Re: [Ifeffit] Possible bug in atoms files generation by Artemis
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 e
Re: [Ifeffit] Possible bug in atoms files generation by Artemis
As I just mentioned to Matt, this conversation is NOT moot because a significant fraction of users have bought access. I wonder if it would be possible to make some sort of 'crippleware' version of FEFF(>6) which ONLY runs from within DemLarchTemis? That might make the UW folks a little more comfortable with letting it be available. FEFF9+ will be a harder case because it seems to have been designed to be run by the jfeff interface and consists of separate programs which have to be run in sequence. I suppose a wrapper could be written to orchestrate that. mam On 3/27/2013 5:44 AM, Bruce Ravel wrote: 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. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Possible bug in atoms files generation by Artemis
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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Possible bug in atoms files generation by Artemis
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 bra...@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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
