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

High-r range EXAFS fitting by Larch
by FAN Dongxiao 05 Jul '24

05 Jul '24

Dear All, I met a problem about the misfit of EXAFS at high-range (around 8 angstrom). My target is the B site EXAFS of perovskite structure (BaSnO3, a=b=c=4.105 angstrom) I want to study the displacement correlation between the Sn and the neighboring Sn atoms. For the first, second, and third Sn neighboring shells, the fitting is good, but the Sn-Sn4 is bad in both amplitude and phase. I try to include the third cumulant, not become better. Can anybody tell me what's the problem? I suspect the high frequency background signal of k space to produce non-structure contribution in the FT spectra. But the data is very clean, I think this should not be the problem. Best, Fan

1 0

Re: [Ifeffit] Creating a structure from EXAFS fitting
by Robert Gordon 27 Jun '24

27 Jun '24

Hi Lisa, Starting from a similar crystal structure could work. Alternatively, building a basic "crystal" structure using symmetry P1 and just putting the atoms where you want them would be feasible - tedious if you have a lot of atoms, easier if you know you have higher symmetry. e.g. Test Symmetry P1 * i.e. no symmetry a = 10 b = 10 c = 10 *Angstroms, easy to scale alpha = 90 beta = 90 gamma = 90 * so metrically cubic Central atom 0.000 0.000 0.000 * at origin, could always displace by 1/2 lattice constants to keep all in the unit cell 1st NNa 0.220 0.000 0.000 * 1st nns at 2.2 Angstroms away 1stNNb 0.000 0.220 0.000 1stNNc 0.000 0.000 0.220 1stNNd -0.220 0.000 0.000 etc... I've used this for modelling molecules, surfaces (with deposited films) as well as 3D crystals. It is a bit of brute force, but should work in any crystal visualization program... cheers, -R. On 2024-06-27 8:47 a.m., Lisa Langlois wrote: > Hello XAFS friends. I would like to know how to create a structure > model for a molecule that was measured with EXAFS, then modeled using > the typical strategies? - So, in the end you have some distances and > bond angles from the central atom > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > ZjQcmQRYFpfptBannerEnd > Hello XAFS friends. > I would like to know how to create a structure model for a molecule > that was measured with EXAFS, then modeled using the typical > strategies? - So, in the end you have some distances and bond angles > from the central atom to the first, and maybe second neighbor. > I was thinking that you start from a similar crystal structure and > then adapt that model using the numbers you got from EXAFS fitting, > using for example the Vesta program. > Best wishes, > Lisa. > > > > > Lisa Langlois, PhD > Beamline scientist > Rm 144 > Phone: +1 225-578-9341 > LSU-CAMD > 6980 Jefferson Hwy, Baton Rouge, LA 70806 > https://urldefense.us/v3/__https://www.lsu.edu/camd/__;!!G_uCfscf7eWS!adSZ4… > <https://urldefense.us/v3/__https://www.lsu.edu/camd/__;!!G_uCfscf7eWS!ZSSym…> > >

1 0

Creating a structure from EXAFS fitting
by Lisa Langlois 27 Jun '24

27 Jun '24

Hello XAFS friends. I would like to know how to create a structure model for a molecule that was measured with EXAFS, then modeled using the typical strategies? - So, in the end you have some distances and bond angles from the central atom to the first, and maybe second neighbor. I was thinking that you start from a similar crystal structure and then adapt that model using the numbers you got from EXAFS fitting, using for example the Vesta program. Best wishes, Lisa. Lisa Langlois, PhD Beamline scientist Rm 144 Phone: +1 225-578-9341 LSU-CAMD 6980 Jefferson Hwy, Baton Rouge, LA 70806 https://urldefense.us/v3/__https://www.lsu.edu/camd/__;!!G_uCfscf7eWS!ZSSym…

1 0

Al and Si references
by Amine EL MESSBAHI 10 Jun '24

10 Jun '24

Hi, Where can I find some Al and Si K-edge normalized data? Thank you, Amine El Messbahi email: amineelmessbahi(a)outlook.com

2 1

alpha and σ2 values for EXAFS data fitting in Artemis came negative
by Arpita Nandy 04 Jun '24

04 Jun '24

Hello Everyone, During one of the data fittings in Artemis, alpha and σ2 came negative!!! What is/are the reason/s behind it? The corresponding file is attached... Regards, Arpita Nandy, PhD student Saha Institute of Nuclear Physics, India

1 0

Issue about plotting simulated EXAFS in Larix
by AowenLi 24 May '24

24 May '24

Dear Matt, I am trying to simulate a theoretical EXAFS with a DFT calculated CIF file via Larix. I performed a FEFF calculation on the CIF file and imported a path to the FEFF fitting panel. However, I didn't get any results when I clicked on the "Plot Current Model" bottom. I get the following error message: TypeError: unsopported format string passed to NoneType.__format__. Could you please help me? Thank you in advance. Best regards, Aowen

2 2

Request for Assistance with Data Import Error of Athena 0.9.26
by Cai, Rui 19 May '24

19 May '24

To whom it may concern, Here's Rui, a PhD student at Georgia Tech. I am writing this email to seek your assistance regarding an import warning I encountered while importing SSRL XAS data collected by uXAS server into Athena 0.9.26, as the Screenshot_Import Warning shows. According to the response from the Ifeffit mailing list, I clicked on all buttons in "Plugin registry", as the Screenshot_Plugin registry shows, and tried to import the same data again. However, there was still the same import warning with the another Athena warning. The data caused error has been attached. I would greatly appreciate it if you could provide guidance on how to resolve this matter. Thank you for your attention to this matter. I look forward to your prompt response. Best regards, Rui Cai

4 3

Choice of E0 in the presence of a huge pre-peak
by Jan-Benedikt Weiss 14 May '24

14 May '24

4 3

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