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

Larch energy calibration
by Schoepfer, Valerie 04 Mar '21

04 Mar '21

Hi, I am using Larch XAS Viewer for the first time to analyze some Mo XANES data. It is fairly straightforward, however I am running into problems with energy calibration, which leads to problems with Linear Combination Fitting. Right now, which is likely wrong, I'm calibrating the energy of a standard to the theoretical edge, then auto-aligning the samples to the standard. But how do reference foils fit in here? Reference foils don't seem to be tied to the sample like they are in Athena. Should I be manually aligning? Is there a general guidance or work flow? Thank you- Valerie Valerie Schoepfer, PhD Postdoctoral Fellow Department of Geological Sciences [cid:image001.jpg@01D5CBC1.8203C730]

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Athena plugin for synchrotrons in Japan
by Yohei Uemura 01 Mar '21

01 Mar '21

Dear Bruce, This is Yohei Uemura. We are using the Athena plugin to read the data format used in synchrotrons in Japan. It is very helpful to read XAFS data directly into Athena. We appreciate the plugin. Recently, we realised that the plugin does not work properly for some data sets. When the data is like below (I0 and I are integers), the plugin works fine. Step scan (or QXAFS) using a counter device [image: image.png] However, if the data is like below (I0 and I are decimal fractions), the outputs of I0 and I are 4digit such as 0.345. QXAFS: I0 and I are decimal fractions [image: image.png] I found the problem was at l. 63. my $pattern = " %9.3f %9.3f %10.6f" . " %12.3f" x $ndet . $/; The output data is terminated by 3 digits after a decimal point. If the plugin is modified as the attached file, both the files were read correctly. The modification is: my $pattern = " %9.3f %9.3f %10.6f" . " %12.3f" x $ndet . $/; *$pattern = " %9.3f %9.3f %10.6f" . " %12.6f" x $ndet . $/ if $list[2+$ndet] =~ m/\d*\.\d+/;* I added the bolded line in order not to truncate the I0 and I by 3 digits. Could you modify the plugin which is provided with the demeter package? Best regards, Yohei -- ================================================ Yohei Uemura (Ph.D) Affiliation : Paul Scherrer Institut (PSI), Laboratory for Environmental Chemistry (LUC) Address : OFLB 106 (PSI Ost), PSI, Forschungsstrasse 111, 5232 Villigen, Switzerland Phone: +41 (0)5-6310-4571 上村洋平所属 : Paul Scherrer Institut (PSI), Laboratory for Environmental Chemistry (LUC) 住所 : OFLB 106 (PSI Ost), PSI, Forschungsstrasse 111, 5232 Villigen, Switzerland 電話 : +41 (0)5-6310-4571 ================================================

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postdoc opportunity at LANL
by Hickam, Sarah Margaret 03 Feb '21

03 Feb '21

Dear all, Los Alamos National Laboratory currently has a postdoc position open for xafs studies of actinide materials. The posting can be found at the following link: https://lanl.jobs/los-alamos-nm/nuclear-forensicsactinide-research-postdoc/… Please feel free to forward this to anyone who might be interested or contact me with any questions. Best regards, Sarah Sarah Hickam Postdoctoral Research Associate Los Alamos National Laboratory MST-16 (505) 695-3515

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Nanocrystalline NiO
by Christian Wittee Lopes 18 Jan '21

18 Jan '21

Dear all, Firstly I would like to wish you a much better year than in 2020. Does anyone have some spectra of nanocrystalline NiO (not bulk standards)? I have a spectrum of a mixed compound and would like to get more insights into what I really have in this sample. Thank you in advance!!! Kind regards, -- *Christian Wittee Lopes* *Visiting Researcher* ANP/FINEP - PRH50 Institute of Chemistry, Universidade Federal do Rio Grande do Sul (UFRGS) Phone: +55 54 992430264

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Larch: AttributeError
by Rachita Rana 13 Jan '21

13 Jan '21

Hi Everyone, I am using Larch for reading and fitting EXAFS data and I get the autobk and Fourier transforms working. But when I try to generate the fefffpaths and fit the data I get an error from the feffit function. I am using the developer version of Larch on MC OS Catalina. Below is the error and the sample script- runfile('/Users/rachita/Box/Larch/Feff_Try2/001.py', wdir='/Users/rachita/Box/Larch/Feff_Try2') Traceback (most recent call last): File "/Users/rachita/Box/Larch/Feff_Try2/001.py", line 27, in <module> fit = feffit(params, dset) File "/Users/rachita/opt/anaconda3/lib/python3.8/site-packages/xraylarch-0.9.50-py3.8.egg/larch/xafs/feffit.py", line 534, in feffit ds.prepare_fit(params=params) File "/Users/rachita/opt/anaconda3/lib/python3.8/site-packages/xraylarch-0.9.50-py3.8.egg/larch/xafs/feffit.py", line 265, in prepare_fit ikmax = int(1.01 + max(self.data.k)/trans.kstep) AttributeError: 'AthenaGroup' object has no attribute ‘k’ #tried this with xdi format data and got the same error Below is the script - #!/usr/bin/env python3 # -*- coding: utf-8 -*- from larch.fitting import param_group, Parameter from larch.io <http://larch.io/> import read_xdi from larch.xafs import feffpath, feffit_dataset, feffit_transform, feffit, feffit_report data = read_xdi('cu_metal_rt.xdi’) #I tried importing Athena project file too path1 = feffpath('feff0001.dat', s02='amplitude', e0='del_e0', sigma2='sigma2', deltar='del_r') trans = feffit_transform(kmin=3, kmax=16, kw=(2,1,3), dk=1, window='hanning', rmin=1.7, rmax=3.1) params = param_group(amplitude= Parameter(1, vary=True), del_e0 = Parameter(1e-7, vary=True), del_r = Parameter(1e-7, vary=True), sigma2 = Parameter(0.003, vary=True)) dset = feffit_dataset(data=data, pathlist=[path1], transform=trans) fit = feffit(params, dset) print(feffit_report(fit)) By printing path groups and transform fit, I confirmed that the data is read correctly. Please let me know if there are ways to fix this or if there is an error in my script. Thank You! Rachita

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Artemis\Plot mismatch\Artemis[Plot]&Artemis [Feff] Atoms and Feff
by Huaming 12 Jan '21

12 Jan '21

Dear all, I am using Artemis for EXAFS data fitting and found that the |χ(R)| plot shown in "Artemis [Plot]" and "Artemis [Feff] Atoms and Feff" are in great difference for a same scattering path. However, the |χ(k)| plots shown in the above two windows is the same. For the plot shown in "Artemis [Feff] Atoms and Feff" window, one path is selected and 'Plot path' is clicked. For the plot shown in "Artemis [Plot]", the same path is dragged into the "Artemis window" and then transfered path and plot in R by click "Action" menu. I would like to know what is the difference of data shown in the two windows. BTW, whether it is possible to have two peaks in the |chi(R)| plot for a single scattering path? For some scatters with high-Z, the f(k) may feature multiple peaks. Thanks, All bests, Huaming Hou

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How do I create a histogram based on R-space values
by Deepak Varanasi 10 Dec '20

10 Dec '20

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How to perform normalisation and background removal of data containing L3 and L2 edges
by Deka, N. 07 Dec '20

07 Dec '20

Dear all I am a student trying to learn Athena for XAS data processing. Attached is a data file which contains L3 and L2 edge of Ru. What should be the right parameters for background removal and normalization of this data set? In the videos from Bruce Ravel, I could not find any example for such a data set containing two edges. Thank you Best Regards, Nipon Deka Leiden University

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Unable to see background and "k", "q", "R" plots for imported data
by Deka, N. 07 Dec '20

07 Dec '20

Dear all I am a new student trying to work with Athena for XAS data processing. Attached is a data file which when I import does not show the background and also Athena cannot plot "k" , "q" , "R" plots for the data. Please suggest me a possible solution. Thank you Best Regards, Nipon Deka Leiden University

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Re: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported
by Mosselmans, Fred (DLSLtd,RAL,SCI) 07 Dec '20

07 Dec '20

Dear Nipon, I suspect you have read the spectrum in as XANEs if you change the data type to mu(e)(e) it should give you what you want Thanks Fred Mosslemans Message: 2 Date: Mon, 7 Dec 2020 15:26:19 +0000 From: "Deka, N." <n.deka(a)lic.leidenuniv.nl> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported data Message-ID: <3088c35cdc4c4e488b2782623526d7bb(a)lic.leidenuniv.nl> Content-Type: text/plain; charset="us-ascii" Dear all I am a new student trying to work with Athena for XAS data processing. Attached is a data file which when I import does not show the background and also Athena cannot plot "k" , "q" , "R" plots for the data. Please suggest me a possible solution. Thank you Best Regards, Nipon Deka Leiden University

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