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Re: [Ifeffit] Ifeffit Digest, Vol 155, Issue 9
by Adi Shivprasad 25 Jan '16

25 Jan '16

Dear all, Thanks for the quick and informative responses! When I mentioned consistency, I should have clarified that, since I am in the Nuclear Engineering field, the audience for my paper may not have any prior experience with XAS, so I wanted to understand how to explain spectrum features in a way that is accurate and easy to understand from their point of view. To that end, I wanted to make sure I had a better understanding before writing anything incorrect. Thanks, Aditya On Mon, Jan 25, 2016 at 10:14 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov > wrote: > 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: XANES pre-edge vs. edge features (Scott Calvin) > 2. Re: XANES pre-edge vs. edge features (Guanghui Zhang) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 25 Jan 2016 10:06:17 -0500 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] XANES pre-edge vs. edge features > Message-ID: <9A201B66-AE18-4F10-A367-7E9A7851F705(a)slc.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Aditya, > > Matt gave a good explanation of what?s responsible for the various > features, which was part of your question. Another aspect of your question > has to do with the way we use terminology. > > (Bruce?s answer, and your response, came in while I was writing this. So > it may be somewhat superfluous, but since it?s already mostly written, I > figure I?ll pass it along.) > > As Matt said, ?edge? is a poorly defined term. One meaning of it is that > it?s the big rise in absorption that occurs at the start of a XAFS > spectrum. That, for example, is the meaning that?s in use when we try to > quantify an ?edge step? or an ?edge jump? so that we can normalize the > data. In that sense, if a feature occurs before most of that rise, it can > be called ?pre-edge.? > > But another use of the word ?edge? is as a synonym for ?E0,? which is > itself a concept that is not unambiguously defined. One definition of E0 > would be ?the energy origin needed to make the EXAFS equation accurate.? > But the EXAFS equation is itself an approximation which is only useful at > energies starting many eV above E0. So there?s no theoretical reason that > the E0 used in EXAFS has to correspond to an energy with a simple > theoretical meaning or to any particular feature in the spectrum. The best > we can say is that it should be within, or sometimes a bit above, the > rising portion of the absorption spectrum. > > But when we?re trying to align and process data we need some working > definition of E0, both for XANES analysis and to get a preliminary chi(k) > for EXAFS analysis. So we come up with other definitions, such as ?the > maximum of the first significant peak in the first derivative spectrum.? As > Bruce said, the exact definition used is not important, but it is important > that the same definition be used with all spectra being compared. > > Depending on the definition chosen, the preliminary value of E0 may very > well be chosen well below the bulk of the rise in the spectrum. If we call > the energy of E0 the ?edge,? but also call features that come before the > big rise "pre-edge features,? we end up with the confusing terminology that > the edge energy may well be below some of the pre-edge features! > > That terminology is unfortunate for people new to the field, but rarely > causes any actual ambiguity. > > ?Scott Calvin > Sarah Lawrence College > > > On Jan 25, 2016, at 9:40 AM, Matt Newville <newville(a)cars.uchicago.edu > <mailto:newville@cars.uchicago.edu>> wrote: > > Aditya, > > The distinction between "edge" and "pre-edge" is not very clear, either > when looking at a single spectrum or even conceptually. > > In broad terms, the main edge is at the energy where the unoccupied > electron levels start - the Fermi energy. For 1s levels, the transition > is to p levels (and for Fe K edge, the 4p level). So, the main edge is at > the energy of the empty 4p levels. This the transition as being to an > atomic level. In a solid (or liquid), the energy levels above the Fermi > level are highly delocalized and spread over many (if not all) atoms in the > systems. Once you get much above the main edge, it's not very easy to > assign transitions to identifiable atomic transitions, or even assign a > good quantum number to them. > > Pre-edge features are generally considered to be unoccupied atomic levels > (that is, still assignable to a particular atom, or at least almost so) > below the main edge. For the transition metal K edges (such as Fe), the > main edge is 1s -> 4p. But Fe has many unoccupied 3d levels. For a K > edge to get to transition to these levels, either you need a quadrupole > transition (unlikely, but not impossible), or (more likely) for > bonding/anti-bonding with ligands (typically oxygen) to mix their > p-orbitals with the metal d-orbitals. This hybridization is often called > a ligand field or crystal field. It often gives very identifiable (and > at very predictable energies) peaks below the main edge. Two and > sometimes even three peaks can be seen and assigned with ligand field > terminology. There's sort of a whole industry built up around these > peaks for transition metal oxides. > > These peaks can "leak" into the main edge, and in some cases (say, Cu1+) > the classification of "sharp features at the edge" is not very clear. For > Fe metal, it's pretty clear that the main edge (derivative at 7110.75 eV, a > small peak on the main edge around 7112.5 eV) is the 4p level, and the rest > of the features are actually explainable as EXAFS. > > Hopefully, someone will correct anything I got wrong! > > --Matt > > > > On Mon, Jan 25, 2016 at 8:13 AM, Aditya Shivprasad <aps202(a)psu.edu<mailto: > aps202(a)psu.edu>> wrote: > Dear list, > > I was looking at the XANES standard for Fe foil from Hephaestus and I > noticed that there was a small, curved feature at the edge (7112 eV), > another inflection point at 7116.4 eV, and then the edge step at around > 7131 eV. My question is: why is the feature at 7112 eV considered as the > edge and not as a pre-edge feature? Are they due to fundamentally different > phenomena? I would like to understand where this type of feature comes from > so as to be consistent in the current paper that I am writing. I have > attached the standard, just in case. > > Thanks > -- > Aditya Shivprasad > > aps202(a)psu.edu<mailto:aps202@psu.edu> > Ph.D Candidate > Nuclear Engineering Department > Pennsylvania State University > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > >

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XANES pre-edge vs. edge features
by Aditya Shivprasad 25 Jan '16

25 Jan '16

Dear list, I was looking at the XANES standard for Fe foil from Hephaestus and I noticed that there was a small, curved feature at the edge (7112 eV), another inflection point at 7116.4 eV, and then the edge step at around 7131 eV. My question is: why is the feature at 7112 eV considered as the edge and not as a pre-edge feature? Are they due to fundamentally different phenomena? I would like to understand where this type of feature comes from so as to be consistent in the current paper that I am writing. I have attached the standard, just in case. Thanks -- Aditya Shivprasad aps202(a)psu.edu Ph.D Candidate Nuclear Engineering Department Pennsylvania State University

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Regarding calculations for scattering amplitude
by pushkar shejwalkar 25 Jan '16

25 Jan '16

Dear All, I sent a related question in the month of Dec but it seems that the question did not appeared on list because of mailbox being full, as we all have received an email. Since mailing list is started again I am sending this question once more. My question is actually regarding finding out the nanoparticle size. In this respect, I am referring to Harris's work in which by using a simple equation we can roughly estimate the nanoparticle size J. Appl. Phys., Vol. 94, No. 1, 1 July 2003 Now the question is that in this paper and another paper I found online as well, it refers to Nnano and Nbulk. I am guessing that this is basically coordination number of nanoparticle and bulk. But my first question is how do I calculate it?? e.g. I am working on Pd K-edge. So should I fit Pd foil with Pd crystal data and get the CN? but that would be 12 anyways. So would Nbulk be 12 in that case? and what will be Nnano then? In another context, CN is proportional to amplitude, so in that case is it directly proportional? as in, can I simply replaced in formula, Nbulk/Nnano with Amplitudebluk/amplitudenano? Third thing is that, if above is true then how should/can I calculated the amplitude? isnt that amplitude is always calculated by Feff? if so could someone help me with the procedure to do so? How will I know amplitude for nanoparticles, because I cannot have FEFF for nanoparticles, right? I went through lot of material, however, so far my calculations give me a solution that is vaguely correlated to TEM images. The TEM value is about 2nm (rouhgly 20 angstrom). my current values I am getting by solving the equation by my current understanding is only 2Ao. about 10 times less. What I am doing is simply plotting the crude data in athena to get x(R) Vs radial distance graph, calculate A-3 for nanoparticles and bulk and using this as amplitudes. It is possible that I may be doing something totally irrelevant, so please help me in this aspect. Thank you Sincerely Pushkar -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

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Re: [Ifeffit] Fwd: Citing XANES standards
by Bruce Ravel 21 Jan '16

21 Jan '16

On 01/21/2016 12:14 PM, Aditya Shivprasad wrote: > Hi Dr. Ravel, > > I am a graduate student in Nuclear Engineering at Penn State. I study > corrosion of Zr-based alloys using microbeam XANES at the APS. For my > linear combination fitting of iron XANES spectra I have used your iron > foil standard that is available through the Hephaestus program. I was > wondering if there was a paper or work I could cite to reference this > standard. Aditya, I am CCing my answer to the Ifeffit mailing list. This seems like a general enough question that it should go onto the list. The advice I have given others who have asked this question is to state that the standard is distributed with the Demeter software package and to use the standard citation for the software. Cheers, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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DAFS calculation
by JeongEunSuk 21 Jan '16

21 Jan '16

Hello I've heard that Atoms 3.0 code is available to calculate DAFS. I would like to calculate it. Do you have any example for it? I don't know how to use keywords in Atoms 3.0 such as dafs, emin, emax and others. Best regards Eun-Suk Jeong

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Ifeffit Mailing List
by Matt Newville 15 Jan '16

15 Jan '16

Hi Folks, As some of you no doubt noticed, the server (millenia.cars.aps.anl.gov) running this mailing list as well as the ifeffit web pages and xafs.org has been down for much of the past month. There was a hard-disk failure that brought this server down on Dec 21. I was out of town at the time, and didn't return until this week. FWIW, I know that Bruce Ravel was also away and unable to answer questions. It's possible the hard disk was telling us we all needed a break over the holidays. If you're getting this message, the mailing list is back up, and should be working now. Any messages you may have posted since Dec 21 are probably lost, and you may want to re-ask them. The ifeffit web site and xafs.org are also back up now. The Atoms web page is not yet functioning, but I'm working on that. If you notice any problems or have any questions, feel free to send me an email either on this list or in private. --Matt Newville <newville at cars.uchicago.edu>

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Solution to running Demeter on an ORNL computer
by Mullins, David R. 17 Dec '15

17 Dec '15

After having run Athena and Artemis for years on my office computer in Oak Ridge they suddenly stopped working. The command prompt window and "credits window" appeared briefly and then shut down. I tried upgrading from v 9.21 to v 9.24. This didn't help. The problem appears to be similar to what was reported in October 2015 by Matt Noerpel on EPA computers. The problem is related to the restricted Administrator privileges imposed by ORNL IT. To install new software we temporarily obtain Administrator privileges. When we do this it changes our User Directory from our standard User Directory to Admin. Demeter's default is to install in the current User Directory which is now the Admin directory and apparently programs installed there won't run when Administrator privileges are gone. To solve the problem I changed the installation directory from Admin to my User Directory name in the long line "Install Demeter in ...". Note that I just substituted my User Directory name for Admin and didn't change any of the other directory specifications. Hope this helps. I suspect that as time goes by many other national labs and companies will institute similarly restrictive Admin privileges. Dave ********************** David R. Mullins Oak Ridge National Laboratory PO Box 2008, MS 6201 Oak Ridge, TN 37831-6201 PH: 865-574-2796 FAX: 865-241-5152 E-MAIL: mullinsdr(a)ornl.gov<mailto:mullinsdr@ornl.gov> WWW:http://www.ornl.gov/sci/csd/Research_areas/SCC_group.html

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Measurment of size of nanoparticles using one measurement of sample
by pushkar shejwalkar 17 Dec '15

17 Dec '15

Dear All, I am currently trying to find out the size of my Pd nanoparticles using EXAFS analysis. But I am totally new to this field and I have no physics background as well. With this I started digging into the email archives as to if it is possible to speculate the size of the nanoparticles that I have. My preliminary information from SEM lets me start from the point where the nanoparticles are around 2-3 nm in size and about spherical in nature. I started with the following thread from archive http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2013-October/011474.html and it was pretty useful as well. I read the documents and other threads involved in it. and then I realized that with the knowledge of amplitude of known (lets say in this case Pd foil) and my sample I can find out the extent to which the Pd atoms are present at the farthest distance. by doing so I can find out what the nanoparticles size. To be specific I am talking about this particular paper. http://scitation.aip.org/docserver/fulltext/aip/journal/jap/94/1/1.1581344.… (http://dx.doi.org/10.1063/1.1581344) I am using this paper since it works with spherical nanoparticles and hence my assumptions can best be supported by this model. I am open to other references as well and I would cite them all if they are useful. Now my question is, in order to make up to the reduced amplitude, it is recommended that for spherical nanoparticles only two variables in fitting parameteres are needed 1) Radius 2) amplitude reduction factor (SO2) I think I have understood the basic concept as to why the amplitude is reduced and somehow we need to increase the number N of number of paths/number of atoms in the cluster so that the amplittude will now increase so much so that it would match the theory. BUT what I have not understood is how to do so? e,g do we do that during fitting? in artemis? in which case the amplitude is by default adjusted to get the fit and now there is no difference in the absolute value of x(R) (A-3Ao) Y-axis. OR have I misunderstood something? Could someone shine a light on this please. Best Pushkar -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

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Mac woes
by Bruce Ravel 15 Dec '15

15 Dec '15

If someone would like to contribute a write-up on how to install the Mac package and how to troubleshoot the most common problems, that would be helpful. I could then replace the text that exists on the Demeter homepage, which does not appear to be sufficient for many Mac users. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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No Plot window (Mac El Capitan)
by Laila Al-Madhagi [fy11lham] 15 Dec '15

15 Dec '15

Hello there, I have installed Demeter with Macports on my Mac recently. My operating system is El Capitan. My issue is that I cannot see the plot area. I have followed two threads discussing this issue. The first one is ''No plot window in Athena/ Demeter on Mac OS X Yosemite'' (http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-September/012739.ht… where George suggested to change the gnuplot to x11 on the Athena preferences menu. I could not find Athena preference menu and I was wondering if anyone could help with that. The second thread is ''No plot window on Mac El Capitan'' (http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg05261.ht… where Chloe could not find Athena Preferences menu as well. Best regards, Laila

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