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

Larch R plot
by Christopher Patridge 25 Oct '21

25 Oct '21

Hello, I am using Larch and Athena together and I just have a question about the magnitude plots and its effect (if any) on EXAFS modeling. Below are plots of the same merged samples using the same setting values. I noted that the plot in Larch begins below 0 and just want to make sure this is not a setting I missed in Larch? Thank you, Chris ********************************************** Dr Christopher Patridge Associate Professor Dept of Chemistry SASE 315 716-829-8096 | patridgc(a)dyc.edu www.dyc.edu <http://www.dyc.edu/> Social: Twitter <http://www.twitter.com/drpatridgc>

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Re: [Ifeffit] Ifeffit Digest, Vol 224, Issue 12
by Lisa Langlois 25 Oct '21

25 Oct '21

XAS Library? Dear Bruce. I was wondering how the XAS library is coming along. I have not seen too much update on that in Hephaestus. Best wishes, Lisa On Wed, Oct 20, 2021 at 9:33 AM <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: [Ext] FW: Problem in installing Larch (Jeffrey Terry) > 2. Re: Problem in installing Larch (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 20 Oct 2021 09:31:56 -0500 > From: Jeffrey Terry <terryj(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] [Ext] FW: Problem in installing Larch > Message-ID: <8D09051C-F118-4DFB-BF91-221C63110D54(a)iit.edu> > Content-Type: text/plain; charset="utf-8" > > ?Hi Raheleh, > > We have submitted a bug fix for this. Expect a new version of Larch to be > released shortly. > > We rely heavily on Larch for our EXAFS Neo analysis package and this has > broken our code as well. > > Jeff > > Jeff Terry > Interim Chair, Department of Social Sciences > Professor of Physics > Professor of Mechanical, Materials, and Aerospace Engineering > Editor, Applied Surface Science > Prairie Chapter Chair, AVS > Illinois Institute of Technology > 3101 S. Dearborn St. > Chicago IL 60616 > 630-252-9708 > > > Sent from my iPhone > > > On Oct 20, 2021, at 9:12 AM, Daneshpour, Raheleh <rmd5926(a)psu.edu> > wrote: > > ? > > > > Hello! > > > > I am Raheleh a PhD student at Penn State working in FeNi catalysis and > using XAS. I am trying to install the Larch, but I constantly get an error > message on different computers and using different installation methods. > The attached file is a screenshot of the error message I got. Could you > please help me to figure out how to solve the problem? > > Thanks, > > Raheleh > > > > <image001.png> > > Raheleh Daneshpour (She/Her) > > Ph.d. student > > > > Email: rmd5926(a)psu.edu > > > > Chemical engineering department > > The Pennsylvania State University > > University Park, PA > > > > > > <Capture-larch.PNG> > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >

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Larch 0.9.56
by Matthew Newville 21 Oct '21

21 Oct '21

Hi Folks, Larch version 0.9.56 is now available on PyPI ( https://pypi.org/project/xraylarch) and should now be installed by default using most installation mechanisms. This really represents a collection of small improvements and bug fixes but includes one emergency bug fix that many people have seen with the latest version of `lmfit` (which was released recently). I believe that this will now work, but please let me know if you continue to have installation problems. Cheers, --Matt Newville

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Re: [Ifeffit] [Ext] FW: Problem in installing Larch
by Jeffrey Terry 20 Oct '21

20 Oct '21

Hi Raheleh, We have submitted a bug fix for this. Expect a new version of Larch to be released shortly. We rely heavily on Larch for our EXAFS Neo analysis package and this has broken our code as well. Jeff Jeff Terry Interim Chair, Department of Social Sciences Professor of Physics Professor of Mechanical, Materials, and Aerospace Engineering Editor, Applied Surface Science Prairie Chapter Chair, AVS Illinois Institute of Technology 3101 S. Dearborn St. Chicago IL 60616 630-252-9708 Sent from my iPhone > On Oct 20, 2021, at 9:12 AM, Daneshpour, Raheleh <rmd5926(a)psu.edu> wrote: > > > Hello! > > I am Raheleh a PhD student at Penn State working in FeNi catalysis and using XAS. I am trying to install the Larch, but I constantly get an error message on different computers and using different installation methods. The attached file is a screenshot of the error message I got. Could you please help me to figure out how to solve the problem? > Thanks, > Raheleh > > <image001.png> > Raheleh Daneshpour (She/Her) > Ph.d. student > > Email: rmd5926(a)psu.edu > > Chemical engineering department > The Pennsylvania State University > University Park, PA > > > <Capture-larch.PNG> > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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Problem in installing Larch
by Daneshpour, Raheleh 20 Oct '21

20 Oct '21

Hello! I am Raheleh a PhD student at Penn State working in FeNi catalysis and using XAS. I am trying to install the Larch, but I constantly get an error message on different computers and using different installation methods. The attached file is a screenshot of the error message I got. Could you please help me to figure out how to solve the problem? Thanks, Raheleh [cid:image001.png@01D7C4CE.9ECA8AE0] Raheleh Daneshpour (She/Her) Ph.d. student Email: rmd5926(a)psu.edu<mailto:rmd5926@psu.edu> Chemical engineering department The Pennsylvania State University University Park, PA

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

12 Oct '21

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

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

11 Oct '21

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

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Open postdoc position in the APS Spectroscopy Group
by Sterbinsky, George E. 04 Oct '21

04 Oct '21

Hello all, The Advanced Photon Source Spectroscopy Group currently has an opening for a Postdoctoral Research Associate in the area of x-ray absorption spectroscopy. Interested candidates can view the full position description and apply at https://argonne.wd1.myworkdayjobs.com/en-US/Argonne_Careers/job/Argonne-Nat…. Best, George George E. Sterbinsky, PhD X-ray Science Division Advanced Photon Source Argonne National Laboratory sterbinsky(a)anl.gov

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S02 selection from reviewer
by Peng Liu 03 Oct '21

03 Oct '21

Dear IFEFFIT members, I am sorry to bother you again. I asked about S02 selection for the first major revision. I just received the second revision. The reviewer is not satisfied with one S02 value for all our samples. " 1. I am still not satisfied with selected SO2 value (it is set to 0.85). SO2 is not transferable between different samples and detection methods. It is not possible to use a value obtained from different compound using transmission measurement mode to completely different other compound measured using fluorescence mode. One method to fix SO2 value is to measure diluted solution (to avoid self-absorption) of reference material in fluorescence mode. Other is to use multiple spectra fitting for all samples of interest (e.g. with Sb(V)) measured using fluorescence mode where SO2 parameter is the same for all samples. At the same time I am confident that CN values 5.6, 7.1 and 6.9 correspond to CN(Sb-O)=6. I suggest reconsidering the SO2 value for measurements in fluorescence mode. " We do get the S02 from a similar reference material measured in transmission mode, and our samples were all measured in fluorescence mode. It is not possible to measure the diluted reference material in fluorescence mode in one or two months. If you could give me some suggestions, that would be great. -- Best Regards, Peng Liu

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Open postdoc position at SSRL for theorist (DFT)
by Bone, Sharon 17 Sep '21

17 Sep '21

Hello Everyone, SSRL has an open postdoc position for a researcher with expertise in DFT, especially in application of DFT to X-ray absorption spectroscopy analysis. Please see the listing here if you are interested: https://careers.slac.stanford.edu/sites/careers.slac.stanford.edu/files/SSR… Thanks! Sharon Sharon Bone, PhD Beamline Scientist Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory (650) 926-3104

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