Re: [Ifeffit] Fit in R or k
Hi Will: The relationship between the data in k-space and R-space is described in this tutorial: https://docs.xrayabsorption.org/tutorials/Basics_of_XAFS_to_chi_2009.pdf Take a look at what a Fourier transform does. In few words I'd say it doesn't matter which representation of the data (k-space or R-space) you model. Both have their good and not so good points. R-space: You can filter out noise, and higher and/or lower frequencies that you might not be interested in. You can also weight the lower or higher part of the spectra you are fitting by using k-weighting. k-space: You are working with less processed data and can directly see the noise and high/lower frequency components "on top of" your signal of interest. If it still isn't clear I'd suggest you start with some of the material at this web site: https://xrayabsorption.org/tutorials/ There is also this very readable book by Scott Calvin: https://www.amazon.com/XAFS-Everyone-Scott-Calvin/dp/1439878633/ref=asc_df_1439878633/?tag=hyprod-20=df0=312091458201==g=7369607741759776259c===9021703=pla-455399119345=1===63669393113===312091458201==g=7369607741759776259==c===9021703=pla-455399119345 I also have an EXAFS chapter that I can send you a copy of, if you send me a request directly. Kind regards, Shelly From: Ifeffit On Behalf Of LIMA DA SILVA, WILL (PGR) Sent: Tuesday, October 12, 2021 4:10 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Fit in R or k Dear IFEFFIT members, I have been fitting some EXAFS data, and my supervisor and I are having doubts if it's better to fit in k or R space. What are the main differences between the two approaches? I have learnt that R space is the right approach, but I am not sure how to explain it. Much appreciated, Will Silva ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] S02 selection from reviewer
Hi Peng: It might be helpful to understanding some of Matt's points regarding S02 transferability, Ei and energy resolution by looking at this paper. Comparison of EXAFS foil spectra from around the world DOI: 10.1088/1742-6596/190/1/012032 Kind regards, Shelly -Original Message- From: Ifeffit On Behalf Of Matthew Marcus Sent: Saturday, October 2, 2021 9:04 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] S02 selection from reviewer Since S02 is a parameter in the description of EXAFS and not of the experiment, it's independent of technique. Overabsorption (misnamed 'self-absorption') can reduce the *measured* amplitude, an effect which can be fudged in analysis by reducing S02. If the sample is truly homogeneous (on the scale of the absorption length), then you can calculate the amount of overabsorption to see if it's significant. However, many kinds of samples, such as concentrated powders mixed with a diluent such as BN, this condition is not met. If the particles are large enough for each to have significant absorption edge jumps, then diluting them in BN doesn't fix the problem. mam On 10/2/2021 12:49 AM, Peng Liu wrote: > Dear IFEFFIT members, > > I am sorry to bother you again. I asked about S02 selection for the > first major revision. I just received the second revision. The > reviewer is not satisfied with one S02 value for all our samples. > " > > 1. I am still not satisfied with selected SO2 value (it is set to 0.85). > SO2 is not transferable between different samples and detection methods. > It is not possible to use a value obtained from different compound > using transmission measurement mode to completely different other > compound measured using fluorescence mode. One method to fix SO2 value > is to measure diluted solution (to avoid self-absorption) of reference > material in fluorescence mode. Other is to use multiple spectra > fitting for all samples of interest (e.g. with Sb(V)) measured using > fluorescence mode where SO2 parameter is the same for all samples. > > At the same time I am confident that CN values 5.6, 7.1 and 6.9 > correspond to CN(Sb-O)=6. I suggest reconsidering the SO2 value for > measurements in fluorescence mode. > > " > > We do get the S02 from a similar reference material measured in > transmission mode, and our samples were all measured in fluorescence > mode. It is not possible to measure the diluted reference material in > fluorescence mode in one or two months. If you could give me some > suggestions, that would be great. > > > -- > Best Regards, > > Peng Liu > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
[Ifeffit] Beamline Scientist position
Hello XAFS community: I'm excited to let you know that we have an opening for beamline scientist within the Spectroscopy group at the Advanced Photon Source. Please help spread the word. https://bit.ly/3iN7Ehe Kind Regards, Shelly Kelly Spectroscopy Group Leader Advanced Photon Source ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] quotation of figures
I'd like to add my 2cents worth about the mean square displacement term. I wrote it up on the EXAFS wiki, since I like to say it over and over. see http://www.xafs.org/Common_Mistakes Shelly From: [EMAIL PROTECTED] on behalf of Scott Calvin Sent: Wed 7/16/2008 3:54 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] quotation of figures Hi Rich, Mean-square radial disorder (MSRD) is one good alternative. I'll also point out another bit of ambiguity with Debye-Waller factor aside from the confusion with the XRD term. Some EXAFS practitioners use Debye-Waller factor to indicate all disorder-type modifications to the EXAFS equation, including higher cumulants. Most use it only for the Gaussian part; i.e. the second cumulant. Another good reason to avoid the term. --Scott Calvin Sarah Lawrence College On Jul 16, 2008, at 4:41 PM, Richard Mayes wrote: I also dislike the phrase Debye-Waller factor for the exafs disorder term. In crystallography, the Debye-Waller factor refers to disorder of atoms about their lattice positions. In exafs, the disorder is about the path length of the N-body configuration -- clearly not the same thing. I am, apparently, in the minority on this topic -- Debye-Waller factor is in wide use in the exafs literature. But, as everyone here knows, I often like to stand up on my soapbox and yell into the crowd. ;-) Bruce, While you're on your soapbox, if we drop Debye-Waller factor to describe the EXAFS disorder term, would you suggest using only disorder or do you have a better phrase to use? Rich ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] quotation of figures
Hi Eckhard, The first slide also has problems. The first path is a single scattering path. All the others are double scattering paths. The word single, double and triple are used to describe the number of atoms that scatter. The number of legs is used to tell the difference between the different kinds of double scattering. So the first (A-B-A) single scattering path has 2 legs (nlegs=2). The next one (A-C-B-A) is a double triangle scattering path with 3 legs. The next one (A-B-C-A) is equivalent to the previous one so that the CN for that path is twice the number of atoms for that path. The last one (A-C-B-C-A) is a double scattering path with 4 legs. HTH Shelly From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] Sent: Wed 7/16/2008 11:04 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] quotation of figures Hi, i have a print out of a talk (about XANES, XAFS and multiple scattering...) and i want to cite some figures (attached). Can anybody tell me the author etc...? I searched everywhere on the web (on several sites of XAFS-Summer Schools...). Unfortunately i do not have the talk as pdf-file only the print out. Maybe the talk is from Matt Newville? Maybe anybody recalls on this talk/slides or recognizes them? Thanks for your help. Have a nice day, Eckhard - Eckhard Bosman [EMAIL PROTECTED] +49 (0)551-39-14441 Raum: E0.104 Institut für Röntgenphysik Friedrich-Hund-Platz 1 37077 Göttingen Germany ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] quotation of figures
Yah know,,,I'm wrong The last one is a triple scattering path with just two scattering atoms. the leg part is right... oops SK From: [EMAIL PROTECTED] on behalf of Kelly, Shelly D. Sent: Wed 7/16/2008 11:45 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] quotation of figures Hi Eckhard, The first slide also has problems. The first path is a single scattering path. All the others are double scattering paths. The word single, double and triple are used to describe the number of atoms that scatter. The number of legs is used to tell the difference between the different kinds of double scattering. So the first (A-B-A) single scattering path has 2 legs (nlegs=2). The next one (A-C-B-A) is a double triangle scattering path with 3 legs. The next one (A-B-C-A) is equivalent to the previous one so that the CN for that path is twice the number of atoms for that path. The last one (A-C-B-C-A) is a double scattering path with 4 legs. HTH Shelly From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] Sent: Wed 7/16/2008 11:04 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] quotation of figures Hi, i have a print out of a talk (about XANES, XAFS and multiple scattering...) and i want to cite some figures (attached). Can anybody tell me the author etc...? I searched everywhere on the web (on several sites of XAFS-Summer Schools...). Unfortunately i do not have the talk as pdf-file only the print out. Maybe the talk is from Matt Newville? Maybe anybody recalls on this talk/slides or recognizes them? Thanks for your help. Have a nice day, Eckhard - Eckhard Bosman [EMAIL PROTECTED] +49 (0)551-39-14441 Raum: E0.104 Institut für Röntgenphysik Friedrich-Hund-Platz 1 37077 Göttingen Germany ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Athena: k-weight=3 in background removal problem
Hi Joseph, I have a book chapter that explains how the different k-weighting affect the chi(k) data produced in the background removal. I'll send it to you directly, so as not to fill up everyone's mail box. Here is the reference for others that might be interested. Kelly, S.D., Hesterberg, D., and Ravel, B., in Analysis of Soils and Minerals Using X-ray Absorption Spectroscopy, (A.L. Ulery and L.R. Drees, Eds.) p. 367. Soil Science Society of America, Madison, WI, USA, 2008. Shelly -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Joseph Washington Sent: Tuesday, July 08, 2008 6:03 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Athena: k-weight=3 in background removal problem Hi Carlo, Since much of our data is located at high k values, it would be an improvement to be using a high k weight in the background removal. Whether or not this will be a vast improvement might be questionable. My main concern is why this occurs for all our Ge edge data across the board, and if this is indicative of an underlying issue in data collection at the beamline or preprocessing. Please see an attached project file containing some scans and a merge. I appreciate the assistance, Joseph Carlo Segre wrote: Hi Joseph: On Mon, 7 Jul 2008, Joseph Washington wrote: Greetings all, I am an APS user and a graduate of XAFS Summer School - class of 2007 :) We have been doing EXAFS analysis on Ge[2]Sb[2]Te[x] thin films. I noticed that at the Ge edge in particular, the k-weight value used in the background removal cannot equal 3, or else the background function no longer follows the data and oscillates wildly and/or it shoots up at the edge energy dominating the plot window. Values of 1 and 2 work fine. Even more puzzling is that this problem is inherent for the Ge edge of data taken over numerous runs, and for various samples (GST-224, GST-225, 226, 227). COuld you tell us why you would like to use a k-weight of 3 in the background removal process? I find that 1 (or 2 sometimes) is sufficient to get a good result. I just checked on a recent data set and I agree that k-weight 1 nd 2 give nearly identical results but that k-weight 3 for the same parameters is slightly different. It would help a lot if you oculd send a project file for us to look at. Carlo -- Joseph Washington Research Assistant Department of Physics North Carolina State University 431 Riddick Hall Raleigh, NC 27695-8202 email: [EMAIL PROTECTED] ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Dodgy Edge Steps
Hi Lachlan, The reason that you want to keep the total absorption less than 3 is because the number of transmitted x-rays becomes small. I=I0 exp(-mu x). So for mu x =3 the number of transmitted x-rays are 5% of the incident x-ray intensity. If you have a lot of x-rays then you can measure spectra with greater total absorption. At most second generation sources we have around 10^6 x-rays /second. That means that only 5 x10^4 x-rays are measured in It for a sample that has a total absorption of 3. Since the statistical noise goes like the square root of N, you will have 5% noise by measuring only 1 second per point, so you will have to measure about 25 sec per point to get usable EXAFS data. As the signal in It becomes smaller, you will find that the oscillatory part of the absorption spectra becomes damped because you can not accurately measure the fluctuations in the transmitted signal. If you have a lot of x-rays and the total absorption is dominated by the element that you measured, your data might be salvageable. Look for a dampening affect. If you see that when comparing to your other data then you are in trouble. I don't know how to reliably fix it. You can use Hephaestus to calculate the number of x-rays per second in It from the voltage and detector gain. Cheers, Shelly From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Stefan Mangold Sent: Monday, April 28, 2008 11:46 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Dodgy Edge Steps Hi, the edge step should be less than 1; the edge step at white line should be not higher than 1.5 and die maximum absorption should not be higher than 2.7 (max. 3) (reason is the signal to noise ratio). The reason for limiting the edge jump are none linearities of your detector systems. So I would not use the data for further analysis. best regards Stefan -- Dr. Stefan Mangold Institut für Synchrotronstrahlung Forschungszentrum Karlsruhe Am 28.04.2008 um 18:27 schrieb LACHLAN MACLEAN: Hi All Long-term lurker, first time poster. I've recently collected some EXAFS data with a large edge step (~3.4) and for some reason didn't pick up on it until it was too late. I've been told that ideally we would want an edge step of 1 and anything above ~1.5-2 is too high. I'm wondering if there is a way to salvage the dataset in order to compare it with EXAFS data that I collected from two other samples (all three are supposed to be synthetic goethite). The first two samples that I want to compare have edge steps of about 0.35. I know Athena allows one to adjust the edge step but wonder how appropriate this is and how much change this would cause the EXAFS data? Trying to adjust the edge step from 3.4 down to ~1 or so seems to be quite a jump. I'm curious whether there is a way to salvage this data rather than wait until the next beamrun. Any help would be appreciated. Cheers Lachlan ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] How to generate the input information for Atom
Hi Fenglong, You can do the next part of the analysis in Artemis. I have a powerpoint tutorial showing the different parts of Artemis on the xafs.org wiki. http://www.xafs.org/Tutorials It is called Basics_of_XAFS_analysis.pdf It is a bit dated now, but the main points are all the same. I recommend Matt's tutorials on that page. Bruce has documentation for Artemis at http://cars9.uchicago.edu/~ravel/software/docs.html And Matt has a data base of crystal structure input files that are already in the correct format for Artemis at http://cars9.uchicago.edu/~newville/adb/ Artemis comes with several working examples that you can find in the distribution package. These links should get you going. Cheers, Shelly From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Fenglong Sun Sent: Monday, November 05, 2007 6:00 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] How to generate the input information for Atom Hi, Bruce, I am working on an experiment of arsenic adsorption on pyrite particles. I have the data of mu(E)~E. I use Anthena to do the Fourier transform. Now I want to know the cordination information of arsenic atom. How can I get the input file for Atom if I want to do the fitting job by using Iffefit package? Thanks! ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Re xanes feff8 sulfur
Hi Eckard, I realize that you have posted a message every month for about 3 months in a row without any reply: Shame on us... I will try to answer some of your questions and maybe that will help to get some discussion going. The energy scale in feff8 is NOT defined as you would expect it to be for determining the absolute energy of an edge. The energy scale in FEFF8 is related to the difference between the energy level of the intersist (potential level inbetween the muffin tins that represent atoms) and the threshold energy level for the excitation of the electron. I realize that this doesn't solve your problem, but hopefully it will spark some discussion. Cheers, Shelly Mon Aug 13 06:00:19 CDT 2007 Does anybody know a person, who has experience respective the topics xanes+feff8 and sulfur K-Edges? I would be very thankful for an answer :-) sincerely yours, Eckhard Bosman Tue Jul 10 10:07:38 CDT 2007 Hello, i have problems with feff-xanes calculations related to pyrite. I try to get the k-edge of sulfur (as absorber) in FeS2. I get the edge at ~2472 eV and i think this is wrong because i get the same energy with gypsum and i think there should be an energyshift related to 2472 eV. My proceeding is as follows: calculate the atomic positions with the asymetric unit from the http://rruff.geo.arizona.edu/AMS/amcsd.php database (Pyrite spacegroup Pa3) respectively http://rruff.geo.arizona.edu/AMS/xtal_data/CIFfiles/00596.cif with powdercell 2.4 feffrun with the feff.inp-file like in the attachment (thanks to Josh Kas for his feff-hints) I started the feff-run on the one hand with 12 atoms (unitcell) and on the other hand with 22 atoms (14x Fe and 8x S in the cube) After this i plotted from xmu.dat the absorbtion mu (column 4) as a function of the energy (column 1). The result is in the attachment too. I don't know why i get everytime the Sulfur-k-edge at the same position (for pyrite or gypsum) respectively without energyshift related to 2472 eV. many thanks for your help :-) Ciao, Eckhard Fri Jun 15 08:48:21 CDT 2007 Hallo @all, (first at all, sorry for my bad english) i'm a student working on my diploma thesis (nexafs/xanes) and my job is to simulate with FEFF 8.4 spectra, for example absorption as a function of energy (mu_(E)). I'm a newbie in this topic and i tried to get the k-edge of Sulfur for the substance gypsum (CaSO4 * 2(H2O)) and pyrite (FeS2). I'm interested in the XANES-range of the spectra not the EXAFS. I get everytime my peaks at ~2472 eV for Sulfur as absorber whatever substance i use (gypsum, pyrite,...). There are no differences with the peak position on the energy-scale or shifts. I'm really confused :-( I think, there should be differences in the spectra... I send you two feff.inp files from my feff-runs. My source is the mineralogy database (http://rruff.geo.arizona.edu/AMS/amcsd.php) where i get the data for the unitcell. Then i put the data in the XtalDraw program to get the positions of the Atoms in Angstrom, by the way i get i nice 3D-View of the unitcell :-). Then i put the values of the positions into feff... I simulated pyrite with 12 atoms and gypsum with 48. I'm appreciative for every help :-) ciao, Eckhard ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] question about Eo and simultaneous fitting
Hi Tony, The approach that I like to take, is to vary the choice of E0 in the background subtraction step so that the chi(k) spectra are well aligned with each other and the theory. Then only one Ezero parameter is needed. Cheers, Shelly -Original Message- From: [EMAIL PROTECTED] [mailto:ifeffit- [EMAIL PROTECTED] On Behalf Of Scott Calvin Sent: Wednesday, February 14, 2007 7:52 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] question about Eo and simultaneous fitting Hi Tony, A quick answer before I try to fight my way through an ice storm to get to work. :) Fitting the three spectra simultaneously makes sense, but if oxidation state is expected to be different, then you really need different E0's. As far as doping, it depends on the details. In some cases, it may require a different E0's, in others, not. Of course, you can try it both ways, and see what the fits think. --Scott Calvin Sarah Lawrence College At 05:04 AM 2/14/2007, you wrote: Hi, first I would like to thank all experienced people answering in this forum!! I have learned really a lot from you. And now my question: Should I fit EXAFS spectra of a doped material and the same material, but oxidized and reduced (three spectra) simultaneously? In my opinion: yes, as I am looking for small differences. Is varying one Eo for the three samples the right approach? I am also wondering, should I vary one Eo for samples with different doping concentrations? ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] question about Eo and simultaneous fitting
Hi Scott, The change in frequency is a bigger affect at high k than the energy shift parameter. The energy shift parameter affects the data more strongly at low k. So I align the data to each other at low k, and then they become out of phase with each other at high k. A similar effect is seen for pressure dependent data where the oxidation state doesn't change but the bond length changes. I also look at how well the data are both aligned to the theory used to describe the data sets independently. The energy shift values should overlap within the uncertainty to justify using a single parameter for them. I suppose that my method might not work for all systems. But if the data are similar enough so that a multiple data set fit has significant overlap in the models used to describe the spectra, then it has worked. Shelly -Original Message- From: [EMAIL PROTECTED] [mailto:ifeffit- [EMAIL PROTECTED] On Behalf Of Scott Calvin Sent: Wednesday, February 14, 2007 9:55 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] question about Eo and simultaneous fitting Hi Shelly, Interesting--I've never tried that method with samples that I expect to differ in oxidation state. If it's differing in oxidation state, the local environment is probably different too...particularly, nearest-neighbor distances should be changed significantly. So how do you align the chi(k) data with each other, when they oscillate at a different frequency? --Scott Calvin Sarah Lawrence College At 10:38 AM 2/14/2007, you wrote: The approach that I like to take, is to vary the choice of E0 in the background subtraction step so that the chi(k) spectra are well aligned with each other and the theory. Then only one Ezero parameter is needed. Cheers, Shelly ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
RE: [Ifeffit] Projekt with the flatten-problem
Hi Jens, I believe the problem is related to the structure in the data before E0. If you choose e0 to be at the beginning of the structure then the normalization is handled better by Athena. Take a look at the attached project file. The first data set with e0 on the edge as you would choose for EXAFS analysis (e1) shows the error that Jens reported. The second data set with a lower value for e0 at the beginning of the structure (e2) gets the job done. 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 [EMAIL PROTECTED] phone: 630-252-7376 -Original Message- From: [EMAIL PROTECTED] [mailto:ifeffit- [EMAIL PROTECTED] On Behalf Of Jens Kruse Sent: Thursday, January 11, 2007 2:38 AM To: Athena mailing List Subject: [Ifeffit] Projekt with the flatten-problem Hi, find attached an example with the flatten-problem. thanks a lot, jens Hi, I have a normalization problem with Athena. If I turn on the flatten option in the background removal section, Athena creates in some of the normalized spectra a step in the pre-edge range. How can I get rid of it? Thanks, jens Flatten.prj Description: Flatten.prj ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
RE: [Ifeffit] Projekt with the flatten-problem
Good going Dave. I think that you are correct. Shelly -Original Message- From: [EMAIL PROTECTED] [mailto:ifeffit- [EMAIL PROTECTED] On Behalf Of Barton, David (DG) Sent: Thursday, January 11, 2007 10:49 AM To: 'XAFS Analysis using Ifeffit' Subject: RE: [Ifeffit] Projekt with the flatten-problem Jens, It appears to me that the E-shift is causing the problems with the step in the pre-edge data. Shelly's data only appears to remove the step because the pre-edge and the extrapolated post-edge plots are nearly parallel. If you adjust the Normalization range in Shelly's data you will see the step appear again. However, if you set the E-shift to zero and reset Eo, pre-edge range, and normalization range (to your liking) you will see that the step is goes away. So the work around would be to subtract the E-shift from your Raw data, then import into Athena and do not use any E-shift. Bruce or Matt may have to comment, but it appears to me that the normalization/flatten routine may not be dealing with the E-shift appropriately. Dave -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Kelly, Shelly D. Sent: Thursday, January 11, 2007 11:11 AM To: XAFS Analysis using Ifeffit Subject: RE: [Ifeffit] Projekt with the flatten-problem Hi Jens, I believe the problem is related to the structure in the data before E0. If you choose e0 to be at the beginning of the structure then the normalization is handled better by Athena. Take a look at the attached project file. The first data set with e0 on the edge as you would choose for EXAFS analysis (e1) shows the error that Jens reported. The second data set with a lower value for e0 at the beginning of the structure (e2) gets the job done. 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 [EMAIL PROTECTED] phone: 630-252-7376 -Original Message- From: [EMAIL PROTECTED] [mailto:ifeffit- [EMAIL PROTECTED] On Behalf Of Jens Kruse Sent: Thursday, January 11, 2007 2:38 AM To: Athena mailing List Subject: [Ifeffit] Projekt with the flatten-problem Hi, find attached an example with the flatten-problem. thanks a lot, jens Hi, I have a normalization problem with Athena. If I turn on the flatten option in the background removal section, Athena creates in some of the normalized spectra a step in the pre-edge range. How can I get rid of it? Thanks, jens ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
RE: [Ifeffit] Is there a physical meaning to a negative SO2
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: [EMAIL PROTECTED] [mailto:ifeffit- [EMAIL PROTECTED] 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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
RE: [Ifeffit] Generating Atom lists using Artemis
--- 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., 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 = 0.3, 0.7,0 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Generating Atom lists using Artemis
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., 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 = 0.3, 0.7,0 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. Cheers, Shelly Pd2Si.cif Description: Pd2Si.cif ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
