Hi everyone, I have the following question: I have a set of spectra collected in transmission with 3 ionization chambers and a standard between 2nd and 3rd ion chambers for calibration, so I know my spectra are nicely calibrated relative to each other. Should I then force Athena(/autobk) to use the same E0 for all of them (e.g. use the atomic value) or let it find E0 independently for each sample? Thanks! Vadim.
Vadim G Palshin schrieb:
Hi everyone, I have the following question: I have a set of spectra collected in transmission with 3 ionization chambers and a standard between 2nd and 3rd ion chambers for calibration, so I know my spectra are nicely calibrated relative to each other. Should I then force Athena(/autobk) to use the same E0 for all of them (e.g. use the atomic value) or let it find E0 independently for each sample? Thanks! Vadim.
Hello, I wrote the message below a few days ago and when I wanted to post it to the mailing list I noticed that Vadim already posed a related question. Sorry for not supplying an answer but to extend the list of questions :( ... Recently I stumled across a behaviour in Athena I did not understand while discussing with a collegue how to choose the right E0 for background subtraction in Athena. I would be glad if I could benefit from the expertise of the members of this mailing-list. The initial question was how to choose a value for E0 when comparing samples with mixtures and the measurements of the pure compounds (e.g. iron, iron-oxide and a sample containing a mixture of both). Usually in this case I set E0 to the atomic value for all samples (Assuming I can be sure that the monochromator was calibrated to return a correct absolute energy. Otherwise I do an appropriate energy-calibration with reference to a standard measured at the same time before entering Athena). I do that to ensure a uniform background subtraction for all samples. However, for a system of e.g. Se, RuSe2 and a mixture of both, the atomic value E0 can be quite far away from the inflection point of the RuSe2- and mixture-samples. So the first question would be: is it better to use the same E0 for all samples or to somehow adjust the E0 to the inflection point of the specific sample? In this context my idea of the algorithm of background subtraction was that a shift of E0 could be completely compensated for by appropriatly shifting all other parameters in the backward direction. E.g. when shifting E0 by 4 eV I should end with the same FT when shifting the values for pre-edge range, normalization range, spline range and k-range by the same amount. However, a test revealed that only the pre-edge lines and post-edge lines are identical. The background splines are different and the FTs differ quite significantly from each other. Is my general assumption wrong? Another question (more cosmetic) concerns the use of 'E0' and 'E shift' as it is irrelevant which parameter to adjust to achieve an energy shift. Is it a good idea to set E0 always to the atomic value and use 'E shift' for entering the offset? Actually this is the way I prefer to do it although Athena initially does not set 'E shift'. I also have a kind of feature request in this context and would be interested if others would also benefit from it: for some samples the initial value Athena picks for E0 is obviously inadequat, e.g. when it chooses a prepeak as inflection point. As a consequence the parameters for background subtraction are also inadequate. After choosing a right value for E0 a new feature could be: "automatically adjust background parameters with regard to the current E0", so one could still benefit from Athenas auto-function. Usually I adjust these parameters anyway but it would simplify doing a quick first look at the data. Thanks for any help, Gerrit -- Gerrit Schmithals Hahn-Meitner-Institute Berlin
Hi Gerrit, My web page has a couple of examples that I think you will find helpful. Take a look at http://www.mesg.anl.gov/Skelly.html . The "Basics of EXAFS data analysis 2004" presentation and the tutorial on background removal for MoO3 will answer most of your questions. The alignment of measured spectra for EXAFS analysis can be different than the alignment of spectra for XANES analysis. My presentations address the issue of alignment for EXAFS analysis. Briefly, The important consideration in EXAFS analysis is aligning the chi(k) data to each other to get a consistent background and aligning the data to the theory. If the different spectra have a similar edge shape then a consistent background removal can be achieved by aligning the spectra relative to each other and choosing exactly the same bkg parameters for all. Go into the align spectra menu, choose the first spectra as the reference and then align all the other spectra to the first spectra. Once that is done go back to the background removal page. Make the background the way you want for the first spectra and then right click on the "background parameters" heading and set those parameters to all the spectra. Then compare the chi(k) spectra with a low k-weight so you can see if they are aligned (spectra should cross zero at the same k-value). Sometimes I need to tweak the value for E0 by ~ 1eV or so to get them exactly the same. BTW, I have a poster at the EXAFS conference later this month about these issues. I will put the poster on my web page when it is done... Good luck 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@anl.gov phone: 630-252-7376 -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Gerrit Schmithals Sent: Thursday, June 29, 2006 8:48 AM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] Right way of choosing E0 in Athena Vadim G Palshin schrieb:
Hi everyone, I have the following question: I have a set of spectra collected in transmission with 3 ionization chambers and a standard between 2nd and 3rd ion chambers for calibration, so I know my spectra are nicely calibrated relative to each other. Should I then force Athena(/autobk) to use the same E0 for all of them (e.g. use the atomic value) or let it find E0 independently for each sample? Thanks! Vadim.
Hello, I wrote the message below a few days ago and when I wanted to post it to the mailing list I noticed that Vadim already posed a related question. Sorry for not supplying an answer but to extend the list of questions :( ... Recently I stumled across a behaviour in Athena I did not understand while discussing with a collegue how to choose the right E0 for background subtraction in Athena. I would be glad if I could benefit from the expertise of the members of this mailing-list. The initial question was how to choose a value for E0 when comparing samples with mixtures and the measurements of the pure compounds (e.g. iron, iron-oxide and a sample containing a mixture of both). Usually in this case I set E0 to the atomic value for all samples (Assuming I can be sure that the monochromator was calibrated to return a correct absolute energy. Otherwise I do an appropriate energy-calibration with reference to a standard measured at the same time before entering Athena). I do that to ensure a uniform background subtraction for all samples. However, for a system of e.g. Se, RuSe2 and a mixture of both, the atomic value E0 can be quite far away from the inflection point of the RuSe2- and mixture-samples. So the first question would be: is it better to use the same E0 for all samples or to somehow adjust the E0 to the inflection point of the specific sample? In this context my idea of the algorithm of background subtraction was that a shift of E0 could be completely compensated for by appropriatly shifting all other parameters in the backward direction. E.g. when shifting E0 by 4 eV I should end with the same FT when shifting the values for pre-edge range, normalization range, spline range and k-range by the same amount. However, a test revealed that only the pre-edge lines and post-edge lines are identical. The background splines are different and the FTs differ quite significantly from each other. Is my general assumption wrong? Another question (more cosmetic) concerns the use of 'E0' and 'E shift' as it is irrelevant which parameter to adjust to achieve an energy shift. Is it a good idea to set E0 always to the atomic value and use 'E shift' for entering the offset? Actually this is the way I prefer to do it although Athena initially does not set 'E shift'. I also have a kind of feature request in this context and would be interested if others would also benefit from it: for some samples the initial value Athena picks for E0 is obviously inadequat, e.g. when it chooses a prepeak as inflection point. As a consequence the parameters for background subtraction are also inadequate. After choosing a right value for E0 a new feature could be: "automatically adjust background parameters with regard to the current E0", so one could still benefit from Athenas auto-function. Usually I adjust these parameters anyway but it would simplify doing a quick first look at the data. Thanks for any help, Gerrit -- Gerrit Schmithals Hahn-Meitner-Institute Berlin _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Vadim, Gerrit, For Vadim's question:
I have the following question: I have a set of spectra collected in transmission with 3 ionization chambers and a standard between 2nd and 3rd ion chambers for calibration, so I know my spectra are nicely calibrated relative to each other. Should I then force Athena(/autobk) to use the same E0 for all of them (e.g. use the atomic value) or let it find E0 independently for each sample? Thanks! Vadim.
Since you know the spectra are well calibrated relative to one another, I would use a single E0 for all background subtractions. In such a situation, I tend to play with the background parameters for one of the spectra and then apply these background parameters to all other spectra. The most important parameters are typically: E0, rbkg, kmin, kweight, and the high-k clamp. For Gerrit's questions:
The initial question was how to choose a value for E0 when comparing samples with mixtures and the measurements of the pure compounds (e.g. iron, iron-oxide and a sample containing a mixture of both). Usually in this case I set E0 to the atomic value for all samples (Assuming I can be sure that the monochromator was calibrated to return a correct absolute energy. Otherwise I do an appropriate energy-calibration with reference to a standard measured at the same time before entering Athena). I do that to ensure a uniform background subtraction for all samples. However, for a system of e.g. Se, RuSe2 and a mixture of both, the atomic value E0 can be quite far away from the inflection point of the RuSe2- and mixture-samples. So the first question would be: is it better to use the same E0 for all samples or to somehow adjust the E0 to the inflection point of the specific sample?
I think there are two different answers (yes and no) depending on how you are treating the data: For linear combination fitting (XANES or EXAFS), I would choose a consistent absolute E0 for all data sets (after appropriate shifts to align the data). For EXAFS analysis with Feff, I would not worry about choosing a consistent E0 -- each Feff calculation puts in an assumption about E0 that has to be refined away anyway.
In this context my idea of the algorithm of background subtraction was that a shift of E0 could be completely compensated for by appropriatly shifting all other parameters in the backward direction. E.g. when shifting E0 by 4 eV I should end with the same FT when shifting the values for pre-edge range, normalization range, spline range and k-range by the same amount. However, a test revealed that only the pre-edge lines and post-edge lines are identical. The background splines are different and the FTs differ quite significantly from each other. Is my general assumption wrong?
I think so (that your general assumption is wrong). E0 sets the definition of k=0, so can have a large impact on the FT and the background subtraction.
Another question (more cosmetic) concerns the use of 'E0' and 'E shift' as it is irrelevant which parameter to adjust to achieve an energy shift. Is it a good idea to set E0 always to the atomic value and use 'E shift' for entering the offset? Actually this is the way I prefer to do it although Athena initially does not set 'E shift'. I also have a kind of feature request in this context and would be interested if others would also benefit from it: for some samples the initial value Athena picks for E0 is obviously inadequat, e.g. when it chooses a prepeak as inflection point. As a consequence the parameters for background subtraction are also inadequate. After choosing a right value for E0 a new feature could be: "automatically adjust background parameters with regard to the current E0", so one could still benefit from Athenas auto-function. Usually I adjust these parameters anyway but it would simplify doing a quick first look at the data.
I'm not sure I understand all that. For non-metals, I'd ignore the "atomic value", since it's wrong (in some sense, that's why we're doing XAFS). For what it's worth, I only use the Energy Shift to align spectra. And, yes, for spectra with large pre-edge peaks, the guessed e0 can be wrong: if you have ideas for how to improve this situation, let me know! But once e0 is set, the rest of athena's background subtraction should still be automatic. Is it not, or am I not understanding something? --Matt
participants (4)
-
Gerrit Schmithals -
Kelly, Shelly D. -
Matt Newville -
Vadim G Palshin