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

Re: [Ifeffit] Trouble downloading Demeter for mac
by Fowler, Joseph W. (Assoc) 09 May '24

09 May '24

Dear Christopher, I have bad news for you. I’m the official MacPorts maintainer of Demeter, and I have not been able to overcome the problems you’re seeing. I’ve seen them too over the last 1-2 years. The ifeffit package has unaddressed problems that have become fatal. I believe they correspond to small incompatibilities with the latest compilers. Over time, code that used to be allowed eventually became deprecated with a warning, and is now an error. As Matt helpfully explained (thanks, Matt!), ifeffit is basically replaced by Larch, and no one wants to update ifeffit to fix problems of that sort. Unfortunately, Demeter, Artemis, and Athena do still depend on ifeffit, and there’s no clear path to integrate that front end with the physics back end of Larch. Or at least, I discussed this a few years ago with the Demeter and Larch authors, and they didn’t see one. If indeed Larch can replace (99% of) the functionality that used to be in the Demeter and ifeffit ports in the MacPorts project, then I am inclined to remove those ports entirely from MacPorts. Otherwise, they are just sitting there, broken. By the way, I have created a `py-xraylarch` port. You could use it, although I don’t particularly recommend that. I’d suggest you use its usual installation options (such as `pip install xraylarch`). Honestly, the pip-based installation is getting so capable these days that I question why we even need MacPorts to package up any python code at all. (Should I ask that in public?) Why not use the MacPorts port? Because I’m the maintainer but not an actual user—I don’t regularly update upstream versions or make it work with the latest Python because of all its dependencies that first have to be updated. For instance, last summer I tried to make a Python 3.11 version, but I was stymied by the lack of Python 3.11 releases by some dependency. I lost interest and haven’t checked in months whether that was resolved. On the other hand, you (obviously) already installed MacPorts, so it’s at least an option if the pip method gives you trouble. Best wishes, Joe Fowler NIST Boulder Labs p.s. Here’s a politically charged question. Has this mailing list’s name falling out of sync with its range of topics, given that ifeffit is finished? On May 9, 2024, at 10:51 AM, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov> To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.us/v3/__https://gcc02.safelinks.protection.outlook.com/?… <https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinf… > or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov<mailto:ifeffit-owner@millenia.cars.aps.anl.gov> When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Trouble downloading Demeter for mac (Christopher Reitwiesner) 2. Re: Trouble downloading Demeter for mac (Matt Newville) From: Christopher Reitwiesner <christopher.reitwiesner(a)uconn.edu<mailto:christopher.reitwiesner@uconn.edu>> Subject: [Ifeffit] Trouble downloading Demeter for mac Date: May 8, 2024 at 1:37:46 PM MDT To: ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov> This Message Is From an External Sender This message came from outside your organization. Hello! I am an undergraduate researcher looking to utilize Demeter. Unfortunately I only have access to a mac. I followed the instructions on the github page. Downloading MacPorts went fine, so did installing Command Line Developer Tools. However when trying to install demeter from Terminal, I eventually run into this error message: Building ifeffit Error: Failed to build ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_ifeffit/ifeffit/main.log for details. Error: Follow https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw… <https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw…> if you believe there is a bug. Error: Processing of port demeter failed I am at a loss on where to go from here and was wondering if someone could point me in the right direction. Thank you for your time! Christopher Reitwiesner From: Matt Newville <newville(a)cars.uchicago.edu<mailto:newville@cars.uchicago.edu>> Subject: Re: [Ifeffit] Trouble downloading Demeter for mac Date: May 9, 2024 at 10:51:01 AM MDT To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>> This Message Is From an External Sender This message came from outside your organization. Hi Christopher, Installing Demeter on macOS has always been painful. The MacPorts solution can work sometimes, but it does require some expertise to use MacPorts and to think about the software as something that needs to be compiled and built. Some of the packages needed (especially "ifeffit" and "wxPerl") are just not very well supported. At this point, I cannot recommend using the old ifeffit - it has too many known issues that will not be fixed. I know that using a virtual Windows interface like Parallels works for some people. But, if you are just getting started, I highly recommend installing Larch, either using the installer at https://urldefense.us/v3/__https://xraypy.github.io/xraylarch/installation.… <https://urldefense.us/v3/__https://xraypy.github.io/xraylarch/installation.…>(you'll have to go into Privacy & Security and allow the installer from "an untrusted source" to run. Also, it might say that it has less than a minute to go for about 5 minutes ;) ), or by downloading and running the GetLarch script at https://urldefense.us/v3/__https://xraypy.github.io/xraylarch/installation.… <https://urldefense.us/v3/__https://xraypy.github.io/xraylarch/installation.…> and running that from a Terminal. With this installed, the Larix App (in the Larch folder on your Desktop: also, the first launch might take a minute) will run and do basically everything that Athena and Artemis do. There are some differences, and there may be a missing feature or two, but many things are better. In general, comments, complaints, and suggestions are welcome. We aim for "highly compatible and familiar" with Demeter and "better than" the underlying ifeffit library. And, it does install and run on macOS. It turns out that most of the development and testing happens on macOS. Cheers, --Matt On Wed, May 8, 2024 at 2:54 PM Christopher Reitwiesner <christopher.reitwiesner(a)uconn.edu<mailto:christopher.reitwiesner@uconn.edu>> wrote: This Message Is From an External Sender This message came from outside your organization. Hello! I am an undergraduate researcher looking to utilize Demeter. Unfortunately I only have access to a mac. I followed the instructions on the github page. Downloading MacPorts went fine, so did installing Command Line Developer Tools. However when trying to install demeter from Terminal, I eventually run into this error message: Building ifeffit Error: Failed to build ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_ifeffit/ifeffit/main.log for details. Error: Follow https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw… <https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw…> if you believe there is a bug. Error: Processing of port demeter failed I am at a loss on where to go from here and was wondering if someone could point me in the right direction. Thank you for your time! Christopher Reitwiesner _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinf… <https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinf…> Unsubscribe: https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options… <https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options…> -- --Matt Newville <newville at cars.uchicago.edu<https://urldefense.us/v3/__http://cars.uchicago.edu__;!!G_uCfscf7eWS!fZTlh9…>> 630-327-7411 _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinf… Unsubscribe: https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options…

1 0

Trouble downloading Demeter for mac
by Christopher Reitwiesner 09 May '24

09 May '24

Hello! I am an undergraduate researcher looking to utilize Demeter. Unfortunately I only have access to a mac. I followed the instructions on the github page. Downloading MacPorts went fine, so did installing Command Line Developer Tools. However when trying to install demeter from Terminal, I eventually run into this error message: Building ifeffit Error: Failed to build ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_ifeffit/ifeffit/main.log for details. Error: Follow https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw… if you believe there is a bug. Error: Processing of port demeter failed I am at a loss on where to go from here and was wondering if someone could point me in the right direction. Thank you for your time! Christopher Reitwiesner

2 1

Save the date: SCC short course at BNL, Oct. 29-31, 2024
by Anatoly Frenkel 03 May '24

03 May '24

Dear subscribers: Please pass it along to your group members who may be interested in this opportunity. In continuation of the annual tradition at the Synchrotron Catalysis Consortium (SCC) at Brookhaven National Laboratory to organize and run XAFS short courses there since 2005, we are planning a first specialized course targeting catalysis and electrocatalysis researchers. The course will follow a successful model of our XAFS courses: the lectures (on the topics ranging from in situ/operando characterization and multimodal instrumentation to data analysis) and software demonstrations on the first two days, followed by the hands-on data analysis session on the last day. The program is being finalized, and we are in the process of getting the necessary approvals from BNL and DOE. In the meantime, please, mark your calendars and contact me if you have any questions. Anatoly ******** On sabbatical leave at Weizmann Institute of Science, Israel ******** ------------------------------------------------------------------- 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://urldefense.us/v3/__https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adz… > https://urldefense.us/v3/__http://you.stonybrook.edu/frenkel__;!!G_uCfscf7e… Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL https://urldefense.us/v3/__http://you.stonybrook.edu/scc2__;!!G_uCfscf7eWS!… Joint Appointment: Senior Chemist Chemistry Division, *Brookhaven National Laboratory* Upton, NY 11973 Email: frenkel(a)bnl.gov https://urldefense.us/v3/__https://www.bnl.gov/staff/frenkel__;!!G_uCfscf7e… -------------------------------------------------------------------

1 0

Re: [Ifeffit] Origin of noise in Ag K-Edge
by Sebastian Kunze 30 Apr '24

30 Apr '24

Dear Shelly, Robert, Matt, thank you for your kind replies, I think I should give more information about the measurement. The sample is a sealed battery anode consisting of silver particles that should undergo alloying with Lithium during charging. This is done at constant temperature and applied pressure. I repeated this experiment under different conditions several times, and each time there is less noise before a certain time during the charging process, after which is persists even when the battery is at rest (not charging/discharging). I0 also did not fluctuate much, and the integration time for each point is indeed the same. Therefore I think it is not instrumental, but rather something happening in the sample. As you can see from the spectra, the silver particles experience a strong decrease of uniform structure when they lithiate. For me, this at least explains why the noise in the post-edge increases, but can it also explain the noise in the edge and pre-edge? In any case, thank you very much for your answers! Best, Sebastian

2 1

question concerning the limitations of the webatoms program
by I. D. 30 Apr '24

30 Apr '24

Dear All, We are studying the gallium oxide polymorph (gamma phase). The *.cif file used is in the appendix. After testing this file with the webatoms program, I believe that there is a limitation of the number of atoms in the list between between 256 and 299. As can be seen in the *.cif file considered structure contains 426 atoms. If we try to use the webatoms program to generate the feff.inp file, error like that appears: "Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error. More information about this error may be available in the server error log." Also there is no possibility to change the cluster size and select the desired absorption atom for generating feff.inp file. Can anyone help and explain how to solve the existing problem? Best regards, Iraida.

3 4

Origin of noise in Ag K-Edge
by Sebastian Kunze 29 Apr '24

29 Apr '24

Greetings, I recently did in-situ QEXAFS at Ag K-edge, expecting to see structure loss starting from crystalline (metallic) state. While we can see that, in addition we also see an increase in noise(?) in the xanes region (compare start and end in the attached image). I am confused by this because the amount of material did not change, so I did not expect a difference in the signal/noise ratio at the absorption edge. And it is reproducible across several samples, so not instrument related. Could anyone point me in the right direction as to what I am missing? Thank you! Best, Sebastian Kunze

4 3

Difficulty in generating XANES for Ni.
by jaskirat brar 22 Apr '24

22 Apr '24

Dear list I am using feff8.2 to generate the XANES for Ni and compare it with the experimental spectra collected on pure Ni. To include the contribution from different scattering paths, I have increased the value of *r_fms* in steps. I find that the intensity ratios of the generated spectra match with that of the experimental spectra when* r_fms* is around 5 angstroms (figure below). Further increasing the* r_fms* produces a mismatch in the intensity ratios of the calculated and the experimental spectra, as shown in the figure. [image: fig.jpg] As per my understanding, increasing the *r_fms* should include more scattering paths and give a better match with the experimental spectra. Please comment on what might be the problem here. Thanks in advance. Jaskirat Brar FMP Lab, South Campus IIT Mandi, H.P., India

1 0

Difficulty with normalization of XAS spectra
by jesse walters 15 Apr '24

15 Apr '24

Hi all, I have some spectra collected by a collaborator, Francesco Ressico, a PhD student at Uni Bologna, (see attached .h5 file below) and we are having trouble normalizing the Fe K edge spectra. The data are for serpentine group minerals and were collected in fluorescence mode. In the attached file, the correct X array value is 'energy_enc', the data type is 'xas', and the y array should be 'mu_fluo_det0'. The spectra are already normalized for the incoming beam energy (although this can also be done using 'flou_det0/i0'). There are multiple spectra in the file, any one of them can be chosen to test the procedure. After loading the spectra, I am able to plot the raw spectra correctly (see attached). But when I try to normalize the pre and post edge regions and plot the normalized spectra, the software only gives a blank plot. I have tried changing the normalization type, polynomial type, range, etc for both the pre and post edge, but nothing seems to work. I also tested different spectra, but with similar results. Does anyone have suggestions for how these data can be normalized? The h5 file is too large, so here is a dropbox link https://urldefense.us/v3/__https://www.dropbox.com/scl/fi/d8k5s67vli0mq97ac… Sincerely, Jesse Walters -- Jesse B. Walters Ambizione Fellow Institut für Geologie Universität Bern

4 7

Re: [Ifeffit] Ifeffit Digest, Vol 254, Issue 4
by Ryan Parmenter 08 Apr '24

08 Apr '24

1 0

Peak-Fitting Process in Larix
by Ryan Parmenter 08 Apr '24

08 Apr '24

Hi All, I have some questions regarding different aspects of the peak-fitting process in Larix. I wish to repeat the process reported in similar studies, but I'm facing challenges in adapting it effectively to my dataset. * Farges 2005: 'One should model the pre-edge feature with either two or three peaks of fixed width and shape pseudo-Voigt functions of 1.3 eV 2σ width and 45% Gaussian'. * Chalmin 2009: 'The pre-edge region was extracted from the normalised XANES spectra and modelled using a series of pseudo-Voigt functions of fixed width (1.3 eV) and fixed Gaussian percent to minimise the number of variable parameters. Two contributions were modelled for Mn2+ and three for Mn3+.' Using Mn2+ as an example, after normalisation, the baseline is fitted within the pre-peak region, followed by fitting an arctangent background function to the data. The parameters for the arctangent function are initially estimated using the 'pick values from plot' feature. However, modifying these parameters doesn't result in corresponding changes in the graph, making it difficult to ascertain if it aligns with the data points. Considering this, would it be acceptable to set the arctangent's amplitude to 1 (normalised edge jump) and position its centre a couple of eV below E0? Following this, two pseudo-Voigt functions are introduced, with their parameters initially estimated. Then, to replicate the conditions of '1.3 eV 2σ width and 45% Gaussian,' do I set the pseud_fraction to 0.45 and pseud_sigma to 2? I'm uncertain about where to input the 1.3 eV width and whether this choice is optimal, especially considering that the natural width of the atomic K level at the Mn edge is 1.16 eV (Krause, 1979). Finally, I couldn't find the specific paper, but the authors stated that due to the significant processing times required for Voigt functions, they opted for pseudo-Voigt functions to model instrumental and core-hole broadening factors. With improvements in processing times, are Voigt functions now the preferred choice, or does the pseudo-Voigt function still hold advantages over both? Any insights and suggestions would be immensely valuable and greatly appreciated. Ryan

2 1