RE: [Ifeffit] Phase corrected Fourier transforms
Anatoly is correct that the phase correction cannot work for all shells in inhomogeneous systems. However, it's *always* possible to remove the central atom phase shift 2 delta_c which often dominates the phase correction. Second, if one corrects by the 1st nn phase, delta_1, the dominant near neighbor shell will appear at the correct distance. The correction is not right for subsequent shells but the error is given by a phase difference delta R = <(1/2)(d/dk) [delta_n-delta_1]> This correction is typically order 0.1 Ang and usually smaller than the typical shift of about 0.3 - 0.4 Ang in uncorrected FT peaks. The upshot is that the phase corrected FT can be correct for the first shell which often dominates the FT and generally better than uncorrected FTs. Corrective lenses for vision aren't perfect either at all distances, but it's hard to argue that it's preferable not to use them for that reason. J. Rehr On Sat, 23 Sep 2006, Anatoly Frenkel wrote: My 0.533 Rouble: In my experience with some Mn oxides, the Mn-O FT magnitude peak's position is 0.5 A lower its corresponding 1NN bond length, while the Mn-Mn are 0.3 A lower than their bond lenghts. Thus, it would be misleading for this and other similar compounds to apply theoretical phase correction of the 1NN to the entire data, as it will shift only one peak correctly. Anatoly -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Matthew Marcus Sent: Saturday, September 23, 2006 4:14 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Phase corrected Fourier transforms OK, I have to put in my US$0.02/e0.02. The phase correction can't mean much if the scattering atoms are different, which is usually the case. If the scattering atoms are very heavy, then the phase correction has a kink in it which could cause strange shapes if applied to light-atom shells. I've played with this phase correction and amplitude correction, while I was at it, and not been very impressed. One place where it might be useful is in the aforementioned case of heavy and light scatterers. If you use the correction for one of these, then the corresponding shells sharpen and the other ones blur out, so you can get a rough idea of who's who. I suspect this works better if you do the amplitude as well. A related technique is to use model compounds+FEFF to get 'semi-empirical' amps and phases which include all the artifacts of the experiment. Suppose, for instance, that you're looking at Cu in a matrix of Fe, and you have data for Cu metal but not for any known Cu->Fe scattering pair. You can synthesize a 'semi-empirical' Cu->Fe phase and amp like this: phi(Cu->Fe) = phi_exp(Cu->Cu)+(phi_theor(Cu->Fe)-phi_theor(Cu->Cu)) amp(Cu->Fe) = amp_exp(Cu->Cu)*amp_theor(Cu->Fe)/amp_theor(Cu->Cu) If you don't want to do this for modeling, you can use this method for comparing two spectra which you think might be alike except for the central atom, by "correcting" one spectrum with the difference to make it comparable to the other. Another aspect to this whole thing is that people are very used to uncorrected FT's and are aware that you have to add 0.3-0.4A to the distances. If you show only corrected FT's, I wonder if that will be satisfying to the audience. mam - Original Message - From: "John J. Rehr" <[EMAIL PROTECTED]> To: "XAFS Analysis using Ifeffit" Cc: "John J. Rehr" <[EMAIL PROTECTED]> Sent: Saturday, September 23, 2006 7:18 AM Subject: Re: [Ifeffit] Phase corrected Fourier transforms Dear Juan Antonio, I personally feel that adding phase correction to the XAFS FT is highly desirable, and I encouraged its implementation in Athena. The reasons are the following: 1) Peaks in non-phase corrected FT are substantially in error. 2) The non-linearity of the phase shifts in high-Z materials leads to multiple-peaks, thus blurring the FT. 3) Theoretical phase shifts are good enough that adding phase correction tends to correct the peak positions and the problems due to non-linearities. 4) Adding phase correction does no-harm to the fits. That is, one gets the same results whether or not phase correction is included. 5) Adding phase correction gives a FT which can be more easily interpreted "by eye", that is the peaks have a more physical interpretation. On the contrary, non-phase corrected FTs can be mis-interpreted. Overall, my view is that the phase correction is like a prescription lens which gives a sharper image. While the image may not be perfect, at least it's generally much superior to the non-phase corrected FT. J. Rehr On Fri, 22 Sep 2006, Juan Antonio [iso-8859-1] Maci? Agull? wrote: Hi all, I have read Phase corrected Fourier transforms in Athena manual and now I have a big doubt, ?phase correction or not in a publication? I have read also that this correction is different (more complete) in Artemis and I am not sure if I should correct also in Artemis and which path should I use and why
RE: [Ifeffit] Phase corrected Fourier transforms
My 0.533 Rouble: In my experience with some Mn oxides, the Mn-O FT magnitude peak's position is 0.5 A lower its corresponding 1NN bond length, while the Mn-Mn are 0.3 A lower than their bond lenghts. Thus, it would be misleading for this and other similar compounds to apply theoretical phase correction of the 1NN to the entire data, as it will shift only one peak correctly. Anatoly -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Matthew Marcus Sent: Saturday, September 23, 2006 4:14 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Phase corrected Fourier transforms OK, I have to put in my US$0.02/e0.02. The phase correction can't mean much if the scattering atoms are different, which is usually the case. If the scattering atoms are very heavy, then the phase correction has a kink in it which could cause strange shapes if applied to light-atom shells. I've played with this phase correction and amplitude correction, while I was at it, and not been very impressed. One place where it might be useful is in the aforementioned case of heavy and light scatterers. If you use the correction for one of these, then the corresponding shells sharpen and the other ones blur out, so you can get a rough idea of who's who. I suspect this works better if you do the amplitude as well. A related technique is to use model compounds+FEFF to get 'semi-empirical' amps and phases which include all the artifacts of the experiment. Suppose, for instance, that you're looking at Cu in a matrix of Fe, and you have data for Cu metal but not for any known Cu->Fe scattering pair. You can synthesize a 'semi-empirical' Cu->Fe phase and amp like this: phi(Cu->Fe) = phi_exp(Cu->Cu)+(phi_theor(Cu->Fe)-phi_theor(Cu->Cu)) amp(Cu->Fe) = amp_exp(Cu->Cu)*amp_theor(Cu->Fe)/amp_theor(Cu->Cu) If you don't want to do this for modeling, you can use this method for comparing two spectra which you think might be alike except for the central atom, by "correcting" one spectrum with the difference to make it comparable to the other. Another aspect to this whole thing is that people are very used to uncorrected FT's and are aware that you have to add 0.3-0.4A to the distances. If you show only corrected FT's, I wonder if that will be satisfying to the audience. mam - Original Message - From: "John J. Rehr" <[EMAIL PROTECTED]> To: "XAFS Analysis using Ifeffit" Cc: "John J. Rehr" <[EMAIL PROTECTED]> Sent: Saturday, September 23, 2006 7:18 AM Subject: Re: [Ifeffit] Phase corrected Fourier transforms Dear Juan Antonio, I personally feel that adding phase correction to the XAFS FT is highly desirable, and I encouraged its implementation in Athena. The reasons are the following: 1) Peaks in non-phase corrected FT are substantially in error. 2) The non-linearity of the phase shifts in high-Z materials leads to multiple-peaks, thus blurring the FT. 3) Theoretical phase shifts are good enough that adding phase correction tends to correct the peak positions and the problems due to non-linearities. 4) Adding phase correction does no-harm to the fits. That is, one gets the same results whether or not phase correction is included. 5) Adding phase correction gives a FT which can be more easily interpreted "by eye", that is the peaks have a more physical interpretation. On the contrary, non-phase corrected FTs can be mis-interpreted. Overall, my view is that the phase correction is like a prescription lens which gives a sharper image. While the image may not be perfect, at least it's generally much superior to the non-phase corrected FT. J. Rehr On Fri, 22 Sep 2006, Juan Antonio [iso-8859-1] Maciá Agulló wrote: > > > Hi all, > > I have read Phase corrected Fourier transforms in Athena manual and now > I have a big doubt, ¿phase correction or not in a publication? > > I have read also that this correction is different (more complete) in > Artemis and I am not sure if I should correct also in Artemis and which > path should I use and why. > > I saw many papers dealing with EXAFS fits and they showed a "calculated" > bond distance, I think it is: d = Reff + deltaR, right? > > I also ask for a paper where I can find that deltaE is ok (even for > high-Z backscatterers) if deltaE < 10eV. > > I have high correlations between ss and SO2, and deltaR and deltaE. I > tried different fits but I can not eliminate them, then...is the fit > wrong? > > Sorry for these easy questions but I am a novice in XAFS. > > Thank you very much. > > Best regards, > JA > > ___ > 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] Phase corrected Fourier transforms
OK, I have to put in my US$0.02/e0.02. The phase correction can't mean much if the scattering atoms are different, which is usually the case. If the scattering atoms are very heavy, then the phase correction has a kink in it which could cause strange shapes if applied to light-atom shells. I've played with this phase correction and amplitude correction, while I was at it, and not been very impressed. One place where it might be useful is in the aforementioned case of heavy and light scatterers. If you use the correction for one of these, then the corresponding shells sharpen and the other ones blur out, so you can get a rough idea of who's who. I suspect this works better if you do the amplitude as well. A related technique is to use model compounds+FEFF to get 'semi-empirical' amps and phases which include all the artifacts of the experiment. Suppose, for instance, that you're looking at Cu in a matrix of Fe, and you have data for Cu metal but not for any known Cu->Fe scattering pair. You can synthesize a 'semi-empirical' Cu->Fe phase and amp like this: phi(Cu->Fe) = phi_exp(Cu->Cu)+(phi_theor(Cu->Fe)-phi_theor(Cu->Cu)) amp(Cu->Fe) = amp_exp(Cu->Cu)*amp_theor(Cu->Fe)/amp_theor(Cu->Cu) If you don't want to do this for modeling, you can use this method for comparing two spectra which you think might be alike except for the central atom, by "correcting" one spectrum with the difference to make it comparable to the other. Another aspect to this whole thing is that people are very used to uncorrected FT's and are aware that you have to add 0.3-0.4A to the distances. If you show only corrected FT's, I wonder if that will be satisfying to the audience. mam - Original Message - From: "John J. Rehr" <[EMAIL PROTECTED]> To: "XAFS Analysis using Ifeffit" Cc: "John J. Rehr" <[EMAIL PROTECTED]> Sent: Saturday, September 23, 2006 7:18 AM Subject: Re: [Ifeffit] Phase corrected Fourier transforms Dear Juan Antonio, I personally feel that adding phase correction to the XAFS FT is highly desirable, and I encouraged its implementation in Athena. The reasons are the following: 1) Peaks in non-phase corrected FT are substantially in error. 2) The non-linearity of the phase shifts in high-Z materials leads to multiple-peaks, thus blurring the FT. 3) Theoretical phase shifts are good enough that adding phase correction tends to correct the peak positions and the problems due to non-linearities. 4) Adding phase correction does no-harm to the fits. That is, one gets the same results whether or not phase correction is included. 5) Adding phase correction gives a FT which can be more easily interpreted "by eye", that is the peaks have a more physical interpretation. On the contrary, non-phase corrected FTs can be mis-interpreted. Overall, my view is that the phase correction is like a prescription lens which gives a sharper image. While the image may not be perfect, at least it's generally much superior to the non-phase corrected FT. J. Rehr On Fri, 22 Sep 2006, Juan Antonio [iso-8859-1] Maciá Agulló wrote: Hi all, I have read Phase corrected Fourier transforms in Athena manual and now I have a big doubt, ¿phase correction or not in a publication? I have read also that this correction is different (more complete) in Artemis and I am not sure if I should correct also in Artemis and which path should I use and why. I saw many papers dealing with EXAFS fits and they showed a "calculated" bond distance, I think it is: d = Reff + deltaR, right? I also ask for a paper where I can find that deltaE is ok (even for high-Z backscatterers) if deltaE < 10eV. I have high correlations between ss and SO2, and deltaR and deltaE. I tried different fits but I can not eliminate them, then...is the fit wrong? Sorry for these easy questions but I am a novice in XAFS. Thank you very much. Best regards, JA ___ 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] Phase corrected Fourier transforms
Dear Juan Antonio, I personally feel that adding phase correction to the XAFS FT is highly desirable, and I encouraged its implementation in Athena. The reasons are the following: 1) Peaks in non-phase corrected FT are substantially in error. 2) The non-linearity of the phase shifts in high-Z materials leads to multiple-peaks, thus blurring the FT. 3) Theoretical phase shifts are good enough that adding phase correction tends to correct the peak positions and the problems due to non-linearities. 4) Adding phase correction does no-harm to the fits. That is, one gets the same results whether or not phase correction is included. 5) Adding phase correction gives a FT which can be more easily interpreted "by eye", that is the peaks have a more physical interpretation. On the contrary, non-phase corrected FTs can be mis-interpreted. Overall, my view is that the phase correction is like a prescription lens which gives a sharper image. While the image may not be perfect, at least it's generally much superior to the non-phase corrected FT. J. Rehr On Fri, 22 Sep 2006, Juan Antonio [iso-8859-1] Maci? Agull? wrote: Hi all, I have read Phase corrected Fourier transforms in Athena manual and now I have a big doubt, ?phase correction or not in a publication? I have read also that this correction is different (more complete) in Artemis and I am not sure if I should correct also in Artemis and which path should I use and why. I saw many papers dealing with EXAFS fits and they showed a "calculated" bond distance, I think it is: d = Reff + deltaR, right? I also ask for a paper where I can find that deltaE is ok (even for high-Z backscatterers) if deltaE < 10eV. I have high correlations between ss and SO2, and deltaR and deltaE. I tried different fits but I can not eliminate them, then...is the fit wrong? Sorry for these easy questions but I am a novice in XAFS. Thank you very much. Best regards, JA ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
