Re: [Ifeffit] Other programs than FEFF - FDMNES

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/EQ... 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@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/

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Message: 3 Date: Sat, 29 Jul 2006 22:42:44 -0500 From: Bruce Ravel To: XAFS Analysis using Ifeffit Message-ID: <200607292242.45091.bravel@anl.gov> Content-Type: text/plain; charset="iso-8859-1"

On Saturday 29 July 2006 17:24, you wrote:

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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@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/

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Message: 4 Date: Sun, 30 Jul 2006 08:20:58 -0400 From: Scott Calvin To: XAFS Analysis using Ifeffit Message-ID: <7.0.1.0.0.20060730075047.020630b8@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

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Message: 5 Date: Sun, 30 Jul 2006 07:29:08 -0700 From: "Matthew Marcus" To: "XAFS Analysis using Ifeffit" Message-ID: <014401c6b3e4$86ef1a50$dd4cf383@lbl.gov> Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=response

...

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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.

...

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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.

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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

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...

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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

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-- Denis Testemale School of Earth and Environmental Sciences, Adelaide University and South Australian Museum North Terrace 5000 Adelaide ph: +61 8 8207 7659