October 2010 - Ifeffit - millenia.cars.aps.anl.gov

Zn foil data
by Jonathan L Keating 21 Oct '10

21 Oct '10

Dear All Firstly, lots of thanks to the contributors of the mailing list for providing such a great platform to discuss and help with exafs analysis. I have a request and wonder if anybody may have some Zn XAS foil data with data extending beyond 13 inverse Angstroms in k-space? Many Thanks Jon

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Re: [Ifeffit] calibration/aligment...2 (Scott Calvin)
by ornella smila castro 15 Oct '10

15 Oct '10

Dear Scott, this is exactly why I was confused about alignment, since I want to see that shift!! Thank you so much for your precious help. it is very clear now.. With best wishes, Ornella > From: ifeffit-request(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 92, Issue 13 > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Thu, 14 Oct 2010 17:54:36 -0500 > > 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: calibration/aligment...2 (Scott Calvin) > 2. Re: MPSE (Joshua Kas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 14 Oct 2010 11:37:43 -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] calibration/aligment...2 > Message-ID: <04C38483-D6F6-4F2D-B206-AFFB25B30429(a)gmail.edu> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > Thanks, Ornella, that clarifies what you're doing. > > My recommendation is to look closely at the 6 reference spectra and > see if there appears to be a systematic energy shift between them. For > example, each spectrum might be shifted by about 0.3 eV from the > spectrum before it. Or the first two spectra might appear aligned, but > then the third through sixth are shifted by 1.5 eV. In either of those > cases, you should align them. In my second example, I might throw out > the second spectrum as an additional precaution (if the shift occurred > "all at once," it might have occurred during the scan before which it > appears). In either case, it doesn't really matter which scan you > choose to align to (and calibrate, if you have a way of doing that). > > If, on the other hand, the 6 reference spectra appear to basically > overplot except for random noise, I would not try to align them further. > > I would treat the 6 spectra for the electrolysed solution similarly-- > align them to each other if there is a systematic energy shift. > > What you should not do, in my opinion, is to align the electrolysed > scans to the reference scans. You actually expect there to be a > chemical shift between the two sets of data, and aligning one to the > other would remove that! > > --Scott Calvin > Sarah Lawrence College > > On Oct 14, 2010, at 11:00 AM, ornella smila castro wrote: > > > Hi Matt and Scott, > > > > First, thank you so much for replying to my questions. > > I realised that I should have been a bit more accurate on the type > > of experiments I am doing. > > To start with, I am doing electrochemistry combined with EXAFS. I am > > using an integrated electrolysis/EXAFS cell. Our experiments are as > > follow: in the case of this experiment in particular, we have a > > solution of ruthenium-based compound that we flow through a channel > > through which the beam passes and that we call "reference". we > > record let's say 6 spectra in a row (we use a flow in order to avoid > > beam damage on our sample).we didn't do any reference spectra (if > > you mean running a scan of a Ru foil before starting the actual > > experiment). then, we make up a new solution but this time we > > electrolysed the solution (by applying a potential) in order to get > > the cationic produced species. (the obtained spectra will therefore > > be a mixture of the neutral and the cationic species). and we record > > as well a set of 6 spectra. > > Here is what I did and what I was wondering if it was the right > > thing to do: I have considered the first spectra of the first set of > > scans as the reference for calibration/alignment. is it ok? > > Thus, I am wondering if when I process the second set of data > > (electrolysed solution), which spectra I should take as a starting > > point for calibrating/aligning my second series of scans: the one I > > used for the first serie or the first of the second set of scans? > > > > I hope this is clear... > > > > Thanks again for your help, > > Ornella > >

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Re: [Ifeffit] MPSE
by Joshua Kas 14 Oct '10

14 Oct '10

Hi Mehmet, The documentation in feff9 for MPSE is (obviously) not very good. What you will need, to start, is a calculation of the bulk loss function L(E) = -Im[1/epsilon(E)] for your material. I can discuss the details with you over email if you like. Cheers, Josh Kas joshua.j.kas(a)gmail.com > 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] calibration/aligment...2
by Scott Calvin 14 Oct '10

14 Oct '10

Thanks, Ornella, that clarifies what you're doing. My recommendation is to look closely at the 6 reference spectra and see if there appears to be a systematic energy shift between them. For example, each spectrum might be shifted by about 0.3 eV from the spectrum before it. Or the first two spectra might appear aligned, but then the third through sixth are shifted by 1.5 eV. In either of those cases, you should align them. In my second example, I might throw out the second spectrum as an additional precaution (if the shift occurred "all at once," it might have occurred during the scan before which it appears). In either case, it doesn't really matter which scan you choose to align to (and calibrate, if you have a way of doing that). If, on the other hand, the 6 reference spectra appear to basically overplot except for random noise, I would not try to align them further. I would treat the 6 spectra for the electrolysed solution similarly-- align them to each other if there is a systematic energy shift. What you should not do, in my opinion, is to align the electrolysed scans to the reference scans. You actually expect there to be a chemical shift between the two sets of data, and aligning one to the other would remove that! --Scott Calvin Sarah Lawrence College On Oct 14, 2010, at 11:00 AM, ornella smila castro wrote: > Hi Matt and Scott, > > First, thank you so much for replying to my questions. > I realised that I should have been a bit more accurate on the type > of experiments I am doing. > To start with, I am doing electrochemistry combined with EXAFS. I am > using an integrated electrolysis/EXAFS cell. Our experiments are as > follow: in the case of this experiment in particular, we have a > solution of ruthenium-based compound that we flow through a channel > through which the beam passes and that we call "reference". we > record let's say 6 spectra in a row (we use a flow in order to avoid > beam damage on our sample).we didn't do any reference spectra (if > you mean running a scan of a Ru foil before starting the actual > experiment). then, we make up a new solution but this time we > electrolysed the solution (by applying a potential) in order to get > the cationic produced species. (the obtained spectra will therefore > be a mixture of the neutral and the cationic species). and we record > as well a set of 6 spectra. > Here is what I did and what I was wondering if it was the right > thing to do: I have considered the first spectra of the first set of > scans as the reference for calibration/alignment. is it ok? > Thus, I am wondering if when I process the second set of data > (electrolysed solution), which spectra I should take as a starting > point for calibrating/aligning my second series of scans: the one I > used for the first serie or the first of the second set of scans? > > I hope this is clear... > > Thanks again for your help, > Ornella

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Re: [Ifeffit] calibration/aligment...2
by ornella smila castro 14 Oct '10

14 Oct '10

Hi Matt and Scott, First, thank you so much for replying to my questions. I realised that I should have been a bit more accurate on the type of experiments I am doing. To start with, I am doing electrochemistry combined with EXAFS. I am using an integrated electrolysis/EXAFS cell. Our experiments are as follow: in the case of this experiment in particular, we have a solution of ruthenium-based compound that we flow through a channel through which the beam passes and that we call "reference". we record let's say 6 spectra in a row (we use a flow in order to avoid beam damage on our sample).we didn't do any reference spectra (if you mean running a scan of a Ru foil before starting the actual experiment). then, we make up a new solution but this time we electrolysed the solution (by applying a potential) in order to get the cationic produced species. (the obtained spectra will therefore be a mixture of the neutral and the cationic species). and we record as well a set of 6 spectra. Here is what I did and what I was wondering if it was the right thing to do: I have considered the first spectra of the first set of scans as the reference for calibration/alignment. is it ok? Thus, I am wondering if when I process the second set of data (electrolysed solution), which spectra I should take as a starting point for calibrating/aligning my second series of scans: the one I used for the first serie or the first of the second set of scans? I hope this is clear... Thanks again for your help, Ornella > From: ifeffit-request(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 92, Issue 11 > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Thu, 14 Oct 2010 12:00:01 -0500 > > 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. MPSE (Mehmet Kaya) > 2. calibration/alignment (ornella smila castro) > 3. Re: calibration/alignment (Scott Calvin) > 4. Re: calibration/alignment (Matt Newville) > 5. Re: calibration/alignment (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Oct 2010 12:23:06 +0200 > From: "Mehmet Kaya" <mehmet.kaya(a)uni-due.de> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] MPSE > Message-ID: <000401cb6ac0$a110d0d0$e3327270$@kaya@uni-due.de> > Content-Type: text/plain; charset="us-ascii" > > 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] calibration/alignment
by Scott Calvin 14 Oct '10

14 Oct '10

On Oct 14, 2010, at 7:39 AM, Matt Newville wrote: > If you're just getting started, I would say to not worry about energy > alignment until it becomes an obvious problem. A cautionary tale (with details made up, since I don't remember them!) from when I was just starting out as to what constitutes an "obvious problem": I collected five transmission EXAFS scans on the same sample. The scans were on top of each other when I looked at the graph, so I merged them...and proceeded to get somewhat screwy fits. The problem? I only looked at the graph across the whole spectra--say, 1500 eV. It turns out there was about a 0.7 eV shift between each scan and the next one, for a total of roughly 3 eV . That was small enough so as to be invisible when looked at on that scale. When I looked at just the XANES, though, the shift did become "obvious." I aligned the spectra and merged them, and suddenly the problems in the fit went away! Since then, I've seen the same thing happen with students to whom I am teaching the technique. On the other hand, there's no magic "blessing" given by the process of alignment. Suppose I have ten scans of very noisy data, and no reference. If I used the auto-align procedure in Athena, it sometimes shifts a scan 0.3 eV one way, sometimes 0.2 eV the other way, with no apparent rhyme or reason. Looking at the graphs, even zoomed in, just shows a bunch of noisy data roughly on top of each other. In that case, there's no reason to believe there are actual shifts between scans, and I would NOT align them prior to merging. Finally, beamline scientists usually have a very good idea whether their line is prone to drifts. Ask them! --Scott Calvin Sarah Lawrence College

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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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