[Ifeffit] Other programs than FEFF - FDMNES
Denis Testemale
denis.testemale at gmail.com
Sun Jul 30 20:19:14 CDT 2006
>
> 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/EQUIPE_SPECTROSCOPIE/SIMUL/EtudFond_Prog.asp
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 at 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 at anl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <200607292242.45091.bravel at 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 at 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 at slc.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <7.0.1.0.0.20060730075047.020630b8 at 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 at lbl.gov>
> To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <014401c6b3e4$86ef1a50$dd4cf383 at 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
>
>
>
> ------------------------------
>
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>
> 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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