February 2004 - Ifeffit - millenia.cars.aps.anl.gov

re:fits
by k-kupiecki＠northwestern.edu 15 Jan '05

15 Jan '05

Thank you Bruce and Shelley! I just wanted to thank Matt, Bruce and everyone involved with IFEFFIT/Artemis/Athena... it has been a Godsend.... I couldn't have stumbled on it at a better time (I'm frantically trying to analyze about 4 beamtimes worth of SEXAFS data for papers and my thesis and WINXAS wasn't really working out for me)!!!!! Does anyone have any suggestions for additional literature in regards to better understanding the quality of fits and the parameters involved?.... or perhaps know when we might be able to expect a updated version of the Artemis literature? (What is currently there has helped me sooo much that I've been checking for an update every couple of weeks hoping to get see sections 2.2-3.2..... ) Also.... I guess I've realized that only knowing IFEFFIT with Artemis I kinda take things for granted (like I didn't know that IFEFFIT was having problems, in certain cases since I had only been checking the "Results" and the error messages on the bottom of the window....) which meant I missed errors like this in the IFEFFIT (since I didn't notice anything unusual in the "Results"): ............ # Do the fit! ## fitting difference of Cov_0_06ML_bl1435_111703.chi and one or more paths ... ## === data set #1 of 1 feffit(1-8, group=data0_fit, chi=data0.chi, k=data0.k, kweight=2.00, rmin=1, rmax=4, kmin=2.5, kmax=15, dk=2, kwindow=kaiser-bessel, fit_space=R, do_bkg=no, data_set=1, data_total=1) feffit fitting 1 data sets fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... no uncertainties estimated! fit gave a warning message: too many fit iterations. try again with better guesses or a simpler problem. ............................................... I guess my question is.... is there anything else I should be looking for in the IFEFFIT printout that I might not otherwise notice by just using Artemis and looking at the error messages and "Results"? Thanks for the input! Sincerely, Kristine Witkowski Northwestern University

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ifeffit and Mac OSX
by Matt Newville 04 Jul '04

04 Jul '04

Hi Raja, On Mon, 7 Oct 2002, rajasekaran swaminathan wrote: > Hi Matt, > > I tried again over the past few days to install the binary > installer on my mac (OS X.2). I couldn't find an attached aquaterm > / pgplot demo. The Aquaterm program opens, but I cannot see any > windows come out from that application. I mean, it is just like a > blank application. When I type ifeffit on Terminal app, it doesnt > recognise the presence of ifeffit in the ifeffitosx directory. i.e. > it says that the command is not found. The executable works > perfectly well on a Windows machine, and I was wondering whether > there are any such equivalents for a Macintosh machine. I also dont > think that the installer comes with athena/artemis/tkatoms etc.. Do > you have any other recommendations to resolve this issue? Also,if > it is possible, can I get a CD of these programs for a Macintosh > equivalent to an executable version for the Windows? > > I appreciate your help in this regard. I have used the binary installer once on a OS 10.1 system. It worked for me (after following the simple included instructions, of course) and plotting with Aquaterm did work. I haven't tried 10.2. I know the Mac binary installer does not include athena, artemis, or tkatoms. I believe it only provides the command-line ifeffit. I'm not sure I can answer many other questions about it. I don't know enough about it or 10.2 v. 10.1 issues to know how well it would work with 10.2. If the aquaterm/pgplot demos don't work, I'd guess it's a more serious problem and that the binary installer may not work. Is the Fink / X-Windows / PGPLOT installation procedure too big of a hassle? I know that can work, and that athena will work too. I also believe that the instructions are simpler for 10.2 than 10.1 (especially with respect to getting perl/Tk to work), but haven't tried this myself. I'm copying this message to the ifeffit mailing list, hoping that someone else may have better answers to these questions. How necessary is a complete binary installer for Mac OSX? Thanks, --Matt

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new release of Athena and Artemis
by Bruce Ravel 09 Mar '04

09 Mar '04

Hi folks, I am announcing the release Athena 0.8.025 and Artemis 0.7.000. You can now run the Windows updater or the horae_update script on your unix machnies to install these new versions. Complete lists of changes can be found in the change logs on my web site. I have increased the minor version number of Artemis because of two significant new features. 1. Atoms is now incorporated into Artemis and there is a simple wrapper around Feff built into Artemis. You no longer need to run Atoms and Feff apart from Artemis. Instead, you now do these chores within Artemis and allow Artemis to organize and manage all of the output files from Feff. By default, Artemis assumes you will be using the version of feff6 that comes with Ifeffit (but that is configurable). 2. Artemis project files are now zip files which contain all data and feff files along with the description of the fitting model. This means that it is easy to share analysis projects with friends and to move analysis projects between computers. The project files are normal zip files that can be examined with PKZip, WinZip, StuffIt, ark, or File Roller. To explain these changes more fully, I have added a chapter to the draft document for Artemis. See chapter 5 in the PDF file at: http://leonardo.phys.washington.edu/~ravel/software/exafs/docs.html Please read this new chapter as it explains the features in full detail. As always, let me know about any bugs, questions, or suggestions. This is a significant new direction for Artemis, so I look forward to hearing about the issues that will, no doubt, come up. You can thank Adam Webb and Paul Fons for all the bugs that *aren't* in Artemis due to their excellent feedback on the new version. B -- ********* PLEASE NOTE MY NEW PHONE, FAX, & ROOM NUMBERS ****************** Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 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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question about S02 (passive electron reduction factor)
by hsnuboy 01 Mar '04

01 Mar '04

Dear Ifeffit folks, This is Yu-Chuan. I am now trying to fit my sample, magnesium orthovanadate. I try to follow Bruce's Cu example and Scott's ZnO example steps and I found a problem come to my fitting. At the beginning of the fitting, the S02(amp) are far away from 0.9 (just about 0.3). It's much different than Bruce's and Scott's examples. For Cu and ZnO examples, the fitting results of amp are close to 0.9 at the beginning even if you set just four parameters (guess:amp, e0, delr, and ss). Also, John have said that the S02 value should be around 0.9. That's why I am wondering if there is anything wrong with my data processing? Does anyone happen to have this kind of problem? Thank you for your help. Good day Yu-Chuan

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*****SPAM***** Re: [Ifeffit] question about S02 (passive electron reduction factor)
by SCalvin100＠aol.com 28 Feb '04

28 Feb '04

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RE: [Ifeffit] question about S02 (passive electron reduction factor)
by Kelly, Shelly D. 27 Feb '04

27 Feb '04

Yu-Chuan, Matt and all, > >> Yu-Chuan wrote: > >> > >> At the beginning of the fitting, the S02(amp) are far away > from 0.9 > >> (just about 0.3). It's much different than Bruce's and Scott's > >> examples. [...] Also, John have said that the S02 value should be > >> around 0.9. That's why I am wondering if there is anything > wrong with > >> my data processing? Does anyone happen to have this kind > of problem? > > > > > > There are several possibilities. One is sample prep. [...] [...] > > Another is normalization.[...] Finally, look at the correlation > > between S02 and sigma2...if it is very high (say 0.95 or > above) it may > > simply be coming up with low estimates for each. > > Yu-Chuan didn't give details of sample prep or data > collection, and I agree with Scott that these are most likely > cause of low S02 factors (Scott mentioned problems with > transmission measurements, and Grant mentioned how > self-absorption can cause similarly low S02 factors for > fluorescence measurements). I also agree with Scott that > poor normalization will affect S02, though S02~0.3 would > indicate an edge step off by a factor of ~3, which is a > pretty big error for normalization. I doubt that is the culprit. > > But: the correlation between S02 and sigma2 is NOT the cause > of a value for S02 being low by a factor of 3. A high > correlation means that a reasonably good fit could also be > found by changing both S02 and sigma2 away from their > best-fit value. This is not at all the same as saying that > either parameter has the wrong best-fit value. In fact, the > correlation between pair of variables says nothing about the > trustworthiness of the best-fit values, only how much the > uncertainties in the best-fit values depend on other variables. > And, just to be clear, the reported uncertainties already > take these correlation into account. > > Yu-Chuan didn't actually say what the reported uncertainties > in S02 were, but it seems that it was small enough so that > S02~=0.3 could be distinguished from S02~=0.9. > > --Matt The degeneracy of the paths included in the fit were not mentioned, and could easily cause the S02 value to be off by a factor of 3. Especially, if you forget that feff has already taken the degeneracy of the path into account, and then you set some N-value to 2 or 3 or 4. I have seen others make this mistake before... Shelly

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Re: [Ifeffit] question about S02 (passive electron reduction factor)
by Grant Bunker 26 Feb '04

26 Feb '04

As a follow-on to Scott's and Bruce's responses, if the samples were measured in fluorescence, the sample self-absorption effects would be a likely explanation for the problem. At the Vanadium edge the absorption length of the sample would probably be short (microns) and you would have to go to some trouble to avoid those problems. There are good correction procedures for that problem (e.g. see papers by Booth and Bridges, Haskell...). grant bunker On Thu, 26 Feb 2004 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: question about S02 (passive electron reduction factor) > (Scott Calvin) > 2. Re: question about S02 (passive electron reduction factor) > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 25 Feb 2004 13:18:29 -0500 > From: Scott Calvin <scalvin(a)slc.edu> > Subject: Re: [Ifeffit] question about S02 (passive electron reduction > factor) > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <3.0.1.32.20040225131829.00acff58(a)mail.slc.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Yu-Chuan, > > There are several possibilities. One is sample prep. If you have an > extremely uneven sample (lots of pinholes, etc.) in transmission it can > lead to results like you're describing. Another is normalization. If you're > using Athena for background subtraction make sure you look at the pre-edge > line and post-edge curve and see that they look reasonable. Sometimes if > the background has a funny shape to it Athena can create a post-edge curve > that shoots way up at the edge energy; this could also lead to the effect > you're describing. Finally, look at the correlation between S02 and > sigma2...if it is very high (say 0.95 or above) it may simply be coming up > with low estimates for each. There are, of course, other possibilities as > well, but in my experience those are the most common. > > --Scott Calvin > Sarah Lawrence College > > >This is Yu-Chuan. I am now trying to fit my sample, magnesium > orthovanadate. > >I try to follow Bruce's Cu example and Scott's ZnO example steps and I > found a > >problem come to my fitting. At the beginning of the fitting, the S02(amp) > are > >far away from 0.9 (just about 0.3). It's much different than Bruce's and > >Scott's examples. For Cu and ZnO examples, the fitting results of amp are > >close to 0.9 at the beginning even if you set just four parameters > (guess:amp, > >e0, delr, and ss). Also, John have said that the S02 value should be around > >0.9. That's why I am wondering if there is anything wrong with my data > >processing? Does anyone happen to have this kind of problem? Thank you for > >your help. > > > > > ------------------------------ > > Message: 2 > Date: Thu, 26 Feb 2004 10:43:48 -0500 > From: Bruce Ravel <ravel(a)phys.washington.edu> > Subject: Re: [Ifeffit] question about S02 (passive electron reduction > factor) > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200402261043.48841.ravel(a)phys.washington.edu> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi, > > Yesterday we had a question about oddly small S02 values. In his > thorough summary of possible explanations, Scott mentioned this: > > On Wednesday 25 February 2004 01:18 pm, Scott Calvin wrote: > > Another is normalization. If you're using Athena for background > > subtraction make sure you look at the pre-edge line and post-edge > > curve and see that they look reasonable. Sometimes if the background > > has a funny shape to it Athena can create a post-edge curve that > > shoots way up at the edge energy; this could also lead to the effect > > you're describing. > > I thought that a word of explanation about why Athena does what she > does might be helpful to folks. In this email I am going to refer to > data taken on an iron foil. To follow along, fire up Athena and > select "Import a demo project" from the Help menu. Select the > `calibrate.prj' file. This contains an iron foil spectrum. > > Set the plotting range in energy to [-200:1500]. Set the upper bound > of the normalization range to 400. Click on the "post-edge line" > button in the plotting options section. This will plot the data, the > background, and the post-edge line. Note that the post-edge line is > U-saped, diverging from the data a bit at low energy and significantly > at high energy. Note also that the edge step is about 3.05. > > Now set the upper bound of the normalization range to 1700 and click > the red E plotting button. Now the post-edge line goes through the > data and the edge step is about 2.86. > > So what's going on? Well, the post-edge line is determined by > regressing a quadratic polynomial to the data in the user-specified > normalization range. When the upper bound was set to 400, the square > term in the polynomial was quite large because *that* was the > regression to the data over that short data range. When the upper > bound was set to 1700, the square term was a lot smaller, the > post-edge line was closer to linear and it was constrained by the > regression to follow the data over the entire data range. > > Setting the upper bound of the normalization range had the effect of > increasing the edge step by about 6%. Remember that the edge step is > the value of the post-edge line extrapolated back to E0 after the > pre-edge line is removed from the data. With the short energy range, > the edge step is too large and the chi(k) is attenuated. In the > subsequent fit, S02 will have to be similarly smaller to compensate. > In this case it was a 6% effect, but if the post-edge line is really > screwy, the attenuation could be much larger. > > So this was the long-winded way of repeating what Scott said -- plot > the post-edge line and make sure the regression was done such that the > post-edge line goes through the entire data in a way that seems > sensible. It is also, as Scott said, prudent to check the pre-edge > line as well. > > B > > > > -- > ********* PLEASE NOTE MY NEW PHONE, FAX, & ROOM NUMBERS ****************** > > Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu > Code 6134, Building 3, Room 405 > Naval Research Laboratory phone: (1) 202 767 2268 > Washington DC 20375, USA fax: (1) 202 767 4642 > > 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/ > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 12, Issue 14 > *************************************** >

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choosing k-weight
by Peter Southon 20 Feb '04

20 Feb '04

Dear Ifeffiters, I'm wondering what principles you have to determine the appropriate k-weight to use for FTs. Until now I've used guidelines from a textbook by Teo, based on the Z of the backscattering atoms: Z > 57; kw = 1 57 > Z > 36; kw = 2 Z < 36; n = 3 Of course you can have different backscatterers around your absorber - I've got C, N and Pt! Are there any other rules you follow? Thanks very much in advance! Peter Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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Re: [Ifeffit] choosing k-weight
by SCalvin100＠aol.com 20 Feb '04

20 Feb '04

Peter, Of course, the bottom line is that the k-weight shouldn't affect the values of the parameters Ifeffit finds. If it does, it's a sign that the parameters should not be trusted. Often, this happens when the k-range chosen to fit is inappropriate (extends up into a range where the data is dominated by noise, down into a range where the background is poorly chosen, or across a small edge due to a contaminant, for example). I always test my "final" fits at all three k-weights separately to make sure the values of the parameters stay fairly stable. --Scott Calvin Sarah Lawrence College

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RE: [Ifeffit] choosing k-weight
by Kelly, Shelly D. 20 Feb '04

20 Feb '04

> Dear Ifeffiters, > > I'm wondering what principles you have to determine the appropriate > k-weight to use for FTs. Until now I've used guidelines from > a textbook by > Teo, based on the Z of the backscattering atoms: > Z > 57; kw = 1 > 57 > Z > 36; kw = 2 > Z < 36; n = 3 > > Of course you can have different backscatterers around your > absorber - I've > got C, N and Pt! Are there any other rules you follow? > > Thanks very much in advance! > > Peter Hi Peter, I have found it very useful to use all three kweights, simultaneously. You can really cut down of the correlation between the different EXAFS parameters by doing so. This paper shows a model that was fit to the data with all three kweights. Geo. Cosmo Acta 66(22): pp 3855-3871, November 2002. I have been thinking about putting together an Artemis project file that shows how to do this. If there is interest, I would be willing. Shelly

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