One reason I can think of for GNXAS to be less popular than FEFF is that it hasn't been compiled for Windows. It exists only for various forms of Unix. The website says that it's fortran, so there's no reason I can see that it couldn't be compiled for Windows, depending on whether it needs some graphic libraries. Other reasons for the popularity of FEFF include its longer history, its distribution as source, so it can be recompiled for any system, and not least, IFEFFIT/Artemis! What is this 'interesting approach'? MXAN seems to have a fit module which allows you to start with a cluster of atoms and automagically move them around to improve the XANES fit. By using XANES instead of EXAFS, you can apparently see quite far out from the absorber. A quick Google search didn't reveal any obvious way to acquire this package, so it may not be publically available. Anyone know where/how to get it? It might make a nice compliment to FEFF. That reminds me - I'm a co-author on a paper, which was submitted to PRL, in which we used FEFF8.1 to simulate EXAFS. A referee complained that FEFF8.1 was for XANES, not EXAFS. What was that about? mam ----- Original Message ----- From: "Matt Newville" To: "XAFS Analysis using Ifeffit" Sent: Thursday, July 27, 2006 12:10 PM Subject: Re: [Ifeffit] Other programs than FEFF - GNXAS and MXAN

Hi Matthew,

I may be biased, but based on what I saw at the recent XAFS13 conference, I would not conclude that the 'international community prefers GNXAS to FEFF' for EXAFS calculations. I think a search of the science citation index would show FEFF to be used somewhat more (say, 10x) than GNXAS. That's not to say that FEFF is better, just that it is in wider use.

GNXAS does include both first principles calculations and analysis. It has a very interesting approach for highly disordered systems such as glasses, where a single-shell cumulant expansion is known to be bad. It seems that these sorts of systems (solutions, glasses, etc) are the primary use for GNXAS, though I don't know why that is.

In principle, it would be possible to use GNXAS calculations in Ifeffit. Similarly, it would also be possible to use the outputs from EXCURVE (which also does both 'first principle calcs' as well as analysis). I have not pursued either of these, but it's not out of the question.

MXAN (which I believe is by M. Benfatto, S. Della Longa, and C. R. Natoli) is a 'full spectrum' XANES analysis program and seems like a nice tool for fitting XANES, including both the white line and first EXAFS oscillations. I've seen it applied (in very nice papers from Benfatto, P. D'Angelo, and others) to ions in solutions and medium- sized biomolecules. I have not seen it applied to EXAFS, and think it may not be appropriate for EXAFS, though I do not know for sure.

--Matt _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Dear all, One of the problems for GNXAS is that it can not be used for actinides like U, Th, Pt etc. I, personally, contacted A. Philiponi (was in 2002) to get right to use GNXAS for natural actinides in natural samples for nuclear waste management (not for nuclear Energy) and he refused. Hope the developers changed their mind since 2002. M. Harfouche Le 27 juil. 06 à 21:22, Matthew Marcus a écrit :

One reason I can think of for GNXAS to be less popular than FEFF is that it hasn't been compiled for Windows. It exists only for various forms of Unix. The website says that it's fortran, so there's no reason I can see that it couldn't be compiled for Windows, depending on whether it needs some graphic libraries. Other reasons for the popularity of FEFF include its longer history, its distribution as source, so it can be recompiled for any system, and not least, IFEFFIT/Artemis!

What is this 'interesting approach'?

MXAN seems to have a fit module which allows you to start with a cluster of atoms and automagically move them around to improve the XANES fit. By using XANES instead of EXAFS, you can apparently see quite far out from the absorber. A quick Google search didn't reveal any obvious way to acquire this package, so it may not be publically available. Anyone know where/how to get it? It might make a nice compliment to FEFF.

That reminds me - I'm a co-author on a paper, which was submitted to PRL, in which we used FEFF8.1 to simulate EXAFS. A referee complained that FEFF8.1 was for XANES, not EXAFS. What was that about? mam

----- Original Message ----- From: "Matt Newville" To: "XAFS Analysis using Ifeffit" Sent: Thursday, July 27, 2006 12:10 PM Subject: Re: [Ifeffit] Other programs than FEFF - GNXAS and MXAN

...

Hi Matthew,

I may be biased, but based on what I saw at the recent XAFS13 conference, I would not conclude that the 'international community prefers GNXAS to FEFF' for EXAFS calculations. I think a search of the science citation index would show FEFF to be used somewhat more (say, 10x) than GNXAS. That's not to say that FEFF is better, just that it is in wider use.

GNXAS does include both first principles calculations and analysis. It has a very interesting approach for highly disordered systems such as glasses, where a single-shell cumulant expansion is known to be bad. It seems that these sorts of systems (solutions, glasses, etc) are the primary use for GNXAS, though I don't know why that is.

In principle, it would be possible to use GNXAS calculations in Ifeffit. Similarly, it would also be possible to use the outputs from EXCURVE (which also does both 'first principle calcs' as well as analysis). I have not pursued either of these, but it's not out of the question.

MXAN (which I believe is by M. Benfatto, S. Della Longa, and C. R. Natoli) is a 'full spectrum' XANES analysis program and seems like a nice tool for fitting XANES, including both the white line and first EXAFS oscillations. I've seen it applied (in very nice papers from Benfatto, P. D'Angelo, and others) to ions in solutions and medium- sized biomolecules. I have not seen it applied to EXAFS, and think it may not be appropriate for EXAFS, though I do not know for sure.

--Matt _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Hello everyone, there seems to be an interesting exchange of ideas going on. Let me contribute a few ideas or bits of information: 1) I don't believe anybody holds the right to speak in the name of the "international community", whatever that means. The scientific process is rather complex and does not even necessarily adapt itself to rules of democratic representation (who votes?...). Obviously the peer review process is not ideal (see the referee with strange ideas about a particular version of feff) but it might be the best we have. 2) Merci, Francois, for reminding us about the recent history of XAS. At the recent XAFS 13 conference there was hardly any mention of AXAFS and multielectron excitations. Is there anyone willing to write a history of XAS to follow on the one by Ch. Brodeur? Might be an interesting endeavor. 3) I have been using both GNXAS and FEFF related software for many (say 15 - 20) years. Most of the differences have come up in replies in the past few days. One extra difference between GNXAS and FEFF I would like to point out is that FEFF treats (linear and circular) polarization dependence while as far as I know GNXAS does not (it didn't for sure until a few years ago). 4) The formalism underlying GNXAS is very elegant and reading the original papers is great. I suggest it is highly worth the effort. 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? Cheers, Federico ----------------------------------------------------------------------------------------------- Prof. Federico Boscherini Department of Physics University of Bologna viale C. Berti Pichat 6/2 40127 Bologna (Italy) e-mail: federico.boscherini@unibo.it tel: ++39 051 209 5805 fax: ++ 39 051 209 5153 research web site: http://www.bo.infm.it/grp/fb/e2_home.htm sito della didattica: http://ishtar.df.unibo.it (seleziona Uni Bo, Scienze, Boscherini) ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov on behalf of Bruce Ravel Sent: Fri 28/07/2006 16:03 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Other programs than FEFF - GNXAS and MXAN On Thursday 27 July 2006 14:22, Matthew Marcus wrote:

Other reasons for the popularity of FEFF include its longer history,

Actually the early references for both GNXAS and FEFF6 date from 1991. To paraphrase Steve Zabinsky (the fellow who did much of the work on Feff6) "if you make it easy to use, everyone will use it -- even if it's not better".

its distribution as source, so it can be recompiled for any system, and not least, IFEFFIT/Artemis!

I'd say that today this mailing list contributes to Feff's wide adoption at least as much as the codes that are the topic of the list.

What is this 'interesting approach'?

Matt and I were solving materials physics problems in grad school, so our codes are very well suited to problems involving crystals or other things with fairly well known atomic positions. Adriano and Andrea were (I think, but I could be mistaken) solving problems more along the lines of solvation chemistry and highly disordered material. Consequently (and explained in broad brushstrokes) GNXAS is well suited to problems for which the g(R) is not described by discrete atomic positions. In essence, GNXAS integrate the exafs equation over a functional form of g(R). It is certainly possible to deal with high disorder in Feff-base analysis and it is certainly possible to do material science-y problems with GNXAS -- they really aren't that fundamentally different. If you are looking at amorphous solids or solvated ions (or really any other system) you would be wise to look into GNXAS. You may find that it fits your problem or fits into your brain better than Feff, Ifeffit, and my software.

That reminds me - I'm a co-author on a paper, which was submitted to PRL, in which we used FEFF8.1 to simulate EXAFS. A referee complained that FEFF8.1 was for XANES, not EXAFS. What was that about?

Ummm.... a high degree of confusion on the part of the referee perhaps? B -- Bruce Ravel ---------------------------------------------- bravel@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/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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

What I like to say is that EXAFS works best when you already know most of the answer. I thought it was so well-known as to need no repeating that putting a completely unknown sample in the beam is futile unless you happen to liuck onto finding an EXAFS spectrum you recognize. mam ----- Original Message ----- From: "Sven L.M. Schroeder" To: "'XAFS Analysis using Ifeffit'" Sent: Sunday, July 30, 2006 1:21 PM Subject: RE: [Ifeffit] Other programs than FEFF - GNXAS and MXAN

Let me add my 2 *pence* worth, as the Manchester team was mentioned too.

I agree with Calvin that a true 'ab initio' EXAFS black-box for a sample about which nothing else is known is probably a non-sensical proposition. As with so many other (any other?) technique that probes molecular level properties one needs additional information about the sample, or more gerenally, 'prior knowledge'. Now, with XAFS we have a technique that is really only let loose on samples (if not the experimentalist then the beamtime committees will usually see to that...) that have already been characterised to quite some level of detail. Even during in situ measurements on dynamic systems (reactions, phase transitions, in vivo, etc), where the nature of the sample is more open-ended, the possibilities are quite restricted. But the range of possible elements in the sample is practically always limited (at least within the concentration ranges that can be probed by XAFS), there are also rules about reasonable ranges for bond lengths out there, phase diagrams, etc. All of these constrain the possible parameter space quite significantly - and that is what is currently done through the human operator.

The conceptual challenge for the design of any 'XAFS black box' is to find a way to integrate this prior knowledge into the analysis process. I, as a physical chemist, sometimes call the challenge 'How to teach a computer chemical intuition'. Bond length rules, or more generally, any knowledge from inorganic chemistry textbooks - there is no principal reason why all this could not be coded into a database for a decision-making system, which would then have to be coupled to a generic EXAFS analysis interface that allows people to constrain a search according to what they already know about their samples. A Herculean job before it becomes elegant...

Also, let's not forget the XANES. In principle that is information that you can almost always get 'for free' with any EXAFS measurement. There is really a lot of information to be mined through proper XANES analysis - but we still have a lot of work to do to get there ...

Good news I guess. Keeps us busy for some years to come!

So that makes roughly 8 cents now (1p = 2c, approximately, at the moment at least).

-- Sven L.M. Schroeder (mailto:s.schroeder@manchester.ac.uk)

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...

-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: 30 July 2006 07:21 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Other programs than FEFF - GNXAS and MXAN

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

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Hi Matthew,

One reason I can think of for GNXAS to be less popular than FEFF is that it hasn't been compiled for Windows.

Oh, I think you're right. FEFF made a conscious effort to be portable, and easy to use. In John's defense of this approach, by aiming for a wide and diverse user base, bugs and mistakes are found quickly, and features important to the experimentalists are added. I think there's an additional point that Feff had a larger group of people working on it, and a more sustained and diverse development. That does not make it the best theory code. But Wu's assertion was about preference, not correctness ;). Feff deliberately did not include graphics or analysis, with the hope / expectation that lots of other people would do this. This turned out to be true, and very many analysis programs use Feff. It is perhaps interesting that this has not happened for GNXAS. In contrast, it is uninteresting for why this did not happen for EXCURVE: they gave an exclusive license to a company, so that regardless of how good that theory is, they chose for it to never be in wide use. I don't know why GNXAS hasn't been ported to Windows. I'm sure it has graphics (it used to be topdrawer?), but I do not know how tightly it is integrated into the code. In any event, GNXAS seems to not aim at being user-friendly.

What is this 'interesting approach'? [ of GNXAS]

Bruce discussed this, and I may get some of the details wrong (hopefully someone will correct me) but: GNXAS models g(R) directly and applies this in an integral of the EXAFS equation. It does not use a sum over paths with a set of cumulants for each path. I do not know what limitations are put on g(R), but I think they may have a few lineshapes used to model g(R) (I do have the documentation somewhere!). If I remember correctly, GNXAS also fits the full mu(E) spectra, including the background and EXAFS, but this is not what I consider "interesting" about GNXAS. The direct modeling of g(R) is definitely a useful approach for highly disordered systems, and the GNXAS authors and collaborators have tended to study glasses, melts, and ion in solutions and biomolecules, which are the sorts of systems where a simple cumulant expansion is most likely to break down. In fairness, this is possible with a sum of paths by using a "histograms" of paths with varying amplitudes. The spatial resolution of EXAFS is such that the "True" g(R) will only be sparsely sampled, and that sampling can be modeled in a variety of ways: it is not the analysis programs which limit the ability to model g(R). For what its' worth, Bruce has a nice demo in one of his many tutorials that uses a histogram to mimic what GNXAS does. 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. For background subtraction, I believe it uses a simple cubic spline with the possibility to add ad-hoc arc-tangents for multi-electron excitations. Again, I could be wrong on these details -- I'm going from memory of the papers and documentation. But I would conclude that GNXAS has no *theoretical" advantages over Feff, but might have a small analytical advantages over Feffit/Artemis for highly disordered systems. OTOH, GNXAS is by all accounts hard to use, so it might be easier to set up a histogram model with Artemis than to run GNXAS at all.

MXAN seems to have a fit module which allows you to start with a cluster of atoms and automagically move them around to improve the XANES fit. By using XANES instead of EXAFS, you can apparently see quite far out from the absorber.

Sure, though I'm not sure that MXAN has been demonstrated to be able to do this better than other XANES approaches. I may have missed some papers, but I've mostly seen it applied to small molecules.

A quick Google search didn't reveal any obvious way to acquire this package, so it may not be publically available. Anyone know where/how to get it? It might make a nice compliment to FEFF.

I got a copy in 2001 by asking Benfatto (Maurizio.Benfatto@lnf.infn.it).

That reminds me - I'm a co-author on a paper, which was submitted to PRL, in which we used FEFF8.1 to simulate EXAFS. A referee complained that FEFF8.1 was for XANES, not EXAFS. What was that about?

That's silly. I would (and often do!) say that Feff8 is not necessary for most EXAFS. But Feff8 is certainly sufficient for EXAFS!! There are a few cases where it's better than Feff6 for EXAFS, but I don't know of any cases where Feff8 is worse. --Matt

Hi Matthew,

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.

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.

My shell-by-shell EXAFS fit program has the option to use as g(r) a Gaussian-broadened exponential tail function, whose FT is analytically simple and which captures the essential features of a somewhat-disordered shell. I prefer it over cumulant expansions because it doesn't assume that C6 and up are 0 and it gives you a physically reasonable g(r) with a minimum of parameters.

C3 seems like a reasonable way to handle small anharmonicities to me. Beyond that, using something else may be useful (if model dependent). In Ifeffit, you can use a set of paths with different Rs and defining the amplitudes for each path to follow some function such as a broadened exponential. Of course, I'm a little skeptical of people claiming that using g(R) is an absolute requirement.

...

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. For MS, Feff includes up to seven-leg paths. (For real EXAFS analysis, I've never heard of a system that needed more than 4). For non-SS paths, Feff uses a filtering method to eliminate MS paths with no weight, and uses the Rehr-Albers approximation to speed up the calculations for the important MS paths. I think GNXAS may do none of that. 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).

Yes, it's for smallish molecules. Typical center-scatterer distances are <4-5A in the examples I've seen. What 'other approaches' to XANES are publically available which work better than FEFF8.1?

I wish I knew! --Matt

...

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

Hi Everyone, All the critical feedback on the various codes (and especially FEFF) to be quite valuable, especially since the main aim of FEFF Project is to develop improved, user-friendly theoretical tools for x-ray and related spectroscopies. In my view the main difference between FEFF and codes like GNXAS and EXCURVE and MXAN is that FEFF only does ab initio theoretical simulations, with a minimum of adjustable parameters. The others named above also do fits, so they are truly ab initio codes. On the other hand, FEFF requires auxilliary codes like IFEFFIT/ARTEMIS, WINXAS, EXAFSPAK, etc. to compare with experiment. Fitting can, of course, even make non-sensical theory fit experiments with enough parameters, so one cannot directly compare fitting codes with theoretical codes. Although we have been interested in MEE for a long time, and know that such excitations must exist (since S_0^2 is not unity!), we have not introduced them into FEFF for lack of a quantitative theory. The sudden approximation does not appear to be very accurate, for example, due to the importance of interference terms, especially near the onset of MEE. However, it may be possible that the quasi-boson model (discussed e.g. at XAFS13) can provide such a theory. J. Rehr