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

Problem in xrayLarch installation
by Latif Ullah Khan 15 Dec '21

15 Dec '21

Dear Sir Madam, I hope you are doing well, I Latif Khan, working as a beamline scientist at XAFS beamline SESAME light source. I was using LARCH on my Anaconda python environment at window PC. Now I re-install and upgrade the Anaconda to python 3.9. I am trying to install the xrayLarch from Anaconda command prompt (python 3.9), using "pip install xraylarch" . However, it is not installing and give me an following error: If you kindly help me in this regard, I will be grateful to you. Thank you in advance Best regards Latif [cid:image001.png@01D7F194.F5C60C50]

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Re: [Ifeffit] XEOL
by Eugenio Otal 06 Dec '21

06 Dec '21

Dear Robert, sorry for the late reply, life... Brilliant suggestion! I will let you know the results if the proposal is approved. Best regards, euG If you can move between Nd L3 and Br K, why not stop at Nd L1 if you want to see if a Nd s-type initial state has any influence on the XEOL? You should not need to go up to Nd K. Some references: https://aip.scitation.org/doi/abs/10.1063/1.477320?journalCode=jcp https://iopscience.iop.org/article/10.1149/1.3211180 and a book chapter https://www.worldscientific.com/doi/10.1142/9789812775757_0015 On 2021-11-25 5:50 p.m., Eugenio Otal wrote: > Hi all, > I am planning XEOL measurements and I have a doubt. > My system is Nd coordinated to Eosin, tetrabromofluorescein. I want to > measure XEOL exciting on the Br K-edge (13.4keV) and the Nd > L3-edge(6.2keV) and measure the emission spectra of the dye and the > Nd. I just measured the emission of the Nd exciting at 530nm and it > worked perfectly. > My question is, I have access to Nd K-edge, is it worthy?to measure > XEOL at the K-edge? I am in the time limit to?request an?extra shift. > I would appreciate some bibliography. > Best regards. > > _______________________________________________ > 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 0.9.57
by Matt Newville 02 Dec '21

02 Dec '21

Hi All, Larch version 0.9.57 has been released and is available on PyPI ( https://pypi.org/project/xraylarch) It should now be installed by default using most installation mechanisms, and you may see a notice to update if running xas_viewer. The updates are described in some at https://github.com/xraypy/xraylarch/releases/tag/0.9.57 and in the github commit history. This includes adding support for reading RIXS data files from ESRF BM16, better support for de-glitching in XAS_Viewer, and fixing of reading of many Athena Project Files that were saved in the "old style" and have non-ASCII characters (the code now correctly reads the 78 Project files at https://github.com/xraypy/xraylarch/tree/master/examples/xafsdata/AthenaPro… ). Much of the work for this release has come from Mauro Rovezzi. In a conversation we had yesterday about this release, we talked about several potential changes going forward, especially for XAS_Viewer, about saving processing history, how to improve the concept of "reference spectrum" for a measurement, and other topics related to keeping track of analysis history and provenance. Some of these ideas are encapsulated in Github Issues at https://github.com/xraypy/xraylarch/issues, and the plan is to work on this. One possibility would be to be able to read and export to Athena Project files but use a different format (probably HDF5) as a new default "Larch Project File" so that more complexly nested data and some sort of "journal" per data set could be saved, displayed, edited, and so on. If anyone here has some thoughts on how such topics could or should be handled, please let us know. If you have other ideas on what might be added or improved, also don't hesitate to speak up, either in conversations here or on Github. Cheers, --Matt Newville

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XEOL
by Eugenio Otal 26 Nov '21

26 Nov '21

Hi all, I am planning XEOL measurements and I have a doubt. My system is Nd coordinated to Eosin, tetrabromofluorescein. I want to measure XEOL exciting on the Br K-edge (13.4keV) and the Nd L3-edge(6.2keV) and measure the emission spectra of the dye and the Nd. I just measured the emission of the Nd exciting at 530nm and it worked perfectly. My question is, I have access to Nd K-edge, is it worthy to measure XEOL at the K-edge? I am in the time limit to request an extra shift. I would appreciate some bibliography. Best regards.

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PostDoc position at Northeastern University
by NUCRET 23 Nov '21

23 Nov '21

Northeastern University Center for Renewable Energy Technology is currently looking for highly qualified candidate to fill a Post-Doctoral Research Associate position with hands-on experience in the area of in situ and operando XAS, XANES, EXAFS spectroscopy, high-energy XRD as applicable to batteries (especially solid-state), fuel cells and electrolyzers. Familiarity with Brookhaven synchrotron facility (or other US-based light source facilities, e.g. ANL, SLAC) is a plus. Candidates should be in the US and authorized to work in the US (visa is _not_ offered). To apply, please use Northeastern University Career Portal: https://careers.hrm.northeastern.edu/cw/en-us/job/508477/postdoctoral-resea…

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Postdoctoral beamline scientist position at Illinois Tech/MRCAT
by Carlo Segre 22 Nov '21

22 Nov '21

Please find attached the advertisement for a postdoctoral position at MRCAT (Sector 10) at the Advanced Photon Source. The position is with Illinois Institute of Technology, which operates MRCAT for its institutional membership. Feel free to share this with any appropriate individuals. Carlo -- Carlo U. Segre (he/him) -- Duchossois Leadership Professor of Physics Professor of Materials Science & Engineering Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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SSRL post-doctoral position
by Ritimukta Sarangi 17 Nov '21

17 Nov '21

Hi, I would like to bring this unique opportunity to the EXAFS user community. I am looking to hire a post-doctoral fellow who will apply spectroscopy tools to the Ni-Fe containing active site in Carbon Monoxide dehydrogenase, which is part of a pathway that biologically captures CO2 and converts it into acetate. This project is funded by the Department of Energy and is extremely relevant to our understanding and remediation of CO2 in the atmosphere. You will work with a diverse team of postdocs working on a variety of X-ray spectroscopy projects and will get the experience of working in a national laboratory setting. See the attached posting for more information. Kind regards, Riti Sarangi

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Fe and Ni carbide XAS reference spectra?
by Valentijn De Coster 17 Nov '21

17 Nov '21

Dear ifeffit mailing list, My name is Valentijn De Coster. I am a PhD student at Ghent University, Belgium, working on Ni and Fe materials for CO2 utilization. I am currently looking for Fe and Ni carbide (Fe3C, Ni3C) reference XAS spectra, at the respective Fe K and Ni K edges, for fingerprinting purposes. As such, I was wondering whether anyone would have such data available. On a side note, I checked the CARS database, and while this has an Fe3C (Fe K edge) reference, the data file does not contain the Energy values of the spectrum. Thank you in advance for your time. Kind regards, Valentijn De Coster [Image result for ghent university logo] Valentijn De Coster PhD Student Laboratory for Chemical Technology (LCT) Department of Materials, Textiles and Chemical Engineering Technologiepark 125, 9052 Ghent, Belgium T: +32 9 331 17 M: +32 (0) 331 17 10 https://www.lct.ugent.be<https://www.lct.ugent.be/> https://helpdesk.UGent.be/e-maildisclaimer.php<https://helpdesk.ugent.be/e-maildisclaimer.php> Member of CSC: https://www.csc.ugent.be<https://www.csc.ugent.be/>

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MacPorts XAFS software: announcing a Port for Larch; and do we actually need Demeter on Macs?
by Fowler, Joseph W. (Assoc) 12 Nov '21

12 Nov '21

Hello XAFS fans: This note is about the Demeter package on MacPorts. If you don’t use Demeter through MacPorts on a Mac, skip this note. I’m the MacPorts “maintainer” of the ports demeter and ifeffit. They have been not installable or upgradeable for something like a year, because of new releases of … something? Probably either Mac OS X, and/or Apple's Xcode development system. I’ve made a ton of progress on my big goal of restoring demeter to life, but I cannot get all the way to finish the project. I have to say here that I’m a poor choice to maintain these ports. I barely understand how MacPorts works, and I don’t understand or use Perl at all. I am not even really an x-ray scientist—I develop superconducting x-ray sensors in a team at NIST, and I happened to be a collaborator of the previous maintainer when he left the field 6 or 8 years ago. I worked on the problem in two parallel paths. One was to create an official port for the Python package Larch. Late last month this was complete, so you can do a “sudo port install py39-xraylarch” and have it. (Replace “py39” with “py38” or “py37” if you use Python 3.8/3.7.) This required creating about a dozen new ports for Larch’s dependencies. (Actually, I know a ton more about how MacPorts works than I did six weeks ago.) Some new ports that might be of interest to this community include: * py39-pymatgen * py39-peakutils * py39-xraydb * py39-spglib * py39-xraylarch My other path was to track down and fix the problem that prevented ifeffit from compiling. (Recall that this package is unmaintained since 2014. See https://github.com/newville/ifeffit/) It looks like Xcode’s C compiler recently turned the “implicit function warning” into an error. A few hours ago, MacPorts accepted my proposed patches, so at least ifeffit should be installable as a port again. Unfortunately, demeter still won’t install completely, owing to problems in certain Perl-based ports that it depends upon, like p5.30-wx. That problem is so far from my expertise that I am completely stuck. I had hoped that if I got ifeffit to work, demeter would follow, but I was wrong. There are four strategies I can imagine from here: 1. Declare the ports ifeffit and demeter to be obsolete. Mac users will need to figure out other ways to do what Athena and Artemis do. 2. Wait until Perl experts fix the Perl dependencies (expect it to take months or more), then I fix demeter. 3. Modify/migrate Demeter so that Athena and Artemis rely completely on Larch and not at all on ifeffit. 4. Ask this mailing list for advice. I don’t know what strategy #3 would entail—again, I know zero Perl and don’t use this software. Demeter’s author told me he doesn’t have much interest in this upgrade. All I can really support alone is strategy #1 or #2: obsoleting or waiting. And that’s why I’m writing. On one side, does anyone care if Athena/Artemis become unavailable through MacPorts? So, does anyone object to path #1? On the other, does anyone here have better ideas? Best wishes, Joe Fowler NIST Boulder Labs

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how to learn wavelet analysis
by 罗昕宇 11 Nov '21

11 Nov '21

Dear IFEFFIT members, I'm a fresh graduate student majoring in chemical engineering. I began to learn XAFS by myself one month ago. I bought and read the book XAFS for Everyone written by Dr. Calvin. I think I have got a clear image of how EXAFS works. Recently, I am attracted by the technique called Wavelet Analysis from literatures. It seems pretty powerful to correlate both temporal and frequency information, but something just went probably beyond my current knowledge base. I understand that a changeable window should be adapted to a make a trade-off between time and frequency, but I don't understand the logic that good time-resolution in high frequency is preferred while in low frequency a good frequency-resolution is better. I would appreciate it very much if you could answer my half-baked question and offer me with some learning material. Best regards Xinyu

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iodine L-edge spectra
by Enyuan Hu 27 Oct '21

27 Oct '21

Hi, Does anybody happen to have the iodine element L-edge spectra (L1 preferred, but L2 and L3 are also okay) and is willing to share? thanks! Enyuan

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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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SSRL User Meeting Sept 20-24: Session on XAS +Theory for Environmental Systems
by Bone, Sharon 17 Sep '21

17 Sep '21

Hi All, The annual SSR:/LCLS User Meeting is coming up Sept 20-24th. I am advertising a session on Thursday, Sept. 23rd, titled: "Enhancing X-ray Spectroscopy with ab initio and classical computational tools to understand environmental processes" Agenda: https://events.bizzabo.com/SLAC-UsersMeeting-2021/agenda/session/565625 In this workshop, we will examine how theoretical tools, such as DFT and MD, can be used to aid interpretation of XAS data and enhance understanding of chemical structure and reactivity in environmental systems (e.g., for biogeochemical and geochemical applications). The User Meeting will be held virtually this year and registration is free. You can find the registration link here: https://events.bizzabo.com/SLAC-UsersMeeting-2021/home We hope to see you there! Best, Sharon Bone, Ritimukta Sarangi and Jocelyn Richardson Sharon Bone, PhD Beamline Scientist Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory (650) 926-3104

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EXAFS Fitting with 2 CIF files
by Zihao Yan 13 Sep '21

13 Sep '21

Dear Ifeffit members: I have a sample which is a mixture of PtFe and PtO2. In order to do the EXAFS fitting, I imported 2 CIF files on Artemis and generated the following 3 paths: >From PtO2: Pt-O @ 2.07 nm >From Pt3Fe: Pt-Pt @ 2.736 nm, Pt-Fe @ 2.736 nm Then, I used these 3 bonds to do the fitting as in the online tutorial (which used 1 CIF file). The fitting result is good in terms of R^2 but it is not scientifically correct. I think I didn't set up a parameter which determines the ratio between CIF(PtO2) and CIF(Pt3Fe). I mean there should be a parameter that regulates how much each CIF contributes to the fitting or the molar ratio between PtO2 and Pt3Fe in my system. Could someone please give me some suggestions on how to do EXAFS fitting with 2 CIF files? Is there anywhere I can set up the molar ratio between PtO2 and Pt3Fe? Yours sincerely, Zihao Yan

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Re: [Ifeffit] Ifeffit Digest, Vol 223, Issue 9
by Moreau, Liane Michelle 08 Sep '21

08 Sep '21

Dear Matts, Thank you for helping Shinhyo sort out his saving problem. Now we can do science! I appreciate your help (as someone who is less technologically inclined I was pretty lost as to suggestions). It was kind of you to take the time to work with him. Thank you, Liane Liane Moreau, PhD Assistant Professor Department of Chemistry Washington State University 509-335-6073 ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Tuesday, September 7, 2021 7:26 PM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 223, Issue 9 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… 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: IFEFFIT file saving issue (Bang, Shinhyo) ---------------------------------------------------------------------- Message: 1 Date: Wed, 8 Sep 2021 02:25:50 +0000 From: "Bang, Shinhyo" <shinhyo.bang(a)wsu.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] IFEFFIT file saving issue Message-ID: <DM6PR01MB48596919474C38ED6664E81F97D49(a)DM6PR01MB4859.prod.exchangelabs.com> Content-Type: text/plain; charset="euc-kr" Dear Matthew, I can certainly save the files onto a folder directly under the C: (although I have to point out that I had/have only English alphabets in the folder names). Thank you very much. I appreciate your support. Best, Shinhyo ________________________________ ?? ??: Matthew Marcus <mamarcus(a)lbl.gov> ?? Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> ?? ??: 2021? 9? 7? ??? ?? 7:14 ?? ??: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> ??: Re: [Ifeffit] IFEFFIT file saving issue This probably isn't relevant, but Desktop is actually a folder under c:. On my computer, it's C:\Users\MAMarcus. I see that 'other Matt' concurs with this and seems to be suggesting that your username may have non-ASCII characters. I'm guessing Korean. Try making a new folder under C:\ with only ASCII characters in the name. mam On 9/7/2021 6:25 PM, Bang, Shinhyo wrote: > Dear Matthew, > > I tried to save a project to "Desktop" which had no parent folder, but > the same problem occurred. I think the non-ASCII character is not the > only problem. > Still, I can save onto a usb from now on. Thank you very much. > > Best, > Shinhyo > ------------------------------------------------------------------------ > *?? ??:* Matt Newville <newville(a)cars.uchicago.edu> ?? Ifeffit > <ifeffit-bounces(a)millenia.cars.aps.anl.gov> > *?? ??:* 2021? 9? 7? ??? ?? 6:06 > *?? ??:* XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > *??:* Re: [Ifeffit] IFEFFIT file saving issue > Hi Shinhyo, > > Again, I would ask to check that the folder you are having trouble > saving to has any non-ASCII characters. For sure, ifeffit and demeter > are not going to be able to handle folder or file names with non-ASCII > characters. > > Larch is slightly better at this - it can work with files with names in > non-ASCII text encodings. To be clear, the situation with Larch is > still not ideal, especially on Windows, because > a) the base installation folder can contain only ASCII characters, > and cannot contain any spaces (apparently this is some problem > with other libraries or possibly some other variation on point b). > b) the concept of "localization" on Windows machines is sort of a > mess and many libraries (at least, from Python) don't handle this very > well. For Larch, we recently had to explicitly set locale to be "simple > C / ASCII". That sort (or should!?) mean that you can read/write files > and folders with non-ASCII characters, though I'm not certain that will > work for all character encoding sets. It's possible this will get > better with time, but it's not something that we can solve. > > For ifeffit / demeter there is simply no hope for non-ASCII text to ever > be handled. > > > On Tue, Sep 7, 2021 at 7:45 PM Bang, Shinhyo <shinhyo.bang(a)wsu.edu > <mailto:shinhyo.bang@wsu.edu>> wrote: > > Dear Matthew, > > I tried to save the project onto a usb, and it WORKed! Thank you so > much for your help. > > Best, > Shinhyo > ------------------------------------------------------------------------ > *?? ??:* Matthew Marcus <mamarcus(a)lbl.gov > <mailto:mamarcus@lbl.gov>> ?? Ifeffit > <ifeffit-bounces(a)millenia.cars.aps.anl.gov > <mailto:ifeffit-bounces@millenia.cars.aps.anl.gov>> > *?? ??:* 2021? 9? 7? ??? ?? 4:11 > *?? ??:* 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>> > *??:* Re: [Ifeffit] IFEFFIT file saving issue > There are other characters that Windoze doesn't like in filenames: > |\/*":<>? > mam > > On 9/7/2021 3:58 PM, Matt Newville wrote: > > Hi Shinhyo, Liane, > > > > On Tue, Sep 7, 2021 at 5:39 PM Bang, Shinhyo <shinhyo.bang(a)wsu.edu <mailto:shinhyo.bang@wsu.edu> > > <mailto:shinhyo.bang@wsu.edu <mailto:shinhyo.bang@wsu.edu>>> wrote: > > > > Thank you for the response. > > The OS is Windows 10. > > In addition to the symptom that was described aforehand, Athena > > freezes when I try to save the file. > > > > > > Is it possible that the folder or file you are saving to has a space or > > other non-ASCII character in it? I believe that non-ASCII characters > > are known to cause problems. > > Can you check whether you can save a file anywhere (maybe even the > > top-level "C:\" folder)? > > > > --Matt > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > <mailto:Ifeffit@millenia.cars.aps.anl.gov> > > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin…> > > > Unsubscribe: https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option…> > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > <mailto:Ifeffit@millenia.cars.aps.anl.gov> > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin…> > > Unsubscribe: > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option…> > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > <mailto:Ifeffit@millenia.cars.aps.anl.gov> > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin…> > Unsubscribe: > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option…> > > > > -- > --Matt Newville <newville at cars.uchicago.edu > <https://urldefense.com/v3/__http://cars.uchicago.edu__;!!JmPEgBY0HMszNaDT!9…>> > 630-327-7411 > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… > Unsubscribe: https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option… > _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… Unsubscribe: https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option…

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IFEFFIT file saving issue
by Moreau, Liane Michelle 08 Sep '21

08 Sep '21

Dear fellow XAFS enthusiasts, My student is running into some trouble in that he can't seem to get any files from IFEFFIT (be it project or exported data files) to save on his computer. When he saves, no files show up in the folder he has saved to. I watched him do this myself to confirm this is indeed the case. I have never run into this issue, nor have I heard of anyone else having this issue previously, but has anyone else run into this issue, and, if so, how did they solve it? I imagine there might be something incompatible with the student's computer settings somehow, although he is able to use the software just fine, it is just that nothing will save. He tried uninstalling and reinstalling Demeter, but unfortunately that did not fix the problem. I appreciate any experience anyone can share that might be helpful. Thank you! Liane Liane Moreau, PhD Assistant Professor Department of Chemistry Washington State University 509-335-6073

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