Athena (Question about LC fitting)
Hi, Related to this issue, I have a question about whether alignment is necessary for LCF when the oxidation state among sample and standards is different. I used to align spectra of samples and standards before LCF while handling P. However, I got confused about Se. For Se speciation, I prepared six Se species with oxidation state of -2 (FeSe), 0 (elemental Se), 0 (seleno-cystine), 0 (seleno-methionine), 4 (selenite), and 6 (selenate) to fit samples collected from sediments and biofilms. I am wondering whether the shift of spectra due to the alignment would make standards mis-fit spectral features of samples. Thank you so much for the help! Yu-Ting Liu Yu-Ting (Lusia) Liu Postdoctoral Associate Duke University Civil and Environmental Engineering Durham, NC, 27708-0287 ------------------------------------------------------------------------------- Belay, I am CCing my response to the Ifeffit Mailing List, which is the appropriate venue for questions about the use fo the software. I encourage you to subscribe to and use the mailing list. On Tuesday, May 10, 2011 08:50:10 am you wrote:
Dear Dr. Ravel, I am doing my PhD in title with identication of Fe-phases in cement hydrates. I am using Athena for LC fitting. I use EXAFS spectra for the fittings. My question is before LC fitting of EXAFS spectra , do I need to calibrate the energy? I have normlized and alligned the spectra very well. The problem is data calibration, when I calibrate the spectra, the energy shifts and it destroys the fitting. Can you please give a clue why this happens or do I make a mistake on the procedure? Thanks so much for your cooperation.
Alignment puts a group of spectra on the same relative energy scale. It is often necessary to do an explicit alignment when working at a beamline with an unstable and unencoded monochromator, as might be found at some older beamlines. Calibration intends to put a single spectrum on the correct absolute energy scale. That is, if you know what point in a spectrum represents a particular absolute energy, then calibration does as I said. LCF requires that the ensemble of data and standards all be aligned -- i.e. put on the same relative energy axis. Once that is done, you can proceed with LCF analysis. LCF does not require that the data be calibrated, only that they be aligned. That is, LCF requires that all the data+standards be on the same relative energy axis, but does not require that that energy axis be calibrated. The reason that is so is because LCF fitting is an abstract, numerical function that treats one data set (the "data") as a linear combination of two or more other data sets (the "standards"). No part of that mathematical process requires knowledge of the species of the absorber atom. Indeed, LCF does not require that the x-axis represent energy, only that it be the same for all data+standards. That said, the interpretation of your data might be easier to consider and easier to present in publcation if your data is calibrated. For instance, the Xray Data Booklet tells us that copper metal has an edge at 8979 eV. Calibration is the process of transforming your data such that its edge does, in fact, happen at 8979 eV. In Athena, using the calibration dialog both does an energy shift and sets the E0 value to 8979. If you want to calibrate your data as well as aligning your data, I find it less confusing to do the calibration first. I believe that the procedures can be commutative, but calibrating after aligning is confusing to me and more prone to error for me. Someone else might give you different advice. Finally, remember that calibration requires actual knowledge (as opposed to some assumption) about what point in a spectrum represents a particular absolute energy value. While you might reasonably assign the first big peak in the first derivative of copper metal to 8979 eV, you cannot correctly assign the first big peak in the first derivative of copper oxide to 8979 eV due to the upwards shift in threshold energy in the oxide. HTH, B
It is really important to have the data for the "unknown" sample and for "standards" correctly aligned in energy. That means that all of them should be measured in an experiment with the same sample located in the "reference" position between the transmitted and reference beam detectors. The absorption coefficients of all the "reference" data should be aligned together in energy. That will ensure that the shifts between the actual data are real and caused by the oxidation state differences. It is sometimes called "alignment in absolute energy" but it simply means that the shifts are real. When this is taken care of, you can align the standards to the unknown using LCF, and do not float the energy origin corrections (delta E0) of any of the samples used in LCF (either data or standards) since they were already set correctly by experimental conditions. Anatoly ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov on behalf of Yu-Ting Liu Sent: Sun 5/15/2011 1:45 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Athena (Question about LC fitting) Hi, Related to this issue, I have a question about whether alignment is necessary for LCF when the oxidation state among sample and standards is different. I used to align spectra of samples and standards before LCF while handling P. However, I got confused about Se. For Se speciation, I prepared six Se species with oxidation state of -2 (FeSe), 0 (elemental Se), 0 (seleno-cystine), 0 (seleno-methionine), 4 (selenite), and 6 (selenate) to fit samples collected from sediments and biofilms. I am wondering whether the shift of spectra due to the alignment would make standards mis-fit spectral features of samples. Thank you so much for the help! Yu-Ting Liu Yu-Ting (Lusia) Liu Postdoctoral Associate Duke University Civil and Environmental Engineering Durham, NC, 27708-0287 ------------------------------------------------------------------------------- Belay, I am CCing my response to the Ifeffit Mailing List, which is the appropriate venue for questions about the use fo the software. I encourage you to subscribe to and use the mailing list. On Tuesday, May 10, 2011 08:50:10 am you wrote:
Dear Dr. Ravel, I am doing my PhD in title with identication of Fe-phases in cement hydrates. I am using Athena for LC fitting. I use EXAFS spectra for the fittings. My question is before LC fitting of EXAFS spectra , do I need to calibrate the energy? I have normlized and alligned the spectra very well. The problem is data calibration, when I calibrate the spectra, the energy shifts and it destroys the fitting. Can you please give a clue why this happens or do I make a mistake on the procedure? Thanks so much for your cooperation.
Alignment puts a group of spectra on the same relative energy scale. It is often necessary to do an explicit alignment when working at a beamline with an unstable and unencoded monochromator, as might be found at some older beamlines. Calibration intends to put a single spectrum on the correct absolute energy scale. That is, if you know what point in a spectrum represents a particular absolute energy, then calibration does as I said. LCF requires that the ensemble of data and standards all be aligned -- i.e. put on the same relative energy axis. Once that is done, you can proceed with LCF analysis. LCF does not require that the data be calibrated, only that they be aligned. That is, LCF requires that all the data+standards be on the same relative energy axis, but does not require that that energy axis be calibrated. The reason that is so is because LCF fitting is an abstract, numerical function that treats one data set (the "data") as a linear combination of two or more other data sets (the "standards"). No part of that mathematical process requires knowledge of the species of the absorber atom. Indeed, LCF does not require that the x-axis represent energy, only that it be the same for all data+standards. That said, the interpretation of your data might be easier to consider and easier to present in publcation if your data is calibrated. For instance, the Xray Data Booklet tells us that copper metal has an edge at 8979 eV. Calibration is the process of transforming your data such that its edge does, in fact, happen at 8979 eV. In Athena, using the calibration dialog both does an energy shift and sets the E0 value to 8979. If you want to calibrate your data as well as aligning your data, I find it less confusing to do the calibration first. I believe that the procedures can be commutative, but calibrating after aligning is confusing to me and more prone to error for me. Someone else might give you different advice. Finally, remember that calibration requires actual knowledge (as opposed to some assumption) about what point in a spectrum represents a particular absolute energy value. While you might reasonably assign the first big peak in the first derivative of copper metal to 8979 eV, you cannot correctly assign the first big peak in the first derivative of copper oxide to 8979 eV due to the upwards shift in threshold energy in the oxide. HTH, B _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
I meant "fit" the standards to the unknown, and I also noticed that Bruce had already replied to the same question below. Anatoly ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov on behalf of Frenkel, Anatoly Sent: Sun 5/15/2011 2:34 PM To: XAFS Analysis using Ifeffit Subject: RE: [Ifeffit] Athena (Question about LC fitting) It is really important to have the data for the "unknown" sample and for "standards" correctly aligned in energy. That means that all of them should be measured in an experiment with the same sample located in the "reference" position between the transmitted and reference beam detectors. The absorption coefficients of all the "reference" data should be aligned together in energy. That will ensure that the shifts between the actual data are real and caused by the oxidation state differences. It is sometimes called "alignment in absolute energy" but it simply means that the shifts are real. When this is taken care of, you can align the standards to the unknown using LCF, and do not float the energy origin corrections (delta E0) of any of the samples used in LCF (either data or standards) since they were already set correctly by experimental conditions. Anatoly ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov on behalf of Yu-Ting Liu Sent: Sun 5/15/2011 1:45 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Athena (Question about LC fitting) Hi, Related to this issue, I have a question about whether alignment is necessary for LCF when the oxidation state among sample and standards is different. I used to align spectra of samples and standards before LCF while handling P. However, I got confused about Se. For Se speciation, I prepared six Se species with oxidation state of -2 (FeSe), 0 (elemental Se), 0 (seleno-cystine), 0 (seleno-methionine), 4 (selenite), and 6 (selenate) to fit samples collected from sediments and biofilms. I am wondering whether the shift of spectra due to the alignment would make standards mis-fit spectral features of samples. Thank you so much for the help! Yu-Ting Liu Yu-Ting (Lusia) Liu Postdoctoral Associate Duke University Civil and Environmental Engineering Durham, NC, 27708-0287 ------------------------------------------------------------------------------- Belay, I am CCing my response to the Ifeffit Mailing List, which is the appropriate venue for questions about the use fo the software. I encourage you to subscribe to and use the mailing list. On Tuesday, May 10, 2011 08:50:10 am you wrote:
Dear Dr. Ravel, I am doing my PhD in title with identication of Fe-phases in cement hydrates. I am using Athena for LC fitting. I use EXAFS spectra for the fittings. My question is before LC fitting of EXAFS spectra , do I need to calibrate the energy? I have normlized and alligned the spectra very well. The problem is data calibration, when I calibrate the spectra, the energy shifts and it destroys the fitting. Can you please give a clue why this happens or do I make a mistake on the procedure? Thanks so much for your cooperation.
Alignment puts a group of spectra on the same relative energy scale. It is often necessary to do an explicit alignment when working at a beamline with an unstable and unencoded monochromator, as might be found at some older beamlines. Calibration intends to put a single spectrum on the correct absolute energy scale. That is, if you know what point in a spectrum represents a particular absolute energy, then calibration does as I said. LCF requires that the ensemble of data and standards all be aligned -- i.e. put on the same relative energy axis. Once that is done, you can proceed with LCF analysis. LCF does not require that the data be calibrated, only that they be aligned. That is, LCF requires that all the data+standards be on the same relative energy axis, but does not require that that energy axis be calibrated. The reason that is so is because LCF fitting is an abstract, numerical function that treats one data set (the "data") as a linear combination of two or more other data sets (the "standards"). No part of that mathematical process requires knowledge of the species of the absorber atom. Indeed, LCF does not require that the x-axis represent energy, only that it be the same for all data+standards. That said, the interpretation of your data might be easier to consider and easier to present in publcation if your data is calibrated. For instance, the Xray Data Booklet tells us that copper metal has an edge at 8979 eV. Calibration is the process of transforming your data such that its edge does, in fact, happen at 8979 eV. In Athena, using the calibration dialog both does an energy shift and sets the E0 value to 8979. If you want to calibrate your data as well as aligning your data, I find it less confusing to do the calibration first. I believe that the procedures can be commutative, but calibrating after aligning is confusing to me and more prone to error for me. Someone else might give you different advice. Finally, remember that calibration requires actual knowledge (as opposed to some assumption) about what point in a spectrum represents a particular absolute energy value. While you might reasonably assign the first big peak in the first derivative of copper metal to 8979 eV, you cannot correctly assign the first big peak in the first derivative of copper oxide to 8979 eV due to the upwards shift in threshold energy in the oxide. HTH, B _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (2)
-
Frenkel, Anatoly -
Yu-Ting Liu