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

Tenure-track academic position advert
by Robert Dryfe 01 Aug '16

01 Aug '16

Dear Sir/Madam, I would be grateful if you could circulate the details of an academic vacancy for an expert in the application of X-ray synchrotron techniques to chemical systems. Details can be found here (please note the application deadline is soon): https://www.jobs.manchester.ac.uk/displayjob.aspx?jobid=11764 Informal inquiries are welcome. regards, Robert Dryfe (School of Chemistry, University of Manchester, UK)

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Postdoc Position
by Jeff Terry 29 Jul '16

29 Jul '16

Hi All, I never remember what the rules are here for posting postdoc positions but I have one position available. You can see more information about the position here: http://mrmac.mr.aps.anl.gov/~jterry/postdoc.html Please let anyone who might be interested know. Thanks, Jeff Jeff Terry Professor, Department of Physics Illinois Institute of Technology Life Sciences Bldg Rm 166 3101 S. Dearborn St. Chicago IL 60616 630-252-9708

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Multiple scattering path parameters
by Neil M Schweitzer 29 Jul '16

29 Jul '16

Are there standard ways of relating the parameters (deltaR and sigma^2) of multiple scattering paths to the parameters of the single scattering paths based on the type of MS path? For example, would deltaR_MS = deltaR_SS*2 if the MS was a "forward through" geometry? What about other geometries and paths that involve different types of atoms? Neil

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Re: [Ifeffit] determining reasonable fitting parameters
by Neil M Schweitzer 27 Jul '16

27 Jul '16

Thanks to everyone for all the previous responses to my emails, I've learned a lot in the few weeks I've been on this list! I was hoping to build off of the last point Bruce made in message 3 below by asking another question. I am fitting a CeO2 reference from paths generated by feff from a cif file. Since this is my starting point, I made SO2 the same for every path (and used the coordination numbers from the cif file). If I am generating what looks to be a reasonable fit, but my SO2 is in the 0.55-0.7 range, what is my fit trying to tell me? Am I doing something wrong in my initial background subtraction in Athena? I'm asking about the background subtraction because I recently discovered that there is a CeO2 reference provided in Hephaestus. I exported the data, and tried to fit it in Artemis using a similar methodology I used for my own sample, and I got an even lower SO2. So I don't think the small SO2 value is an artifact of the way the experiment was run (although I might be wrong, I wasn't present when the data was actually collected). The observed difference seems real because the magnitude of the signal in E-space, k-space, and R-space is lower for the Hephaestus sample compared to my experimental sample (see attached image... One note, I'm not sure why the signals are off set in the Energy plot. The Eo's are the same, and if I plot the spectra together in E-space alone, they are not offset. Maybe a bug?). Neil -----Original Message----- From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, July 21, 2016 8:01 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 161, Issue 20 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia.cars.aps.anl.g… 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. demeter installation in OSX El Capitan (Ping, Yuan) 2. Re: determining reasonable fitting parameters (Bruce Ravel) 3. Re: determining reasonable fitting parameters (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Thu, 21 Jul 2016 05:37:10 +0000 From: "Ping, Yuan" <ping2(a)llnl.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] demeter installation in OSX El Capitan Message-ID: <D3B5AD95.32BB2%ping2(a)llnl.gov> Content-Type: text/plain; charset="windows-1252" Dear all, I recently upgraded my mac to OSX El Capitan, and tried to install demeter following the steps at https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_de… XQuartz 2.7.9 (xorg-server 1.17.4), Xcode 7.3.1, command line tools, ?sudo port -v self update?, ?port upgrade outdated? were all OK. When I tried ?sudo port install xorg-server demeter?, it showed: ---> Computing dependencies for xorg-server ---> Cleaning xorg-server ---> Computing dependencies for demeter ---> Dependencies to be installed: ifeffit libgcc cctools llvm-3.8 ---> libcxx libffi llvm_select gmp isl ld64 ld64-latest libmpc mpfr ---> pgplot gcc5 ... (a long list) Then after many attempts to fetch libcxx-3.7.1_0.darwin_15.x86_64.tbz2 from various websites, it showed: Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.7.1_0 Error: Failed to install libcxx Please see the log file for port libcxx for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_libcxx/libcxx/main.log The log file is attached. What should I do to fix it? Any suggestion will be appreciated. Thanks. Yuan

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Re: [Ifeffit] determining reasonable fitting parameters
by Neil M Schweitzer 27 Jul '16

27 Jul '16

Thanks for the responses. Seems like it is a problem without a simple solution, especially after the experiment has already been performed. When my users rerun the samples, I'll have to make sure they are very careful. In terms of the question about fitting the Hephaestus reference, when you plot it in Hephaestus it only shows out to ~50eV, but when you save the data file the data goes out much further. You can see from the plots I had included that the data goes out past k=10 A^-1. Neil -----Original Message----- From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, July 27, 2016 4:09 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 161, Issue 39 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia.cars.aps.anl.g… 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: determining reasonable fitting parameters (Matthew Marcus) 2. Re: determining reasonable fitting parameters (Bruce Ravel) 3. Re: determining reasonable fitting parameters (Matthew Marcus) 4. Re: determining reasonable fitting parameters (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 27 Jul 2016 13:39:03 -0700 From: Matthew Marcus <mamarcus(a)lbl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] determining reasonable fitting parameters Message-ID: <c2c71f99-44d9-f17f-ab52-399f53d8bb83(a)lbl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed I'm not sure I get your point about ion-chamber response. Shouldn't that normalize out in post-edge spline? If the I0 chamber gets less sensitive as a function of energy, then the post-edge background rises by the same amount as the wiggles get bigger, so it divides out. Similarly for probe-depth effects, depending on concentration. Another couple of possible sources of amplitude error: 1. The model for the pre-edge background is inaccurate, so that its extrapolation to the EXAFS region is incorrect. For instance, if there's a lot of elastic scatter getting into the fluorescence detector, then the pre-edge is curved, and if you model that with a straight line fitted near the edge, them you'll be off far from the edge. Similarly, in a long transmission scan, both pre- and post-edge are curved. My background-sub program has simple models for thse shapes which aren't perfect but help. This effect is really hard to control for because you have no real way to know what the 'right' answer is, most of the time. 2. Overabsorption will definitely reduce the amplitude of the wiggles, and I'm surprise Bruce didn't menntion it. It looks much like pinhole effect. Harmonics do similar things as well in transmission. I still haven't heard how you do EXAFS analysis using the short spectrum from Hepheastus. mam On 7/27/2016 1:23 PM, Bruce Ravel wrote: > On 07/27/2016 03:53 PM, Neil M Schweitzer wrote: >> Thanks to everyone for all the previous responses to my emails, I've >> learned a lot in the few weeks I've been on this list! I was hoping >> to build off of the last point Bruce made in message 3 below by >> asking another question. I am fitting a CeO2 reference from paths >> generated by feff from a cif file. Since this is my starting point, I >> made SO2 the same for every path (and used the coordination numbers >> from the cif file). If I am generating what looks to be a reasonable >> fit, but my SO2 is in the 0.55-0.7 range, what is my fit trying to >> tell me? Am I doing something wrong in my initial background >> subtraction in Athena? >> >> I'm asking about the background subtraction because I recently >> discovered that there is a CeO2 reference provided in Hephaestus. I >> exported the data, and tried to fit it in Artemis using a similar >> methodology I used for my own sample, and I got an even lower SO2. So >> I don't think the small SO2 value is an artifact of the way the >> experiment was run (although I might be wrong, I wasn't present when >> the data was actually collected). The observed difference seems real >> because the magnitude of the signal in E-space, k-space, and R-space >> is lower for the Hephaestus sample compared to my experimental sample >> (see attached image... One note, I'm not sure why the signals are off >> set in the Energy plot. The Eo's are the same, and if I plot the >> spectra together in E-space alone, they are not offset. Maybe a >> bug?). > > I don't remember much about the provenance of that CeO2 spectrum. I > don't remember how calibration was done (or even if it is reliable). > I don't remember much about the sample -- it was a pellet, but I have > no way of knowing if it was homogeneous or even if the particles were > of the size reported. > > I guess what I am trying to say is this -- if you trust your CeO2 > measurement, you should have more faith in that (or the one Matthew > just sent) than in the one from Hephaestus. > > As for your S02 question, here's some of the standard litany: > > + the mean free path used by feff was too long. > > + S02 and sigma^2 are highly correlated. > > + you did a lousy job normalizing the data (although it sure doesn't > look that way from your picture). > > + your sample had a lot of pinholes. > > + there is some source of loss in CeO2 that is neglected in Feff > (which is, practically speaking, the same as the mean free path > comment). You could try fixing S02 and floating an Ei parameter. > Or floating both S02 and Ei, although they will be highly > correlated. > > + There is also an energy response to the ionization chambers at such > a low energy -- that is, the absorption of the gas in the detector > is weaker at the end of the spectrum than at the beginning. In > fluorescence, that serves to attenuate the edge0step-normalized > spectrum in a way that looks like an enhancement to sigma^2. But > it's an attenuation, which could show up in S02. > > I should mention that in my favorite teaching example -- FeS2 -- by > the end of the lecture I have a S02 of something like 0.69. And I > just walk away from the lecture at that point :) The reason I do so is > that all the rest of the parameters are defensible and I chalk the > small S02 up to one of the points above (along with some enthusiastic > hand waving -- usually it's time for coffee or lunch by the time I've > finished the FeS2 demo!). > > B > > ------------------------------ Message: 2 Date: Wed, 27 Jul 2016 16:45:26 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] determining reasonable fitting parameters Message-ID: <e0a93edf-8a8b-97a5-aa14-f595fc385c31(a)bnl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed On 07/27/2016 04:39 PM, Matthew Marcus wrote: > I'm not sure I get your point about ion-chamber response. Shouldn't > that normalize out in post-edge spline? Athena edge-step normalizes (i.e. normalizes by a constant) by default. It does not do a functional (or energy dependent) normalization by default in the way you are suggesting. > If the I0 chamber gets less sensitive as a function of energy, then > the post-edge background rises by the same amount as the wiggles get > bigger, so it divides out. Similarly for probe-depth effects, > depending on concentration. Another couple of possible sources of > amplitude error: > 1. The model for the pre-edge background is inaccurate, so that its > extrapolation to the EXAFS region is incorrect. > For instance, if there's a lot of elastic scatter getting into the > fluorescence detector, then the pre-edge is curved, > and if you model that with a straight line fitted near the edge, > them you'll be off far from the edge. Similarly, in > a long transmission scan, both pre- and post-edge are curved. My > background-sub program has simple models for thse > shapes which aren't perfect but help. This effect is really hard > to control for because you have no real way to know > what the 'right' answer is, most of the time. > > 2. Overabsorption will definitely reduce the amplitude of the > wiggles, and I'm surprise Bruce didn't menntion it. It looks > much like pinhole effect. Harmonics do similar things as well in > transmission. My brain is really tiny and it's getting to be late in the afternoon here. It's amazing that many bullet points actually made it into the email! 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: https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_ho… Software: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bruceravel&… Demeter: https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_de… ------------------------------ Message: 3 Date: Wed, 27 Jul 2016 13:56:41 -0700 From: Matthew Marcus <mamarcus(a)lbl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] determining reasonable fitting parameters Message-ID: <3ee04494-5113-2994-3d96-e9e5bd2ebecc(a)lbl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed Oh, so it assumes that chi(k) = (mu(E(k))-spline(k))/const.? Mine does (mu(E(k))-spline(k))/spline(k), which I guess has its own problems - any wiggles driven in the spline will multiply the EXAFS. I haven't seen any effect from this, though. Maybe the right thing is (mu(E(k))-spline(k))/smooth(E(k)) where smooth is a smooth post-edge background such as a polynomial or spline with fewer knots than the subtraction spline or even a tensioned spline. I'd be willing to bet that this refinement will make no detectable difference, especially if you do the reference data the same way. I've found that you can do the most amazingly bogus things and get away with it as long as you do them equally to your reference and unknown, especially if the reference is very similar to the unknown. Of course, you can't rely on that. mam On 7/27/2016 1:45 PM, Bruce Ravel wrote: > On 07/27/2016 04:39 PM, Matthew Marcus wrote: >> I'm not sure I get your point about ion-chamber response. Shouldn't >> that normalize out in post-edge spline? > > Athena edge-step normalizes (i.e. normalizes by a constant) by default. It does not do a functional (or energy dependent) normalization by default in the way you are suggesting. > >> If the I0 chamber gets less sensitive as a function of energy, then >> the post-edge background rises by the same amount as the wiggles get >> bigger, so it divides out. Similarly for probe-depth effects, >> depending on concentration. Another couple of possible sources of >> amplitude error: >> 1. The model for the pre-edge background is inaccurate, so that its >> extrapolation to the EXAFS region is incorrect. >> For instance, if there's a lot of elastic scatter getting into >> the fluorescence detector, then the pre-edge is curved, >> and if you model that with a straight line fitted near the edge, >> them you'll be off far from the edge. Similarly, in >> a long transmission scan, both pre- and post-edge are curved. My >> background-sub program has simple models for thse >> shapes which aren't perfect but help. This effect is really hard >> to control for because you have no real way to know >> what the 'right' answer is, most of the time. >> >> 2. Overabsorption will definitely reduce the amplitude of the >> wiggles, and I'm surprise Bruce didn't menntion it. It looks >> much like pinhole effect. Harmonics do similar things as well in >> transmission. > > My brain is really tiny and it's getting to be late in the afternoon here. It's amazing that many bullet points actually made it into the email! > > B > > ------------------------------ Message: 4 Date: Wed, 27 Jul 2016 17:08:58 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] determining reasonable fitting parameters Message-ID: <a632df68-e115-cda0-3ace-4c066230b85f(a)bnl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed On 07/27/2016 04:56 PM, Matthew Marcus wrote: > Oh, so it assumes that chi(k) = (mu(E(k))-spline(k))/const.? Mine > does (mu(E(k))-spline(k))/spline(k), which I guess has its own > problems Exactly. Both solutions have problems. The potential for trouble with "/const" seems less severe to me and easier to support (in the sense of supporting the use of a software package). So that's why Athena does what she does. 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: https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_ho… Software: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bruceravel&… Demeter: https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_de… ------------------------------ Subject: Digest Footer _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia.cars.aps.anl.g… Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia.cars.aps.anl.g… ------------------------------ End of Ifeffit Digest, Vol 161, Issue 39 ****************************************

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Re: [Ifeffit] Athena Question
by tyson 27 Jul '16

27 Jul '16

Thanks for the fast response.TAT Sent via the Samsung GALAXY S® 5, an AT&T 4G LTE smartphone -------- Original message -------- From: Bruce Ravel <bravel(a)bnl.gov> Date: 7/27/2016 12:34 PM (GMT-06:00) To: "Tyson, Trevor A." <trevor.a.tyson(a)njit.edu> Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: Athena Question On 07/27/2016 12:01 PM, Tyson, Trevor A. wrote: > Hi Bruce, > > I know that you are very busy building beaminles but I could not > resist adding more to your load. I have an Athena question. I have > aligned a large set of data to a reference. Now for each data set > Athena records the energy shift. Is it possible to export the list of > shifts? Thanks. > > Trevor > Hi Trevor, Hope you don't mind that I am CCing this to the Ifeffit mailing list. The question seems broadly interesting, so leaving an answer in a place that can be found by google seems like a good idea. There are a several ways of doing this: 1. Right click on the label that says "Energy shift". one of the options is "Show energy shifts of all groups". That will post a dialog like the one in the attached picture. Click the "Save" button to write the contents as a text file. 2. Click on the File menu, then on the Export submenu. Select "Excel report on marked groups". This will write an XLS file. You can open that up in Excel or any other spreadsheet program. Column E has the energy shifts. 3. For the sake of completeness, if you are a command line kinda guy, you can use the "dlsprj" program that gets installed when you install the rest of demeter: dlsprj myproject.prj --params=bkg_eshift,bkg_delta_eshift This will print the shifts and their uncertainties to the screen. 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/

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Re: [Ifeffit] Athena Question
by Bruce Ravel 27 Jul '16

27 Jul '16

On 07/27/2016 12:01 PM, Tyson, Trevor A. wrote: > Hi Bruce, > > I know that you are very busy building beaminles but I could not > resist adding more to your load. I have an Athena question. I have > aligned a large set of data to a reference. Now for each data set > Athena records the energy shift. Is it possible to export the list of > shifts? Thanks. > > Trevor > Hi Trevor, Hope you don't mind that I am CCing this to the Ifeffit mailing list. The question seems broadly interesting, so leaving an answer in a place that can be found by google seems like a good idea. There are a several ways of doing this: 1. Right click on the label that says "Energy shift". one of the options is "Show energy shifts of all groups". That will post a dialog like the one in the attached picture. Click the "Save" button to write the contents as a text file. 2. Click on the File menu, then on the Export submenu. Select "Excel report on marked groups". This will write an XLS file. You can open that up in Excel or any other spreadsheet program. Column E has the energy shifts. 3. For the sake of completeness, if you are a command line kinda guy, you can use the "dlsprj" program that gets installed when you install the rest of demeter: dlsprj myproject.prj --params=bkg_eshift,bkg_delta_eshift This will print the shifts and their uncertainties to the screen. 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/

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Problem with Artemis opening an Athena project
by Irina Pi 27 Jul '16

27 Jul '16

Dear all, I have a problem opening an Athena project with Artemis. When I have selected it, it appears this error: Use of uninitialized value in addition (+) at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Prj.pm line 132 And after selecting OK and import selected data, everything closes. This Prj.pm file is attached in the mail, if it is of any help. Thank you. Best regards, Irina Pi.

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about sigma square
by Bruce Ravel 26 Jul '16

26 Jul '16

Shaofeng Wang asked this question on the mailing list that some may not have seen because it got marked as spam somewhere along the line. Kinda weird. Not quite sure why that happened.... > I have a question about sigma square. Must this parameter be in the > range of 0.003-0.02? I obtained some of it in the range of > 0.0001-0.002. Is this reasonable? Could please provide some > reference? There are no hard rules for anything. That sigma^2 is 0.00something is a good guideline and often the case, but not an actual rule. The problem with a sigma^2 in the range of 0.0something is that it tends to attenuate the path so much that it doesn't really have an impact on the quality of the fit. In that case the uncertainty is often very large precisely because the path no longer contributes significant spectral weight to the fit. A sigma^2 in the range of 0.000something means that the bond is very stiff. In some situations, that would be correct. As an example, consider the sort of negative thermal expansion material that is a network of metal-ligand octahedra. The NTE effect happens in that case because, as the material heats, up the octahedra tilt within the network, pulling the network inwards. This happens because the metalligand (usually metal-oxygen) bond is very strong -- much stronger than the forces connecting the octahedra. In an EXAFS measurement of an NTE material, you will likely find a very small sigma^2 for the first shell. (And a very large one for the second shell.) Regardless of the size of sigma^2, the bottom line is that the value is defensible. This means that you can understand and explain why sigma^2 is the size that it is. It also means that the uncertainty is such that you can support your conclusion. While the red line might overplot the blue with sigma^2=0.0003+0.001, that may be a troubling result because sigma^2 is not positive definite! Executive summary: a reasonable value is a defensible value. If you are willing to explain a result to your thesis committee or let one of us review it in a manuscript, then the result is probably reasonable. HTH, 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/

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Help with Athena
by Irina Pi 26 Jul '16

26 Jul '16

Dear all, I am just getting started with XAFS projects and I am using Athena software for processing and analysing the data. I am learning how to use it, and I have a little problem. The thing is that when I plot the XANES data, the automatic created plot is not labeled and plus it doesn't have the option of selecting a point of the spectrum. I mean, when I want to choose E0 for example, I need to do it changing the number in the Athena screen, and I don't know exactly what I am choosing because it doesn't appear anything in the graph. Was I clear? Do you know any way which I could solve it? Thank you very much, Regards, Irina Pi.

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Re: [Ifeffit] Regarding time resolved XAS
by Chris Milne 26 Jul '16

26 Jul '16

Hi Mazhar, Usually time-resolved (pump-probe) XAS is measured in data set pairs at each X-ray energy: one with laser on, one with laser off. This means that you can always directly reference your laser-excited measurement to your laser un-excited measurement. To calibrate to an absolute scale you would then use a reference foil as normal and shift both data sets according to the reference values. If you had significant delays between your laser on/off measurements then drifts and other noise sources will affect your data, making it very difficult to determine a reliable difference signal. You could try to use a reference foil measurement to correct for these kinds of drifts but you need to be very careful with the corrections to ensure you aren’t just seeing an artifact. Ideally you would be measuring laser on/off differences on a millisecond to microsecond timescale between acquisitions, this gets rid of most of the possible noise sources. Best, Chris > On 30 May 2016, at 19:00 , 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. Regarding time resolved XAS (mazhar iqbal) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 May 2016 06:20:36 +0000 (UTC) > From: mazhar iqbal <mazharphy_05(a)yahoo.com> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Regarding time resolved XAS > Message-ID: > <349705754.1395970.1464589236411.JavaMail.yahoo(a)mail.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > hello.. I am sorry if am not posting on right place. > I want to ask about the aligning the XAS spectra that is given in Athena. Can we do the alignment of time resolved spectra? As you know that the resolved spectra (IR pump X-ray probe) may have edge shift due to laser pumping. Do you think that the same method of the alignment can be applied here as well. An additional piece of information is that ?we have a reference fluorescence line always on the screen that well behind the K absorption edge. > Hoping to see your response.? > Best Regards >

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Bug Report importing file.
by Samy Ould-Chikh 25 Jul '16

25 Jul '16

Hello, I have some issue to import a file in Athena: just a simple x-y column (.txt attached with this email). Ti K-edge. Data range in the file : 4916.30 up to 5436.88 eV. Issue: only data up to 5260 eV are imported (see screenshot: bug-importation). Version: Demeter 0.9.24 System: Windows 7 Professional SP1 Well, I hope it's just not me not being able to find a proper way to import the file... 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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Re: [Ifeffit] Bug Report importing file.
by Samy Ould-Chikh 25 Jul '16

25 Jul '16

Just a quick idea on why I cannot import the .txt file attached with previous email. I realized that the files contain 11948 points ! (it's QEXAFS data). Athena might have an hard limit of 8200 points that may be imported in a single file. 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 -----Original Message----- From: Samy Ould-Chikh Sent: Sunday, July 24, 2016 10:56 AM To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Bug Report importing file. Hello, I have some issue to import a file in Athena: just a simple x-y column (.txt attached with this email). Ti K-edge. Data range in the file : 4916.30 up to 5436.88 eV. Issue: only data up to 5260 eV are imported (see screenshot: bug-importation). Version: Demeter 0.9.24 System: Windows 7 Professional SP1 Well, I hope it's just not me not being able to find a proper way to import the file... 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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demeter installation in OSX El Capitan
by Ping, Yuan 21 Jul '16

21 Jul '16

Dear all, I recently upgraded my mac to OSX El Capitan, and tried to install demeter following the steps at http://bruceravel.github.io/demeter/ XQuartz 2.7.9 (xorg-server 1.17.4), Xcode 7.3.1, command line tools, “sudo port -v self update”, “port upgrade outdated” were all OK. When I tried “sudo port install xorg-server demeter”, it showed: ---> Computing dependencies for xorg-server ---> Cleaning xorg-server ---> Computing dependencies for demeter ---> Dependencies to be installed: ifeffit libgcc cctools llvm-3.8 libcxx libffi llvm_select gmp isl ld64 ld64-latest libmpc mpfr pgplot gcc5 ... (a long list) Then after many attempts to fetch libcxx-3.7.1_0.darwin_15.x86_64.tbz2 from various websites, it showed: Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.7.1_0 Error: Failed to install libcxx Please see the log file for port libcxx for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_libcxx/libcxx/main.log The log file is attached. What should I do to fix it? Any suggestion will be appreciated. Thanks. Yuan

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Re: [Ifeffit] demeter installation in OSX El Capitan
by Ping, Yuan 21 Jul '16

21 Jul '16

Hi Joe, Thanks for your reply. In my first email I forgot to mention that I did install MacPorts-2.3.4-10.11-ElCapitan. Yuan On 7/21/16, 11:27 AM, "Ifeffit on behalf of Fowler, Joseph W. (Assoc)" <ifeffit-bounces(a)millenia.cars.aps.anl.gov<mailto:ifeffit-bounces@millenia.cars.aps.anl.gov> on behalf of joe.fowler(a)nist.gov<mailto:joe.fowler@nist.gov>> wrote: Dear Yuan, Thanks for the log file, but I’m afraid I don’t know what your Mac Ports problem is. The log file indicates a failure to fetch the archive at all. After waiting a day, did the problem go away? My workplace has lots of rules about how and when to upgrade to El Cap. As a result, I have not done it myself yet. Have you visited the Mac Ports team’s page on OS X 10.11? https://trac.macports.org/wiki/ElCapitanProblems There are no specific problems mentioning libcxx, I notice. Did you remember to re-install Mac Ports itself? If not, then problems are inevitable. Also, are Xcode and its command-line tools both updated to match the OS? If you’ve followed all the upgrade instructions and cannot install libcxx, then I think you have a Mac Ports problem and should look to that project’s issue tracker (possibly filing an issue yourself). Best wishes, Joe Fowler NIST Boulder Labs

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demeter installation in OSX El Capitan
by Fowler, Joseph W. (Assoc) 21 Jul '16

21 Jul '16

Dear Yuan, Thanks for the log file, but I’m afraid I don’t know what your Mac Ports problem is. The log file indicates a failure to fetch the archive at all. After waiting a day, did the problem go away? My workplace has lots of rules about how and when to upgrade to El Cap. As a result, I have not done it myself yet. Have you visited the Mac Ports team’s page on OS X 10.11? https://trac.macports.org/wiki/ElCapitanProblems There are no specific problems mentioning libcxx, I notice. Did you remember to re-install Mac Ports itself? If not, then problems are inevitable. Also, are Xcode and its command-line tools both updated to match the OS? If you’ve followed all the upgrade instructions and cannot install libcxx, then I think you have a Mac Ports problem and should look to that project’s issue tracker (possibly filing an issue yourself). Best wishes, Joe Fowler NIST Boulder Labs

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determining reasonable fitting parameters
by Neil M Schweitzer 21 Jul '16

21 Jul '16

Being somewhere between a novice and an advanced user of XAS, I have two "philosophical" questions about EXAFS fitting (I hope this is the correct forum to ask them!). I also have a bug to report. I have included a project file of a CeO2 powder for those interested. 1) Generally, I have developed my own methodology for EXAFS fitting which I think generates ok fits, at least from the standpoint that the red line seems to follow the blue line pretty closely. My question relates to interpreting the statistics of the fit. Generally, I am studying catalyst (i.e. very small metal or oxide nanoclusters supported on a different oxide phase). Due to the size of the clusters of interest, I wouldn't expect them to resemble a bulk crystal, and therefore it is difficult for me to reduce the number of independent variables using know crystal structures. For example in this reference material, I am giving every single scattering path its own delR and ss, and using a single delE and SO2 for all the paths since they come from the same feff calculation. Once I am through with my own methodology, I can usually get a close fit even while making every variable a guess (refer to fit 17 in the project file). Admittedly, the reduced chi is rather large (5262) and the error of each of the DWF's is the same magnitude as the value itself, which is troubling. However, if I use the best fit values of fit 17 and set all of the values except for the 3 DWF's and generate a new fit, all of the statistics significantly improve even though the values of the DWF's did not change at all (Fit 19). That is, merely setting the other variables improved the fit (the reduced chi square is now 2951) and improved the error of the guess variables (the errors of the DWF's are cut close to half). Why is the fit better since none of the values actually changed, and why do the errors improve? How should I be reporting the statistics (i.e. the errors) in a publication? Should I report the fit 17 errors or the fit 19 errors for the DWF's? 2) In terms of the DWF's in general, what value is considered too high? I know the DWF's have a component that relates to temperature induced disorder in the scattering shell and a component that relates to physical disorder in the scattering shell, but what value would be considered too big for a sample measured at room temperature. I have seen values as high as 0.03 and 0.04 in presentations (sorry, no references) but these seems too large to me. At some point, if the sample is disordered enough, it seems like EXAFS is no longer an appropriate characterization tool to use. What value of DWF would that represent (for a sample measured at room temperature)? 3) I found a bug in the log files in the history window. I am running Demeter 0.9.21 on Windows 7. When I generate a new fit, if I change the k-range of the fit, the k-range of previous fits in the history window will also change to the current range (e.g. fit 19 was run from 2.1-9.3, as shown in the data window. Fits 14-16 were run in smaller ranges). What's even stranger, is if I go to a very old fit (i.e. fit 1 or 2 in the project file) and then go back to the new fit, the log file will report the k-range from the earlier fit, not the current fit. Obviously, this is making it very difficult to keep track of fits generated with different k-ranges. I have not tested to see if the R-range behaves similarly. Neil

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fitting of S XANES with arctans and gaussians
by Matthew Marcus 19 Jul '16

19 Jul '16

I'm trying to fit 37 micro-XANES spectra taken at the S K-edge, using the method discussed in the paper by Manceau and Nagy "Quantitative analysis of sulfur functional groups in natural organic matter by XANES spectroscopy", Geochimica et Cosmochimica Acta 99 (2012) 206–223. In this paper, they fit spectra to two arctangents and 6 gaussians, with widths of the arctans slaved together and widths of gaussians 1-3 and 4-6 slaved (or all 6 to one value). I'm looking for recommendations as to how to do the fit. They give prescriptions for how to set the initial estimates to give robust values. Manceau has told me that 'Athena works quite well', but I don't see any obvious way there to do the parameter constraints called for, or to keep peak heights from going negative. Athena also has a habit of assuming you want it to do the normalization for you; I've already done that and need no further 'help'. Any ideas? I've tried using Genplot, but that offers no way to restrain parametsrs to ranges to keep them from going nuts. PCA seems to want 6-8 components, so it's not all that helpful. These spectra were taken at various spots on a biological structure (abalone radula) so there's no sense of sequence which would enable the use of evolving factor analysis or something like that. LCF doesn't give satisfying fits with the references I have. I've attached a couple of the files, truncated to the range Manceau&Nagy fit to. The originas were taken over the range 2460-2550eV. mam

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Artemis - Atom/Feff issues
by M.F.Bertuzzo 18 Jul '16

18 Jul '16

Dear all, Having a spot of trouble with Feff calculations at the moment, any help would be much appreciated. A little info before I describe the problem: I have performed Crystal14 calculations on a system to optimise its geometry. After completing this, I opened the output file in J-Ice so that I could then save the file in .pdb format, so I could then open it inside of Mercury (v3.8) which would then allow me to save the file as a .CIF, to be used for Feff a calculation in Artemis. All okay so far. But, when I open the CIF file inside of Artemis it thinks that some of the atoms sit only 0.02Angstroms apart from one another - obviously wrong. Yet when the file is viewed in Mercury (or whatever graphical interface you wish to use) it correctly displays the atoms, as opposed to Artemis which is somehow populating 500+ atoms within a small distance of just 5 Angstroms. Is this something to do with the Cluster size? I have tried to arbitrarily increase it to a higher number to prevent it from finding atoms just 0.02Angstroms apart, but even then it locates atoms 0.14Angstroms apart which is still wrong. I have attached the structure (in .XYZ format) I am trying to work on so you can view it as well as its CIF format that I have been trying to open up inside of Artemis to run Feff. Thanks for any assistance! Marcus Postgraduate Researcher in Chemistry University of Kent

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Artemis - Atoms/Feff issues
by M.F.Bertuzzo 18 Jul '16

18 Jul '16

Dear all, Having a spot of trouble with Feff calculations at the moment, any help would be much appreciated. A little info before I describe the problem: I have performed Crystal14 calculations on a system to optimise its geometry. After completing this, I opened the output file in J-Ice so that I could then save the file in .pdb format, so I could then open it inside of Mercury (v3.8) which would then allow me to save the file as a .CIF, to be used for Feff a calculation in Artemis. All okay so far. But, when I open the CIF file inside of Artemis it thinks that some of the atoms sit only 0.02Angstroms apart from one another - obviously wrong. Yet when the file is viewed in Mercury (or whatever graphical interface you wish to use) it correctly displays the atoms, as opposed to Artemis which is somehow populating 500+ atoms within a small distance of just 5 Angstroms. Is this something to do with the Cluster size? I have tried to arbitrarily increase it to a higher number to prevent it from finding atoms just 0.02Angstroms apart, but even then it locates atoms 0.14Angstroms apart which is still wrong. I have attached the structure (in .XYZ format) I am trying to work on so you can view it as well as its CIF format that I have been trying to open up inside of Artemis to run Feff. Thanks for any assistance! Marcus Postgraduate Researcher in Chemistry University of Kent

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Artemis Antisite Simulation
by #GUPTA DISHA# 15 Jul '16

15 Jul '16

Dear All I am trying to simulate data for antisite disorder for LFP data. I import the CIF file and make sum of all the paths and save the file as an artemis file. I do this for different ratios of Li/Fe sites. However, I want to compare all these data in Origin. How do I open these artemis files in Origin to see how my data varies with different Li/Fe antisites? Thank you and Kind Regards Ms. Disha Gupta PhD Student School of Materials Science & Engineering (MSE) Nanyang Technological University 50 Nanyang Avenue, Singapore 639798 Tel: (65) 84087404 | Email: disha001(a)e.ntu.edu.sg ________________________________ 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: Wednesday, July 13, 2016 1:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 161, Issue 9 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. Artemis (FEFF) question (Louis Forto) 2. Re: Artemis (FEFF) question (Matt Newville) 3. Re: Artemis (FEFF) question (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Tue, 12 Jul 2016 10:13:17 +0100 From: Louis Forto <cforto10(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Artemis (FEFF) question Message-ID: <CAOfHeiQnRSZX98TrKvDasc2t1WB1gq1xBmboA_T3k3RwkBNbhQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear All, I am trying to run a FEFF calculations on a quaternary glass , when I import crystalline data obtained from ICSD website and try to run FEFF to calculate the scattering paths of nearest neighbour atoms relative to absorbing atom, I get an error message that says " generate one or more common positions and their occupancies sum to more than 1". I don't know how to go about this, any help , I will appreciate. Thanks.

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No Reference Foil... Continued
by Neil M Schweitzer 14 Jul '16

14 Jul '16

Thanks for the responses. When I had originally tried fitting the CeO2 data, the fit was awful, but I think it was because the Eo was really far off. I set it close to where it should be and was able to find a common feature in Io to calibrate the rest of the samples to. That being said, fitting CeO2 is still quite difficult. I found a reference online (EXAFS analysis of the L3 edge of Ce in CeO2: effects of multielectron excitations and final-state mixed valence: J. Synchrotron Rad. (1999). 6, 34-42) that, from my understanding, essentially suggests duplicating all the paths and using a second delta_Eo value for the duplicated paths while also weighing the SO2 of each set of paths based on the degeneracy of the excitations. This does tend to make the fit better (as one would expect from doubling the number of paths!), but does anyone know if this is a generally accepted correction for fitting ceria materials? Does anyone have a different reference that might help me? Thanks for all the help! Neil

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No Reference Foil
by fred.mosselmans＠diamond.ac.uk 13 Jul '16

13 Jul '16

Dear Neil, Sorry this may be too exact an interpretation of your English, but if you are looking at the exafs then calibration is normally pretty irrelevant as long as it is not wildly out, as you refine E0 anyway in the fitting. The bond distances will be very little altered by this. If you are looking at XANES and it is 3/4 then CeL3 as I am sure you know has two "white lines" for four and one for three and the ratio of the two peaks can be used to Look at oxidation state mixtures, I think you should be able to align the peaks and fit the area e.g. Burnham AD, Berry AJ, 2014, The effect of oxygen fugacity, melt composition, temperature and pressure on the oxidation state of cerium in silicate melts, Chemical Geology, Vol:366, ISSN:0009-2541, Pages:52-60 Best wishes 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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No Reference Foil
by Neil M Schweitzer 12 Jul '16

12 Jul '16

Hello, Long time follower/user and first time subscriber! I work at Northwestern University, and one of the services I provide is analyzing XAS data for users who collect data at APS. Generally, I am not at APS to help them collect spectra, I help analyze the data afterwards. A user came to me recently with some Ce L3 data that does not have reference foil data. If I am trying to compare the EXAFS of several different samples (all which should be similar oxidation state, and of which I have other references of similar oxidation state). Does anyone have a suggestion how to work up the data if I can't calibrate it? ------ Neil M. Schweitzer, Ph.D Operations Director, CleanCat Core Facility Research Assistant Professor Chemical and Biological Engineering Northwestern University 2137 Sheridan Road Evanston, IL 60208-3000 Office: 847-491-2955 http://cleancat.northwestern.edu

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Artemis (FEFF) question
by Louis Forto 12 Jul '16

12 Jul '16

Dear All, I am trying to run a FEFF calculations on a quaternary glass , when I import crystalline data obtained from ICSD website and try to run FEFF to calculate the scattering paths of nearest neighbour atoms relative to absorbing atom, I get an error message that says " generate one or more common positions and their occupancies sum to more than 1". I don't know how to go about this, any help , I will appreciate. Thanks.

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