[Ifeffit] Re: larixite: a WebAtoms-like app for converting crystallographic information into XAS input files

Hi Dongxiao, >Thank you very much for the great work of Larixite. > Can I propose a function for creating input files of FEFF or FDMNES? >This function may be not realistic to achieve but can be very helpful if we >have. It can already create FEFF input files, either from the web app or fro

[Ifeffit] larixite: a WebAtoms-like app for converting crystallographic information into XAS input files

Hi Folks, As some of you have noticed, the WebAtoms application stopped working on millenia.cars.aps.anl.gov a month or so ago. We now have a start of an alternative at https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/larixite__;!!G_uCfscf7eWS!ZXQ2kUFpdV0HV2BeHhKF9ERcYZ6TtE1u0wvLQ

[Ifeffit] Re: demo data for XAFS tutorial

Hi Yohei, Sorry for the trouble. I think that most of the data described there is at https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/data/xraylarch/Workshop2022/__;!!G_uCfscf7eWS!Z8D7nSK4wW_eUYUbja-qyVIf-Snw7GwtZU-S-0aNwd2uhyewvGbGcq1WBG8GBhPN4wE51MkO2cFEi_JnT_LTyyDdHOFijdW9Y2b_hTg$

[Ifeffit] Re: Can't get access to WebAtoms via http://millenia.cars.aps.anl.gov/webatoms/

. --Matt From: Mangold, Stefan (IPS) Date: Sunday, September 29, 2024 at 6:21 AM To: Matthew Newville Cc: XAFS Analysis using Ifeffit Subject: Re: Can't get access to WebAtoms via https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/webatoms/__;!!G_uCfscf7eWS!dakoWTvspWy2zk4u

[Ifeffit] Re: Can't get access to WebAtoms via http://millenia.cars.aps.anl.gov/webatoms/

Hi Stefan, Yes, we know this is down, and sorry for that. In fact, we talked about this at the most recent Larch developers meeting (which is more of a discussion with people interested in influencing its development, so if anyone is interested in giving feedback on these tools or joining such

[Ifeffit] Re: updates to this mailing list

gov/webatoms/__;!!G_uCfscf7eWS!YuZ2y0nxkvdnPQ7rBdIHiNjAoaN0RbWf_h15ZUCrafnxFCIfxd91hKHNnNCcPRnVUHMSV4zmT2j2c37tS9zZWefZUAR9WomFhfTA3qI$ <https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/webatoms/__;!!G_uCfscf7eWS!b58nhCAItwj3aeUVit764sZVSzfzbg-3Yo_RuaaU0RCs81-tv3u4Vi34mBFSkzCbqva5SI202KLW8fCxW7IaTfplXf7ISdR92r4$> thanks for any insights, Chris

[Ifeffit] updates to this mailing list

Hi Folks, We needed to upgrade the operating system on the machine running this mailing list late last week. That went well, but part of that process involved upgrading the "mailman" software used for this mailing list to the latest version. That upgrade was long overdue (the web pages looked

Re: [Ifeffit] Problem with XRF mapviewer post-update

Hi Sarah, Very sorry for the trouble. I have fixed this (or: I fixed one error like this, and it runs for me ;)). On macOS, If you open a Terminal, you should be able to run this: ~/xraylarch/bin/python -pip install https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/xraylarch/dow

[Ifeffit] Larch 0.9.80

Hi Folks, I have released Larch version 0.9.80. It's been a few months since the last announced release, and there have been a few important bug fixes and changes, especially to the Larix GUI.A list of changes is at https://urldefense.us/v3/__https://github.com/xraypy/xraylarch/releases/ta

Re: [Ifeffit] Modeling a spinel structure with fractional occupancy

Hi Matthew, Larix and its CIF Parser (based on pymatgen) can help turn such a CIF file into feff.inp files. For sites with multiple fractional occupations, the feff.inp generated will try to be randomly filled according to those fractions. Of course, with small numbers of neighboring atoms it

[Ifeffit] Upcoming Q2XAFS, Data Formats, and request for data files

Hi Folks, As some of you may have heard, there will be a virtual Q2XAFS (Quality and Quantity for X-ray Absorption Fine Structure) symposium series this summer, with presentations from Working Groups defined and formed at the 2023 Q2XAFS meeting in Melbourne last August. Details for this summe

Re: [Ifeffit] Al and Si references

Hi Amine, There are some Al and Si XAFS spectra at https://urldefense.us/v3/__https://mdr.nims.go.jp/__;!!G_uCfscf7eWS!crCmM50CeBbWwZ_tfXvFPu17hbvtZp74A07Ng4D5n193umyyDeSFe66LGzWZ5ofsugZM8FhB6aaVA-oe7itgv2US8mWeOLAsNXANG_c$ . These spectra are not always the easiest to find or work with but th

Re: [Ifeffit] Issue about plotting simulated EXAFS in Larix

Hi Aowen, Sorry for the trouble. I think you are seeing a “known but not-yet solved” problem. The Feffit Panel in Larix needs to have an experimental data set to show a simulated EXAFS spectrum. That should not be necessary, but it is for now to work around this bug. This is on the list of

Re: [Ifeffit] Request for Assistance with Data Import Error of Athena 0.9.26

Hi Rui, It seems that you probably attached the Apple resource file "_2.1 CH4_006_001.dat" (note the leading underscore). That won't have the data in it -- it's meant to be a File System resource file. There probably is (or should be) also a file named "2.1 CH4_006_001.dat" (without the leadi

Re: [Ifeffit] Choice of E0 in the presence of a huge pre-peak

Hi Jan, Yes, it can be confusing to select the E0 value for spectra like this. The complication is that we basically use E0 for two purposes: for XANES and normalization, we use it as the energy where absorption starts. In this case, the first derivative at the Cu1+ position is perfectly rea

Re: [Ifeffit] Origin of noise in Ag K-Edge

Sebastian, What is happening “in situ”? Are you heating the sample, flowing gas, or changing some other external conditions? The cleaner spectra are also those with larger oscillations, implying a more uniform local environment. That might suggest that the less clean spectra are from samples

Re: [Ifeffit] Difficulty with normalization of XAS spectra

Hi Jesse, Sorry for the trouble. I see the same behavior with your data. What is happening is that the first data point for the "mu_fluo_det0" array (and the "fluo_det0" array, and a few other arrays too) is NaN. That looks to be the case for most, if not every scan in this file. That is

Re: [Ifeffit] Imidazole multiple scattering in Artemis

Hi Chris, Using the single-scattering and multiple-scattering paths that have the same scattering atoms is not double counting. In general, including all the paths from a Feff calculation is what you ought to do to account for all of the EXAFS. But many paths will have weak contributions, and

[Ifeffit] Larch 0.9.75

Hi Folks, Larch 0.9.75 has been released and is now available. You may see a prompt to install this the next time you launch the Larix GUI. It's been several months since the last release of Larch, and there have been many updates, especially for the Larix GUI, and for using Larch for XAS anal

Re: [Ifeffit] Larix.desktop on Arch Linux AttributeError: 'list' object has no attribute 'shape'

Hi Cristian, You tell us you are using a particular Linux distribution. I doubt this matters – if you got as far as Larix running, then the OS-specific or distribution-specific challenges are almost all solved. But then you also say that you are opening a ".xlsx" data file. Are you really ope

Re: [Ifeffit] [IFEFFIT] Polarized FEFF calculation

Hi Soyoung, I would not place too much importance to the value of the "Importance" factor ;)That is, it is a quick estimate of the importance of a Path so that it might be filtered out.As you'll notice, the first path always has an Importance factor of 100, making comparisons between ca

Re: [Ifeffit] Ifeffit Digest, Vol 224, Issue 12

Hi Lisa, On Fri, Oct 22, 2021 at 8:03 PM Lisa Langlois wrote: > 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 > > This is not exactly an answer about the XAS data available with H

Re: [Ifeffit] Larch 0.9.56

install and the other updates worked well > > best regards > > Stefan > > > Am 20.10.2021 um 20:22 schrieb Matthew Newville : > > Hi Folks, > > Larch version 0.9.56 is now available on PyPI ( > https://pypi.org/project/xraylarch) and should now be installed by >

[Ifeffit] Larch 0.9.56

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

Re: [Ifeffit] Running FEFF 8 in Artemis

On Fri, Sep 13, 2019, 11:58 AM Farideh Jalilehvand wrote: > Hi everyone, > > I am trying to do EXAFS data analysis using Artemis and FEFF 8. > > To do so, I have followed these steps: > >1. Changed FEFF executable file path >2. Changed Process from Demeter to FEFF8 > > > > FEFF 8.10 runs,

Re: [Ifeffit] Problem building latest demeter on Debian 32bit Stretch

Hi Al, Bruce, Is there a need to run analysis codes running 32-bit Linux? I haven't seen one of those in a long time, and don't plan on testing or supporting any codes on that platform. I'm not even excited about supporting 32-bit Windows. --Matt ___ I

Re: [Ifeffit] data table for larch data group

Hi Bruce, At the moment, No. But that should be easy and a very good idea to separate reading headers plus the data table from naming of the 1d arrays... Like, I often run into cases where I want to rename arrays after reading the file. I'll work on that. I'd also like to be able to sensibly h

Re: [Ifeffit] Issues with larch built-in shape functions for fitting

Hi Sean, On Fri, Nov 18, 2016 at 6:09 PM, Sean Fackler wrote: > Dear Matt, > > I’ve been fitting with Larch and found a few issues with some of the > functions from code based on the example: examples/fitting/doc_example2a.lar. > It’s for fitting two gaussians and an error function. Briefly, th

Re: [Ifeffit] port for demeter failure

Hi Jason, On Nov 2, 2016 6:28 PM, "justin park" wrote: > Hello, > > I have followed the steps to install macports on my mac and it seems to be > working. However when I went to port in demeter it start and fails rather > quickly giving this error message. > > Error: org.macports.archivefetch for

Re: [Ifeffit] trouble installing deter on a mac

Hi Justin, Hmm, I'm not sure. Are you certain that all of Macports actually installed correctly. Can you give a more complete set of commands and any error messages? On Nov 2, 2016 3:02 PM, "justin park" wrote: > Hello, > > I have followed the steps to install macports on my mac and it seems

Re: [Ifeffit] updating ifeffit manually

Hi Aranwela, Thanks, that's a very helpul description of how to install the zip files.  I'd like to understand why it doesn't work for some accounts and privilege levels, as the problem will surely happen for someone else... Any Windows gurus who understand this? --MattOn Aug 19, 2010 2:21 PM,

Re: [Ifeffit] IFEFFIT update (windows7)

Can you create ana delete a file in C:\Proagram Files\Ifeffit ? How about removing or overwriting an existing file?   These are the things unzip will need to do, with your permissions. In reporting such problems, please be specific about what you did and what does happen, including error messages