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

more fun with FFT's
by Grant Bunker 09 Jun '04

09 Jun '04

This is in response to Scott's remarks about zero padding and windows. The basic point is that you *always* have fourier truncation effects if you are using a finite k range. If you Fourier transform a pure sine wave over a finite range you will get side lobes that go like |sin(x)/x|. This is true whether you zero pad or not. You won't be able to resolve the side lobe structure if you don't zero-pad however. All you will see is a single point. A useful way to think about it is to view the discrete FFT as a sampled version of the continuous transform (side lobes and all) where the r-space sampling is controlled by size N of the zero padded array (and dk). Hhe zero padding doesn't change the window distortions, it just allows you to see them better. You can of course mitigate the side lobes by applying a k-window to taper the amplitude down to zero at the cutoff, but at the expense of broadening the central part of the peaks. There also is a common myth that if you choose the cutoff to be where chi is zero anyway, that you don't get fourier truncation effects. This is not true. Even if chi (Amplitude*sin(phase)) is zero at a particular k value the amplitude may not be. Imagine a thought experiment in which you shift the phase of chi by a Pi/2, so a node becomes an antinode. Mathematically this is the same as multiplying the complex chi A exp(i phi) by exp(i Pi/2). Since the fourier transform is linear, the filtered (transformed, r-windowed, and inverse transformed) data are just shifted in phase by Pi/2. The fourier filtering distortions are precisely the same when you cut at a node or an antinode. I'll try to dig up some simulations I did many moons ago and post them. grant On Tue, 8 Jun 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. more fun with FFTs (Grant Bunker) > 2. E0 correction in EXAFS fitting (Wojciech Gawelda) > 3. Re: more fun with FFTs (Scott Calvin) > 4. beginning with ARTEMIS (doug pease) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 8 Jun 2004 12:34:58 -0500 (CDT) > From: Grant Bunker <bunker(a)biocat1.phys.iit.edu> > Subject: [Ifeffit] more fun with FFTs > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <Pine.LNX.4.44.0406081222050.25188-100000(a)biocat1.phys.iit.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Just to amplify Matt's remarks - the purpose of padding with zeros is to > deliver a finer grid in r-space. There is a relationship between the > r-space grid dr, the k-space grid dk, and the number of points in the > array (N): N dk dR = Pi. So, for a k-space grid of .05/A and 2048 > points, you get an r-grid spacing of .0307 A. This gives pretty good > sampling of the fourier transform. If you only use say 256 points in your > array (i.e. you don't pad with zeroes) the r-space sampling is .245 A, > which is too coarse to be useful. > > You might ask whether zero padding botches up the data. It can be shown > (I worked it out once) that zero padding is exactly equivalent to > an interpolation of the unpadded data witha specific interpolation kernel > (a sinc function or something as I recall). What happens is that as you > pad with more zeros into a longer array, the sampling in r-space increases, > and ultimately the curve looks just like what you would get with a continuous > fourier transform (with cutoff effects from the finite k-space window). > > grant > > On Tue, 8 Jun 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: FFT in Ifeffit (Matt Newville) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 7 Jun 2004 22:55:28 -0500 (CDT) > > From: Matt Newville <newville(a)cars.uchicago.edu> > > Subject: Re: [Ifeffit] FFT in Ifeffit > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Message-ID: <Pine.LNX.4.44.0406072214290.13810-100000@corvette> > > Content-Type: TEXT/PLAIN; charset=US-ASCII > > > > Hi Scott, > > > > All Fourier transforms in Ifeffit use arrays of length 2048, > > padding with zeros as needed. > > > > In earlier versions of Feffit, doing repeated FTs in the fitting > > loop was noticeably slow. This is probably one of the reasons > > fitting in R-space was uncommon. Anyway, using arrays of length > > N_fft = 1024, 512, or 256 definitely helped speed things up. > > > > In principle, one could use N_fft ~= N_idp, but it turns out that > > if you use too few FT points, you can easily get into a real > > 'false, local, minima'. So Feffit used 1024,512,or 256 for fits, > > and then go back to 2048 to write out the data. Strictly speaking, > > the FFT doesn't need to use an array size that is a power of 2, > > but it turns out to make a very noticeable difference with the FFT > > routines used. > > > > With Ifeffit, several "anti-optimizations" were made that make > > the fits slightly slower but be more straightforward and simple > > (relatively speaking, anyway!). The use of double precision and > > N_fft=2048 being the main examples. Part of the reason for > > sticking with 2048 is that you want to be able to view the data at > > any point in the process so 'pretty output' is always needed. > > Also, I doubt many people will be trying to run artemis on a 386 > > or a microVAX. > > > > --Matt > > > > > As I was working on my talk for the EXAFS workshop, I came across a > > > rather technical question: how does Ifeffit choose the number of > > > points for the Fourier transforms? As I recall, FEFFIT used an > > > algorithm which required an integer power of 2, so its default > > > behavior was to use the smallest integer power of 2 greater than the > > > number of points in the chi(k) data, and then pad the rest with 0's. > > > This default behavior could also be over-ridden if desired. > > > > > > It doesn't look to me like Ifeffit is handling that in the same > > > way--is it always using a very large number of points and padding > > > with 0's, or is it using an algorithm that doesn't require the > > > integer power of 2, or is it interpolating the chi(k) on to a grid of > > > the appropriate size first, or...? > > > > > > I appreciate any info you can give me on this. > > > > > > --Scott Calvin > > > Sarah Lawrence College > > > _______________________________________________ > > > 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 > > > > > > End of Ifeffit Digest, Vol 16, Issue 7 > > ************************************** > > > > > > ------------------------------ > > Message: 2 > Date: Tue, 8 Jun 2004 20:04:25 +0200 > From: "Wojciech Gawelda" <wojciech.gawelda(a)epfl.ch> > Subject: [Ifeffit] E0 correction in EXAFS fitting > To: <ravel(a)phys.washington.edu> > Cc: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <!~!UENERkVCMDkAAQACAAAAAAAAAAAAAAAAABgAAAAAAAAA+oqSCNd0OEmvPV/OsrrrucKAAAAQAAAAqvlml9Ymw0KfPXsmOeouUQEAAAAA(a)epfl.ch> > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Bruce and other mailing list users, > > I have a very basic question concerning the choice of E0 in EXAFS data > analysis. Recently I have been working on Ru solvated complex. I dont > go into too many details but I can say its a pretty large molecule in > aqueous solution with 3 ligands containing 6 N atoms and 30 C atoms in > D3 symmetry. Now, we have measured the L3 edge XANES and EXAFS of this > molecule and I have recently tried to analyze it. Now, what bothers me a > lot is the following observation: once I start processing the data > (meaning background removal, pre-edge subtraction etc.) AUTOBK in both > Ifeffit and Athena proposes to place the edge energy E0 at the > inflection point of the spectrum which lies at about 2838-2839 eV (which > corresponds to atomic Ru L3 edge absorption energy). You might say its > ok but I cannot accept this value. The inflection point lies on a huge > pre-edge peak which is the 4d bound-to-bound transition (white line) > which in principle I dont want to include in my chi(k) because its > still below the ionization energy as I understand it. I guess the > continuum states should start higher in energy and actually from other > spectroscopies one would suspect the E0 to be around 2847 eV (so about > 7-8 eV higher in energy space). Now I set my E0 to this value and I > started fitting the spectrum with FEFF calculation performed on > crystalline structure of the same complex. What I end up with is always > E0 correction for the first shell of neighbors (meaning N atoms) between > -6 to -7.5 eV. I check in chi.dat and xmu.dat files that in my FEFF > calculation the k=0 value was assigned to approx. 2839 eV so its the > same atomic value again. However I know it shouldnt be like that (apart > from a simple fact that Ru in my compound is in its 2+ oxidation state > which surely moves the E0 toward higher energies, doesnt it?). So, I > tried to fool FEFF and make some tricks like shift my data in energy > space or fit the white line and subtract it form the data but it always > consistently converges to place the E0 value at the first inflection > point meaning between 2839-2842 eV. I thought that when fitting the > experimental data with FEFF scattering paths one can choose E0 and then > refine its value by shifting the FEFF-calculated E0 by the amount which > comes out of the fit. So if I have some value of E0 coming out of my fit > then I just shift the initial k=0 value as estimated by FEFF using k -> > sqrt( k-E0(2m/h_bar^2) ) (in other words the negative E0 correction > would always shift the origin in k-space towards larger k values which > means lower values in energy space). Ok, so now my question is the > following: is there an explicit way to set E0 value before letting FEFF > to do its job or it will always use the tabulated atomic value? So, if I > dont know my E0 a priori how can I refine it for a complex or molecule > which has different oxidation state than 0? I mean its a serious > question in my opinion and I wish I could get some feedback from people > who have been doing it for so many years. > I hope I made my point clear enough to you. Let me know if you need any > more feedback in order to answer my question. Ill be glad to give more > details. > Best regards, > > Wojciech > > ********************************************************************* > Wojciech Gawelda > > Laboratoire de Spectroscopie Ultrarapide (LSU) > Institut des Sciences et Ingénierie Chimiques (ISIC), > Faculté des Sciences de Base (SB-BSP) > Ecole Polytechnique Fédérale de Lausanne (EPFL) > > CH-1015 Lausanne-Dorigny, Switzerland > Tel.: +41 (21) 693 0452 > Fax.: +41 (21) 693 0422 > E-mail: <mailto:wojciech.gawelda@epfl.ch> wojciech.gawelda(a)epfl.ch > WWW: <http://lsu.epfl.ch> http://lsu.epfl.ch > ********************************************************************* > >

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E0 correction in EXAFS fitting
by Wojciech Gawelda 09 Jun '04

09 Jun '04

Dear Bruce and other mailing list users, I have a very basic question concerning the choice of E0 in EXAFS data analysis. Recently I have been working on Ru solvated complex. I dont go into too many details but I can say its a pretty large molecule in aqueous solution with 3 ligands containing 6 N atoms and 30 C atoms in D3 symmetry. Now, we have measured the L3 edge XANES and EXAFS of this molecule and I have recently tried to analyze it. Now, what bothers me a lot is the following observation: once I start processing the data (meaning background removal, pre-edge subtraction etc.) AUTOBK in both Ifeffit and Athena proposes to place the edge energy E0 at the inflection point of the spectrum which lies at about 2838-2839 eV (which corresponds to atomic Ru L3 edge absorption energy). You might say its ok but I cannot accept this value. The inflection point lies on a huge pre-edge peak which is the 4d bound-to-bound transition (white line) which in principle I dont want to include in my chi(k) because its still below the ionization energy as I understand it. I guess the continuum states should start higher in energy and actually from other spectroscopies one would suspect the E0 to be around 2847 eV (so about 7-8 eV higher in energy space). Now I set my E0 to this value and I started fitting the spectrum with FEFF calculation performed on crystalline structure of the same complex. What I end up with is always E0 correction for the first shell of neighbors (meaning N atoms) between -6 to -7.5 eV. I check in chi.dat and xmu.dat files that in my FEFF calculation the k=0 value was assigned to approx. 2839 eV so its the same atomic value again. However I know it shouldnt be like that (apart from a simple fact that Ru in my compound is in its 2+ oxidation state which surely moves the E0 toward higher energies, doesnt it?). So, I tried to fool FEFF and make some tricks like shift my data in energy space or fit the white line and subtract it form the data but it always consistently converges to place the E0 value at the first inflection point meaning between 2839-2842 eV. I thought that when fitting the experimental data with FEFF scattering paths one can choose E0 and then refine its value by shifting the FEFF-calculated E0 by the amount which comes out of the fit. So if I have some value of E0 coming out of my fit then I just shift the initial k=0 value as estimated by FEFF using k -> sqrt( k-E0(2m/h_bar^2) ) (in other words the negative E0 correction would always shift the origin in k-space towards larger k values which means lower values in energy space). Ok, so now my question is the following: is there an explicit way to set E0 value before letting FEFF to do its job or it will always use the tabulated atomic value? So, if I dont know my E0 a priori how can I refine it for a complex or molecule which has different oxidation state than 0? I mean its a serious question in my opinion and I wish I could get some feedback from people who have been doing it for so many years. I hope I made my point clear enough to you. Let me know if you need any more feedback in order to answer my question. Ill be glad to give more details. Best regards, Wojciech ********************************************************************* Wojciech Gawelda Laboratoire de Spectroscopie Ultrarapide (LSU) Institut des Sciences et Ingénierie Chimiques (ISIC), Faculté des Sciences de Base (SB-BSP) Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne-Dorigny, Switzerland Tel.: +41 (21) 693 0452 Fax.: +41 (21) 693 0422 E-mail: <mailto:wojciech.gawelda@epfl.ch> wojciech.gawelda(a)epfl.ch WWW: <http://lsu.epfl.ch> http://lsu.epfl.ch *********************************************************************

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starting artemis
by doug pease 09 Jun '04

09 Jun '04

Hello All, My oversight not specifying the platform. When the ATOMS in ARTEMIS fills up the whole screen and the run button is off screen I am in Windows XP. I also have a - perhaps non standard - ViewSonic flat screen monitor, for what that is worth. Carlo, thank you for your interest. Do you or anyone else have a suggestion? Overnight I thought of perhaps trying to change my monitor settings to shrink my monitor display?? Sincerely, Doug Pease

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RE: [Ifeffit] starting artemis
by Kelly, Shelly D. 09 Jun '04

09 Jun '04

-----Original Message----- From: doug pease [mailto:dougpease@comcast.net] Sent: Wednesday, June 09, 2004 6:57 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] starting artemis Hello All, My oversight not specifying the platform. When the ATOMS in ARTEMIS fills up the whole screen and the run button is off screen I am in Windows XP. I also have a - perhaps non standard - ViewSonic flat screen monitor, for what that is worth. Carlo, thank you for your interest. Do you or anyone else have a suggestion? Overnight I thought of perhaps trying to change my monitor settings to shrink my monitor display?? Sincerely, Doug Pease Hi Doug, If you can, you should increase the resolution of the display. On a win2k machine you go to the control panel and choose the Display icon. >From there you can increase the resolution by going to the setting tab and increase the screen area to be 1280 by 1024 pixels. (-I think that winXP should be similar.:) Shelly

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beginning with ARTEMIS
by doug pease 09 Jun '04

09 Jun '04

Hello All, Just starting ARTEMIS for first time. Seems o.k. until I come to the place where I am to run ATOMS in ARTEMIS. The ATOMS view in ARTEMIS takes up the whole monitor screen and the button for running ATOMS is out of site. I cannot drag the view high enough to reveal the ATOMS run button. Any suggestions? Sincerely, Doug Pease

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Re: [Ifeffit] more fun with FFTs
by Scott Calvin 08 Jun '04

08 Jun '04

First of all, thanks to Matt for the info--this seems to me to be a very sensible way for Ifeffit to handle the issue. In terms of Grant's comments, the interesting part to me (and I admit I am getting esoteric here) is that zero-padding has the potential to change the cutoff effects in some circumstances. If you're using a window that goes to zero anyway, then I think it has exactly the effect that Grant describes. But not all windows do this. As a particularly simple example, consider a perfect cosine function over an integer number of periods, with no window. Even though the transform is applied to a finite interval, the result is a spike to within the resolution discussed in Grant's post. (As I recall, the finite sampling also causes the transform to be periodic, but the period is large enough to be disregarded in EXAFS analysis.) But now consider the identical function over the identical interval with zero-padding. This introduces a sharp discontinuity, and causes lots of sidebands on the Fourier transform. Of course, I chose a very special case. Windows reduce this effect considerably, so I would certainly agree that zero-padding does not "botch up" the data. But I wonder if some reduction in sidebands could be achieved by, for example, using a window that goes to the average of the values of the function at the two ends of the interval rather than to 0 (and adjusting the windowing function accordingly). It's on my list of things to try when I get the chance...I don't expect it will make a dramatic difference, but it might make an incremental one. --Scott Calvin Sarah Lawrence College At 12:34 PM 6/8/2004 -0500, Grant wrote: >You might ask whether zero padding botches up the data. It can be shown >(I worked it out once) that zero padding is exactly equivalent to >an interpolation of the unpadded data witha specific interpolation kernel >(a sinc function or something as I recall). What happens is that as you >pad with more zeros into a longer array, the sampling in r-space increases, >and ultimately the curve looks just like what you would get with a continuous >fourier transform (with cutoff effects from the finite k-space window). >

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more fun with FFTs
by Grant Bunker 08 Jun '04

08 Jun '04

Just to amplify Matt's remarks - the purpose of padding with zeros is to deliver a finer grid in r-space. There is a relationship between the r-space grid dr, the k-space grid dk, and the number of points in the array (N): N dk dR = Pi. So, for a k-space grid of .05/A and 2048 points, you get an r-grid spacing of .0307 A. This gives pretty good sampling of the fourier transform. If you only use say 256 points in your array (i.e. you don't pad with zeroes) the r-space sampling is .245 A, which is too coarse to be useful. You might ask whether zero padding botches up the data. It can be shown (I worked it out once) that zero padding is exactly equivalent to an interpolation of the unpadded data witha specific interpolation kernel (a sinc function or something as I recall). What happens is that as you pad with more zeros into a longer array, the sampling in r-space increases, and ultimately the curve looks just like what you would get with a continuous fourier transform (with cutoff effects from the finite k-space window). grant On Tue, 8 Jun 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: FFT in Ifeffit (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 7 Jun 2004 22:55:28 -0500 (CDT) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] FFT in Ifeffit > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <Pine.LNX.4.44.0406072214290.13810-100000@corvette> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi Scott, > > All Fourier transforms in Ifeffit use arrays of length 2048, > padding with zeros as needed. > > In earlier versions of Feffit, doing repeated FTs in the fitting > loop was noticeably slow. This is probably one of the reasons > fitting in R-space was uncommon. Anyway, using arrays of length > N_fft = 1024, 512, or 256 definitely helped speed things up. > > In principle, one could use N_fft ~= N_idp, but it turns out that > if you use too few FT points, you can easily get into a real > 'false, local, minima'. So Feffit used 1024,512,or 256 for fits, > and then go back to 2048 to write out the data. Strictly speaking, > the FFT doesn't need to use an array size that is a power of 2, > but it turns out to make a very noticeable difference with the FFT > routines used. > > With Ifeffit, several "anti-optimizations" were made that make > the fits slightly slower but be more straightforward and simple > (relatively speaking, anyway!). The use of double precision and > N_fft=2048 being the main examples. Part of the reason for > sticking with 2048 is that you want to be able to view the data at > any point in the process so 'pretty output' is always needed. > Also, I doubt many people will be trying to run artemis on a 386 > or a microVAX. > > --Matt > > > As I was working on my talk for the EXAFS workshop, I came across a > > rather technical question: how does Ifeffit choose the number of > > points for the Fourier transforms? As I recall, FEFFIT used an > > algorithm which required an integer power of 2, so its default > > behavior was to use the smallest integer power of 2 greater than the > > number of points in the chi(k) data, and then pad the rest with 0's. > > This default behavior could also be over-ridden if desired. > > > > It doesn't look to me like Ifeffit is handling that in the same > > way--is it always using a very large number of points and padding > > with 0's, or is it using an algorithm that doesn't require the > > integer power of 2, or is it interpolating the chi(k) on to a grid of > > the appropriate size first, or...? > > > > I appreciate any info you can give me on this. > > > > --Scott Calvin > > Sarah Lawrence College > > _______________________________________________ > > 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 > > > End of Ifeffit Digest, Vol 16, Issue 7 > ************************************** >

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Re: [Ifeffit] Using more than one E0
by Scott Calvin 08 Jun '04

08 Jun '04

Hi Wojciech, I have another suggestion. It is my secret, completely untested belief (which I am now revealing to everyone on this mailing list!), that some of the cases of "successful" fits using multiple E0's are masking problems caused by not considering a third cumulant. For those who may not know the role of this parameter, it in essence measures asymmetry in the distribution associated with a path. For example, if a pair of atoms are more likely to separated by a distance considerably larger than the mean separation than by a distance considerably smaller than the mean separation, then the third cumulant is positive. (The mathematical definition is that the third cumulant is the mean cube of the difference from the mean, in the same sense that sigma2 is the mean square of the difference from the mean.) In most cases, the third cumulant is small. Nevertheless, if it were 0 in all cases, then materials would not show any expansion with temperature! Through symmetry arguments, it is pretty clear that the third cumulant is most likely to be significantly nonzero for nearest-neighbor paths. What does this have to do with fitting different E0's? E0 and the third cumulant both affect the phase of the EXAFS signal, although they are weighted in different ways by k. Nevertheless, if a nonzero nearest-neighbor third cumulant is called for, allowing a different E0 for the nearest-neighbor instead would probably also improve the fit statistically. In this case, however, while the use of a third cumulant can be justified on physical grounds relatively easily, the use of a separate E0 is an arbitrary non-physical attempt to improve the statistics. So as far as I am concerned, I am more inclined, if my fit is not quite working out, to try allowing the third cumulant for paths in the first coordination shell to vary than I am to introduce multiple E0's. In fact, I usually do this at some point during the fitting process even if my fit is behaving fairly well to reassure myself that the third cumulant is 0 to within the uncertainty of the fit, and that constraining it to 0 is not distorting the values of the parameters I am interested it. Take all of this with a grain of salt; I wrote my dissertation on the third cumulant, and, to paraphrase Bruce, since I've spent a lot of time making a nice hammer, everything tends to look like a nail... --Scott Calvin Sarah Lawrence College > >I would like to address a couple of questions which are partially >related to my recent struggles in fitting some EXAFS data. I'm >trying to fit my data using several shells of different neighbors >including a few single scattering paths and also so multiple >scattering contributions (mainly collinear multiple scattering >paths) all calculated with the help of FEFF 8.20. Now, I found once >in the FEFFIT manual the following suggestion: one might consider >using several different E0's for different paths in order to improve >the fit. Ok, the explanation was based on some approximations coming >from FEFF code which include incomplete core-hole shielding, lack of >angular variations of the valence charge distribution and charge >transfer between atoms in polar materials. >My question is the following: does anyone of you have some >experience with such procedure? And if yes, shall than distinguish >between the first shell of nearest neighbors and the rest of the >atoms in terms of their E0 corrections (using 2 parameters)? Or >perhaps one can use separate E0's for each path?

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trouble with Atoms on Mac OSX
by Michel Jaouen 04 Jun '04

04 Jun '04

Hi folks, I'm using a PM (2X1.8 MHz processors) under OSX v 10.3.4 (Panther latest version). I have installed ifeffit-1.2.5a two weeks ago and used Atoms many times since. It works well till yesterday when I loose the ability to use the space group browser with an error reported on the herre attached file. It looks that I have a problem with Tk, but I don't understand why. I have tried to make a new install from scratch after putting in the trash the ifeffit and perl (the one I assume to be put by the iffit installer in the home/lib folder): it didn't fix the problem. I found rather puzzling to find several perl folders (one coming from ifeffit and one from Fink). Looking my environnement, I found the following: PERL5LIB=/sw/lib/perl5:/sw/lib/perl5/darwin. I therefore modify my profile making a setenv to force to use the perl from ifeffit without any change. So it seems some hidden file is responsible of this behavior. I must say that if I enter the space group by hand, Atoms runs (e.g. it creates the feff.inp file). If anybody has a solution, I will appreciate. Additional point: I have compliled feff7 using the GNU g77 from Fink, but it stops the run with a segmentation fault. Any hint? Best regards Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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Debian packages
by Carlo U. Segre 04 Jun '04

04 Jun '04

Hello All: I have now packaged the latest horae (036) for Debian stable and unstable. There was a problem in previous versions for stable which I just now figured out how to fix and it involved making a back port of a newer perl module for the archiving/zipping of the project files. Sorry if this caused anyone problems. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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