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

FW: Data summation - missing groups
by Godfrey, Ian 01 Feb '16

01 Feb '16

Sorry, I've just seen that this has already been reported. Ian From: Godfrey, Ian Sent: 27 January 2016 11:21 To: 'XAFS Analysis using Ifeffit' <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Data summation - missing groups Dear All, When using the data summation tool in Athena (0.9.24 x64 on Win10 Pro) the first group in the group list seems to be missing from the dropdown showing the potential components of a summation (see attached screenshot). To reproduce: 1) Open attached project file and import with "select all" on the import dialogue box 2) Change to data summation window 3) Try and add the first data group (234) to the summation from the dropdown menus. (In the screenshot I've changed the default normmu(E) to mu(E), but the same behaviour is displayed in both cases.) On a related note, I'm not sure I fully understand how the data summation is different from the merge? Clearly data summation allows you more control (arbitrary weighting of groups etc.) and is intended for XANES analysis, but is it a fundamentally different procedure or just a different interface for the same thing? Thanks, Ian Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London, And School of Materials Science, Japan Advaned Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp> 02076 794864

2 5

Re: [Ifeffit] pi/2deltak
by Avakyan L.A. 31 Jan '16

31 Jan '16

Hello Riti, the criterion of R-resolution of pi/2deltak can be drawn from the Nyquist theorem. The amount of information in the spectra is limited by Nidp = 2 deltak deltaR / pi. Then, in assumption of equal distribution of information over the R-interval, the minimal interval can be estimated as deltaR / Nidp = pi/2deltak. The problem is that exact formula for Nidp is not known. Sometimes it has addition of +1 or +2 to represent the fact that single point (deltak=0) still contains information. Moreover, information is not equally distributed: some k-regions are more rich, other are less... And when energy interval is very short (glass, liquid) this question becomes vital. Sometimes, this resolution limit can even be overcome as it is shown in [http://dx.doi.org/10.1103/PhysRevB.82.064204] Best regards, Leon Leon Avakyan PhDr, Physics Faculty, Southern Federal University laavakyan(a)sfedu.ru On 31.01.2016 21:00, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Message: 2 > Date: Sat, 30 Jan 2016 17:35:04 -0800 > From: Ritimukta Sarangi<ritimukta(a)gmail.com> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] pi/2deltak > Message-ID: > <CAMWiF7ymrKEDSZw31pcgwCzZH5tsFvFk+151gxfjRz9jUARH4w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I was recently asked about the accuracy of this formulation for obtaining > EXAFS resolution and I did not have a good answer. Can someone point to a > reference or explain here? > Thank you for your time, > Best, > -Riti

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 155, Issue 16
by Christopher Thomas Chantler 30 Jan '16

30 Jan '16

Dear Jason Good topic We have published a few papers discussing analysis with thickness distributions and roughness. Normally the XERT method will address this especially for small samples. Particularly see J. L. Glover, C. T. Chantler, M. D. de Jonge, ‘Nano-roughness in gold revealed from X-ray signature,’ Physics Letters A373 (2009) 1177-1180. The general topic of thickness effects is of course wider, and partially addressed in a couple of other papers. Hope this helps Chris ------------------------------------------------------------ Christopher Chantler, Professor, FAIP Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS President, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au chantler(a)me.com http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html http://optics.ph.unimelb.edu.au/~chantler/home.html ________________________________________ From: Ifeffit [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Sunday, 31 January 2016 5:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 155, Issue 16 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: Effect of gradual thickness variation in beam (Jason Gaudet) ---------------------------------------------------------------------- Message: 1 Date: Fri, 29 Jan 2016 14:32:43 -0500 From: Jason Gaudet <jason.r.gaudet(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Effect of gradual thickness variation in beam Message-ID: <CANMcWtOLubiomegk-GM6SMS6CSpw0B0Hg21rMe9-hV8uQEkxhw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Anatoly, Sorry, I meant to write 1000 um inner diameter. Energies will be V and Fe, 5465 & 7112 eV. Samples are roughly 1 absorption length thick for the metal (V, Fe) and about 2-2.5 absorption lengths for the entire sample. Bruce, I may just flip over the sample holder and have the sample tubes in plane with the storage ring to take advantage of the greater horizontal spread, rather than focusing on the vertical. Cutting the vertical slits down to 100-300 um while keeping the horizontal around 500 um ought to get me the most beam at the least variation in mu(E), especially if I go with 1500 um ID tubes. The samples are nice and concentrated so I can afford to give up a lot of photon flux. Bar-napkin calculations tell me with a 1500 um ID tube and 200 um V 750 um H slits I'll lose an acceptable amount of photon flux and have a <1% thickness variation. I'm fairly confident I've made pressed pellets with as much or more variation from one spot to another, without noticeable mu(E) changes from spot to spot, in the vicinity of this energy range. I'll go ahead and take your advice, and amend my setup procedure with some measurements of Io intensity and mu(E) reproducibility as a function of slit width. While a bit of a bother, it's still worth it to keep our sample prep simple and inexpensive. Thanks, Jason On Thu, Jan 28, 2016 at 9:12 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > On 01/27/2016 07:05 PM, Jason Gaudet wrote: > >> I'm planning on some transmission-mode XAS with smaller than usual >> sample tubes. I'm realizing I might be in danger of creating excessive >> non-uniformity in my samples by having the beam size on the same order >> of magnitude as the sample tube radius. >> >> For example, let's say I want to measure liquid in a sample tube with a >> 1000 micron outer diameter, with a beam 500 microns wide and centered on >> the sample tube. If the tube is orthogonal to the ring plane, the entire >> vertical portion of the beam will pass through the same length of >> liquid. But in the horizontal plane, the center of the beam will pass >> through 1000 microns of sample while the edges of the beam will pass >> through 866 microns of sample, due to the curvature of the sample cell >> across the horizontal plane. >> >> Most of what I know about the statistics of thickness effects are about >> leakage and pinholes - nonlinearity caused by a few spots having very >> low or negligible sample thickness. But I don't know how significant a >> "mild" thickness distribution might be. If this sort of thickness >> distribution is going to be an issue it would be great to know that >> beforehand and either go with larger samples, smaller beam size, or more >> creative orientation. >> > > > Jason, > > There may be some distortion to the data due to the varying thickness. > On the plus side, liquids tend to be very homogeneous. > > Probably the best solution to this situation, if it's available at the > beamline, is to focus the beam in the vertical, for example, using a > flat mirror on a bender. Focusing to a spot would also address the > thickness situation, but you need to be mindful that the intense beam > could generate radicals from the liquid, causing sample damage. > > If the sample is sufficiently concentrated, then you could simply slit > the beam down to 100 or 200 microns and still have enough for a > transmission measurement. In fact, that would be the way to decide if > you are seeing a big problem from the shape of the tube. Compare the > mu(E) with the slits at 500 to mu(E) with the slits at 100 (carefully > aligning the sample both times, of course). If they are the same, > then, then you're golden. > > 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/ > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >

1 0

Effect of gradual thickness variation in beam
by Jason Gaudet 29 Jan '16

29 Jan '16

Sample cell Hi all, I'm planning on some transmission-mode XAS with smaller than usual sample tubes. I'm realizing I might be in danger of creating excessive non-uniformity in my samples by having the beam size on the same order of magnitude as the sample tube radius. For example, let's say I want to measure liquid in a sample tube with a 1000 micron outer diameter, with a beam 500 microns wide and centered on the sample tube. If the tube is orthogonal to the ring plane, the entire vertical portion of the beam will pass through the same length of liquid. But in the horizontal plane, the center of the beam will pass through 1000 microns of sample while the edges of the beam will pass through 866 microns of sample, due to the curvature of the sample cell across the horizontal plane. Most of what I know about the statistics of thickness effects are about leakage and pinholes - nonlinearity caused by a few spots having very low or negligible sample thickness. But I don't know how significant a "mild" thickness distribution might be. If this sort of thickness distribution is going to be an issue it would be great to know that beforehand and either go with larger samples, smaller beam size, or more creative orientation. Thanks, Jason

3 3

Data summation - missing groups
by Godfrey, Ian 27 Jan '16

27 Jan '16

Dear All, When using the data summation tool in Athena (0.9.24 x64 on Win10 Pro) the first group in the group list seems to be missing from the dropdown showing the potential components of a summation (see attached screenshot). To reproduce: 1) Open attached project file and import with "select all" on the import dialogue box 2) Change to data summation window 3) Try and add the first data group (234) to the summation from the dropdown menus. (In the screenshot I've changed the default normmu(E) to mu(E), but the same behaviour is displayed in both cases.) On a related note, I'm not sure I fully understand how the data summation is different from the merge? Clearly data summation allows you more control (arbitrary weighting of groups etc.) and is intended for XANES analysis, but is it a fundamentally different procedure or just a different interface for the same thing? Thanks, Ian Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London, And School of Materials Science, Japan Advaned Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp> 02076 794864

2 1

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 > >

1 0

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

6 5

Regarding calculations for scattering amplitude
by pushkar shejwalkar 24 Jan '16

24 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

4 5

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/

1 0

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

3 3