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

INCREASE NOVP Error
by Anis Attiaoui 04 Dec '24

04 Dec '24

Dear Matt and Community, I am having a problem related to a specific .inp file when I am trying to generate the inp file from its corresponding cif with feff8. I am attaching the .cif and feff.inp. The error I am getting is the following: '' Calculating potentials ... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 initial state energy overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 muffin tin radii and interstitial parameters : ipot, Norman radius, Muffin tin radius, Overlap 0 1.49498E+00 1.39776E+00 1.15000E+00 1 1.20678E+00 8.53844E-01 1.15000E+00 2 1.56883E+00 1.42805E+00 1.15000E+00 tell authors to INCREASE NOVP '' I did try to run the same cif using ARTEMIS and it worked wo any issues using the feff6L instead of version 8. Thus, I tried to use the new Larixite ciff2feffinp module and use the feff6L instead of version 8 but I noticed this is not installed yet. I also found that a similar issue has previously been documented but I didn't find any clear answers in there. https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/feff/feffusers… Any suggestions will be tremendously appreciated. Thank you very much. Dr. Anis Attiaoui, Stanford University, GLAM Dept. Material Science and Engineering, McCullough Building, 476 Lomita Mall, Stanford California, USA, 94305 Office/shipping: McC-203 Tel: +1(650)485-0501 Web: https://urldefense.us/v3/__https://mcintyre.stanford.edu__;!!G_uCfscf7eWS!d… <https://urldefense.us/v3/__https://mcintyre.stanford.edu/__;!!G_uCfscf7eWS!… >

2 1

Larch: noise in chi(k) - another try
by Kirill LOMACHENKO 26 Nov '24

26 Nov '24

3 3

Larch: noise in chi(k)
by Kirill LOMACHENKO 22 Nov '24

22 Nov '24

1 0

Re-Installing Larch for Windows
by Daria Boglaienko 18 Nov '24

18 Nov '24

Hello, I'm sorry if I missed information related to troubleshooting of larch installation. My earlier larch version stopped loading and I uninstalled it in order to install the latest one. After doing that I can't find XAS viewer. No folder containing it was created after installation (unlike before). I went to “Scripts” in "xraylarch", found larch exe and many other exe files but they don’t load (open and crash). I uninstalled and installed it around 4 times. I also uninstalled anaconda and python for potential conflict, after that Larch installation went without errors, but still … the same issue. Please, let me know. Thank you in advance! Daria

4 4

Generating feff.inp from .cif file issues
by Anis Attiaoui 15 Nov '24

15 Nov '24

Dear Ifeffit Community, I am struggling to generate the feff.inp file using the following .cif file (attached). I am using py-Larch for this project. I tried using these 2 functions: from larch.xrd.cif2feff import cif2feffinp and from larch.xrd.structure2feff import structure2feffinp. For some reason both of them, they cannot seem to read the cif cluster file (attached). The snippet of the code I am using is : inp_file = cif2feffinp(cif_file, 'Sn', edge='K', absorber_site=1, version8=False) I am trying to generating inp_file using feff6. I keep getting the error output of inp_file: "# could not read CIF file". I am wondering if this is because the .cif file is bad or there is sthg else going on. Any suggestions will be tremendously helpful. Best regards, Dr. Anis Attiaoui, Stanford University, GLAM Dept. Material Science and Engineering, McCullough Building, 476 Lomita Mall, Stanford California, USA, 94305 Office/shipping: McC-203 Tel: +1(650)485-0501 Web: https://urldefense.us/v3/__https://mcintyre.stanford.edu__;!!G_uCfscf7eWS!a… <https://urldefense.us/v3/__https://mcintyre.stanford.edu/__;!!G_uCfscf7eWS!… >

4 6

XANES-Linear Combination Fitting (LCF) Au standard sample
by liyy15＠outlook.com 09 Nov '24

09 Nov '24

Hi, All I am recently learning to use XAS to characterize some Au mixture solution samples. I would like to study the chemical valence by XANES. Unfortunately, I have only gotten Au foil data. Could I use the standard data from literature like [AuCl4]-, [AuCl2]-, Au hydroxide etc? Best regards, Yu

1 0

demo data for XAFS tutorial
by Yohei Uemura 30 Oct '24

30 Oct '24

Dear Matt, I'm wondering if the demo data for the Larch tutorials is still available. https://urldefense.us/v3/__https://youtu.be/5mYRqpAWK-o?si=MS7_aqBiYF_cQTtf… My colleague wants to learn how to use Larch from the tutorial, but the link to the demo data is expired. Best regards, Yohei -- ================================================ Yohei Uemura (Ph.D) Instrument scientist FXE beamline, European XFEL GmbH Address : Holzkoppel 4, 22869 Schenefeld, Germany Phone: +49-40-8998-6006 上村洋平所属 : FXE beamline, European XFEL GmbH, 住所 : Holzkoppel 4, 22869 Schenefeld, Germany 電話 : +49-40-8998-6006 ================================================

2 2

larixite: a WebAtoms-like app for converting crystallographic information into XAS input files
by Matthew Newville 30 Oct '24

30 Oct '24

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… This uses PyMatGen to convert CIF files into Feff.inp files. This includes a simple searchable interface to data collected from the American Mineralogist Crystal Structure Database (https://urldefense.us/v3/__https://rruff.geo.arizona.edu/AMS/amcsd.php__;!!… ) of published mineral structures that has been included in xraylarch for some time. You can upload a CIF file – and most should work. We expect to be able to add inputs for FDMNES soon, and we’re looking into formats for other calculations (say, Ocean) as well. On a practical note, we thought it would be best to pull this code out of the main Larch repository and start a fresh project just for “working with crystallographic information and atomic clusters to generate inputs for XAS calculations”. This code is now under https://urldefense.us/v3/__https://github.com/xraypy/larixite__;!!G_uCfscf7… (and does not rely on the larger xraylarch package). At some point soon we plan to remove this code from xraylarch itself and use this project for that functionality. This is all sort of new, so suggestions on any part of this and bug reports are most welcome. --Matt

3 3

MD EXAFS comparison with Experimental EXAFS
by awade9＠bu.edu 25 Oct '24

25 Oct '24

Hello, I'm trying to compare my experimental EXAFS data for a molten salt (NaF-ZrF4) sample (extracted through Athena), with EXAFS obtained through running FEFF iteratively on multiple atomic configuration files obtained through MD to get an average EXAFS out. This has been performed before by Pauvert et al. (https://doi.org/10.1021/jp203137h) for a similar salt as well as others for different materials. In our comparison, there seems to be a phase shift in MD EXAFS (to higher k) compared to experimental EXAFS and I would like to know if that's normal. I've read that there is an energy shift when we use FEFF and this might be affecting the MD EXAFS here but all the comparisons I've come across in literature overlay quite well... Thank you. Best, Anubhav

2 1

SIXPACK Background Removal not reading averaged data file from SamView
by Muretta, Julie 21 Oct '24

21 Oct '24

Hello, I have been using SIXPACK to process my S K-edge XANES data from SSRL beamline 4-3. I am using SamView to average 5 scans (to improve S/N) for each sample. Then I save the averaged file (.avg) and open in the SIXPACK Background Removal application for normalization. All data sets seem to be working great with this method except one. This one opens fine in SamView, but Background Removal cannot open the averaged file. Here is the error message: *** read_data: error opening file *** C:\sixpack/test.inp pre_edge: no energy array? pre_edge: no energy array? I have saved the averaged file as a .txt file to look at it (.avg and .txt files attached), and I see an energy array. How can I open and use this in SIXPACK Background Removal? Thank you in advance, Julie Muretta

1 0