April 2016 - Ifeffit - millenia.cars.aps.anl.gov

XASLIB (was Re: data availability)
by Matt Newville 27 Apr '16

27 Apr '16

Hi Nino, Thanks for bringing this up and for the kind words. I agree that not only is access to measured XAFS spectra a problem now, it's been a problem for a long time, as evidenced by the Farrel Lytle database. In fact, it has long been a topic of discussion in the XAFS community of how to provide such databases, and developments over the past few years on data formats have been driven at least partly by the desire to have better spectral databases. For everyone: please try out XASLIB at http://cars.uchicago.edu/xaslib and let us know if you have any questions, comments, or suggestions for improving this database. Right now, there is not a lot of data here, but it is enough to give you an idea of how it works. Comments can either come here or as github Issues at the source repository for this code: https://github.com/XraySpectroscopy/XASDataLibrary There is a bit of documentation and wiki pages at https://github.com/XraySpectroscopy/XASDataLibrary/wiki A longer explanation: The standard XDI format for XAFS data (largely the work of Bruce) was presented at an IXAS workshop (Q2XAFS) in Tsukuba, Japan in 2011. At the most recent Q2XAFS meeting in Hamburg last August (as a satellite meeting of the XAFS conference), I presented an initial version of an on-line database based on this format, and intended for general use in the community. With feedback from that meeting, the version linked above is now ready for beta testing and comments. The plan is to move this to the IXAS Portal http://www.ixasportal.net/ixas/, but we'd like to get community suggestions and features and testing before we make that move. The database uses proper relational database to store the actual data, and tries to use modern web technologies for the interface. Some of the main features of this database are: - spectra can be uploaded from XDI files through the web interface. - multiple spectra can be tagged as belonging to the same Suite. - individual spectra or Suites can be rated and/or commented on by anyone, giving "Amazon-like" reviews. - in order to upload or comment, one has to log in by email address. The ratings and reviews are meant to provide some mechanism for data quality assurance, but to avoid having one person "police" the data before it can be added. This is trying to recognize that no one person can actually curate all the spectra, that truly bad data can be best identified by experts on that system, and also that there is actually some value to imperfect data. The requirements for data to be uploaded are fairly minimal except that the data must be in XDI format (basically so that metadata can be parsed easily and the columns are well-labeled), and that the monochromator lattice constant must be provided (so that energy re-calibration can be done if needed). We can help translate existing data into XDI so it can be uploaded into this database. There are several features to add or improve including: - adding some information about energy resolution. - being able to export a Suite of spectra as a single zip file or Athena project. - better web page interface to setting citation information. - better web page interface to setting sample information. But suggestions from anyone would be greatly appreciated. Finally, although the database is meant to provide a public, on-line databases useful to anyone, and uses modern relational database engines as the backend, the software can actually run on an individual machine to provide a local, private database of XAS spectra, with the same web-based interface. This is not very well documented at the moment, but if anyone is interested in trying to set such a database at their home institution, let me know. --Matt Newville

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Farrel Lytle IXAS XAFS database data energy calibration
by bajnoczi 26 Apr '16

26 Apr '16

Dear List Members, I need some nickel reference spectra, and I thought to use the Farrel Lytle IXAS XAFS database. I have found some proper ones, e.g.: http://ixs.csrri.iit.edu/data/Farrel_Lytle_data/RAW/Ni/nifl.090 and http://ixs.csrri.iit.edu/data/Farrel_Lytle_data/RAW/Ni/nicl.047 , but it is not clear from the files how these spectra are energy calibrated. Can somebody help and give some detailed information about it for me? Thank you for your help in advance. Best Regards, Eva Bajnoczi

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data availability
by pereira 26 Apr '16

26 Apr '16

New to this mailing list, so excuse my innocence: Today I see two questions about standards. Some time ago I was looking for what I think is similar, and was pointed to the XAS data base http://cars.uchicago.edu/xaslib/about/. If I understand the questions properly, this database may be of great help. It was to me. I thank the people organizing it, Matt Newville and Bruce Ravel, for their great service to the community in volunteering to make seemingly reliable data available in a convenient way. Nino

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Request for CuCl and CuSO4 XAFS/ XANES standard data
by Halder, Avik 26 Apr '16

26 Apr '16

I was trying to find the bulk standards for CuCl and CuSO4. If you would have this data could you please share with me. Best regards, Avik Halder

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how to use the data in the XAN library to estimate the transmission of an x-ray filter
by pereira 13 Apr '16

13 Apr '16

Hi All, new to this list and to the field, so please be patient and kind and helpful in any response you may have. So far everyone I've reached on this topic has been extraordinary good. I still have to learn the lore though. I'd like to compute the x-ray transmission as function of the x-ray energy, for a particular mass per unit area of a substance, say Zn. In the XAS data base I find Zn foil at room temperature, recently measured and even more recently put into the data base just in time for my purpose. Thank you! The question is: is there a ready-made program to use those data? I see that your community has a whole slew of programs that do the opposite, go from the attenuation and/or fluorescence measured on a beam line to the attenuation coefficient, apparently without having to know the mass per unit area of the filter. I see Demeter, Athena, Larch, and various others but they all seem to go the wrong way for (and much further than) what I need. Instead, I'd like to pick up the data you guys measured on the synchrotron, and convert those into the X-ray transmission of a filter for which I select the mass per unit area. In trying to figure out how to do this I look at the graphs in the database, and the numbers behind Zn foil.xdi. The graph on the top left side gives the "Raw XAFS" (y, say) as function of energy. I interpret that as y = - ln (itrans/i0), where i0 and itrans are in Zn foil.xdi as the intensity of the incoming x-ray beam, and the beam behind the particular filter. Far from the edge, at 9600 eV, I see i0=93769.049842 and itrans=56429.849906, so that y=0.508. I can't tell from the graph whether this is indeed the case, so I go to the NIST tables. They give 35.05 cm^2/g on the low side of the edge. Then, the mass per unit area of this particular foil must have been 14.5 mg/cm^2. At 10000 eV the same thing gives y=3.603. This is pretty close to what I see in the graph, so I'm tempted to think that guessing "Raw XAFS"= ln(i0/itrans). However, for (mu/rho) NIST gives 233.1 cm^2/g, so I get for the foil's mass per unit area 16 mg/cm^2. Not quite right. Any comments on what I might have done wrong? It seems to me that by measuring the transmission of a particular filter on some X-ray source we might have available would then in effect measure the mass per unit area, so that this can be taken into account by simply exponentiating itrans/i0 with the right exponent ( = multiplying the logs with the right factor). Is something like this already implemented in one of your programs? If so, which one? Thank you, Nino

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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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