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

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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Question about Io during data collection
by Luxton, Todd 01 Apr '16

01 Apr '16

All: Recently our group was at the APS collecting Pb L(III) spectra on an ID line using quick XAFS. Data was collected from -200 to +800 eV for Pb L(III) at 0.2 eV steps with a count rate of 0.025 seconds. Each scan took about 2.5 minutes to complete. During our measurements we began noting issues with the linearity of scans collected in the extended region of the same sample. After poking around in the data we noticed that Io was not linear throughout the measurement for a portion of the scans. This was not always the true (see Athena project attached to the email, and images attache to the email). I was always under the impression that Io should ideally remain linear throughout the energy region scanned, or at least remain unchanged between replicate scans. We worked with the beamline scientists to try alleviate/fix the issue, but it kept persisting. I realize this is not an IFEFFIT issue, but I was hoping someone might be able to help me understand what was going on and why this was happening? If I have not included enough information for the question please let me know. [cid:image001.jpg@01D18B37.F66BD820] [cid:image002.jpg@01D18B37.F66BD820] All the Best, todd All the Best, Todd Luxton, Ph.D. Office of Research and Development National Risk Management Research Laboratory Land Remediation and Pollution Control Division Waste Management Branch Mailing Address: 5995 Center Hill Ave Cincinnati, OH 45243 Phone: Office: (513) 569-7210 Cell: (513) 319-5104 Fax: (513) 569-7879 Email: Luxton.todd(a)epa.gov<mailto:Luxton.todd@epa.gov> "A nation that destroys its soils destroys itself" Franklin D. Rosevelt

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Chi(E) data export and import
by Matteo Busi 01 Apr '16

01 Apr '16

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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Questions to Bruce
by Dien.Li＠srs.gov 24 Mar '16

24 Mar '16

HI, Bruce and Matt I have two questions for you, please help me. 1. I collected U EXAFS data on APS 10-ID, while I input a single data file with reference data in Athena, it was OK, however, when I input multiple data files (scans) also with reference data, it was crushed. I could input multiple data files without reference data, which Matt helped me trouble shoot. The Demeter 8.24 version is used on my computer, I believe. Matt suggested me to update to the current version. I do not know if other users have this problem. 2. I have a U EXAFS data file which was collected at SSRL, however, I could not input this data file using Athena, how to fix this? format? See the attachment. thanks you so much. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Running Examples for larch
by Panagiotis Mougkogiannis 19 Mar '16

19 Mar '16

Hello Dear all, I am struggling to run the larch-0.9.27 examples. >From previous email messages in IFEFFIT info page I managed to install larch and the icons appeared in my desktop (see attached picture larch_1) but when I am trying to run the example http://cars.uchicago.edu/xraylarch/xafs/autobk.html#examples I received this message (see attached picture larch_2) what is happened? what is the working directory of larch? Is it like something python ? If you use the commands import os print os.getcwd() you 'll find your working directory and after you can run your modules? Many thanks Regards Panagiotis

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where can I acquire quantitative date on the attenuation at the low-energy end of Zn and some of its compounds
by Nino Pereira 18 Mar '16

18 Mar '16

Dear All, I'm not part of your community, but I've been at the APS synchrotron enough to know that you might have the information I'm looking for, and willing to share it. My question is in the subject line. The reason for this question is an upcoming measurement of the ionization energy shift in a hot plasma. We have chosen Ta, because its Lbeta-2 line happens to be slightly lower in energy than the nominal energy of the Zn K-edge. Hence, a small increase, perhaps as low as 1 eV, should produce a substantial change in the attenuation of a sufficiently thick K-edge filter. Crystal spectrometers of the type we use rarely have a resolution that exceeds 2000, so that for a 10 keV l-line we could as best see a 5 eV energy change. With the same approach we could measure a ~10 eV shift on the ~63,000 eV Kalpha_2 line of Ir, with a K-edge filter of Lu. It so happens that their nominal energies are 27 eV apart (according to the x-ray data booklet, not according to Deslattes et al, 2001), so that the line and the K-ege overlap. Both are life time broadened by about 40 eV, so as the energy of the line increases, the transmission of a filter decreases. We first separate the two Kalpha lines (which are 1.3 keV apart), and then measured the decrease in the intensity behind the filter. The idea is to preferentially absorb the high-energy side of the Ir Kalpha_2 line, so that an increase in the line center becomes a decrease in line intensity behind the filter. I appreciate any comment you may have on this matter. Thank you, Nino

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