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

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

2 1

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.

3 3

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

2 1

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.

1 0

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* >

1 0

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*

1 0

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

2 4

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

2 5

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

3 2

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

3 3