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

beamline scientist position at NSLS-II beamline XFM
by Matt Newville 22 Nov '23

22 Nov '23

Hi Folks, The University of Chicago is looking to hire a beamline scientist to be stationed at the NSLS-II XFM (4-BM) beamline. Details are at: https://uchicago.wd5.myworkdayjobs.com/en-US/External/details/Research-Prof… --Matt Newville

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Help with Larch install on MacOSX 14 (Sonoma)
by Sandeep Haripuria 19 Nov '23

19 Nov '23

Hi Matt, I’m trying to install Larch on MacOSX 14 (Sonoma) using the 64 bit binary installer (new install, new laptop). It created the xraylarch folder in my home folder, and installed the python library there. However, it did not create a Larch folder on the desktop (or anywhere else I can find). I tried the command from the terminal console ($HOME/xraylarch/bin/larch -m) but get the message of no such file or directory. Not sure what to do next… Hope all is well and thanks for your help, Sandeep Haripuria [ThePlattery.Com](https://theplattery.com/)

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Help with Larch install on MacOSX 14 (Sonoma)
by Peggy O'Day 17 Nov '23

17 Nov '23

Hi Matt, I’m trying to install Larch on MacOSX 14 (Sonoma) using the 64 bit binary installer (new install, new laptop). It created the xraylarch folder in my home folder, and installed the python library there. However, it did not create a Larch folder on the desktop (or anywhere else I can find). I tried the command from the terminal console ($HOME/xraylarch/bin/larch -m) but get the message of no such file or directory. Not sure what to do next… Hope all is well and thanks for your help, Peggy

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Errors when I try to export CSV file
by Yi Sang 12 Nov '23

12 Nov '23

Dear developer, I met an error when I try to export my XANES data as CSV file. Below is the error message: Traceback (most recent calls last): File "/Users/yisang/xraylarch/lib/python3.11/site-packages/larch/wxxas/xasgui.py", line 684, in onExportCSV groups2csv(savegroups, outfile, x=res.xarray, y=res.yarray, TypeError: groups2csv() got an unexpected keyword argument '_larch' How do you think I should resolve this problem? Thanks, Yi

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upcoming Webinar on Synchrotron for Earth and Environmental Science
by Matt Newville 09 Nov '23

09 Nov '23

Hi Folks, For the Earth and environmental scientists on the list, there will be a webinar introducing the newly formed "Synchrotron for Earth and Environmental Science" on Tuesday, November 14th, at 3 PM Chicago time, as presented by SEES Director Andy Campbell. If you are interested in learning more, you can sign up for the Zoom link for the webinar at: https://cars.uchicago.edu/sees/2023/09/27/sees-webinar-sees-the-light/ For a little more background: SEES (Synchrotron Earth and Environmental Science) is a new cooperative agreement with NSF to manage and enhance NSF Earth Science-supported beamline operations for Earth and environmental science research at four DOE synchrotron facilities: the Advanced Photon Source (APS), the Advanced Light Source (ALS), the National Synchrotron Light Source II (NSLS-II), and the Stanford Synchrotron Radiation Lightsource (SSRL). See https://cars.uchicago.edu/sees/ for more information. SEES will support many beamlines across the US for Earth and environmental science, including a few X-ray microprobe beamlines for XAS and other spectroscopy and imaging experiments such as the one I run at the APS. This new organization will also be the source of most of my support for the foreseeable future, with a healthy fraction of that explicitly earmarked for work on cyber-infrastructure, including the XAFS-related software discussed here. Cheers, --Matt

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Postdoc position at Argonne National Laboratory - X-ray characterization of low-temperature fuel cell and electrolyzers
by Myers, Deborah J. 30 Oct '23

30 Oct '23

https://argonne.wd1.myworkdayjobs.com/Argonne_Careers/job/Lemont-IL-USA/Pos…

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Re: [Ifeffit] Differences between Larch and Artemis when performing FEFF calculations
by Ava Rajh 18 Oct '23

18 Oct '23

Hello Matt! thank you for the response. In putting together all the project files for the minimal working example I tested a bunch more .cif files of various materials including different graphite file, and there was no difference in Larch and Athena in any of them (as long as the same FEFF version and input settings are used) as expected. Looking closely at the feff input file for the C.cif I was having trouble with, there were some differences which I haven't noticed when looking through them before. So as far as I am concerned, this was a user error on my part, as the generated input files weren't exactly the same. If I save the input feff file from Larch and use that in Artemis or the other way around, as you suggested, the results match exactly. The compared spectra in my previous message were calculated separately, exported and plotted together. thank you for very much for the help and kind regards, Ava > Message: 1 > Date: Mon, 16 Oct 2023 15:24:26 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Differences between Larch and Artemis when > performing FEFF calculations > Message-ID: > <CA+7ESbrWm5UoBYggLmi+-WZRU6mn4Y_-z1OBVg57pAu4rsXM7w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Ava, > > I think you'll have to give us more details about what you have done. > The > figures you show are all in R-space, so after at least some > processing... > So, yes, project files and/or scripts would be helpful. Yes, there > can be > subtle changes in the background subtraction (and in the normalization > process too) between Larch and Ifeffit/Athena/Artemis. > > By default, Artemis uses Feff 6.10 and Larch uses Feff 8. For the C K > edge, that could have a noticeable difference, especially in the > placing of > the k=0 value, though I do not know how big that effect would be for C > (graphite?). But also, Artemis and Larch can both read the inputs > from > the other calculations: it might be that this is what you have done to > make the plots, but that wasn't 100% clear to me. > > > > > On Mon, Oct 16, 2023 at 2:08?PM Ava Rajh <ava.rajh(a)ijs.si> wrote: > >> Dear all! >> >> I haven't been able to find a similar question/issue in the previous >> threads, so I hope someone can help me figure out what is going on. >> >> I am trying to fit a Carbon EXAFS spectra, using graphite as a model. >> I >> am first focusing on just the first two single scattering paths, so I >> calculated the theoretical paths with FEFF in Larch and tried using >> them >> to fit the spectra. I was consistently getting slightly lower >> distances >> than expected, but otherwise an OK fit. >> >> The issue is, I tried to compare the analysis with a colleague who is >> using Athena. At first glance the EXAFS spectra, using the exact same >> parameters, looked very similar (but not exactly the exactly the same, >> this I attributed to Larch using a different autobk procedure). I >> would >> have however expected the theoretical paths to match exactly, if they >> were calculated and plotted with the same parameters. But they were >> also >> slightly different. I then downloaded Athena and spent time trying to >> find where the differences come from. If I compare the first two >> calculated shells from Larch with the ones from Athena, with exactly >> the >> same set of test parameters (S02 = 1, E0 = 0, dr1 = 0, s2_1 = 0, dr2 = >> 0, s2_2 = 0), the resulting models do not match. I made sure the paths >> are calculated from the came .cif file in both cases, use FEFF6, have >> the same calculated reference distances, same FT... >> >> So, my main question is, am I missing something important in regards >> to >> calculations, why would the calculated paths be different and which >> one >> would be the "correct" one to use for the fit? And the other question >> would be about the fact that EXAFS spectra of experimental data look >> slightly different using Larch and Athena, am I right in disregarding >> this, or should I dig deeper and find the source of discrepancy? >> >> I am enclosing a plot of just the calculated first two shells from >> Athena and Larch (FT: kmin = 2, kmax = 7.5, Fittting in R space, kw = >> 3, kWindow = Hanning, dk = 1.0, Rmin = 0.6, Rmax = 2.1) along with the >> cif file I ended up using for testing the differences. If it would be >> helpful, I can also provide the project files and larch script I used >> for the dataset, but I am mainly interested in understanding the >> differences seen in the theoretical parts first. I tested this using >> Larch v 0.9.72 and Demeter 0.9.26 >> >> Thank you ver much for the help, and If I need to provide any >> additional >> info please let me know. >> kind regards, Ava >> >> -- >> Ava Rajh_______________________________________________

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EXAFS fitting - Reff command not recognized
by van der Veer, Siebe 17 Oct '23

17 Oct '23

Hi all, I'm having an issue where I want to use a * reff (also tried a*reff, a * Reff, a*Reff) as the expression for delta R, but instead of recognizing the command Reff, Larix now considers this a parameter it should fit, whereas in the past it would just use the value for Reff contained in the path in question. Is anyone else experiencing this issue as well and if so, how can I fix this? Best, -- *Siebe van der Veer* | *PhD student* Nanostructures of Functional Oxides | Zernike Institute for Advanced Materials University of Groningen | Nijenborgh 4, 9747 AG Groningen | The Netherlands Email: s.van.der.veer(a)rug.nl |

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Differences between Larch and Artemis when performing FEFF calculations
by Ava Rajh 16 Oct '23

16 Oct '23

Dear all! I haven't been able to find a similar question/issue in the previous threads, so I hope someone can help me figure out what is going on. I am trying to fit a Carbon EXAFS spectra, using graphite as a model. I am first focusing on just the first two single scattering paths, so I calculated the theoretical paths with FEFF in Larch and tried using them to fit the spectra. I was consistently getting slightly lower distances than expected, but otherwise an OK fit. The issue is, I tried to compare the analysis with a colleague who is using Athena. At first glance the EXAFS spectra, using the exact same parameters, looked very similar (but not exactly the exactly the same, this I attributed to Larch using a different autobk procedure). I would have however expected the theoretical paths to match exactly, if they were calculated and plotted with the same parameters. But they were also slightly different. I then downloaded Athena and spent time trying to find where the differences come from. If I compare the first two calculated shells from Larch with the ones from Athena, with exactly the same set of test parameters (S02 = 1, E0 = 0, dr1 = 0, s2_1 = 0, dr2 = 0, s2_2 = 0), the resulting models do not match. I made sure the paths are calculated from the came .cif file in both cases, use FEFF6, have the same calculated reference distances, same FT... So, my main question is, am I missing something important in regards to calculations, why would the calculated paths be different and which one would be the "correct" one to use for the fit? And the other question would be about the fact that EXAFS spectra of experimental data look slightly different using Larch and Athena, am I right in disregarding this, or should I dig deeper and find the source of discrepancy? I am enclosing a plot of just the calculated first two shells from Athena and Larch (FT: kmin = 2, kmax = 7.5, Fittting in R space, kw = 3, kWindow = Hanning, dk = 1.0, Rmin = 0.6, Rmax = 2.1) along with the cif file I ended up using for testing the differences. If it would be helpful, I can also provide the project files and larch script I used for the dataset, but I am mainly interested in understanding the differences seen in the theoretical parts first. I tested this using Larch v 0.9.72 and Demeter 0.9.26 Thank you ver much for the help, and If I need to provide any additional info please let me know. kind regards, Ava -- Ava Rajh

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Re: [Ifeffit] Ifeffit Digest, Vol 248, Issue 2
by bikov＠phys.uni-sofia.bg 13 Oct '23

13 Oct '23

Dear Edmund Welter, Dear Matt Newville, Thank you for the answers and very informative explanations. With best regards, Konstantin > 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. Fitting mechanism of Artemis (bikov(a)phys.uni-sofia.bg) > 2. Re: Fitting mechanism of Artemis (Edmund Welter) > 3. Re: Fitting mechanism of Artemis (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 6 Oct 2023 11:09:55 +0300 > From: bikov(a)phys.uni-sofia.bg > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Fitting mechanism of Artemis > Message-ID: > <1936f567bb85f017cc9aa404a2a49fda.squirrel(a)mail.phys.uni-sofia.bg> > Content-Type: text/plain;charset=utf-8 > > Dear all, > I have a general question regarding the mechanism employed in the fitting > procedures implemented in Artemis. > How exactly is performed a fit? Do we have a fixed > central atom (absorbing/emitting atom) and only the distances to the > neighbors included in the probed pathways are varied, i.e. by varying the > coordinates of the corresponding neighbor atoms, or during > the fitting process Artemis can vary the position of the absorption center > too? Could the procedure be constrained in such a way that the scattering > pathways are adjusted by only varying the coordinates of the central atom? > > With kind regards, > Konstantin Bikov > PhD Student at the Physics Department > of the University of Sofia, Bulgaria > > > > ------------------------------ > > Message: 2 > Date: Fri, 6 Oct 2023 11:05:26 +0200 > From: Edmund Welter <edmund.welter(a)desy.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Fitting mechanism of Artemis > Message-ID: <1ac7d9c6-e37f-2b17-82c5-bb382af973ba(a)desy.de> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Dear Konstantin, > > why would you want to do that? If you change the distance between A-B > you the distance between B-A changes by the same amount. If you move the > absorber away from let's say the centre of an octaeder you would split > the (next) nearest neighbours shell into different shells with different > distances. If the differences are large enough and the resolution of > your EXAFS spectrum sufficient you would see more than one (first > neighbours) peak in the FT of your EXAFS spectrum. But that would be > another model that you would feed into FEFF before you start your second > fit. Technically you would fneed to define the position of all atoms in > your model in world-coordinates. So the absorber would no longer be at > 0,0,0. I would guess that this would make the computation and the model > more complex or at least less intuitive. > > Best regards, > > Edmund > > > On 06.10.23 10:09, bikov(a)phys.uni-sofia.bg wrote: >> Dear all, >> I have a general question regarding the mechanism employed in the >> fitting >> procedures implemented in Artemis. >> How exactly is performed a fit? Do we have a fixed >> central atom (absorbing/emitting atom) and only the distances to the >> neighbors included in the probed pathways are varied, i.e. by varying >> the >> coordinates of the corresponding neighbor atoms, or during >> the fitting process Artemis can vary the position of the absorption >> center >> too? Could the procedure be constrained in such a way that the >> scattering >> pathways are adjusted by only varying the coordinates of the central >> atom? >> >> With kind regards, >> Konstantin Bikov >> PhD Student at the Physics Department >> of the University of Sofia, Bulgaria >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ------------------------------ > > Message: 3 > Date: Fri, 6 Oct 2023 11:41:17 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Fitting mechanism of Artemis > Message-ID: > <CA+7ESbpV-FtSVhjEpoTdV72ntx4wAibjZHqZdeAq7ShpSZZiiw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Konstantin, > > > > On Fri, Oct 6, 2023 at 3:11?AM <bikov(a)phys.uni-sofia.bg> wrote: > >> Dear all, >> I have a general question regarding the mechanism employed in the >> fitting >> procedures implemented in Artemis. >> How exactly is performed a fit? > > > > That is a pretty open-ended question to be able to answer with precision. > Is the question more about how fitting works in general, or about what is > modeled and allowed to change in the mode for EXAFS? > > There are plenty of writeups and resources on both topics, including > program documentation. > > Do we have a fixed central atom (absorbing/emitting atom) and only the >> distances to the >> neighbors included in the probed pathways are varied, i.e. by varying >> the >> coordinates of the corresponding neighbor atoms, or during >> the fitting process Artemis can vary the position of the absorption >> center >> too? > > > > Within the context of the software here, the answer is sort of that the > central atom is fixed. > > The way we model EXAFS is effectively (more below, as some might object > to > this) as a 1-dimensional problem. Single scattering EXAFS depends only on > the scalar distance between the atoms (or path length for the > photo-electron). Now, some aspects of EXAFS scattering definitely depend > on more than just distance. The Z of the scattering atom definitely has a > large effect. The angle of the X-ray polarization vector with the > three-dimensional bond direction can also have an effect. These are > folded into the scattering amplitude and phase shift. But even the > disorder terms, sigma^2, and so on, are really capturing the disorder in > R, > not the 3-D disorder. > > For sure, multiple-scattering paths will have 3D information baked into > them. With Feff and the way we use it, this 3D info *is* folded into the > scattering amplitudes and phase shifts calculated for a path and all we > really vary is the distribution of path lengths for those paths. > > In 1-D, it does not matter whether the absorber or scatterer moves, the > only thing that matters is the distance. In fact, to the extent that > neighboring atoms move together in the same direction, there is no effect > on the EXAFS -- an atom in a solution or melt will have EXAFS (it might be > weak, but it does not fall to 0 at a phase transition). EXAFS is much > more > sensitive to "optical phonons" (neighboring atoms moving in opposite > direction) than to "acoustic phonons" (neighboring atoms moving in the > same > direction). > > Now, one can take a reverse-monte-carlo approach: calculate a lot of > different local structures, sum the EXAFS for each calculation, and see > which is best. One can also do something sort of in-between: calculate > a > set of "undistorted paths" and one or more sets of "distorted paths" and > then do a linear (or for some multiple-scattering case, quadratic) model > to > combine these. > > > Could the procedure be constrained in such a way that the scattering >> pathways are adjusted by only varying the coordinates of the central >> atom? >> > > Yes. In fact, this has been done several times. If you imagine a metal > ion > (let's say Ti) surrounded by six neighbors (let's say O) in an octahedron, > a common thing to try to model is if that Ti atom moves away from the > center of the octahedron, say in a perovskite-like structure. > > For the simplest case (ie, what I would start with ;)), you could > calculate > the EXAFS with Ti at the center of a perfect octahedron and get 6 > equivalent paths, and add those to give the EXAFS. If the octahedron is > distorted, you might have 2, 3, 4, or 6 paths. Let's go all the way to > "general" 6 paths. Each path would use a different Feff calculation (or > a > copy). You would not be limited to varying the change in each of the six > path lengths (our 'delr' parameter) to have the same delr for all paths. > Instead, you could define 3 new fitting variables, let's say "dx", "dy", > and "dz" for the displacement of the absorbing Ti from the position used > in > the Feff calculation (let's just call that "origin"). > > If you only have "dz", then one path gets shorter by dz, one gets longer > by > dz, and the other four get longer by sqrt(reff*2 + dz**2), where "reff" is > the magic "R used for each path Feff calculation. I'll leave the more > general case for you ;). > > Hope that gets you started, > > --Matt >

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