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

Re: Re: Re: XAFS Analysis using Ifeffit
by jana padeznik 04 Aug '06

04 Aug '06

>How do you get those absorption backgrounds, free of EXAFS? I can see it >for Kr, but how did you do it for the other, >chemically-reactive elements? > mam > In short: we've chosen at least two compounds of each element with especially simple EXAFS signal (mostly glasses), modeled this signal and eliminated it from the original data. This residual is used as an approximate atomic absorption background for the other sample, whose spectrum, after subtraction of this background, is the basis for an improved EXAFS model. Afterwards, the role of the two spectra is switched. After a few steps the published estimates were obtained. The procedure is described in the article: Padeznik Gomilsek, J., Kodre, A., Arcon, I., Loireau-Lozac'h, A., Benazeth, Multielectron photoexcitations in x-ray-absorption spectra of 4p elements. Phys. rev., A, 1999, vol. 59, no. 4, 3078-3081 Some information can be found on Iztok Arcon's website: http://www.p-ng.si/~arcon/xas/ <http://www.p-ng.si/%7Earcon/xas/> Best regards, Jana

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Re: [Ifeffit] Re: XAFS Analysis using Ifeffit
by Alojz Kodre 03 Aug '06

03 Aug '06

Sorry, forgot the attachment. Lojz

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Re: [Ifeffit] Re: XAFS Analysis using Ifeffit
by Alojz Kodre 03 Aug '06

03 Aug '06

Dear Matt, >I'm still confused about the right way to handle these in practice. It >seems that >a choice of "arc-tangent", "lorenztian", or "mimic the shape of the main edge" >should work for most cases -- do you agree? It also seems there ought to be >a reasonable way for the algorithm to pick which of these lineshapes to use. Maybe you`ll find the two graphs in the attachment helpful - they are from our paper cited at the top and also accessible on Iztok Arcon`s homepage. The first graph shows the usual range of EXAFS (~ 1000 eV above the edge) on the horizontal scale, and the atomic number on the vertical scale, with inserted energies of the main MPE. You can see that for 3d elements (Ti-Zn) the EXAFS range is almost free of MPE, the prominent 1s3p still within 100 eV of the edge, and the weak 1s2p at the end of the usual EXAFS range. For 4p elements(Ga-Kr) the 1s3p slowly moves into the EXAFS region. And beyond Kr, the strong 1s3d excitation gets beyond the 100 eV mark, so that two prominent MPE are to be taken into account. The L EXAFS are, as seen from the graph, practically all infested by MPE, so that there are no "clean" or "safe" ranges of Z. In the second graph, the "real" atomic backgrounds, extracted from EXAFS spectra, are shown for 4p elements. ALthough very noisy, they show what kind of an ansatz would be necessary to approximate at least crudely their shape. I imagine that two functional terms with proper energy position and amplitude (these are mostly transferable, prepared in tables) but with a small common fittable energy shift (to account for different energy calibrations or small chemical shifts). To allow the usual sloppines in the practical EXAFS analysis regarding the use of proper "matrix" subtraction etc, it would be sensible to retain some smooth background function, either a spline or a polynomial, but with much less free parameters. My feeling is that a 4-interval spline or 4th degree polynomial should be sufficient since the spline would not need to simulate the sharp jumps of MPE. Best wishes Lojz

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Other programs than FEFF - GNXAS and MXAN
by Matthew Marcus 02 Aug '06

02 Aug '06

I heard a talk by Ziyu Wu of Beijing Synchrotron Radiation Facility in which he said that the international community prefers a package called GNAXS to FEFF for EXAFS calculations. He also has his own package called MXAN for XANES fitting. What do other people think of these programs? Would it be possible/worthwhile to modify Athena/IFEFFIT to use one of these other programs? I haven't investigated them, so I don't know whether it would be possible to put a shell around GNAXS which would make it look like FEFF and therefore be usable directly by IFEFFIT. mam

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Re: XAFS Analysis using Ifeffit
by jana padeznik 02 Aug '06

02 Aug '06

Hi Matt, > Personally, I'd like to see more data with >clear MEE to play >with, and would like to model these better than with an ad hoc arc-tanget. I'd >also like to see a real case where including MEE transitions gave different >structural results than an analysis that did not include them. Any takers? > I've chosen three real chemical problems from our work where multielectron excitations had to be taken into account in order to obtain structural information. I'm sending you original data together with our articles: - cetyl-trimethylammonium bromide (CTAB) adsorbed on carbon black with very weak structural signal (Br_CTAB.nor, Br-O bond). Spectrum of aqueous solution of KBr (Br_sol.nor) helped to separate atomic and structural features. Article: Kodre, A., Padeznik Gomilsek, J., Arcon, I., Preseren, R., Separation of weak EXAFS signal from atomic background in Br and Rb samples. J. synchrotron radiat., 1999, vol. 6, 306-307. - iodine in electrolyte, again weak EXAFS signal (I_MPE.mue, I-I bond). Due to simplicity of EXAFS signal we used shorter k-range to avoid distortion from MPE. Article: Padeznik Gomilsek, J., Arcon, I., Kodre, A. Atomic effects in EXAFS structural analysis of redox I[sup]-/I[sup]-[sub]3 solid state electrolites. Acta chim. slov.. 2006, 53, 18-22. Available online: http://acta.chem-soc.si/issues.html - CeO2 thin films annealed in air (Ce_air.mue) or Ar (Ce_Ar.mue). I'm sending a spectrum of CeO2 powder as well (CeO2.mue). As in some other lanthanides, MPE signal is very strong and affects structural analysis even in case of CeO2 powder. We subtracted (valence dependent) MPE estimate prior to EXAFS analysis. In this case MPE resonances are more important than arc-tanget. Article: Padeznik Gomilsek, J., Kodre, A., Bukovec, N., Kozjek-Skofic, I. Atomic effects in EXAFS structural analysis of mixed Ce oxide thin films. Acta chim. slov., 2004, 51, 23-32. Available online: http://acta.chem-soc.si/issues.html Best regards, Jana

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Re: XAFS Analysis using Ifeffit
by Jana Padeznik Gomilsek 02 Aug '06

02 Aug '06

Since only my zip files (spectra and articles) have appeared on the Ifeffit Mailinig list, here is once again the accompanying text: Hi Matt, > Personally, I'd like to see more data with >clear MEE to play >with, and would like to model these better than with an ad hoc arc-tanget. I'd >also like to see a real case where including MEE transitions gave different >structural results than an analysis that did not include them. Any takers? > I've chosen three real chemical problems from our work where multielectron excitations had to be taken into account in order to obtain structural information. I'm sending you original data together with our articles: - cetyl-trimethylammonium bromide (CTAB) adsorbed on carbon black with very weak structural signal (Br_CTAB.nor, Br-O bond). Spectrum of aqueous solution of KBr (Br_sol.nor) helped to separate atomic and structural features. Article: Kodre, A., Padeznik Gomilsek, J., Arcon, I., Preseren, R., Separation of weak EXAFS signal from atomic background in Br and Rb samples. J. synchrotron radiat., 1999, vol. 6, 306-307. - iodine in electrolyte, again weak EXAFS signal (I_MPE.mue, I-I bond). Due to simplicity of EXAFS signal we used shorter k-range to avoid distortion from MPE. Article: Padeznik Gomilsek, J., Arcon, I. , Kodre, A. Atomic effects in EXAFS structural analysis of redox I[sup]-/I[sup]-[sub]3 solid state electrolites. Acta chim. slov.. 2006, 53, 18-22. Available online: http://acta.chem-soc.si/issues.html - CeO2 thin films annealed in air (Ce_air.mue) or Ar (Ce_Ar.mue). I'm sending a spectrum of CeO2 powder as well (CeO2.mue). As in some other lanthanides, MPE signal is very strong and affects structural analysis even in case of CeO2 powder. We subtracted (valence dependent) MPE estimate prior to EXAFS analysis. In this case MPE resonances are more important than arc-tanget. Article: Padeznik Gomilsek, J., Kodre, A., Bukovec, N., Kozjek-Skofic, I. Atomic effects in EXAFS structural analysis of mixed Ce oxide thin films. Acta chim. slov., 2004, 51, 23-32. Available online: http://acta.chem-soc.si/issues.html Best regards, Jana

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XAFS Analysis using Ifeffit
by FARGES Francois 31 Jul '06

31 Jul '06

Dear all, to mam : your referee is a dumb, clearly ! feff8 can do both. One more quick and dirty referee. Some journals do money nowadays. Easy to answer there is an EXAFS card, which is not made for XANES, clearly... to all : gnxas is not designed to be easy to use; it is not designed as a "black box". it needs some effort and that's an opposite way to feff. this strategy has its own pros and cons; and corresponds to what was taught in Italy and France in the 90's on XAFS ("work hard school"). I survived it ... But the authors have considerably modified they vision recently (open to actinides) and it is becoming more more accessible, tough not as easy as feff. For instance, the great biotech group at SSRL widely use it. One advantage of their strategy is that not everyone can claim to do "state of the art" EXAFS simulation without some deep understanding of what's going on. I've seen, in contrast, papers in which people were claiming so much about feff (so-call "good and bad things") but their calculations were far from optimum (they are never, I know for sure myself !) so their feff "evaluation" was quite very poor in fact. also gnxas is not just for glasses. it is for everything of course. they applied it often to glasses because it corresponds to what physicists where highly interested in the 90's. Nowadays the situation is quite different because environmental and biological sciences invaded the field but gnxas is highly involved in the biotech field at SSRL, for instance. With gnxas, this is not to happen soon because you always feel to be a "primitive and modest gnxas user", given the intrinsic complexity of the program and its numerous options and, I must say, its documentation that is not always updated as the code is; leaving some perplexity, if not bad mood sometimes. Also, the graphical subroutine uses some kind of unpopular primitive odd (dumb) library that is not always very easy to find or to install (many alternatives would be much more easier ...) Finally, their supported plateforms is not typical of what users now use nowadays. Surprisingly, they promote either very expensive proprietary (HP UNIX, VMS etc) or so-calmled "open source" free plateforms (Linux)(Red Hat is no more but a gnxas distribution for RedHat is still available; so there is some inconsistencies here in the gnxas policies). That's their choice but it is getting more and more 90's outdated, not reflecting 2006. But basically, a modernized front end of gnxas would be great. But one has to get into that programming to make it easy-to-click (like many would like too). With Atoms of Bruce Ravel, there are options to prepare these so-odd files needed for gnxas. this is already a wonderful first step. Any decent model of the EXAFS for high Z cations should be done with that program, basically. Sixpack, ifeffit, but mostly FEFF, are missing the multi-electronic excitation (MEE) modeling. This is well known and their authors are well aware of this limitation. The atomic-XAFS vs. MEE "battle" a few years ago contributed to this unfortunate segmentation. But most users don't even "smell" these MEE's (or AXAFS if you prefer) in their data and process them straight away. they cannnot be 100% blamed, MEE are also quite vicious features. but more and more is done that is not appropriate because of these nice GIUs (athena, sixpack). so it is difficult to decide what to do. Also, like others, I ve found that MEE are more and more visible as much as the metal concentration probed is getting lower and lower (comparative study of Mn permanganate solutions at more and more dilutions makes that the MEE is increadingly more detected in the normalized EXAFS). And this now standard to look at diluted metals, in environmental samples with these 3rd generation, highly-stabilized sources (SLS for instance). But we are getting more or less overflowded with data with all these new sources everywhere and funding agencies need papers and we go straight into it... MAM : I won't blame them not to have Windows version as I know many other GREAT programs, incl. yours, that run only on Windows (still, what a limitation to be better quoted...) as they could easily run on other plateforms... (get rid of these registers !). I'm thinking also to the viper/xanda series. So, any close future to get more gnxas done, if one does not want to jump into it... and still the best exafs-fitting package for sure. We all wish to be using it more but this is not gonna happen soon. FF

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Re: [Ifeffit] Other programs than FEFF - FDMNES
by Denis Testemale 30 Jul '06

30 Jul '06

> > My memory is that Yves Joly's FDMNES codes is available for the > asking, but the last time I looked at it (many years ago by now) I was > unable to get it compiled on my linux machine. I cannot say I managed to compile it on my linux machine because I got a bin already compiled (at ESRF), and my newbie status prevented me to try the fortran compilation. However I also use the Windows version which works straightly. FDMNES has changed since last time you had a look, Bruce (was it when you spent time at the laboratoire de Cristallographie? I was doing my phD there, at that time, we kicked the ball together once or twice! Sorry guys for that). You can download it at http://cristallo.grenoble.cnrs.fr/LDC/LE_LABORATOIRE/Equipes_de_recherche/E… There is now a small fitting module embedded in it. I also heard very recently of a program which uses the multidimensional interpolation method (you probably know better than me what this means) and which is compatible by default with FEFF8 and FDMNES ( but you can apparently use any of your XANES XANES calculation code): it allows you to vary parameters within a specified range (at this point I don't know if it is only structural parameters) and save time by selecting the calculations you really need to do (the other spectra are interpolated). This program is made by Smolentsev and Soldatov (Rostov Uni). See here: http://www.esrf.fr/computing/scientific/FitIt/MAIN.htm 2 (euro) cents more... denis It is possible that Delphine Cabaret's pseudopotential approach may be > available for outside use as well, but I do not know for sure -- it's > been a while since I last spoke with her. > > The folks associated with Rostov have codes for computing XANES > spectra. I believe Victor Kraizman reads this list and may be able to > elaborate. > > B > > > -- > Bruce Ravel ---------------------------------------------- bravel(a)anl.gov > > Molecular Environmental Science Group, Building 203, Room E-165 > MRCAT, Sector 10, Advance 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/ > > > > > ------------------------------ > > Message: 3 > Date: Sat, 29 Jul 2006 22:42:44 -0500 > From: Bruce Ravel <bravel(a)anl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200607292242.45091.bravel(a)anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > On Saturday 29 July 2006 17:24, you wrote: > > 4) The formalism underlying GNXAS is very elegant and reading the > original > > papers is great. I suggest it is highly worth the effort. > > This is true. They are indeed very interesting papers. The physics > or physical chemistry students reading this list would be well advised > to seek them out. > > I would also put in a plug for the PRB from 1990 by Rehr and Albers > about the fast separable formalism for computing the photoelectron > propagator. That paper was my constant companion for about a year in > grad school and is really quite lovely. > > > 5) Regarding ease of use: is XAS amenable to a "black box" approach? > > Despite the fact that this clashes with what many of us teach to physics > > students, it might be very useful e.g. in the field of bioXAS. But can > this > > be done? Or is the underlying physics too complex? > > Ah! The "black box" discussion. That's a fun way to waste lots of > time. ;-) > > The physics has its complicated parts, but I suspect that we have a > sufficient understanding of the problems. There are many applications > where a black box is reasonable to consider and probably would even > work pretty well. At the recent XAFS conference, the group from > Manchester, UK presented a high-throughput scheme that involves > automate processing of larfge quantities of data. They seem to get > good results with minimal human intervention. And Harald Funke gave a > really neat talk about Feff-based wavelets that could be a very useful > approach to a first-shell black-box. > > There will always be a large part of exafs analysis that falls well > outside the scope the black box. The sorts of crazy fits published by > some of the frequent contributors to this list (I am thinking > specifically of Scott Calvin and Shelly Kelly) will always defy > automation. > > Well, that was my US$0.02 worth... > B > > > -- > Bruce Ravel ---------------------------------------------- bravel(a)anl.gov > > Molecular Environmental Science Group, Building 203, Room E-165 > MRCAT, Sector 10, Advance 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/ > > > > > ------------------------------ > > Message: 4 > Date: Sun, 30 Jul 2006 08:20:58 -0400 > From: Scott Calvin <SCalvin(a)slc.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <7.0.1.0.0.20060730075047.020630b8(a)slc.edu> > Content-Type: text/plain; charset=us-ascii; format=flowed > > Well, I have some time to waste, and since my name was just mentioned... > > I think a black box is a wonderful idea for cases where the space of > possible solutions is very limited. At the same conference that the > UK group presented, Wolfram Meyer-Klaucke gave a very nice talk on a > black-box system for determining protein structure around an active > site. The talk was opposite the UK group's, so unfortunately no one saw > both. > > In any case, that's a perfect situation for automation: there are a > very limited number of ligands that could be present, and their > structures are very well understood. It's much more than > fingerprinting, since the combination of ligands might never have > seen before. Their system even allows for the ligands to be at > slightly unusual distances. But it only works because the > biochemistry is already pretty well understood and quite limited. > Although a very different system, I suspect the UK automation of > supported metal catalysts has similarly limited scope; neither system > would probably work very well when fed data meant for the other! > > I think there's sometimes a wish for a system that acts like a Star > Trek tricorder: stick any spectrum in, and the computer can say "it > appears to be an oxide with coordination number 6." In my opinion, > that kind of system will never be developed, because there just isn't > that much information sitting in the EXAFS. (Some of you new to EXAFS > may be puzzled by that--it doesn't sound like very much information > at all. But if you're going to allow me the space of all possible > structures along with less-than-perfect data, it's hard to > distinguish disorder from coordination number changes, for example, > and it's in turn hard to distinguish true disorder from splitting > below the resolution of the data.) > > In other words, current experts in EXAFS analysis don't act as black > boxes to the outside world. If <pick-your-favorite-expert> were > brought a spectrum and asked "OK, tell me the structure," the expert > would immediately start asking questions to gain additional > information (or would say "no," and walk off in a huff). If experts > don't act as black boxes, then neither can a computer. > > OK, with my two cents added to Bruce, that now makes four... > > --Scott Calvin > Sarah Lawrence College > > > > >Ah! The "black box" discussion. That's a fun way to waste lots of > >time. ;-) > > > >The physics has its complicated parts, but I suspect that we have a > >sufficient understanding of the problems. There are many applications > >where a black box is reasonable to consider and probably would even > >work pretty well. At the recent XAFS conference, the group from > >Manchester, UK presented a high-throughput scheme that involves > >automate processing of larfge quantities of data. They seem to get > >good results with minimal human intervention. And Harald Funke gave a > >really neat talk about Feff-based wavelets that could be a very useful > >approach to a first-shell black-box. > > > >There will always be a large part of exafs analysis that falls well > >outside the scope the black box. The sorts of crazy fits published by > >some of the frequent contributors to this list (I am thinking > >specifically of Scott Calvin and Shelly Kelly) will always defy > >automation. > > > >Well, that was my US$0.02 worth... > >B > > > > > ------------------------------ > > Message: 5 > Date: Sun, 30 Jul 2006 07:29:08 -0700 > From: "Matthew Marcus" <mamarcus(a)lbl.gov> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <014401c6b3e4$86ef1a50$dd4cf383(a)lbl.gov> > Content-Type: text/plain; format=flowed; charset="iso-8859-1"; > reply-type=response > > >> Including only bare-bones ASCII in/out is, IMHO, the only way to obtain > >> true portability, and it has worked. I vaguely recall that they use > >> some > >> sort of verifier on their code to screen out system dependencies. > > > > I don't understand this. > > A verifier is a program that inspects programs, looking for probable bugs > such as un-initialized > variables, non-standard syntax, and system dependencies. In fortran and > C, > graphics is > not natively provided, so much be called from a library. Such libraries > vary from system to system. > > > > >> If it uses a g(r) approach, then I imagine that it doesn't handle > >> multiple > >> scattering. On the > >> other hand, it could be argued that *in the EXAFS range* a system which > >> needs a g(r) approach > >> won't have detectable MS. That still leaves XANES, though. > > > > Actually, GNXAS does handle MS. It's not clear to me how well it > handles > > small crystallographic distortions, mixed shells, and so on, but it does > > include MS. I agree with you that requiring one of g(R) and MS seems > > to suggest that the other isn't necessary. > > It may use MS for systems in which the atomic positions are defined, but > g(r) alone > does not define them. To get both *at one time* would require some way of > specifying > baseline atoms positions plus some random distortions with specified > distributions, plus > models for how those distortions are correlated. Essentially, calculating > MS requires assuming > things about 3-body correlations at least. > > > >> > That's not about "theory" as analysis. I don't know what theoretical > >> > advantages GNXAS might have. I believe it includes curved wave > >> > effects, > >> > and that it uses the Hedin-Lunqvist exchange (perhaps the only > >> > option?). > >> > I think that it has a simple polarization model (perhaps only > >> > dipole??). > >> > I > >> > believe it does multiple-scattering only out to four-leg paths (good > >> > enough > >> > for almost all cases), and don't know how it does this. I recall > from > >> > one of > >> > the GNXAS papers that they talked about correlating Debye-Waller > >> > factors > >> > for MS paths with those of SS paths, but I don't know that works in > >> > practice. > >> > >> All that sounds like what FEFF has. > > > > Err, no. Feff has multiple options for exchange potentials, and decent > > models for loss terms. Feff has polarization dependence beyond dipole, > > which is needed for L edges, and can do elliptical polarization fot > XMCD. > > I think GNXAS has none of that. > > I meant that FEFF's options are a superset, not that they are identical. > > > > > For DW factors for MS paths, Feff can use the correlated Debye model. > > GNXAS claims to do something different and more complicated, but I've > > never understand this, or why that would be important for systems that > > needed to be treated with a g(R). > > If GNXAS provides two different systems, one for disordered systems > described by g(r) > and one for systems described by atomic positions, then maybe the > 'different&more complicated' > part is only for the atom-position case. > mam > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 41, Issue 14 > *************************************** > -- Denis Testemale School of Earth and Environmental Sciences, Adelaide University and South Australian Museum North Terrace 5000 Adelaide ph: +61 8 8207 7659

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mxan and gnxas
by Francesco Giannici 29 Jul '06

29 Jul '06

1. how to get mxan: as far as i know, mxan is available free of charge, although not ready for download. you should directly contact maurizio dot benfatto @ lnf dot infn dot it. caveat: the documentation is *very* short, and there is no interface, so here's another reason to keep in touch with the developer. mxan means "minuit xanes", so it uses the minuit minimization procedures to fit either structural (i.e. atomic positions) or physical (i.e. broadening, plasmon, etc.) parameters. it seems the best choice if you deal with a few atoms (biomolecules, coordination compounds, and such). 2. my two cents on gnxas: this package is either very powerful, and very scary. you have to be always aware of what you're doing, because it's no black box. but once you manage to learn the basics, you are awarded with wonderful quality and stability of the fit (minuit is used to avoid false minima during minimization), and total control of the background subtraction (spline and multi-electron excitation refined simultaneously during the fit). other useful features are asymmetric distributions, and the automatic inclusion of all ms paths in the n-body signal generation. the cons: there's no fourier filtering (the fit is done on chi(E)), there are a few bugs in the potential calculation that prevent a smooth generation of signals above 7 angstrom, and you have to spend a lot of time learning the various modules of the package. hope this can help, -- francesco giannici dept. of inorganic and analytical chemistry università di palermo giannici(a)pa.ismn.cnr.it

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Problems with GeO2
by Andreas Schacht 22 Jul '06

22 Jul '06

Hello, my name is Andreas Schacht and I am working with germanium and germanium oxides in my diploma thesis. Therefore I was trying to simulate the XANES spectra of both with feff. The results for germanium seem to be very good in comparison to the experimental data but the simulated spectra of GeO2 in the alpha-quartz structure is far away from all the experimental spectra I have seen. So I was wondering if someone has some experience with calculating the XANES spectra of germanium oxides. Thanks for any help. Best regards Andreas -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/

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