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

Re: [Ifeffit] Installing Demeter on Mac (Apple M1)
by Fowler, Joseph W. (Assoc) 05 Dec '22

05 Dec '22

Dear Anthony, I’m the official MacPorts maintainer of Demeter. Although I have an M1 mac, I have not even tried to install it there. This fact might give you an idea of how active my efforts have been lately. (Sorry about that, community. Volunteers who use Demeter in their daily life on a Mac would be most welcome to take over or share the load here!) I suspect your immediate problem is with your shell’s path. Can you… 1. Make sure demeter installed what you expect it to install? Try “port contents demeter | less”. I expect to find /opt/local/bin/athena in the list of contents. 2. Make sure the directory where athena is installed is “in your path”. Specifically, try “echo $PATH” and make sure that /opt/local/bin is in the colon-separated list of path elements. 3. If athena is installed, but not in the path, you can do “/opt/local/bin/athena” to start it. For future convenience, you can read up on how to add to your PATH variable via zsh startup files. However, even after all that, you might still have a problem. The root of the bigger problem is that ifeffit is no longer actively maintained, but it’s required for Demeter. The authors of the two packages have discussed the problem with me, but we have not come up with any satisfactory solution. You might investigate whether Larch (ifeffit’s successor) could help solve your problems outside of Athena? (That’s available in a port named py-xraylarch, which we added earlier in 2022. Or you can use pypi/pip to install Larch using Python’s package management outside of the MacPorts framework.) In principle, Larch might be capable of being mixed in to Demeter as a replacement for ifeffit, but in practice it would take some real work. (Or so the authors think.) Bruce, Matt: please correct any misunderstandings I’ve expressed in the previous paragraph! Best wishes, Joe Fowler NIST Boulder Labs On Dec 4, 2022, at 6:22 PM, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov> To subscribe or unsubscribe via the World Wide Web, visit https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c… or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov<mailto:ifeffit-owner@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. Installing Demeter on Mac (Apple M1) (agironda) From: agironda <agironda(a)uw.edu<mailto:agironda@uw.edu>> Subject: [Ifeffit] Installing Demeter on Mac (Apple M1) Date: December 4, 2022 at 5:33:43 PM MST To: "ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>" <ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>> Hi, I’m a graduate student in Gerald Seidler’s group at University of Washington. I’ve gone through the process of installing Demeter on my M1 mac using macports. I believe it has completed successfully and all dependencies have been installed/established. However, calling “athena” or other commands do nothing -here’s a screenshot from my terminal. <image001.png> Transcription: anthonygironda@Anthonys-MacBook-Air-4 ~ % sudo port install xorg-server demeter Password: ---> Computing dependencies for xorg-server ---> Cleaning xorg-server ---> Computing dependencies for demeter ---> Cleaning demeter ---> Scanning binaries for linking errors ---> No broken files found. ---> No broken ports found. anthonygironda@Anthonys-MacBook-Air-4 ~ % athena zsh: command not found: athena anthonygironda@Anthonys-MacBook-Air-4 ~ % I understand Demeter compatibility on Mac is not largely supported, but has someone encountered this and found a workaround? I’m a bit of a novice at command line, so I appreciate your consideration and help. Sincerely, Anthony Gironda _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@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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Artemis: Importing VPaths Crash Error
by Ryan Parmenter 03 Dec '22

03 Dec '22

Hello, I'm having an issue with opening a data file in Artemis. As usual, I started by importing an Athena data file and a CIF. The paths were calculated and plotted (all worked ok). Then, I opened a second Athena data file and attempted to copy over the paths to check the fit; however, transferring the path parameters from the first data set to the second crashed the programme and will no longer open that data file. I have replicated the problem by using a new data file with fewer paths. Again, when exporting the path parameters to a second data set causes the file to crash and no longer open. I have tried both versions, 0.9.26 and 0.9.25, on two different laptops - one with windows 10 and the other with Windows 11. The same issue occurs. Opening the .fpj file directly from the desktop opens Artemis, but it soon crashes and closes; however, opening Artemis and loading the file causes Artemis to get stuck on 'importing VPaths'. (see image). I have left this open for a couple of hours, and its remains on importing v paths. Checking the dartemis file log, it states: Can't call method "parent" without a package or object reference at C:/Users/rap/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/Fit.pm line 1717. '-q' is not recognized as an internal or external command, operable program or batch file. %PGPLOT, Unable to read font file: grfont.dat %PGPLOT, Use environment variable PGPLOT_FONT to specify the location of the PGPLOT grfont.dat file. I had a look in visual studio to look at line 1716 - 1719 in fit.pm This is: my $path = $this -> mo -> fetch(['Path','SSPath'], $pg); $path->parent(Demeter->mo->fetch("Feff", $path->parentgroup)) if not $path->parent; ##print $path->name, "|", $path->group, "|", $path->parent, $/; $this->push_paths($path); I could not debug due to being a newbie with visual studio and unable to debug without the 'Perl' language installed. I have tried to install this language, but that's a separate issue. Thanks, Ryan

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PosDoc position at KIT
by Zimina, Anna (IKFT) 30 Nov '22

30 Nov '22

Dear all, Postdoc position for operando X-ray absorption studies on Fischer-Tropsch catalysts for the CARE-O-SENE Project is open now in our group at IKFT/KIT: https://www.pse.kit.edu/karriere/joboffer.php?id=91688 <https://www.pse.kit.edu/karriere/joboffer.php?id=91688&new=true> &new=true https://care-o-sene.com/en/ Feel free to apply and distribute the information further. Best regards, Anna Zimina ____________________________________________________________________________ __________ Karlsruhe Institute of Technology (KIT) Institute of Catalysis Research and Technology (IKFT) Dr. Anna Zimina Senior scientist Hermann-von-Helmholtz-Platz 1 Building 345 Office 304 76344 Eggenstein-Leopoldshafen Phone: +49 721 608 28673 Fax: +49 721 608 26789 E-Mail <mailto:anna.zimina@kit.edu> anna.zimina(a)kit.edu

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Re: [Ifeffit] XANES temperature estimation (Robert Gordon)
by Gabriele Garofalo 21 Nov '22

21 Nov '22

Hi Gordon, I have just one spectrum per sample, all taken at different T (unknown, due to technical problems) and P (known). I'd like to find T and using an EoS is not a viable option. I was thinking that maybe, assuming that the Debye-Waller term is explained only by thermal disorder, the Debye temperature is P independent, and there are no structural or electronic transformations, I could retrieve T by fitting the Debye-Waller term and using the reference spectra. Is this possible? Best regards Gabriele > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 21 Nov 2022 16:16:50 +0100 > From: Gabriele GAROFALO <gabriele.garofalo(a)esrf.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] XANES temperature estimation > Message-ID: <0ce690cc-ca47-5507-76b3-848bba8d7db8(a)esrf.fr> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Hi everyone, > > I'd like to estimate the temperature of some samples from some XANES > spectra, is there a way to do that? I couldn't find an answer in the > mailing list archive. > > Thanks! > > > > ------------------------------ > > Message: 2 > Date: Mon, 21 Nov 2022 10:23:10 -0500 > From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] XANES temperature estimation > Message-ID: <B288F5DB-33C3-4F6C-A4A3-D41D713157B1(a)stonybrook.edu> > Content-Type: text/plain; charset=utf-8 > > Only evaporation temperature, when XANES spectrum disappears?:) > > Anatoly > >> On Nov 21, 2022, at 10:20 AM, Gabriele GAROFALO >> <gabriele.garofalo(a)esrf.fr> wrote: >> >> ?Hi everyone, >> >> I'd like to estimate the temperature of some samples from some XANES >> spectra, is there a way to do that? I couldn't find an answer in the >> mailing list archive. >> >> Thanks! >> >> _______________________________________________ >> 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 > > > > ------------------------------ > > Message: 3 > Date: Mon, 21 Nov 2022 09:13:19 -0800 > From: Robert Gordon <ragordon(a)alumni.sfu.ca> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] XANES temperature estimation > Message-ID: > <CA+FiM0EvUpbWH2=WzqjKTRMwZsw2w-DSgJ-2J9XgAVAScbiSTg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Gabriele, > > To qualify Anatoly's cheerful, pre-morning coffee response, if your > samples > are part of a sequence of measurements > of a material whose XANES has been measured at different temperatures, > and > said XANES does have some changes > owing to changes in physical or electronic behavior with temperature > (i.e. > a phase transition), then you could estimate > where your samples fit within that determined behavior. > > Are you familiar with how temperature dependence manifests in a typical > XAFS measurement? > ...through the Debye-Waller term..the effects of which become less > pronounced at lower k... > > Temperature is more typically a controlled parameter during > measurements. > > So no, not really...unless there is a known behavior for comparison. > > -R.

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XANES temperature estimation
by Gabriele GAROFALO 21 Nov '22

21 Nov '22

Hi everyone, I'd like to estimate the temperature of some samples from some XANES spectra, is there a way to do that? I couldn't find an answer in the mailing list archive. Thanks!

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How to normalize tens of thousands of XAS data?
by 张驰 15 Nov '22

15 Nov '22

How to normalize tens of thousands of XAS data? I measured a series of the spectra of sample over time by in situ XAS, the results contained tens of thousands of sets of XAS data, and it was impossible to normalize each set of data individually.I would like to ask where to find the normalized source code of Athena, I can modify the code so I can use my computer to achieve a large number of processing.Thanks!

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found some issues found in larch (read-in issues)
by Mangold, Stefan (IPS) 26 Oct '22

26 Oct '22

Dear All, dear Matt, all tests were done on Macs (one M1 & one Intel) with the latest version your software & latest OS. 1. Read-In of spec files works, but only one file at once. Even if multiple files are selected 2. If one tries to load text-files it is possible to load data form multiple files as long as you don’t try to load also the reference spectra. If you load the reference also the read-in stopps at the transmission/fluorescence spectrum of the second file selected. 3. Trouble, that I sometimes can’t unmount network volumes after reading from them, larch saved on local discs. MacOS claims that python has files open; no other python program running 4. unable to save the data of one XAS-viewer while having two xas-viewer open. best regards Stefan Mangold

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Xraylarch installation
by Dien.Li＠srnl.doe.gov 14 Oct '22

14 Oct '22

Dear Matt With help of our IT folk, we downloaded Larch for windows binary installer file and installed the xraylarch 9.65 on my computer, however, the LARCH subdirectory with the five application platforms (e.g., XAS viewer) were NOT generated automatically. We tried to uninstall and install three times, it is still the same, could you please suggest what we may do to correct this? Thank you so much. Dien Li Savannah River National Laboratory

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[Larch] S02 value larger than 1
by dxfan＠post.kek.jp 04 Oct '22

04 Oct '22

Dear All, � I have a very common question, which is already asked many times: the S02 value is larger than 1. I measure the Sr K-edge EXAFS of SrTiO3 with temperature dependence. The S02 value is larger than 1. I check the book of “XAFS for everyone”, in which say maybe because of the distorted data or wrong structure model. I check the data measured by other beamline with the same sample, the S02 value still is larger than 1. I change the background reduction parameters, same result. I also modify the model, still same result. � I am very confused with these results. I attached the data, FEFF paths, and the fitting python Code the package. Can anyone help me check my fitting procedure. � Best regards, Fan

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Co2P spectrum
by Christian Wittee Lopes 21 Sep '22

21 Sep '22

Dear XAFS community, Does anyone have a spectrum of Co2P sample or standard? Thank you in advance. Best, Christian Wittee Lopes -- Christian Wittee Lopes Visiting Researcher - ANP/FINEP - PRH 50.1 Institute of Chemistry, Universidade Federal do Rio Grande do Sul (UFRGS) chriswittee(a)gmail.com LinkedIn <https://www.linkedin.com/in/christian-wittee-lopes-561855219/> | ORCID <https://orcid.org/my-orcid?orcid=0000-0001-8420-1958> | Lattes <http://lattes.cnpq.br/4953371870936050>

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