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

Deglitch the data
by Shailendra 17 Jul '23

17 Jul '23

Hi, IFEFFIT community, I am Rachna, a Ph.D. student working on IrO2 based OER catalyst. I am a new XAS user. Recently, we recorded some XAS on amorphous IrO2 electrode samples however some of the samples show a dip in adsorption at high energy. The glitches are similar to the one in the attached photo. I am attaching the Athena file for the measurements too. I was wondering if there is a way to remove such glitches. I would greatly appreciate any tips or tricks you may have for dealing with this situation. Thanks, Kavya Rachna

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Re: [Ifeffit] Help installing Demeter on a Mac
by Fowler, Joseph W. (Assoc) 01 Jul '23

01 Jul '23

Hello Kyle, I agree that putting /opt/local/bin in your PATH should be adequate, so this isn’t totally obvious. The executables athena, hephaestus, and artemis should all be in /opt/local/bin/. Are they? What is the result if you execute the following? $ port contents demeter I’m the official maintainer of the Macports version of Demeter. Unfortunately, I’m not a regular user. In fact, it’s not installed on the everyday computer that I’ve had for four years (to give you an idea of what “not regular” means to me). Worse, there’s a chronic problem that I have never worked out how to solve. The Demeter ports depends on many things. One is ifeffit, which is not really still supported, but Demeter can’t just magically start using Matt Newville’s replacement for ifeffit, known as Larch. It feels to me like Mac-Demeter is doomed to break permanently pretty soon, if it has not already. [Bruce, Matt, have I stated that accurately? Please correct me if I’m wrong.] Still, there exists a port for ifeffit and for demeter, and one should be able to install them. I’m trying it right now on a Mac that lacks them. It will take me a while, because I’m not a Perl user either, and there are dozens of dependencies to install first. Let’s see how it goes for me… This install is taking a very long time. I’m going to send this note as-is and report later about whether I can make athena run, and where the executable is located. (But I’m sure it will be /opt/local/bin/ ) Could I suggest that, if you get it to work, and you use it regularly, and you’re an open-source supporter, would you think about helping as a second official maintainer of the Demeter port? Other users could benefit from me teaming up with an actual demeter user, to be sure! Best wishes, Joe Fowler NIST Boulder Labs On Jun 30, 2023, at 11:00 AM, 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…<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<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. Help installing Demeter on a Mac (Kluherz, Tk) From: "Kluherz, Tk" <Tk.Kluherz(a)nrel.gov<mailto:Tk.Kluherz@nrel.gov>> Subject: [Ifeffit] Help installing Demeter on a Mac Date: June 30, 2023 at 10:02:03 AM MDT 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>> Hello All, I’m a new postdoc at NREL, trying to install Demeter on my NREL Mac. I have previously only installed it on a Linux system. I followed the instructions<https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.h…> for installing on a Mac, including the logout/login, and the installation appeared to be successful, with no errors. However, when I then try to run athena/artemis/hephaestus from the command line, I get a ‘command not found’ error. Has anyone encountered this problem before? I thought I found a thread in the archives from 2014, but there was not response to the issue. I suspect it may be that the command location was not added to the $PATH, but am not sure where it is in order to add it. Here’s the output from echo $PATH: /opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin Any help would be appreciated! Thanks, Kyle _______________________________________________ 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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Help installing Demeter on a Mac
by Kluherz, Tk 30 Jun '23

30 Jun '23

Hello All, I’m a new postdoc at NREL, trying to install Demeter on my NREL Mac. I have previously only installed it on a Linux system. I followed the instructions<https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.h…> for installing on a Mac, including the logout/login, and the installation appeared to be successful, with no errors. However, when I then try to run athena/artemis/hephaestus from the command line, I get a ‘command not found’ error. Has anyone encountered this problem before? I thought I found a thread in the archives from 2014, but there was not response to the issue. I suspect it may be that the command location was not added to the $PATH, but am not sure where it is in order to add it. Here’s the output from echo $PATH: /opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin Any help would be appreciated! Thanks, Kyle

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EXAFS course at BNL: Nov. 1-3, 2023
by Anatoly Frenkel 29 Jun '23

29 Jun '23

Dear subscribers: The information about the upcoming XAFS short course is here: https://www.bnl.gov/xafscourse/ The course will be taught in-person. The place in the course is limited, and, due to the emphasis on advanced methods, the preference will be given to those participants who have prior experience with EXAFS data modeling and analysis. The info about the past course topics (2005-2022) is at the SCC website: https://you.stonybrook.edu/scc2/xafs-workshops/ Regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering (primary appointment) Department of Chemistry (affiliate appointment) * Stony Brook University * Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 Joint Appointment: Senior Chemist Chemistry Division, *Brookhaven National Laboratory* Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/staff/frenkel -------------------------------------------------------------------

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Postdoc position at BM23 ID24 XAS beamlines
by Kirill LOMACHENKO 28 Jun '23

28 Jun '23

Dear all, we are looking for an excellent postdoc to work with us at BM23 and ID24 XAS beamlines of the ESRF (Grenoble, France) in the field of chemistry (catalysis, electrochemistry, energy materials, etc). Cutting-edge research, state-of-the-art equipment, friendly team, competent users, great location, competitive salary and all other things to make a scientist happy. If you are good at applying XAS for chemistry (or know someone who is), please find the link to the position below (in case the link is not visible, just google "ESRF jobs"). Do not hesitate to contact me for more details. Best regards, Kirill Lomachenko -- Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu

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Brain teaser
by Anatoly Frenkel 15 Jun '23

15 Jun '23

Hello, all. It is a low- to medium- level brain teaser. Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It detectors were both Ar filled ionization chambers. Because of the energy dependence of reflectivity of the Pt mirror, I0 intensity was strongly nonlinear (blue curve). However, the transmission intensity in the It detector was almost linear (red curve). Why? Anatoly [image: image.png]

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Re: [Ifeffit] [Ext] Brain teaser
by Anatoly Frenkel 15 Jun '23

15 Jun '23

Thank you, Robert, Matthew, Jeff, Kirill, Terry and Sirine for great suggestions. I initially thought that the explanation for the linearity or the transmission signal is a superposition of two opposite trends: 1) increase of flux with energy due to the mirror effect and 2) similar decrease with energy due to the photon removal by first effect in the I0 detector. But I did not look into the main reason for the curving up of the I0 signal and I agree it is not a result of the reflectivity. I fill follow up on all suggestions, and, if something more definitive transpires, will report back. Thanks again for your time and advice! Anatoly > On Jun 15, 2023, at 2:10 AM, matthew marcus <mamarcus(a)lbl.gov> wrote: > The mirror was set up for a run at the Pd K-edge, according to the problem statement. Therefore, its nominal angle must be such as to put the critical energy >25keV. An angle of 3mrad would do it. At that angle, the reflectivity (assuming no roughness) goes up with energy in the relevant range, but only by a few percent. > > We're not told what the ratio of gains of the current amps is, or whether the ion chambers have the same path length, so we can't tell whether the signals are comparable, as shown on the graph, or orders of magnitude different. > mam > > On 6/14/2023 10:17 PM, Jeffrey Terry wrote: >> Well, I’ll take a shot. Looks like the mirror angle is totally fubared, you are getting Bragg peaks from the coating or substrate that are giving you the peaks in Io. Since you have no idea what angle those are going through Io, they are unlikely to make it into either the sample or It. Since those photons are removed from the beam hitting the sample, they would show up as intensity dips in It. I’d bet that most (all?) of the reflected beam is not going into the sample. I’m kind of surprised It signal is as clean as it is, but then I don’t know the gains on either measurement amplifiers. I couldn’t find a flat mirror angle that would cause the cutoff at 12870? eV but since it is a collimating mirror who knows what range of angles were actually being hit. >> Jeff Terry >> Interim Chair, Department of Biology >> Interim Chair, Department of Social Sciences >> Professor of Physics >> Professor of Mechanical, Materials, and Aerospace Engineering >> Editor, Applied Surface Science >> Illinois Institute of Technology >> 3101 S. Dearborn St. >> Chicago IL 60616 >> 630-252-9708 >>> On Jun 14, 2023, at 7:27 PM, Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu <mailto:anatoly.frenkel@stonybrook.edu>> wrote: >>> Hello, all. It is a low- to medium- level brain teaser. >>> Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It detectors were both Ar filled ionization chambers. Because of the energy dependence of reflectivity of the Pt mirror, I0 intensity was strongly nonlinear (blue curve). However, the transmission intensity in the It detector was almost linear (red curve). Why? >>> Anatoly >>> <image.png> >>> _______________________________________________ >>> 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 >> _______________________________________________ >> 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] Brain teaser
by Kirill LOMACHENKO 15 Jun '23

15 Jun '23

Hi Anatoly, maybe the high voltage of the I0 chamber is off? All the best, Kirill Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu On 15/06/2023 08:09, 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: Brain teaser (Anatoly Frenkel) > 2. Re: [Ext] Brain teaser (Jeffrey Terry) > 3. Re: [Ext] Brain teaser (matthew marcus) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 15 Jun 2023 00:30:41 -0400 > From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Brain teaser > Message-ID: <866EACCF-DAD2-4486-AAE0-AC3F6B28023E(a)stonybrook.edu> > Content-Type: text/plain; charset=utf-8 > > Amazing idea. I thunk you were the only one who succeeded to use third harmonic of Si for taking EXAFS at high atomic number elements. But that does not explain the peaks and dips. > > Anatoly > >> On Jun 15, 2023, at 12:22 AM, matthew marcus <mamarcus(a)lbl.gov> wrote: >> >> ?Suppose the mono is being used at the 333 reflection (for Si), intentionally working at the 3rd harmonic. In that case, if the fundamental isn't filtered out, you could get just what we see, with the sample doing the filtering before the beam gets to the transmission chamber. >> mam >> >>> On 6/14/2023 9:16 PM, Anatoly Frenkel wrote: >>> Thank you, Matthew and Robert, but I think the explanation is more simplle. The fact that there are peaks in I0 and dips in transmission is a clue that explains why transmission is almost linear while I0 curves up. >>> Anatoly >>>>> On Jun 14, 2023, at 11:34 PM, matthew marcus <mamarcus(a)lbl.gov> wrote: >>>> ?One thing that's pretty odd is that the glitches are peaks in I0, and dips in It. It would be much easier to explain if It was the one that increased steeply and I0 was more linear, but the presence of the edge in It shows that you didn't switch them. Red = It. What's that sudden drop at the end? >>>> >>>> Could it be that the I0 chamber is misaligned so that beam is scraping one of the plates? That could cause all sorts of odd things to happen. >>>> mam >>>> >>>>> On 6/14/2023 5:27 PM, Anatoly Frenkel wrote: >>>>> Hello, all. It is a low- to medium- level brain teaser. >>>>> Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It detectors were both Ar filled ionization chambers. Because of the energy dependence of reflectivity of the Pt mirror, I0 intensity was strongly nonlinear (blue curve). However, the transmission intensity in the It detector was almost linear (red curve). Why? >>>>> Anatoly >>>>> image.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 >>>> _______________________________________________ >>>> 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 >> _______________________________________________ >> 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: 2 > Date: Thu, 15 Jun 2023 00:17:35 -0500 > From: Jeffrey Terry <terryj(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] [Ext] Brain teaser > Message-ID: <C024E52C-2EDF-49C0-9B5A-168A2B14F8D3(a)iit.edu> > Content-Type: text/plain; charset="utf-8" > > Well, I?ll take a shot. Looks like the mirror angle is totally fubared, you are getting Bragg peaks from the coating or substrate that are giving you the peaks in Io. Since you have no idea what angle those are going through Io, they are unlikely to make it into either the sample or It. Since those photons are removed from the beam hitting the sample, they would show up as intensity dips in It. I?d bet that most (all?) of the reflected beam is not going into the sample. I?m kind of surprised It signal is as clean as it is, but then I don?t know the gains on either measurement amplifiers. I couldn?t find a flat mirror angle that would cause the cutoff at 12870? eV but since it is a collimating mirror who knows what range of angles were actually being hit. > > Jeff Terry > Interim Chair, Department of Biology > Interim Chair, Department of Social Sciences > Professor of Physics > Professor of Mechanical, Materials, and Aerospace Engineering > Editor, Applied Surface Science > Illinois Institute of Technology > 3101 S. Dearborn St. > Chicago IL 60616 > 630-252-9708 > > > > > >> On Jun 14, 2023, at 7:27 PM, Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> wrote: >> >> Hello, all. It is a low- to medium- level brain teaser. >> >> Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It detectors were both Ar filled ionization chambers. Because of the energy dependence of reflectivity of the Pt mirror, I0 intensity was strongly nonlinear (blue curve). However, the transmission intensity in the It detector was almost linear (red curve). Why? >> >> Anatoly >> >> <image.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 0.9.70 released
by Matt Newville 09 Jun '23

09 Jun '23

Hi Folks, We have been releasing a version of X-ray Larch every few months, steadily adding features and improving bugs in XAS Viewer and in the general library. We have not felt the need to announce every release, but I would like to address a problem that many people have seen with automated updates, especially on Windows. Basically, automated updates from XAS Viewer do not work on Windows, and running the automated updates can (and I think even "usually will") lead to a broken installation. This can be (and needs to be) fixed by running C:\Users\YourName\xraylarch\Scripts\pip install --upgrade xraylarch from a Command Prompt terminal. With the latest version, XAS Viewer will only inform you (in the status bars at the bottom of the main window) when an update is available, and not continually prompt you to update now. A new desktop application called "Larch Updater" will also be installed that will run the above command. Unfortunately, the current version you have installed will still prompt you for an automated update. I recommend that you do not do this, but run the above command yourself, and then going forward, we'll all be able to use the updater at our own pace. --Matt PS: Some of the other changes in the latest version can be seen at https://github.com/xraypy/xraylarch/releases/tag/0.9.70

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Post-doc position at SSRL
by Ritimukta Sarangi 06 Jun '23

06 Jun '23

Hello Folks, We have an open post-doc position in XAS/EXAFS/advanced spectroscopy at SSRL. We are looking for someone with expertise in or interest in biological/molecular applications of XAS. Please see the job listing here: https://careers.slac.stanford.edu/sites/default/files/SSRL_X-ray_Spectrosco… If you have any questions, please do not hesitate to reach out. We are hoping to fill this position asap but can wait for for a few months for the right candidate! Kind regards, Riti Sarangi SSRL Sent from my iPhone

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python accesses outlook PST files during X-ray larch binary installation on Windows 10 computer
by Voegelin, Andreas 06 Jun '23

06 Jun '23

Dear All I apologize for this question related to IT safety rather than science and the use of Larch. Today, I installed Larch for Windows on an institute computer using the latest Windows 64-bit binary installer (0.9.68). Now I got the following alert from our IT security: “The process c:\users\%USER%\appdata\local\xraylarch\python.exe accessed Outlook files. The user who ran the process was XXXX. The accessed files were: XXXX.pst, YYYY.pst”. It seems that during the installation of Larch, python.exe accessed some outlook archive files in another folder on the C drive, and I do not know if this should be a matter of concern. Has anyone experienced a similar behavior before, or does anyone with Larch/python skills have an explanation for this? Cheers, Andreas

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calibrated Fe(CP)2 and beam effect
by Esmael Balaghi 26 May '23

26 May '23

Dear All, Does anyone happen to have a spectrum of bulk ferrocene (Fe K edge), by any chance? It would be even more helpful if it includes the spectrum of Fe foil or calibrated ferrocene. I'm trying to determine the extent of the beam effect, whether it caused reduction/oxidation or decomposition, during data acquisition. I would greatly appreciate any tips or tricks you may have for dealing with this situation. Thank you in advance. Esmael

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Re: [Ifeffit] Problems with FEFF calculation using CIF file (Matt Newville)
by Volker, Anouk 26 May '23

26 May '23

Dear Matt, Thank you for the quick response. The first error gets indeed resolved by removing the atoms labeled with a B. I was not very clear in my first post that I had to do this to have the ATOMS window run properly in Artemis. The problem I am stuck on is that when I have them removed and then run the FEFF window, it seems to all work fine, until I try and drag the paths into the Path window in Artemis. At that point the paths seem to no longer exist. I hope this clears up my question a bit more. Kind regards, Anouk On Thu, May 25, 2023 at 7:02 PM <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: Problems with FEFF calculation using CIF file (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 24 May 2023 12:29:01 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Problems with FEFF calculation using CIF file > Message-ID: > <CA+7ESbpH97zi+-xbK2R62m8ND-MG+6OgMB= > R16zSqXE2za7yCA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Anouk, > > I am not sure what is happening with that CIF file. When I try to read > that with pymatgen, I get > > >>> from pymatgen.io.cif import CifParser > >>> structs = CifParser('VOXZAJ.cif') > >>> structs.get_structures() > .../site-packages/pymatgen/io/cif.py:1145: UserWarning: Error is Species > occupancies sum to more than 1!. > warnings.warn(f"Error is {str(exc)}.") > .../site-packages/pymatgen/io/cif.py:1148: UserWarning: Issues encountered > while parsing CIF: Some occupancies ([2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, > 2, 2, 2, 2, 2, 2, 2, 2]) sum to > 1! If they are within the > occupancy_tolerance, they will be rescaled. The current occupancy_tolerance > is set to: 1.0 > Species occupancies sum to more than 1! > warnings.warn("Issues encountered while parsing CIF: " + > "\n".join(self.warnings)) > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > .../site-packages/pymatgen/io/cif.py", line 1150, in get_structures > raise ValueError("Invalid cif file with no structures!") > ValueError: Invalid cif file with no structures! > > If you remove all the atomic sites that have a "B" in their name, that gets > resolved, but I do not know if that is still the correct structure - or > what the "B" means. > > CIF is complicated, but just from a practical point of view, I think we are > going to take `pymatgen` as the arbitrator of "valid CIF". > > > On Wed, May 24, 2023 at 11:30?AM Volker, Anouk <a.volker(a)student.rug.nl> > wrote: > > > Dear all, > > > > I hope this email finds you well. I have encountered a problem that I > have > > not been able to fix on my own. I have a specific CIF file (from the > CCDC > > database) that is attached to the e-mail. After removing the duplicate > > atoms in the file, the ATOMS window seems fine. The FEFF calculation will > > run without any errors and within the FEFF window the paths are displayed > > and can be plotted. The problem arises when I try to take some of the > paths > > from the FEFF window and drag them into the Path window. Now the paths > can > > no longer be plotted and when trying to use them to fit, it seems like > the > > paths are non-existent as well. > > > > Is there something wrong with the CIF file that causes this to happen and > > if so, what can be done to fix it? I have already tried to make a > feff.inp > > file from the xyz data (after opening the CIF file in any viewer), but > this > > gives the same problem. > > > > Thank you in advance, > > > > Kind regards, > > Anouk Volker > > > > Master student, Browne Group > > Stratingh Institute, University of Groningen > > _______________________________________________ > > 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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Problems with FEFF calculation using CIF file
by Volker, Anouk 24 May '23

24 May '23

Dear all, I hope this email finds you well. I have encountered a problem that I have not been able to fix on my own. I have a specific CIF file (from the CCDC database) that is attached to the e-mail. After removing the duplicate atoms in the file, the ATOMS window seems fine. The FEFF calculation will run without any errors and within the FEFF window the paths are displayed and can be plotted. The problem arises when I try to take some of the paths from the FEFF window and drag them into the Path window. Now the paths can no longer be plotted and when trying to use them to fit, it seems like the paths are non-existent as well. Is there something wrong with the CIF file that causes this to happen and if so, what can be done to fix it? I have already tried to make a feff.inp file from the xyz data (after opening the CIF file in any viewer), but this gives the same problem. Thank you in advance, Kind regards, Anouk Volker Master student, Browne Group Stratingh Institute, University of Groningen

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Re: [Ifeffit] [Attachment Removed] Re: Low amplitude chi signal of first shell calculated by FEFF
by Matt Newville 24 May '23

24 May '23

Hi Fan, If you included an attachment, I did not see it. If so, can you send it some other way? I would not expect that the Sr K-edge of SrTiO3 needs much playing around with parameters in the feff.inp file prior to running Feff. I would advise against doing that unless you know what you are doing. Don't set Vi to be below 0. I would be more inclined to believe that the data treatment had problems or that the use of the feff paths had problems. Without knowing what you did, it is very hard to speculate what might be going wrong. On Tue, May 23, 2023 at 9:38 PM Dongxiao <dongxiaofan01(a)gmail.com> wrote: > An attachment on this email message was removed because it contained > potentially dangerous content. If you are expecting a file from the sender, > request that they provide access to it via a file sharing service. > ------------------------------ > > Hello, Matt, cc: who is interested, > > > > Thank you very much for your reply. > > The low amplitude chi signal is common when I calculated the A site EXAFS > signal of perovskite structure. > > Especially the chi signal of first single scattering path (A-O) is > unreasonable low. > > In my case (Sr K-edge EXAFS of SrTiO3), the intensity of calculated chi is > smaller than the low-temperature experimental chi. > > I have been struggling with this problem for some time. I am looking > forward to somebody who can give me some advice.. > > I attached the related files for your check. > > > > I try to vary Vr and Vi value and want to see how the amplitude change. > > If set the Vi to negative, it indeed can increase the amplitude, but I > don’t know if it is proper. > > Maybe the problem is caused by the bad muffin-tin potential, but I don’t > know how to improve it. > > > > Can you give me some advice? > > > > Best regards, > > Fan > > > > -----Original Message----- > > Matt Newville > <https://www.mail-archive.com/search?l=ifeffit@millenia.cars.aps.anl.gov&q=f…> > Fri, 12 May 2023 14:25:36 -0700 > <https://www.mail-archive.com/search?l=ifeffit@millenia.cars.aps.anl.gov&q=d…> > > > > Hi Fan, > > > > On Fri, May 12, 2023 at 9:56 AM <dx...(a)post.kek.jp> wrote: > > > > > Hi, All > > > > > > > > > > > > The problem I meet is the low amplitude chi signal of first shell > > > calculated by FEFF. > > > > > > The consequence of the fitting is large value of SO2 (1.5-2.0), which is > > > quite unacceptable. > > > > > > I tried to fit the dataset measured by different people at different > > > beamline, the consequence is same. > > > > > > > > > > > > My data is T-dependent Sr K-edge EXAFS of SrTiO3, path file generated by > > > FEFF10, fitting process by Larch+python. > > > > > > By check the email list, it seems the long shell distance (2.7 A) is the > > > origin of the problem. I am not sure for that. > > > > > > I also try to vary the Vi value to improve the amplitude, the change is > > > small. > > > > > > Can any body give me some advice? > > > > > > > I would not expect that a Sr-O distance of 2.7 to 2.8Ang would cause an > > amplitude problem. I would tend to expect that being off by a factor of 2 > > would > > imply normalization issues. You could try to vary Vi, but I would not > > guess that you need to do that. Why do you set Vi to 2 (eV)? > > > > Do you have data and/or analysis steps (script or Larch session file) you > > can share? > > > > > > > > > > > Best regards, > > > > > > Fan > > > > > > > > > > > > My feff.inp file is like: > > > > > > -------------------------------------------- > > > > > > * This feff8 file was generated by Demeter 0.9.26 > > > > > > * Demeter written by and copyright (c) Bruce Ravel, 2006-2019 > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * space = 221 > > > > > > * a = 3.90500 b = 3.90500 c = 3.90500 > > > > > > * alpha = 90.00000 beta = 90.00000 gamma = 90.00000 > > > > > > * rmax = 9.00000 core = Sr > > > > > > * polarization = 0 0 0 > > > > > > * shift = 0 0 0 > > > > > > * atoms > > > > > > * # el. x y z tag > > > > > > * Sr 0.00000 0.00000 0.00000 Sr > > > > > > * Ti 0.50000 0.50000 0.50000 Ti > > > > > > * O 0.00000 0.50000 0.50000 O > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * total mu*x=1: 32.298 microns, unit edge step: 44.289 microns > > > > > > * specific gravity: 5.118 > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * normalization correction: 0.00029 ang^2 > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * Sr K edge energy = 16105 eV > > > > > > EDGE K > > > > > > S02 1.0 > > > > > > > > > > > > * pot xsph fms paths genfmt ff2chi > > > > > > CONTROL 1 1 1 1 1 1 > > > > > > > > > > > > PRINT 1 0 0 0 0 3 > > > > > > > > > > > > * ixc [ Vr Vi ] *** ixc=0 means to use Hedin-Lundqvist > > > > > > EXCHANGE 0 2 1 -1 > > > > > > *** Radius for self-consistent pots (2 shells is a good choice) > > > > > > * r_scf [ l_scf n_scf ca ] *** l_scf = 0 for a solid, 1 for > > > a molecule > > > > > > SCF 7 0 100 0.1 1 > > > > > > * kmax [ delta_k delta_e ] *** Upper limit of XANES > > > calculation. > > > > > > * XANES 4.0 > > > > > > * r_fms l_fms *** Radius for Full Mult. Scatt. l_fms = 0 > > > for a solid, 1 for a molecule > > > > > > * FMS 16.77392 0 > > > > > > * emin emax eimag *** Energy grid over which to calculate DOS > > > functions > > > > > > * LDOS -30 20 0.1 > > > > > > *** for EXAFS: RPATH 5.0 and uncomment the EXAFS card > > > > > > CRITERIA 0 0 > > > > > > * POLARIZATION 0 0 0 > > > > > > COREHOLE FSR > > > > > > RPATH 7.0 > > > > > > LDOS -30 20 0.1 > > > > > > EXAFS 20.0 > > > > > > > > > > --Matt

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Re: [Ifeffit] Ifeffit Digest, Vol 243, Issue 10
by Shuting Xiang 17 May '23

17 May '23

Thank you very much! We really appreciate it! Shuting On Wed, May 17, 2023 at 12:02 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. In2O3 and In foil XAFS spectra in need (Shuting Xiang) > 2. Re: In2O3 and In foil XAFS spectra in need (Robert Gordon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 16 May 2023 22:29:22 -0400 > From: Shuting Xiang <shuting.xiang(a)stonybrook.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov, "Li, Zhengyuan (li3zn)" > <li3zn(a)mail.uc.edu>, "Jimenez, Juan" <jjimenez1(a)bnl.gov> > Subject: [Ifeffit] In2O3 and In foil XAFS spectra in need > Message-ID: > < > CAPi4yra21_O6RT+KoZCJRUL8rk2ST-USoB_wMpRB7XFPyF5GZA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I hope this email finds you well. I am writing to inquire if any of you > might have the XAFS spectra of In oxide (In2O3) and In foil. We are in need > of these spectra as references for our ongoing research. If anyone would be > kind enough to share these spectra with us, we would greatly appreciate it. > > Please feel free to reach out to me if you are able to assist. Your support > would be greatly appreciated. > > Thank you very much for your attention and consideration. > > Best, > > Shuting Xiang > Department of Material Science and Engineering > Stony Brook University > Shuting.xiang(a)stonybrook.edu >

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Question about EXAFS fitting of mixtures
by Soyoung Kim 17 May '23

17 May '23

Dear all, While fitting EXAFS for tiny Pt nanoparticles, a simple question occurred to me. For these two scenarios: 1. All Pt atoms are coordinated to 3 O atoms and 3 Pt atoms each. 2. Half of the Pt atoms are coordinated to 6 O atoms and half to 6 Pt atoms. If we fit only single-scattering paths, would it be possible to tell apart these two scenarios with EXAFS fitting? What about linear combination analysis of the XANES? Thank you, Soyoung

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Not possible to install larch on actual system and Mac M1 system
by Mangold, Stefan (IPS) 17 May '23

17 May '23

Dear all, from binary package: can’t write to system partition by script and by anaconda I got the following message back: Collecting fabio Using cached fabio-2023.4.1.tar.gz (724 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... error error: subprocess-exited-with-error System ist 13.3.1, tried to install the newest version completely from scratch, because the update killed my larch version …. best regards Stefan

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In2O3 and In foil XAFS spectra in need
by Shuting Xiang 17 May '23

17 May '23

Dear all, I hope this email finds you well. I am writing to inquire if any of you might have the XAFS spectra of In oxide (In2O3) and In foil. We are in need of these spectra as references for our ongoing research. If anyone would be kind enough to share these spectra with us, we would greatly appreciate it. Please feel free to reach out to me if you are able to assist. Your support would be greatly appreciated. Thank you very much for your attention and consideration. Best, Shuting Xiang Department of Material Science and Engineering Stony Brook University Shuting.xiang(a)stonybrook.edu

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customized dead-time correction in Larch
by Esmael Balaghi 16 May '23

16 May '23

Dear Matt, Dear All, Is there a way to use our customized dead-time correction function in XAS viewer/Larch? Bests, Esmael

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Question about Artemis
by María Elena Montero Cabrera 13 May '23

13 May '23

Dear IFEFFIT-friends, I am working with Demeter version 0.9.26. In older versions of Artemis, I remember being able to load FEFF9 to produce the model for fitting, but I can't figure out how to do it in this version. I have only found how to write the Atoms results to be read by FEFF8. Is there a way to use the version of FEFF9 for this version of Artemis? Can anyone tell me how it's done or instead recommend where to get documentation on it? Thank you very much in advance Regards María Elena Dra. María Elena Montero Cabrera Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Complejo Industrial Chihuahua Chihuahua CP 31136, Chih. México Tel (614) 4391123

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Low amplitude chi signal of first shell calculated by FEFF
by dxfan＠post.kek.jp 12 May '23

12 May '23

Hi, All The problem I meet is the low amplitude chi signal of first shell calculated by FEFF. The consequence of the fitting is large value of SO2 (1.5-2.0), which is quite unacceptable. I tried to fit the dataset measured by different people at different beamline, the consequence is same. My data is T-dependent Sr K-edge EXAFS of SrTiO3, path file generated by FEFF10, fitting process by Larch+python. By check the email list, it seems the long shell distance (2.7 A) is the origin of the problem. I am not sure for that. I also try to vary the Vi value to improve the amplitude, the change is small. Can any body give me some advice? Best regards, Fan My feff.inp file is like: -------------------------------------------- * This feff8 file was generated by Demeter 0.9.26 * Demeter written by and copyright (c) Bruce Ravel, 2006-2019 * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- * space = 221 * a = 3.90500 b = 3.90500 c = 3.90500 * alpha = 90.00000 beta = 90.00000 gamma = 90.00000 * rmax = 9.00000 core = Sr * polarization = 0 0 0 * shift = 0 0 0 * atoms * # el. x y z tag * Sr 0.00000 0.00000 0.00000 Sr * Ti 0.50000 0.50000 0.50000 Ti * O 0.00000 0.50000 0.50000 O * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- * total mu*x=1: 32.298 microns, unit edge step: 44.289 microns * specific gravity: 5.118 * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- * normalization correction: 0.00029 ang^2 * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- * Sr K edge energy = 16105 eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 3 * ixc [ Vr Vi ] *** ixc=0 means to use Hedin-Lundqvist EXCHANGE 0 2 1 -1 *** Radius for self-consistent pots (2 shells is a good choice) * r_scf [ l_scf n_scf ca ] *** l_scf = 0 for a solid, 1 for a molecule SCF 7 0 100 0.1 1 * kmax [ delta_k delta_e ] *** Upper limit of XANES calculation. * XANES 4.0 * r_fms l_fms *** Radius for Full Mult. Scatt. l_fms = 0 for a solid, 1 for a molecule * FMS 16.77392 0 * emin emax eimag *** Energy grid over which to calculate DOS functions * LDOS -30 20 0.1 *** for EXAFS: RPATH 5.0 and uncomment the EXAFS card CRITERIA 0 0 * POLARIZATION 0 0 0 COREHOLE FSR RPATH 7.0 LDOS -30 20 0.1 EXAFS 20.0

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Beamline Scientist at APS
by Kelly, Shelly Diane 09 May '23

09 May '23

Hello Fellow XAS scientists: We have a position open for beamline scientist in the Spectroscopy Group at the APS. Please reach out to all those that might be interested in joining our team here in Chicago-land area. https://argonne.wd1.myworkdayjobs.com/en-US/Argonne_Careers/job/Lemont-IL-U… Kind regards, Shelly Kelly

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Co(OH)2 spectrum
by Christian Wittee Lopes 09 May '23

09 May '23

Hi folks, Does anyone have a spectrum of bulk cobalt hydroxide Co(OH)2 by chance? Thank you in advance. 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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Re: [Ifeffit] Ifeffit Digest, Vol 242, Issue 18
by Jyoti Pandey 26 Apr '23

26 Apr '23

Thank you! With Best Regards Dr. Jyoti Pandey, Ph.D. Postdoctoral Researcher Department of Physics Central Michigan University, MI, USA Mobile No. +1-928-265-0599 ..................................... On Tue, Apr 25, 2023 at 9:52 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: (no subject) (Anatoly Frenkel) > 2. Re: (no subject) (Kelly, Shelly Diane) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 24 Apr 2023 13:04:16 -0400 > From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] (no subject) > Message-ID: > < > CAFsMoZZZy_-1G5hnw1UNEbGMA+zB6pRMBZR2OPCpXqd8bBUjCg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Joyti, > > The coordination number of Rh-C bonds is defined as the total number of > Rh-C bonds in the sample divided by the total number of Rh atoms in the > sample. > Anatoly > ------------------------------------------------------------------- > Anatoly I. Frenkel > Professor > Department of Materials Science and Chemical Engineering (primary > appointment) > Department of Chemistry (affiliate appointment) > Stony Brook University > Stony Brook, NY 11794 > Email: anatoly.frenkel(a)stonybrook.edu > < > https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb… > > > http://you.stonybrook.edu/frenkel > Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL > http://you.stonybrook.edu/scc2 > > Joint Appointment: > Senior Chemist > Chemistry Division, Brookhaven National Laboratory > Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 > Email: frenkel(a)bnl.gov > https://www.bnl.gov/staff/frenkel > ------------------------------------------------------------------- > > > On Mon, Apr 24, 2023 at 12:25?PM Jyoti Pandey <jyotipandey51092(a)gmail.com> > wrote: > > > Hello everyone, > > > > I have a cluster of 13 Rh atoms above the graphene sheet. The first > > coordination number that I am getting is around 1.65 (which is obtained > by > > choosing a Rh-C) path. I am curious to know whether this value is the > > "exact" or the "average" coordination number w.r.t all the Rh atoms. > > > > Thanks > > > > With Best Regards > > > > Dr. Jyoti Pandey, Ph.D. > > Postdoctoral Researcher > > Department of Physics > > Central Michigan University, MI, USA > > Mobile No. +1-928-265-0599 > > ..................................... > > > > _______________________________________________ > > 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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