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

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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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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Re: [Ifeffit] Ifeffit Digest, Vol 157, Issue 9
by Matteo Busi 14 Mar '16

14 Mar '16

Hi Bruce, Sorry if I insisted, didn't mean to be rude. By the way the solution you proposed is exactly what I meant and I thank you. Anyways if you're going to implement this in the new release, personally I would prefer to have the mu(E) data in the .chi saved file as it simplifies my work. Don't know if it is the same to everybody. Thank you very much and have a good Easter Matteo Busi, UiS 2016-03-11 19:00 GMT+01:00 <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: Exporting Athena projects data (Bruce Ravel) > 2. Re: Exporting Athena projects data (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Mar 2016 08:57:50 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Exporting Athena projects data > Message-ID: <56E2CEDE.3040803(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/11/2016 06:52 AM, Matteo Busi wrote: > > Hi Bruce I'm sending this again, probably the latest message was lost in > > the confusion. > > Or ... perhaps ... I've been really busy lately. > > I understand what you are looking for and will have a solution for you > soon, once I get some other, more pressing things done. > > B > > > I would like to have an output file containing chi(E) and mu(E) using the > > same energy (E) grid. > > If I export them separately ( the only available way I think right now) > > they have > > different energy grid. > > > > The previous messaging was: > >> Hi Mateo, > > > >> I'm not quite clear on what you are asking for. Do you want an ascii > >> output file that has a column containing chi(E) using the energy grid of > >> the original data? > > > >> If so, would it suffice to add a column to the mu(E) ascii output file? > >> That seems to me like a natural solution. > > > >>Cheers, > >>B > > > > Thanks and Regards > > Matteo, UiS > > > > > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > > -- > 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/ > > > ------------------------------ > > Message: 2 > Date: Fri, 11 Mar 2016 11:56:22 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Exporting Athena projects data > Message-ID: <56E2F8B6.7060508(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > Matteo, > > A fully correct solution to this will have to wait until the next > release, but I can offer a partial solution which you can implement > immediately. > > Locate the file > "perl\site\lib\Demeter\templates\process\ifeffit\save_xmu.tmpl" in > whatever location Demeter was installed on your computer. > > Grab this: > > > https://raw.githubusercontent.com/bruceravel/demeter/master/lib/Demeter/tem… > > and replace the previous "save_xmu.tmpl". When you download the > replacement, be sure that its filename is "save_xmu.tmpl" and that > your browser does not "helpfully" add a .txt extension. > > When you next save current group as mu(E), there will be an additional > column which contains the chi(E) on the grid of the original data. > That column will be 0 below the lower bound of the spline range and > above the upper bound of the spline range (i.e. in the energy range > over which chi is not defined). It is un-k-weighted. If you want to > look at k-weighted chi(E), /you/ will have to apply the k-weighting > /yourself/. > > I think that addresses your request. Let me know what you think. > > B > > > On 03/11/2016 06:52 AM, Matteo Busi wrote: > > Hi Bruce I'm sending this again, probably the latest message was lost in > > the confusion. > > > > I would like to have an output file containing chi(E) and mu(E) using the > > same energy (E) grid. > > If I export them separately ( the only available way I think right now) > > they have > > different energy grid. > > > > The previous messaging was: > >> Hi Mateo, > > > >> I'm not quite clear on what you are asking for. Do you want an ascii > >> output file that has a column containing chi(E) using the energy grid of > >> the original data? > > > >> If so, would it suffice to add a column to the mu(E) ascii output file? > >> That seems to me like a natural solution. > > > >>Cheers, > >>B > > > > Thanks and Regards > > Matteo, UiS > > > > > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > > -- > 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/ > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ------------------------------ > > End of Ifeffit Digest, Vol 157, Issue 9 > *************************************** >

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Exporting Athena projects data
by Matteo Busi 11 Mar '16

11 Mar '16

Hi Bruce I'm sending this again, probably the latest message was lost in the confusion. I would like to have an output file containing chi(E) and mu(E) using the same energy (E) grid. If I export them separately ( the only available way I think right now) they have different energy grid. The previous messaging was: > Hi Mateo, > I'm not quite clear on what you are asking for. Do you want an ascii > output file that has a column containing chi(E) using the energy grid of > the original data? > If so, would it suffice to add a column to the mu(E) ascii output file? > That seems to me like a natural solution. >Cheers, >B Thanks and Regards Matteo, UiS

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Absorption length
by 이국승(에너지환경소재연구팀) 11 Mar '16

11 Mar '16

Dear members, I have seen many times the absorption length in materials for introduction of XAFS. The absorption length equals 1/mu, which is the thickness that I0 is attenuated to 1/e. But I do not understand why the absorption length is important. More importantly, I do not understand why the particle size in samples should be smaller than the absorption length. Could any one explain the absorption length including the question above and the relation between the absorption length and edge step calculations? Thanks in advance. Kug-Seung Lee Kug-Seung Lee, Ph.D. Staff Scientist Manager, 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Researcher ID: http://www.researcherid.com/rid/D-7088-2011

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Error in N (Number of Scatterers)
by Carolyn Carr 09 Mar '16

09 Mar '16

Hello Mailing List, I have read papers describing that EXAFS has an error regarding N the number of scatters of +/- 20%. The only original reference I can see to support this is "The effect of statistical noise on structural parameters in EXAFS data analysis" by L. Incoccia, S. Mobilio (1984, Il Nuovo Cimento D). However, in the more recent D. C. Koningsberger review "XAFS spectroscopy; fundamental principles and data analysis" (2000, Topics in Catalysis) he cites an error of 5% for N (although the paper cites slightly varying error for different absorber-scatterer pairs). Several months ago, I wrote to the mailing list regarding the difference of fitting in R- and k-space in Artemis and received several responses revealing that some comments made in the Koningsberger review are no longer valid in Artemis. In my literature search, I did not find additional papers describing the error inherent in N when fitting in Artemis. Since the paper cited by Koningsberger (X-ray-absorption fine-structure standards: A comparison of experiment and theory, G. G. Li, F. Bridges, and C. H. Booth, Physical Review B, 1995) utilized Feff6 for their theoretical standards and so does Artemis, is the error in N still the same? I was wondering if there is some literature that I have missed, or if the developers of the Demeter package can shed some light on this issue. Thank You, Carolyn Carr

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Path Missing Using Artemis
by lijuncha＠msu.edu 08 Mar '16

08 Mar '16

Hi all, During my use of Artemis, I found out that the FEEF paths finder had some problem with my atom, which is Cu12Sb4S13 in the attachment. I firstly ran atom on Cu12e, then ran the FEFF calculation. Then I found that the S24g.1 path was missing. Since S24g is near the core atom Cu12e and the path should exist, I was confused to send the message and hopefully get your response. Thanks, Junchao

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Any XAFS schools in North America this year?
by Robert Gordon 07 Mar '16

07 Mar '16

Hi All, I have a couple of students who are novices. I was hoping that one could go to a school to learn and perhaps get some hands-on experience before they get into the meat of their thesis work. I haven't seen any notices yet about schools taking place in the late spring or summer and was wondering if there are any plans to hold such. I am aware of the 1/2-day workshop planned for the DXC. Are there other options? Thanks, Robert

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Re: [Ifeffit] Ifeffit Digest, Vol 157, Issue 1
by Matteo Busi 07 Mar '16

07 Mar '16

> Hi Mateo, > I'm not quite clear on what you are asking for. Do you want an ascii > output file that has a column containing chi(E) using the energy grid of > the original data? > If so, would it suffice to add a column to the mu(E) ascii output file? > That seems to me like a natural solution. >Cheers, >B Hi Bruce I would like to have an output file containing chi(E) and mu(E) using the same energy (E) grid. If I export them separately ( the only available thing right now) they have different energy grid. Thanks and Regards 2016-03-04 15:18 GMT+01:00 <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. Exporting Athena projects data (Matteo Busi) > 2. Collected k-space and fitting range (Taehoon Kim) > 3. Re: Collected k-space and fitting range (Scott Calvin) > 4. Re: Exporting Athena projects data (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 3 Mar 2016 23:53:54 +0100 > From: Matteo Busi <basebush(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Exporting Athena projects data > Message-ID: > <CAOyEiGi7jNury5oTAostBixxinOF+Vxcg2= > 8Sf8VeM9rywEmrg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Bruce, hi mailing list readers. > With the project I'm working with, it came out that would be really useful > for me to export groups in both .xmu and .chi . > More in details I have to deal with a function that depends on both the chi > and xmu data. I tried to look at all the chances and through the guide but > I didn't find any function to do that. I was thinking of exporting > separately the .chi and .xmu data, but they have different point of the > Energy(eV) and that makes hard the programming of my evaluating scripts. > Should I use the spline function to estimate the .xmu data and use it > combined to the .chi data? > > Hope it's all clear. Thanks > Best Regards, > Matteo, UiS >

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Collected k-space and fitting range
by Taehoon Kim 04 Mar '16

04 Mar '16

Hello, I am a bit confused about the range of k-space, which may affect the quality of EXAFS fitting. I would like to understand whether there is a difference between the fitting using an identical fitting range of k-space obtained from different range of k-space collected. For example, is there a notable difference between a fitting of k = 2.3-11 which was deduced from a spectra data collected up to k=12 and a spectra data collected up to k=13 ? Kind regardsTerry

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Exporting Athena projects data
by Matteo Busi 04 Mar '16

04 Mar '16

Hi Bruce, hi mailing list readers. With the project I'm working with, it came out that would be really useful for me to export groups in both .xmu and .chi . More in details I have to deal with a function that depends on both the chi and xmu data. I tried to look at all the chances and through the guide but I didn't find any function to do that. I was thinking of exporting separately the .chi and .xmu data, but they have different point of the Energy(eV) and that makes hard the programming of my evaluating scripts. Should I use the spline function to estimate the .xmu data and use it combined to the .chi data? Hope it's all clear. Thanks Best Regards, Matteo, UiS

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Re: [Ifeffit] fluo_corr() script
by Matt Newville 26 Feb '16

26 Feb '16

Hi Gerome, (I'm CCing this to the Ifeffit mailing list) On Thu, Feb 25, 2016 at 9:30 PM, Gerome Melaet <gmelaet(a)lbl.gov> wrote: > Dear Dr. Newville, > I have tried to use the flu_corr() function to correct some of my recent > x-ray data on the cobalt K-edge. > Unfortunately, after multiple tryout I am unable to get it to work > properly. > I have received this error message a couple of time. > > > *File > "/Volumes/Python/anaconda/lib/python2.7/site-packages/larch/__init__.py", > line 37, in wrapper* > * return fcn(*args, **keywords)* > * File "/Volumes/Python/anaconda/share/larch/plugins/xafs/fluo.py", line > 57, in fluo_corr* > * muvals = material_mu(formula, energies, density=1, _larch=_larch)* > * File > "/Volumes/Python/anaconda/lib/python2.7/site-packages/larch/__init__.py", > line 37, in wrapper* > * return fcn(*args, **keywords)* > * File "/Volumes/Python/anaconda/share/larch/plugins/xray/materials.py", > line 68, in material_mu* > * mater = _materials.get(name.lower(), None)file <stdin>, line 0* > *AttributeError: ‘int' object has no attribute 'lower'* > > I have a .dat file two column with energy and normalized mu (I have done > most of the energy corrections during my shift at the synchrotron). > I am able to load both energy and mu, yet I am not sure I handle the > different args correctly in the fluo_corr() function. > > Here is how I tried: > > fluo_corr(dat.energy, dat.mu, formula=None, elem=‘Co’, edge=‘K’) > > Thanks in advance for your help, > > Best, > Gerome > Yes, you need to pass a valid (even if approximate) formula for the chemical composition of the material. See http://xraypy.github.io/xraylarch/xray/index.html#x-ray-properties-of-mater… for some further details. You might want to do something like fluo_corr(dat.energy, dat.mu, formula='Co0.5Fe0.5S04', elem=‘Co’, edge=‘K’) Perhaps obviously, getting the composition of light elements perfect is not critical. It's often noticed that one has to lower the concentration of the absorbing element some (perhaps even by half) to avoid over-correcting. As with many things, it's always good to practice on a system where you're pretty confident what the right answer should be. --Matt

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Re: [Ifeffit] problem with transfer of prj fils
by fred.mosselmans＠diamond.ac.uk 22 Feb '16

22 Feb '16

Hi Thomas Are you sure both the users have the same version of Athena. I have seen this behaviour when discussing analysis with my users and they are not using the latest version of Demeter and I am. Then the prj crashes Athena for the person with the old version. Thanks Fred -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Problem with transfer of prj files
by Huthwelker Thomas (PSI) 22 Feb '16

22 Feb '16

Dear All, I find this Problem with the transfer of Athena project files: An Athenae project file is created on a one computer and saves on a harddisk. This file is then transferred to another person working on another computer. When opening the *.prj file on the new PC, Athena crashes. This happens if Athena is opened first and one tries to import the prj file into an open Athena, or if one just double clicks the *.prj file to start Athena. Operating system: Windows 7 Thanks for information, Thomas

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problem with Artemis crashing on mac
by Katherine M. Davis 16 Feb '16

16 Feb '16

Hello all, I was wondering whether anyone had experienced this problem or had some advice for what I can try. I have Demeter installed successfully on my mac (Yosemite 10.10.5). Athena works just fine. However, when I try running Artemis, it begins to open fine and all the GUI windows look good, but then a popup that says 'Restore from an autosave file' with buttons for 'Cancel' or 'OK' appears. I'm not able to click on anything and the program does not progress from this point. I don't remember this happening when I first installed. Is there an easy way to go in and trash some potential autosave file I have that is causing problems? If so, where would that be located? I dug around a bit, but couldn't find anything obvious. It's a little odd, because I've not really used the program. I simply tested it when I first installed to ensure it worked and that was it. Any thoughts or comments would be useful. If additional information would help in diagnosing the issue, I'm happy to provide it. Thanks, Kate

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Re: [Ifeffit] Ifeffit Digest, Vol 156, Issue 6
by Adi Shivprasad 10 Feb '16

10 Feb '16

Dear Riti, Thanks for the response. It was very helpful in better understanding my system. Adi On Wed, Feb 10, 2016 at 1:00 PM, <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. Feature near edge of Ni XANES spectrum (Aditya Shivprasad) > 2. Re: Feature near edge of Ni XANES spectrum (Ritimukta Sarangi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 9 Feb 2016 21:19:21 -0500 > From: Aditya Shivprasad <aps202(a)psu.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Feature near edge of Ni XANES spectrum > Message-ID: > <CAFbAhodYDnzzK1keVptQVfhS4OJMR-VgB-vR= > wFL8TKVCfEBHw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear list, > > I have obtained nickel XANES spectra (attached) from metallic Zircaloy-2 > nuclear fuel cladding (Zr, 1.5% Sn, 0.15% Fe, 0.1% Cr, 0.05% Ni). > > In the spectrum, I identify the edge as being approximately 8331-8332 eV > (based on maximum of first derivative), as it is for pure Ni. However, I > also identify a sharp feature at less than 1 eV past the edge. If anyone on > the list could help me to understand the origin of this feature, that would > be very helpful. > > Thanks > -- > Aditya Shivprasad > > aps202(a)psu.edu > Ph.D Candidate > Nuclear Engineering Department > Pennsylvania State University >

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