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

SSRL post-doctoral position
by Ritimukta Sarangi 17 Nov '21

17 Nov '21

Hi, I would like to bring this unique opportunity to the EXAFS user community. I am looking to hire a post-doctoral fellow who will apply spectroscopy tools to the Ni-Fe containing active site in Carbon Monoxide dehydrogenase, which is part of a pathway that biologically captures CO2 and converts it into acetate. This project is funded by the Department of Energy and is extremely relevant to our understanding and remediation of CO2 in the atmosphere. You will work with a diverse team of postdocs working on a variety of X-ray spectroscopy projects and will get the experience of working in a national laboratory setting. See the attached posting for more information. Kind regards, Riti Sarangi

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Fe and Ni carbide XAS reference spectra?
by Valentijn De Coster 17 Nov '21

17 Nov '21

Dear ifeffit mailing list, My name is Valentijn De Coster. I am a PhD student at Ghent University, Belgium, working on Ni and Fe materials for CO2 utilization. I am currently looking for Fe and Ni carbide (Fe3C, Ni3C) reference XAS spectra, at the respective Fe K and Ni K edges, for fingerprinting purposes. As such, I was wondering whether anyone would have such data available. On a side note, I checked the CARS database, and while this has an Fe3C (Fe K edge) reference, the data file does not contain the Energy values of the spectrum. Thank you in advance for your time. Kind regards, Valentijn De Coster [Image result for ghent university logo] Valentijn De Coster PhD Student Laboratory for Chemical Technology (LCT) Department of Materials, Textiles and Chemical Engineering Technologiepark 125, 9052 Ghent, Belgium T: +32 9 331 17 M: +32 (0) 331 17 10 https://www.lct.ugent.be<https://www.lct.ugent.be/> https://helpdesk.UGent.be/e-maildisclaimer.php<https://helpdesk.ugent.be/e-maildisclaimer.php> Member of CSC: https://www.csc.ugent.be<https://www.csc.ugent.be/>

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MacPorts XAFS software: announcing a Port for Larch; and do we actually need Demeter on Macs?
by Fowler, Joseph W. (Assoc) 12 Nov '21

12 Nov '21

Hello XAFS fans: This note is about the Demeter package on MacPorts. If you don’t use Demeter through MacPorts on a Mac, skip this note. I’m the MacPorts “maintainer” of the ports demeter and ifeffit. They have been not installable or upgradeable for something like a year, because of new releases of … something? Probably either Mac OS X, and/or Apple's Xcode development system. I’ve made a ton of progress on my big goal of restoring demeter to life, but I cannot get all the way to finish the project. I have to say here that I’m a poor choice to maintain these ports. I barely understand how MacPorts works, and I don’t understand or use Perl at all. I am not even really an x-ray scientist—I develop superconducting x-ray sensors in a team at NIST, and I happened to be a collaborator of the previous maintainer when he left the field 6 or 8 years ago. I worked on the problem in two parallel paths. One was to create an official port for the Python package Larch. Late last month this was complete, so you can do a “sudo port install py39-xraylarch” and have it. (Replace “py39” with “py38” or “py37” if you use Python 3.8/3.7.) This required creating about a dozen new ports for Larch’s dependencies. (Actually, I know a ton more about how MacPorts works than I did six weeks ago.) Some new ports that might be of interest to this community include: * py39-pymatgen * py39-peakutils * py39-xraydb * py39-spglib * py39-xraylarch My other path was to track down and fix the problem that prevented ifeffit from compiling. (Recall that this package is unmaintained since 2014. See https://github.com/newville/ifeffit/) It looks like Xcode’s C compiler recently turned the “implicit function warning” into an error. A few hours ago, MacPorts accepted my proposed patches, so at least ifeffit should be installable as a port again. Unfortunately, demeter still won’t install completely, owing to problems in certain Perl-based ports that it depends upon, like p5.30-wx. That problem is so far from my expertise that I am completely stuck. I had hoped that if I got ifeffit to work, demeter would follow, but I was wrong. There are four strategies I can imagine from here: 1. Declare the ports ifeffit and demeter to be obsolete. Mac users will need to figure out other ways to do what Athena and Artemis do. 2. Wait until Perl experts fix the Perl dependencies (expect it to take months or more), then I fix demeter. 3. Modify/migrate Demeter so that Athena and Artemis rely completely on Larch and not at all on ifeffit. 4. Ask this mailing list for advice. I don’t know what strategy #3 would entail—again, I know zero Perl and don’t use this software. Demeter’s author told me he doesn’t have much interest in this upgrade. All I can really support alone is strategy #1 or #2: obsoleting or waiting. And that’s why I’m writing. On one side, does anyone care if Athena/Artemis become unavailable through MacPorts? So, does anyone object to path #1? On the other, does anyone here have better ideas? Best wishes, Joe Fowler NIST Boulder Labs

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how to learn wavelet analysis
by 罗昕宇 10 Nov '21

10 Nov '21

Dear IFEFFIT members, I'm a fresh graduate student majoring in chemical engineering. I began to learn XAFS by myself one month ago. I bought and read the book XAFS for Everyone written by Dr. Calvin. I think I have got a clear image of how EXAFS works. Recently, I am attracted by the technique called Wavelet Analysis from literatures. It seems pretty powerful to correlate both temporal and frequency information, but something just went probably beyond my current knowledge base. I understand that a changeable window should be adapted to a make a trade-off between time and frequency, but I don't understand the logic that good time-resolution in high frequency is preferred while in low frequency a good frequency-resolution is better. I would appreciate it very much if you could answer my half-baked question and offer me with some learning material. Best regards Xinyu

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iodine L-edge spectra
by Enyuan Hu 26 Oct '21

26 Oct '21

Hi, Does anybody happen to have the iodine element L-edge spectra (L1 preferred, but L2 and L3 are also okay) and is willing to share? thanks! Enyuan

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Larch R plot
by Christopher Patridge 25 Oct '21

25 Oct '21

Hello, I am using Larch and Athena together and I just have a question about the magnitude plots and its effect (if any) on EXAFS modeling. Below are plots of the same merged samples using the same setting values. I noted that the plot in Larch begins below 0 and just want to make sure this is not a setting I missed in Larch? Thank you, Chris ********************************************** Dr Christopher Patridge Associate Professor Dept of Chemistry SASE 315 716-829-8096 | patridgc(a)dyc.edu www.dyc.edu <http://www.dyc.edu/> Social: Twitter <http://www.twitter.com/drpatridgc>

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Re: [Ifeffit] Ifeffit Digest, Vol 224, Issue 12
by Lisa Langlois 25 Oct '21

25 Oct '21

XAS Library? Dear Bruce. I was wondering how the XAS library is coming along. I have not seen too much update on that in Hephaestus. Best wishes, Lisa On Wed, Oct 20, 2021 at 9:33 AM <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: [Ext] FW: Problem in installing Larch (Jeffrey Terry) > 2. Re: Problem in installing Larch (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 20 Oct 2021 09:31:56 -0500 > From: Jeffrey Terry <terryj(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] [Ext] FW: Problem in installing Larch > Message-ID: <8D09051C-F118-4DFB-BF91-221C63110D54(a)iit.edu> > Content-Type: text/plain; charset="utf-8" > > ?Hi Raheleh, > > We have submitted a bug fix for this. Expect a new version of Larch to be > released shortly. > > We rely heavily on Larch for our EXAFS Neo analysis package and this has > broken our code as well. > > Jeff > > Jeff Terry > Interim Chair, Department of Social Sciences > Professor of Physics > Professor of Mechanical, Materials, and Aerospace Engineering > Editor, Applied Surface Science > Prairie Chapter Chair, AVS > Illinois Institute of Technology > 3101 S. Dearborn St. > Chicago IL 60616 > 630-252-9708 > > > Sent from my iPhone > > > On Oct 20, 2021, at 9:12 AM, Daneshpour, Raheleh <rmd5926(a)psu.edu> > wrote: > > ? > > > > Hello! > > > > I am Raheleh a PhD student at Penn State working in FeNi catalysis and > using XAS. I am trying to install the Larch, but I constantly get an error > message on different computers and using different installation methods. > The attached file is a screenshot of the error message I got. Could you > please help me to figure out how to solve the problem? > > Thanks, > > Raheleh > > > > <image001.png> > > Raheleh Daneshpour (She/Her) > > Ph.d. student > > > > Email: rmd5926(a)psu.edu > > > > Chemical engineering department > > The Pennsylvania State University > > University Park, PA > > > > > > <Capture-larch.PNG> > > _______________________________________________ > > 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 >

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Larch 0.9.56
by Matthew Newville 21 Oct '21

21 Oct '21

Hi Folks, Larch version 0.9.56 is now available on PyPI ( https://pypi.org/project/xraylarch) and should now be installed by default using most installation mechanisms. This really represents a collection of small improvements and bug fixes but includes one emergency bug fix that many people have seen with the latest version of `lmfit` (which was released recently). I believe that this will now work, but please let me know if you continue to have installation problems. Cheers, --Matt Newville

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Re: [Ifeffit] [Ext] FW: Problem in installing Larch
by Jeffrey Terry 20 Oct '21

20 Oct '21

Hi Raheleh, We have submitted a bug fix for this. Expect a new version of Larch to be released shortly. We rely heavily on Larch for our EXAFS Neo analysis package and this has broken our code as well. Jeff Jeff Terry Interim Chair, Department of Social Sciences Professor of Physics Professor of Mechanical, Materials, and Aerospace Engineering Editor, Applied Surface Science Prairie Chapter Chair, AVS Illinois Institute of Technology 3101 S. Dearborn St. Chicago IL 60616 630-252-9708 Sent from my iPhone > On Oct 20, 2021, at 9:12 AM, Daneshpour, Raheleh <rmd5926(a)psu.edu> wrote: > > > Hello! > > I am Raheleh a PhD student at Penn State working in FeNi catalysis and using XAS. I am trying to install the Larch, but I constantly get an error message on different computers and using different installation methods. The attached file is a screenshot of the error message I got. Could you please help me to figure out how to solve the problem? > Thanks, > Raheleh > > <image001.png> > Raheleh Daneshpour (She/Her) > Ph.d. student > > Email: rmd5926(a)psu.edu > > Chemical engineering department > The Pennsylvania State University > University Park, PA > > > <Capture-larch.PNG> > _______________________________________________ > 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

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Problem in installing Larch
by Daneshpour, Raheleh 20 Oct '21

20 Oct '21

Hello! I am Raheleh a PhD student at Penn State working in FeNi catalysis and using XAS. I am trying to install the Larch, but I constantly get an error message on different computers and using different installation methods. The attached file is a screenshot of the error message I got. Could you please help me to figure out how to solve the problem? Thanks, Raheleh [cid:image001.png@01D7C4CE.9ECA8AE0] Raheleh Daneshpour (She/Her) Ph.d. student Email: rmd5926(a)psu.edu<mailto:rmd5926@psu.edu> Chemical engineering department The Pennsylvania State University University Park, PA

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