv.net> > Content-Type: text/plain; charset=us-ascii; format=flowed > > Hi Ruoshuang, > > Following up on Anatoly's excellent post, I would say that I > personally distinguish between a "reference" and a "standard." > > When I talk about a reference, I usually mean something I'm > measuring simultaneously with the sample. The primary purpose is > energy alignment, although it also gives a check on beam quality > issues > (e.g. harmonics). For this purpose, I generally use whatever is > convenient and well known, such as a metal foil. Sometimes I'll > measure the reference by itself, particularly if it's a beamline or > edge that is new to me. > > On the other hand, I think of a standard as a known compound that is > similar to my sample. I often work with nanoparticles, so my > standard might be the corresponding bulk material. Or if I'm working > with a doped compound, the standard might be the undoped version. > The standard is measured under the same conditions as the > sample...in fact, that means that I measure the standard with a > reference in place, if that makes sense. :) > > So I use a reference for Anatoly's purpose (1) and a standard for > Anatoly's purposes (2) and (3). > > I hope that's helpful. > > --Scott Calvin > Sarah Lawrence College > > At 03:28 PM 3/22/2007, you wrote: > >Hi Ruoshuang, > > > >I am cc'ing this email to IFEFFIT mailing list. There are several > >reasons (I am listing just a few) you should measure a reference > >sample simultaneously with unknown materials. > > > >1) to align the unknown sample scans prior to merging. If those data > >are noisy, reference sample can be used for the alignment. In > >addition, if you want to compare samples before and after some > >changes that may affect their energy positions (e.g., oxidation, > >reduction, doping, metal-insulator transition, etc.) you want to > >align all of their references to reliably analyze these changes. > > > >For this purpose, it does not matter whether you use a metal or a > >metal oxide or any other standard with the same resonant element. > > > >2) to find S02 value. It is usually the same in most samples which > >have the same resonant element. > > > >For this purpose, what matters the most is whether you can reliably > >find S02 from your standard (and then impose it on your unknown > >sample). Thus, some exotic reference which may still be good for 1) > >may not be as good for 2) since it may be difficult to refine its > >structure and get precise value for S02. The metals would be the > >best, but if you have other materials with "open lattices", e.g., > >fcc, rock salt, etc., with well defined first shell that you can fit > >with the miniumum parameters, they will all work fine. > > > >3) to use as a model for your analysis. > > > >If you analyze an alloy, as in your case, you want to compare EXAFS > >results in your alloys against those in relevant pure compounds. For > >binary alloys, the best reference will be a pure metal, for ternary > >- an intermetallic compound, etc. An oxide would not be so useful > >for modeling. For that reason, people often measure more than one > >reference, as per 1),2) and 3). > > > > > > ------------------------------ > > Message: 3 > Date: Thu, 22 Mar 2007 16:03:34 -0400 > From: "Frenkel, Anatoly" <frenkel(a)bnl.gov> > Subject: Re: [Ifeffit] EXAFS reference materials > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <0D9ED6BC247DA847A3855B6726D6E34421854F(a)exchangemb1.bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Thanks, Scott! - Good point. > A. > > ________________________________ > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Scott Calvin > Sent: Thu 3/22/2007 3:48 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] EXAFS reference materials > > Hi Ruoshuang, > > Following up on Anatoly's excellent post, I would say that I > personally distinguish between a "reference" and a "standard." > > When I talk about a reference, I usually mean something I'm measuring > simultaneously with the sample. The primary purpose is energy > alignment, although it also gives a check on beam quality issues > (e.g. harmonics). For this purpose, I generally use whatever is > convenient and well known, such as a metal foil. Sometimes I'll > measure the reference by itself, particularly if it's a beamline or > edge that is new to me. > > On the other hand, I think of a standard as a known compound that is > similar to my sample. I often work with nanoparticles, so my standard > might be the corresponding bulk material. Or if I'm working with a > doped compound, the standard might be the undoped version. The > standard is measured under the same conditions as the sample...in > fact, that means that I measure the standard with a reference in > place, if that makes sense. :) > > So I use a reference for Anatoly's purpose (1) and a standard for > Anatoly's purposes (2) and (3). > > I hope that's helpful. > > --Scott Calvin > Sarah Lawrence College > > At 03:28 PM 3/22/2007, you wrote: > >Hi Ruoshuang, > > > >I am cc'ing this email to IFEFFIT mailing list. There are several > >reasons (I am listing just a few) you should measure a reference > >sample simultaneously with unknown materials. > > > >1) to align the unknown sample scans prior to merging. If those data > >are noisy, reference sample can be used for the alignment. In > >addition, if you want to compare samples before and after some > >changes that may affect their energy positions (e.g., oxidation, > >reduction, doping, metal-insulator transition, etc.) you want to > >align all of their references to reliably analyze these changes. > > > >For this purpose, it does not matter whether you use a metal or a > >metal oxide or any other standard with the same resonant element. > > > >2) to find S02 value. It is usually the same in most samples which > >have the same resonant element. > > > >For this purpose, what matters the most is whether you can reliably > >find S02 from your standard (and then impose it on your unknown > >sample). Thus, some exotic reference which may still be good for 1) > >may not be as good for 2) since it may be difficult to refine its > >structure and get precise value for S02. The metals would be the > >best, but if you have other materials with "open lattices", e.g., > >fcc, rock salt, etc., with well defined first shell that you can fit > >with the miniumum parameters, they will all work fine. > > > >3) to use as a model for your analysis. > > > >If you analyze an alloy, as in your case, you want to compare EXAFS > >results in your alloys against those in relevant pure compounds. For > >binary alloys, the best reference will be a pure metal, for ternary > >- an intermetallic compound, etc. An oxide would not be so useful > >for modeling. For that reason, people often measure more than one > >reference, as per 1),2) and 3). > > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

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Some more questions
by Shantanu Behera 22 Mar '07

22 Mar '07

Dear Ifeffiters I have some more questions. 1. There is a k-weight button in the background removal column in Athena. How's that used and what's its significance? 2. Assume that I have collected data up to 14k, and I see that the signal beyond 12k is very noisy. I want to use the data up to 12k and within that data range pick a F-filter window of 2-10k or 3-10k. How do I go about this? Can I do that with the spline range (in k or E) options in bkg removal (Athena) column? I have gone through Bruce's documentations and have some sense, but not quite clear. Would appreciate your help. Warm regards. Shan -- ||||||||||||||||||||||||||||||||| Shantanu Behera Center for Advanced Materials and Nanotechnology Lehigh University 5, East Packer Avenue Bethlehem, PA 18015, USA

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