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

Accelerated Specotroscopy post-doc position at LBNL
by Santosh Suram 23 Aug '18

23 Aug '18

Hi everyone, I would like to bring to your attention an upcoming post-doc position on accelerated spectroscopy and analysis of XANES and EXAFS data. Please see the brief advertisement below and if interested please email your resume to jyano(a)lbl.gov and santosh.suram(a)tri.global -- best, Santosh -- Confidential or protected information may be contained in this email and/or attachment. Unless otherwise marked, all TRI email communications are considered "PROTECTED" and should not be shared or distributed. Thank you.

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Fe K-edge EXAFS spectra for Fe-silicates
by Paul Francisco 22 Aug '18

22 Aug '18

Dear Everyone, Hello! I'm working on iron silicates and I'm wondering if anybody here would be willing to share some Fe K-edge EXAFS spectra (preferably ones that go up until k=14-15 A-1) for phyllosilicates (e.g. chlorite/saponite/serpentine); or if anybody can recommend some database or reference for these. Thanks in advance and I would really appreciate any help! Cheers, Paul

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Modelling texture in Artemis
by Kirstine Dalgaard 20 Aug '18

20 Aug '18

Dear all How can texture in a powder sample be modeled in ARTEMIS? My samples are fine powders of a layered material, mixed with cellulose and pressed to pellets. The data were collected in fluorescence mode with a 45 degree tilt. PXRD data reveal that the samples are highly textured, including standards. I am new to XAFS, and I need some advise to deal with this issue. Best regards Kirstine Dalgaard

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Re: [Ifeffit] using the mail list archive for mac install
by Matt Newville 17 Aug '18

17 Aug '18

Hi Joel, > I ran into the problem that some people seem to have with Demeter on mac while > upgrading to High Sierra. I found a fix on this mail list, but… Yeah, Demeter on MacOS is a continuing challenge. Even when it can be installed, parts of the GUI interaction are pretty buggy (I believe this must be due to wxPerl on Mac). MacPorts seems to need a fair amount of attention and expects the end user to know Unix command line tools well enough to be able to run updates and understand and react to error messages. For sure, it is a useful resource for developers, but it seems like it is not really designed for deploying end-user software. Still , I don't know of a better alternative for getting Demeter working on MacOS. I've tried many of the alternatives, and wxPerl seems to be a real stumbling block for all of them. > 1) I can’t download Template.pm from the archive (bin file that uncompresses to cpgz file > that uncompresses back to a bin file…) I think that the advice from Luke and Bruce back in April was to try to find and install version 1.47 of Text::Template. You might find this at https://metacpan.org/source/MSCHOUT/Text-Template-1.47/lib/Text and try unpacking and installing that. There may be a way to specify particular versions with the "cpan" program, but I do not know how to do it. I don't think we want "install old version of some library" to be a long term solution (this will break other things eventually), but it might work for you. > 2) Matt mentions that he installed 0.9.26 from macports, but I see only 0.9.25 (stable & develop). To clarify, in April I updated MacPorts to the latest versions, installed the packages for Demeter 0.9.25. Then I installed Demeter 0.9.26 from source code on top of that. That might also work , but it's probably more work than most folks would want to do. Cheers, --Matt

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Re: [Ifeffit] Ifeff calculation
by Dien.Li＠srnl.doe.gov 15 Aug '18

15 Aug '18

Hi, Carlo and Matt or others Attached please find the cif crystal structure data file for NaReO4 that was downloaded from Crystallography Open database. As I added it into Artemis for calculation, it gave error message saying that it has more than 500 atoms that exceeds the limit. Could you help to troubleshooting?? Thanks a lot. Dien Li -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Tuesday, August 14, 2018 5:29 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 186, Issue 13 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: LCF on Larch - EXAFS Region (Matt Newville) 2. Re: wavelet transforms for EXAFS (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 14 Aug 2018 12:33:35 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] LCF on Larch - EXAFS Region Message-ID: <CA+7ESbr8s-gQOeLOo302hTdtT+XLS8g55goXvYm6hqJFiLCkaQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Martin and Mike, Thanks -- I'll take a closer look at your paper on this! I think we all basically agree that linear analysis of EXAFS can work, but also that compared to linear analysis of XANES, linear analysis of EXAFS has a few more caveats and issues that need to be addressed for each case. On Mon, Aug 13, 2018 at 8:26 PM Martin McBriarty <memcbr(a)gmail.com> wrote: > Matt, > > Glad to read your impressions of EXAFS LCF. I've had reasonable success > with LCF using EXAFS spectra generated by ab initio molecular dynamics > (AIMD) to figure out the local structure of dopants whose preferred > coordination is symmetrically dissimilar from the crystals they inhabit, > i.e. for which there are no good experimental standards. This can be pretty > tough to do accurately with shell-by-shell fitting. > > As you point out, disorder is a huge hurdle (in both LCF and > shell-by-shell EXAFS analysis). We assume that a good AIMD model will > simulate thermal disorder pretty well, but there are likely differences in > configurational disorder between a periodic infinite structure and the real > material due to defects. Fortunately, defects can be explicitly accounted > for in a simulation, assuming you have the computational capability to > screen a set of defect configurations. > > Background subtraction should ideally be done using the same procedure for > all data. Theoretical data could be used to refine a background subtraction > procedure; spline fit parameters such as Rbkg or clamping may be tweaked to > improve agreement between a simulated chi(k) and a measured standard over a > reasonable k-range. > > Simulating spectra with a range of binding energy offsets can explicitly > address the problem of E0 choice, but it can also be used as a fudge factor > for strain. In my LCFs, dE0 is the only parameter besides the fractions of > the chosen phases. > > To address the above problems, benchmarking is key. Quantitative agreement > should be sought between simulated spectra and experimental standards to > ensure the theory is sound and the chi(k) extraction is reasonable. > However, there are probably still systematic sources of error which are > larger than the uncertainties Athena's LCF tool will report; I agree with > Mike's practical estimate of 10% or so. > > I discuss these issues in somewhat greater detail in my recent (open > access!) article that demonstrates how LCF using AIMD-simulated spectra > yields answers that shell-by-shell fitting struggles with due to multiple > overlapping components: https://pubs.acs.org/doi/10.1021/acs.est.8b00297 > > Martin > > > On Sun, Aug 12, 2018 at 10:19 PM, Matt Newville < > newville(a)cars.uchicago.edu> wrote: > >> Hi Mike, >> >> On Thu, Aug 9, 2018 at 10:04 PM Mike Massey <mmassey(a)gmail.com> wrote: >> >>> This is interesting. Could you say more about your skepticism of the >>> robustness of EXAFS LCF, Matt? >>> >>> To be fair, it suffers from many of the same drawbacks of XANES LCF, >>> plus others. But I'm curious about your thoughts on it since yours seems to >>> be what amounts to a "strong opinion" on the subject. >>> >> >> >> I would not say that no one should ever do linear combination fitting for >> EXAFS. For sure, linear analysis of XANES is quite robust and verified >> many times to give good results, at least at level of a few percent. >> Linear analysis of EXAFS suffers more data processing challenges and >> conceptual problems that limit its robustness. For sure, there are cases >> for which it can work well. >> >> Longer answer: >> Any linear analysis (LCF, PCA, MCR-ALS, etc) of XANES works reasonably >> well (typically to a few percent) because: >> a) the processing needed is minimal. Data need to have a common >> energy calibration better than the intrinsic energy resolution -- typically >> energy calibration of 0.25 eV or better will be OK. Data need to have a >> consistent normalization of mu(E), typically to a few percent. Variations >> in these processing steps will have a direct and negative effect on the >> results. >> >> b) conceptually, the assumption is that there exists a nearly 1 to 1 >> correspondence between "local chemical configuration" and "measured XANES", >> and that the "local chemical configurations" that are being investigated >> are discrete and well-defined (ie "iron carbonate") and not continuous. >> That is, if you determine that your Fe XANES spectra is "50% iron >> carbonate and 50% iron sulfate" then implicit conclusion is that 50% of the >> iron atoms are iron carbonate and 50 percent are iron sulfate, not that all >> irons are 50% carbonate and 50% sulfate. >> >> To be clear, linear analysis of XANES does not work well to ppm levels, >> partly due to the poor experimental contrast (that is, mu(E) tend to all >> look alike and features are intrinsically broadened to the ~eV level), but >> also conceptually, because at the ppm level, local chemical configurations >> are not always limited to 3 to 10 discrete states. >> >> Linear Combination EXAFS is more challenging from both the processing and >> conceptual point of view. >> >> For Processing, EXAFS requires more data processing than XANES. The >> selection of E0 and the background mu0(E) will have an effect on linear >> analysis of EXAFS if not done consistently. It is not really obvious how >> E0 or mu0(E) can be selected consistently for very different spectra. >> >> Conceptually, EXAFS is much more sensitive to disorder and subtle >> variations in the bond lengths (thermal or static disorder) and can have >> significant variation in its sensitivity to second and further neighbors. >> In that sense, EXAFS is much less discrete and much more continuous in its >> variability across different kinds of local structures. >> >> Again, this is not to say that linear analysis of EXAFS cannot ever work, >> just that is probably more limited in applicability and absolute accuracy >> than linear analysis of XANES. Of course, for EXAFS you can also do an >> actual fit of structural parameters. The information content is somewhat >> limited so that refining multiple overlapping components may not always be >> possible, and linear combinations of end-member spectra may look >> attractive.... >> >> Hopefully, anyone who has other insights or experiences will be able to >> correct any of my misunderstandings. >> >> --Matt >> >> >> _______________________________________________ >> 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 >> >> > _______________________________________________ > 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 > -- --Matt Newville <newville at cars.uchicago.edu> 630-252-0431

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Basic questions about the preliminary data processing in Athena
by Haifeng Li 14 Aug '18

14 Aug '18

Dear ALL, I am a beginner in Athena. Recently I got the spectra and I am confusing about the data calibration and alignment. The manual shows that calibrate the reference data of one scan and align other reference data to that calibrated one. Here I want to show examples. I have two samples A and B, Each sample has three scans with the corresponding reference data. For sample A, 1st scan is calibrated and the other two scans are aligned to 1st scan. Then merge them into merged A. The same procedures for sample B and get merged B. If I want to compare XANES of sample A and B, do I need to align the merged reference data between A and B? If so, why? My understanding is that all scans (original data and merged data) in sample A and B are calibrated to standard edge energy. Why do they need to align? I appreciate your help. Thanks, Haifeng

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Re: [Ifeffit] wavelet transforms for EXAFS
by Clark Adam Hugh (PSI) 14 Aug '18

14 Aug '18

Hi Matt I recently had some problems incorporating the larch Cauchy wavelet transform into my program for rapid bulk processing of QEXAFS data (discussed http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-April/007250.html) I particular after importing the relevant module into python the cauchy_wavelet(cwsam, kweight=kwwt, _larch=mylarch) function raises the error 'not callable'. As a work around I have explicitly copied the module code for the definition into my own script and this seems to resolve the issue. I also notice that at present that it is not possible to apply a windowing function within the wavelet transform, is this just a case of windowing the K space data that is fed to the module? I would also have interest in trying to fit the EXAFS data in the wavelet space, has there been any progress in Larch for performing this? As briefly discussed at the EXAFS conference another feature that I think would be very nice to include would be the possibility to use a Victoreen function for the post edge normalisation instead of a polynomial function. I also briefly discussed the application of the MBACK algorithm. Unless I am doing something incorrect, when trying to use the MBACK algorithm in Larch within python the following error is raised ' 'XrayDB' object has no attribute _getChantler'. In some cases it would be very interesting to apply the MBACK algorithm particularly when only a short data range is collected in some experiments. Thanks Adam Clark __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/133 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark(a)psi.ch

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LCF on Larch - EXAFS Region
by Garret Bland 14 Aug '18

14 Aug '18

Hello! I've recently been trying to use Larch instead of Athena for EXAFS analysis, and I mainly do linear combination fitting for my samples. It seems that the XANES fitting is doing just fine requesting a specified region to fit (-25 to +75 eV). When I try to fit in the k-space however, Larch does not request a specific region in k space. I try to input the eV values corresponding to the k value I want to fit, but it is still plotting in mu rather than k . Is there anyway I can change this and/or do it manually on the larch GUI? Any help would be appreciated! Thanks, Garret -- Garret Bland Graduate Student Carnegie Mellon University Civil and Environmental Engineering Porter Hall 207C Pittsburgh, PA, 15213

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Ph.D and Postdoctoral positions- Time-resolved X-ray Spectroscopy in Biological/Chemical Catalysis
by dooshaye.moonshiram 11 Aug '18

11 Aug '18

Dear all. We have a Ph.D and postdoctoral position available in time-resolved X-ray spectroscopy in biological and chemical catalysis. The details of the positions are attached. Please contact me or forward the attached positions if you or anyone you know might be interested. Many thanks and Best Regards, Dooshaye Moonshiram Group Leader IMDEA Nanociencia Calle Faraday 9, Madrid, Spain

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Demeter on ubuntu 14.04
by Edmund Welter 09 Aug '18

09 Aug '18

Dear all, I am hitting a wall trying to install the latest Demeter version on my ubuntu laptop. System: Ubuntu 14.04 Demeter: 0.9.26 perl: 5.18.2 pdl and pdl::stats from repositories. (I tried a newer versions from cpan, but ot no avail) moose: initially from repositories, than vs. 2.2011 from cpan I did follow the installation instructions on https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h… and tried to install demeter in ~/perl5 and also the instructions in: https://bruceravel.github.io/demeter/documents/SinglePage/installation.html to install Demeter as sudo Both attempts ended with the same result when I start dathena in a terminal the image of the goddess appears briefly and I get the following error messages in the terminal: --------------------------------------------------------------------- Invalid version format (non-numeric data) at /usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11, <DATA> line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Moose.pm line 15, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Moose.pm line 15, <DATA> line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Demeter.pm line 123, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Demeter.pm line 123, <DATA> line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24, <DATA> line 90. Compilation failed in require at /usr/local/bin/dathena line 31, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/bin/dathena line 31, <DATA> line 90. Use of uninitialized value $Larch::larch_exe in concatenation (.) or string at /usr/local/lib/perl/5.18.2/Larch.pm line 288, <DATA> line 90. Can't exec "-q": No such file or directory at /usr/local/lib/perl/5.18.2/Larch.pm line 288, <DATA> line 90. -------------------------------------------------------------------- When i try to start denv to create the nice overview of installed components I only get the following errors: -------------------------------------------------------------------- [PDL->Version: 10 PDL_CORE_VERSION: 8 XS_VERSION: ] PDL::Stats::Distr needs to be recompiled against the newly installed PDL at /usr/lib/perl/5.18/DynaLoader.pm line 207. Compilation failed in require at (eval 1130) line 5. BEGIN failed--compilation aborted at (eval 1130) line 5. BEGIN failed--compilation aborted at /usr/local/bin/denv line 24. Use of uninitialized value $Larch::larch_exe in concatenation (.) or string at /usr/local/lib/perl/5.18.2/Larch.pm line 288. Can't exec "-q": No such file or directory at /usr/local/lib/perl/5.18.2/Larch.pm line 288. ---------------------------------------------------------------------- This is insofar interesting as I got the same error about PDL when I tried to start dathena before I installed the pdl::stats module from cpan, that means when both, pdl and pdl::stats were installed from repositories. Any hint would be welcome, upgrading ubuntu to a newer LTS version might be useful (It is absolutely possible that something is weird with this installation after a lot of playing around) but I am currently reluctant to do so, because it will for sure break other things... Best regards, Edmund

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