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

calibration/alignment
by ornella smila castro 14 Oct '10

14 Oct '10

Hi everyone, I am trying to do some data processing with Athena but I am already stuck at the first step. The thing is: I read the worked example section of the "Athena's user guide" and on the example on the iron foil, it is mentioned to calibrate the data at the right energy (until here evrything is fine) but then it is said to align the data. Can anyone explain to me what does "alignment" exactly means, and what is the aim of "aligning the data". The data that I have collected were through a channel through which a solution flow (~200 microliters/hr) so I am not convinced that alignment makes sense. Many thanks, Ornel

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Re: [Ifeffit] calibration/alignment
by Scott Calvin 14 Oct '10

14 Oct '10

Hi Ornel, Alignment is used to compensate for monochromators that do not maintain stable energy calibration between scans. In conventional measurements, you'll generally have several scans that are supposed to be of the same sample under identical conditions, and those scans may need to be aligned with each other. That is not the case for a time series, which is what I think you are saying you have. So in a time series, how do you compensate for any energy drift of the monochromator? If you are recording a simultaneous reference spectrum, you can align the reference spectra to each other. (Athena automatically will shift the sample spectra by the same amount that the reference spectra are shifted.) If you have a time series but don't have a simultaneous reference spectra, it becomes tougher. If you collected a reference spectrum before and after the time series, you could try to interpolate any shift that's seen, although that's dicey; shifts sometimes occur in jumps. But if there's no shift, you're probably OK! If you have a time series and no reference at all, or a reference only before the series, you're out of luck. You're relying then on the assumption of energy stability, which on some beamlines might be OK...but it is best to confirm that by at least measuring a reference before and after. --Scott Calvin Sarah Lawrence College On Oct 14, 2010, at 2:46 AM, ornella smila castro wrote: > Hi everyone, > > I am trying to do some data processing with Athena but I am already > stuck at the first step. The thing is: I read the worked example > section of the "Athena's user guide" and on the example on the iron > foil, it is mentioned to calibrate the data at the right energy > (until here evrything is fine) but then it is said to align the > data. Can anyone explain to me what does "alignment" exactly means, > and what is the aim of "aligning the data". The data that I have > collected were through a channel through which a solution flow (~200 > microliters/hr) so I am not convinced that alignment makes sense. > > Many thanks, > Ornel > <ATT00001..txt>

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MPSE
by Mehmet Kaya 13 Oct '10

13 Oct '10

Dear all, i want to run FEFF with the many pole self energy MPSE. In the documentation to FEFF9 is written that I have to use the formula detailed in 'EpsInvFormula.ps' to calculate the optical constants. Where can I get this file? Many thanks Mehmet from University Duisburg-Essen in Germany

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Re: [Ifeffit] schemes for delr and sigma2 for multiple scattering paths
by Jatinkumar Rana 12 Oct '10

12 Oct '10

Hi Matt, Thank you very much. I have gone through the chapter in your Tutorial and things are more convincing now. With best regards, Jatin Rana HZB Berlin On 09.10.2010 19:00, 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: schemes for delr and sigma2 for multiple scattering paths > (Matt Newville) > 2. Re: schemes for delr and sigma2 for multiple scattering paths > (Jatinkumar Rana) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 8 Oct 2010 13:13:23 -0500 > From: Matt Newville<newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] schemes for delr and sigma2 for multiple > scattering paths > Message-ID: > <AANLkTimBJbC9EqyUs31kiHuU9F+fHSVv+ib5oXBKq5Kb(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Jatin, > > I tried to answer both of these question in chapter 3 of > http://xafs.org/Tutorials?action=AttachFile&do=view&target=Newville_xas_fun… > > Does the explanation there help? If not, do you have any suggestions > for making it clearer? > > The basic physics is that an absorbed x-ray creates a photo-electron > which will scatter from its neighbors. A portion of the scattered > portion (so, a small amount) of that photo-electron will return to the > absorbing atom. But Pauli's exclusion principle tells us that if an > electron is at the absorbing atom, and has the same energy (and other > quantum numbers) as the outgoing photo-electron, the outgoing > photo-electron cannot be created in the first place. Thus, the > scattering of the photo-electron from the neighbors affects whether > the photo-electron can be created, and so whether the x-ray will be > absorbed. > > The effect can be either destructive or constructive, as with nearly > any wave-like phenomenon. It does seem a bit circular that the > photo-electron scattering affects the existence of the photo-electron, > but quantum mechanics leads to many much stranger behaviors. > > --Matt > > > ------------------------------ > > Message: 2 > Date: Sat, 09 Oct 2010 09:41:12 +0200 > From: Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] schemes for delr and sigma2 for multiple > scattering paths > Message-ID:<4CB01C98.4020103(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hello Chris, Bruce, > > Thank you so very much for your detailed explanations. > > With best regards, > Jatin Rana > HZB Berlin > > > > > > On 08.10.2010 19:00, 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: schemes for delr and sigma2 for multiple scattering paths >> (Chris Patridge) >> 2. Re: schemes for delr and sigma2 for multiple scattering paths >> (Bruce Ravel) >> 3. Re: schemes for delr and sigma2 for multiple scattering paths >> (Bruce Ravel) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 8 Oct 2010 10:09:34 -0400 >> From: Chris Patridge<patridge(a)buffalo.edu> >> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] schemes for delr and sigma2 for multiple >> scattering paths >> Message-ID:<68FC92BB-B842-48F2-8596-7675D168EB16(a)buffalo.edu> >> Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes >> >> Hello Jatin, >> >> I don't confess expertise but i think the absorption coeff. relates to >> the overlap between the initial and final wavefunction. Therefore the >> interference between outgoing and backscattering modulates the final >> wavefunction which manifests as the exafs fluctuations past the edge >> which in turn changes the It signal so we can use the difference >> between Io and It to measure exafs data. Any additional comments are >> welcomed if I am mistaken as I said I am not an expert. >> >> Buena salud, >> >> Chris Patridge >> >> >> On Oct 8, 2010, at 9:30 AM, Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de >> > wrote: >> >> >> >>> Hi Scott, >>> >>> Nice to see you back-in-action from holidays. Thank you very much >>> for your suggestions. >>> >>> Since last few days i was trying to visualize the physical process >>> going on inside an absorbing atom when we measure EXAFS, i met few >>> really basic questions, which of course, could be due to lack of my >>> understandings. Therefore, I tried to go through literatures and >>> EXAFS books but i am not satisfied. >>> >>> Therefore, i decided to put them to mailing list >>> >>> My first question is : >>> >>> In EXAFS, the oscillations are due to the intereference between the >>> outgoing photo electron from absorbing atom and incoming >>> backscattered photoelectron from the scatterer. Depending upon, how >>> much they are out of phase w.r.t each other we get oscillations in >>> EXAFS curve. These oscillations are nothing but the variation in the >>> absobtion coefficient of sample as the energy of incident photon is >>> varied. >>> >>> I wonder, how, the intereference between the photo electrons is >>> related to absorbtion coefficient of sample ?? >>> >>> because, It = I0 * exp (-ut) >>> >>> My second question is : >>> >>> While measuring EXAFS at beamline, we only measure the intial >>> intensity (Io) and the transmitted intenstiy from sample (It). In >>> other words, we only measure the number of photons before and after >>> the sample and variation in abs.coeffi.(u) is related to variation >>> in It. >>> >>> How interference between photoelectrons will be reflected as >>> variation in abs.coeffi. (u) of sample while we never measure photo >>> electrons in EXAFS?? >>> >>> We only measure Io and It. >>> >>> Also, whether the intereference between photo electrons is >>> constructive or destructive, the incident photon will lose its >>> energy once it knocks an electron from say K-shell of absorbing atom >>> and hence photon is said to have absorbed. >>> >>> I will be really thankful to you for your valuable explanation. >>> >>> With Best regards, >>> Jatin Rana >>> HZB, Berlin >>> >>> >>> >>> >>> >>> On 07.10.2010 19:00, 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: Multiple scattering paths in fitting (Frenkel, Anatoly) >>>> 2. Re: schemes for delr and sigma2 for multiple scattering >>>> paths >>>> (Scott Calvin) >>>> >>>> >>>> --- >>>> ------------------------------------------------------------------- >>>> >>>> Message: 1 >>>> Date: Thu, 7 Oct 2010 09:38:26 -0400 >>>> From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> >>>> To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> >>>> Subject: Re: [Ifeffit] Multiple scattering paths in fitting >>>> Message-ID: >>>> <CCBF39F82283424BBB90EA208CD9DE80014175C7(a)exchangemb5.bnl.gov> >>>> Content-Type: text/plain; charset="iso-8859-1" >>>> >>>> For relationships between sigma2 for MS and SS paths, some are >>>> listed in the Appendix to this article: >>>> >>>> P. Shanthakumar, et al, Physical Review B 74, 174103 (2006). >>>> >>>> Anatoly >>>> >>>> >>>> >>>>

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Re: [Ifeffit] schemes for delr and sigma2 for multiple scattering paths
by Jatinkumar Rana 09 Oct '10

09 Oct '10

Hello Chris, Bruce, Thank you so very much for your detailed explanations. With best regards, Jatin Rana HZB Berlin On 08.10.2010 19:00, 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: schemes for delr and sigma2 for multiple scattering paths > (Chris Patridge) > 2. Re: schemes for delr and sigma2 for multiple scattering paths > (Bruce Ravel) > 3. Re: schemes for delr and sigma2 for multiple scattering paths > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 8 Oct 2010 10:09:34 -0400 > From: Chris Patridge<patridge(a)buffalo.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] schemes for delr and sigma2 for multiple > scattering paths > Message-ID:<68FC92BB-B842-48F2-8596-7675D168EB16(a)buffalo.edu> > Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes > > Hello Jatin, > > I don't confess expertise but i think the absorption coeff. relates to > the overlap between the initial and final wavefunction. Therefore the > interference between outgoing and backscattering modulates the final > wavefunction which manifests as the exafs fluctuations past the edge > which in turn changes the It signal so we can use the difference > between Io and It to measure exafs data. Any additional comments are > welcomed if I am mistaken as I said I am not an expert. > > Buena salud, > > Chris Patridge > > > On Oct 8, 2010, at 9:30 AM, Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de > > wrote: > > >> Hi Scott, >> >> Nice to see you back-in-action from holidays. Thank you very much >> for your suggestions. >> >> Since last few days i was trying to visualize the physical process >> going on inside an absorbing atom when we measure EXAFS, i met few >> really basic questions, which of course, could be due to lack of my >> understandings. Therefore, I tried to go through literatures and >> EXAFS books but i am not satisfied. >> >> Therefore, i decided to put them to mailing list >> >> My first question is : >> >> In EXAFS, the oscillations are due to the intereference between the >> outgoing photo electron from absorbing atom and incoming >> backscattered photoelectron from the scatterer. Depending upon, how >> much they are out of phase w.r.t each other we get oscillations in >> EXAFS curve. These oscillations are nothing but the variation in the >> absobtion coefficient of sample as the energy of incident photon is >> varied. >> >> I wonder, how, the intereference between the photo electrons is >> related to absorbtion coefficient of sample ?? >> >> because, It = I0 * exp (-ut) >> >> My second question is : >> >> While measuring EXAFS at beamline, we only measure the intial >> intensity (Io) and the transmitted intenstiy from sample (It). In >> other words, we only measure the number of photons before and after >> the sample and variation in abs.coeffi.(u) is related to variation >> in It. >> >> How interference between photoelectrons will be reflected as >> variation in abs.coeffi. (u) of sample while we never measure photo >> electrons in EXAFS?? >> >> We only measure Io and It. >> >> Also, whether the intereference between photo electrons is >> constructive or destructive, the incident photon will lose its >> energy once it knocks an electron from say K-shell of absorbing atom >> and hence photon is said to have absorbed. >> >> I will be really thankful to you for your valuable explanation. >> >> With Best regards, >> Jatin Rana >> HZB, Berlin >> >> >> >> >> >> On 07.10.2010 19:00, 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: Multiple scattering paths in fitting (Frenkel, Anatoly) >>> 2. Re: schemes for delr and sigma2 for multiple scattering >>> paths >>> (Scott Calvin) >>> >>> >>> --- >>> ------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Thu, 7 Oct 2010 09:38:26 -0400 >>> From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> >>> To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> >>> Subject: Re: [Ifeffit] Multiple scattering paths in fitting >>> Message-ID: >>> <CCBF39F82283424BBB90EA208CD9DE80014175C7(a)exchangemb5.bnl.gov> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> For relationships between sigma2 for MS and SS paths, some are >>> listed in the Appendix to this article: >>> >>> P. Shanthakumar, et al, Physical Review B 74, 174103 (2006). >>> >>> Anatoly >>> >>> >>> >>>

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Re: [Ifeffit] schemes for delr and sigma2 for multiple scattering paths
by Jatinkumar Rana 08 Oct '10

08 Oct '10

Hi Scott, Nice to see you back-in-action from holidays. Thank you very much for your suggestions. Since last few days i was trying to visualize the physical process going on inside an absorbing atom when we measure EXAFS, i met few really basic questions, which of course, could be due to lack of my understandings. Therefore, I tried to go through literatures and EXAFS books but i am not satisfied. Therefore, i decided to put them to mailing list My first question is : In EXAFS, the oscillations are due to the intereference between the outgoing photo electron from absorbing atom and incoming backscattered photoelectron from the scatterer. Depending upon, how much they are out of phase w.r.t each other we get oscillations in EXAFS curve. These oscillations are nothing but the variation in the absobtion coefficient of sample as the energy of incident photon is varied. I wonder, how, the intereference between the photo electrons is related to absorbtion coefficient of sample ?? because, It = I0 * exp (-ut) My second question is : While measuring EXAFS at beamline, we only measure the intial intensity (Io) and the transmitted intenstiy from sample (It). In other words, we only measure the number of photons before and after the sample and variation in abs.coeffi.(u) is related to variation in It. How interference between photoelectrons will be reflected as variation in abs.coeffi. (u) of sample while we never measure photo electrons in EXAFS?? We only measure Io and It. Also, whether the intereference between photo electrons is constructive or destructive, the incident photon will lose its energy once it knocks an electron from say K-shell of absorbing atom and hence photon is said to have absorbed. I will be really thankful to you for your valuable explanation. With Best regards, Jatin Rana HZB, Berlin On 07.10.2010 19:00, 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: Multiple scattering paths in fitting (Frenkel, Anatoly) > 2. Re: schemes for delr and sigma2 for multiple scattering paths > (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 7 Oct 2010 09:38:26 -0400 > From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> > To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Multiple scattering paths in fitting > Message-ID: > <CCBF39F82283424BBB90EA208CD9DE80014175C7(a)exchangemb5.bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > For relationships between sigma2 for MS and SS paths, some are listed in the Appendix to this article: > > P. Shanthakumar, et al, Physical Review B 74, 174103 (2006). > > Anatoly > > > >

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Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin/Shelly Kelly/Abhijeet Gaur); Re: Ifeffit Digest, Vol 92, Issue 5
by Scott Calvin 07 Oct '10

07 Oct '10

Not at all unusual, Han Sen. If you think about the EXAFS equation, you'll see that sigma^2 and amplitude primarily affect the amplitude of the signal, while distances affect the position of the peak in the Fourier transform (or equivalently, the spacing of peaks in chi(k)). So sigma^2 and amplitude can trade off without affecting distance- based aspects of the fit much. That's why I suggested you try forcing the sigma^2 to a "reasonable" value to see what happened to your fit. Sometimes none of the aspects of the fit you're interested in depend strongly on the sigma^2 of low- amplitude paths--particularly if what you're interest in is distances or information that is in part derived from distances, like phase identification. In those cases, the anomalous sigma^2 can be a "yellow flag" (think about what might be causing it and decide if it's a problem to your scientific case) rather than a "red flag" (drop everything and resolve the problem before proceeding). Also, note from the EXAFS equation that sigma^2 is weighted by k^2, and amplitude is not. If fits using different k-weights result in significantly different values of sigma^2, that can be a clue that the issue is actually one of amplitude, as in your case. At any rate, I'm glad you solved your issue in such a satisfying way! --Scott Calvin Sarah Lawrence College On Oct 7, 2010, at 11:22 AM, Han Sen Soo wrote: > Hello Shelly and Scott, > Thank you both again for your suggestions. It seems that after > making the MS path more linear in my cif file, the FEFF calculation > increased the amplitude value of the path and dramatically > increased the sigma^2 value in the fit. Strangely, the fit values > for the distances remain pretty much the same and the statistical > figures of merit have improved, but the sigma^2 values are now much > more reasonable (about twice as large, but I have a more triangular > than linear model, so you're right Scott, your explanation does not > work for my case). I guess the increased amplitude made a difference? > > Hello Abhijeet, I used a rudimentary geometrical way to get my bond > angles. For a 3 atom triangle M-O-A, the effective MS path length > (R_MOA) is twice the sum of the individual bond distances. So if you > have the R_MOA, R_MO, and R_MA distances from your fits, you can use > R_MOA - R_MO - R_MA to get the O-A bond length. And with the 3 sides > of the triangle, you can use the geometrical Cosine Rule to get any > of the 3 bond angles. This is just geometry so I don't know what the > error propagation for this would be. > > Thanks again everyone! > han sen

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Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin/Shelly Kelly/Abhijeet Gaur); Re: Ifeffit Digest, Vol 92, Issue 5
by Han Sen Soo 07 Oct '10

07 Oct '10

Hello Shelly and Scott, Thank you both again for your suggestions. It seems that after making the MS path more linear in my cif file, the FEFF calculation increased the amplitude value of the path and dramatically increased the sigma^2 value in the fit. Strangely, the fit values for the distances remain pretty much the same and the statistical figures of merit have improved, but the sigma^2 values are now much more reasonable (about twice as large, but I have a more triangular than linear model, so you're right Scott, your explanation does not work for my case). I guess the increased amplitude made a difference? Hello Abhijeet, I used a rudimentary geometrical way to get my bond angles. For a 3 atom triangle M-O-A, the effective MS path length (R_MOA) is twice the sum of the individual bond distances. So if you have the R_MOA, R_MO, and R_MA distances from your fits, you can use R_MOA - R_MO - R_MA to get the O-A bond length. And with the 3 sides of the triangle, you can use the geometrical Cosine Rule to get any of the 3 bond angles. This is just geometry so I don't know what the error propagation for this would be. Thanks again everyone! han sen On Oct 7, 2010, at 6:36 AM, 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: More than 256 paths on Mac OS 10.5? (Scott Calvin) > 2. Re: sigma^2 values for multiple scattering paths (Scott > Calvin); Re: Ifeffit Digest, Vol 92, Issue 4 (Han Sen Soo) > 3. Re: sigma^2 values for multiple scattering paths (Scott > Calvin); Re: Ifeffit Digest, Vol 92, Issue 4 (Scott Calvin) > 4. Multiple scattering paths in fitting (Abhijeet Gaur) > 5. schemes for delr and sigma2 for multiple scattering paths > (Jatinkumar Rana) > 6. Re: Multiple scattering paths in fitting (Frenkel, Anatoly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 6 Oct 2010 10:01:27 -0700 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] More than 256 paths on Mac OS 10.5? > Message-ID: <6DD333D2-F58C-4E55-AB0D-430483EF97F4(a)gmail.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Thanks, Matt! > > --Scott Calvin > Sarah Lawrence College > > On Oct 6, 2010, at 9:08 AM, Matt Newville wrote: > >> Hi Scott, >> >> >> The attached zip file has dynamic libraries (and static program >> ifeffit) built with 1024 paths and feff files. It contains the files >> >> lib/libifeffit.dylib >> lib/libifeffit.so >> bin/ifeffit >> >> The zip file should be unzipped under >> /Applications/iXAFS.app/Contents/Resources/local/ >> to overwrite the above files. You should be able to open the iXAFS >> Shell and type >> >> cd /Applications/iXAFS.app/Contents/Resources/local/ >> unzip ~/Downloads/iXAFS_1024paths.zip >> athena >> >> >> Athena and Artemis will automatically use the new dynamic library. >> > > > > ------------------------------ > > Message: 2 > Date: Wed, 6 Oct 2010 10:36:25 -0700 > From: Han Sen Soo <hssoo(a)lbl.gov> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths > (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4 > Message-ID: <BC995EC7-578E-4256-9D62-DE5E73831893(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii > > Hello Scott, > Just to make sure I understand what you mean, are you saying that in your 3 atom system, the S1 and S2 atoms have relatively fixed locations but A may have large vibrational amplitudes in the A-S1 and A-S2 directions? So the round-trip 3 atom MS path has a small sigma^2 value since the variation in the A-S1-S2-A path is dictated by the more or less fixed S1 and S2 end-points (with minimal perpendicular contribution), whereas the 2 individual SS paths have large sigma^2 value due to the large A-S vibrations? > > I tried setting the sigma^2 value to a reasonable number for the MS path and it appears to increase the R factor slightly and tries to maximize the floating degeneracy I set (with a restrain to be physically reasonable based on my model). It does not look as good but at least it seems more plausible. I will try out Shelly's suggestions to see if they work too. I guess what I wanted to find out is whether the model I included is telling me that something is terribly wrong. > > Thank you all again for your responses! > han sen > > On Oct 6, 2010, at 10:00 AM, 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: sigma^2 values for multiple scattering paths (Scott Calvin) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 6 Oct 2010 09:39:49 -0700 >> From: Scott Calvin <dr.scott.calvin(a)gmail.com> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Cc: "Dr.Scott.Calvin(a)gmail.com" <Dr.Scott.Calvin(a)gmail.com> >> Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths >> Message-ID: <AB39966C-893D-4947-BED2-A26FC6534315(a)gmail.edu> >> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes >> >> Although I agree with the main points that Bruce makes, I do want to >> comment on one piece: >> >> On Oct 6, 2010, at 7:03 AM, Bruce Ravel wrote: >> >>> . >>> >>> In no case can I understand a physical explanation for the the MS >>> sigma^2 being smaller than for the SS. >> >> Actually, there is a physical situation where something like that can >> occur, although it sounds like it's not the one that Han Sen has. >> >> Consider an absorbing atom rattling around in a relatively fixed cage >> or lattice. And then consider a linear (or near-linear) arrangement: >> >> S1 -- A -- S2 >> >> One multiple scattering path that can sometimes have a sizable >> contribution is A --> S1 --> S2 --> A. This path will have a sigma^2 >> that is a bit larger than the single-scattering path S1 --> S2 --> S1, >> because of the perpendicular component of the motion of A. >> >> But it's quite frequently the case that S1 --> S2 --> S1 is not >> modeled in a fit, because the S edge is not measured. >> >> On the other hand, the single scattering paths A --> S1 --> A and A -- >>> S2 --> A ARE included in the fit. Those two have high sigma^2's, >> because A is rattling around a lot. >> >> Under that circumstance, a multiple-scattering path included in the >> fit may indeed have a lower sigma^2 than the single-scattering paths >> included in the fit. >> >> The moral, of course, is that it's not hard to think physically about >> what sigma^2 means for a multiple scattering path. If one appears to >> have an "unphysically" small sigma2, then the explanation is probably >> one of the ones given by Bruce or Shelly. >> >> One more thought on this. How much does it change your fit, Han Sen, >> if you set the sigma^2 for the multiple-scattering path to some >> "reasonable" value. If the scientific information you want from your >> fit is not sensitive to exactly what sigma^2 the MS path gets, and is >> not significantly different when given a "reasonable" value than when >> allowed to find its "best-fit" value, then there's probably no need to >> resolve the issue. In my experience, this is often the case with low- >> amplitude MS paths: the fit is improved by their inclusion, but may >> not be particularly sensitive to the details of their path parameters. >> >> --Scott Calvin >> Sarah Lawrence College >> >> >> ------------------------------ >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> End of Ifeffit Digest, Vol 92, Issue 4 >> ************************************** > > > > > ------------------------------ > > Message: 3 > Date: Wed, 6 Oct 2010 10:51:59 -0700 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths > (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4 > Message-ID: <CBC93BEC-49EA-40CB-B700-4CD1E421D1A5(a)gmail.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > > On Oct 6, 2010, at 10:41 AM, Han Sen Soo wrote: > >> Hello Scott, >> Just to make sure I understand what you mean, are you saying that in >> your 3 atom system, the S1 and S2 atoms have relatively fixed >> locations but A may have large vibrational amplitudes in the A-S1 >> and A-S2 directions? So the round-trip 3 atom MS path has a small >> sigma^2 value since the variation in the A-S1-S2-A path is dictated >> by the more or less fixed S1 and S2 end-points (with minimal >> perpendicular contribution), whereas the 2 individual SS paths have >> large sigma^2 value due to the large A-S vibrations? >> > > Yes--you explained it far better than I did. :) > > --Scott Calvin > Sarah Lawrence College > > > > ------------------------------ > > Message: 4 > Date: Thu, 7 Oct 2010 12:51:01 +0530 > From: Abhijeet Gaur <abhijeetgaur9(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Multiple scattering paths in fitting > Message-ID: > <AANLkTim8q3nucice-cVa-F2jpqCR=abDbkKk=AJj2X87(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > I just read the discussion on "sigma^2 values for multiple > scattering paths ". One thing is clear that inclusion of multiple scattering > path may increase the quality of fit. I have also some questions related to > MS paths. > 1. What else information can be obtained from multiple scattering paths? > 2. What values of delr should be relevant for MS paths. > 3. How can we determine the bond-angles from multiple-sacttering paths using > Artemis fitting method. > > With thanks > Abhijeet Gaur > School of Studies in Physics > Vikram University, Ujjain. >

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Re: [Ifeffit] schemes for delr and sigma2 for multiple scattering paths
by Scott Calvin 07 Oct '10

07 Oct '10

Jatin, IF the uniform expansion model is valid for single scattering paths, then it is for multiple scattering paths as well. For some materials, particularly those with cubic space groups, that's got a good chance of being a useful model. Others tends to distort with changes in temperature, doping, etc., and it may not work as well. But even in those cases, if you've decided how to constrain the delr for single- scattering paths, you'll do reasonably well by using some kind of appropriate average of the delr's for related single-scattering paths. --Scott Calvin Sarah Lawrence College On Oct 7, 2010, at 3:05 AM, Jatinkumar Rana wrote: > Dear all, > > It is reasonable to assign a constant fraction by which unit cell > expands at a given temperature of XAFS measuremnt and so the variation > in the path lengths for every single scattering paths could be > assigned > as delr = alpha * Reff. Similarly, one can assign sigma2 value for > each > single scattering path depending on both type of scatterer and its > distance from the absorbing atom. > > Now coming to multiple scattering paths, Sigma2 for multiple > scattering > paths can be constrained based on the sigma2 of related single > scattering paths and a definite path-geometry-dependent scheme > (Triangle, collinear, reversed etc.) could be applied. > > Is there any such scheme for delr of multiple scattering paths ? or we > can simply assume that all paths (single scattering and multiple > scattering) undergo uniform expansion by a factor alpha. > > Thank you so much in advance for your valuable time... > > With best regards, > Jatin Rana > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Multiple scattering paths in fitting
by Abhijeet Gaur 07 Oct '10

07 Oct '10

Hi all, I just read the discussion on "sigma^2 values for multiple scattering paths ". One thing is clear that inclusion of multiple scattering path may increase the quality of fit. I have also some questions related to MS paths. 1. What else information can be obtained from multiple scattering paths? 2. What values of delr should be relevant for MS paths. 3. How can we determine the bond-angles from multiple-sacttering paths using Artemis fitting method. With thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain.

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