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

Re: [Ifeffit] Ifeffit Digest, Vol 163, Issue 10
by Matteo Busi 13 Sep '16

13 Sep '16

Dear Bruce, Attached is an example of multiple data sets project, Please try to: 1. Load all the data sets of the project 2. Mark only the data set: "merge" 3. Save current group as: "____" 4. Save marked group as "____" 5. Open both files in a notepad 6. Notice the differences I hope this is detailed enough, ( I have attached my saved files as well) Best regards, Matteo 2016-09-12 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: Saving Bug (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 12 Sep 2016 09:34:52 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Saving Bug > Message-ID: <96f04ebb-4477-3911-d6e2-e5eef2973cdb(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 09/10/2016 07:03 PM, Matteo Busi wrote: > > > > It occurs when I try to save groups to files, it seems that the saving > > option change the output while it shouldn't. When I save using the "Save > > current group as ..." option I get the full log with many columns, > > whereas when I save using the "Save marked group as ..." option I only > > get 2 columns. > > (I saved only as xmu and norm but I guess it is occuring for every > > extension) > > I do not see this behavior. It's not that I don't believe you, it is > that you have not provided enough information for me to see the problem > on my own computer. > > I need to know things about the state of Athena that should be contained > in the project file. Specifically, I want to know that you have > actually marked groups before trying to "Save marked groups as ..." > > So, post a project file that displays this behavior AND provide an > explicit recipe of mouse clicks so I can reproduce it on my computer. > > B > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 743, Room 114 > 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 163, Issue 10 > **************************************** >

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Saving Bug
by Matteo Busi 12 Sep '16

12 Sep '16

Dear Bruce and all, I think I found a minor bug in the Athena package (0.9.25). It occurs when I try to save groups to files, it seems that the saving option change the output while it shouldn't. When I save using the "Save current group as ..." option I get the full log with many columns, whereas when I save using the "Save marked group as ..." option I only get 2 columns. (I saved only as xmu and norm but I guess it is occuring for every extension) It is a minor bug but I think if it doesn't take much time it is worth correcting. Regards, Matteo Busi

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Re: [Ifeffit] Help in background removal with Athena
by fred.mosselmans＠diamond.ac.uk 07 Sep '16

07 Sep '16

-----Original Message----- From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 06 September 2016 14:57 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 163, Issue 6 Dear Irina, Your efforts are probably sadly in vain. C K-edge NEXAFS or XANES is common, but the data range is rarely long enough for exafs analysis. You have ca 160 eV of data that is not enough for EXAFS analysis. Hence I don't think there is a way to get a good background and then FT for your data. Certainly looking at your data the noise level and thus uncertainty in which features are real and which may not be will probably prevent anything but a XANES analysis. There probably is an oscillation there but with the limited data range getting meaningful numbers from a fit is most unlikely. Best wishes Fred 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. Help in background removal with Athena (Irina Pi) ---------------------------------------------------------------------- Message: 1 Date: Tue, 6 Sep 2016 13:56:19 +0000 From: Irina Pi <Irina.Pi(a)icfo.eu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Help in background removal with Athena Message-ID: <VI1PR0601MB22877AFA6B07BEE3CFDCEC798DF90(a)VI1PR0601MB2287.eurprd06.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Dear all, I am sorry to bother you with my tiny problems, but I have been struggling with it for a long time. The thing is I have XAS data from a graphite sample, and I don't know if I'm plotting the background correctly in it with Athena software, which determines a lot the response in the Fourier transform, and thus in our results. I'm attaching the data as data_exafs.txt, and also two different Athena projects of different backgrount fittings, graphite_exafs1.prj and graphite_exafs2.prj. Just in case projects cannot be seen, I'm also attaching screenshots (1-01deg.png and 2-01deg.png) of the different background fittings and the parameters used in Athena in only one set of data (01deg), because they are the same in the others (02deg and 35deg). Also, the final R-space plot in both fittings are sent (1-rspace.pdf and 2-rspace.pdf). What I wanted to ask is why it is so different the result according to the background removal. And are they correct the fittings I've done? I would like to have a background line similar to the other figure attached (0deg.pdf, but take into account that it is from different data), but I cannot get it. I guess this last fitting seems better, doesn't it? What could I do to have good results in the Fourier transform? Again, sorry but I don't have much experience and it seems to be so subjective that I fear doing it all wrong. Thank you very much, Best regards, Irina Pi Jauma.

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Re: [Ifeffit] Help in background removal with Athena
by fred.mosselmans＠diamond.ac.uk 06 Sep '16

06 Sep '16

Hi Irina, I guess in a normal situation you would want to FT at least 5 k(1/A) range to get some sort of shape to your FT peaks which would normally be a range of about 2 -7 k so maybe 190 eV above the edge. However added to that the data has to be good, I am not a C XAS expert but looking at your data I am unsure that all the oscillations are due the x-rays scattering , some might be experimental artefact which would then make the analysis even less trustworthy. WRT your data after the signal begins to die about 400 eV, i.e. you have ca 110 eV of data I might trust on a good day and even then I'd be more reassured if these were several scans added rather than just one. (I can't tell if this is the case). I doubt there is useful stuff that can be extracted past that point. Hence I think all that is probably there is the pre-edge changes in the XANES which I presume you are looking at as well. 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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Help in background removal with Athena
by Irina Pi 06 Sep '16

06 Sep '16

Dear all, I am sorry to bother you with my tiny problems, but I have been struggling with it for a long time. The thing is I have XAS data from a graphite sample, and I don't know if I'm plotting the background correctly in it with Athena software, which determines a lot the response in the Fourier transform, and thus in our results. I'm attaching the data as data_exafs.txt, and also two different Athena projects of different backgrount fittings, graphite_exafs1.prj and graphite_exafs2.prj. Just in case projects cannot be seen, I'm also attaching screenshots (1-01deg.png and 2-01deg.png) of the different background fittings and the parameters used in Athena in only one set of data (01deg), because they are the same in the others (02deg and 35deg). Also, the final R-space plot in both fittings are sent (1-rspace.pdf and 2-rspace.pdf). What I wanted to ask is why it is so different the result according to the background removal. And are they correct the fittings I've done? I would like to have a background line similar to the other figure attached (0deg.pdf, but take into account that it is from different data), but I cannot get it. I guess this last fitting seems better, doesn't it? What could I do to have good results in the Fourier transform? Again, sorry but I don't have much experience and it seems to be so subjective that I fear doing it all wrong. Thank you very much, Best regards, Irina Pi Jauma.

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Re: [Ifeffit] need help to get better fitting (Dali Yang)
by Dali Yang 06 Sep '16

06 Sep '16

Hi, Mia, In your Artemis file “Cs1.33Fe1.33_FeKedge_Fit.fpj”, It seems that you are using a Ti atom as the core atom instead of an Fe atom. So, you are trying to fit a Fe_K_edge EXAFS using a "Ti-O” and ”Ti-Ti" path? That is probably the major problem. However, I tried to replace the core atom in your feff input file, but I can not get a reasonable fitting for the first shell either(see the attachment). I guess you are using a cif file which is not your real Fe dopant sample. The Fe dopant might expand your structure to make Fe-O path(bond length, coordination) very different from Ti-O, so we can not get a decent fitting for this data. Meanwhile, I can not see the meaning by using a Fe foil to extract the S0^2 for your data fitting. Good luck, Dali > Message: 1 > Date: Mon, 5 Sep 2016 15:58:47 -0400 > From: Yun Xu <yunxulanl(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] need help to get better fitting > Message-ID: > <CAKGyrcG_CuCNQDBWQc1b48XQks33VJgdnMnF20RhEo8MHo1GPw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > *Hello, This is Mia From Clemson University.* > *I have problem with my fitting, this has bothered me for long time.* > *So the thing is I use Fe metal foil as reference, and I was able to get > S02 from fitting the Fe metal foil XAS as seen in the attached file > Fe_metal foil fit.* > *Then I used this S02 value to fit the Fe_kedge exafs data of Hollandite > sample, Cs1.33Fe1.33Ti6.67O16. The hollandite crystal structure cif file is > also attached as hollandite.cif. Fe and Ti sit in the six oxygen > coordinated octahedral. the crystal structure is shown in the attached > figure as hollandite.jpg. (neglect the color of octahedra) This cif file is > the original structure without dopant as BaTi8O16 (I4/m space group). so I > set the core atom as Fe in the Feff, and assume second and third shell as > Ti, in the DFT calculation, Fe octahedra tend to have a Ti octahedra as > neighbor rather than a Fe ocatahedra. * > *I've also attached my artemis file to see anybody could help me get a > better fitting. I just need to fit the range up 3.5A which includes the > first oxygen shell and Two Ti shell.* > *A specific question is I always get negative S02 value, can any body tell > me what I should do if I get negative S02.* > *Thank you very much* > *Mia* >

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need help to get better fitting
by Yun Xu 05 Sep '16

05 Sep '16

*Hello, This is Mia From Clemson University.* *I have problem with my fitting, this has bothered me for long time.* *So the thing is I use Fe metal foil as reference, and I was able to get S02 from fitting the Fe metal foil XAS as seen in the attached file Fe_metal foil fit.* *Then I used this S02 value to fit the Fe_kedge exafs data of Hollandite sample, Cs1.33Fe1.33Ti6.67O16. The hollandite crystal structure cif file is also attached as hollandite.cif. Fe and Ti sit in the six oxygen coordinated octahedral. the crystal structure is shown in the attached figure as hollandite.jpg. (neglect the color of octahedra) This cif file is the original structure without dopant as BaTi8O16 (I4/m space group). so I set the core atom as Fe in the Feff, and assume second and third shell as Ti, in the DFT calculation, Fe octahedra tend to have a Ti octahedra as neighbor rather than a Fe ocatahedra. * *I've also attached my artemis file to see anybody could help me get a better fitting. I just need to fit the range up 3.5A which includes the first oxygen shell and Two Ti shell.* *A specific question is I always get negative S02 value, can any body tell me what I should do if I get negative S02.* *Thank you very much* *Mia*

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Co fitting questions
by Neil M Schweitzer 02 Sep '16

02 Sep '16

I have been trying to fit a Co(OH)2 reference sample and think I have a good fit, but I have a couple reservations about it and wanted to run it by some people for an expert opinion. If you are interested, I have included the Athena file, an image of the fit, and the fit log file. Please read on! If not, sorry I spammed you. As you can see, the fit contains four paths. They are all single scattering paths, and the paths with the four largest ranks according to feff. All paths share the same SO2 and deltaE. Each path has its own delR and ss. After some work, I got it to the point that the fit looks pretty (R-factor<0.02), but I have several reservations about it: 1) Generally, the ss values are all higher than I would like. 0.007 even seems high to me for a metal-O bond. Am I right about this? Would this indicate that this may have been a poor choice for reference sample (I should mention it is a powder) and it is not very crystalline? Could it mean there was something we overlooked when we recorded the data? 2) The biggest problem with the fit is the large error on ss_O2 and ss_O3. The largest feature at ~2.75 is obviously Co-Co scattering, but the Co-O paths help to fit the shoulder (or feature at ~3.1 in the Real part) in R-space. If I take them out, then the Co path has a large ss with an equally large error. So here is my question. If I add more paths, the error of ss_O2 and ss_O3 will go down, but then the errors on the new path will consequently be large, so when do I stop adding paths? For the purpose of my samples, I am only interested in the first Co-O path and the Co-Co path. Is this fit good enough you would publish it? Please feel free to critique any other aspect of the fit too. Thanks for your input! Neil

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Larch user base?
by Sean Fackler 01 Sep '16

01 Sep '16

Hello all! Do you have an idea of Larch user base or Larch package download stats? Thanks for any information. Regards, Sean Fackler, PhD Joint Center for Artificial Photosynthesis Lawrence Berkeley National Lab 1 Cyclotron Rd Mail Stop 30R0205 Berkeley CA, 94720 Mobile: 609-613-8734

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Phase correction not working in Athena
by Sebastian George 31 Aug '16

31 Aug '16

Dear all, I hope that I am writing this in the correct place, and if I am not, I apologize. The problem I'm having is pretty much summed up in the Subject line. I'm analyzing some experimental EXAFS data in Athena, and it seems that ticking the "phase correction" box has no effect on my Forward Fourier transform. Has anybody run into this problem, and if so, were you able to fix it? The material I'm studying is amorphous SmCo. Could it be that having multiple backscattering species or a lack of crystalline structure causing problems for the phase correction? More generally, I'm wondering how exactly this phase correction is determined anyway. If used, is it the sort of thing that can put the first peak in my FT fairly close to the true nearest neighbor distance? Perhaps a better phrased question is: when can the phase transformation be expected to give a quantitatively accurate radial distribution (in terms of peak positions), and when is it more likely to only be qualitatively useful? Also, I would have assumed that a backscattering species would need to be given in order to calculate the phase shift, but I haven't found anywhere to do that. Have I missed something? Thank you for any help in advance! Regards, Sebastian

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pgplot and ifeffit installation on current linux systems
by Loges, Anselm G 26 Aug '16

26 Aug '16

Dear all, I hope this is the right platform for my question. If not, sorry to bother anyone. The question: Has anyone successfully installed pgplot and ifeffit on a recent Arch Linux system and could provide a quick how-to guide (also for the Demeter website maybe)? Although I have not yet tested it, my problem may also be relevant for current Debian/Ubuntu systems. Here's the situation: I am trying to install ifeffit on a current Arch Linux machine and therefore need to install pgplot first. The PGPLOT_install script on the respective GitHub page (as linked by a tutorial on the Demeter page, see links below) does not work because it relies on several outdated paths to dependencies. The one culprit I was able to isolate and fix was the path to the X11 libraries, which the script looks for here: /usr/X11 or /usr/X11R6 but in current Arch Linux (at least in mine, which is Manjaro to be precise, link below) is here: /usr/share/X11 This alone does not fix all problems, there are several dependencies missing in the X11 directory and I could not find out what the actual relevant package names are in Arch (Debian/Ubuntu names cannot be found). Also the config files of pgplot seem to have a bunch of similar problems that (at least partially) seem to stem from use of an old fortran-to-c translator (f2c) instead of the gcc fortran frontend and missing dependencies for that. If I am not mistaken, the latest Ubuntu LTS (16.04.) also has the /usr/share/X11 path, so the script should not work there either. I'd be happy to provide an updated installation script if I ever get it running but I thought I'd ask if someone has done that already or has solved the related problems so as not to invent the wheel anew. Links: <https://bruceravel.github.io/demeter/documents/SinglePage/installation.html>https://bruceravel.github.io/demeter/documents/SinglePage/installation.html https://github.com/newville/ifeffit <https://manjaro.github.io/>https://manjaro.github.io/ Best regards, Anselm

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Demeter Installation issues
by Gaurab Rimal 23 Aug '16

23 Aug '16

Hello, I have been trying to install demeter in my archlinux machine but have issues in the build process. I had issues installing pgplot from ifeffit git source so I installed pgplot separately (as outlined in the original pgplot instructions). After installing ifeffit and after all dependencies were met, I ran ./Build and got an error about 'cpg/libgcc_path.sh'. Below is the full output from ./Build. I am unsure of this error because it seems to be related to ifeffit and pgplot and do not know how to resolve this. $ ./Build Ifeffit's installations directory is /usr/local/share/ifeffit (found by capturing `ifeffit -i`) Compilation flags (from /usr/local/share/ifeffit/config/Config.mak): -L/usr/local/lib -lifeffit -L/usr/local/pgplot/ -lpgplot -lX11 `/cpg/libgcc_path.sh` -lgcc -lm -lc -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../.. -lgfortran -lm -lgcc_s -lquadmath cc -I/usr/lib/perl5/core_perl/CORE -fPIC -L/usr/local/lib -lifeffit -L/usr/local/pgplot/ -lpgplot -lX11 `/cpg/libgcc_path.sh` -lgcc -lm -lc -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../.. -lgfortran -lm -lgcc_s -lquadmath -c -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -o src/ifeffit_wrap.o src/ifeffit_wrap.c cc: error: `/cpg/libgcc_path.sh`: No such file or directory error building src/ifeffit_wrap.o from 'src/ifeffit_wrap.c' at /usr/share/perl5/core_perl/ExtUtils/CBuilder/Base.pm line 174, <C> line 11. Gaurab

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Re: [Ifeffit] Ifeffit Digest, Vol 162, Issue 17
by Christopher Thomas Chantler 13 Aug '16

13 Aug '16

Topic 1: We have a routine /edit within ifeffit (our modified version) which propagates and fits uncertainty. Working on a couple of minor details before passing it on to Matt and Bruce for general use. Topic 3: Monochromator glitches should be eliminated in absorption spectra under normal circumstances if the dark current estimation is well defined. I recommend careful measurement and recording of this for all spectra. ------------------------------------------------------------ Christopher Chantler, Professor, FAIP Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS President, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au chantler(a)me.com http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html http://optics.ph.unimelb.edu.au/~chantler/home.html ________________________________________ From: Ifeffit [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Friday, 12 August 2016 11:22 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 162, Issue 17 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. Statistical errors in linear combination fits (Joshua Kas) 2. Re: Statistical errors in linear combination fits (Bruce Ravel) 3. Athena interpolation when removing mono glitches (Michael Gaultois) 4. Re: Athena interpolation when removing mono glitches (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Thu, 11 Aug 2016 13:31:45 -0700 From: Joshua Kas <joshua.j.kas(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Statistical errors in linear combination fits Message-ID: <CAHuhYRm_Dx5+_HAUuOZ0nCwzXwCrS-Subxb9dmBXDsQp8wmSRQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi All, I was wondering if it is possible to pass a value for the uncertainty in the data to Athena when doing linear combination fits. We have calculated chi^2 values using a simple estimate of the statistical uncertainty, and find that our values differ by several factors of 10 when compared to the reported values from Athena. I assume that this has to do with value of the uncertainty that Athena is using, but I certainly could be mistaken. In any case, the reduced chi^2 reported by Athena is much smaller than 1, while the fit is off by fairly large amounts compared to any reasonable estimate of the statistical error. Thanks in advance for any help and sorry if this info is already available in the archives, Josh Kas

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Athena interpolation when removing mono glitches
by Michael Gaultois 12 Aug '16

12 Aug '16

Dear members of the Ifeffit list, I recently collected some EXAFS data with some significant monochromator glitches that I am looking to remove. I have used a python script graciously written by the beamline scientist to remove the offending regions, but when I import the data into Athena, Athena does some funny business in an attempt to join together the regions outside of the data gap. (See the bending away in the dataset and/or attached image.) I have confirmed by plotting with other software that the strange step-like behaviour in the mu(E) is present only after importing into Athena (the raw data is fine). I have looked through the mailing list archives and also the user manual, but can't seem to find anything that explains it, or other people who have experienced this problem in the past. From what I can determine, Athena joins together the segments to obtain a linear interpolation in the norm(E)? This leads to a warping in the mu(E). ==How does Athena try to treat this data?== I was wondering if other people have had similar issues, and what steps can be taken to remedy the problem. For example, replacing removed data points with artificial points along a linear interpolation would be possible, but the act of adding artificial points that don't exist is concerning to me. ==What is the best way to treat data with mono glitches to reduce spurious features not intrinsic to the sample?== If you are interested, I have included links to .prj datasets and images to highlight these problems below. With thanks for your time, Michael ---------- .prj file with 4 ways of working up the same data: http://bit.ly/2bnfNZ5 1) raw data 2) mono glitches removed 3) rebinned data 4) rebinned and manually removed points (This leads to some strange-looking features in k-space, and this would be less than desireable on the many datasets we have collected) images to highlight these problems: a) mu(E) http://bit.ly/2aYaJIf b) norm(E) http://bit.ly/2aYaX27 c) k http://bit.ly/2baWh0h

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Statistical errors in linear combination fits
by Joshua Kas 11 Aug '16

11 Aug '16

Hi All, I was wondering if it is possible to pass a value for the uncertainty in the data to Athena when doing linear combination fits. We have calculated chi^2 values using a simple estimate of the statistical uncertainty, and find that our values differ by several factors of 10 when compared to the reported values from Athena. I assume that this has to do with value of the uncertainty that Athena is using, but I certainly could be mistaken. In any case, the reduced chi^2 reported by Athena is much smaller than 1, while the fit is off by fairly large amounts compared to any reasonable estimate of the statistical error. Thanks in advance for any help and sorry if this info is already available in the archives, Josh Kas

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Converting PDF files to CIF files for usage in Artemis
by Ed Han 09 Aug '16

09 Aug '16

Hello All, I apologize in advance if this is not the correct method to reply to the thread. Thank you for your replies and suggestions. I will look further into determining the atomic structure of the Hf-Al intermetallics through their papers. Once I obtain this information, how do I go about creating the actual CIF file? Can I just open up any arbitrary CIF file and then change the parameters and name to match that of the Hf-Al systems? Lastly, going through some CIF files from crystallography.net, I notice that some of the 3D models from the CIF has a different stoichiometry from the designated crystal. For example, I have attached a CIF file of SiO2 that I have found; however, the 3D representation only has 1 Silicon atom and 1 Oxygen atom. Do you have any insight on this disparity? Regards, Ed Han

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Ti data problem
by Siliang Chang 08 Aug '16

08 Aug '16

Dear all, I am new to XAFS data analysis. Im currently working on the XAFS data of atomic layer deposited mixed oxide thin film: SnTiOx. I have both Sn and Ti K edge data, and was able to fit Sn edge using a model of (Sn,Ti)O2 solid solution. However, Ti data really confuses me (please see attached file). With Rbkg set to 1, there is a doublet in 1-2 Å region in every data, this is something I have never seen in the literature. Im wondering if this is normal? Does this mean I should set a larger Rbkg value, say, around 1.5? Ive tried to fit the abovementioned Ti data using several models: anatase, rutile, (Sn,Ti)O2 solid solution, perovskite (N is fixed at 6 for all of those), so far no success. I would really appreciate if you can comment on my data processing, any suggestions are welcomed, as Im new to this, Im not sure if Im doing it the right way. Thank you very much. Best regards, Siliang Chang

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Converting PDF files to CIF files for usage in Artemis
by Ed Han 08 Aug '16

08 Aug '16

Dear All, In the upcoming fall, my research group plans on performing XAS studies observing the Hf L3-edge for various Hf-Al intermetallic samples. In preparation for the experiments, I am looking for CIF files of the various Hf-Al intermetallic systems, including HfAl3, HfAl2, Hf4Al3, etc. Upon scavenging through a multitude of crystallographic databases, I was not able to find any CIF files of Hf-Al intermetallics. However, I have acquired powder diffraction files (PDF) for said intermetallics. Seeing as how PDFs cannot be used in Artemis for EXAFS data analysis (to my knowledge), is there a way to convert PDFs into CIFs? I have attached one of the PDF files to demonstrate what information it contains. I would really appreciate your help! Regards, Edmund Han

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Amorphous
by Carlos Triana Estupinan 08 Aug '16

08 Aug '16

Dear Bruce I want to know if it is possible to obtain a 3D structure (.cif file) of an amorphous material from the EXAFS fitting carried out from artemis. I mean, there is a way to extract a .cif file with the structural data obtained from the refined spectra. Also, in amorphous materials there must be a distribution of interatomic bond distances and coordination, and so, how can I address such a structural distribitions. Regards.

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Multi-electron peak in Yb
by Matthew Marcus 05 Aug '16

05 Aug '16

Does anyone know of data on multi-electron peaks at the Yb L3 edge? One of the users here was just running Yb and finds on every spectrum a bump at the same energy. It's not a Bragg glitch from the sample or an I0 glitch or any other obvious artifact. It reminds me of the two little bumps at Ce. If someone has analyzed and parameterized this peak as a fraction of edge jump, then it would be possible to subtract it off. The attached papers show exmples for almost every lanthanide *execpt* Yb. For those doing Ce, I've written a program which does the correction, essentially as presented in the attached Gomilsek paper. Like Ce, Yb hs 2 valence states (other than 0), but the user is sure that his sample is all 3+. mam

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Re: [Ifeffit] Questions about fitting of EXAFS
by Scott Calvin 04 Aug '16

04 Aug '16

Just to clarify: the shape of the FT may certainly change when you change kmax. But if the data and the model change in the same way, then the fit is insensitive to the choice of kmax, in the sense that the fitted parameters remain stable to within their reported uncertainties. —Scott Calvin Sarah Lawrence College On Aug 4, 2016, at 2:50 PM, Fuxiang Zhang <zhangfx(a)umich.edu<mailto:zhangfx@umich.edu>> wrote: The Kmax effect on the shape of magnitude of FTs of one of my samples may come from the low signal/noise ratio.

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Questions about fitting of EXAFS
by Fuxiang Zhang 04 Aug '16

04 Aug '16

Hi, Everyone, I have several detailed questions about EXAFS processing and fitting 1. Are there any physical meaning for DeltaE0 in the paths, why it should be less than 10eV 2. The cutting range of Kmax (FT transform parameters) has great effect on FTs of EXAFS, how do I know to use the best value of Kmax; 3. How to make refinement equation for multi-scattering paths? Such as in NiFe alloys (simple fcc structure), the path [Ni-FM-3m] Fe1.1 Ni1.4 Fe1.1., I use 0.67*Efe+0.33*Eni for DeltaE0, and 0.67*ssFe1+0.33*ssNi4 for sigma2, is that right? Many thanks Fuxiang Zhang

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Applicable scope of delr=alpha*reff
by woschangqiang 03 Aug '16

03 Aug '16

Hi, everyone. delr=alpha*reff is very powerful in the fit of cubic system. And I want to know whether this function can be used in other crystal system. Thank for your patient answer.

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Reference spectra for brookite, anatase, rutile, Amorphous TiO2 at Ti K-edge
by Samy Ould-Chikh 03 Aug '16

03 Aug '16

Dear, I received some data at Ti K-edge to analyse. The spectra corresponds to samples which are different mixture of titania allotropes. I started to do standard EXAFS fitting, but it doesn't seem relevant in this case. Probably, an attempt to do linear combination fitting with brookite, anatase, rutile, and amorphous titania references will be more useful. Unfortunately, the set of data I was given do not include those standards. Is there anyone who have the spectra corresponding to those titania compounds and willing to share with us the raw data ? If yes, would you mind to provide also the citation I should you use to acknowledge those standards ? Many thanks for your kind help. Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa Website: http://kcc.kaust.edu.sa/Pages/Home.aspx ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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2016 Introduction to Synchrotron Radiation Course
by Carlo Segre 01 Aug '16

01 Aug '16

This fall semester I will be offering an introductory graduate level course entitled Introduction to Synchrotron Radiation at Illinois Tech. This course has been offered on a regular basis over the past 5 years and it is avilable as an online course through IIT/Online. Through a special arrangement with the Dean of the College of Science, online students can take this course as non-degree students at a 67% tuition discount. We have had students from Italy and Brazil in past sessions of this course. Registering for this course as a non-degree student requires a simple application which can be completed online and will be approved in only a few days. The course description is below. Please share this with interested parties and direct any questions to Carlo Segre <segre(a)iit.edu> Course Description: This is a graduate course which introduces students to the production, manipulation and use of synchrotron radiation in research. The course will include visits to, and possibly hands-on experience with, beamlines at the Advanced Photon Source (APS) at Argonne National Laboratory but is not specific to the APS. Students will be expected to give presentations and write a General User Proposal to the APS as their final projects. Graduate students in any science or engineering program are welcome to register as are undergraduates with senior standing and permission of instructor. It is particularly recommended for students wishing to make use of synchrotron radiation in their research. The class meets Mondays and Wednesdays 17:00-18:15 and the lectures are available online as an Internet section for students not on the IIT campus or even in the United States. Textbook: Elements of Modern X-Ray Physics, 2nd ed., Jen Als-Nielsen and Des McMorrow, (John Wiley & Sons, Ltd. 2011). Topics Covered: X-rays and their interaction with matter Sources of x-rays Refraction and reflection from interfaces Kinematical Diffraction Diffraction by perfect crystals Photoelectric absorption Resonant scattering Small angle scattering Other topics as appropriate Course Organization: The grade will be based equally on homework assignments, student presentations and a draft General User Proposal to the Advanced Photon Source. There will be at least one field trip to the Advanced Photon Source for experiment demonstrations. For more information please contact Carlo Segre <segre(a)iit.edu> -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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