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

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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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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