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

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 23 May '23

23 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 16 May '23

16 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 08 May '23

08 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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White line position shift
by Otal Eugenio 25 Apr '23

25 Apr '23

Hi all, I am dealing with in-situ battery measurements. While I am changing the voltage, the white line of TM is changing its position and intensity. The change in intensity can be related to the order as pointed out here: https://pubs.acs.org/doi/10.1021/acsami.0c13161 But what about energy shifts when there is no change in the oxidation state? Any reference where to dig? Best regards. (^ㅇᆽㅇ^)(=˃ᆺ˂=)(=🝦 ༝ 🝦=) Eugenio H. OTAL Assistant Professor Dept. of Materials Chemistry Shinshu University 4-17-1 Wakasato, Nagano 380-8553, JAPAN eugenio_otal(a)shinshu-u.ac.jp https://sites.google.com/view/zettsu-laboratory/news-updates

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(no subject)
by Jyoti Pandey 25 Apr '23

25 Apr '23

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 .....................................

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XAS Data pre-processing
by Kumar Jena 23 Apr '23

23 Apr '23

Hi Ifeffit community, I am Kumar Jena, a PhD student at the University of Auckland. I have recently collected XAS data from amorphous anatase samples. I have read and seen many resources on performing data preprocessing, such as corrections, energy calibrations, etc. However, my question is, is there a specific order for doing so, or does it vary from data set to data sets? The order in which I have done it is as follows: (I have used Athena) - Import > Align data sets > Choose E0 and apply for all the scans > Merge them > Deglith the merged data > Rebin > Normalize Please advise if it's the right way to start. I appreciate your time and help. Kind regards, Kumar -- [image: University of Auckland (UOA) - WEGO-ITN] *Kumar Debajyoti Jena* *M.Tech (IIT Kanpur)* *Ph.D. Student* Department of Chemical and Materials Engineering Faculty of Engineering The University of Auckland Mob: *(+64) 225155447* *THERE IS NO PLAN*ET *B*. Please think of the environment before you print this email.

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SO2 for samples with non-planar geometry
by Joel Brugger 22 Apr '23

22 Apr '23

Dear list, We are trying to fit EXAFS from data collected on solutions within a capillary. The capillary has OD 1mm, ID 0.8mm, and was placed horizontally. The beam is 1x2 mm (VxH). Fitting the copper reference foil, we get the expected SO2 value of ~0.7. However, the solution containing the Cu(II) aqua ion gives a coordination of 2, instead of the expected 5-6. So our SO2 for this solution is apparently ~0.25. I couldn’t find a discussion of the effect of geometry (in our case cylindrical rather than planar) on SO2. Is it possible that the low SO2 is a result of the odd geometry? Confused as ever, JOEL Joël Brugger Professor of Synchrotron Geosciences Monash University School of Earth, Atmosphere and Environment Room 257A, Level 2, 9 Rainforest Walk <x-apple-data-detectors://2> Clayton, Victoria 3800 <x-apple-data-detectors://2> Australia <x-apple-data-detectors://2> T: +61 3 9905 4898 <tel:+61%203%209902%209095> E: Joel.Brugger(a)monash.edu <mailto:Andrew.Mackintosh@monash.edu> Twitter: @JoelBrugger

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Argument "h_rmax = 4" isn't numeric in array or hash
by Ryan Parmenter 15 Apr '23

15 Apr '23

Hi all, I have been using the Demeter package for a year now and have recently been experiencing an issue when importing data. The following message pops up when importing data into Athena: 10:23:55: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139. Line 139 contains: coerce Window, from Str, via { ($_ =~ m{[0-5]}) ? $window_list[$_] : $_ }; This usually pertains to line 139, but the following errors appear after the data import window is closed. 10:23:58: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139, <F> line 19. 10:23:58: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139, <F> line 27. 10:23:58: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139, <F> line 35. 10:23:58: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139, <F> line 43. 10:23:58: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139, <F> line 51. 10:23:58: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139, <F> line 59. 10:23:58: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139, <F> line 67. The programme still runs; however, this pop-up is becoming slightly frustrating, given the amount of data I have. I have tried to use an older version, but the issue persists. This occurs with new and old data files, which were fine in the past. Do you have any ideas on how I can resolve this? I appreciate any help you can give me.

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Re: [Ifeffit] Ifeffit Digest, Vol 242, Issue 9
by Jyoti Pandey 14 Apr '23

14 Apr '23

Thank you so much for the information. With Best Regards Dr. Jyoti Pandey, Ph.D. Postdoctoral Researcher Department of Physics Central Michigan University, MI, USA Mobile No. +91-9555347259 ..................................... On Thu, Apr 13, 2023 at 4:31 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: Scattering paths in Artemis (Matt Newville) > 2. Re: Stand Alone Atoms (Matt Newville) > 3. Re: Issue with Larch interacting with other software > (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 13 Apr 2023 12:57:16 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Scattering paths in Artemis > Message-ID: > < > CA+7ESbriDraZ4TvE7afH_gFj_Aa9R_Hyw64d9WY+0j22wa4v2Q(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Jyoti, > > The scattering paths are held in the "feffNNNN.dat" files, and do not > necessarily need the feff.inp file that was used to generate them. It is > fine to move those around, rename them, etc. That just means that you are > then taking charge of managing and organizing them instead of letting > Artemis (or, say XAS Viewer) do that for you. > > You can definitely use different scattering paths from multiple > calculations, including those done elsewhere. > > > On Thu, Apr 13, 2023 at 10:30?AM Jyoti Pandey <jyotipandey51092(a)gmail.com> > wrote: > > > Hello everyone, > > > > I have a question regarding the scattering paths. > > Can we manually feed the scattering paths in artemis or it will only read > > from the feff input file. > > > > Thank you. > > > > > > > > With Best Regards > > > > Dr. Jyoti Pandey, Ph.D. > > Postdoctoral Researcher > > Department of Physics > > Central Michigan University, MI, USA > > Mobile No. +1-9282650599 > > ..................................... > > > > _______________________________________________ > > 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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Issue with Larch interacting with other software
by Luke Townsend 13 Apr '23

13 Apr '23

Hi All, Apologies if this has been brought up previously but I wanted to see if anyone else has had some issues with other software installed on the computer interacting with Larch (particularly XAS Viewer) and resulting in Larch no longer functioning. A couple of colleagues/students have been running into this issue with the SEM software AZtec. The error code that has been reported is (I'm not sure how helpful this is): 'Entry Point Not Found - The procedure entry point H5Literate could not be located in the dynamic link library C:\Program Files\Oxford Instruments NanoAnalysis\AZtec\x64\HDF5_hl.dll.' If anyone has any suggestions for resolving this (without having to run two separate computers for each software which is our current work around) it'd be thoroughly appreciated. All the best, Luke -- Dr Luke Townsend | Research Associate | MinSoc Environmental Mineralogy Group Early Career Representative & Newsletter Editor | Department of Materials Science & Engineering | The University of Sheffield | S1 3JD | +44(0)7464724397 | Twitter: @LukeTTownsend *I may sometimes send emails outside of standard office hours as this suits my working habits. Please note I do not expect an out of hours response in return.* *Latest research:* Cr2+ solid solution in UO2 evidenced by advanced spectroscopy ( https://doi.org/10.1038/s42004-022-00784-3) Sulfidation and Reoxidation of U(VI)-Incorporated Goethite: Implications for U Retention during Sub-Surface Redox Cycling ( https://doi.org/10.1021/acs.est.2c05314)

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