Just to put my bit in, I believe that the most significant advantage of higher FEFF versions for EXAFS analysis is that it results in more reasonable values for E0 for high-Z elements. I forget whether the issue is high-Z scatterer or absorber. If you use any of the common prescriptions for defining E0 with, say, Pt metal in FEFF6l, your fit will want large values of enot. That said, I have not done a real test by comparing FEFF8 and FEFF6 paths. Has anyone done that? It would be interesting to know what happens if you simulate a k^n*chi(k) with one program and fit it with the other. mam On 3/26/2013 1:10 PM, Ravel, Bruce wrote:

This is more a documentation bug in the sense that I have not written any documentation explaining how to use Feff8 with Demeter. What's more, I have not completely tested using Feff8 and there are probably still missing features. I would not expect Feff8 to work completely to your satisfaction at this stage.

Even once I get Feff8 support fully implemented, I have no intention of distributing a copy of the Feff8 executable with Demeter. Indeed, I do not have the authority to do so.

That said, you need to go to the File menu -> Preferences, the Feff->executable. Change the value of that parameter to the location on your computer where the Feff8 executable can be found. Demeter is not currently smart enough to choose a Feff executable according to how you selected to generate the feff.inp file. It is entirely up to you to do that correctly.

Feff6 input files often work, in some sense, with the Feff8 executable. Feff8 input files will not work with the feff6 executable. That is the issue you are reporting as a bug.

In closing, I'll say two things. (1) Feff8 is not yet fully supported in Demeter -- use it at your own peril. I will eventually get it fully implemented, but it is at this time near the top of my list of priorities. (2) You should go back to the mailing list archives and find the last discussion about the relative merits of feff6 and feff8 for EXAFS analysis. I was then and remain now rather unconvinced that feff8 does anything substantive for you in the context of your EXAFS analysis.

B

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--

*From:* ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Devender [devend@rpi.edu] *Sent:* Tuesday, March 26, 2013 3:26 PM *To:* XAFS Analysis using Ifeffit *Subject:* [Ifeffit] Possible bug in atoms files generation by Artemis

Hi,

I ran updater for Demeter 0.9.15. I was using Artemis to calculate paths for Bi L3 in Bi2Te3. I saw now the option of using both (FEFF 6 and FEFF 8 style) for atoms. Previously, I was using only available option of FEFF6 style. When I tried to run atoms selecting FEFF 8, it generated atoms files but when I tried to run FEFF calculations it produced following errors.

Error#1 " Unknown keyword: "EDGE" at line: EDGE L3"

Error#2 "Unknown keyword: "exchange" at line: exchange"

I worked around first error by replacing

"EDGE L3 S02 1.0 "- which was generated by atoms when FEFF8 style is selected.

with "HOLE 4 1.0" and deleting Exchange keyword from feff file. After making these edits in feff files, I was able to run FEFF without showing any errors. I have attached all the files with appropriate name.

-- Devender Graduate Student, Materials Science and Engineering Rensselaer Polytechnic Institute, Troy, NY Website https://sites.google.com/site/devendermaun/

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

Some users do have FEFFx (x>6l) on their own, so it would be useful to prepare Artemis/Demeter/Larch... for them and provide methods for using higher versions if an executable is present. What does the multipole self-energy do? Is that the thing that requires the dielectric response? As you point out, the purpose of the exercise is to analyze unknowns, so by definition one doesn't have the dielectric response. We can't expect a program that runs on a PC to do a proper, all-electrons, excited-state calculation. One thing I do is to use experimental data from models as sources of amplitudes and phases. At present, I do this using my own multishell fit program. Is there an easy way to do this in your programs? What I think would be nice is a subsystem which allows one to do the filtering and extraction of amp and phase from a model .chi file from within the program, rather than having to create FEFF-path-like files. As long as we're talking wish-list, I'd love to have some way of defining atom positions using symbolic variables and have the system compute the path distances automatically as functions of those variables. That way, I could, for instance, define a dopant system in terms of the displacements of the near-neighbors without having to do the geometry by hand, which is difficult, tedious and error-prone. mam On 3/26/2013 9:24 PM, Matt Newville wrote:

Hi Matthew,

On Tue, 26 Mar 2013, Matthew Marcus wrote:

...

Just to put my bit in, I believe that the most significant advantage of higher FEFF versions for EXAFS analysis is that it results in more reasonable values for E0 for high-Z elements. I forget whether the issue is high-Z scatterer or absorber. If you use any of the common prescriptions for defining E0 with, say, Pt metal in FEFF6l, your fit will want large values of enot. That said, I have not done a real test by comparing FEFF8 and FEFF6 paths. Has anyone done that? It would be interesting to know what happens if you simulate a k^n*chi(k) with one program and fit it with the other. mam

It's been a very long time since I've tried, but, yes I've made such comparisons in the past, as well as comparing Feff6 and Feff8 to the same "very good data".

Feff 8 actually has a long history. Initially, EXAFS was noticeably worse with Feff8, but it got better over the years to the point where I think it's hard to say that Feff8 is worse than Feff6 for EXAFS. As you say, E0 is better (though still needs refinement), as is S02. Feff8 also appears that it is better for heavy elements (perhaps Z > 50, but I'm not sure anyone has looked at that carefully). But: the multi-pole self-energy introduced around Feff8.5 or so can make a very large improvement for the EXAFS. Whether this can be made generally applicable is a separate question.

Just to echo some of Bruce's frustration and build on that (and, speaking only for myself): Basically, we're stuck with Feff6 because we do not have access to Feff8. Last I heard, John and Josh were working on this, so that Feff8-for-EXAFS would be made freely available. I haven't seen the code yet, but I'm optimistic that it will be released someday.

Once this happens, I'll happily start incorporating this into Larch. I'd very much like to replace the pathfinder (as Bruce has done in Perl for Demeter) so that distortions are easier to track, and allow the EXAFS calculation for a Path to be done automatically inside the fitting loop. That will be some real work (anyone out there interested in helping?), and could take awhile, but could actually make a difference for modeling.

I'm pretty sure that getting the multi-pole self-energies more universally useful would be a big help, but I think there still some unknowns there (basically -- how well do you have to know the dielectric response for a general system?) that have to be worked out. Getting 1/epsilon for Cu metal is one thing (a first step!), but getting it for As sorbed onto ferrihydrite or would be more challenging....

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

Many years back, when FEFF stopped being free, I was told that the decision was not Rehr's but forced by the university. Blame them. It's always easier and more pleasant for us to blame faceless university beauraucrats than scientists anyway :-) I agree that FEFF input is broken. This was, perhaps, inevitable as FEFF evolved over the years. It may be (I haven't studied the matter) that the old format, which was perfectly good in its day, simply can't accommodate new features just by adding new keywords. I really can't blame the Project very much for changing the format. Still, the formats are documented, so I don't buy the idea that nothing can be done with FEFF8 until the Project changes its format or goes open-source. I can understand a reluctance to go open-source because they now keep tight control over portability and the embodied physics, such that everybody knows exactly what 'we used FEFF8.4' means. If it went open-source, it may be imagined that there'd be a proliferation of versions, some of them with dubious hacks. One fix I could imagine the Project doing is to release as open-source an input module for FEFF9, which is broken up into separate modules anyway. That way, people could have whatever input format they wanted, but the integrity of FEFF would be preserved. As to dielectric response, what is the effect of improving that model on EXAFS predictions? Does it affect the self-energy, hence lifetime broadening and E0? I knbow it affects XANES, but that's a whole other subject not covered by DemLarchTemis discussions. mam mam On 3/27/2013 7:32 PM, Matt Newville wrote:

Hi Matthew, Bruce,

On Wed, Mar 27, 2013 at 10:33 AM, Matthew Marcus wrote:

...

Some users do have FEFFx (x>6l) on their own, so it would be useful to prepare Artemis/Demeter/Larch... for them and provide methods for using higher versions if an executable is present.

I completely agree that this would be valuable, and that it's not quite moot because many people do have Feff8 or Feff9 available to them.

But, I also want to be clear that I totally agree with Bruce's point on this as well. It's really hard to support code that is actually poorly defined and cannot be changed. The Feff input file format is a complete mess, and it's not Bruce's (or my) fault. In fact, this *is* what the original question was about. Feff changed form one awful form to another -- why is this Bruce's problem to solve? There is no API or library provided for reading feff.inp. We are forbidden from changing it or redistributing a changed version of Feff8. It is, to be very clear, the choice of the Feff project to break these input files. If we had a "Feff8 for EXAFS" that could be relied upon and redistributed, it would be a totally different story. We don't.

We've lobbied (begged) for changes in the i/o and freer access to the code for many, many years. I can't explain the restrictions in any rational terms, fathom why this restriction is a priority for John or anyone else, or understand how anyone who writes scientific software would use anything except an open-source license. I've given up on pestering them about it. I was told last summer that a version of Feff8 for EXAFS that we can distribute would be made, but haven't heard a thing about it since. It could happen soon .... that would be great. The license they use is their choice, and I respect that even if I don't actually like their choice, and actually have real reservations about the choice being solely theirs to make. Ultimately, science will demand that all versions of Feff will be made free or be forgotten. It is completely believable that Feff6L will be what is used twenty years from now. I expect that Feff8 for XANES calculations codes will never be made free and will be forgotten in time.

I actually don't have a copy of Feff9. Kevin J did a great job with JFEFF, and emulating or including this approach of using a remote cluster in the analysis codes would be interesting to think about.

...

From a practical point of view, it would be easier to reproduce a similar system than to have to argue about licensing. Then again, without the calculation engine being freely available, running it on a cluster actually seems like a problem... wouldn't you need a license key or something? Right, sorry, the Feff license actually makes no sense -- it's better to not think about this.

...

What does the multipole self-energy do? Is that the thing that requires the dielectric response? As you point out, the purpose of the exercise is to analyze unknowns, so by definition one doesn't have the dielectric response. We can't expect a program that runs on a PC to do a proper, all-electrons, excited-state calculation.

Yes, the multipole self-energy uses a better model for the self-energy based on the dielectric response of the system in the low (electron) energy regime -- in short, how a "free" photo-electron will travel through the multi-electron system. So, yes, in principle one needs to know the dielectric function. That's conceivable for Cu metal, and maybe an ion in an aqueous solution, but not so much for lots of systems really studied. Still, if you think that a single-pole model works pretty well (the current normal implementation of the self-energy), perhaps a mediocre dielectric response function (say, treating 'iron oxides' as all more or less the same) would be an improvement.

...

One thing I do is to use experimental data from models as sources of amplitudes and phases. At present, I do this using my own multishell fit program. Is there an easy way to do this in your programs? What I think would be nice is a subsystem which allows one to do the filtering and extraction of amp and phase from a model .chi file from within the program, rather than having to create FEFF-path-like files.

Creating a model "Path" from experimental data is definitely possible, but not conveniently encapsulated in Larch -- it would not be hard to do, and is a fine idea. It's now on the to-do list. In years past, Anatoly has done similar things by making "fake feff.dat files" and using them in Feffit. It can work, but it should be made easier.

...

As long as we're talking wish-list, I'd love to have some way of defining atom positions using symbolic variables and have the system compute the path distances automatically as functions of those variables. That way, I could, for instance, define a dopant system in terms of the displacements of the near-neighbors without having to do the geometry by hand, which is difficult, tedious and error-prone. mam

Oh yes, this is a major motivation for wanting to replace the PathFinder with a version that was reversible (ie, which atoms in the cluster correspond to this structure, and vice versa) and for wanting to move the GenerateFeff_MuffinTin(Potentials, Path) into the fitting loop. Ultimately, we'd like to replace the sum-over-paths with a sum-over-atoms-in-a-cluster, where the x,y,z coordinates would be the variables. I think it's completely possible, though a fair amount of work. Probably needs a person to really dedicate some serious time to it... Sorry to sound like a broken record, but if anyone is interested in this, let me know.

Cheers,

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

On Tuesday, March 26, 2013 01:21:58 PM Matthew Marcus wrote:

Just to put my bit in, I believe that the most significant advantage of higher FEFF versions for EXAFS analysis is that it results in more reasonable values for E0 for high-Z elements. I forget whether the issue is high-Z scatterer or absorber. If you use any of the common prescriptions for defining E0 with, say, Pt metal in FEFF6l, your fit will want large values of enot. That said, I have not done a real test by comparing FEFF8 and FEFF6 paths. Has anyone done that?

This is *exactly* my point. Except, as Matt said, for the rather limited, unpublished tests made by him and John many years ago, no one has reported on a substantive test comparing the efficacy of feff6 and feff8 for analysis of EXAFS. (Of course, computation of XANES and other spectroscopies is a different topic entirely.) Perhaps I would be more interested in fully implementing use of feff8 in my software if someone would offer a better justification than "8 is a bigger number than 6". FWIW, I agree with Matt that the multi-pole self-energies is a very promising thing that could have a substantial impact on EXAFS analysis. But few of those who claim to want to use feff8 with my software are actually computing and using the multi-pole self-energies. In any case, I do not have permission to redistribute feff8. So, on a very real level, this conversation is moot. B

It would be interesting to know what happens if you simulate a k^n*chi(k) with one program and fit it with the other.

-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel