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

SSRL XAS Summer School 2016 - update
by Ritimukta Sarangi 12 Apr '16

12 Apr '16

Hello Everyone, The agenda and application pages are online for the XAS summer school at SSRL in July. Please note that there are two hands-on tracks and you can choose to attend one of either XAS-imaging or EXAFS sessions. The lecture part is the same for both the sessions and both sessions will benefit from the XANES and advanced spectroscopy lectures on the final day of the summer school. Note that the deadline for application is May10th. Accepted participants will be emailed before the 20th of May. http://ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html <http://ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html> Best Wishes, -Riti Sarangi Staff Scientist SSRL, SLAC > On Apr 4, 2016, at 12:32 PM, Ritimukta Sarangi <ritimukta(a)gmail.com> wrote: > > Hello Everyone, > This is an announcement for the XAS summer school to be held at SSRL between July 18-22, 2016. We will cover XAS, EXAFS and Imaging beamlines with hands on data collection sessions at beamlines, followed by in-depth data analysis in a classroom setting. You can find more information at :http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html <http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html>. The agenda and application pages will be finalized within a week and I will post an update once it is up and running. But I wanted interested users and participants to get a heads up. > > > > >

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Importing chi(k) data
by Matteo Busi 12 Apr '16

12 Apr '16

Hi, I am experiencing several bugs when trying to import data as chi(k). I have the data as a .dat ascii files with k the second column and the relevant chi(k) and corrected chi(k) as the 4th and 5th columns. This data was previously exported as .xmu from athena, the k grid column was obtained as k ~= sqrt(0.262468*(E-E0)). When I try to import this new data back in athena, I get something totally different from expectations! However sometimes by clicking repeatedly in the importing menu I get the expected result. This looks like a bug to me! You can find the file as attachment. Regards

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Bug report
by Lorenzo Stievano 11 Apr '16

11 Apr '16

Hi, I have to report a bug on a computer where Demeter 0.9.24 is installed. Athena worked fine until a few days ago, but from a certain point it started to crash when I try to import a simple text data file (which worked well before). I have tried reinstalling Demeter (I actually did it twice) but the problem persist. The computer works under WIndows 7 Professional, SP1, 64 bits. Can you help me? Thank you in advance, Lorenzo PS: The athena log after the crash is attached.

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(no subject)
by Matteo Busi 08 Apr '16

08 Apr '16

Hi Matt. Thanks for the hints, they are very useful. What would you suggest to use if not the bkg? Regarding the xmu(E) I have been using exactly the values exported through the .xmu ascii file. I have been reading though the Athena's user guide and I didn't find any hint about which unit I could assign to them. Anyway I would like to get them with the cm^-1 units which would suit with the correction expression I want to perform. How can this be done? My idea was to divide the xmu data by the penetration depth in the sample (i.e. the radius of the capillar sample). Is this correct? Can this be applied to the bkg data aswell? Moreover the data I have is not scanned through the Cu fluorescence energy you have mentioned (8046 eV). Would you recommend to use data from Chantler or Cromer-Liberman? And how can I merge it with my other measured data to make it unit meaningful? Thanks and regards, Matteo I report our previous conversation for reference: > What I am trying to do is to perform a new developed self-absorption > correction using collected fluorescence absorption coefficient data on a > CuSO4 (pentahydrate) capillar (cylinder) and spherical sample with Cu as > absorber, having different values of molarity and penetration depth. > The correction expression requires these measured quantity: > ?X(E) : the absorption coefficient due to a given core excitation of the > absorbing atom > - I used the background function for this ( bkg(E)) Wouldn't using bkg(E) suppress the fine-structure you are trying to recover? Anyway what are the units, are you normalizing bkg(E) to something meaningful? I would suggest using data from Chantler or Cromer-Liberman here. Or perhaps match mu(E) or bkg(E) to these. > ?o = ?(E) : photoelectric total linear absorption coefficient of the > sample at incident energy E > - I used the xmu(E) for this > Again, be mindful of what the units are. > ?h = ?(E) :photoelectric total linear absorption coefficient of the sample > at fluorescence emission Ef > - I used the xmu(Ef) with Ef the K absorption edge of > Cu ( 8.9789 eV) > I am pretty sure that this is not what you want. You probably want mu(E) at the Cu fluorescence energy (8.046 keV). This can make a significant difference.

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Fuzzy degeneracy
by Panagiotis Mougkogiannis 07 Apr '16

07 Apr '16

Dear Bruce, Hello I am quite new in the field and I was reading your paper : ''Path degeneracy and EXAFS analysis of disordered materials, Journal of Synchrotron Radiation,volume 21, issue 6, pages 1269-1274,year 2014''. A simple question, Where can I find the Ti K-edge data of CaZrTi2O7 in order to manipulate EXAFS data analysis by myself? and something more How do you plot in the same figure the paths of strict and fuzzy degeneracy -Figure1a-? What I managed to do is in the attached picture ( 4 figures with the strict and fuzzy degeneracy)... Many Thanks Yours Faithfully Panagiotis

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frequently asked questions
by Bruce Ravel 06 Apr '16

06 Apr '16

Hi all, I am making a new stab at creating a list of frequently asked questions about the software and other topics on this mailing list. Here's my first draft: http://bruceravel.github.io/demeter/documents/SinglePage/faq.html I want to solicit suggestions for good questions and answers. If there is a topic that you think would make a good question for the FAQ, please open an issue at Demeter's GitHub page: https://github.com/bruceravel/demeter/issues There is a "FAQ question" label that can be used as a tag. If you would like to edit the FAQ directly and submit a diff file or make a pull request, here is the source file: https://github.com/bruceravel/demeter/blob/master/documentation/SinglePage/… You'll get a copy when you clone the demeter repository or you can click the "raw" button to get the source for the faq page. Thanks in advance! Bruce -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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SSRL XAS Summer School 2016
by Ritimukta Sarangi 04 Apr '16

04 Apr '16

Hello Everyone, This is an announcement for the XAS summer school to be held at SSRL between July 18-22, 2016. We will cover XAS, EXAFS and Imaging beamlines with hands on data collection sessions at beamlines, followed by in-depth data analysis in a classroom setting. You can find more information at :http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html <http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html>. The agenda and application pages will be finalized within a week and I will post an update once it is up and running. But I wanted interested users and participants to get a heads up. Best Wishes, Ritimukta Sarangi SSRL

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Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 3
by Matteo Busi 04 Apr '16

04 Apr '16

Hi Bruce, Thanks for your help, it's really appreciated. I was trying to keep it simple but it seems I'm just messing around. What I am trying to do is to perform a new developed self-absorption correction using collected fluorescence absorption coefficient data on a CuSO4 (pentahydrate) capillar (cylinder) and spherical sample with Cu as absorber, having different values of molarity and penetration depth. The correction expression requires these measured quantity: μX(E) : the absorption coefficient due to a given core excitation of the absorbing atom - I used the background function for this ( bkg(E)) μo = μ(E) : photoelectric total linear absorption coefficient of the sample at incident energy E - I used the xmu(E) for this μh = μ(E) :photoelectric total linear absorption coefficient of the sample at fluorescence emission Ef - I used the xmu(Ef) with Ef the K absorption edge of Cu ( 8.9789 eV) χ: and here I used the chi(E) values of the exported ascii .xmu file Hope it's clear now. Matteo 2016-04-02 19:00 GMT+02:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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: Ifeffit Digest, Vol 158, Issue 1 (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Apr 2016 15:56:29 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 1 > Message-ID: > <CA+7ESbrsbsFQGMGLwGNPJmVO= > fGzksbv1SezR3M5pRkXanNyDg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Matteo, > > > On Fri, Apr 1, 2016 at 8:35 AM, Matteo Busi <basebush(a)gmail.com> wrote: > > > Hi Bruce, > > Now this is clear. > > In my case the correction I have to perform requires these > > measured/evaluated parameters: chi, mu (not sure if it's better to work > > with normmu here) and the background function. > > Is it physically meaningless to have the mu(k) and bkg(k) data? If that > is > > not the case I would like to have these two columns exported in the ascii > > chi(k) file. > > So then I can perform the correction and re-import the new corrected > > chi(k) and make comparison with the uncorrected. > > > > Kind regards, > > Matteo > > > > > It would certainly help (and by that I mean "help you get the answers > you're looking for") if you gave us more details about what you're trying > to do rather than ask for how to what you think you want to do. > > Just to be clear: Converting from E to k does not involve a Fourier > transform, just > k = sqrt((2m*e/hbar**2)*(E-E0)) > > for k in Ang^-1 and E in eV, that's k ~= sqrt(0.262468*(E-E0)) > > I'm not sure what you're trying, but I would image you want to use > normalized mu(E) or at least pre-edge subtracted mu(E). That is, what we > call mu(E) is typically really -ln(I/I0) > where I and I0 are not the actual intensities before and after the sample, > but counts or counts per time in some detector that samples the flux. > These values include more or less arbitrary scale factors (amplifier gains, > etc) included. That means that (unless you very careful) mu(E) does not > have meaningful units, certainly not cm^-1 or cm^2/gram. > > Normalized mu(E) doesn't have such units either, but it's an easier place > to start. > > --Matt >

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Self-absorption xmu units
by Matteo Busi 04 Apr '16

04 Apr '16

Hi Matt. Thanks for the hints, they are very useful. What would you suggest to use if not the bkg? Regarding the xmu(E) I have been using exactly the values exported through the .xmu ascii file. I have been reading though the Athena's user guide and I didn't find any hint about which unit I could assign to them. Anyway I would like to get them with the cm^-1 units which would suit with the correction expression I want to perform. How can this be done? My idea was to divide the xmu data by the penetration depth in the sample (i.e. the radius of the capillar sample). Is this correct? Can this be applied to the bkg data aswell? Moreover the data I have is not scanned through the Cu fluorescence energy you have mentioned (8046 eV). Would you recommend to use data from Chantler or Cromer-Liberman? And how can I merge it with my other measured data to make it unit meaningful? Thanks and regards, Matteo I report our previous conversation for reference: > What I am trying to do is to perform a new developed self-absorption > correction using collected fluorescence absorption coefficient data on a > CuSO4 (pentahydrate) capillar (cylinder) and spherical sample with Cu as > absorber, having different values of molarity and penetration depth. > The correction expression requires these measured quantity: > ?X(E) : the absorption coefficient due to a given core excitation of the > absorbing atom > - I used the background function for this ( bkg(E)) Wouldn't using bkg(E) suppress the fine-structure you are trying to recover? Anyway what are the units, are you normalizing bkg(E) to something meaningful? I would suggest using data from Chantler or Cromer-Liberman here. Or perhaps match mu(E) or bkg(E) to these. > ?o = ?(E) : photoelectric total linear absorption coefficient of the > sample at incident energy E > - I used the xmu(E) for this > Again, be mindful of what the units are. > ?h = ?(E) :photoelectric total linear absorption coefficient of the sample > at fluorescence emission Ef > - I used the xmu(Ef) with Ef the K absorption edge of > Cu ( 8.9789 eV) > I am pretty sure that this is not what you want. You probably want mu(E) at the Cu fluorescence energy (8.046 keV). This can make a significant difference.

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Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 1
by Matteo Busi 01 Apr '16

01 Apr '16

Hi Bruce, Now this is clear. In my case the correction I have to perform requires these measured/evaluated parameters: chi, mu (not sure if it's better to work with normmu here) and the background function. Is it physically meaningless to have the mu(k) and bkg(k) data? If that is not the case I would like to have these two columns exported in the ascii chi(k) file. So then I can perform the correction and re-import the new corrected chi(k) and make comparison with the uncorrected. Kind regards, Matteo 2016-04-01 15:06 GMT+02:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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. Chi(E) data export and import (Matteo Busi) > 2. Re: Chi(E) data export and import (Bruce Ravel) > 3. Re: Question about Io during data collection (Luxton, Todd) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Apr 2016 13:58:23 +0200 > From: Matteo Busi <basebush(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Chi(E) data export and import > Message-ID: > < > CAOyEiGhFhPbQ5Xn1is+R4MPVDQ4mxS4wXCcWM-j2qBcO5117-g(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Bruce, > this message il linked to the previous solutions you find for me. > > For the reference, I asked to have a column of the chi(E) in the exported > mu(E) data. > This has worked correctly so far. > > Now for my master thesis, I'm performing a correction to chi(E) in the E > space regarding to some geometrical properties of the sample. > I have also tried to re-import the corrected data as a chi(k), having > reproduced the right k grid column, but it looks totally wrong. > The thing I'm not sure about is if the chi(E) needs to be fourier > trasnformed into chi(k) or not. > That's because I would have liked to make comparison in the Athena software > between the two chis, but if that's not possible I will keep it to the > external software (mathematic) with which the correction is performed. > Or if you can share me the fourier transform routine performed I can > include it to my correction script. > > Hope the message is clear, > Kind Regards, > > Matteo >

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