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

Bi L3 standards
by Schlesinger, Danielle R. 29 Jun '21

29 Jun '21

Hi everyone, Does anyone have a set of Bi L3 edge standards that they would be willing to share? Thank you! Danielle Danielle R. Schlesinger, Ph.D. Post Doctoral Fellow – AOS/QPC Johns Hopkins University – Applied Physics Laboratory Tel: (240) 592-5243

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Cannon start larch on ubuntu 20.04.2 LTS
by Don Baker, Dr. 29 Jun '21

29 Jun '21

Hi Folks, I think I am missing something obvious and am hoping that you can quickly tell me my mistake, so let me begin my story: I downloaded xraylarch-2021-060Linux-x86_64.sh into downloads on a Asus Zenbook using ubuntu 20.04.2 LTS I ran the command bash ./xraylarch-2021-060Linux-x86_64.sh Larch appears to have been correctly installed, but because I am using a gnome desktop no shortcuts appeared on my desktop (as promised) and there were no files that I could identify as shortcuts in my Downloads directory (which was set to display hidden files) I then moved to the /xraylarch/bin and tried to launch larch using python and this is what happened: python larch Traceback (most recent call last): File "larch", line 5, in <module> from larch.apps import run_larch File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/__init__.py", line 52, in <module> from . import builtins File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/builtins.py", line 27, in <module> from . import xrd File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/xrd/__init__.py", line 25, in <module> from .amscifdb import CifStructure, get_amscifdb, get_cif, find_cifs File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/xrd/amscifdb.py", line 40, in <module> from pymatgen.io.cif import CifParser File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/io/cif.py", line 25, in <module> from pymatgen.core.composition import Composition File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/core/__init__.py", line 21, in <module> from .lattice import Lattice # noqa File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/core/lattice.py", line 23, in <module> from pymatgen.util.coord import pbc_shortest_vectors File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/util/coord.py", line 17, in <module> from . import coord_cython as cuc File "pymatgen/util/coord_cython.pyx", line 1, in init pymatgen.util.coord_cython ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject I also tried to use python to start larch_server and xas_viewer and had the same results. I also have the same results if I try to launch larch using ./larch This is the information on the version of Python that I am running: Python 3.8.10 (default, Jun 4 2021, 15:09:15) [GCC 7.5.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information. Any suggestions anyone has to offer will be appreciated. Wishing you all the best, Don -- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, McGill University

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Cannot start larch on ubuntu 20.04.2 LTS
by Don Baker, Dr. 28 Jun '21

28 Jun '21

Hi Folks, I think I am missing something obvious and am hoping that you can quickly tell me my mistake, so let me begin my story: I downloaded xraylarch-2021-060Linux-x86_64.sh into downloads on a Asus Zenbook using ubuntu 20.04.2 LTS I ran the command bash ./xraylarch-2021-060Linux-x86_64.sh Larch appears to have been correctly installed, but because I am using a gnome desktop no shortcuts appeared on my desktop (as promised) ,and there were no files that I could identify as shortcuts in my Downloads directory (which was set to display hidden files) I then moved to the /xraylarch/bin and tried to launch larch using python and this is what happened: python larch Traceback (most recent call last): File "larch", line 5, in <module> from larch.apps import run_larch File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/__init__.py", line 52, in <module> from . import builtins File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/builtins.py", line 27, in <module> from . import xrd File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/xrd/__init__.py", line 25, in <module> from .amscifdb import CifStructure, get_amscifdb, get_cif, find_cifs File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/xrd/amscifdb.py", line 40, in <module> from pymatgen.io.cif import CifParser File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/io/cif.py", line 25, in <module> from pymatgen.core.composition import Composition File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/core/__init__.py", line 21, in <module> from .lattice import Lattice # noqa File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/core/lattice.py", line 23, in <module> from pymatgen.util.coord import pbc_shortest_vectors File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/util/coord.py", line 17, in <module> from . import coord_cython as cuc File "pymatgen/util/coord_cython.pyx", line 1, in init pymatgen.util.coord_cython ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject I also tried to use python to start larch_server and xas_viewer and had the same results. I also have the same results if I try to launch larch using ./larch This is the information on the version of Python that I am running: Python 3.8.10 (default, Jun 4 2021, 15:09:15) [GCC 7.5.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information. Any suggestions anyone has to offer will be appreciated. Wishing you all the best, Don -- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, McGill University

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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 26 May '21

26 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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Larch 0.9.51
by Matt Newville 27 Apr '21

27 Apr '21

Hi Folks, Larch 0.9.51 is now available for download and use. It's been several months since the last release, and there have been some important improvements to XAFS data processing and to the XAS Viewer application: - Parameters saved in an Athena Project File are now correctly saved and read into XAS Viewer (thanks Tyler Valentine!) - There is now a simple "Apply to all marked groups" feature for pre-edge peak fitting. That is, you can define a pre-edge peak model with one data set and then apply it to many others, either inspecting the individual fits or saving a CSV file with all the parameters and uncertainties for each fit to each data set. - XAS Viewer can now import multiple scans from a Spec file (thanks Mauro Rovezzi for help with this). It may seem that Specfiles are "legacy", but the reader should also be able to handle the ESRF Bliss HDF5 files (as read in with the silx package, from ESRF), which is their way of efficiently stacking multiple scans into a single binary file. While support for this here should be considered "beta" (or maybe "alpha"!), it is also reasonable to expect that this or a similar HDF5 format file will become a common way to collect and store XAFS data. - There are binary installers for Windows, MacOSX, and Linux. There are also now "GetLarch.sh" and "GetLarch.bat" scripts (that are very short) that can be run to do the download and install, essentially mimicking what the binary installer does. This may be useful for folks wanting to install Larch on multi-user servers or in existing (or "other") Python environments. This might also be useful for those who run into permissions issues, especially on MacOS, where installing a package from an untrusted source is often blocked by default. With the installer script, the unprivileged user is simply running a script that downloads a bunch of files and places them in the home folder. These scripts might also be useful for those who run into problems downloading very large files from millenia.cars.aps.anl.gov, as the installer scripts will use Anaconda and PyPI resources that are better distributed throughout the world. ... which brings me to a final note (I'll send out another message next week): The APS will have a planned power outage from April 30 to May 4 . This will take millenia.cars.aps.anl.gov off-line for those 5 +/- 1 days. That machine hosts the binary installers and also this mailing list. Mail sent to this list during that time will likely be lost (email routing servers can handle destination servers being down for a few hours, but not days). So, if you're planning on sending announcements here, either do it before April 29 or wait until May 5. If you have any questions, problems, or suggestions, please let me know. --Matt

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Fourier transform parameters not saved in Larch XAS Viewer
by Tyler Valentine 19 Apr '21

19 Apr '21

Hello, I am using Larch XAS Viewer. I noticed that when I save my work to an Athena project file (.prj) and reopen it later, the Fourier transform parameters are reset. It seems to be correctly saving other values that I set such as the pre-edge and normalization ranges, so I am unsure why it does not also save the transform parameters. Is it possible to have these values saved? Thank you, Tyler

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XAFS 2021 Virtual Conference deadlines
by Matt Newville 19 Apr '21

19 Apr '21

Hi Folks, I hope most of you have seen information about the 2021 Virtual XAFS Conference this summer: https://xafs2021.org/ There will be an in-person conference in the summer of 2022 in Sydney and a briefer, virtual conference this summer: 11-13 July 2021. I especially want to draw your attention to the Virtual Poster session for students and early-career scientists. The abstract deadline is 1 May, a little less than two weeks from now: see https://xafs2021.org/call-for-abstracts.php for details. Please consider submitting a poster or encouraging your colleagues to do so. There will also be a Virtual Workshop on Data Analysis with Larch: I'll be pre-recording lectures, and then going over some of the finer details of using XAS Viewer and doing simple XAFS analysis during the workshop. Hope to see you there, --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

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Looking for the XAS of Zn3P2
by Madeleine Han 16 Apr '21

16 Apr '21

Dear Ifeffit community, I am looking for the X-ray absorption spectrum of Zn3P2 to use as a reference to determine the composition of an unknown compound. Does anyone know if it has already been recorded? If so, where can I find it? Thank you in advance for your help, Yours sincerely Madeleine Han

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Re: [Ifeffit] Artemis fit error - chi-square and R-factors are always equal to 0
by Ava Rajh 27 Mar '21

27 Mar '21

HI, I hope I am replying to the thread correctly. Thank you for your insights, I have spent a lot of time tinkering with installation and I have a partial solution. To first answer your questions: - yes, the fit ran ok and comparing it to the same fit using ifeffit (done by a a machine using ifeffit that works correctly), the calculated parameters are almost the same, with slight differences of 10-5 order of magnitude. The plot after the fit also looks fine. -the log I attached was from the example Cu data set, but the issue happens on every fit I try to run. -I'm not sure about the feff.dat file used, I haven't been able to locate it in my installation. - Feff6 (or Feff6l if I set it in preferences) are able to run as far as I can tell -I have run the example larch scripts to which you pointed me, and most of them were able to run ok, with no obvious issues (the parameters looked ok and reduced chi-square and R vales were reported). There was an error in running a few of the tests something to do with PlotDisplay, but I'm pretty sure these aren't related issues. To me, all of this points to some trouble Artemis has communicating with larch. I have tried downgrading the installation from 0.9.50 (that installs with pip) to 0.9.49 (that the website says is the current) and an even older ones but no luck. The solution war disappointingly trivial: If I completely removed larch and demeter suite along with everything else I installed in the last few days, from my computer and tried to compile it again, this time with ifeffit, I finally managed to get the reduced-chi square and R values. I have no idea why it didn't work when I tried it a few times before before but now I am able to get the fit and all required parameters. It still doesn't work with larch, but for now, at least I'm able to get the results. I'll re-install Larch and tinker with it a bit more to try to figure out where the error was coming from and report back if I find anything that might help someone else facing the same issue. Thanks again for the help Best, Ava

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Unable to load Demeter modules with Perl
by Tyler Valentine 27 Mar '21

27 Mar '21

Hello, I am learning how to use a perl script to structure a fit with Demeter. However, when I input the 'use Demeter;' command into my script, I receive the following error: Can't load 'C:/Users/Tyler/AppData/Roaming/DemeterPerl/perl/site/lib/auto/Ifeffit/Ifeffit.dll' for module Ifeffit: load_file:The specified module could not be found at C:/Users/Tyler/AppData/Roaming/DemeterPerl/perl/lib/DynaLoader.pm line 193. I have changed the @INC to include all the directories where Demeter modules should be located, so I am not sure why I am receiving this error. I would appreciate hearing back from you about ways I could resolve this. Thank you for your time, Tyler

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Artemis fit error - chi-square and R-factors are always equal to 0
by Ava Rajh 26 Mar '21

26 Mar '21

Hello, I have recently installed Demeter suite on my LinuxMint 20 machine with all required dependencies met. Athena works well and Demeter passed all tests during installation. When running Artemis however, there is an issue with fits that persists with provided examples any any other projects I open (including the ones done by colleagues and just re-run on my machine). After the fit (which completes fine and returns expected fit that looks ok when comparing it to experiment), when inspecting the log file, chi-square, reduced chi-square and R values are equal to 0 (example log file attached bellow). No errors accompany the fit. I am using Larch installed with anaconda, and Artemis uses Feff6 executable. I have re-installed Demeter and tried to get it to work with Ifeffit but the error persists. I have found an existing git hub thread dealing with similar issue (https://github.com/bruceravel/demeter/issues/62) but no solution that I could discern. Could it be an issue with my perl version (5.30.0)? If someone has any ideas what the issue could be and how to fix it, I would appreciate the help. Please let me know if I can provide any additional information, and I apologize if there is something obvious I may have missed. Sincerely, Ava -- Ava Rajh

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FW: Postdoc position at BNL for studying molten salts using synchrotron methods
by Gill, Simerjeet 24 Mar '21

24 Mar '21

Hello XAFS Community, On behalf of Energy Frontier Research Center on Molten Salts in Extreme Environments (MSEE) at Brookhaven National Laboratory (BNL), I would like to bring your attention to postdoctoral Research Associate position within the Energy Frontier Research Center (EFRC) on Molten Salts in Extreme Environments. The position requires a Ph.D. degree in chemistry, physics, materials science or a related field. The interdisciplinary research will focus on structural and spectroscopic investigation of molten salts, solutes in them, and liquid-solid interfaces. You can find the detailed description of the position requirements and apply online, go to https://jobs.bnl.gov<https://jobs.bnl.gov/> under Job ID 2335 (https://jobs.bnl.gov/job/upton/post-doc-synchrotron-studies-of-molten-salts…) The postdoc will investigate molten salt systems using NSLS-II beamline facilities at Brookhaven National Laboratory, with X-ray absorption fine structure along with x-ray scattering techniques. This position will be in Nuclear Science and Technology Department at Brookhaven National Lab, Under supervision of Dr. Simerjeet Gill. Responsibilities will include performing synchrotron experiments on molten salt systems with and without actinides and collaborating with other participants of MSEE-EFRC. For inquiries, please email me at gills(a)bnl.gov<mailto:gills@bnl.gov>. Thank you, Simerjeet K Gill, Group leader, Nuclear Science and Technology Department, Brookhaven National Lab, Upton, NY 11973

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Cobalt carbide EXAFS spectrum
by Antonio Aguilar 18 Mar '21

18 Mar '21

Dear community, I'm struggling with the data analysis of some Co samples, i think it might be some cobalt carbide. I was wondering if someone would be willing to share the spectrum of the Co2C reference please? That would be very helpful. Thank you in advance! Cheers, Antonio Aguilar -- Postdoctoral fellow Beamlines CRG FAME (BM30B) & FAME-UHD (BM16) | ESRF ESRF - The European Synchrotron 71 Avenue des Martyrs, 38043 Grenoble, France Tel: +33 (0)4 76 88 25 46 - Bureau : LOB 2-50

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Not possible to install Larch MacOS X 10.12.6 via anaconda (see report)
by Mangold, Stefan (IPS) 16 Mar '21

16 Mar '21

Dear all, I tried to reinstall; before I updated and couldn’t open larch anymore conda install -yc GSECARS xraylarch Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed UnsatisfiableError: The following specifications were found to be incompatible with each other:

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Normalization of LCF coefficients when fitting experimental spectra with theoretical spectra
by Patricia Poths 11 Mar '21

11 Mar '21

Hi, I am a theoretical chemistry PhD student working on fitting experimental spectra with computed spectra in order to get a better understanding of the composition. In the LCF process with athena, I have found that when I allow "sum coefficients to 1", I get an unphysical negative coefficient of the last standard- after reading through the mailing list I understood why, and so no longer use that. The sum of my coefficients during the fitting now is close to 1- generally within the range of 0.95-1.1 at the absolute extremes, but more often around ~0.98- ~1.05. In order to compare these coefficients, I renormalize them to 1, so they can represent the fractions of each component present. However, to test this I took the new normalized coefficients and summed up the standards with their respective weights to create this normalized "fit", and found that it is worse than the initial one. Is this something I should be concerned about when reporting the qualitative trends in how the composition changes? And if so, is there a better way to do the fits in a more normalized way? Many thanks, Patricia

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Re: [Ifeffit] Ifeffit Digest, Vol 217, Issue 6
by Clark Adam Hugh (PSI) 10 Mar '21

10 Mar '21

Dear Valerie Sorry! I don't know where I got the idea that it was Fe, I was probably working on Fe data at the time of writing. Having looked back I can see Mo. "I am using Larch XAS Viewer for the first time to analyze some Mo XANES data. It is fairly straightforward, however I am running into problems with energy calibration, which leads to problems with Linear Combination Fitting." For Mo I also have some standards, maybe these would be helpful for you. These are all calibrated with the first derivative of the Mo foil and so are consistent with each other. Although measured on a different monochromator, the likely would serve well to compare the edge position to make sure the calibration is done consistently for the standards you have from the canadian light source to give some idea of if things are reliable. Si(111): Mo MoO2 MoO3 Fe2Mo3O12 Mo2C NiMoO4 Adam __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/129 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark(a)psi.ch ________________________________ 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: Tuesday, March 9, 2021 7:00:01 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 217, Issue 6 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: Re. Larch Energy Calibration (Mangold, Stefan (IPS)) 2. Re: Larch Energy calibration (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 9 Mar 2021 11:20:38 +0000 From: "Mangold, Stefan (IPS)" <stefan.mangold(a)kit.edu> To: "Schoepfer, Valerie" <valerie.schoepfer(a)usask.ca> Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Re. Larch Energy Calibration Message-ID: <45116D6C-9314-4822-8E1B-7FB929333D72(a)kit.edu> Content-Type: text/plain; charset="utf-8" Dear Valerie, The reason why I'm currently not using Larch for my data-evaluation chain is, that I didn?t found some features (like energy calibration; not as I use it; like Calibration of references, absorption and fluorescence spectra in one group) in Larch, which I need for my data evaluation process. They might be there, but I didn?t found them. for the XANES data evaluation your energy region might be a bit to short to fit a good background to the data. Anyway you have to fine-tune the parameters to reach a good background fit in the XANES region. While the automatic process in Athena produces quite good results for a lot of absorption edges, one has to be careful not add artefacts to the data in the XANES. Best regards Stefan > Am 08.03.2021 um 14:17 schrieb Schoepfer, Valerie <valerie.schoepfer(a)usask.ca>: > > Hi Chris and Adam, > > I'm actually looking at Mo, so the energy range is from about 19800 through 20200 eV on a Si(220) monochromator. (But thank you for your Fe offer!) > The standards seem to be all from the Canadian Light Source, but going as far back as 2013... > I'm not looking to make the LCF perfect at this point, but it does seem like the deeper I go, the less confident I am that I have the correct standards. > > I'm doing alright in Athena with respect to the process, its just that I can't get Larch to align properly. I'll probably just use Athena for data prep, Larch just seemed nice to learn. > But then in Athena I run into trouble with incorrect standards. One thing after another, you know? > > Thanks- > Valerie > > -----Original Message----- > From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov > Sent: Thursday, March 4, 2021 12:00 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 217, Issue 3 > > CAUTION: External to USask. Verify sender and use caution with links and attachments. Forward suspicious emails to phishing(a)usask.ca > > > 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: Larch energy calibration (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 3 Mar 2021 18:38:24 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Larch energy calibration > Message-ID: > <CA+7ESbrGYtdjidL4X+rCUEi+DfmL3dUyG-R2R-FHffeqshSGTQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Valerie, > > On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie < valerie.schoepfer(a)usask.ca> wrote: > >> Hi, >> >> >> >> I am using Larch XAS Viewer for the first time to analyze some Mo >> XANES data. It is fairly straightforward, however I am running into >> problems with energy calibration, which leads to problems with Linear >> Combination Fitting. >> >> >> >> Right now, which is likely wrong, I?m calibrating the energy of a >> standard to the theoretical edge, then auto-aligning the samples to the standard. >> But how do reference foils fit in here? Reference foils don?t seem to >> be tied to the sample like they are in Athena. Should I be manually aligning? >> >> >> >> Is there a general guidance or work flow? >> > > It's possible that I do not fully understand the question or that this answer will veer a bit off the topic of your question. > > For sure, energies need to be aligned properly for any multi-spectra comparison or linear method to work well. But it should be that you will have groups of spectra that all share a consistent energy calibration, say from the same beamline/beamtime. > > If you do have a reference channel for every measurement, you can compare those reference channels. Ideally, these will not vary for every > measurement - that would indicate a serious problem. So, I think you > should be able to group spectra together as uniformly calibrated (hopefully all data from a day or more of beamtime at a particular beamline) and then make sure that the different groups of spectra. Does that seem reasonable? > > I have to admit that at my beamline I don't often have the luxury or need to run a reference foil for every scan, so we calibrate consistently ahead > of time. I'm sure that leads to a bias in the software. I guess I forgot > that Athena had the ability to read and tie a second spectrum as a "reference" and use that to auto-apply calibration. > > Is it generally necessary to calibrate many spectra individually, or do people find that doing them in a few large groups is sufficient? > > --Matt >

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