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

Larch 0.9.58
by Matt Newville 16 Jan '22

16 Jan '22

Hi Folks, Larch version 0.9.58 has been released. It should now be installed by default using all installation mechanisms, and you may see a notice to update if running xas_viewer. Coming only 6 weeks after 0.9.57, and with the holidays in between, this is mostly a set of bug fixes, especially surrounding installation and errors associated with our use of deprecated features of silx and numpy. Thanks mostly to Mauro for this, and for updating the documentation for installation, especially for existing Anaconda Python users, and on Linux. FWIW, I checked that a fresh install works on Windows 10, MacOS 12, CentOS 7, CentOS 8 Stream, and that "auto-updates" work with "larch -u" or from XAS Viewer works on MacOS 12 and on Fedora 34. But, of course, let us know if you have suggestions, comments, or problems. There are a few fixes for reading some kinds of data files and with de-glitching XAS spectra. The plans discussed in the previous release message (see https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2021-December/010345.ht…) about saving more complex projects and how to think "reference spectra" have not had much work done on them. The request for suggestions and comments on these topics still stands. --Matt

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Re: [Ifeffit] Question--FEFF calclulated atom coordinates and labels
by Ming Zhang 14 Jan '22

14 Jan '22

sorry for the trouble, I forgot to register this email. -----原始邮件----- 发件人:"Ming Zhang" <mzhang17(a)zju.edu.cn> 发送时间:2022-01-13 14:41:04 (星期四) 收件人: ifeffit(a)millenia.cars.aps.anl.gov 抄送: 主题: Question--FEFF calclulated atom coordinates and labels Dear IFEFFIT members, I’m practicing EXAFS fitting with some standard crystal data. I GOT SOME QUESTIONS when I imported the CIF File into the FEFF calculation. 1)I’m confused with the atom label. The VESTA GUI shows that there are C1, C2, and C3 carbons in a unit cell. However, after FEFF calculation, they become C1.1 C2.1 C3.1, so do the other atoms like nitrogen and hydrogen. Since I need to set some geometry constraints, I have to figure out the nomenclature of the atom coordinates calculated by FEFF and link those atoms to real physical images. 2)I’m also confused with the calculated degeneracy, like the path of @ C1.1 @ (I have no idea about the atom C1.1 stands for). It’s a zinc absorber placed in a tetrahedron coordinated by the N atom of imidazole. Very intuitively, the degeneracy of @ N1.1 @ (row 1) is 4, and YES IT IS. But how comes the single scattering path (row 2) of the C atom next to N become 8? Also in row 5, degeneracy of @ N1.1 C2.1 @ is 8. Notably, we only got 3 C atoms in a coordinated molecule, so even treating closely located C atoms into the same one couldn’t help explain this. FEFF calculation VESTA GUI The CIF file is attached. I would appreciate it very much if you could help me out. Best regards Ming Zhang

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How do I launch Larch GUIs?
by Swanner, Elizabeth S [GE AT] 12 Jan '22

12 Jan '22

I use a Mac recently updated to Big Sur (11.6). I used the Binary Installer File for Larch and am a little stuck on what to do next. I was able to run the installer, and I have an xraylarch folder on my computer. However, I was hoping to use the XAS Viewer and do not see it within the folder. Should it be there? I had an old version of XAS Viewer I got while at APS but needed to replace that as it did not have all the modules. I did not check before removing that whether it was working on this OS. I am also not clear how to use Larch in general (i.e., the Basic Larch GUI). Do I need to install python? I see there is a python application in the folder but when I try to open that nothing happens. I’m not sure if these are issues with my OS or if I am missing something really basic about how to launch Larch. Best, Betsy Swanner

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Issues reinstalling Larch, error creating desktop shortcut for macOS
by Lauren N. Pincus 05 Jan '22

05 Jan '22

Hi Matt, I'm having an issue with reinstalling Larch. I'm using macOS Catalina 10.15.7. I had Larch previously installed and it was working well, but found I was no longer able to open up XAS Viewer. The application would start and then quit. So, I removed Larch from my system and tried to reinstall it. I first used the mac installer but would get an error that the "Installation failed. The installer encountered an error that caused the installation to fail." I then tried the installation using the script in terminal. This appeared successful, but no desktop shortcut was created. I tried to create a desktop shortcut using larch -m but get the following error: (base) laurenpincus@lnp24mbp2020 ~ % larch -m Traceback (most recent call last): File "/Users/laurenpincus/xraylarch/bin/larch", line 5, in <module> from larch.apps import run_larch File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/__init__.py", line 52, in <module> from . import builtins File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/builtins.py", line 22, in <module> from . import io File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/io/__init__.py", line 39, in <module> from .specfile_reader import (str2rng_larch, read_specfile, open_specfile, File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/io/specfile_reader.py", line 26, in <module> from silx.io.convert import write_to_h5, _is_commonh5_group ImportError: cannot import name '_is_commonh5_group' from 'silx.io.convert' (/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/silx/io/convert.py) (base) laurenpincus@lnp24mbp2020 ~ % Thanks, Lauren Lauren Pincus, PhD NSF Earth Sciences Postdoctoral Fellow Princeton University Department of Geosciences

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Re: [Ifeffit] [Ext] Re: Problem in xrayLarch installation
by Jeffrey Terry 20 Dec '21

20 Dec '21

We’ve had to come up with a slightly different install plan for Windows users of our analysis package EXAFS Neo that is built on top of xrayLarch. We recommend a slightly different route using both conda and pip. You can read through out full recommended analysis route for xrayLarch in the Prerequisites section of our readme file at: https://github.com/laumiulun/EXAFS-Neo-Public We are pretty confident that the installation method given there works for xrayLarch installation on Mac, Windows, and Linux. 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 Dec 15, 2021, at 2:42 AM, Mauro Rovezzi <mauro.rovezzi(a)esrf.fr> wrote: > Dear Latif, > > Thanks for reporting this. Unfortunately `pip` is not able to correctly install all dependencies of Larch. The way to go is to install those dependencies via `conda`. > > Under Windows, this is achieved by running the script `GetLarch.bat` (https://raw.githubusercontent.com/xraypy/xraylarch/master/installers/GetLar…) This script will download and install a minconda distribution, plus install Larch in it. > > Seen you already have Anaconda installed, you could simply run the following commands from your Anaconda prompt: > > conda install -yc conda-forge wxpython tomopy scipy matplotlib scikit-image scikit-learn pymatgen pycifrw > pip install wxmplot wxutils lmfit asteval pyshortcuts pyfai xraylarch > > If this does not work, please, let me know. I have created a related Github issue in order to avoid such troubles in the future: > > https://github.com/xraypy/xraylarch/issues/333 > > Best, > Mauro > > On 2021-12-15 08:20, Latif Ullah Khan wrote: >> Dear Sir Madam, >> I hope you are doing well, I Latif Khan, working as a beamline scientist at XAFS beamline SESAME light source. I was using LARCH on my Anaconda python environment at window PC. Now I re-install and upgrade the Anaconda to python 3.9. I am trying to install the xrayLarch from Anaconda command prompt (python 3.9), using “pip install xraylarch” . However, it is not installing and give me an following error: >> If you kindly help me in this regard, I will be grateful to you. >> Thank you in advance >> Best regards >> Latif >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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Re: [Ifeffit] Ifeffit Digest, Vol 226, Issue 9_Problem in wavelet code
by Latif Ullah Khan 20 Dec '21

20 Dec '21

Dear Matt Newville and Mauro, Many thanks for the kind reply and great support in installation of the XrayLarch through window. Unfortunately, I could not install through Anaconda prompt using command " conda install -yc conda-forge wxpython tomopy scipy matplotlib scikit-image scikit-learn pymatgen pycifrw pip install wxmplot wxutils lmfit asteval pyshortcuts pyfai xraylarch" as suggested by Mauro. Fortunately I succeeded to install through window command prompt using the source code. Now I am using through VS Studio code. I just adopted the code for wavelet transformation written by Matt Newville, however, I faced some problem in plotting the 2D CCWT image, I am sharing the code with input data and also the code. Its showing some error in following syntax, probably "imopts" has problem: plt.imshow(f.wcauchy_mag, win=1, label='Wavelet Transform: Magnitude', **imopts) plt.imshow(f.wcauchy_re, win=2, label='Wavelet Transform: Real Part', **imopts) If you kindly help me in this regard, I will be grateful to you. Thank you in advance Best regards Latif -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, December 15, 2021 6:08 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 226, Issue 9 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: Problem in xrayLarch installation (Matt Newville) 2. Re: Any coorelation about 'white line" in K-edge XAS with oxidation states? (Robert Gordon) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Dec 2021 09:23:47 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: "Ifeffit-request(a)millenia.cars.aps.anl.gov" <Ifeffit-request(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem in xrayLarch installation Message-ID: <CA+7ESbqCSsM+==XmUgzkjzjPHTOJjfLRGw8JRDqN5CGUxzJCuQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Latif, Sorry for the trouble. As Mauro said, some of the packages needed (and pymatgen is one of these) are not super-well supported for installing with pip. FWIW, I agree that the needed combination of conda and pip is sort of unfortunate. But most of the "problem packages" are either Windowing systems (wxPython: that have been challenging to have consistent binary support on Linux is very challenging) or packages of scientific code written by and for scientists, some with excellent engineering support and some (like us!) with "less" support. Conda is a popular option for many of these. We try to support the simpler / more ubiquitous pip where we can. Anyway, that's basically why we have the binary installers and installation scripts. But also: thanks for the report and we are trying to clean up or at least document some of these kinds of issues where we can: https://github.com/xraypy/xraylarch/issues/333 --Matt

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Any coorelation about 'white line" in K-edge XAS with oxidation states?
by Marco Wang 16 Dec '21

16 Dec '21

Dear everyone: Ihave some questions about the interpretation of "white line", from anarticle (https://doi.org/10.1038/s41467-021-27116-8) and the figure was attached. In the article, it is said that “the sample was fully reduced to Ni (0) state at ~480 °C judging from the edge position and ‘white-line’ profiles”. First, we assumed that the metal was coordinated with the same anion. We all know that K-edge transition in 3d and 4d metalis' spin forbidden, so it may be inappropriate to conclude that the intensity of the "white line" is correlated with metals' oxidation states. But in other words, the probability for s→d transition may be proportional to thenumber of empty d orbitals, so it seems like if the the intensity of "white line" is higher, the oxidation state is higher. So, how should we correctly interpret the “white line” and edge energy from XAS spectrum of metals’ K-edge and L-edge? Thank you in advance for your time. Marco Wang

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Problem in xrayLarch installation
by Latif Ullah Khan 15 Dec '21

15 Dec '21

Dear Sir Madam, I hope you are doing well, I Latif Khan, working as a beamline scientist at XAFS beamline SESAME light source. I was using LARCH on my Anaconda python environment at window PC. Now I re-install and upgrade the Anaconda to python 3.9. I am trying to install the xrayLarch from Anaconda command prompt (python 3.9), using "pip install xraylarch" . However, it is not installing and give me an following error: If you kindly help me in this regard, I will be grateful to you. Thank you in advance Best regards Latif [cid:image001.png@01D7F194.F5C60C50]

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Re: [Ifeffit] XEOL
by Eugenio Otal 06 Dec '21

06 Dec '21

Dear Robert, sorry for the late reply, life... Brilliant suggestion! I will let you know the results if the proposal is approved. Best regards, euG If you can move between Nd L3 and Br K, why not stop at Nd L1 if you want to see if a Nd s-type initial state has any influence on the XEOL? You should not need to go up to Nd K. Some references: https://aip.scitation.org/doi/abs/10.1063/1.477320?journalCode=jcp https://iopscience.iop.org/article/10.1149/1.3211180 and a book chapter https://www.worldscientific.com/doi/10.1142/9789812775757_0015 On 2021-11-25 5:50 p.m., Eugenio Otal wrote: > Hi all, > I am planning XEOL measurements and I have a doubt. > My system is Nd coordinated to Eosin, tetrabromofluorescein. I want to > measure XEOL exciting on the Br K-edge (13.4keV) and the Nd > L3-edge(6.2keV) and measure the emission spectra of the dye and the > Nd. I just measured the emission of the Nd exciting at 530nm and it > worked perfectly. > My question is, I have access to Nd K-edge, is it worthy?to measure > XEOL at the K-edge? I am in the time limit to?request an?extra shift. > I would appreciate some bibliography. > Best regards. > > _______________________________________________ > 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 0.9.57
by Matt Newville 02 Dec '21

02 Dec '21

Hi All, Larch version 0.9.57 has been released and is available on PyPI ( https://pypi.org/project/xraylarch) It should now be installed by default using most installation mechanisms, and you may see a notice to update if running xas_viewer. The updates are described in some at https://github.com/xraypy/xraylarch/releases/tag/0.9.57 and in the github commit history. This includes adding support for reading RIXS data files from ESRF BM16, better support for de-glitching in XAS_Viewer, and fixing of reading of many Athena Project Files that were saved in the "old style" and have non-ASCII characters (the code now correctly reads the 78 Project files at https://github.com/xraypy/xraylarch/tree/master/examples/xafsdata/AthenaPro… ). Much of the work for this release has come from Mauro Rovezzi. In a conversation we had yesterday about this release, we talked about several potential changes going forward, especially for XAS_Viewer, about saving processing history, how to improve the concept of "reference spectrum" for a measurement, and other topics related to keeping track of analysis history and provenance. Some of these ideas are encapsulated in Github Issues at https://github.com/xraypy/xraylarch/issues, and the plan is to work on this. One possibility would be to be able to read and export to Athena Project files but use a different format (probably HDF5) as a new default "Larch Project File" so that more complexly nested data and some sort of "journal" per data set could be saved, displayed, edited, and so on. If anyone here has some thoughts on how such topics could or should be handled, please let us know. If you have other ideas on what might be added or improved, also don't hesitate to speak up, either in conversations here or on Github. Cheers, --Matt Newville

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XEOL
by Eugenio Otal 26 Nov '21

26 Nov '21

Hi all, I am planning XEOL measurements and I have a doubt. My system is Nd coordinated to Eosin, tetrabromofluorescein. I want to measure XEOL exciting on the Br K-edge (13.4keV) and the Nd L3-edge(6.2keV) and measure the emission spectra of the dye and the Nd. I just measured the emission of the Nd exciting at 530nm and it worked perfectly. My question is, I have access to Nd K-edge, is it worthy to measure XEOL at the K-edge? I am in the time limit to request an extra shift. I would appreciate some bibliography. Best regards.

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PostDoc position at Northeastern University
by NUCRET 23 Nov '21

23 Nov '21

Northeastern University Center for Renewable Energy Technology is currently looking for highly qualified candidate to fill a Post-Doctoral Research Associate position with hands-on experience in the area of in situ and operando XAS, XANES, EXAFS spectroscopy, high-energy XRD as applicable to batteries (especially solid-state), fuel cells and electrolyzers. Familiarity with Brookhaven synchrotron facility (or other US-based light source facilities, e.g. ANL, SLAC) is a plus. Candidates should be in the US and authorized to work in the US (visa is _not_ offered). To apply, please use Northeastern University Career Portal: https://careers.hrm.northeastern.edu/cw/en-us/job/508477/postdoctoral-resea…

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Postdoctoral beamline scientist position at Illinois Tech/MRCAT
by Carlo Segre 22 Nov '21

22 Nov '21

Please find attached the advertisement for a postdoctoral position at MRCAT (Sector 10) at the Advanced Photon Source. The position is with Illinois Institute of Technology, which operates MRCAT for its institutional membership. Feel free to share this with any appropriate individuals. Carlo -- Carlo U. Segre (he/him) -- 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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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 11 Nov '21

11 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 27 Oct '21

27 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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Fit in R or k
by LIMA DA SILVA, WILL (PGR) 12 Oct '21

12 Oct '21

Dear IFEFFIT members, I have been fitting some EXAFS data, and my supervisor and I are having doubts if it's better to fit in k or R space. What are the main differences between the two approaches? I have learnt that R space is the right approach, but I am not sure how to explain it. Much appreciated, Will Silva

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Bug report: Athena, multiple data export
by Soyoung Kim 11 Oct '21

11 Oct '21

Dear Bruce and IFEFFIT community, Hope all is well. I found a bug with Athena's file export function. I had two normalized mu(E) data with very similar spectra but different x-axis values (collected with different energy step settings). [image: image.png] When I batch exported them to a .dat file using the purple E button while "Save next plot to a file" was turned on, the resulting data only had a single x-axis column, which was taken from the first data. Hence, when I plot the two spectra from this .dat file, they now look different: [image: image.png] If I export each data individually to .dat files, then they are correct. [image: image.png] I'm attaching the Athena project file containing the two data and the .dat files I exported, both together and individually. Please let me know if anything is unclear. Thank you in advance for your help. Best, Soyoung Kim

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