- Ifeffit - millenia.cars.aps.anl.gov

one more thing...
by Bruce Ravel 30 Oct '03

30 Oct '03

Hi folks, The one very obvious change in how Athena behaves is how it plots normalized mu(E) spectra. If you dislike this new feature and would prefer to always see the normalized data as they were previously plotted, it is easy to disable by going to the preferences dialog, selecting the variable Bkg -> flatten, and setting it to false. Below is the description of this new feature from the NEWS page on my web site. B 1. FLATTENED DATA. I added a new features for plotting normalized spectra which I call flattening. In short, this works by subtracting the linear and quadratic portions of the polynomial regressed to the post-edge region of the data from the normalized data after the edge. This has the effect of shifting the oscillatory portion of the spectrum such that it oscillates about 1. That is, the flattened spectrum is presented with its baseline at 0 and it's post-edge at 1. This is purely a plotting device and has no impact on the calculation of chi(k). It can be turned on and off for a data set using a toggle button in the background removal section of the main window. Whether flattening is on or off by default is configurable in preferences dialog. Flattening is sensitive to how the post-edge line is chosen, particularly in XANES data which have a limited energy range. The idea for this feature was blatantly swiped from SixPack. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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... and lots of new stuff in Athena and Artemis, too!
by Bruce Ravel 30 Oct '03

30 Oct '03

Hey! As a followup to Matt's announcement, I wanted to mention that the brand new Ifeffit release contains the latest versions of Athena and Artemis, both of which contain lots of new features. Here is an explanation of the new goodies: http://leonardo.phys.washington.edu/~ravel/software/exafs/NEWS Windows users can just run the updater or the installer and you will get the latest codes. Linux and other unix users can grabthe latest tarball from my web site. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Ifeffit 1.2.4
by Matt Newville 30 Oct '03

30 Oct '03

Hi Everyone, I've uploaded Ifeffit version 1.2.4 to the Ifefft web pages, and to Sourceforge.net. This version has a few long-promised fixes, and improvements. == Bug fixes: the bug of 'n_varys' not being correct is now fixed. Several of the program limits were increased (lengths of strings, number of Feff paths, etc) and better reporting of these limits. Long label lines should be handled better now in read_data() and athena. Feff6 now works on Windows. A few more bug fixes are mentioned in the ChangeLog file. == Feff6, Feffit, Autobk: these 'input-file' based programs can now all take the name of an input file with a name other than 'feff.inp', 'feffit.inp', and 'autobk.inp' as a command line argument (on Unix, Mac OS X, and Windows). On Windows, the batch files now pop up a file browser so that you can browse for a feff.inp file, and Feff6 will be run with that input file, in that directory (and similarly for feffit and autobk). == Diffkk: This has (finally!) been updated to allow f1->f2 transforms. This still needs testing, but works for a test case. Sorry for taking so long, Michel! == Mac OS X: There is now a disk image with a crude installer that will install the latest versions of ifeffit, feff6, feffit, autobk, athena, artemis, tkatoms, and a few other programs for Mac OS X (but not gifeffit or sixpack -- yet). Fink is NOT required to run these programs, but there are a few important caveats: This installer will work only with OS 10.2, requires X11 to run (the X11 beta3 from Apple works OK for me), and assumes the Apple-supplied perl 5.6 (it won't work with perl 5.8). I realize that OS 10.3 just came out (which ships with X11 and perl 5.8) -- I don't yet have it installed yet, but expect to support it relatively soon. If anyone gives this installer a try, please let me know how it works. If you want to get these programs to work with 10.3 and/or 10.2 with perl5.8, let us know: we can make it go much smoother now than in the past. == Windows: There is a full installer (30Mb) or an update (8Mb) from Ifeffit 1.2.3 that can be automatically installed. These include latest versions of athena and artemis (and ifeffit, feff6l, feffit, and autobk) are included. If you install from the update, make sure you double-click on make_bats.exe afterwards!!! == Other Announcements: As some of you may know, , my wife Julie had a baby two weeks ago. We're very happy, and everybody's doing well. But as a result I'm spending a lot less "extra time" at work these days, and it will probably stay that way. This will cut down on my ability to support Ifeffit, especially to build and fix the Windows versions which I have to do at work (though I do count it as real work, it's not always the highest priority). On the other hand, I can work on the source and Mac versions from home between diaper changes and other real work. The Windows installer and updater for 1.2.4 are much less tested than they should be: please report problems and be patient, as it will take time to fix any problems!!! I'd also like to repeat Bruce's plea for help earlier this week. It's likely that the level of support and ability to respond to problems will drop, and we really do need help. If you're using these programs as an integral part of your research, please consider what they're worth to you and what you would have to do if these programs didn't exist. If you can help, either with making releases for Windows or Macs, with program documentation or web pages, or in any other way, please contact us. As always, let us know if there are any questions or problems, --Matt

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Re: [Ifeffit] This might be a silly question....
by k-kupiecki＠northwestern.edu 29 Oct '03

29 Oct '03

Thank you so much! That's very helpful! BTW... so far I've found the Artemis manual very helpful in getting started (especially the explanation of IFEFFIT)... thanks!!!! -Kristine On Wed, 29 Oct 2003 18:44:03 -0400 Bruce Ravel wrote: > On Wednesday 29 October 2003 04:55 pm, k-kupiecki(a)northwestern.edu wrote: > > Hi, > > > > I'm also a novice with the Athena/Artemis Ifeffit software. > > > > I've read through the online documentation for both and I'm now > trying to > > go through the Cu example in Chapter 2 of the Artemis manual. > > > > Can someone please tell me where I input the following information into > > Artemis (I've tried in the fields on the Path parameter screen, but it > > gives me an error when I go to fit)? (from page 19 of the manual): > > > > We will then define extremely simple math exressions for the > > corresponding path parameters of the first shell. > > > > s02 0:1 amp > > e0 0:1 e0 > > delr 0:1 delr > > sigma2 0:1 ss > > > Kristine, > > Hmmm.... this is a little embarassing. I have to apologize for the > state of the Artemis document. It suffers rather alot right now from > bad stream-of-consciousness writing. > > My goal in the chapter on the copper fit was to walk through the steps > of an increasingly complicated fit. Start with single shell, then two > shells, then three. Then do four shells + all the necessary multiple > scattering. Then introduce the concept of multiple-data-set fitting. > As I was writing it a few months ago, I didn't want to interupt my > (ever-so-brilliant) train of thought to make a bunch of screenshots > demonstrating what I was talking about, so I tried to develop a > text-only shorthand to explain what I meant. > > The "0:1" was my shorthand for indicating that this was path number 1 > (i.e. the first one) from data set number 0 (also intended to be the > first one). Obviously confusing. Sigh. > > In an attempt to clarify the situation, I made four screenshots from > the single shell project file that gets distributed with the program. > > Point your browser at this directory: > http://feff.phys.washington.edu/~ravel/misc/ > > You will find the four screenshots I just made: > > artemis_cu1.png the view of the data > artemis_cu2.png the view of the guess and set parameters > artemis_cu3.png the view of the description of the feff > calculation > artemis_cu4.png the view of the first path > > I think this should make it clear what goes where. Note that these > shots were taken of Artemis getting ready to fit just the fist shell > of the copper data. Thus paths contained in feff0002.dat through > feff0005.dat are not included in the fit. The ones not included in > the fit are written in brown text in the list on the right side of the > window. In subsequent fits, when those included in the fit, you can > edit their parameters by clicking on them. That will display > something that looks very much like the artemis_cu4.png image, but > with the information relevant to that path. > > Taking language from those images on my web site, the bit in the > document that you are asking about would have been much better > written as: > > FEFF0: feff0001.dat > s02 = amp > e0 = e0 > delr = delr > sigma2 = ss > > That would have, perhaps, been clearer. Certainly more consistent > with the appearence of the program. And still more concise than an > entire screenshot at that point in the doc. > > > Hope that helps, sorry for the confusion, and don't hesitate to keep > asking questions on the mailing list. And, contrary to the sentiment > in your subject line, there are no silly questions, just silly > programmers. > > B > > > > -- > Bruce Ravel ----------------------------------- > ravel(a)phys.washington.edu > Code 6134, Building 3, Room 222 > Naval Research Laboratory phone: (1) 202 > 767 5947 > Washington DC 20375, USA fax: (1) 202 > 767 1697 > > NRL Synchrotron Radiation Consortium (NRL-SRC) > Beamlines X11a, X11b, X23b > National Synchrotron Light Source > Brookhaven National Laboratory, Upton, NY 11973 > > My homepage: http://feff.phys.washington.edu/~ravel > EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/ >

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This might be a silly question....
by k-kupiecki＠northwestern.edu 29 Oct '03

29 Oct '03

Hi, I'm also a novice with the Athena/Artemis Ifeffit software. I've read through the online documentation for both and I'm now trying to go through the Cu example in Chapter 2 of the Artemis manual. Can someone please tell me where I input the following information into Artemis (I've tried in the fields on the Path parameter screen, but it gives me an error when I go to fit)? (from page 19 of the manual): We will then define extremely simple math exressions for the corresponding path parameters of the first shell. s02 0:1 amp e0 0:1 e0 delr 0:1 delr sigma2 0:1 ss Thanks, Kristine Witkowski Northwestern University

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Re: [Ifeffit] Novice seeks advice
by SCalvin100＠aol.com 29 Oct '03

29 Oct '03

Oops. Scott meant to send this to the list, of course. --Scott In a message dated 10/29/03 10:21:28 AM Eastern Standard Time, ravel(a)phys.washington.edu writes: On Wednesday 29 October 2003 10:12 am, SCalvin100(a)aol.com wrote: > I would like to add to Bruces' post one other quick "reality check." > Look at Athena and see where E0 was picked there. It's possible that > for some reason you have an E0 in Athena way above the actual rising > portion of the energy spectrum, in which case Artemis is actually > doing the right thing by moving it back to the correct energy > origin. You really don't want to depend on Artemis to fix a poor E0 > choice in Athena, though, so if that is the case then you should > choose a more reasonable E0 in Athena and feed the resulting chi > file back in to Artemis. Scott, Did you send this to the list or just to me? The headers seem to suggest the latter -- in which case it is weird the Scott is referring to Bruce in the third person ;-) B

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Another stab at the data
by Dave Baker 29 Oct '03

29 Oct '03

Bruce, Thanks for the advice. I've run through the list, redone processing and started the analysis with said list in mind, and the most plausible solution is that I shouldn't be using a crystalline material for the FEFF calculation. One interesting thing (at least to my untrained eye) to note is that the shapes of the first path and the peak that I'm trying to fit (this is before any attempt at fitting) are nearly identical, but the FEFF path is shifted about 2~3 angstroms higher than the peak. The only improvement that I could muster is that the e0 variable has gone down from 80 to 50. -Dave Baker ------------------------------------------------------------------------ -- North Carolina State University Dept. of Physics 2700 Stinton Dr. Box 8202 Raleigh, NC 27695 Ph: 919-515-5017 Fax:919-515-7331 email: dabaker(a)unity.ncsu.edu ------------------------------------------------------------------------ -- On Tuesday 28 October 2003 11:00 pm, Dave Baker wrote: > I am a novice student in the EXAFS world, and I am starting to work my > way through Athena and Artemis. Currently, I'm working with amorphous > GeTe and the Atoms/FEFF runs are based on the crystalline data. I have > performed a fit in Artemis of the Ge K edge, and my e0 for three > contributing paths is exceedingly large, (-70 ~ -80 volts). Two > questions: 1.) What symptom is this an indicator of, and 2.) What are > some possible solutions? Hi Dave, Glad to see you were able to get started using the software after that very short conversation we had at X11A a couple weeks ago. I have seen this effect on occassion when, for some silly reason, I have made the Feff calculation using the wrong edge (i.e. K instead of L3 or vice versa). Another possible indication of an absurdly large e0 shift might be if the distances between atoms in the feff calculation are very different than the distances between atoms in the real material. That is, if the material used in the feff calculation is a very poor approximation of the real material. Another possibility that occurs to me from the way you phrased your question is that you are allowing e0 to float independently for each path. That's almost certainly not physically supportable. At least as a first stab at theproblem, you should use the same e0 for each path. One thing you might try is to not allow everything to vary in the fit. Try fixing e0 to be something sensible -- like 0.0. Vary all the rest of the parameters to get a sense of how the parameters behave and how well they describe the data. This sort of manual examination of the parameter space might help give you a clue of why you are getting such an odd result. HTH, B

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Novice seeks advice
by Dave Baker 29 Oct '03

29 Oct '03

I am a novice student in the EXAFS world, and I am starting to work my way through Athena and Artemis. Currently, I'm working with amorphous GeTe and the Atoms/FEFF runs are based on the crystalline data. I have performed a fit in Artemis of the Ge K edge, and my e0 for three contributing paths is exceedingly large, (-70 ~ -80 volts). Two questions: 1.) What symptom is this an indicator of, and 2.) What are some possible solutions? -Dave Baker

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contributing to the Ifeffit family
by Bruce Ravel 28 Oct '03

28 Oct '03

Hi folks, On occassion, the topic comes up of contributions to the ifeffit universe from other people besides Matt, Sam, and myself. Indeed, there have been some excellent examples centered around this mailing list. For example, a few months ago, we had a really useful discussion, including code examples, about rebinning data. As a somewhat smaller example, two fine souls responded to my request for some example data from NSLS X10C. Last week, Scott asked this: Oh, and I've been thinking. [Matt and Bruce] spend enormous amounts of time on this software, and it's a big contribution to the field. As I explained above, I'm not willing to help on the coding end, but I'd like to support the project in some way. I know Bruce has mentioned the need for more/better Athena and Artemis documentation...I was hesitant to suggest I help with that until I got more familiar with the software, but I think I'm now getting to that point. So Bruce--what is the most pressing need in that area? I'll see if I can start devoting some time to it... I thought I would answer Scott's question in public. Who knows, maybe I'll start something ;-) I will divide this up into a few categories. If you dig into any of these, we should probably communicate so that you produce something in a format that will be useful to us developers. Pure documentation ================== 1. Edit and expand upon the documentation that exists for Athena. The Athena doc is actually in pretty good shape. Most parts of the code are at least mentioned in the doc. If you are not familiar with the POD markup that is used in Athena's docs, don't worry. If you do some significant editing, I'll be happy to touch up the mark-up. 2. The Artemis document needs serious work. Pick a topic that interests you (or one of the unwritten topics in the current document) and start writing. You don't have to write in Latex. If you write in Word or some other format, all I'd ask is that you not format what you write too heavily and that you provide me with external copies of all images in appropriate formats. 3. Write a FAQ (frequently asked/answered/anticipated questions). Documentation by example ======================== One of the neat (IMHO, anyway) ways that I have documented Athena is the collection of demo projects, which are just normal Athena projects with extensive commentary in the Journal area. 1. Make more Athena projects. Improve upon the ones that are already there. 2. Make some nice Artemis projects. Even better, make a sequence of Artemis projects which demonstrate the steps one might take in building a sophisticated fitting model. Programming and related chores ============================== If you are inclined to deal with code, but don't necessarily want to dive into Athena or Artemis, here are some smaller projects. 1. Write an object-oriented module in Perl for accessing Spec data files. I could then use this in Athena. 2. Volunteer to maintain and build the Windows distribution and updates. 3. Collect examples of data from every dedicated XAFS beamline in the world. (Really, I mean it, every one.) Figure out which ones can be read by Ifeffit and which cannot. Figure out how to preprocess the ones that aren't read properly by Ifeffit and explain to us how to recognize them and how to preprocess them. 4. Think up a battery of tests. Subject Athena and Artemis to those tests soon after (or even prior to) every release. Let me know about any problems. Web-based projects ================== 1. Set up a web site for a FAQ which allows searching the FAQ for keywords. 2. Set up a web page which indexes the Ifeffit mailing list archives and allows searching by keywords. 3. Set up and administer a Wiki so everyone can participate in the process of documenting Ifeffit, SixPack, Athena, and Artemis. 4. Set up and administer a community discussion board. My inclination would be to use Slash (http://slashcode.com) which has a comination of features that I think could provide a valuable service to the XAFS community. 5. Collect and organize new material for the databases that Matt maintains which contain atoms input files and standards spectra. Well, that ought to be enough suggestions to get anyone started. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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questions
by J. M. An 28 Oct '03

28 Oct '03

On Monday 27 October 2003 03:10 pm, J. M. An wrote: >/ Dear IFEFFIT helper, />/ />/ I am a novice of IFEFFIT and would like to ask some questions about />/ fitting variables used in the program. />/ I've been trying to fit my FEFF 8 calculation result to an experimental />/ data for a bulk compound CdSe. />/ Essentially, the fitting variables, S02 and DW factor (the correlated />/ Debye model) for the first-shell, />/ are used for the fit. I can manage to fit quite nicely with those />/ variables, but the problem is that I want to use the values />/ of the resulting fitting variables as input for CdSe quantum dot />/ calculations. />/ />/ Normally, S02 and Debye keywords in FEFF are global paramaters, not />/ restricted to a single shell, so there seems to be />/ no way that I can put the fitting values obtained from the fit into new />/ FEFF calculations. />/ I was wondering if someone has experience to use bulk fitting values as />/ input in a new FEFF calculation. / I don't think I quite understand what you want to do, but here are a couple pieces of advice: 1. It is my strong preference never to introduce S02 or sigma^2 into the feff calculation when I am doing exafs analysis. It is much easier and much less confusing to use S02=1.0 and all sigma^2=0 in the feff calculation. That way, any values that you get for those parameters from a fit using ifeffit are absolute numbers and do not require that you remember what you did in feff in order to interpret the ifeffit result. 2. I do think that redoing the feff calculation might be useful at some time during the fit, but only if I have reason to believe that the *structural* parameters used in the feff calculation were in error relative to the real material. If the distance between atoms in the real material are quite different from what you used in the feff calculation, then you might worry that the phase shifts and scattering amplitudes are not as good as they might be. Given all that, I am not sure what you hope to accomplish by your new feff calculation. Hope that helps, B *********************************************************************** Thank you for the advice. The idea behind my research is (1) to extract information S02 and Sigma2 by fitting my feff result to experiment in crystal CdSe. (2) then to use this information to perform feff calculations for quantum dots CdSe of a certain shape. In other words, the info in (1) will be used as input to quantum dot calculations in (2). The reason is that no one knows how the surface terminates in the dot. To this end, I need to know reasonable fitting values of S02 and Sigma2 to be used in a feff input file. Suppose that I have obtained S02 and Sigma2 by doing (1) only for the first shell, leaving all other shells intact. (This is because in crystal CdSe, our calculated FEFF chi(k) using correlated Debye model differs from experiment for large k.) However, my problem is how we put these fitting values in (2), since SO2 and Sigma2 are global to all paths in Feff. Another complication may be that in (2) I am performing a set of calculations for different Se absorbing atomic sites. At the end, add all contribution from different Se sites to total chi(k), which is exactly what experimentalists measure. That is why I need to put resonable S02 and Sigma2 before I essentially perform quantum dot calculations. I will appreciate any further advice of yours on this, and let me know if this is not sufficient for you to understand what I intend to do. Joon Lawrence Berkeley National Lab

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