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

Re: [Ifeffit] R-factor uncertainty
by Scott Calvin 10 Jan '07

10 Jan '07

Hi Lisa, >At 07:23 AM 1/5/2007, you wrote: > >I have a question about the R factor: how can I decide if the >difference between the R factors of 2 fits is statistically >significant, i.e, how can I calculate the uncertainty which has to >be associated to the R factor? > As I understand it, you can't. The R-factor is not a proper statistical measure, as it doesn't incorporate any measure of data quality. That's the great weakness of this measure of quality-of-fit. It is also its strength, as estimating the uncertainty in EXAFS data is notoriously problematic. The complementary statistic is reduced chi-square. It does incorporate a measure of data quality. By default, ifeffit uses noise from high in the FT to estimate this. That's a reasonable idea, but can be problematic. It has been shown (by Matt and/or Shelly, as I recall), that there may in some cases be signal in the part of the FT ifeffit is using to estimate noise. There are also cases where the noise may not be "white," that is, the noise high in the FT may be a poor estimate of the noise low in the FT. Ifeffit does allow you to specify a value of the measurement uncertainty instead, so if you think you have a way of doing this, go ahead. What does all this mean in practice? It means, in my opinion, that the actual =value= of the reduced chi-square statistic is usually meaningless, unless you have a good way of coming up with the measurement uncertainty (for example, your sample may be so dilute that errors are dominated by counting statistics). But reduced chi-square is a great statistic for comparing two fits to a given set of data, particularly if the k-range, k-weighting, and k-window are the same for the two fits. For example, you can apply statistical tests of significance, if you'd like. The R-factor then provides the reality check that the fit is "good" at all. The R-factor isn't doing anything other than what you can see by looking at a graph, but is a nice shorthand for tables showing the results of many fits and similar applications. If there's a big R-factor (say, 0.20), the question of statistical significance isn't necessary to tell you that you haven't got a conclusive positive result: maybe the R-factor is big because the fitting model is lousy, or maybe it's big because the data quality is lousy, but either way the fit shouldn't be trusted. I'd also add that your eye tells you considerably more than the R-factor, because you can tell the character of the mismatch. Is it in the high part of the FT, low, or evenly throughout? Is the miss primarily in amplitude, or phase? I often find I choose a fit with an R-factor of 0.03 over one with 0.01, if, for example, the 0.03 reproduces qualitatively all the features in the data but has small errors in the amplitude of the peaks, while the 0.01 fits the first part of the spectrum perfectly but misses some peak altogether. Hope that helps... --Scott Calvin Sarah Lawrence College

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RE: [Ifeffit] Is there a physical meaning to a negative SO2
by Kelly, Shelly D. 09 Jan '07

09 Jan '07

Hi Todd, One thing to try is to set s02 to a positive value and all the other variables to reasonable values and then look at the real or imaginary parts of the Fourier transform and also look at the chi(k) spectra. You should "see" the affect that Scott mentioned. Shelly > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin > Sent: Tuesday, January 09, 2007 10:27 AM > To: 'XAFS Analysis using Ifeffit' > Subject: Re: [Ifeffit] Is there a physical meaning to a negative SO2 > > Hi Todd, > > Your paragraph below is correct; i.e. you do not have a physically > realistic model. One common cause of a negative S02 is that the model > also is off by half an oscillation. After all, the negative S02 turns > the signal upside down, shifting it by half an oscillation can then > cause a rough (but spurious) alignment between model and data. > > In any case, the model needs work; depending on your system and > degree of prior knowledge, you might be assuming the wrong species of > scattering atom, for example. > > --Scott Calvin > Sarah Lawrence College > > At 10:41 AM 1/9/2007, Todd Luxton wrote: > >I am very new to XAFS analysis, I am wondering if there is a > >physical meaning to a negative value for SO2. Based on the XAFS > >equation I can't understand what the physical significance of a > >negative SO2 value would be, therefore I am assuming that my > >modeling results using Athena are not representative of a physically > >realistic model due to the negative value calculated fro SO2 or more > >specifically the amp variable in the guess set. Any insight would > >be greatly appreciated. > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Is there a physical meaning to a negative SO2
by Todd Luxton 09 Jan '07

09 Jan '07

I am very new to XAFS analysis, I am wondering if there is a physical meaning to a negative value for SO2. Based on the XAFS equation I can't understand what the physical significance of a negative SO2 value would be, therefore I am assuming that my modeling results using Athena are not representative of a physically realistic model due to the negative value calculated fro SO2 or more specifically the amp variable in the guess set. Any insight would be greatly appreciated. thanks

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RE: [Ifeffit] Generating Atom lists using Artemis
by Kelly, Shelly D. 08 Jan '07

08 Jan '07

--------------------------- Shelly Kelly Argonne National Laboratory Bldg 203, RM E113 > > On Saturday 06 January 2007 10:53, Kelly, Shelly D. wrote: > > Hello Artemis users, > > > > I found an interesting feature in Artemis when generating a list of > atoms > > from the attached cif file worth sharing on the list. In the attached > cif > > file for Pd2Si the position of the Si2 atoms are at x,y,z = 0.3333, > 0.6667, > > 0 with a space group of p -6 2 m. Using this cif file and choosing > either > > Pd1 or Pd2 as the core atom results in errors in the atom list. For > > example for the Pd2 site there are 4 Si neighbors with the 1st and 3rd > and > > the 2nd and 4th on top of each other. If you edit the atomic positions > so > > that the Si2 atoms are correct to an additional digit x,y,z = 0.33333, > > 0.66667,0 then the atom list is fixed with only two Pd2-Si neighbors at > > each of the unique positions. The interesting feature is that the > > coordinates on the atoms page need to be correct to the 5 decimal place. > > > This has been discussed many, many times on the mailing list and is > explained in question 3 at > http://cars9.uchicago.edu/iffwiki/FAQ/RunningFeff > > The version of Feff that ships with Ifeffit (and, I believe, all > others) uses 5 significant figures in the path finder. Since Atoms > main purpose is to interact with Feff, it interprets the 5 digit thing > quite strictly. > > B > > [sdk] Hi Bruce, Well, I thought that I had skipped your "here is a link describing that response" by searching the Ifeffit wiki. I didn't run FEFF, so I missed the description of the problem under the FEFF error message of overlapping atoms. I think that it would be helpful for the ATOMS page within Artemis to contain a note of some sort indicating that the 5th digit is significant. Now that I have had additional time to ponder this problem, I realize that I have learned it several times only to forget it again....:) Cheers, Shelly

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RE: [Ifeffit] R-factor uncertainty
by Kelly, Shelly D. 08 Jan '07

08 Jan '07

Hi Lisa, In general the R-factor is good if it is less than a few percent. The value reported is 0.01 or 1% then the fit is satisfactory. Just as a note the R-factor is calculated over the entire data range given by rmin and rmax of the fit, so make sure that they are reasonable values. To compare two different models, use the reduced-chi-square (RCS) value. One standard deviation in the RCS value is SQRT(2/nu), where SQRT is square-root and nu is the number of independent points. If the first model has RCS1 and nu1 and the second model has RCS2 and nu2 then the second model is better than the first model if their difference (RCS1-RCS2) is greater than 2*SQRT((2*RCS1*RCS1)/nu1 + (2*RCS2*RCS2)/nu2)) which is twice the fluctuation of the difference. The number of independent points is equal to the number of data points minus the number of variables in the model. I do this kind of comparison in this paper: S.D. Kelly, K.M. Kemner, G.E. Fryxell, J. Liu, S.V. Mattigod, K.F. Ferris, "X-ray Absorption Fine-Structure Spectroscopy Study of the Interactions Between Contaminant Tetrahedral Anions and Self-Assembled Monolayers on Mesoporous Supports," The Journal of Physical Chemistry B 105 (27) 6337-6346, Aug 2001. The paper can be found here: http://www.mesg.anl.gov/sdkpublist.html. Cheers, Shelly --------------------------- Shelly Kelly Argonne National Laboratory Bldg 203, RM E113 9700 S. Cass Ave Argonne, IL 60439 Molecular Environmental Science Group www.mesg.anl.gov skelly(a)anl.gov phone: 630-252-7376 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Lisa Giachini > Sent: Friday, January 05, 2007 6:23 AM > To: XAFS Analysis using Ifeffit; FEFF Users > Cc: XAFS Analysis using Ifeffit > Subject: [Ifeffit] R-factor uncertainty > > > > Dear all, > > I have a question about the R factor: how can I decide if the difference > between the R factors of 2 fits is statistically significant, i.e, how can > I calculate the uncertainty which has to be associated to the R factor? > > B.R., > > Lisa > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Feffusers] thermal stage
by Matt Newville 05 Jan '07

05 Jan '07

Hi Igor, (and sorry for the double posting, but I thought some people on the Ifeffit list might be interested and have something to say too). I (well, GSECARS) have a Linkam TS-1500 heating stage, which can go to 1500C. It works well. We use it in our x-ray microprobe, where we're usually very concerned with contaminating signals from metals, so we run it open to air without any cover plates on it. It can easily get to 800C with this configuration (that is, no vacuum, a lot less insulation than intended), but we tend to consume the heating elements a little faster than we'd like. In fact, we just ordered some replacements. Julie (well, PNCCAT) has the Linkam THMS-600 (I think that's the model -- it goes down to LN2 temperature, and up to ~600C). The APS equipment pool also has one of these. It also works well, and really does get down to -196C. I does tend to consume LN2 and the connecting line between the stage and dewar is a little short. I think Julie had Linkam modify the basic design to open the back hole enough to allow transmission signal be measured while the stage was at 45degrees to the beam, and then also made some in-house modifications of her own (to improve the low temperature insulation, mostly). The heating element on hers also broke this fall, but she was able to repair it. Anyway, these are definitely reasonable choices, and being commercial products, probably cheaper, safer, and more reliable than anything you can build at home. I think Oxford Danfysik has (or used to have, anyway) a similar microscope heating/cooling stage that could be adapted for synchrotron work, but don't recall the details. --Matt On 12/15/06, Igor Levin <igor.levin(a)nist.gov> wrote: > Hi, > > We are considering to purchase a variable-temperature stage for the XAS > work. Linkam's THMS600 thermal stage came up as an option. Does anybody > have an experience with this stage? What are the alternatives? > > Thanks, > > Igor Levin > > Materials Research Scientist > Ceramics Division > National Institute of Standards and Technology > Gaithersburg MD 20899 > > > _______________________________________________ > Feffusers mailing list > Feffusers(a)u.washington.edu > http://mailman1.u.washington.edu/mailman/listinfo/feffusers >

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Fwd: Re: Independent data poins in Artemis
by Bruce Ravel 04 Jan '07

04 Jan '07

Whoops! I just sent this to Han earlier and meant to send it to the whole list. Silly me! B ---------- Forwarded Message from Bruce Ravel <Bruce Ravel <bravel(a)anl.gov>> ---------- Subject: Re: Independent data poins in Artemis Date: Thursday 04 January 2007 14:50 From: Bruce Ravel <bravel(a)anl.gov> To: "Sang-Wook Han" <swhan(a)chonbuk.ac.kr> On Thursday 04 January 2007 11:48, Sang-Wook Han wrote: > I have checked the Matt's note. > Although I understand the problem, it is still not clear for me. > If we have only one data point in k-space, it is a delta function. For > 2DrDk/pi, it should be zero. When we do Fourier transformation of the one > data point, we still have data points in real and imaginary r-space. That > is not zero. Han, This question and the other answers to it are all charmingly pedantic with regards to the formalism of measurement theory ;-) The main point, IMHO, is that the Nyquist criterion is only true for a properly packed signal. EXAFS resembles a sum of sine waves, but is *not*, in fact, a sum of pure sines waves. The Nyquist criterion, then, is a statement about the maximum possible amount of information in your data, but does not tell you the amount of information that you actually have. Quantifying the information content of an improperly packed signal is the point of the Baysian approach that Scott discussed in in his earlier message. The bottom line is that real EXAFS data tends to have somewhat less than Nidp independent points. One could apply Baysian formalism. Or one could be conservative in the use of parameters and mindful of the level of correlation between parameters. In either case, asserting +0, +1, or +2 in your statement of the Nyquist criterion is pedantry. Indeed, by focussing on that fairly trivial aspect of formal information theory, you are missing a much more improtant point about your real EXAFS measurement. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced 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/

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RE: [Ifeffit] Re: Independent data poins in Artemis
by Scott Calvin 04 Jan '07

04 Jan '07

Thanks, Jeremy. Good point. As a practical matter, what you actually get when a Fourier transform algorithm is applied to a data set consisting of a single point will depend on the algorithm. If the algorithm pads with 0's, it gets a transform that starts to look more and more "white," that is, like a constant function in transform space. If it doesn't pad with 0's, but instead takes the usual Fourier integral and let the limits of integration tend toward 0, so that it only includes the non-zero point, the transform approaches a delta function located at 0 in transform space. Those results are as different as they could be, and they depend entirely on how the truncation is handled. (A typical ifeffit calculation, as I understand it, lies between these two extremes. It integrates over a finite interval, but pads with 0's to get to a convenient number of points.) I think that nicely demonstrates that you can't extract information from the "Fourier transform" of a single point. --Scott Calvin Sarah Lawrence College At 03:20 PM 1/4/2007, you wrote: >Rigorously speaking, a single point is not a delta function. To have a >delta function, only one point has a non-zero value, all other points >are zero. If you have only one data point and you assume all other >points are zero, you are adding information not contained in your data. > >Jeremy Kropf

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Re: Independent data poins in Artemis
by "Sang-Wook Han" 04 Jan '07

04 Jan '07

Hi! Bruce, I have checked the Matt's note. Although I understand the problem, it is still not clear for me. If we have only one data point in k-space, it is a delta function. For 2DrDk/pi, it should be zero. When we do Fourier transformation of the one data point, we still have data points in real and imaginary r-space. That is not zero. Han. ----- Original Message ----- From: "Bruce Ravel" <bravel(a)anl.gov>, To: "Sang-Wook Han" <swhan(a)chonbuk.ac.kr>,"XAFS Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov>, Date: 2007-01-04 23:53:20 Subject: Re: Independent data poins in Artemis On Thursday 04 January 2007 03:06, Sang-Wook Han wrote: > Hi! Bruce > > I have a question of the independent data points. > I calculate the indenpent data points using Stern's idea, > N = 2(Kmax - Kmin)*(Rmax-Rmin)/3.14 + 2. > As you can see the attached file, the result of the Artemis is different > from this method. How do you determine the independent data points? Hi Han, I am taking the liberty of CCing my response to the Ifeffit mailing list since this is a very common question and quite approriate for discussion in that forum. The issue of enumerating independent points is one that has been discussed at some length already on the mailing list. Here are some links. In this one, Matt summary is quite consistent with my view on this issue: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-December/002222.html Here Scott makes reference to a paper applying Baysing approaches to EXAFS data analysis and to the fact that the EXAFS measurement is not, in fact, an ideally packed signal. http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-December/002221.html It seems to me that if your analysis requires the "+2", then you are almost certainly placing excessive demand on your data. Almost certainly, you are using parmaters that are highly correlated and are seeing quite large error bars. If that is the case, you will need to think about how to use constraints to simplify your fitting problem. See question 3 at http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling. Regards, B P.S. It would be very helpful if someone could make am entry on that same FAQ page discussing the issue of enumerating Nidp. -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced 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/

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Re: Independent data poins in Artemis
by Bruce Ravel 04 Jan '07

04 Jan '07

On Thursday 04 January 2007 03:06, Sang-Wook Han wrote: > Hi! Bruce > > I have a question of the independent data points. > I calculate the indenpent data points using Stern's idea, > N = 2(Kmax - Kmin)*(Rmax-Rmin)/3.14 + 2. > As you can see the attached file, the result of the Artemis is different > from this method. How do you determine the independent data points? Hi Han, I am taking the liberty of CCing my response to the Ifeffit mailing list since this is a very common question and quite approriate for discussion in that forum. The issue of enumerating independent points is one that has been discussed at some length already on the mailing list. Here are some links. In this one, Matt summary is quite consistent with my view on this issue: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-December/002222.html Here Scott makes reference to a paper applying Baysing approaches to EXAFS data analysis and to the fact that the EXAFS measurement is not, in fact, an ideally packed signal. http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-December/002221.html It seems to me that if your analysis requires the "+2", then you are almost certainly placing excessive demand on your data. Almost certainly, you are using parmaters that are highly correlated and are seeing quite large error bars. If that is the case, you will need to think about how to use constraints to simplify your fitting problem. See question 3 at http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling. Regards, B P.S. It would be very helpful if someone could make am entry on that same FAQ page discussing the issue of enumerating Nidp. -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced 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/

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Re: [Ifeffit] CN and bond distances in Artemis
by Juan Antonio Maciá Agulló 21 Dec '06

21 Dec '06

Hi all, First of all, I would like to thanks Anatoly for his file and everybody for useful comments. I have analysed Anatoly's data and I have obtained a good value for S02 = 0.85 or 0.82 (depending on the number of variables used). So, my data is the problem, and it is not my analysis, but maybe my measurements need a more accurate analysis with Athena as Scott suggested. I was not at synchrotron measuring platinum samples and I only know that are measured in fluorescent mode. As Bruce said, I have no beamtime now for more measurements. I have more questions, related and not related to the last subject, but I am still thinking about them: The first one is easy, it is about the Nyquist theorem. I read in a paper that the formula is 2·deltak·deltaR/pi + 2. The last "+2" is new for me and I am afraid that Artemis does not consider it. I am sure that it is a silly thing. I will try to correct again Ptfoil considering self-absorption in order to obtain a spectrum similar to Anatoly's or Bruce's one. And then, I will apply the same correction for supported platinum catalysts, right? I also observed that Anatoly's Pt foil shows good signal even for large k (20 A-1). Nevertheless, obviously platinum catalysts spectra possess lower signal and specially for high values of k where the noise is big. The question is, despite Pt foil has a good signal until 20 A-1, it is usually used a smaller k-range (i.e. 3-12 A-1), right? I normally use a k-range of 3-12. And finally, how to calculate bond distances from Reff and deltaR? Thank you very much Best regards, JA

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Yttrium in alumina GBs
by Shantanu Behera 21 Dec '06

21 Dec '06

Thanks Carlo and Scott for ur response. Some numbers from my fits in this regard and some more queries. When I make a cluster based on the Alumina structure (replacing the central Al with Y with relaxed lattice parameters) I get DW 0.0025 +- 0.002, without any restraint. While I restrain the DW to 0.005, my CN jumps from 4.8 to 5.2. When I make a cluster based on Yttria structure, I get DW factor of 0.008 +- 0.002, unrestrained. While I restrain the DW to 0.01, it again jumps from 4.8 to 5.2. First query...if you can pin down on the CN change (Carlo..you wanted some numbers) Second...what are ur comments on the above 2 models and the change in DW factors. I might add that ther is no appreciable difference with k=2, 3 or 2&3 fittings. All the fits produce red-chi-sqr less than 100 (~50-70), all R-factors are <0.01 and no unphysical reports after the fit. And I have only 1 peak to worry about, there is no second shell correlation seen. I would appreciate your 2 cents on this. Warm regards Shan -- ||||||||||||||||||||||||||||||||| Shantanu Behera Center for Advanced Materials and Nanotechnology Lehigh University 5, East Packer Avenue Bethlehem, PA 18015, USA

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Re: [Ifeffit] Yttrium in alumina GBs
by Scott Calvin 20 Dec '06

20 Dec '06

Hi Shan, Nothing at all surprising here. In fact, you're getting pretty good results, in my opinion. Your CN insists on being "about" 4.8. When you push the ss, with which CN is correlated, to the top of its fitted range, the CN increases to about 5.2. To me, that says your CN is 4.8 +/ 0.4. A 10% uncertainty in CN is quite good for EXAFS! Of course, your real uncertainty is greater than that, because there are some possible systematic errors (e.g. normalization, sample effects) that might be present. But still, you're doing about as well as can be expected. Of course, that's assuming that CN's are what you're after. If finding out whether it's Alumina or Yttria is what you're after, the quality of fit and CN are not distinguishing between the two possibilities. That leaves bond distance as the best EXAFS indicator of which phase is present. --Scott Calvin Sarah Lawrence College At 05:49 PM 12/20/2006, you wrote: >Thanks Carlo and Scott for ur response. > >Some numbers from my fits in this regard and some more queries. > >When I make a cluster based on the Alumina structure (replacing the >central Al with Y with relaxed lattice parameters) I get DW 0.0025 +- >0.002, without any restraint. While I restrain the DW to 0.005, my CN >jumps from 4.8 to 5.2. > >When I make a cluster based on Yttria structure, I get DW factor of >0.008 +- 0.002, unrestrained. While I restrain the DW to 0.01, it >again jumps from 4.8 to 5.2. > >First query...if you can pin down on the CN change (Carlo..you wanted >some numbers) >Second...what are ur comments on the above 2 models and the change in >DW factors. > >I might add that ther is no appreciable difference with k=2, 3 or 2&3 >fittings. All the fits produce red-chi-sqr less than 100 (~50-70), all >R-factors are <0.01 and no unphysical reports after the fit. And I >have only 1 peak to worry about, there is no second shell correlation >seen. > >I would appreciate your 2 cents on this.

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RE: [Ifeffit] Athena problem
by Barton, David (DG) 20 Dec '06

20 Dec '06

The oddity that Jeff describes also occurs on the Windows platform (Athena 0.8.050). If you hit the "OK" button in the File-Open window a couple of times while a dataset is being loaded you will multiple instances loaded into the data group list that cannot be selected or deleted. The message trapped by Athena message can be seen in attached image. Dave >-----Original Message----- >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >Of Jeff Terry >Sent: Wednesday, December 20, 2006 12:55 PM >To: XAFS Analysis using Ifeffit >Subject: Re: [Ifeffit] Athena problem > >Since everyone is bringing up oddities in Athena, at least >under Debian, if you click on the load file button a second >time after setting up the input file parameters before it has >completed loading, you get a second group with the identical >name but it is not selectable and cannot be deleted. > >Jeff > > >On Dec 20, 2006, at 11:39 AM, Matt Newville wrote: > >> Hi, >> >> I agree that there have been several unrelated "issues" brought up >> here. Some of them are definitely reproducible, if not necessarily >> easy to capture as an isolated bug report. >> >> The "out of memory" problem that Paul Fons mentioned is >definitely due >> to ifeffit's limited, and fixed memory. This can be changed changed >> at compile time, but is (sadly) unavoidable in the current >> implementation. Someday there will be an Ifeffit 2 that eliminates >> this problem. >> >> The problem with 'clicking on the file/group area' in Athena on >> Windows is a long-standing issue. It's fairly common (for >me, anyway) >> to get an Athena session in this state, in which clicking on an >> existing group does not highlight it or make it current, and moving >> the mouse over it does not change the font. Sometimes a group can >> still be chosen as a member of a set. I don't know of an foolproof >> way to get to this state, but it seems to be more common >when reading >> in several data sets, and after a project has been open and >used for a >> while. This is definitely an irritation and it's been >like this for >> awhile. The rest of athena still runs fine. The easiest and most >> reliable workaround (that I know of) is to click into a real >widget in >> the Main Panel (so that it actually responds) and then go >back to the >> group list and click on another group. >> >> I haven't experienced very many random crashes of Athena. >> >> --Matt >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Athena problem
by Maura H. Jordao 20 Dec '06

20 Dec '06

Dear all, Im having some problems to run Athena (Ifeffit 1.2.9) in my Windows XP (Home Edition, Version 2002), and Im writing to this list to get a help. One of them is if I plot a graph using different options (E or k for example) for many times, the graphics window freeze and I need obligatory to close the program. The other is the Pre and Post-edge lines do not appear when I marked them to plot. If somebody had experienced similar problems and know how to solve, please, write me. Ill be glad to receive some solution. Thanks, Maura ____________________________________________________________________________________ Want to start your own business? Learn how on Yahoo! Small Business. http://smallbusiness.yahoo.com/r-index

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RE: [Ifeffit] Athena problem
by Barton, David (DG) 20 Dec '06

20 Dec '06

Bruce, I believe I have a sequence of events that you can reproduce this problem of the data selection window locking up in Windows (tested in XP-SP2 and Win2000-SP4) using Athena 0.8.050. #1) Open three data sets #2) Right-click on first dataset choose Plot This Curve..In energy (Left click to choose) #3) The other datasets are now locked. Cannot select another dataset. #4) The fix: Right-click on any other dataset. Data selection begins working fine again. It appears that Athena is waiting for another Right-click after something is chosen off the popup context menu. This glitch is reproducible on WinXP and Win2000 platforms. Dave >-----Original Message----- >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >Of Bruce Ravel >Sent: Wednesday, December 20, 2006 9:06 AM >To: XAFS Analysis using Ifeffit >Subject: Re: [Ifeffit] Athena problem > > >Hi folks, > >I have been following the discussion in the last few days >about problems people are having on Windows with Athena and >Artemis. I trust that everyone appreciates that my commitment >to providing useful, usable software is strong and that I work >very hard to meet that commitment. Unfortunately, nothing in >this thread has provided me with actionable information. >While I understand that some of you are having problems, no >one has yet provided enough information for me even to begin >solving the problem (whatever it might be). >The fundamental rule of good bug reporting is that you need to >provide sufficient information that I can reproduce the >problem on my computer. If I cannot reproduce the problem, I >cannot understand it and cannot solve it. > >On my bug reporting page >(http://cars9.uchicago.edu/~ravel/software/bugs.html) >there is a box on the left side of the screen with links to >two excellent articles in how to communicate with software >developers. If you are interested in how to best help me to >understand and solve problems with my software, please read >through those articles and take the authors' suggestions to heart. > >Regards, >B > >-- > Bruce Ravel ---------------------------------------------- >bravel(a)anl.gov > > Molecular Environmental Science Group, Building 203, Room >E-165 MRCAT, Sector 10, Advanced 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/ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Re: [Ifeffit] High Correlation betn SO2 and ss
by Scott Calvin 20 Dec '06

20 Dec '06

Hi Sham, I agree with Carlo. I would also add that you should try different k-weights, including multiple k-weights at once. Since the dependence of S02 and ss on k is quite different, that can often reduce the correlation between the two. --Scott Calvin Sarah Lawrence College At 11:58 PM 12/19/2006, Shantanu Behera wrote: >Hi Folks > >I have a small doubt. I work on the structural features of Y that are >segregated to Alumina grain boundaries (very dilute amounts of Yttrium >in polycrystalline alumina). > >In some of my fits, I find a correlation ~0.85 between SO2 and ss. If >I restrain the ss, from 0.004 to 0.007, the CN changes by ~0.5 (not >considering +/-0.3). I would appreciate if someone can explain me how >to interpret the results from a structural point of view.

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High Correlation betn SO2 and ss
by Shantanu Behera 20 Dec '06

20 Dec '06

Hi Folks I have a small doubt. I work on the structural features of Y that are segregated to Alumina grain boundaries (very dilute amounts of Yttrium in polycrystalline alumina). In some of my fits, I find a correlation ~0.85 between SO2 and ss. If I restrain the ss, from 0.004 to 0.007, the CN changes by ~0.5 (not considering +/-0.3). I would appreciate if someone can explain me how to interpret the results from a structural point of view. Warm regards Shan -- ||||||||||||||||||||||||||||||||| Shantanu Behera Center for Advanced Materials and Nanotechnology Lehigh University 5, East Packer Avenue Bethlehem, PA 18015, USA

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XAFS: Industrial Career Opportunity
by Barton, David (DG) 19 Dec '06

19 Dec '06

The Dow Chemical Company has openings for Ph.D. Chemists, Polymer Scientists and Materials Scientists in our Global Analytical Sciences Laboratory. If you are highly qualified and are interested in this job, please submit your electronic resume directly to tdominowski att dow.com Location of Jobs: Midland, Michigan and Freeport, Texas Job Title: Senior Research Scientist Degree: Ph.D Discipline: Analytical Chemistry, Physical Chemistry, Inorganic Chemistry, Materials Science, Physics, Chemical Physics or Polymer Science Job Description Overview: Candidate will be responsible for providing advanced Materials Characterization by developing new techniques in the area of surface science and/or Synchrotron techniques (XAFS, XRD, tomography). For this position we are seeking candidates who are strong in Materials Science and Materials Characterization. Candidates must be proficient in characterization techniques. Candidates must have significant analytical chemistry and thin film characterization specialization and excellent problem solving skills. Qualifications: Ph.D. in Analytical Chemistry, Physical Chemistry, Inorganic Chemistry, Materials Science. Experience and deep capability in Materials Characterization is preferred. Capability in techniques such as XPS/TEM/EXAFS. Experience and expertise in one or more of the following is highly valued: inorganic chemistry, ceramics, materials science. Candidates must have strong quantitative analysis and analytical problem solving skills. Feel free to email me with any questions (dgbarton att Dow.com) Regards, Dave _________________________________ David Barton The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA Ph: (989) 636-4753 Fax: (989) 638-6225 dgbarton att dow.com

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staff position available for BLADE beamline at Diamond Light Source
by Van Der Laan, G (Gerrit) 16 Dec '06

16 Dec '06

Dear Collegue, We are currently looking for a beamline scientist for BLADE (BeamLine for Advanced Dichroism Experiments) at Diamond, which will be operational in 2010/11 at the Diamond Light Source, near Oxford, United Kingdom. I would be very grateful if you could pass on the following advert (see below for the text of the announcement). http://www.diamond.ac.uk/Jobs/CurrentVacancies/Scientific/DIA0271SB.htm Deadline for applications is 5 January 2007. Informal enquiries can be made to Dr Paul Steadman (Paul.Steadman(a)diamond.ac.uk, Tel: +44 (0)1235 778156), who is the principal beamline scientist of BLADE. Best Regards, Gerrit van der Laan Chair of the BLADE user working group Daresbury Laboratory, UK Tel: +44 (0)1925 603448 email: g.vanderlaan(a)dl.ac.uk -------------------------------- Text of the announcement: DIA0239/LV - Beamline Scientist: Beamline for advanced dichroism experiments (BLADE) A beamline for the study of magnetic dichroism and magnetic structure using soft x-ray resonant scattering (reflection and diffraction) and x-ray absorption, allowing a broad range of novel studies focused on the spectroscopic properties and magnetic ordering of novel nanostructured systems This beamline will provide variable linear and circular polarised x-rays covering the energy range 0.4 to 2 KeV, which includes important absorption edges such as 3d transition metal L2,3 and rare earth M4,5 edges. The highly brilliant source of polarised soft x-rays will allow ultrasensitive studies using magnetic dichroism in x-ray absorption, soft x-ray resonant scattering and (resonant) photoemission. The beamline will comprise two branches for (i) a 9T superconducting magnet with UHV environment, cooling to 1K for x-ray magnetic circular and linear dichroism (XMCD and XMLD) and (ii) a multi-circle UHV diffractometer with liquid helium cooling and sample magnetisation for soft x-ray resonant magnetic scattering (SXRMS). There will also be the possibility of attaching user stations such as for photoemission and resonant Raman scattering. This beamline, which will be world leading in terms of its flux, coherence and design for extreme sample conditions, provides a ke! y resource to scientists in the national and international research communities and will have a very significant impact in some of the most topical subjects of contemporary solid state. The combination of XMCD/ XMLD and SXRMS will enable a broad range of exciting new phenomena in novel nanostructures and correlated materials to be explored using soft x-ray spectroscopy and diffraction. Key Duties Working in support of the Principal Beamline Scientist in the following areas: * To assist in the design, testing, installation and commissioning of the Beamline * Assist in the procurement of the beamline components * Liaise with the suppliers of the beamline components * Assist in the testing, installation and commissioning of the beamline components. * Support the operation of the beamline and interact closely with the users of this facility * Carry out own research in an area relevant to the beamline Skills and experience Essential * Appropriate first degree or equivalent qualification * Relevant synchrotron research experience * Experience or knowledge of synchrotrons * Ability and initiative to get to the heart of the problem and take it effectively through to completion * Good interpersonal, communication and presentational skills * Ability to interact effectively with staff at all levels * Ability to work as part of a multi-disciplinary team * Self motivated * Desirable * Experience of beamline design * Experience of magnetic circular dichroism and magnetic linear dichroism * Experience of soft X-ray scattering * Experience of working with high magnetic fields * Experience of low temperature measurements * Experience of ultra high vacuum * Second degree in appropriate subject * Ability to manage a small team * Project management experience * Further Information * Must be available to travel occasionally within the UK and abroad, including overnight absences Salary c£30,000 If you would like to apply please visit our website at <http://www.diamond.ac.uk/Jobs/How+to+apply/ApplicationForm.htm>

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Re: Ifeffit Digest, Vol 46, Issue 7
by Mehdi Ali 14 Dec '06

14 Dec '06

I have a question what does Rbkg option in athena does. What is its physical significance. I am new to exaf data analysis. Thanks Mehdi Mehdi Ali, PHD Canditate, Department of Physics, Illinois Institute of Technology, Chicago,IL (773)-895-6144 ----- Original Message ----- From: ifeffit-request(a)millenia.cars.aps.anl.gov Date: Thursday, December 7, 2006 12:00 pm Subject: Ifeffit Digest, Vol 46, Issue 7 > 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: Re: question on Athena data import (Gerrit Schmithals) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 07 Dec 2006 15:15:27 +0100 > From: Gerrit Schmithals <schmithals(a)hmi.de> > Subject: Re: [Ifeffit] Re: question on Athena data import > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <457821FF.30400(a)hmi.de> > Content-Type: text/plain; charset="iso-8859-1" > > Matt Newville schrieb: > >> Very nice! I'd be happy to give you some space on > >> http://cars9.uchicago.edu/~ravel/software/contrib.html, if that > would>> help. > > > > You could use the wiki for this. > Hello Bruce, Hello Matt, > > I appended the script file along with a couple of textfiles for > testing.There is a description at the top of the file that explains > how to use it. > > I think both the wiki and the Athena homepage are good places to offer > it. Can I leave it up to you where you want to have it? > > I only tested it on Windows so maybe you want to give it a try on > Linux/Mac first. > > Cheers, > Gerrit > >

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FEFF and XANES
by Frommer Jakob 11 Dec '06

11 Dec '06

Dear all, I have a FEFF related question (I know that this is an IFEFFIT list, but I guess the subjects are closely related). I try to model some of my Cr XANES data with FEFF (following the procedure outlined in an excellent publication in Chem Phys 300 (2004) 13-22 the authors have shown that it is possible to explain the Cr XANES spectra at least qualitatively by the means of FEFF calculations). I have however still some trouble to understand the difference (or the relation) between the XANES results given in the xmu.dat file and the l-projected density of states results (ldosXX.dat). Due to rho(E)=rho_0(E)[1+chi(E)] I would expect them to conincide (if the rho is calculated for the correct l i.e. if the matrix element is non-zero). However I observed that the ldos and the xmu do not always coincide is this possible? Furthermore at the white line position (from what I know, the white line is commonly interpreted as being due to the transition into unoccupied but bound states) the xmu shows strong intensity whereas the ldos do not (maybe one comment: I assume that the e-scales in the ldos-file and in the xmu-file are the same). I am using FEFF8.2 with the SCF, DOS, XANES and FMS card. I would be obliged for your help. Thanks Jakob P.s.: for hydroxide structures FEFF is always returning bad counts if I include the protons into the FEFF calculation however this might be also due to bad input structures. ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 Email: jakob.frommer(a)env.ethz.ch http://www.ito.ethz.ch/SoilChem/

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Re: question on Athena data import
by Jay Brandes 11 Dec '06

11 Dec '06

Ended up looking at the older threads and the fix posted a few months ago, to use the program textwrangler and save in UNIX text format, worked. The problem seems to be that the normal Mac text handling programs do not have this option and Athena requires it. Just looking at the files in another text editing program does not reveal the problem. Anyway, problem solved.

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Hack and slash
by Paul Fons 06 Dec '06

06 Dec '06

I hacked and slashed and have succeeded in building the wrapper and making a new version of horae. It is getting rather late here so I will have to turn in, but I think the idea of making a different Makefile for the wrapper is a good one. As it didn't seem to be particularly difficult, I assume that I will have no trouble putting one together. I will post a new tarball later tommorrow on sourceforge with a new Mac installer (power pc). This problem with the tarball was new -- there was no conflict before (or was there). The error associated warning message occurred when tar attempted to write the file "atoms" on top of the directory "Atoms". I wonder if the archive order was different before hiding the conflict? Paul On Dec 6, 2006, at 11:59 PM, Bruce Ravel wrote: > On Wednesday 06 December 2006 08:30, Paul Fons wrote: >> Alas Bruce, not everyone has a unix without training wheels. The >> darwin OS is case insensitive. Sort of a good thing in many ways. >> For instance take the example of "atoms" and "Atoms" in the horae-063 >> directory. This frozzed tar in the unpacking stage and I didn't >> realize the conflict until today (I was in Italy until last Friday so >> didn't get a chance to compile horae until today). > > Hmmm... not so trivial. But I'll try to have a trial tarball for you > later today. > >> Can you remove the conflict with uppercase and lowercase "atoms/ >> Atoms" in the horae directory so this doesn' happen every time. It >> would also be sort of neat if there were a some sort of "honest" way >> to compile the ifeffit_wrapper.c source without having to hack the >> ucky MakeMaker output (a switch perhaps). All this is of course, >> when you have time. Thanks for the new release. > > If I knew how to honestly compile the wrapper, I'd be happy to do so. > > Are you able to compile other C code from perl packages "out of the > box"? For example, if you downloaded (to suggest an example that > horae uses) Compress::Zlib and did the typical perl-y build > incantation, does it run to completion without further input? If so, > then I can simply remove all darwin-specific code from my > makefile.PL. If not, then you need to tell me what to do. > > One option is for you to provide me with a makefile that builds > ifeffit_wrapper. I'll add that to the tarball and simply have > Makefile.PL skip the compilation of ifeffit_wrapper. Then your > external makefile can be used to build ifeffit_wrapper. That adds a > step to the build incantation, but that's not so bad. > > Perhaps better, I can simply skip the build of ifeffit_wrapper for > darwin on the assuption that it is already installed or has been > installed some other way. That way, the wrapper can be part of the > installer package, not part of the tarball update for darwin. That > is, in fact, what my Makefile.PL does for debian. > > B > > > > > -- > Bruce Ravel ---------------------------------------------- > bravel(a)anl.gov > > Molecular Environmental Science Group, Building 203, Room E-165 > MRCAT, Sector 10, Advanced 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/exafs/ >

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CN and bond distances in Artemis
by Juan Antonio Maciá Agulló 06 Dec '06

06 Dec '06

Hi all, I read your papers Anatoly. You fixed the value of S02 found in the Pt metal, and the expression in Artemis would be like this: N:1 x S02: amp·N, right?? I have a low value of S02 in the case of platinum (0.53), how can I solve the problem? Bond distances = delR + Reff (with phase correction)? Thank you very much, Best regards, JA

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