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

Re: [Ifeffit] Ifeffit Digest, Vol 220, Issue 2
by Danilo Oliveira de Souza 15 Jun '21

15 Jun '21

Hi Teresa and Matt, Concerning the SPOIL function, some months ago I digged on that and I found the first paper (I guess) on this topic, which is from Edmund R. Malinowski in an Analytical Chimica Acta, 1978 ( 10.1016/S0003-2670(01)83099-3 <https://doi.org/10.1016/S0003-2670(01)83099-3> ). Instead of reproducing this paper here (it is not just a couple of lines), I let to you read the precise definition of such a function. I have the copy on pdf of the paper if any of you is interested in it. Cheers, Danilo *Danilo OLIVEIRA DE SOUZA* *Research Fellow @ ELETTRA Sincrotrone, XAFS beamline* * Strada Statale 14 - km 163,5 in AREA Science Park* * 34149 Basovizza, Trieste ITALY* *http://www.elettra.trieste.it/elettra-beamlines/xafs.html <http://www.elettra.trieste.it/elettra-beamlines/xafs.html>* * e-mail: danilo.oliveiradesouza(a)elettra.eu <danilo.oliveiradesouza(a)elettra.eu> * * mobile: (+39) 351 50.30.731 bureau: (+39) 040-375-8604* Em qui., 10 de jun. de 2021 às 19:00, < ifeffit-request(a)millenia.cars.aps.anl.gov> escreveu: > 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: PCA Sixpack results compared to Athena (etc.) (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 10 Jun 2021 07:08:19 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] PCA Sixpack results compared to Athena (etc.) > Message-ID: > <CA+7ESbq= > J9fZ3Y0PPuyjShk+XNFOGjOTktX4m7oyu6PFfTwM5w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Teresa, > > I'm sorry that I cannot give you a definitive answer. I should admit that > when adding PCA methods to Larch and XAS Viewer (which I invite you to try > out), I tried to follow the scikit-learn approach but also to follow the > Athena implementation. I think I never tried to test against the results > from SixPack. FWIW, Larch only does (easily) PCA on normalized mu(E) or > its derivative. I suppose PCA on chi(k) could be added, but I'm a bit sort > of skeptical of this. > > In fact, the code at > https://github.com/xraypy/xraylarch/blob/master/larch/math/pca.py (and, > just to be clear, having this both in Python and publicly available is > motivated by having these conversations of "what does it do?") has a few > different methods to train a PCA set: one directly from scikit-learn, one > basically reproducing Demeter's PCA.pm (modulo slight differences in > underlying math libraries, which should be insignificant), one that aims to > use only non-negative components (not really worth in my opinion), and one > that is sort of hand-coded and including the IND statistic. I don't know > what SixPack does. > > I cannot really explain why, but the default "readily exposed in Larch XAS > Viewer" is to use the hand-coded version of `pca_train`. In fact, they > should be all more or less interchangeable. I did some tests with these > but that was now several years ago, but it might be worth trying that > again. If you're up for that, please do try. If not and would like to > send your project and an outline of what you get, I might be able to look > at this too. > > For "target transformation", this is implemented as `pca_fit`: how well can > a data set be explained by the first N components of a training model? > > For fit statistics: I have seen "SPOIL" used several places in the EXAFS > literature but am afraid I do not actually know of a definition for this. > If anyone can explain what these are, that would be helpful. Larch can > calculate the F1 and IND statistics that are more common in the PCA > literature. XAS Viewer exposes and automatically plots IND - it's a very > useful way to select how many components are significant. > > I'm pretty sure that does not answer your actual question, but maybe it > will be helpful. If you or anyone else has suggestions for additions, > improvements, or other optional methods or statistics for PCA and/or > related methods, please let me know. > > --Matt > > > On Tue, Jun 8, 2021 at 7:43 AM <t.zahoransky(a)mineralogie.uni-hannover.de> > wrote: > > > > > Dear XAS Community, > > > > I stumbled over the issue that a PCA on 20 EXAFS spectra (k?, k = > > 2.0-11.0 ?-1) perfomed in Sixpack does not give the same results > > (Eigenvalues, variance) as in Athena. However, when I use other > > statistical programs (i.e., TIBCO Statistica or SPSS), I get the same > > results as reported in Athena. I tested this with another EXAFS > > dataset of over 30 samples and the problem persited. > > > > An old entry from 2017 in the ifeffit mailing list ("[Ifeffit] > > Calculation of SPOIL value for the reconstruction of standard > > spectra"), told me that as of Sixpack version 1.4 on, a new/different > > PCA algorithm from the scikit-learn Python package is used. > > > > So I downloaded older versions of Sixpack (i.e. 1.3) and used "Use Old > > PCA"-selection in the "Rotation" menu bar, which actually gave > > different results. However, they are still different from the > > Athena/Statistical program results. > > > > My question is: What is behind this? Is there some sort of > > normalization or axis rotation, that leads to the different values? Is > > there any way to change this so that the results are comparable to > > other programs? > > > > As I need to use the Target Transform option after PCA, which is not > > yet possible in Athena, I am at a loss as to how to deal with these > > different results and where they come from. > > > > > > Thank you very much for your help, > > > > Teresa > > > > > > -- > > Teresa Zahoransky > > > > Soil Mineralogy > > > > Gottfried Wilhelm Leibniz Universit?t Hannover > > > > Institute of Mineralogy > > > > Callinstr. 3, Room 325 > > > > D-30167 Hannover, Germany > > > > > > > > Phone: +49 (0)511 762-8058 > > > > Email: t.zahoransky(a)mineralogie.uni-hannover.de > > > > _______________________________________________ > > 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> 630-327-7411 >

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TiFe EXELFS Two Phase Co-Refinement Question
by Wilson, Catrina 10 Jun '21

10 Jun '21

Hello, I am using Artemis to fit EXELFS data on a TiFe alloy. There are multiple interfaces between two phases (Im-3m, and P63/mmc) present in the data. I am attempting to co-refine using both phases to create a path list and using paths from both phases in the fit. My understanding of this process is that the software uses a linear combination of each path. However, that would imply that there is a weighting factor applied to each phase that would be correlated to the phase weight for that region. I was wondering if there is a way to determine what the weighting factors during a co-refinement to multiple phases are in Artemis, assuming my initial understanding of the co-refinement process is correct? Thanks for your time, Catrina Wilson Ph.D. Candidate The Ohio State University Doan-Nguyen Group and McComb Group Materials Science and Engineering Center for Electron Microscopy, 1305 Kinnear Rd., Columbus, OH 43212 (614) 643-3110 Office wilson.3981(a)osu.edu<mailto:wilson.3981@osu.edu> / osu.edu<http://osu.edu/> Pronouns: she/her/hers

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PCA Sixpack results compared to Athena (etc.)
by t.zahoransky＠mineralogie.uni-hannover.de 10 Jun '21

10 Jun '21

Dear XAS Community, I stumbled over the issue that a PCA on 20 EXAFS spectra (k², k = 2.0-11.0 Å-1) perfomed in Sixpack does not give the same results (Eigenvalues, variance) as in Athena. However, when I use other statistical programs (i.e., TIBCO Statistica or SPSS), I get the same results as reported in Athena. I tested this with another EXAFS dataset of over 30 samples and the problem persited. An old entry from 2017 in the ifeffit mailing list ("[Ifeffit] Calculation of SPOIL value for the reconstruction of standard spectra"), told me that as of Sixpack version 1.4 on, a new/different PCA algorithm from the scikit-learn Python package is used. So I downloaded older versions of Sixpack (i.e. 1.3) and used "Use Old PCA"-selection in the "Rotation" menu bar, which actually gave different results. However, they are still different from the Athena/Statistical program results. My question is: What is behind this? Is there some sort of normalization or axis rotation, that leads to the different values? Is there any way to change this so that the results are comparable to other programs? As I need to use the Target Transform option after PCA, which is not yet possible in Athena, I am at a loss as to how to deal with these different results and where they come from. Thank you very much for your help, Teresa -- Teresa Zahoransky Soil Mineralogy Gottfried Wilhelm Leibniz Universität Hannover Institute of Mineralogy Callinstr. 3, Room 325 D-30167 Hannover, Germany Phone: +49 (0)511 762-8058 Email: t.zahoransky(a)mineralogie.uni-hannover.de

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Analyzing EXAFS data on Artemis
by Alexandros Deltsidis 28 May '21

28 May '21

Dear mailing list, I am currently analyzing some EXAFS data. I am studying a Lix(C5H5N)FeSe system in a temperature grid that extends from 20 K to 300 K and I have 4 such datasets which correspond to different amount of doping (x). Right now, im focusing on fitting the 1st coordination cell, in Artemis for the Se K-edge. My starting model is the simple P4/nmm FeSe. So, in my system the 1st coordination cell, in the Se K-edge, corresponds to the Se (absorber) - Fe (backscatterer) pair. I have 2 questions: 1) I realize now, that I have a certain impurity in the high doping range on my system, namely Li2Se. I try to include a scattering path from the respective Li2Se crystal model in my fits, since a Se (absorber) - Li (backscatterer) pair is present in the R-range of my fit in the Forward Fourier Transform. My question here is if this makes sense since Li is much smaller scatterer compared to Se. In other words, does it make sense to look for physical parameters (Li-Se bond length and DW factor respectively) of a signal (Se-Li) that is "tucked" in below the main peak coming from the "majority" Se-Fe signal in the FFT? 2)Also, I'm attempting to extract an Einstein temperature for each of those datasets, by utilizing the "eins(T, thetae)" function implemented in Artemis. What is the equation that is parametrized here? Does it include the s0^2 offset term that accounts for the overall configuration disorder in the system? And if that is the case is there same way to separate it from the temperature dependent s^2 term? Thank you in advance, Deltsidis Alexandros PS:I am attaching a png. file exported from Artemis that is relative to my question 1) Ph.D candidate, Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology - Hellas (FORTH)

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Free Oxford Ion Chambers Available [SEC=OFFICIAL]
by MITCHELL, Valerie 25 May '21

25 May '21

Dear All, The XAS beamline at the Australian Synchrotron has four Oxford IC SPEC ion chambers available for free (picture attached). If interested please let me know, and I'm happy to answer any questions. Kind regards, Valerie Mitchell OFFICIAL

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APS/IIT EXAFS Summer School
by Carlo Segre 19 May '21

19 May '21

Hello All: I am attaching the announcement for the 2021 APS/IIT EXAFS Summer School which will be held virtually this year from August 1-4, 2021. Please see the attached for more detail. To register, please send email to Grant Bunker <bunker(a)iit.edu> Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Professor of Materials Science & Engineering 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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IMP: Inquiry for a postdoc position
by Nirmalendu Patra 18 May '21

18 May '21

Dear XAS group Members, I apologize in advance for spamming everyone with this posting. I am Nirmalendu Patra (Ph.D). I have been working as a postdoc in Dr. Simon R. Bare’s group at Stanford Synchrotron Radiation Light Source (SSRL), SLAC National Accelerator Laboratory, California, USA since June of 2020. My current role in the group is to support the team effort to broaden the experimental capabilities by conducting the in-situ XAS (XANES / EXAFS) experimental plan, data acquisition and analysis using IFEFFIT software package (Athena and Artemis) and finally preparing the manuscript. I am also working on the Principal component analysis (PCA) and clustering using TXM XANES Wizard to visualize the unidentified chemical species and the pattern in a large dataset. Before my current postdoc position, I graduated with a Ph.D. in Physics, working on the X-ray Absorption Spectroscopy studies on magnetic thin films and bulk materials at the Indus-2 Synchrotron, RRCAT, Indore, India under the guidance of Dr. Dibyendu Bhattacharyya, BARC, Mumbai, India. The title of my thesis was “Investigation on local structures of various thin film Heusler alloys by XAS and XMCD measurements”. The main objective of my thesis study the local atomic structure, surface morphology and elemental composition of the PLD deposited Heusler alloy thin ﬁlms and correlate their atomic structure with their magnetic properties. My postdoctoral fellowship with Dr. Bare is ending on June 25th, 2021. I am looking for a new postdoctoral position that will enable me to study materials for energy conversion and storage. I am also interested in studying electronic, structural, physio-chemical properties and morphology of materials using advanced spectroscopy techniques. XAS study on metallic alloys or metal oxide thin ﬁlms for spintronic applications are also a part of my research interest. My resume is attached here, and more details can be found from my LinkedIn profile (www.linkedin.com/in/nirmalendu-patra-82701365) If any group has an opening for a postdoc position, kindly respond to my email. Because of the COVID situation in India, I don't want to return now. So trying hard to find a new position. I am available for hiring and will appreciate your help to find a postdoc position. Thank you. With kind regards, *Nirmalendu Patra*

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Illinois Tech Synchrotron Radiation Course
by Carlo Segre 09 May '21

09 May '21

Hello All: Illinois Tech is offering the graduate Introduction to Synchrotron Radiation course once again in Fall 2021. Please see the attached course summary. The course is offered online and it is very straightforward to apply as a non-degree graduate student as late as the second week of classes in September. The online course will be a one (1) credit course instead of the three (3) credits taken by degree-seeking Illinois Tech students. If you are interested or have interested students please contact me for more details on the course or how to apply and register. Cheers, Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Professor of Materials Science & Engineering 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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Postdoc positon in synchrotron characterization of lithium-ion batteries available at SOLEIL
by BELIN Stephanie 06 May '21

06 May '21

Dear All, I would like to share information about one funded Postdoc positions at SOLEIL synchrotron. We are looking for a Postdoc candidate on advanced synchrotron characterization of lithium-ion batteries within the framework of the Battery Interface Genome Materials Accelerated Platform (BIG-MAP<http://www.big-map.eu>, www.big-map.eu<http://www.big-map.eu>). The Postdoc position is dedicated to the development of versatile electrochemical cells and set-ups for operando experiments using spectroscopic and scattering techniques such as synchrotron X-ray absorption spectroscopy (XAS), X-ray emission spectroscopy (XES), X-ray diffraction (XRD), and small-angle X-ray scattering (SAXS), combined with conventional laboratory techniques, such as Raman scattering. Please find the advertisement in the attachment. https://www.synchrotron-soleil.fr/en/job-offers/post-doctoral-position-adva… Please pass on to suitable candidates you are aware of and disseminate to relevant networks! Thank you for your help. With kind regards, Stéphanie &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Dr Stéphanie BELIN ROCK beamline scientist tel. (0033) 01 69 35 96 45 ROCK (0033) 01 69 35 81 46 Fax (0033) 01 69 35 94 57 Email : stephanie.belin(a)synchrotron-soleil.fr<mailto:stephanie.belin@synchrotron-soleil.fr> Synchrotron SOLEIL - Division Expériences L'orme des Merisiers - Saint Aubin BP48 91192 GIF sur YVETTE [cid:image002.png@01D105CE.75C2FD50] http://www.synchrotron-soleil.fr<http://www.synchrotron-soleil.fr/> &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&

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millenia.cars.aps.anl.gov outage starting April 29
by Matt Newville 29 Apr '21

29 Apr '21

Hi Folks, The server millenia.cars.aps.anl.gov that hosts this mailing list and related services including Webatoms and the binary installers for Larch will be offline due to a planned power outage at the APS. We'll gracefully shut down this server on the afternoon (Chicago time) of April 29th, a bit more than 24 hours from now. The estimate for restoring power is May 4th, but it is possible that the outage will go for another day or so. During that time, any messages sent to this list are likely to be lost. In the meantime, please do consider submitting an abstract for the Virtual XAFS Conference! --Matt PS: if you need to contact me directly by email that will (or should) still work during the APS power outage.

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