July 2006 - Ifeffit - millenia.cars.aps.anl.gov

Debye-Waller factors for metal oxides ?
by Ian James Drake 16 Apr '09

16 Apr '09

Hi, There is little discussion over the significance of fitted Debye-Waller factors (ss2) found for metal centers in metal oxides of heterogeneous catalysts. I am searching for a better way of determining how reasonable these values are in the fits I get. 1. Are phenomenological models like the correlated Debye model and Einstein model appropriate? It seems that Debye temperatures are hard to find for oxides. 2. Is there an equivalent value for ss2 in x-ray crystallography data that I can refer to for comparison in these materials? What should I look for in reviewing published x-ray crystallographic data? 3. Is the temperature dependence reported for the ss2 for some metals (like Cu and Al) similar to their respective oxides? For example, in Debye-Waller factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three between 25C and 300C. Would I expect a factor of three increase in crystalline zeolites (AlO4 structural units). 4. Specific to my work: I have studied Al containing oxides at temperatures between 25 and 300 C. I would like to quantify coordination changes by doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at temperature and I observe no change in the broadening of the data. Likewise, the fitting shows no sensitivity in the Debye-Waller factor. It is nearly constant at 0.001 A over the temperatures of interest. Since ss2 and the coordination number (CN) are correlated, I would like a way to bind the error on the fitted CN by modeling real physical changes in the Debye-Waller factors. Do you have any suggestions? Looking forward to your thoughts. Ian Drake Graduate Student UC Berkeley

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New Method for Normalization?
by Barton, David (DG) 30 Mar '09

30 Mar '09

XANES Aficionados, I know most users on this list are hard-core EXAFS analysts, but some of us use XANES analysis to decipher mixed phases or use it to get structural clues when data quality isn't sufficient for EXAFS analysis. Anyway, I have a question for those interested in quantitative analysis of XANES or those that are willing to offer an opinion on methods to normalize raw spectra to get reliable, repeatable comparisons of near-edge features. Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below: J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines? Dave _________________________________ David Barton The Dow Chemical Company

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Re: [Ifeffit] OS X: (was: new release (061) of my codes)
by Matt Newville 28 Nov '06

28 Nov '06

Bruce, everyone Mac-interested: I believe many of the problems that have been seen come from the idea that one can install the binary, and then expect upgrading from source to work. I believe this will always be fragile: Mac OS X does not come with an installed compiler for C or Fortran (they are available). For these machines, the standard 'perl Makefile.PL' will fail. Whether this is the cause of the recent problems is a separate question. The way I see it, there are two ways to go here: A) assume that Mac is "just-another-version-of-Unix" so that installations and upgrading from source should work. B) assume that Mac is as special as Windows, and that ALL installations and upgrades need an actual installer or a simple, foolproof upgrade mechanism that involves no users typing at a terminal. An "upgrade" could simply consist of a zip file of new files, but we'd need a program (like exists for Windows) that did this upgrading semi-automatically. If the perl upgrades were "pure perl" and did not include a compilation, it could probably be made to work more reliably. But I don't quite see that as the right solution, because it still expects upgrades to happen with a different model than the original installation. Personally, I'm not thrilled about having to support option A. Option B means that someone will have to do the work of making and testing binary installers and upgrades. It will probably mean having to stick close to Mac OS X upgrade cycle. But I think we need a consensus on this. Any opinions? --Matt

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silly me!
by Bruce Ravel 06 Sep '06

06 Sep '06

Hi folks, It just occured to me that I didn't mention the web page where I document all the changes to my codes in the most recent release. Athena especially has a number of interesting new features. You might want to take a look at this http://cars9.uchicago.edu/iffwiki/HoraeVersion062 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/exafs/

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Re: Ifeffit Digest, Vol 40, Issue 10
by Michel Jaouen 07 Aug '06

07 Aug '06

>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. data file format (emmanuelle montarges-pelletier) > 2. Re: data file format (Matthew) > 3. Re: data file format (Bruce Ravel) > 4. The most important fitting parameters (Bridget Ingham) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 21 Jun 2006 10:25:47 +0200 >From: emmanuelle montarges-pelletier > <emmanuelle.montarges(a)ensg.inpl-nancy.fr> >Subject: [Ifeffit] data file format >To: ifeffit(a)millenia.cars.aps.anl.gov >Message-ID: <1F268809-6D80-4EE8-996D-209DFF3FEE07(a)ensg.inpl-nancy.fr> >Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed > >Hello >I have some problems with data file format as I try to import exafs >files in Artemis or in Athena. >I am working on a powerbook G4, with OSX 10.4.6. I installed the >ifeffit package, including Athena and Artemis. Athena could open any >XAS "raw" file from fluorescence or transmission measurements. >However, if I perform any modifications on these raw files with >exterior programs (Michalowicz programs, Kaleidagraph) and try to >import the new files , saved as text files, Athena or Arthemis can >not open them. I guess it may come from the encoding of the text >file. Do you have any clue on this encoding issue? Do you know any >program which would allow me to transform these text files in >readable files for Artemis? >Thank you for your answer >sincerely >Emmanuelle > > >There are two types of encodings which may differ among text files from >different countries and OSs. I >don't know how Athena&Co. handle either of them. One is that numbers and >decimals can differ per country. If >Kgraph is using a local encoding other than the American standard, say, >using commas instead of periods, it's possible >that Artemis won't understand it. I have the same problem with my analysis >programs. Every so often I get a panicky email >from a user whose files won't open. The other variation is in what >constitutes the end of a line, which is OS-dependent. It could >be carriage return, linefeed, or CR-LF. > mam > > >Salut Emmanuelle, > >Matthew's suggestion of floats with commas is a good suggestion. A&A >make no attempt at respecting localization. (That is, a number >between one and two might be written as 1,234 -- which would confuse >A&A -- rather than 1.234.) If that is the case, your best bet is to >go back to the exterior program and ask it nicely to write out points >instead of commas. Or you might need to edit the file by hand. > >I thought that the end-of-line issue (Matthew's other suggestion) was >one that was solved in A&A years ago. If that proves not to be the >case, please let me know. > >Another possibility is that the exterior program added other text to >the file that is confusing A&A. Here is my explanation of how Athena >reads ascii data files > > http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions > >and here is the explanation of the file-reading function in Ifeffit >which Athena uses: > > http://cars9.uchicago.edu/~ifeffit/refman/node24.html > >The situation in Artemis is similar, although restricted in the sense >that Artemis is expecting its data to be chi(k). > >If none of that clarifies the issue for you, I'll need to see an >example of the data file which is causing the problem. > >The easiest way to move data from Athena to Artemis is to have Artemis >import its data directly from the Athena project file. > >If there is some data processing feature that Athena does not do but >which you require before moving on to data analysis, you should >consider making a feature request here on the mailing list. Athena >will never get the features that you need if I am not aware that they >are needed! > >B > Just an additional point: take care to save the file as unix file and not standard Mac (use a free text editor as TextWrangler to do this kind of manipulation). Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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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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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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