June 2021 - Ifeffit - millenia.cars.aps.anl.gov

Postdoc position for XAFS analysis
by 이국승(에너지환경소재연구팀) 30 Jun '21

30 Jun '21

Dear Ifeffit members, We are looking for a postdoc candidate for XAFS analysis in PAL. Tasks will be 1. XAFS analysis of electrochemical energy materials 2. Beamline management at Nano-probe XAFS beamline (BL8C) 3. One's own research The position requires PhD degree in Electrochemistry, Chemistry, Materials science or Physics, Excellent writing and communication skills in English, Experience in XAFS analysis. The position begins at any time in this year but earlier is better. If you are interested in this position, please send your CV including list of publications to Dr. Kug-Seung Lee. (lks3006(a)postech.ac.kr) Additional documents can be required including references. Kind regards, Kug-Seung Lee Kug-Seung Lee, Ph.D. Staff Scientist Manager, 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Scopus : https://www.scopus.com/authid/detail.uri?authorId=56953635300 Researcher ID: http://www.researcherid.com/rid/D-7088-2011

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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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