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

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 11 Jan '21

11 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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Postdoctoral research opportunity in photocatalysis and x-ray spectroscopy
by Sokaras, Dimosthenis 06 Dec '20

06 Dec '20

Hello XAFS Community, We have a new postdoctoral research opportunity in the field of photocatalysis, aiming to study photocatalytic conversion of CO2 to liquid fuels. The selected candidate will be performing time-resolved and operando x-rays characterizations of photocatalytic materials in order to extract fundamental electronic-structure insights that can correlate and guide catalytic activity and photocatalysts material’s properties. An extensive part of the research will take place at LBNL/SLAC where the candidate will be developing and performing novel x-ray spectroscopy methodologies. Applicants interested in this opportunity may reach out to Junko Yano (LBNL, jyano(a)lbl.gov) and Dimosthenis Sokaras (SLAC, dsokaras(a)slac.stanford.edu) Thank you, Junko Yano and Dimosthenis Sokaras

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LARCH- XRF- fitting the spectrum
by Ana Mijo 04 Dec '20

04 Dec '20

Hello, I have images from GSECARS. I am trying to improve the background reduction by fitting the spectrum and getting new ROIs. I did a fit but I don’t manage to update the ROI’s. I tried saving to a .mca file and uploading again but I don’ t see a change. Since I come from other software I may have pre-concepts, maybe the first question is: can a new fit be done and get new (maybe cleaner) images? or Can I only work with the ROI’s from the experiment? If it can be done, how should I proceed after doing the fit to update ROI’s? I have emailed this question to Matt also (before finding this mailing list). Thanks in advance, Best regards, Ana Ana Mijovilovich Czech Republic ana_mijo(a)yahoo.com

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Pd nanoparticle K-edge XANES
by Eva Bajnoczi 30 Nov '20

30 Nov '20

Dear Mailing List Readers, I wonder if there is anyone who has and also would be willing to provide a K-edge XANES spectrum measured on Pd nanoparticles. Or to point me to a source where I can find one. Our particles most probably around 5nm, so this size-range would be ideal, but anything would be very much appreciated, as that would be a better reference than metallic Pd foil. We have got some interesting reviewer questions on a paper and to answer them a Pd nanoparticle XANES would be highly useful, but under the circumstances, it is not possible to measure it on our own in the forseeable future. Thank you for any kind of help in advance! Best regards, Eva Bajnoczi -- Bajnóczi Éva / Éva Bajnóczi tudományos munkatárs / research fellow Wigner Fizikai Kutatóközpont / Wigner Research Centre for Physics 1121 Budapest, Konkoly-Thege Miklós út 29-33. Magyarország / Hungary

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Workshop Opportunity for XAS users in the field of Biogeochemistry.
by Ritimukta Sarangi 24 Nov '20

24 Nov '20

Hello, Apologies for the mass email. SSRL, in conjunction with EMSL is organizing a Workshop titled "Spectroscopy and Modeling for Molecular Insights into Environmental Processes" on 26, Jan 2021. The main focus is to encourage and provide help in getting started with the use of theory and modeling (such as DFT and MD) in the interpretation of EXAFS/XAS data. Please find more information in the event flyer below: https://www.dropbox.com/s/vvshxqpji4yok2s/SSRL_EMSL_Workshop_Flyer.pdf?dl=0 We encourage interested users and research groups to register and attend the workshop. Looking forward to your participation. Best regards, Riti Sarangi SSRL

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Two phases EXAFS fitting-help
by Chen, Danting 10 Nov '20

10 Nov '20

Hi Mr/Ms, I have a sample and get a two major phases result by linear combination analysis, one dominate 59.5% of hydrozincite( and another is 33.5% zinc phosphate (. I would like to use Artemis to fit the k-space and the first shell of R-space. For R-space, my idea is to fit the first Zn-O shell since both dominate phases are both tetrahedral and octahedral coordination and the first shell is the similar environment. For k-space, shall I fit each phase with the sample individually and then sum the different weight of fitting curve together to see how it fit finally? If it is right, may I ask how exactly it fits? I have no idea how the weight is set in Artemis or it can only be summed half by half? Also, since my sample numbers are only two, I am unable to use PCA to fit. Except the above mentioned, is there anything else that I can do? Sorry, I am a new learner of XAS and have many things to learn. Best Wishes, Danting Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Re: [Ifeffit] Postdoctoral positions in MSEE EFRC at Brookhaven National Lab
by Gill, Simerjeet 09 Nov '20

09 Nov '20

Hello XAFS Community, On behalf of Energy Frontier Research Center on Molten Salts in Extreme Environments (MSEE) at Brookhaven National Laboratory (BNL), I would like to bring your attention to two postdoctoral Research Associate positions within the Energy Frontier Research Center (EFRC) on Molten Salts in Extreme Environments. The positions require a Ph.D. degree in chemistry, physics, materials science or a related field. The interdisciplinary research will focus on structural and spectroscopic investigation of molten salts, solutes in them, and liquid-solid interfaces. The positions are located in the BNL Nuclear Science and Technology Department (Job ID 2335) and Chemistry Department (Job ID 2341). Experiments will be performed at the National Synchrotron Light Source II (NSLS-II), BNL's new, state-of-the-art synchrotron, the BNL Chemistry Division and the BNL Center for Functional Nanomaterials. To find detailed descriptions of the position requirements and apply online, go to https://jobs.bnl.gov<https://jobs.bnl.gov/>. For Job ID 2335, hands-on experience in either X-ray scattering, spectroscopy and reflectivity is required. For Job ID 2341, demonstrated experience in electrochemical methods or working with molten salts is required. Experience with the chemical and physical properties of materials at high-temperature is highly desirable for both positions. If you have follow up questions, please don't hesitate to contact: Jim Wishart: wishart(a)bnl.gov<mailto:wishart@bnl.gov> or Simerjeet Gill: gills(a)bnl.gov<mailto:gills@bnl.gov>. For position 2335, postdoc will investigate molten salt systems using NSLS-II beamline facilities at Brookhaven National Laboratory, with primary technique being X-ray absorption fine structure. This position will be in Nuclear Science and Technology Department at Brookhaven National Lab, Under supervision of Dr. Simerjeet Gill. Responsibilities will include performing synchrotron experiments on molten salt systems with and without actinides and collaborating with other participants of MSEE-EFRC. For inquiries, please email me at gills(a)bnl.gov<mailto:gills@bnl.gov>. Thank you, Simerjeet K Gill, Group leader, Nuclear Science and Technology Department, Brookhaven National Lab, Upton, NY 11973

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Postdoctoral position in MSEE EFRC at Brookhaven National Lab
by Gill, Simerjeet 03 Nov '20

03 Nov '20

Hi, I would like to post below message regarding postdoc positions in MSEE EFRC at BNL, with attached flyer to XAFS community. Thanks, Simer Hello XAFS Community, On behalf of Energy Frontier Research Center on Molten Salts in Extreme Environments (MSEE) at Brookhaven National Laboratory (BNL), I would like to bring your attention to two postdoctoral Research Associate positions within the Energy Frontier Research Center (EFRC) on Molten Salts in Extreme Environments. Information about the positions is summarized in a flyer attached to this message. For position 2325, postdoc will investigate molten salt systems using NSLS-II beamline facilities at Brookhaven National Laboratory, with primary technique being X-ray absorption fine structure. This position will be in Nuclear Science and Technology Department at Brookhaven National Lab, Under supervision of Dr. Simerjeet Gill. Responsibilities will include performing synchrotron experiments on molten salt systems with and without actinides and collaborating with other participants of MSEE-EFRC. For inquiries, please email me at gills(a)bnl.gov<mailto:gills@bnl.gov>. Thank you, Simerjeet K Gill, Group leader, Nuclear Science and Technology Department, Brookhaven National Lab, Upton, NY 11973

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XAS question
by Chen, Danting 29 Oct '20

29 Oct '20

Hi Mr/Ms, I am a new learner of XAS and meet a problem like before and hope you can give me some hints. [cid:image001.png@01D6ADDA.9D016B40] [cid:image005.png@01D6ADDA.9D016B40] I have a data set after merged and alignment. But at 11-13 A-1, the amplitude of k is much higher than normal but there seems no weird points at XAS spectrum. I wonder how I could deal with this part? If I shorter kmax and it must lose some important information. Best Wishes, Danting Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Advanced XAS Workshop at CLS
by Gosia Korbas 27 Oct '20

27 Oct '20

Hi all, On behalf of the BioXAS team at the Canadian Light Source, I would like to invite you to participate in the virtual Advanced XAS Data Analysis and Modeling Workshop to be conducted in four half-day (8 AM to 1 PM, UTC-6, Saskatchewan Time) remote sessions through WebEX on November 10, 13, 20 and 24. The workshop is organized by the BioXAS-Spectroscopy senior scientist, Roman Chernikov. For more details and registration (free) please follow the link: https://bioxas-spectroscopy.lightsource.ca/advanced-spectroscopy-workshop-2… We hope to see you there! Gosia Korbas --------------------------------------------------------------------- Gosia Korbas, Ph.D. BioXAS-Imaging Senior Scientist BioXAS-Sector Responsible Canadian Light Source Phone: +1-306-657-3859 BioXAS-Imaging website<https://bioxas-imaging.lightsource.ca/> gosiakorbas.net<https://gosiakorbas.net/>

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Athena error on Linux mint
by Kyle Kluherz 26 Oct '20

26 Oct '20

I recently successfully installed the Demeter suite on my Linux Mint 19 machine. Last week, I updated to Linux Mint 20, and now I get the following error when trying to run athena from the command line: Can't locate Demeter/Here.pm in @INC (you may need to install the Demeter::Here module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/local/bin/dathena line 7. BEGIN failed--compilation aborted at /usr/local/bin/dathena line 7. I was wondering if there was a relatively easy way to fix this, or if the best recourse is to simply reinstall Demeter? It took some fiddling to install initially, so I don't want to reinstall it unless that's the easiest way to fix the issue. Also, the mailing list link on the Demeter home page (http://cars9.uchicago.edu/mailman/listinfo/ifeffit/) times out. Fortunately I was able to get a working link (https://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) from a friend. Sincerely, Kyle Kluherz -- Kyle (Tk) Kluherz Graduate Student Gamelin & De Yoreo groups Department of Chemistry, UW Materials Science Division, PNNL

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Wyartite XAS spectrum?
by Mike Massey 17 Oct '20

17 Oct '20

Hi All, And now for something not-phosphorus... Does anyone happen to have a wyartite U L3-edge XAS spectrum laying around? If you do, and happened to be willing to talk with me about it, I would be most grateful. Kind Regards, Mike

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Re: [Ifeffit] P K-edge XANES spectrum question (Mangold, Stefan (IPS))- (Mike Massey); Re: Ifeffit Digest, Vol 212, Issue 7 (Luis Carlos Colocho Hurtarte)
by Ganga Hettiarachchi 16 Oct '20

16 Oct '20

Mike, Thanks, we will try diluted samples to make sure that this is not an issue due to concentration. Luis, Thanks for sharing those papers. We have plenty of OC in these systems, but Pb or other trace elements concentrations are very small (below 10 mg/kg). Best regards, Ganga -------------------- Ganga M. Hettiarachchi

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Re: [Ifeffit] Ifeffit Digest, Vol 212, Issue 7
by Ganga Hettiarachchi 16 Oct '20

16 Oct '20

Hello Dean, Thanks for this interpretation; it makes sense. I was (am still) quite surprised by the intense of Al(III) pre-edge feature as we did not detect anything else in our XRD work, except some Fe oxides (the product is X-ray amorphous most likely). Hello Mike, Thanks. We diluted this sample already to bring P concentration below 5000 mg/kg. We can potentially try further diluting, but when we go below that, sometimes we have a hard time getting a reasonable P spectrum in environmental samples. Best regards, Ganga -------------------- Ganga M. Hettiarachchi, Ph.D. Professor of Soil and Environmental Chemistry Department of Agronomy 2107 Throckmorton Plant Sciences Center 1712 Claflin Road Kansas State University Manhattan, KS 66506 USA 785-532-7209 (office) 785-532-6094 (FAX) http://www.agronomy.k-state.edu/research/soil-and-environment/soil-environm… http://www.agronomy.k-state.edu/people/faculty/hettiarachchi-ganga/index.ht… -----Original Message----- From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Friday, October 16, 2020 4:53 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 212, Issue 7 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. Re: P K-edge XANES spectrum question (Dean Hesterberg) 2. Re: P K-edge XANES spectrum question (Mike Massey) ---------------------------------------------------------------------- Message: 1 Date: Fri, 16 Oct 2020 05:21:58 -0400 From: Dean Hesterberg <dean_hesterberg(a)ncsu.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] P K-edge XANES spectrum question Message-ID: <CANEgao_RuxGJ7khkrwypyqu4FM333aw3iozgtPJHuZP6Sx9KSA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello Ganga, That is a very interesting spectrum. Given what you said about the system, the lower energy feature at ~ 2146 eV should be Fe(III)-bonded phosphate and the feature at ~2149 eV should be Al(III)-bonded phosphate. Both produce pre-white line absorption peaks, but the Al-bonded phosphate peak is closer to the white line and less distinct in spectra of Al-phosphates like variscite and non-crystalline Al-phosphate, for example (see Khare et al. 2007. *Geochimica et Cosmochimica Acta* 71:4405, Fig. 5C). A significant proportion of the phosphate in your system apparently precipitated with Al-13 polymer structures in the aluminum chlorohydrate. Dean On Fri, Oct 16, 2020 at 1:26 AM Ganga Hettiarachchi <ganga(a)ksu.edu> wrote: > All, > > Can anyone provide some insight into the pre-edge ?features? in this P > XANES spectrum? > > This is the P XANES spectrum we got for a recovered P-product (rich in > Fe and Al) from wastewater using the AnMBR technology. During the > coagulation process, our collaborators (environmental engineers) used > stock solutions of aluminum chlorohydrate (ACH) and FeCl3. > > > > Thanks very much. > > > > Best regards, > > > > Ganga > > > > -------------------- > > > > Ganga M. Hettiarachchi, Ph.D. > > Professor of Soil and Environmental Chemistry > > Department of Agronomy > > 2107 Throckmorton Plant Sciences Center > > 1712 Claflin Road > > Kansas State University > > Manhattan, KS 66506 USA > > > > 785-532-7209 (office) > > 785-532-6094 (FAX) > > > > > http://www.agronomy.k-state.edu/research/soil-and-environment/soil-env > ironment-chem/ > > > http://www.agronomy.k-state.edu/people/faculty/hettiarachchi-ganga/ind > ex.html > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- DEAN HESTERBERG William Neal Reynolds Distinguished Professor of Soil Chemistry Dept. of Crop and Soil Sciences NC State University email: dean_hesterberg(a)ncsu.edu

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Re: [Ifeffit] P K-edge XANES spectrum question (Mangold, Stefan (IPS))
by Ganga Hettiarachchi 16 Oct '20

16 Oct '20

Stefan, Thanks for sharing your thoughts. Please share if you do have spectra for any other P (i.e., not +5). Best regards, Ganga -------------------- Ganga M. Hettiarachchi, Ph.D. Professor of Soil and Environmental Chemistry Department of Agronomy 2107 Throckmorton Plant Sciences Center 1712 Claflin Road Kansas State University Manhattan, KS 66506 USA 785-532-7209 (office) 785-532-6094 (FAX) http://www.agronomy.k-state.edu/research/soil-and-environment/soil-environm… http://www.agronomy.k-state.edu/people/faculty/hettiarachchi-ganga/index.ht…

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P K-edge XANES spectrum question
by Ganga Hettiarachchi 16 Oct '20

16 Oct '20

All, Can anyone provide some insight into the pre-edge "features" in this P XANES spectrum? This is the P XANES spectrum we got for a recovered P-product (rich in Fe and Al) from wastewater using the AnMBR technology. During the coagulation process, our collaborators (environmental engineers) used stock solutions of aluminum chlorohydrate (ACH) and FeCl3. Thanks very much. Best regards, Ganga -------------------- Ganga M. Hettiarachchi, Ph.D. Professor of Soil and Environmental Chemistry Department of Agronomy 2107 Throckmorton Plant Sciences Center 1712 Claflin Road Kansas State University Manhattan, KS 66506 USA 785-532-7209 (office) 785-532-6094 (FAX) http://www.agronomy.k-state.edu/research/soil-and-environment/soil-environm… http://www.agronomy.k-state.edu/people/faculty/hettiarachchi-ganga/index.ht…

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Postdoctoral Position(s) at SSRL - DOE BOTTLE Project.
by Ritimukta Sarangi 15 Oct '20

15 Oct '20

Hello XAFS Community, On behalf of the BOTTLE team at SLAC, I would like to bring three post-doctoral fellowship openings to your attention. Please visit: https://careers.slac.stanford.edu/jobs-slac/ra-and-postdocs The three positions with "Postdoc BOTTLE" in their names are the relevant postings. I am also including a pdf version of the position I have available in this email for easy reference. We look forward to hearing from interested candidates to join our team! Thank you, Riti Sarangi

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EXAFS, Spectroscopy and Imaging Summer School Youtube Page
by Ritimukta Sarangi 13 Oct '20

13 Oct '20

Hello EXAFS enthusiasts, We have uploaded our 2020 summer school material on the Youtube Channel : https://www.youtube.com/channel/UC3sd8ZqQkNfDK11jM8cOWzw/videos You may find useful material for your synchrotron XANES/EXAFS/Imaging research. You can subscribe and share the page with colleagues as an educational resource. In the future (TBD), we plan to include recorded videos on advanced spectroscopy techniques including soft and hard X-ray RIXS and XES methods. If there are SSRL related material that you would like us to prepare, please let us know and we can put it on the list. Thank you for your time. Best regards, Riti Sarangi SSRL.

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Ifeffit Question
by Nicholas Weingartz 08 Oct '20

08 Oct '20

Hello List, I'm having a strange problem with my EXAFS fits in Artemis in which they seem to fly off at higher k. I was having trouble with background fitting a particularly messy data set and I wanted more control over this so I used the program PySpline to fit the background after I did the rest of the preprocessing in Athena. I then imported the data into Athena and loaded the project into Artemis. Interestingly, when I only include a single path in the fit and plot both the single path and the overall fit, the single path does not fly off but the overall fit does. I have attached an image of the issue. When I use the spline fitting built into athena, I do not encounter this issue. Has anyone ever experienced this issue before? Thanks for your help! Nicholas Weingartz Ph.D Student Department of Chemistry Northwestern University [image: image.png]

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Core-hole Lifetimes in Hephaestus 0.9.26
by Daniel Przyrembel 28 Sep '20

28 Sep '20

To Whom it may concern, I am quite sure there is a general lifetime/energy-width conversion error in Hephaestus: All core-hole lifetimes seem to come out too long by a factor of - as it seems exactly - 10: E.g. the lifetime of the F K-edge with a width of 0.25 eV is given as 25.30 fs instead of ca. 2.6 fs (width = h_bar / lifetime). This glitch was present in 0.9.25 already and, as I noticed after updating, prevails in 0.9.26. I have not tried earlier versions. Best regards, Daniel

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EXAFS fitting sum of all paths in R space
by Ashwini Kumar Poswal 23 Sep '20

23 Sep '20

Dear All, I have one problem regarding the sum of all paths (R-space) after fitting. If we include many paths for the fitting, the fitting shows a good fit but after fitting, I select all paths and export (using Artemis [Data] window: save data + marked paths as |χ(R)|. I plotted all paths in origin as well as the sum of all paths. But when I add up all the contributions from all the paths, the deviation at larger paths is extraordinarily high and not equal to final fit. I am attaching a figure for illustration. It is clearly seen that the final fit is lesser compared to one of the path and the sum of all paths is quite high compared to fit (as shown in second figure. Can anybody suggest, how to sum different paths? [image: image.png] [image: image.png] Regards *Ashwini Kumar Poswal* *Mumbai* *Tel.-+91 (022) 25595081*

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Requesting guidance in understanding results from Athena
by Deepak Varanasi 13 Sep '20

13 Sep '20

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Postdoctoral fellowship in AI - related field
by Anatoly Frenkel 12 Sep '20

12 Sep '20

Please pass this info to anyone interested in this opportunity, particularly, those students who are about to obtain their PhD and looking for postdoctoral fellowships. This one may be suitable for those who plan to use data science approaches for interpreting XANES and EXAFS data and apply them to interdisciplinary research projects. https://www.stonybrook.edu/commcms/iacs/opportunities/fellowships/Postdocto… You are welcome to contact me if you are interested. Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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XAFS short course at BNL: Nov. 18-20, 2020
by Anatoly Frenkel 11 Sep '20

11 Sep '20

Dear mailing list subscribers: Please pass this information along to your group members or others who may be interested in this. As it has done every year since 2005, on* Nov. 18-20, 2020*, Synchrotron Catalysis Consortium (SCC) will run an annual short course on X-ray absorption fine structure techniques and applications. *Date of Event:* November 18-20, 2020 *Official Name of Event: * Short course on X-ray Absorption Fine Structure: Application to Nanomaterials *Description: * Every year Synchrotron Catalysis Consortium, in partnership with NSLS-II, organizes and runs a 3-day short course to those interested in learning about the use of x-ray absorption spectroscopy methods. This year, the course will be offered online from November 18–20, 2020. The course will be useful for those scientists' who already possess basic experience with XANES and EXAFS methods, including experiment and data analysis, and are interested in advanced analysis and modeling methods applicable for nanomaterials research. The course will be run in a flip classroom mode. Participants will study video-presentations of leading experts in XAFS methods and applications in advance of the workshop. The video-lectures will be assembled to follow the workshop agenda. During the workshop, the instructors will divide participants in breakout sections for in-depth problem solving, data analysis and modeling, to best match participants and their research interests. There will be Q&A sessions on the subject of the lectures, and in depth practicums of the EXAFS and XANES analysis software programs. The course will be open to 80 participants, selected based on their application materials. Further info about the course, including the application materials and the deadlines, is available here: https://www.bnl.gov/xafs2020/ Note the application deadline: September 27, 2020. For past XAFS workshops, and information about the SCC-supported beamlines and capabilities, please visit the SCC web sites: https://you.stonybrook.edu/scc2/xafs-workshops/ For any questions, please contact me. Best regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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Unable to Import Data In Athena
by Angshuman Gupta 04 Sep '20

04 Sep '20

Dear sir, I am new to this mailing list and excuse me if the question had already been asked. I am not able to import data in the Athena software. I tried to import some of the examples data like Fe_lepidocrocite.000 in the Fe standards folder while importing the data I encountered an error (screenshot has been attached along with the log file generated in the terminal). I am using Linux Mint 18.3 Sylvia OS and perl 5, version 22, subversion 1 (v5.22.1). I followed the instruction for installation here " https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h… " I will be thankful if you could suggest something to getting rid of this issue. Thank you Angshuman Gupta PhD scholar IIT Bombay

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Co K-edge XAS spectra of Co(OH)2 and CoOOH
by Carlos Triana Estupinan 27 Aug '20

27 Aug '20

Dear mailing list, I am looking for the Co K-edge XAS spectra of Co(OH)2 and CoOOH containing both the XANES and EXAFS regions at room temperature. Thank you in advance. Kind regards, -- *Carlos A. Triana* PHD. - LIC.PHIL. Sciences Physics MSC.*-* BSC. Sciences Physics Postdoctoral research fellow University of Zürich Switzerland TEL: +41 076 814 41 60

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web apps for X-ray data and XAS library
by Matt Newville 14 Aug '20

14 Aug '20

Hi Folks, I was fortunate enough to have a summer student this crazy summer and had them work (from home, of course!) on web applications for X-ray data resources, including absorption calculations for materials. The result is a bit like a web version of Hephaestus and is currently at both https://xraydb.xrayabsorption.org/ and https://millenia.cars.aps.anl.gov/xraydb/ While similar to Hephaestus, there are some differences too. There are pages for absorption and fluorescence lines, absorption length calculations, ion chamber flux calculations, mirror reflectivities, scattering factors, and mono Darwin widths. Many of the calculations will show interactive plots, links to data, and/or a link to a python script to reproduce the calculation. Questions, comments, complaints, or suggestions for making this better are most welcome. We may have missed your favorite Hephaestus feature - is so, please let us know. Also: the X-ray Data Library - a collection of XAS spectra - has moved to https://xaslib.xrayabsorption.org/ <https://xraydb.xrayabsorption.org/> This has also expanded some (well, now with about 270 spectra), and added several features, notably interactive plots. Again, any comments or suggestions for making this better would be most welcome. I will be adding more data to this library, but I also ask that if anyone has data they can and would like to share on this site, please let me know. Thanks for any feedback or suggestions you might have. --Matt

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RE-REGISTRATION Request for SSRL Summer School
by Ritimukta Sarangi 05 Aug '20

05 Aug '20

Hello everyone, This message is going out at *11:23 AM PST on Aug 5, 2020*. Our registration website for the summer school has been overwhelmed by requests and we had to stop registration and fix some of the errors. I request that *if you registered before that time, please go ahead and re-register* for the summer school program. I apologize for the issues and request your continued patience with us in determining the best way to support smooth operations for this unprecedented amount of interest in the school. Thank you, Riti Sarangi p.s -please email me at ritis(a)slac.stanford.edu, if you have any questions.

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Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9
by Abhinav Prabhakar 05 Aug '20

05 Aug '20

Hello, Thank you for your reply. Attached is the CIF file in question. The crystal is Tobermorite 14A, taken from COD website. However, the structure has partial occupancy and it is modified to include full occupancy. The modified CIF file shows a space group of B11b (and cannot be recognized by Artemis). I tried a C1c1 space group (it works) but it shows the same structural values as a P11b. Regards, AP On Tue, Mar 14, 2017 at 1:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. Re: Space group type in Artemis (Bruce Ravel) > 2. Data export and coordination number (Abhinav Prabhakar) > 3. Re: Data export and coordination number (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Mar 2017 09:20:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Space group type in Artemis > Message-ID: <3853f1f7-61fd-6886-306f-040c540ecae1(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/11/2017 05:56 AM, Abhinav Prabhakar wrote: > > Hello, > > > > I have a question about the working of Artemis as a new user. > > > > Artemis does not recognize the space group B11b. When importing a cif > > file of a crystal with this symmetry, it sends a prompt message that the > > space group symbol cannot be recognized. As a result, I changed it to > > P11b and it works. But would this change any crystal information (for > > eg. Degen, Reff values) significantly? > > I am not a crystallography expert in any sense. When I wrote Artemis, I > meticulously followed what I found in the fourth edition of the > International Tables for Crystallography, Volume A. Every symbol > defined in there is recognized by Artemis. (Well, I guess I should say > that every symbol is /supposed to be/ recognized by Artemis. If one is > missing, that's a bug and should be reported.) > > "B11b" is not a symbol that I found in my copy of ITC volume A. As > Robert suggested, there may be a way to rotate group 9 so that "B11b" is > an interpretable symbol in the abstract. But Artemis does not know how > to do that. (Nor do I.) > > "P11b" is a setting for space group #7. If, as Robert suggests, your > CIF file is for space group #9, then the answer to your last question is > yes. It is plainly obvious that using a different space group will > change the degeneracies and distances. > > > Of course, you did not bother to include a copy of the CIF file in > question to your original email, so it is not actually possible for > Robert or I or anyone else to actually help you effectively. > > At the risk of sounding like an annoyingly broken record, everyone > should take the time to ask a good question or write an actionable bug > report: > > http://bruceravel.github.io/demeter/documents/SinglePage/help.html > http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 743, Room 114 > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Mar 2017 21:48:31 +0800 > From: Abhinav Prabhakar <abhi.prabhakar(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Data export and coordination number > Message-ID: > <CA+nbL85FJReunY1Am1oeNTMtFskXMd8FmH_OgaO00mnmew2c-g(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > As a new user, I have some questions related to the use of Athena and > Artemis: > > i) Is it possible to extract the normalized/background corrected data from > Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)? > > ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess' > parameters (Artemis allows only numerical values for N)? > > Thank you. > > Regards, > > Abhinav Prabhakar (Mr.) >

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Jupyter/python question for Larch
by Garret Bland 04 Aug '20

04 Aug '20

Hello! I have a Python/Larch related question. I have been developing some python script via jupyter and incorporating Larch as a module. I was able to read an athena prj file with the following code *import larch as lc* *athena_prj = lc.io.read_athena(prjfilename)* Python stores this object as a 'Group' object with each spectrum being an instance. I would like to go through more processing with all spectra. Example: *for spectrum in athena_prj:* * lc.xafs.find_e0(spectrum.energy, spectrum.mu <http://spectrum.mu>, group = spectrum)* This does not work since the 'Group' object is not iterable. I tried to look up some other built-in functionality with python, but couldn't find an efficient way other than manually typing out each spectrum (athena_prj.spectrum1, athena_prj.spectrum2, .... etc). Is there any built-in functionality in larch that can iterate this 'Group' object? Any help would be appreciated. Thank you for your time! Garret -- Garret Bland PhD Student Carnegie Mellon University Civil and Environmental Engineering Porter Hall 201 Pittsburgh, PA, 15213

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Writing a Script for MD Simulations / Scripting Atoms
by David Sprouster 28 Jul '20

28 Jul '20

Dear IFEFFIT Experts, My colleagues and I are working on preparing Python scripts which: 1) run about 20,000 cif files from MD simulations through Atoms, 2) produce feff.inp files, 3) run feff.inp files through Feff (for XANES), 4) average all the XANES spectra. We are having trouble opening the stand alone Atoms program through Python – we can get Athena and Artemis to open, but for some reason Atoms will not. A snipet of our code which includes the file path is attached below. *Code:* ### def openAtoms(): try: subprocess.run([r"C:\Users\ADIAZ\AppData\Roaming\DemeterPerl\perl\site\bin\datoms.bat"]) except: print('Error') openAtoms() ### We have searched the Ifeffit archive for some answers but came up short, and we were wondering if anybody on the list has any suggestions for a potential fix to this problem? Additionally, has anybody prepared a similar series of scripts (in Python) to generate XANES spectra from MD simulations? We note that Marcus Karolewski did discuss something similar in a past post: https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02744.html Thanks in advance, Dave -- ---------------------------------------------------------------------------------- David J. Sprouster, Ph.D. Assistant Research Professor Department of Materials Science and Chemical Engineering Stony Brook University 222 Old Engineering Stony Brook, NY 11794 Phone: (631) 294-8983 web: http://stonybrook.edu/emrel ----------------------------------------------------------------------------------

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Cool math expression
by Anatoly Frenkel 19 Jun '20

19 Jun '20

I thought I share a really good idea I found in someone's fit project that was shared with me. Instead of varying deltaR and then doing something like: "after R_final = 2.79 + deltaR" to have Artemis calculate the actual bond length (and then looking for its uncertainty in the list of guess parameters in the log file for the corresponding deltaR variable's uncertainty), it can be written in the Artemis data window as: [image: image.png] where A_Cr is the bond length, and its uncertainty will be written in the same place with the best fit value in the guess parameters list. Probably I am the only one not using this trick, but I still thought it would be good to share. Anatoly

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Exporting fit from ARTEMIS_problem with k-weight
by Manju 19 Jun '20

19 Jun '20

Hello there I got an issue with k-weight of fit whileexporting the fit from ARTEMIS I fitted the data in k2, but it is exporting k3. I saved the fit at k2 weight and when I opened again, it was again set at k3. Is there any way I could choose the k-weight of my choice while exporting? Regards Manju Junior Research Fellow Department of Basic and Applied Sciences Punjabi University, Patiala- 147 002 Punjab, India.

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Ga standards
by Christian Wittee Lopes 17 Jun '20

17 Jun '20

Dear colleagues, Does anyone have the XANES spectra of the different Ga2O3 polymorphs (alfa, beta, gamma) and α-GaOOH? I'm treating some data and I need to rule out the presence of such phases in my samples. Thanks in advance!!! -- *Christian Wittee Lopes* *Postdoctoral Researcher* Institute of Physics, Universidade Federal do Rio Grande do Sul (UFRGS) Phone: +55 54 992430264

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Requested: NiFe2O4 Fe K and Ni K XAS spectra
by Valentijn De Coster 17 Jun '20

17 Jun '20

Dear mailing list, I am looking for Fe K and Ni K edge XAS spectra of NiFe2O4 - if possible, containing both the XANES and EXAFS region. Then again, if energy regions of 7100-7200 eV (Fe K) and 8320-8420 eV (Ni K) are available, this is already sufficient. Spectra obtained at room temperature would be much obliged. This is with the intention of a comparative study for XANES features of an as prepared Ni-Fe catalyst. Thank you in advance. Kind regards, Valentijn

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Re: [Ifeffit] FOLP error in Feff calculation
by Kewei Zhao 26 May '20

26 May '20

Dear Matthew, Thanks for the suggestion. The cluster structure is generated from molecular dynamics trajectories, and I just picked a random one out of 10k+ clusters. The Ca-Cl distance varies between 3-8 A. And not all calculations of Cl-containing clusters return such error. The cluster is not charge-neutral. But using the ION card did not solve the problem. Best, Kewei -- Kewei Zhao Ph.D. Student Myneni Lab Princeton University From: Matthew Marcus<mailto:mamarcus@lbl.gov> Sent: Tuesday, May 26, 2020 5:50 PM To: Kewei Zhao<mailto:keweiz@princeton.edu> Subject: Re: [Ifeffit] FOLP error in Feff calculation Here is your feff.inp, reworked as follows: 1. Subtract the position of Atom 0 (Ca) from all others. 2. Sort on distance from Ca, which is the new column. As you can see, a lot of the distances are way too close to Ca, which is a big atom. That may be part of the problem. Your lone Cl is almost 7A from the Ca. Was that intended? It does seem odd that this only happened when you included that distant atom. Also, I didn't count - is this cluster charge-neutral? Sincerely, Matthew Marcus On 5/26/2020 1:10 PM, Kewei Zhao wrote: > Dear colleagues, > > I'm using Feff to simulate the EXAFS of an aqueous Ca cluster. But I got this error when I tried to include Cl in the structure (potential type 0 is Ca, 1 is O, 2 is H, and 3 is Cl): > > Feff 8.50L > Ca in water > 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 > free atom potential and density for atom type 3 > 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 > overlapped potential and density for unique potential 3 > muffin tin radii and interstitial parameters > FOLP for POTENTIAL type 3 is too big. > Reduce overlap using FOLP and rerun > MOVRLP-1 > > If I change the type 3 atom to other elements or move its position, the error is gone. However, I do not want to change the input structure. Including FOLP or AFOLP cards in the input file did not work. Is there anyway to bypass this error? Please find my input file attached. > > Thanks, > Kewei Zhao > > -- > > Kewei Zhao > > Ph.D. Student > > Myneni Lab > > Princeton University > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >

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FOLP error in Feff calculation
by Kewei Zhao 26 May '20

26 May '20

Dear colleagues, I'm using Feff to simulate the EXAFS of an aqueous Ca cluster. But I got this error when I tried to include Cl in the structure (potential type 0 is Ca, 1 is O, 2 is H, and 3 is Cl): Feff 8.50L Ca in water 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 free atom potential and density for atom type 3 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 overlapped potential and density for unique potential 3 muffin tin radii and interstitial parameters FOLP for POTENTIAL type 3 is too big. Reduce overlap using FOLP and rerun MOVRLP-1 If I change the type 3 atom to other elements or move its position, the error is gone. However, I do not want to change the input structure. Including FOLP or AFOLP cards in the input file did not work. Is there anyway to bypass this error? Please find my input file attached. Thanks, Kewei Zhao -- Kewei Zhao Ph.D. Student Myneni Lab Princeton University

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Artemis crash upon empirical standard import.
by George Sterbinsky 22 May '20

22 May '20

Hello, I am trying to import an empirical standard (.es file created in Athena) into Artemis. Upon import, Artemis crashes. This occurs with both the latest mac and windows releases (0.9.25 on mac and 0.9.26 on windows). I have attached an Athena project file containing the data used to generate the .es file (Co1-13C-std) and the data to be fit (Co1-57C-toFit). I have also attached the .es file. Following the instructions at https://bruceravel.github.io/demeter/documents/Artemis/extended/empirical.h…, I import Co1-57C-toFit into Artemis and the choose "import an empirical standard" in the data window. When I choose the .es file from the file selection dialog, Artemis crashes. Thank you, George

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FEFF: problem with calculations of La and Eu XANES spectra with UNFREEZEF card
by Павел Засимов 15 May '20

15 May '20

Dear XAFS community, I have got a problem with FEFF9 calculations of La and Eu XANES spectra with UNFREEZEF card (The calculation don't converge, but it runs without any problems if I do not use UNFREEZEF card). This problem does not depend on the chemical form of the element (i.e. it occurs in La2O3, EuPO4, LaTp3, EuTp3, where Tp is trispyrazolylborate) and seems to be element-specific: the same feff.inp files where La/Eu are replaced with Ce or U are processed by FEFF program without the problem. To note, SCF settings were the same as recommended in the FEFF9.6 manual: SCF 3.7 0 30 0.05 10. Logfile (log1_er.dat), as well as an example of an input file (feff_er.inp), are attached to this mail. The fragment of logfile reporting about the error is shown below: Electronic configuration iph il N_el 0 0 1.683 Found bad counts. Occupation number in getorb is 4.000 Will repeat this iteration. 0 1 7.372 0 2 10.521 Found bad counts. Occupation number in getorb is 1.000 Will repeat this iteration. 0 3 0.727 ... 3 3 0.000 Core-valence separation Bad counts found repeatedly - pot will exit now. Did anyone notice anything similar? Thanks for any help, Zasimov Pavel

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Change in fixed baseline after fit in XAS Viewer
by George Sterbinsky 11 May '20

11 May '20

Hello, I have observed changes in fixed parameters while running a pre-edge peak fit in XAS Viewer. I first run a baseline fit. This provides a good match to the data in the baseline fitting region. I would like to subtract the baseline from the data and then numerically integrate the data. In order to export the baseline fit and data, I fix all of the fitting parameters for bline and bpeak and then click "fit model". This generates a baseline and fit that no longer match the data well in the baseline fitting region. Additionally, in the "Fit Results" window, the reported best-fit values of the fixed parameters are slightly different from the values reported in the "Value" field after the baseline fit, to which they were fixed. This appears to be the result of rounding of the baseline fit parameters at some point after the baseline fit. For example bline_slope was fixed to "-0.0024752483" but the best-fit value is "-0.00247500". I realize I am using XAS Viewer in a way that it was not exactly designed for, and perhaps no one anticipated someone fixing a parameter out to 10 decimal places. However, what I am doing still seems reasonable, and I would greatly appreciate it if XAS Viewer could be updated so that all digits entered in the Value field for a fixed parameter will be maintained for the fit. I am happy to provide a project file and instructions to reproduce my observation if they would be helpful. Thank you, George

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Reported W L3-edge and L2-edge energy
by Bare, Simon R 08 May '20

08 May '20

All: We are wondering if others agree that the reported values for the W L3 and W L2 edges are incorrect. We recently noticed the following: The "Edge" - defined by the inflection point of the absorption edge step When using the Ir L3 edge (11215.0 eV) as a calibration, the W L3- and L2-edges are 10203.4 eV and 11542.4 eV, respectively. When using the Pt L3 edge (11564.0 eV) as a calibration, the W L3- and L2-edges are 10203.3 eV and 11542.4 eV, respectively. These observations are thus different than the reported values of 10207.0 eV and 11544.0 eV for the L3 and L2 edges, respectively. Thanks in advance for the discussion and feedback. Simon R Bare Distinguished Scientist SSRL, MS69 SLAC National Accelerator Lab 2575 Sand Hill Road Menlo Park CA 94025 simon.bare(a)slac.stanford.edu<mailto:simon.bare@slac.stanford.edu> Ph: 650-926-2629 [co_access_logo_text]

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Re: [Ifeffit] Ifeffit Digest, Vol 207, Issue 14
by Christopher Chantler 07 May '20

07 May '20

Dear all This is an excellent thread. Just to give some background literature, you will be aware of the calibration of X-ray energies by diffraction (either like Kraft or better accuracy from the NIST group and Dick Deslattes, etc). This remains the best method for beamline calibration, though the mono is usually affected by heatload and detuning to shift the energies. [So you want either a 4-bounce or an analyser 'mono']. You will also be aware of the International Tables of Crystallography Volume C Section 4.2.2 [Not our XAFS one, Volume I, but the main Physical Tables Volume]. The old issue summarised a lot of details about current known and not-known accuracy of X-ray energies and is embedded in the NIST website, though the original publication[s] Deslattes et al. are in many ways superior. However, Volume C is coming out with a new edition [soon*] and the summary of the known and unknown accuracies and what to do about them is in the new section 4.2.2. It should be available this year, I understand. Secondly, by far the best edge energy determinations are those of Kraft et al., and these were based around the subset of transition metals and K edges. Most other edges have not been published with an absolute energy measurement, so they really do flop around in the literature. This is a major and important [urgent] task that maybe we can all help with. The issue of stability of lines, crystals etc. is a closely related and important issue. The issue is compounded at lower energies and for L edges. One of the best current examples is that of the recent Mendenhall et al. publication on copper... I hope this thread has emphasised the importance of this work and that we would all like more progress in this area Very best wishes Chris -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Friday, 8 May 2020 8:55 AM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 207, Issue 14 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. Re: Reported W L3-edge and L2-edge energy (Matthew Marcus) 2. Re: Reported W L3-edge and L2-edge energy (Mike Massey) ---------------------------------------------------------------------- Message: 1 Date: Thu, 7 May 2020 15:17:20 -0700 From: Matthew Marcus <mamarcus(a)lbl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Reported W L3-edge and L2-edge energy Message-ID: <c838484f-6689-8a82-78f3-a6ef211d1068(a)lbl.gov> Content-Type: text/plain; charset=utf-8; format=flowed For elements like P and S, people often use the energies of peaks. These are more immune to noise, energy-resolution effects and overabsorption than inflection points are. For instance, on ALS 10.3.2, I used the sulfate peak of gypsum set at 2482.74eV. I forget where I got that number. Going down to soft X-rays, a common convention for the carbon edge is to use a pair of sharp peaks in CO2 gas at 292.74 and 294.96eV. mam On 5/7/2020 3:09 PM, Mike Massey wrote: > Hi Matt, > > > Indeed, in my experience (which is limited to one beamline at one > synchrotron facility for P XAS), once it is calibrated, the energy > selection tends to be quite stable, so I think you're on-target there. > > The trouble I still run into, though, is comparability of data between > studies. The difficulty is magnified by the fact that people tend to > identify certain near-edge features by the energy range at which they > occur. I do the same, of course, but I also try to carefully document > the material and energy I used to calibrate the monochromator. > > For the P K-edge, it doesn't really seem like people have settled on a > convention for calibrating the monochromator, unlike in the case of > iron, for example (where one just uses a foil and sets some feature of > that spectrum to their preferred value). If everyone was using the same > thing all would be happy, but most people use different materials and > different values. So datasets for P at the K-edge really aren't too > comparable just yet. > > Sorry to hijack the conversation, it's just an issue I've been mulling > over for a few years. The discussion of energy calibration values made > me think of it again. > > > Best, > > > > Mike > > > > >> On May 8, 2020, at 8:51 AM, Matt Newville <newville(a)cars.uchicago.edu> >> wrote: >> >> ? >> Hi Mike, >> >> >> On Tue, May 5, 2020 at 10:56 PM Mike Massey <mmassey(a)gmail.com >> <mailto:mmassey@gmail.com>> wrote: >> >> On a tangentially related topic, I find that phosphorus K-edge XAS >> energy calibration conventions are still in a bit of a "Wild West" >> state, with a wide variety of materials and values in use for >> energy calibration. As an extreme example, one or two frequently >> cited papers in my field from the 2000s don't even report the >> material or value used for energy calibration, and only show >> portions of the spectra on an energy axis with values relative to >> an unknown E0. >> >> >> I have never measured a P K edge, or indeed any edge lower in energy >> than the S K edge (ignoring some X-ray raman work).? But if one is >> using a Si(111) double-crystal monochromator where P or S is >> approximately the low-energy (high-angle) limit, then it really should >> be that the calibration does not drift much and cannot be too wrong at >> low energies. >> >> That is, a mono calibration is controlled by a d-spacing and angular >> offset. Normally (or perhaps, in my experience), "re-calibrating" is >> done by changing the angular offset, leaving the d-spacing alone. >> That is, the d-spacing is presumably known, at least to within some >> thermal drift. >> If that is the case that the d-spacing really is not changing and what >> needs to be refined is the angular?offset, then setting the offset at >> relatively high energy edges will be much more sensitive, and changing >> the angular offset to that a high-energy edge is correct should move >> lower energy edges by a smaller amount.? ?The corollary is that you >> have to move the offset a lot to move the P? K edge around, and that >> would have a larger (and ever-increasing) impact on higher energy >> edges such as Ca, Fe, Cu or Mo. >> >> The counter-argument is also true:? d-spacing has a bigger effect on >> the high-angle / low-energy edges. >> >> So, if you believe the mono d-spacing (or you believe the beamline >> scientist who believes it ;)) then calibrate at the highest energy you >> can.? ?The Kraft values don't go very low in energy. >> >> All that said, if using a different mono crystal such as InSb or more >> exotic crystals, I have no idea how stable those are. >> >> >> I too have picked my own material and value, and will be the first >> to acknowledge that I did so out of necessity and ease of >> comparison to other available data, rather than because I thought >> it was correct. >> >> The issue of calibration conventions and values definitely seems >> to be one that merits continued discussion. It has been >> interesting to watch things evolve over time in the case of iron, >> for example (it's good to know that 7110.75 is a candidate >> calibration value...) I appreciate Matt's detailed thoughts, and >> the data that he's been working with. Thanks Matt! >> >> >> Cheers, >> >> >> >> Mike >> >> >> >> >> >>> On May 6, 2020, at 3:32 PM, Matt Newville >>> <newville(a)cars.uchicago.edu <mailto:newville@cars.uchicago.edu>> >>> wrote: >>> >>> ? >>> Hi Simon, >>> >>> This is definitely a timely discussion for me, as I've been >>> spending part of the quartine?working on collating data and >>> expanding datasets for an XAFS spectral database.? I'm hoping to >>> have something ready for public comment and to start asking for >>> contributions of data in a few weeks, but I'll be happy to have >>> more discussion about that sooner too. >>> >>> I generally believe that the monochromator I use at GSECARS is >>> both well-calibrated and reasonably accurate.? That is, with 2 >>> angular encoders with a resolution of >130,000 lines per degree >>> and an air-bearing, I believe the angular accuracy and >>> repeatability are very good.? I believe there are equally good >>> moons in existence.? ?As Matthew Marcus pointed to the Kraft >>> paper (which used an older source but 4-bounce mono to improve >>> resolution), we find that Fe foil is definitely?better defined as >>> 7110.75 and Cu foil is between 8980.0 and 8980.5 eV.? That is, >>> we've measured multiple foils, found their first derivatives, and >>> refined the d-spacing and angular offset.? We do this about once >>> per run, and the offsets tend to be very consistent.? ?For sure, >>> there is some question about whether the Kraft numbers are >>> perfect.? ?For sure, putting Fe foil at 7110.75?+/- 0.25 eV >>> appears to be "most right" to us. >>> >>> I also believe that we should probably re-measure these metal >>> foils (and other compounds) with a single calibration set for >>> both Si(111) and Si(311).? We will probably have time to do that >>> this summer in the time between "beamline staff can get back to >>> the beamline" and "open for outside users". >>> >>> What I can tell you now is:? I have some data on W metal, WO2, >>> and WO3 measured all at the same time on our bending magnet line, >>> with Si(111).? An Athena project for this is attached (W.prj). >>> ?I cannot vouch for the absolute calibration. >>> >>> I also attach a set of foils (V, Fe, Cu, Mo) measured with the >>> same calibration (and Si(111) on our ID line), after adjusting >>> d-space and offset?to be close to the Kraft values >>> (CalibratedFoils2013.prj). >>> >>> I also attach a set of foils (Fe, Cu, Au L3, Au L2, Au L1, Pb L3, >>> Pb L2, Pb L1 edges) measured in 2016 (again, using Si(111) on our >>> ID line), also with the same calibration values >>> (FeCu_Au_Pb.prj).? I'm pretty certain these use the same >>> d-spacing as the 2013 Foils to?at least 5 digits.? ?For >>> completeness, all of the raw data files are also under >>> https://github.com/XraySpectroscopy/XASDataLibrary/tree/master/data >>> >>> In my experience, the Pb L3 edge value has the biggest variation >>> in the literature, with values ranging from 13035 to 13055 eV >>> (possibly a typo somewhere along the line).? Fortunately, the >>> Kraft-based calibration splits the difference and puts the value >>> at 13040 eV. >>> >>> For W in particular, I will look if I have measured this recently >>> on our ID line.? I can tell you that I use CdWO4 as a phosphor >>> and use that to focus our X-ray beam.? ?I use this trick all the >>> time: any tail from the beam penetrating the phosphor is shortest >>> at the peak of the white-line and for CdWO4 that is always >>> between 10210 and 10215 eV. >>> >>> I hope that helps.? I am interested in trying to get all these >>> values as accurately as possible, so any comments or suggestions >>> would be most welcome. >>> >>> --Matt >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On Tue, May 5, 2020 at 5:14 PM Bare, Simon R >>> <srbare(a)slac.stanford.edu <mailto:srbare@slac.stanford.edu>> wrote: >>> >>> All:____ >>> >>> __ __ >>> >>> We are wondering if others agree that the reported values for >>> the W L3 and W L2 edges are *incorrect*. We recently noticed >>> the following:____ >>> >>> __ __ >>> >>> The ?Edge? ? defined by the inflection point of the >>> absorption edge step____ >>> >>> __ __ >>> >>> When using the Ir L_3 edge (11215.0 eV) as a calibration, the >>> W L_3 - and L_2 -edges are *10203.4 eV* and *11542.4 eV*, >>> respectively. ____ >>> >>> __ __ >>> >>> When using the Pt L_3 edge (11564.0 eV) as a calibration, the >>> W L_3 - and L_2 -edges are *10203.3 eV* and *11542.4 eV*, >>> respectively.____ >>> >>> __ __ >>> >>> These observations are thus different than the reported >>> values of *10207.0 eV* and *11544.0 eV* for the L_3 and L_2 >>> edges, respectively.____ >>> >>> __ __ >>> >>> Thanks in advance for the discussion and feedback.____ >>> >>> __ __ >>> >>> __ __ >>> >>> Simon R Bare____ >>> >>> /Distinguished Scientist____/ >>> >>> /SSRL, MS69____/ >>> >>> /SLAC National Accelerator Lab____/ >>> >>> /2575 Sand Hill Road____/ >>> >>> /Menlo Park CA 94025____/ >>> >>> __ __ >>> >>> simon.bare(a)slac.stanford.edu >>> <mailto:simon.bare@slac.stanford.edu>____ >>> >>> Ph: 650-926-2629____ >>> >>> __ __ >>> >>> <image001.png> >>> ____ >>> >>> __ __ >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> <mailto:Ifeffit@millenia.cars.aps.anl.gov> >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> Unsubscribe: >>> http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >>> >>> >>> >>> -- >>> --Matt Newville <newville at cars.uchicago.edu >>> <http://cars.uchicago.edu>> 630-252-0431 >>> <W.prj> >>> <CalibratedFoils2013.prj> >>> <FeCu_AuPb.prj> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> <mailto:Ifeffit@millenia.cars.aps.anl.gov> >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> <mailto:Ifeffit@millenia.cars.aps.anl.gov> >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> >> >> >> -- >> --Matt Newville <newville at cars.uchicago.edu >> <http://cars.uchicago.edu>> 630-252-0431 >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > ------------------------------ Message: 2 Date: Fri, 8 May 2020 10:54:07 +1200 From: Mike Massey <mmassey(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Reported W L3-edge and L2-edge energy Message-ID: <CC4875F1-C227-4726-8D25-CD597ED4592D(a)gmail.com> Content-Type: text/plain; charset=utf-8 I agree Matthew, I also tend to use the primary K-edge peak for P calibration, but one issue to be wary of is attenuation/flattening of the primary peak (if one is using a concentrated sample). Gypsum sounds like a good material to use for S, since it is commonly available and probably not too variable. My material of choice for P (lazulite) might fail on both counts, so it might be a poor choice. Mike > On May 8, 2020, at 10:19 AM, Matthew Marcus <mamarcus(a)lbl.gov> wrote: > > ?For elements like P and S, people often use the energies of peaks. These are more immune to noise, energy-resolution effects and overabsorption than inflection points are. For instance, on ALS 10.3.2, I used the sulfate peak of gypsum set at 2482.74eV. I forget where I got that number. Going down to soft X-rays, a common convention for the carbon edge is to use a pair of sharp peaks in CO2 gas at 292.74 and 294.96eV. > mam > >> On 5/7/2020 3:09 PM, Mike Massey wrote: >> Hi Matt, >> Indeed, in my experience (which is limited to one beamline at one synchrotron facility for P XAS), once it is calibrated, the energy selection tends to be quite stable, so I think you're on-target there. >> The trouble I still run into, though, is comparability of data between studies. The difficulty is magnified by the fact that people tend to identify certain near-edge features by the energy range at which they occur. I do the same, of course, but I also try to carefully document the material and energy I used to calibrate the monochromator. >> For the P K-edge, it doesn't really seem like people have settled on a convention for calibrating the monochromator, unlike in the case of iron, for example (where one just uses a foil and sets some feature of that spectrum to their preferred value). If everyone was using the same thing all would be happy, but most people use different materials and different values. So datasets for P at the K-edge really aren't too comparable just yet. >> Sorry to hijack the conversation, it's just an issue I've been mulling over for a few years. The discussion of energy calibration values made me think of it again. >> Best, >> Mike >>>> On May 8, 2020, at 8:51 AM, Matt Newville <newville(a)cars.uchicago.edu> wrote: >>> >>> ? >>> Hi Mike, >>> >>> >>>> On Tue, May 5, 2020 at 10:56 PM Mike Massey <mmassey(a)gmail.com <mailto:mmassey@gmail.com>> wrote: >>> >>> On a tangentially related topic, I find that phosphorus K-edge XAS >>> energy calibration conventions are still in a bit of a "Wild West" >>> state, with a wide variety of materials and values in use for >>> energy calibration. As an extreme example, one or two frequently >>> cited papers in my field from the 2000s don't even report the >>> material or value used for energy calibration, and only show >>> portions of the spectra on an energy axis with values relative to >>> an unknown E0. >>> >>> >>> I have never measured a P K edge, or indeed any edge lower in energy than the S K edge (ignoring some X-ray raman work). But if one is using a Si(111) double-crystal monochromator where P or S is approximately the low-energy (high-angle) limit, then it really should be that the calibration does not drift much and cannot be too wrong at low energies. >>> >>> That is, a mono calibration is controlled by a d-spacing and angular offset. Normally (or perhaps, in my experience), "re-calibrating" is done by changing the angular offset, leaving the d-spacing alone. That is, the d-spacing is presumably known, at least to within some thermal drift. >>> If that is the case that the d-spacing really is not changing and what needs to be refined is the angular offset, then setting the offset at relatively high energy edges will be much more sensitive, and changing the angular offset to that a high-energy edge is correct should move lower energy edges by a smaller amount. The corollary is that you have to move the offset a lot to move the P K edge around, and that would have a larger (and ever-increasing) impact on higher energy edges such as Ca, Fe, Cu or Mo. >>> >>> The counter-argument is also true: d-spacing has a bigger effect on the high-angle / low-energy edges. >>> >>> So, if you believe the mono d-spacing (or you believe the beamline scientist who believes it ;)) then calibrate at the highest energy you can. The Kraft values don't go very low in energy. >>> >>> All that said, if using a different mono crystal such as InSb or more exotic crystals, I have no idea how stable those are. >>> >>> >>> I too have picked my own material and value, and will be the first >>> to acknowledge that I did so out of necessity and ease of >>> comparison to other available data, rather than because I thought >>> it was correct. >>> >>> The issue of calibration conventions and values definitely seems >>> to be one that merits continued discussion. It has been >>> interesting to watch things evolve over time in the case of iron, >>> for example (it's good to know that 7110.75 is a candidate >>> calibration value...) I appreciate Matt's detailed thoughts, and >>> the data that he's been working with. Thanks Matt! >>> >>> >>> Cheers, >>> >>> >>> >>> Mike >>> >>> >>> >>> >>> >>>> On May 6, 2020, at 3:32 PM, Matt Newville >>>> <newville(a)cars.uchicago.edu <mailto:newville@cars.uchicago.edu>> >>>> wrote: >>>> >>>> ? >>>> Hi Simon, >>>> >>>> This is definitely a timely discussion for me, as I've been >>>> spending part of the quartine working on collating data and >>>> expanding datasets for an XAFS spectral database. I'm hoping to >>>> have something ready for public comment and to start asking for >>>> contributions of data in a few weeks, but I'll be happy to have >>>> more discussion about that sooner too. >>>> >>>> I generally believe that the monochromator I use at GSECARS is >>>> both well-calibrated and reasonably accurate. That is, with 2 >>>> angular encoders with a resolution of >130,000 lines per degree >>>> and an air-bearing, I believe the angular accuracy and >>>> repeatability are very good. I believe there are equally good >>>> moons in existence. As Matthew Marcus pointed to the Kraft >>>> paper (which used an older source but 4-bounce mono to improve >>>> resolution), we find that Fe foil is definitely better defined as >>>> 7110.75 and Cu foil is between 8980.0 and 8980.5 eV. That is, >>>> we've measured multiple foils, found their first derivatives, and >>>> refined the d-spacing and angular offset. We do this about once >>>> per run, and the offsets tend to be very consistent. For sure, >>>> there is some question about whether the Kraft numbers are >>>> perfect. For sure, putting Fe foil at 7110.75 +/- 0.25 eV >>>> appears to be "most right" to us. >>>> >>>> I also believe that we should probably re-measure these metal >>>> foils (and other compounds) with a single calibration set for >>>> both Si(111) and Si(311). We will probably have time to do that >>>> this summer in the time between "beamline staff can get back to >>>> the beamline" and "open for outside users". >>>> >>>> What I can tell you now is: I have some data on W metal, WO2, >>>> and WO3 measured all at the same time on our bending magnet line, >>>> with Si(111). An Athena project for this is attached (W.prj). I cannot vouch for the absolute calibration. >>>> >>>> I also attach a set of foils (V, Fe, Cu, Mo) measured with the >>>> same calibration (and Si(111) on our ID line), after adjusting >>>> d-space and offset to be close to the Kraft values >>>> (CalibratedFoils2013.prj). >>>> >>>> I also attach a set of foils (Fe, Cu, Au L3, Au L2, Au L1, Pb L3, >>>> Pb L2, Pb L1 edges) measured in 2016 (again, using Si(111) on our >>>> ID line), also with the same calibration values >>>> (FeCu_Au_Pb.prj). I'm pretty certain these use the same >>>> d-spacing as the 2013 Foils to at least 5 digits. For >>>> completeness, all of the raw data files are also under >>>> https://github.com/XraySpectroscopy/XASDataLibrary/tree/master/data >>>> >>>> In my experience, the Pb L3 edge value has the biggest variation >>>> in the literature, with values ranging from 13035 to 13055 eV >>>> (possibly a typo somewhere along the line). Fortunately, the >>>> Kraft-based calibration splits the difference and puts the value >>>> at 13040 eV. >>>> >>>> For W in particular, I will look if I have measured this recently >>>> on our ID line. I can tell you that I use CdWO4 as a phosphor >>>> and use that to focus our X-ray beam. I use this trick all the >>>> time: any tail from the beam penetrating the phosphor is shortest >>>> at the peak of the white-line and for CdWO4 that is always >>>> between 10210 and 10215 eV. >>>> >>>> I hope that helps. I am interested in trying to get all these >>>> values as accurately as possible, so any comments or suggestions >>>> would be most welcome. >>>> >>>> --Matt >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> On Tue, May 5, 2020 at 5:14 PM Bare, Simon R >>>> <srbare(a)slac.stanford.edu <mailto:srbare@slac.stanford.edu>> wrote: >>>> >>>> All:____ >>>> >>>> __ __ >>>> >>>> We are wondering if others agree that the reported values for >>>> the W L3 and W L2 edges are *incorrect*. We recently noticed >>>> the following:____ >>>> >>>> __ __ >>>> >>>> The ?Edge? ? defined by the inflection point of the >>>> absorption edge step____ >>>> >>>> __ __ >>>> >>>> When using the Ir L_3 edge (11215.0 eV) as a calibration, the >>>> W L_3 - and L_2 -edges are *10203.4 eV* and *11542.4 eV*, >>>> respectively. ____ >>>> >>>> __ __ >>>> >>>> When using the Pt L_3 edge (11564.0 eV) as a calibration, the >>>> W L_3 - and L_2 -edges are *10203.3 eV* and *11542.4 eV*, >>>> respectively.____ >>>> >>>> __ __ >>>> >>>> These observations are thus different than the reported >>>> values of *10207.0 eV* and *11544.0 eV* for the L_3 and L_2 >>>> edges, respectively.____ >>>> >>>> __ __ >>>> >>>> Thanks in advance for the discussion and feedback.____ >>>> >>>> __ __ >>>> >>>> __ __ >>>> >>>> Simon R Bare____ >>>> >>>> /Distinguished Scientist____/ >>>> >>>> /SSRL, MS69____/ >>>> >>>> /SLAC National Accelerator Lab____/ >>>> >>>> /2575 Sand Hill Road____/ >>>> >>>> /Menlo Park CA 94025____/ >>>> >>>> __ __ >>>> >>>> simon.bare(a)slac.stanford.edu >>>> <mailto:simon.bare@slac.stanford.edu>____ >>>> >>>> Ph: 650-926-2629____ >>>> >>>> __ __ >>>> >>>> <image001.png> >>>> ____ >>>> >>>> __ __ >>>> >>>> _______________________________________________ >>>> Ifeffit mailing list >>>> Ifeffit(a)millenia.cars.aps.anl.gov >>>> <mailto:Ifeffit@millenia.cars.aps.anl.gov> >>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>>> Unsubscribe: >>>> http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >>>> >>>> >>>> >>>> -- --Matt Newville <newville at cars.uchicago.edu >>>> <http://cars.uchicago.edu>> 630-252-0431 >>>> <W.prj> >>>> <CalibratedFoils2013.prj> >>>> <FeCu_AuPb.prj> >>>> _______________________________________________ >>>> Ifeffit mailing list >>>> Ifeffit(a)millenia.cars.aps.anl.gov >>>> <mailto:Ifeffit@millenia.cars.aps.anl.gov> >>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> <mailto:Ifeffit@millenia.cars.aps.anl.gov> >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >>> >>> >>> >>> -- >>> --Matt Newville <newville at cars.uchicago.edu <http://cars.uchicago.edu>> 630-252-0431 >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ------------------------------ Subject: Digest Footer _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ------------------------------ End of Ifeffit Digest, Vol 207, Issue 14 ****************************************

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 207, Issue 10
by Caliebe, Wolfgang 06 May '20

06 May '20

Dear All, there is another publication about high precision measurements of X-Ray Absorption Edges from the early 90ies from the same group: Measurement of the Energy of X‐Ray Absorption Edges J. Stümpel P. Becker St. Joksch R. Frahm G. Materlik First published: 16 April 1991 https://doi.org/10.1002/pssa.2211240224 The trick is that the authors don't use the monochromator in order to determine the energy of the edge, but instead an analyzer-crystal on a rotary stage with an encoder. This analyzer-crystal can be rotated to two different angles, where it fulfills the Bragg condition. Instead of measuring an absolute angle, they measure a difference of two angles, which is twice the Bragg-angle. This is more precise. They also measure the temperature of the crystal, which is essential to determine the lattice constant and to calculate the correct energy. More than 15 years ago, Syed Khalid used the values from the PTB-publications to calibrate the monochromator at X18b, and he used these values to determine the temperature of the monochromator crystal. All energies of the edges of the 3d-metals could be nicely reproduced, and the deviations from the PTB-values were rather small and not jumping by several eV as the Bearden-values from the yellow book. Unfortunately, the web-page got lost after NSLS was shut-down (at least, I cannot find it again). Syed tried to convince his users to use the PTB-values for calibration, but they all refused since they had used the old values for decades and did not want to switch. There might have been also users from UOP. Those, who listen to Jerry Seidler's Global XAFS Journal Club might remember the lecture by Joe Fowler: The tabulated values for the energies of fluorescence lines are ancient, some were still measured with photographic paper, and it is not much different for absorption edges. I agree with Matt that new values are required, and we should compare our results! With best regards, Wolfgang ----- Original Message ----- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Wednesday, 6 May, 2020 05:32:08 Subject: Ifeffit Digest, Vol 207, Issue 10 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. Re: Reported W L3-edge and L2-edge energy (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 5 May 2020 22:31:27 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Reported W L3-edge and L2-edge energy Message-ID: <CA+7ESbpcjj0QNkTNFTax9W2e=SB4JeezJ2Lmfb-KMEKsQotCAw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Simon, This is definitely a timely discussion for me, as I've been spending part of the quartine working on collating data and expanding datasets for an XAFS spectral database. I'm hoping to have something ready for public comment and to start asking for contributions of data in a few weeks, but I'll be happy to have more discussion about that sooner too. I generally believe that the monochromator I use at GSECARS is both well-calibrated and reasonably accurate. That is, with 2 angular encoders with a resolution of >130,000 lines per degree and an air-bearing, I believe the angular accuracy and repeatability are very good. I believe there are equally good moons in existence. As Matthew Marcus pointed to the Kraft paper (which used an older source but 4-bounce mono to improve resolution), we find that Fe foil is definitely better defined as 7110.75 and Cu foil is between 8980.0 and 8980.5 eV. That is, we've measured multiple foils, found their first derivatives, and refined the d-spacing and angular offset. We do this about once per run, and the offsets tend to be very consistent. For sure, there is some question about whether the Kraft numbers are perfect. For sure, putting Fe foil at 7110.75 +/- 0.25 eV appears to be "most right" to us. I also believe that we should probably re-measure these metal foils (and other compounds) with a single calibration set for both Si(111) and Si(311). We will probably have time to do that this summer in the time between "beamline staff can get back to the beamline" and "open for outside users". What I can tell you now is: I have some data on W metal, WO2, and WO3 measured all at the same time on our bending magnet line, with Si(111). An Athena project for this is attached (W.prj). I cannot vouch for the absolute calibration. I also attach a set of foils (V, Fe, Cu, Mo) measured with the same calibration (and Si(111) on our ID line), after adjusting d-space and offset to be close to the Kraft values (CalibratedFoils2013.prj). I also attach a set of foils (Fe, Cu, Au L3, Au L2, Au L1, Pb L3, Pb L2, Pb L1 edges) measured in 2016 (again, using Si(111) on our ID line), also with the same calibration values (FeCu_Au_Pb.prj). I'm pretty certain these use the same d-spacing as the 2013 Foils to at least 5 digits. For completeness, all of the raw data files are also under https://github.com/XraySpectroscopy/XASDataLibrary/tree/master/data In my experience, the Pb L3 edge value has the biggest variation in the literature, with values ranging from 13035 to 13055 eV (possibly a typo somewhere along the line). Fortunately, the Kraft-based calibration splits the difference and puts the value at 13040 eV. For W in particular, I will look if I have measured this recently on our ID line. I can tell you that I use CdWO4 as a phosphor and use that to focus our X-ray beam. I use this trick all the time: any tail from the beam penetrating the phosphor is shortest at the peak of the white-line and for CdWO4 that is always between 10210 and 10215 eV. I hope that helps. I am interested in trying to get all these values as accurately as possible, so any comments or suggestions would be most welcome. --Matt On Tue, May 5, 2020 at 5:14 PM Bare, Simon R <srbare(a)slac.stanford.edu> wrote: > All: > > > > We are wondering if others agree that the reported values for the W L3 and > W L2 edges are *incorrect*. We recently noticed the following: > > > > The ?Edge? ? defined by the inflection point of the absorption edge step > > > > When using the Ir L3 edge (11215.0 eV) as a calibration, the W L3- and L2-edges > are *10203.4 eV* and *11542.4 eV*, respectively. > > > > When using the Pt L3 edge (11564.0 eV) as a calibration, the W L3- and L2-edges > are *10203.3 eV* and *11542.4 eV*, respectively. > > > > These observations are thus different than the reported values of *10207.0 > eV* and *11544.0 eV* for the L3 and L2 edges, respectively. > > > > Thanks in advance for the discussion and feedback. > > > > > > Simon R Bare > > *Distinguished Scientist* > > *SSRL, MS69* > > *SLAC National Accelerator Lab* > > *2575 Sand Hill Road* > > *Menlo Park CA 94025* > > > > simon.bare(a)slac.stanford.edu > > Ph: 650-926-2629 > > > > [image: co_access_logo_text] > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-252-0431

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Re: [Ifeffit] Ifeffit Digest, Vol 207, Issue 8
by Christopher Chantler 05 May '20

05 May '20

Dear Simon, good work Currently most synchrotron beamlines will report calibrations of the edge according to the inflection point, or first peak in the derivative spectrum. As we know, this changes with experimental resolution, monochromation pre-edge structure and bandwidth, so is neither a fixed definition nor fully portable. However, apart from direct [powder or single crystal] diffraction measurement post monochromation, this is one of the best markers we have to date. The discrepancy you mention is quite large prima facie to be just the above, so more likely is a calibration error or even monochromation calibration error [of one or the other]. These studies are very important to make progress in the field and to cross-calibrate, and to question theoretical predictions based around the edge structure, which are ongoing. [PS I did not directly answer your question!] Best wishes Chris -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Wednesday, 6 May 2020 8:14 AM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 207, Issue 8 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. Reported W L3-edge and L2-edge energy (Bare, Simon R) ---------------------------------------------------------------------- Message: 1 Date: Tue, 5 May 2020 22:14:12 +0000 From: "Bare, Simon R" <srbare(a)slac.stanford.edu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Reported W L3-edge and L2-edge energy Message-ID: <MWHPR07MB38690FD1A9915311AC5859A491A70(a)MWHPR07MB3869.namprd07.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" All: We are wondering if others agree that the reported values for the W L3 and W L2 edges are incorrect. We recently noticed the following: The "Edge" - defined by the inflection point of the absorption edge step When using the Ir L3 edge (11215.0 eV) as a calibration, the W L3- and L2-edges are 10203.4 eV and 11542.4 eV, respectively. When using the Pt L3 edge (11564.0 eV) as a calibration, the W L3- and L2-edges are 10203.3 eV and 11542.4 eV, respectively. These observations are thus different than the reported values of 10207.0 eV and 11544.0 eV for the L3 and L2 edges, respectively. Thanks in advance for the discussion and feedback. Simon R Bare Distinguished Scientist SSRL, MS69 SLAC National Accelerator Lab 2575 Sand Hill Road Menlo Park CA 94025 simon.bare(a)slac.stanford.edu<mailto:simon.bare@slac.stanford.edu> Ph: 650-926-2629 [co_access_logo_text]

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Problem with XAS Viewer
by Xinyue Wang 04 May '20

04 May '20

Hi, I am Xinyue, a student who interested in using XAS Viewer. My issue is when I tried baseline fitting, I followed the document. But there was no region, no centroid, and no fitting line shown. Here is a screenshot of my work. Could you please help me with this? Thanks for your help. Thanks, Xinyue

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unable to export xdi file in xas viewer
by George Sterbinsky 04 May '20

04 May '20

Hello, When attempting to export an xdi file for a pre-edge peak fit in XAS viewer, the error message below prints to the terminal and the xdi file is not generated. I can provide the project file and instructions for generating the error message if that would be helpful. Thank you, George Traceback (most recent call last): File "/anaconda3/lib/python3.7/site-packages/larch/wxxas/prepeak_panel.py", line 369, in onExportFitResult yerr=yerr, x=x) File "/anaconda3/lib/python3.7/site-packages/larch/io/export_modelresult.py", line 60, in export_modelresult delta_fit = result.eval_uncertainty(result.params, **kwargs) File "/anaconda3/lib/python3.7/site-packages/lmfit/model.py", line 1488, in eval_uncertainty dval = pars[pname].stderr/3.0 TypeError: unsupported operand type(s) for /: 'NoneType' and 'float'

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Open postdoc position at DESY XAFS beamline
by Edmund Welter 30 Apr '20

30 Apr '20

Dear colleagues, in case you are interested in an interesting post doc position at a XAFS beamline at DESY in Hamburg (a place where you usually do not suffer from drought!) please have a look at the following job offer: https://www.desy.de/career/job_offers/index_eng.html?joboffer=103168 If you know of a colleague who might be interested please forward this mail to her/him. For any questions concerning the advertised position please do not hesitate to contact me via e-mail but please take care that you do not send your reply to the mail list. Best regards, Edmund Welter

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How Artemis handle crystal structure data with partial occupancy in vorlanite (cubic CaUO4)
by Dien.Li＠srnl.doe.gov 28 Apr '20

28 Apr '20

HI, Matthew and Bruce and Carlo As I want to fit a U L3-edge EXAFS spectrum using a crystal structure model of vorlanite (cubic CaUO4), I was not able to load the crystal structure data, with an error message of "could not input the data file because of partial occupancy" or something like this. I believe that the reason is that Ca and U are on the same site (coordination), and they are completely disordered, it is like (Ca,U)O2, a CaF2 structure, and the occupancy for each of Ca and U is 0.5. Is there any way to handling of such crystal structure data in Artemis? Please see the attached crystal data file in cif. Thank you so much for your instruction. Dien Li Savannah River National Laboratory

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Larch 0.9.47
by Matt Newville 18 Apr '20

18 Apr '20

Hi Everyone, Larch 0.9.47 is now available, with installers and source code at https://xraypy.github.io/xraylarch/installation.html. For python users, there is a plain python package available on PyPI and conda packages for Anaconda Python. See the installation docs for more details. There have been several improvements and bug fixes, especially for the XAS Viewer application and for XRF modeling in the nearly six months since the last release. In particular, there have been two improvements to basic XAFS and XANES data processing, both based on user reports and comparisons to older versions of Ifeffit/Athena and give a noticeable change in XAFS and XANES processing. First, the ranges used in by the pre_edge() function for finding the edge step for normalization are now better determined from the actual data range rather than simply being hard-wired numbers. These improvements were long over-due and give noticeably better default results for XANES data, especially for relatively low-energy edges such as S and Cl K edges. When reading Athena Project files (say, to import into XAS Viewer), the pre-edge and normalization ranges from the Athena Project file will be preserved. When reading in new raw data, or if you select the "Use Default Setting" button on the Normalization Panel for any group in XAS Viewer, the newer defaults will be used. You can always alter these values, but in playing around with this with a range of datasets, the new defaults seem to give a noticeable improvement in almost all cases and rarely bad. Second, as a few users have pointed out or gently hinted at over many months, there were sometimes significant differences in the background removals between classic Autobk/Ifeffit/Athena and Larch, with Larch sometimes being noticeably and inexplicably worse. I believe this involved two different problems. One was introduced a while back when implementing an estimate of delta_chi - the variance in chi due to the background subtraction. This estimate is important, but I botched some of the configurations of the number of knots, fit range, and Rbkg. The other problem was that "spline clamps" were just done too differently in Larch and Ifeffit/Athena. I believe this is now working much better: the background results are much more consistent, and do not occasionally get "very bad". They also happen to be generally closer to Autobk/Ifeffit/Athena, and perhaps slightly better because the fit range in R-space is now more consistently determined (instead of wandering +/- a few R data points around Rbkg where the misfit will often be the largest). In addition, `delta_chi` (never calculated in Ifeffit/Athena) is now also more consistent. One consequence of this change is that a very small change in Rbkg (of say 0.01 to 0.05 Ang) may actually give no difference at all in mu0(E) or in chi(k). I bring these changes up because I think they will be noticeable. I think they are both improvements, but let me know if you find cases for which you think are now made worse. Possibly related: one thing that I definitely noticed in going through several example data sets was that I tended to favor a k-weight of 2 instead of 1 for background subtraction -- so much so that it seemed like this might be a better default. I did not change this default yet, but if you have a strong opinion on this, that might be a good topic for discussion here. There are some documentation improvements, but this is an ongoing process and never complete. It is also one area where help and feedback would greatly be appreciated. If you or your students have time to work through the larch examples and/or documentation and make improvements or even suggestions for improvements in readability or completeness, it would be greatly appreciated. Thanks, --Matt Newville

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Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 206, Issue 8
by Dien.Li＠srnl.doe.gov 13 Apr '20

13 Apr '20

Hi, all I fitted my Cr EXAFS data, but E0 was -2.5. I calibrated the spectrum in energy space by +10 eV, the spectra in K and R space were identical before and after this calibration, in contract to my understanding that the k space oscillations and R magnitude should shift. Could you please provide any direction on how to get E0 to position values or negative E0 is acceptable? Thank you so much. Dien Li Savannah River National Laboratory -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Monday, April 13, 2020 12:04 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 206, Issue 8 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. Artemis crash upon empirical standard import. (George Sterbinsky) ---------------------------------------------------------------------- Message: 1 Date: Mon, 13 Apr 2020 11:02:34 -0500 From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Artemis crash upon empirical standard import. Message-ID: <CALoY8YzT1C+eGx_o2FUmwBbzRYYNeZL8tigM9zTzQMT0QKox5A(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello, I am trying to import an empirical standard (.es file created in Athena) into Artemis. Upon import, Artemis crashes. This occurs with both the latest mac and windows releases (0.9.25 on mac and 0.9.26 on windows). I have attached an Athena project file containing the data used to generate the .es file (Co1-13C-std) and the data to be fit (Co1-57C-toFit). I have also attached the .es file. Following the instructions at https://bruceravel.github.io/demeter/documents/Artemis/extended/empirical.h…, I import Co1-57C-toFit into Artemis and the choose "import an empirical standard" in the data window. When I choose the .es file from the file selection dialog, Artemis crashes. Thank you, George

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errors in bond lengths
by George Sterbinsky 13 Apr '20

13 Apr '20

Hello, As is well known, EXAFS is more accurate at determining relative changes in bond lengths than absolute changes in bond lengths due to cancelation of systematic errors in relative comparisons. When comparing the relative changes in bond lengths determined from EXAFS fits, as one might for a temperature series for example, is it appropriate to use the uncertainties returned by Artemis? My question arises in part from Phys Rev Lett vol. 100 pg. 055901 (2008), where the authors state that errors for changes in bond length in a temperature series were determined by empirical means rather than statistical means. This then raises the question as to if the authors believe that statistical means would overestimate the error. My inclination is to think that the uncertainties reported by Artemis would be appropriate because of the scaling by the square root of reduced chi squared. However, I want to see what others think about this before committing to it. Thank you, George

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larch can not deconvolve my data
by Shaofeng Wang 10 Apr '20

10 Apr '20

Dear all, Recently I am trying to deconvolve a As K-edge xafs data using larch. But the xas viewer program always crash. I tried other K edge spetra, it worked well. I attached my data, please give me some help. 祝好运！ Best regards, 王少锋，Shaofeng Wang, Ph.D 中国科学院沈阳应用生态研究所，Institute of Applied Ecology, CAS Email: wangshaofeng(a)iae.ac.cn; sf.wang(a)hotmail.com Address: Wenhua Road 72, Shenyang

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Fe 4+ reference
by George Sterbinsky 05 Apr '20

05 Apr '20

Hello, Does anyone have Fe K-edge XANES from an Fe4+ reference or sample (for example SrFeO3) that they can share? Thank you, George

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Re: [Ifeffit] Ifeffit Digest, Vol 206, Issue 1
by Christopher Chantler 04 Apr '20

04 Apr '20

Dear Anatoly and all Excellent question. The Guest Editors have been working very methodically and professionally through the manuscripts, with several undergoing multiple revisions. Today they have just submitted the last manuscript being the Guest Editorial, so I expect it will reach production within a couple of weeks [even with Covid]. In particular the referees have I believe kept everything to a high standard and perhaps that has taken an extra couple of revisions. Very best wishes to all Chris -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Friday, 3 April 2020 4:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 206, Issue 1 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. Chris Chantler, Re: XAFS conference proceedings (Anatoly Frenkel) 2. As(0) XAS spectrum (Richard Collins) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Apr 2020 14:22:06 -0400 From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Chris Chantler, Re: XAFS conference proceedings Message-ID: <CAFsMoZYbgj_YKE38Wv5kUiqeeCmQoiT2AJWJN93ai34PfDQFeA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Chris (if you are reading this), Do you know when the Rad. Phys. Chem. issue with the latest XAFS conference proceedings will be finalized and published online? It currently shows "corrected proofs" but not the articles with pages. Perhaps, it is a bad time to follow up and I am sorry for bothering you. Hope everyone is safe and well. Best regards, Anatoly

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As(0) XAS spectrum
by Richard Collins 01 Apr '20

01 Apr '20

Dear XAFS community, I’m writing to see if anyone has an As(0) K-edge XAS spectrum that they would be willing to share with me. A spectrum obtained at room temperature would be ideal. Many thanks in advance, Richard Dr Richard N Collins Senior Lecturer School of Civil and Environmental Engineering UNSW Sydney Sydney, NSW 2052, Australia Tel: (02) 9385 5214 From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of Anatoly Frenkel Sent: Thursday, April 2, 2020 5:22 AM To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Chris Chantler, Re: XAFS conference proceedings Dear Chris (if you are reading this), Do you know when the Rad. Phys. Chem. issue with the latest XAFS conference proceedings will be finalized and published online? It currently shows "corrected proofs" but not the articles with pages. Perhaps, it is a bad time to follow up and I am sorry for bothering you. Hope everyone is safe and well. Best regards, Anatoly

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Chris Chantler, Re: XAFS conference proceedings
by Anatoly Frenkel 01 Apr '20

01 Apr '20

Dear Chris (if you are reading this), Do you know when the Rad. Phys. Chem. issue with the latest XAFS conference proceedings will be finalized and published online? It currently shows "corrected proofs" but not the articles with pages. Perhaps, it is a bad time to follow up and I am sorry for bothering you. Hope everyone is safe and well. Best regards, Anatoly

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Question on (Combo-) LCF plot output
by t.zahoransky＠mineralogie.uni-hannover.de 30 Mar '20

30 Mar '20

Dear Mailing list, I am a relatively new user in terms of XAS data handling and I encountered a strange problem during LCF in Athena. I am working on LCF-combo fittings for Mn minerals as described in Manceau et al. 2012*. Fitting f.ex. a cryptomelane sample of myself with the open source monovalent manganese mineral standards of Manceau et al. 2012 in a fit range of -20 to +30 k, gives the following result shown below (I´ll attach the Athena project): " LCF fit of Cryptomelane_T_20K_ecd as flattened mu(E) from 6536.79 to 6586.79 Fit included 100 data points and 6 variables, and approximately 41.333 measurements Weights sum to 1: no Weights forced between 0 and 1: no Overall e0 shift used: yes Noise added to data: 0 R-factor = 0.0003537 Chi-square = 0.00815 Reduced chi-square = 0.0000858 . standard weight e0 ======================================================== . Manganosite.dat 0.042 (0.006) 1.631 (0.044) . Groutite.dat 0.030 (0.029) 1.631 (0.044) . Ca2Mn3O8.dat 0.288 (0.026) 1.631 (0.044) . Ramsdellite.dat 0.584 (0.022) 1.631 (0.044) . Mn2O3.dat 0.044 (0.025) 1.631 (0.044) . sum ........... 0.988 " Note that the box “all standards share an E0” is checked before clicking on “Fit this group”. Optically, the fit itself “looks” good compared to the data, yet, it is somewhat shifted on the x-axis compared to the data. I was wondering why, as this was not the first sample where this was the case. When I now uncheck the “All standards share an E0” box, leave everything else just the way it is and just click “Fit this group” again, the fit suddenly is shifted perfectly on my data. The strange thing is: Nothing else in the output-results changes – weights, R-factor, chi-square etc. just stay the same. Only slight changes in the numbers in brackets after the reported weights. The "new" result is: " LCF fit of Cryptomelane_Mikon_T_20K_ecd_reb-a-m as flattened mu(E) from 6536.79 to 6586.79 Fit included 100 data points and 5 variables, and approximately 41.333 measurements Weights sum to 1: no Weights forced between 0 and 1: no Overall e0 shift used: no Noise added to data: 0 R-factor = 0.0003537 Chi-square = 0.00815 Reduced chi-square = 0.0000849 . standard weight e0 ======================================================== . Mn2O3.dat 0.044 (0.024) 1.631 (0.000) . Manganosite.dat 0.042 (0.006) 1.631 (0.000) . Ca2Mn3O8.dat 0.288 (0.024) 1.631 (0.000) . Ramsdellite.dat 0.584 (0.019) 1.631 (0.000) . Groutite.dat 0.030 (0.026) 1.631 (0.000) . sum ........... 0.988 " Can anybody tell me, what is actually happening? I exported both data to excel to replot the fits to exclude a simple plot-bug, but the data behind show that this is real. So, I am changing the data behind the plot, but actually not the output data … what is going on here? You find the project attached – I hope someone can tell me, how to cope with that! Thank you very much, Teresa *Manceau, A., Marcus, M. A., & Grangeon, S. (2012). Determination of Mn valence states in mixed-valent manganates by XANES spectroscopy. American Mineralogist, 97(5-6), 816-827. -- Teresa Zahoransky Soil Mineralogy Gottfried Wilhelm Leibniz Universität Hannover Institute of Mineralogy Callinstr. 3, Room 325 D-30167 Hannover, Germany Phone: +49 (0)511 762-8058 Email: t.zahoransky(a)mineralogie.uni-hannover.de

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Yoshio Waseda database
by Pierre LECANTE 12 Mar '20

12 Mar '20

Dear XAS users, I have a problem and maybe you can help or point me to a suitable source: from time to time I used the database from Professor Yoshio Waseda, especially the structural database on molten metals measured by X-ray scattering, just like Farell-Lytle Database but for PDF studies; address was: http://ies.tagen.tohopku.ac.ip/~waseda/scm/AXS/index.html however it seems to be no more accessible and the change is relatively recent; any information on the problem or actually on a way to access such structural information should be greatly appreciated! sincerely, Pierre -- Groupe SINanO CEMES-CNRS, 29 rue Jeanne Marvig, 31055 Toulouse Cedex 4, France Tel: +33 (0)5 62 25 78 51, Fax: +33 (0)5 62 25 79 99 Email: lecante(a)cemes.fr http://www.cemes.fr/SINanO-Surfaces-Interfaces-et-Nano-Objets Full list of publications: http://www.researcherid.com/rid/A-8745-2011 http://orcid.org/0000-0001-6337-6855

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Unable to access content on millenia.cars.aps.anl.gov website
by Jullieta Lum 09 Mar '20

09 Mar '20

Good Day, I need assistance with accessing content on the iffefit website. I am subscribed to the mail list and receive the digest. However, I am unable to open any of the past questions and answers which I could do before. Hoping you can assist. Kind Regards, Jullieta

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PhD position in XAS for catalysis at ESRF
by Kirill LOMACHENKO 05 Mar '20

05 Mar '20

Dear all, it is my pleasure to inform you that we have opened a PhD position at BM23 and ID24 XAS beamlines of the ESRF (Grenoble, France). The focus of the PhD project is on the operando XAS and XES studies of novel industrial deNOx catalysts. The position is funded by a European program InnovaXN. The student will be hosted in ESRF, but will also have internships at Umicore Denmark (industrial partner) and University of Turin (academic partner). Full description of the project and the application form are here: https://esrf.gestmax.eu/1396/1/phd-position-operando-xas-dor-denox-catalysi… I would be grateful if you could forward this info to your colleagues and students who might be interested. Best regards, Kirill Lomachenko -- Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu

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APS/IIT XAFS Summer School Announcement
by Carlo Segre 20 Feb '20

20 Feb '20

The 2020 APS/IIT Summer XAFS School will be held from July 12-17, 2020 in Chicago. Please see attached document for details and contact Grant Bunker <bunker(a)iit.edu> by email for more information with the subject line "2020 XAFS School". -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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XAFS detection limit
by Christian Wittee Lopes 09 Feb '20

09 Feb '20

Dear all, Recently I was questioned about the EXAFS detection limit when describing different metal species in a bimetallic sample. By checking Pd and Cu K-edges, for example, I found Pd metal nanoparticles and CuO clusters, respectively. But additional techniques tell me I can have copper atoms in intimate contact with the Pd nanoparticles. What would be the minimum amount of these "single atoms" needed to be detected by EXAFS? is there a detection limit or it depends on several parameters? Thanks!!! -- *Christian Wittee Lopes* *Postdoctoral Researcher* Institute of Physics, Universidade Federal do Rio Grande do Sul (UFRGS) Phone: +55 54 992430264

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Re: [Ifeffit] Ifeffit Digest, Vol 204, Issue 1
by Christopher Chantler 07 Feb '20

07 Feb '20

Dear Christian and all I think we do not know yet, as the limits are getting better with improved techniques and error analysis, but it is a really good question. One can discuss limits from transmission versus fluorescence, in mM, in ppm; and separately perhaps in mass or mL or microL; or in e.g. atoms or molecules. I think every beamline has some guidelines, for their implementation. So yes it depends a lot on atomic number, density, need for a particular k range (e.g. XANES, normal XAFS, XERT etc.), beamline flux, and experimental method. Some of these estimates will be in the forthcoming International Tables for Crystallography, and earlier estimates are in earlier treatises. Best wishes, Chris -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Saturday, 8 February 2020 5:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 204, Issue 1 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. XAFS detection limit (Christian Wittee Lopes) ---------------------------------------------------------------------- Message: 1 Date: Thu, 6 Feb 2020 23:39:13 -0300 From: Christian Wittee Lopes <chriswittee(a)gmail.com> To: Ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] XAFS detection limit Message-ID: <CAJHLRaEz1SJ8dsA+WySAq4Uc2JR=cHApDQ+yZ+yHguqELU+tOw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear all, Recently I was questioned about the EXAFS detection limit when describing different metal species in a bimetallic sample. By checking Pd and Cu K-edges, for example, I found Pd metal nanoparticles and CuO clusters, respectively. But additional techniques tell me I can have copper atoms in intimate contact with the Pd nanoparticles. What would be the minimum amount of these "single atoms" needed to be detected by EXAFS? is there a detection limit or it depends on several parameters? Thanks!!! -- *Christian Wittee Lopes* *Postdoctoral Researcher* Institute of Physics, Universidade Federal do Rio Grande do Sul (UFRGS) Phone: +55 54 992430264

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XAFS.ORG WEBSITE??
by Bare, Simon R 30 Jan '20

30 Jan '20

Talking of websites does anyone know what happened to the International XAFS website? I can't access it. And what is going on with this organization? Thanks. Simon

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what happened to the website?
by Matthew Marcus 29 Jan '20

29 Jan '20

The http://millenia.cars.aps.anl.gov/ website seems to have gone off-line, which means that WebAtoms doesn't work anymore. Is there a replacement? Of course, I can use the stand-alone Atoms in Demeter. -- Sincerely, Matthew Marcus

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color of fonts in demeter
by Ricardo Faccio 29 Jan '20

29 Jan '20

Dear all After installing Demeter in MacOS I am having some problems related to the color of fonts and background. Since they look identical is diffcult to see and read. How could be possible to change the color of fonts? I am attaching an example. Best regards Ricardo -- ------------------------------------------------------------------------- Dr. Ricardo Faccio Prof. Agregado de Física (Assoc. Prof.) Mail: Área Física, DETEMA, Facultad de Química, Universidad de la República Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio(a)fq.edu.uy Phone: (+598) 2924 9859 (+598) 2929 0648 Fax: (+598) 2924 1906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm

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Fw: Re: request help about Zn standard spectra
by Qiang Chang 27 Jan '20

27 Jan '20

Dear Mauro, Thank you so much for your kind and quick help. Best reards, Qiang From: Mauro Rovezzi Date: 2020-01-27 09:45 To: ifeffit Subject: Re: [Ifeffit] request help about Zn standard spectra Dear Qiang, Here some Zn K-edge spectra from the SSHADE/FAME database: https://www.sshade.eu/search?db=fame&query=%22Zn%20K%20edge%22 Best regards, Mauro On 2020-01-26 21:06, Qiang Chang wrote: > Hi all, > > May I ask if you have some standard spectra for Zn elements, like > metallic Zn, ZnO, ZnNx, etc. I am vey appreciative if you could send me > some copies. > > Thank you very much. > > Best regards, > Qiang > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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request help about Zn standard spectra
by Qiang Chang 27 Jan '20

27 Jan '20

Hi all, May I ask if you have some standard spectra for Zn elements, like metallic Zn, ZnO, ZnNx, etc. I am vey appreciative if you could send me some copies. Thank you very much. Best regards, Qiang

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interesting job posting at NSLS-II
by Ravel, Bruce 25 Jan '20

25 Jan '20

Hi all, A colleague of mine here at NSLS-II has an interesting post-doc position open right now. https://jobs.bnl.gov/job/upton/postdoctoral-research-associate-in-total-sca… This position is for a person doing total scattering (aka PDF). Strictly speaking, not an XAS position, but perhaps of interest to someone with an XAS background who is looking for a post-doc. Regards, Bruce -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 6BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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smoothing XAS data
by Daria Boglaienko 23 Jan '20

23 Jan '20

Hello, In what case smoothing of the data is OK? My data have a lot of noise and smoothing really helps (visually). I compared fit done in Artemis for smoothed and non-smoothed data sets and the result is very similar, however when I searched about it online, it looks like it is not recommended. What is a good way to justify it? Thank you! -Daria

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Re: [Ifeffit] Ifeffit Digest, Vol 203, Issue 5
by Christopher Chantler 22 Jan '20

22 Jan '20

Dear all I agree with Mike and Scott too. I might suggest Schalken, M. J. and Chantler, C. T. "Preservation of uncertainty in experiment: structures of Ni (II) coordination complexes" (2018) J. Synchrotron Rad., 25, 920-934 as a partial discussion around this topic if people are interested. It could be read as 'don't smooth data if you can avoid it'. Very best wishes to all Chris -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Thursday, 23 January 2020 4:05 PM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 203, Issue 5 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. smoothing XAS data (Daria Boglaienko) 2. Re: smoothing XAS data (Carlo Segre) 3. Re: smoothing XAS data (Scott Calvin) 4. Re: smoothing XAS data (Mike Massey) 5. Re: smoothing XAS data (Will Bennett) ---------------------------------------------------------------------- Message: 1 Date: Wed, 22 Jan 2020 17:38:43 -0800 From: Daria Boglaienko <dbogl003(a)fiu.edu> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] smoothing XAS data Message-ID: <CAACWq8BmJFr0QNUHk1YrsB7w3BLGhzyus9pXow0Ng+ER3eAZDQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello, In what case smoothing of the data is OK? My data have a lot of noise and smoothing really helps (visually). I compared fit done in Artemis for smoothed and non-smoothed data sets and the result is very similar, however when I searched about it online, it looks like it is not recommended. What is a good way to justify it? Thank you! -Daria

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Larch Mac OS X 10.15 Catalina
by Jeff Terry 10 Jan '20

10 Jan '20

Hi Matt, I had to upgrade my Mac to OS X 10.15 and it blew up my Anaconda distribution which has forced me to reinstall everything from scratch. Now whether I install larch from source or by using conda, I get the following error: Traceback (most recent call last): File "/Users/jterry/anaconda3/lib/python3.7/ctypes/__init__.py", line 97, in CFUNCTYPE return _c_functype_cache[(restype, argtypes, flags)] KeyError: (None, (<class 'epics.dbr.access_rights_handler_args'>,), 1) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/jterry/anaconda3/bin/larch", line 11, in <module> load_entry_point('xraylarch==0.9.46', 'console_scripts', 'larch')() File "/Users/jterry/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 489, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/Users/jterry/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2852, in load_entry_point return ep.load() File "/Users/jterry/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2443, in load return self.resolve() File "/Users/jterry/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2449, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "/Users/jterry/anaconda3/lib/python3.7/site-packages/larch/__init__.py", line 50, in <module> from . import builtins File "/Users/jterry/anaconda3/lib/python3.7/site-packages/larch/builtins.py", line 33, in <module> from . import epics File "/Users/jterry/anaconda3/lib/python3.7/site-packages/larch/epics/__init__.py", line 9, in <module> import epics File "/Users/jterry/anaconda3/lib/python3.7/site-packages/epics/__init__.py", line 29, in <module> from . import ca File "/Users/jterry/anaconda3/lib/python3.7/site-packages/epics/ca.py", line 761, in <module> dbr.access_rights_handler_args) File "/Users/jterry/anaconda3/lib/python3.7/site-packages/epics/dbr.py", line 339, in make_callback return ctypes.CFUNCTYPE(None, args)(func) File "/Users/jterry/anaconda3/lib/python3.7/ctypes/__init__.py", line 99, in CFUNCTYPE class CFunctionType(_CFuncPtr): TypeError: item 1 in _argtypes_ passes a struct/union with a bitfield by value, which is unsupported. I think that line 11 is: load_entry_point('xraylarch==0.9.46', 'console_scripts', 'larch')() Any ideas on how to address this issue? Thanks, Jeff Jeff Terry Professor of Physics, Illinois Institute of Technology terryj(a)iit.edu

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X-ray analysis books available if you want them
by Mike Massey 08 Jan '20

08 Jan '20

Hi all, I have a small selection of x-ray books I'm happy to give you if you want them. Please contact me privately if you do. I'd rather give them away to a good home than send them to book heaven. Koningsberger and Prins, X-Ray Absorption Attwood, Soft X-rays and Extreme Ultraviolet Radiation Stohr, NEXAFS Spectroscopy Stock, MicroComputed Tomography RIMG vol 18, Spectroscopic Methods in Mineralogy and Geology ...And maybe one or two more. Kind Regards, Mike

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Installation problems on MacOS catalina, macports
by Ricardo Faccio 30 Dec '19

30 Dec '19

Dear all I followed al the instructions in https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.h…. In principle, I got a clean installation without errors. But when running athena I get: MacBook-Pro-de-Ricardo:~ rfaccio$ athena Can't locate Demeter/Here.pm in @INC (you may need to install the Demeter::Here module) (@INC contains: /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.4 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /opt/local/bin/athena line 7. BEGIN failed--compilation aborted at /opt/local/bin/athena line 7. Any hint will be appreciated. Best regards Ricardo -- ------------------------------------------------------------------------- Dr. Ricardo Faccio Prof. Agregado de Física (Assoc. Prof.) Mail: Área Física, DETEMA, Facultad de Química, Universidad de la República Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio(a)fq.edu.uy Phone: (+598) 2924 9859 (+598) 2929 0648 Fax: (+598) 2924 1906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm

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Re: [Ifeffit] Ifeffit Digest, Vol 202, Issue 8
by Christopher Chantler 17 Dec '19

17 Dec '19

Dear Fred and Matt, thanks for raising the notice for the IUCr 2020 in Prague. We [XAFS, CXAFS] have a strong list of speakers and XAFS sessions, together with all the Crystallography sessions. We also have a tutorial workshop the day before the Congress at the venue, which is free [with registration for the Congress] and especially for early career researchers, crystallographers finding out about XAS and students. We have been awarded two keynote speakers on XAS, together with nine XAS and XAS-related Microsymposia, including Fred's one: 1) Advanced Methods for analysis of XAFS and Crystallographic data 2) Spectroscopy applied to electrochemistry: operando studies 3) Catalysis: functionalized materials studied by XRD and XAFS 4) XAS and crystallography allied for geomaterials and environmental problems 5) Disordered materials: spectroscopic and scattering techniques 6) Matter at extreme conditions at SR and XFEL: complementarity of spectroscopy and diffraction 7) X-ray spectrometry and X-ray diffraction in Art and Archaeology 8) 4th generation SR and XFEL Facilities 9) Combining x-ray diffraction and spectroscopy to characterize materials We welcome all submissions, abstracts etc. and hope this will be a great programme. Prague is also a beautiful place. Very best wishes to everyone... Particular thanks to Giuliana, Sofia, Dibyendu, Valerie and all the session chairs. -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Wednesday, 18 December 2019 4:07 AM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 202, Issue 8 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. IUCR conference 202 prague (Mosselmans, Fred (DLSLtd,RAL,SCI)) 2. La-Oxide La K edge reference spectrum (Benedikt Eggert) 3. Re: La-Oxide La K edge reference spectrum (Barton, David (DG)) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 Dec 2019 07:53:14 +0000 From: "Mosselmans, Fred (DLSLtd,RAL,SCI)" <fred.mosselmans(a)diamond.ac.uk> To: "'ifeffit(a)millenia.cars.aps.anl.gov'" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] IUCR conference 202 prague Message-ID: <AM0PR01MB62282DF052E6E196004245A4A3500(a)AM0PR01MB6228.eurprd01.prod.exchangelabs.com> Content-Type: text/plain; charset="us-ascii" Please excuse this email, but I'd like to draw your attention to the IUCR congress<https://www.xray.cz/iucr/> in Prague next year, (August 22 -30). I'd like to draw your attention to a session I am co-chairing with Annalisa Martucci entitled "XAS and crystallography allied for geomaterials and environmental problems."<https://www.xray.cz/ctfc/chairs-speakers.asp?id=61> Professors Rizlan Bernier-Latmani and Giuseppe Cruciani will be our invited speakers. The abstract deadline for talks is 31/3/2020, while for posters it is 30/6/2020. (The International XAFS Society is affiliated to the IUCR and thus a number of the congress sessions are based on the use of X-ray Absorption Spectroscopy.) Regards Fred Mosselmans Principal Beamline Scientist I20 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7419362123 E fred.mosselmans(a)diamond.ac.uk orcid.org/0000-0001-6473-2743 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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La-Oxide La K edge reference spectrum
by Benedikt Eggert 17 Dec '19

17 Dec '19

Hello all, Has someone a reference XAS spectrum of La2O3 at the La K edge in his repository? Thanks a lot in advance for your help. Best regards, Benedikt -- -------------------------------------------------------------------- M.Sc. Benedikt Eggert Fakultät für Physik - AG Wende Universität Duisburg-Essen, MD 450 Lotharstraße 1, 47057 Duisburg, Germany Benedikt.Eggert(a)uni-due.de Tel.: +49203/379-2389 --------------------------------------------------------------------

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IUCR conference 202 prague
by Mosselmans, Fred (DLSLtd,RAL,SCI) 17 Dec '19

17 Dec '19

Please excuse this email, but I'd like to draw your attention to the IUCR congress<https://www.xray.cz/iucr/> in Prague next year, (August 22 -30). I'd like to draw your attention to a session I am co-chairing with Annalisa Martucci entitled "XAS and crystallography allied for geomaterials and environmental problems."<https://www.xray.cz/ctfc/chairs-speakers.asp?id=61> Professors Rizlan Bernier-Latmani and Giuseppe Cruciani will be our invited speakers. The abstract deadline for talks is 31/3/2020, while for posters it is 30/6/2020. (The International XAFS Society is affiliated to the IUCR and thus a number of the congress sessions are based on the use of X-ray Absorption Spectroscopy.) Regards Fred Mosselmans Principal Beamline Scientist I20 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7419362123 E fred.mosselmans(a)diamond.ac.uk orcid.org/0000-0001-6473-2743 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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PhD opportunity available at IMDEA Nanociencia/University Autonoma Madrid
by dooshaye.moonshiram 16 Dec '19

16 Dec '19

Dear Colleagues, The time-resolved spectroscopy group and theoretical chemistry group at IMDEA Nanociencia and University Autonoma Madrid, Spain is currently looking for a Ph.D student with intention to apply for by the “la Caixa” fellowship (https://obrasociallacaixa.org/en/investigacion-y-becas/becas-de-la-caixa/do…) Deadline: 4/02/2020. The project will consist in studying solar fuel catalysts through static and ultrafast in-situ X-ray spectroscopy and electrochemistry. The main objectives of the project will be to probe the electronic and structural changes occurring near the active catalytic site through time-resolved X-ray absorption, emission and resonant inelastic scattering spectroscopy. The student will also be trained in Raman, Electron Paramagnetic Resonance, and X-ray photoelecron spectroscopy. Quantum chemistry approaches will be used throughout the project’s duration to determine the geometries of proposed intermediates based on correlation of theory to spectroscopic observables. The results of these studies are expected to have a profound impact on modern catalysis research by identifying the critical requirements for water splitting reactions. For further information, please contact Dooshaye Moonshiram (dooshaye.moonshiram(a)imdea.org) or Antonio Picon (antonio.picon(a)uam.es) Best Regards, -- Dooshaye Moonshiram Group Leader IMDEA Nanociencia Calle Faraday 9, 28049 Madrid, Spain https://moonshiram.wordpress.com/

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Download Demeter in Ubuntu 18.04
by sri tapaswi 13 Dec '19

13 Dec '19

Hello all, Please guide me on the ways to download, install, and run Demeter software such as Athena on linux distribution, Ubuntu 18.04. Thanks, Sri Tapaswi Nori

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Mac installation error "Failed to build demeter"
by Rebecca Goncalves 09 Dec '19

09 Dec '19

Hi all, I'm getting this error message after entering the command "install xorg-server demeter": [image: Screen Shot 2019-12-02 at 9.52.07 AM.png] Has anyone encountered this issue when installing the program on a Mac? This is what the end of the suggested log files reads: [image: Screen Shot 2019-12-05 at 8.06.09 AM.png] Thanks, Rebecca

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Mac installation error "Failed to build demeter"
by Fowler, Joseph W. (Assoc) 05 Dec '19

05 Dec '19

Hi Rebecca, I am the macports maintainer of Demeter, and it certainly worked for me when I installed on my desktop Mac. But given your note, I decided to try installing demeter on my Mac laptop. To my surprise, I see the same error that you did. I don’t have a great idea what this signifies. How can ’string.h’ not be found?? If anyone out there can suggest how to fix this problem, I can try to get the macports version fixed. Otherwise, I’m stumped. Joe Fowler On Dec 5, 2019, at 11:36 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://gcc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c… or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. Mac installation error "Failed to build demeter" (Rebecca Goncalves) From: Rebecca Goncalves <rbg(a)u.northwestern.edu> Subject: [Ifeffit] Mac installation error "Failed to build demeter" Date: December 5, 2019 at 7:06:53 AM MST To: ifeffit(a)millenia.cars.aps.anl.gov Hi all, I'm getting this error message after entering the command "install xorg-server demeter": <Screen Shot 2019-12-02 at 9.52.07 AM.png> Has anyone encountered this issue when installing the program on a Mac? This is what the end of the suggested log files reads: <Screen Shot 2019-12-05 at 8.06.09 AM.png> Thanks, Rebecca _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov https://gcc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c… Unsubscribe: https://gcc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c…

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Mac installation error "Failed to build demeter"
by Rebecca Goncalves 05 Dec '19

05 Dec '19

Hi all, I'm getting this error message after entering the command "install xorg-server demeter": [image: Screen Shot 2019-12-02 at 9.52.07 AM.png] Has anyone encountered this issue when installing the program on a Mac? This is what the end of the suggested log files reads: [image: Screen Shot 2019-12-05 at 8.06.09 AM.png] Thanks, Rebecca

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Trouble with energy spacing in .nor files Athena
by Berryman, Eleanor (NRCAN/RNCAN) 22 Nov '19

22 Nov '19

I have run into a problem with Athena binning the energies of my imported spectra without being told to. This problem is best explained by example: I am processing XANES data collected around the Cr edge (5989 eV). I load a datafile that has data collected in 5 eV steps from 5789.2 to 5969.2 eV; in 0.5 eV steps from 5969.2 to 6019.2 eV; in 1 eV steps from 6019.2 to 6139.2 eV. In the 'Import Data' popup window (Athena: column selection), the preview of the raw data shows the current energy resolution. The raw data is processed in Athena using column 1 as Energy, column 10 as Numerator, and column 4 as denominator. 'Perform rebinning' is unselected. I save the processed data as norm(E) to produce the attached result, which has data in the following steps: 5 eV steps from 5789.2 to 5969.2 eV; 1 or 1.5 eV steps from 5970.2 to 6018.7; 1 or 2 eV steps from 6020.2 eV to 6138.2 eV. I have used the rebinning feature during import to circumvent this problem. When I rebin, the saved .nor file obeys the rebinned energy spacing. I need to find a better solution than this. I need to find a way for Athena to obey the energy spacing of the imported dataset. Details on my version of Athena: Demeter 0.9.26 Downloaded last week and today. Installation run as user and as administrator. The problem persists even after reinstallation. System details: 64-bit Windows 10 Operating System Thanks in advance for any direction in finding a solution to this problem. Eleanor Berryman, PhD Mineralogist & Geochemist, CanmetMINING Land & Minerals / Natural Resources Canada / Government of Canada eleanor.berryman(a)canada.ca<mailto:eleanor.berryman@canada.ca> / Tel : 613-995-4479 Minéralogiste & Géochimiste, CanmetMINES Secteur des terres et des minéraux / Ressources naturelles Canada / Gouvernement du Canada eleanor.berryman(a)canada.ca<mailto:eleanor.berryman@canada.ca> / Tél : 613-995-4479

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Illinois Tech Synchrotron Radiation Course
by Carlo Segre 22 Nov '19

22 Nov '19

Hello All: Illinois Tech is offering the graduate Introduction to Synchrotron Radiation course once again in Spring 2020. Please see the attached course summary. The course is offered online and it is very straightforward to apply as a non-degree graduate student as late as the second week of classes in January. The online course will be a one (1) credit course instead of the three (3) credits taken by degree-seeking Illinois Tech students. If you are interested or have interested students please contact me for more details on the course or how to apply and register. Cheers, Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Directory, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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selection of pixels by criteria
by E. Rasbury 22 Nov '19

22 Nov '19

I have used larch some for XRF maps. I like the feature for defining ROI's and then looking at the statistics of the data. I have some samples that are an intimate mix of two or more phases and I would like to extract pixels based on a criteria- like high Sr or low Fe, etc, from across a whole map region. I wonder if this feature is available, or would be easy to create on larch? Thanks! E. Troy Rasbury Associate Professor Department of Geosciences Stony Brook University Stony Brook NY 11794 631-632-1488

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no plot window with Demeter on Ubuntu 18.04
by Joseph Zsombor-Pindera 21 Nov '19

21 Nov '19

Dear mailing list members; I've successfully built Demeter from source on my computer running Ubuntu 18.04. Running "dathena", for example opens the familiar Athena window. Once I try to plot something, however, I get no plot window. It appears as if the program has done something, but the window just doesn't appear. I have installed gnuplot-x11. running 'gnuplot -e "plot sin(x)"' produces no window, but 'gnuplot -p -e "plot sin(x)"' produces a plot, and if I just run 'plot sin(x)' within gnuplot, then I get the plot, so it appears that gnuplot itself is working correctly. 'show terminal' results in: terminal type is wxt 0 enhanced I have tried changing the terminal to 'wxt' under preferences>gnuplot>terminal in Athena, which didn't fix the problem. I have also tried changing the terminal to 'qt' and installing gnuplot-qt. This didn't work, so I purged it and switched back to gnuplot-x11. I haven't managed to get gnuplot to run with x11 as its default terminal. It seems that the default terminal of gnuplot-x11 is wxt. I'm not sure if these matter, but when I run Athena, I get errors in the terminal like this: (dathena:16207): Gtk-CRITICAL **: 11:55:29.414: gtk_box_gadget_distribute: assertion 'size >= 0' failed in GtkCheckButton thanks, Joseph -- *Joseph Zsombor-Pindera, BSc* PhD Student, UBC Chemistry C

2 1

about WebAoms
by Park Gyuchul 20 Nov '19

20 Nov '19

Hi All, I am trying to simulate the EXAFS spectrum of pure molybdenum through FEFF9 software. I got the atomic configurations of molybdenum from molecular dynamics simulations, and I'd like to import it into FEFF 9. In order to do that, I converted lammps file into cif file, and I am trying to convert cif file into feff.inp. I am using Webatoms to convert cif file into feff.inp. The default value of cluster size and longest path is 8 and 5, respectively (in angs). However, when I try to increase the cluster size and the longest path to 10, it stops working, and I got the internal error. I am working with 1024 atoms (8x8x8 cells, bcc crystal structure). Are 1024 atoms too many to deal with in webatoms? or is there other ways to convert cif file into feff.inp? I don't have any problems when I use the ideal cif file (not from molecular dynamics simulations). Sincerely, Gyuchul Park

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Re: [Ifeffit] webatoms for large cluster
by Gentle, Cecilia M 20 Nov '19

20 Nov '19

Hi Gyuchul, Have you tried using Stand Alone Atoms (it comes with the demeter package) instead of webatoms? In my experience, stand alone atoms should not have a problem with 10 angstrom cluster. Hope this helps, Cecilia -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, November 20, 2019 12:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 201, Issue 11 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. about WebAoms (Park Gyuchul) ---------------------------------------------------------------------- Message: 1 Date: Wed, 20 Nov 2019 02:27:27 +0000 From: Park Gyuchul <park855(a)purdue.edu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] about WebAoms Message-ID: <MN2PR22MB209315A18585A0B381D2FEB9934F0(a)MN2PR22MB2093.namprd22.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hi All, I am trying to simulate the EXAFS spectrum of pure molybdenum through FEFF9 software. I got the atomic configurations of molybdenum from molecular dynamics simulations, and I'd like to import it into FEFF 9. In order to do that, I converted lammps file into cif file, and I am trying to convert cif file into feff.inp. I am using Webatoms to convert cif file into feff.inp. The default value of cluster size and longest path is 8 and 5, respectively (in angs). However, when I try to increase the cluster size and the longest path to 10, it stops working, and I got the internal error. I am working with 1024 atoms (8x8x8 cells, bcc crystal structure). Are 1024 atoms too many to deal with in webatoms? or is there other ways to convert cif file into feff.inp? I don't have any problems when I use the ideal cif file (not from molecular dynamics simulations). Sincerely, Gyuchul Park

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Including MS paths with an aggregate feff calculation in Artemis
by Jamie Hart 15 Nov '19

15 Nov '19

Dear mailing list subscribers, Is it possible to perform an aggregate feff calculation in Artemis, and then perform a fit using multiple scattering paths? It appears that the aggregate feff calculation is able to successfully compute MS paths, but Artemis will not let me include these paths in a fit. I am only able to perform an (aggregate) fit using single scattering paths. Please let me know if there is anything I can do to perform an aggregate fit with MS paths. Thank you, Jamie

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Installation problems for Demeter on Ubuntu 16.04
by Jo Melville 13 Nov '19

13 Nov '19

Hello all, I am having some troubles successfully building Demeter from source on my Linux machine. All dependencies appeared to install correctly -- a few errors pop up upon running ./Build test (full error report attached), but as best I could discern, the errors produced were the same as those reported in this recent message <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06782.html> ( https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06782.html ). Athena appear to install correctly and even start correctly, but upon attempting to import *any* data file into Athena, the following error message pops up (screenshot also attached): > 03:50:59 PM: Unknown warnings category 'experimental::script_run' at > /usr/share/perl/5.22/warnings.pm line 254. > warnings::Croaker("Unknown warnings category 'experimental::script_run'") > called at /usr/share/perl/5.22/warnings.pm line 332 > warnings::unimport("warnings", "experimental::script_run") called at (eval > 2455) line 1 > Pod::Simple::BlackBox::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > eval 'no warnings "experimental::script_run"; > qr/(*script_run: ^ .* $ )/x' called at > /usr/local/share/perl/5.22.1/Pod/Simple/BlackBox.pm line 74 > require Pod/Simple/BlackBox.pm called at > /usr/local/share/perl/5.22.1/Pod/Simple/LinkSection.pm line 7 > Pod::Simple::LinkSection::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Simple/LinkSection.pm called at > /usr/local/share/perl/5.22.1/Pod/Simple.pm line 9 > Pod::Simple::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Simple.pm called at /usr/share/perl/5.22/Pod/Text.pm line 34 > Pod::Text::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Text.pm called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/PluginRegistry.pm > line 13 > Demeter::UI::Athena::PluginRegistry::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Demeter/UI/Athena/PluginRegistry.pm called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm line 2114 > Demeter::UI::Athena::make_page(Demeter::UI::Athena=HASH(0x28f21b0), > "PluginRegistry") called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line 260 > Demeter::UI::Athena::IO::test_plugins(Demeter::UI::Athena=HASH(0x28f21b0), > "/home/melville/Documents/XAFS/Sample Projects/Athena and Arte"...) called > at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line > 168 > Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x28f21b0)) > called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm > line 890 > Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0xab38570), > Wx::CommandEvent=SCALAR(0xdaee6e0), Demeter::UI::Athena=HASH(0x28f21b0)) > called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm > line 808 > Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0xab38570), > Wx::CommandEvent=SCALAR(0xdaee6e0)) called at /usr/local/bin/dathena line 35 > eval {...} called at /usr/local/bin/dathena line 35 > > 03:50:59 PM: Unknown warnings category 'experimental::script_run' at > /usr/share/perl/5.22/warnings.pm line 254. > warnings::Croaker("Unknown warnings category 'experimental::script_run'") > called at /usr/share/perl/5.22/warnings.pm line 332 > warnings::unimport("warnings", "experimental::script_run") called at (eval > 2455) line 1 > Pod::Simple::BlackBox::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > eval 'no warnings "experimental::script_run"; > qr/(*script_run: ^ .* $ )/x' called at > /usr/local/share/perl/5.22.1/Pod/Simple/BlackBox.pm line 74 > require Pod/Simple/BlackBox.pm called at > /usr/local/share/perl/5.22.1/Pod/Simple/LinkSection.pm line 7 > Pod::Simple::LinkSection::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Simple/LinkSection.pm called at > /usr/local/share/perl/5.22.1/Pod/Simple.pm line 9 > Pod::Simple::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Simple.pm called at /usr/share/perl/5.22/Pod/Text.pm line 34 > Pod::Text::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Text.pm called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/PluginRegistry.pm > line 13 > Demeter::UI::Athena::PluginRegistry::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Demeter/UI/Athena/PluginRegistry.pm called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm line 2114 > Demeter::UI::Athena::make_page(Demeter::UI::Athena=HASH(0x28f21b0), > "PluginRegistry") called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line 260 > Demeter::UI::Athena::IO::test_plugins(Demeter::UI::Athena=HASH(0x28f21b0), > "/home/melville/Documents/XAFS/Sample Projects/Athena and Arte"...) called > at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line > 168 > Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x28f21b0)) > called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm > line 890 > Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0xab38570), > Wx::CommandEvent=SCALAR(0xdaee6e0), Demeter::UI::Athena=HASH(0x28f21b0)) > called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm > line 808 > Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0xab38570), > Wx::CommandEvent=SCALAR(0xdaee6e0)) called at /usr/local/bin/dathena line 35 > eval {...} called at /usr/local/bin/dathena line 35 > BEGIN failed--compilation aborted at (eval 2455) line 1. > Ignoring this message allows Athena to import data correctly at first, but clicking some buttons will consistently and immediately cause the program to close, without even an error message popping up. Actions that will induce a crash range from selecting any Energy value besides 1 in column selection to things as innocuous as clicking Help>Show Tip. As a result, though the program is (barely) usable, it is very unstable and prone to crashing without warning, causing frustrating data loss. I'm sure that this is due to some fault on my part during the installation process, and would welcome any guidance on how best to approach this issue. Thanks, Jo Melville -- Jonathan "Jo" Melville <https://stuff.mit.edu/~melville/> PhD Candidate, Surendranath Group <http://www.interphases.org/> (2016-) Contact: (620)-842-8756 *“People think of education as something they can finish.”* *--Isaac Asimov*

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Bug in Artemis
by Natasa Diklic 12 Nov '19

12 Nov '19

Greetings! I encounter an issue for which I find no explanation so far. When I try to export data and fit in k weight 2, the data gets exported in k weight 3 all the time. I can see that Artemis k weight is 2 but Artemis output k weight is 3. Everything was working properly until today. Does anyone knows how to change this Artemis output k weight? Thank you very much in advance! Natasa

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Problem with installation of demeter on MAC (Catalina v10.15)-Can't locate Demeter/Here.pm
by wei zhang 08 Nov '19

08 Nov '19

After installation of both xorg-server and demeter, when I launch Athena, the problem is as follows: Can't locate Demeter/Here.pm in @INC (you may need to install the Demeter::Here module) (@INC contains: /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.4 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /opt/local/bin/athena line 7. So, what should I do to solve this problem? Thank you all! Wei Zhang

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Solved concatenation bug Arrays.pm line 115
by FonsPaul 06 Nov '19

06 Nov '19

I wanted to update the mailing list on my encounter with a concatenation bug. I discovered that the cause was having (Japanese) Chinese characters in the pathname. Moving the folder solved the problem. Paul Fons

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Athena problem on MacOS 10.15
by FonsPaul 05 Nov '19

05 Nov '19

Hi All, I am using demeter on Mac OS 10.15 (the latest release) and am encountering some problems that I was hoping could be cleared up, in particular with Athena. The Athena version is 0.9.25, the latest version from MacPorts. Athena starts and properly plots existing projects without trouble, but trying to open a new data set using the PFBL12C plug in. From the Perl error messages below, it appears that the underlying cause is not from the Plugin, but from some problem within Demeter, with an uninitialized values in particular at line 115 that starts with the “my $text” assignment. Any ideas on what could be going wrong or what other debugging information might be useful. Paul Fons Arrays.pm sub get_array { my ($self, $suffix, $part) = @_; $part ||= q{}; if (not $self->plottable) { my $class = ref $self; croak("Demeter: $class objects have no arrays associated with them and are not plottable"); }; my $group = $self->group; my $text = ($part =~ m{(?:bkg|fit|res|run)}) ? "${group}_$part.$suffix" : "$group.$suffix"; my @array = $self->fetch_array($text); return @array; }; Perl error messages: 16:07:51: Use of uninitialized value $suffix in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Arrays.pm line 115. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 231. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 232. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 233. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 233. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 234. Fragment of example data set causing trouble 9809 SPring-8 01b1 GeTe_reference 19.10.31 11:20 - 19.10.31 11:22 Te standard Ring : 8.0 GeV 99.5 mA - 99.5 mA Mono : SI(311) D= 1.63747 A Initial angle= 7.06039 deg 01b1 Transmission( 2) Repetition= 1 Points= 4798 Param file : angle axis (1) Block = 1 Block Init-ang final-ang Step/deg Time/s Num 1 7.00000 6.52000 -0.000100 0.03 4798 Ortec( 0) NDCH = 4 Angle(c) Angle(o) time/s 2 3 4 Mode 0 0 1 2 1 Offset 0 0 49961.200 49083.900 1124.500 6.99980 7.00417 0.025 121003 450174 6.99970 7.00407 0.025 120103 447134 6.99960 7.00398 0.025 120212 447353 6.99950 7.00388 0.025 120465 448618 6.99940 7.00379 0.025 121167 450721 6.99930 7.00370 0.025 120510 448136 6.99920 7.00361 0.025 120907 450140 6.99910 7.00352 0.025 120063 446166 6.99900 7.00343 0.025 120656 449360 6.99890 7.00335 0.025 120901 450062 6.99880 7.00326 0.025 120820 449932 6.99870 7.00317 0.025 120655 448835 6.99860 7.00308 0.025 120869 449502 6.99850 7.00299 0.025 120818 449723 6.99840 7.00290 0.025 121239 450978 6.99830 7.00280 0.025 120744 449404

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Postdoctoral position
by Anatoly Frenkel 31 Oct '19

31 Oct '19

Our group has an opening for a postdoctoral position in heterogeneous catalysis. Expert knowledge of X-ray absorption spectroscopy and in situ/operando characterization of catalysts are required. The postdoc will be stationed at Brookhaven National Laboratory. For inquires, please email me at my Stony Brook University address, with a subject line: Postdoc in heterogeneous catalysis. Thank you, Anatoly Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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Fwd: 32 bit package for install
by Ravel, Bruce 28 Oct '19

28 Oct '19

http://bruceravel.github.io/demeter/#old -------- Forwarded Message -------- Subject: 32 bit package for install Date: Mon, 28 Oct 2019 20:30:40 +0200 From: Margaret Blazhynska <blazhynska(a)gmail.com> To: ifeffit-owner(a)millenia.cars.aps.anl.gov To whom it may concern, Could you please send me the 32-bit installer package of ifeffit? I am a student of a masters degree in Chemistry and I really need this pack to practice on XAS Thank you in advance -- Best regards, Margaret Blazhynska -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 6BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Issue with the Athena software - Athena Warning: redundant argument in sprintf
by Clarissa Baldo 15 Oct '19

15 Oct '19

Good Afternoon, I am a new user of the Athena software. I am trying to fit my XANES spectra using the linear combination fitting tools in Athena. However, every time I run the fitting I receive the following warning message: [cid:image002.png@01D58286.ED191450] Would you please give me some advice to solve this problem? I am using the latest version of the Demeter system (version 0.9.26) for windows. I have attached a copy of the warning log and a screenshot of the error. Thanks, Clarissa

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trouble installing Demeter from source on Ubuntu 18.04
by Joseph Zsombor-Pindera 15 Oct '19

15 Oct '19

Dear mailing list members; I'm trying to build Demeter from source according to Bruce Ravel's guide (https://bruceravel.github.io/demeter/documents/SinglePage/installation.html) I have mostly been able to install the dependencies, but I had trouble with the libwxgtk packages, so I installed 3.1.0 according to these instructions: https://gist.github.com/abdulhalim-cu/f3ae4be0b45baabef5623ccdd20ca584. wx-config --version results in: 3.1.0, so I think it's installed correctly. libgif4 is no longer in the repository, so I installed libgif-dev and libgif7. WxPerl 0.9932 is installed. Iffeffit is installed, and gnuplot-x11 and pgplot5 are installed. I ran ./Build installdeps and it ran but eventually got stuck in a loop saying "please tell me where I can find your apache src", which I ignored. The script terminated with "/usr/bin/make install -- OK" and then I installed apache2 anyways. Now, if I rerun it, it outputs "all prerequisites satisfied". I ran perl Build.PL, which seemed to complete successfully, and then finally ./Build and ./Build test, however ./Build test fails one test: Test Summary Report------------------- t/003_config.t (Wstat: 512 Tests: 22 Failed: 2) Failed tests: 17, 22 Non-zero exit status: 2 Files=44, Tests=2671, 89 wallclock secs ( 0.34 usr 0.07 sys + 85.03 cusr 3.94 csys = 89.38 CPU) Result: FAIL Failed 1/44 test programs. 2/2671 subtests failed. corresponding to: # Failed test 'configuration system introspection works: groups 38 artemis' # at t/003_config.t line 66. # Failed test 'introspection after reading new group: groups' # at t/003_config.t line 80. # Looks like you failed 2 tests of 22. t/003_config.t .......... Dubious, test returned 2 (wstat 512, 0x200) Failed 2/22 subtests line 80 in demeter/t/003_config.t is: ok( ($#groups == $number_of_groups), 'introspection after reading new group: groups'); I'm not sure what's going wrong here. Does anyone know how to resolve this problem? any help would be much appreciated, Joseph -- *Joseph Zsombor-Pindera, BSc* PhD Student, UBC Chemistry Cell: 514.804.0798 6201 Cecil Green Park Road Vancouver BC, V6T 1Z1 C

2 1

Geting Trouble in Fitting CuZr2 strucutr with Cu33Zr67 alloy using simulations
by Akash Deshmukh 11 Oct '19

11 Oct '19

I am trying to do EXAFS fitting using simulations for Cu33Zr67 (Cu33). After running lammps program, I have got.XYZ files for the Cu33. While running edamd command, I am not getting output files. However, the program is running continuously for more than 12 hours. I am considering CuZr2 crystal structure as an input file to fit with Cu33. Can anyone please help me to figure out this? _______________________________________________________________________________ With Best Regards, Akash A. Deshmukh, +91 9175477696

1 0

XAS fitting
by Wang, Maoyu 11 Oct '19

11 Oct '19

Hi I am running an EXAFS fitting for spinel Co3O4. As we know, the Co3O4 will have two different two local coordinations. One is 6 Co-O coordinated octahedral site, and another one is 4 Co-O coordinated tetrahedral site. When we run the Feff calculation, we can only use one Co site to do the calculation once, and we can only get one site coordination by one calculation. However, the EXAFS will tell us the average local structure. How could we use these two different calculation paths to do the fitting? Sincerely, Maoyu Wang Chemical Engineering Oregon State University wangma(a)oregonstate.edu 541-602-1707

3 2

software installation
by Shultz, Mary Jane 11 Oct '19

11 Oct '19

Has anyone had issues with software installation? I have installed it on a Windows machine (64 bit, 7 pro). It appears to install, but when I try to run it, it starts but immediately shuts down. Am I missing something? Thanks M Three colleagues are having the same issue.

3 3

Larch install error
by Mangold, Stefan (IPS) 05 Oct '19

05 Oct '19

Dear Matt, I tried to install larch via Anaconda. Install of Anaconda and larch seems to work fine, but I couldn’t create the Links via larch -m [numexpr.utils] INFO : NumExpr defaulting to 8 threads. Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/larch Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/larch --wxgui Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/xas_viewer Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/gse_mapviewer Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/gse_dtcorrect Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/xrfdisplay Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/dioptas_larch Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/xrd2d_viewer Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/xrd1d_viewer I have MacOS Sierra installed On a similar system I installed larch half a year ago without any issues. best regards Stefan Mangold

2 2

Mac problems
by Enrico Tusini 04 Oct '19

04 Oct '19

Hey there, I have this problem with the installation of Athena package on Mac Mojave : Failed to build pgplot: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_graphics_pgplot/pgplot/main.log for details. Error: Follow https://guide.macports.org/#project.tickets to report a bug. Error: Processing of port demeter failed I’ll be very thankful for any suggestion. Best regards Tusini Enrico

2 1

Install for Mac error
by Wu Xiaohan 03 Oct '19

03 Oct '19

Hello everyone, I tried to install demeter on my Mac and run Athena. And get the error shown below: 16:59:44: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 16:59:44: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 16:59:44: Name "Demeter::Templates::F" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 16:59:44: Name "Demeter::Templates::PT" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 16:59:44: Name "Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 16:59:44: Name "Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. I would like to ask help to correct this error. Thank you so much. Best regards Kelsey

2 1

Re: [Ifeffit] Fluorescence sample thickness
by Wallick, Rachel 01 Oct '19

01 Oct '19

The complex is 13% by mass of the absorbing element (Copper K-edge). The solvent will be acetonitrile and by control the concentration, I mean that I can dictate how much of the sample may be put into the capillary. I won’t be able to control the amount of the absorbing element. Rachel Wallick Chemistry Graduate Student | van der Veen Group University of Illinois at Urbana-Champaign 3011 Materials Research Laboratory

1 0

Fluorescence sample thickness
by Wallick, Rachel 01 Oct '19

01 Oct '19

I'm preparing for an XAS measurement in fluorescence of a solution-phase sample that will be measured in a capillary tube. I anticipate being able to control the concentration fairly easily, and I'm trying to figure out what the best capillary diameter would be. Is there a good way to figure this out? Rachel Wallick Chemistry Graduate Student Van der Veen Group University of Illinois at Urbana-Champaign 3011 Materials Research Laboratory

2 1

About Athena
by Pankaj Singh Rawat 30 Sep '19

30 Sep '19

Hey There, Good Morning.I am using Athena to analyse O-k edge XAS data. After uploading the data to the Athena, Fourier transform parameters are not showing. attaching a screenshot of home page. I'll be thankful to you for any suggestion. Thank you. hoping to hear from you soon. -- Pankaj Singh Rawat PhD Research Scholar GBPUA&T Pantnagar

2 1

Athena data uploading: Fourier transform parameters are not showing
by Pankaj Singh Rawat 30 Sep '19

30 Sep '19

Hey There, Do anyone have idea about following problem: I uploaded C-k edge on Athena but fourier transform parameters are not showing/open for modifications. Attaching the screenshot. Is this because of the data format of any software issue ? any suggestions? I'll be grateful to you for valuable suggestions. -- Pankaj Singh Rawat PhD Research Scholar GBPUA&T Pantnagar

2 1

Larch single-file installers problem on Mac
by 朱宥銓 17 Sep '19

17 Sep '19

Hi everyone, I had a problem when I tried to launch XAS software “Larch” on Mac through single-file installers. After I followed the tutorial and installed it (double click the dmg file), when I typed the command “larch”, the terminal showed the followings: could not read history from /Users/willie/.larch/history.lar [Errno 13] Permission denied: '/Users/willie/.larch/init.lar' [Errno 13] Permission denied: '/Users/willie/.larch/history.lar' [Errno 13] Permission denied: '/Users/willie/.larch/history_larchgui.lar' [Errno 13] Permission denied: '/Users/willie/.larch/matplotlib/README' [Errno 13] Permission denied: '/Users/willie/.larch/dlls' [Errno 2] No such file or directory: '/Users/willie/.larch/dlls/README' [Errno 13] Permission denied: '/Users/willie/.larch/modules' [Errno 2] No such file or directory: '/Users/willie/.larch/modules/README' [Errno 13] Permission denied: '/Users/willie/.larch/plugins' [Errno 2] No such file or directory: '/Users/willie/.larch/plugins/README' Traceback (most recent call last): File "//anaconda3/bin/larch", line 11, in <module> load_entry_point('xraylarch==0.9.46rc1', 'console_scripts', 'larch')() File "//anaconda3/lib/python3.7/site-packages/larch/apps.py", line 230, in run_larch cli = shell(quiet=options.quiet, with_wx=with_wx) File "//anaconda3/lib/python3.7/site-packages/larch/shell.py", line 56, in __init__ maxhistory=maxhist) File "//anaconda3/lib/python3.7/site-packages/larch/interpreter.py", line 177, in __init__ for pname in sorted(os.listdir(plugins_dir)): FileNotFoundError: [Errno 2] No such file or directory: '/Users/willie/.larch/plugins’ Does anyone face this problem as well? How can I fix this problem? Thank you, Youchiuan

2 1

Running FEFF 8 in Artemis
by Farideh Jalilehvand 16 Sep '19

16 Sep '19

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, but it does not generate paths that I can pick for fitting. The console shows that paths have been found, but does not write it. When I run FEFF outside the Artemis program, it does write the paths as the PRINT card in FEFF.inp file is set at (PRINT 1 1 1 3). So, greatly appreciate if you can help me finding a solution for this problem. Kind regards, Farideh ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Farideh Jalilehvand, Ph.D. Associate Professor, and Associate Head (Undergraduate) Department of Chemistry, University of Calgary 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada Tel: (403) 220-3855 / 220-5353│E-mail: faridehj(a)ucalgary.ca URL: http://www.chem.ucalgary.ca/research/groups/faridehj/

5 6

Larch 0.9.46
by Matt Newville 14 Sep '19

14 Sep '19

Hi Folks, Larch 0.9.46 is now available, with installers for Windows, MacOS, and Linux at https://millenia.cars.aps.anl.gov/xraylarch/ It has been several months since I announced a release. For XAFS and XANES analysis, there have been several recent improvements: - add reading and visualizations tools for RIXS plane data (thanks, Mauro Rovezzi!). - better support for reading older Athena Project files. I think all Athena files are now supported, but if you run into trouble, please send me the file you are having problems with. - better support for reading and parsing data files from more XAFS beamlines, at least those in North America. If you have data files that are not being read correctly (or even "well", including figuring out how columns should be labeled), please send an example file and how you expect it to read. - several fixes to the XAS Viewer application. There is still a To-Do list for this, but if you have suggestions, problems, or irritations using this, please let me know. There have been steady improvements in using Larch as a Python library, especially from Jupyter consoles and Notebooks. Some improvement in the docs and examples have been made. These are still behind but will continue to be worked on over the next few months. If you having any questions or suggestions, please let us know. --Matt Newville

1 0

Anyone use OCEAN?
by Matthew Marcus 12 Sep '19

12 Sep '19

OCEAN is the U. Washington program for doing XANES sims using ab-initio, Bethe-Salpeter methods (http://monalisa.phys.washington.edu/OCEAN/ocean-about.html) It seems to require a certain amount of experience and expertise to get it to produce any result, let alone correct results. I wonder if this might be a good forum for getting advice on solving problems with this code. Unlike ABINIT, which is one of the ab-inito engines OCEAN can use, OCEAN doesn't have a forum of its own. -- Sincerely, Matthew Marcus

1 0

Occupation number error getorb
by Patridge, Christopher 12 Sep '19

12 Sep '19

Hello, I have searched back on the mailing list regarding the occupation number error and found bad counts with getorb. I have tried a number of settings as per the email thread, however nothing seems to correct the error. I trying to calculate a vanadium oxide K-edge but as the earlier email stated, it just hangs trying to iterate SCF. This email was quite a while ago and just wondered if anyone has had these issues come up again and were able to find conditions that worked for them? Attached is the feff.inp which triggers this error. Any guidance or suggestions beyond the thread would be greatly appreciated, Thanks, Chris ********************************************** Dr Christopher Patridge Associate Professor Dept of Chemistry SASE 315 716-829-8096 | patridgc(a)dyc.edu<mailto:patridgc@dyc.edu> www.dyc.edu<http://www.dyc.edu> Social: Twitter<http://www.twitter.com/drpatridgc> [cid:0edd417e-b4aa-4ba7-af9d-5051c7441a0a@namprd14.prod.outlook.com]

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need version for 32 bit
by Seham Kamal 12 Sep '19

12 Sep '19

Dears, Good morning, Is it possible to send the version that works on 32 bit best regards Seham -- Seham K. Abdel-Aal (PhD) Lecturer, Physics department Faculty of Science, Cairo University 12613 Giza, Egypt Phone: 00201229131402 Email: seham(a)sci.cu.edu.eg Cairo University Scholar http://scholar.cu.edu.eg/?q=seham/biocv/cv Google scholar citation https://scholar.google.com/citations?user=VGVf2l0AAAAJ&hl=en Research gate page https://www.researchgate.net/profile/Seham_Kamal/publications -- **Disclaimer:** This E-mail represents the views of its author only and does not necessarily reflect the opinions of Faculty of Science (*SCI <http://www.sci.cu.edu.eg>*). We do not assume responsibility for any loss, damage (including direct, indirect, punitive, special, or consequential loss or damage), which you may directly or indirectly suffer from this email or its contents or through the ways of handling this email which includes sending, receiving, replying, forwarding, deleting, saving or changing and adjusting its content in any way.

2 2

Larch import error
by Patridge, Christopher 10 Sep '19

10 Sep '19

Good morning, I have OSX Larch installed and attempting to open XAS data files. It cannot read the file and Larch returns an error: Error trying to read '/Users/DrPatridge/Desktop/2019-03-21/CaVO_50-40-10_vs_Zn.002': _tmp_file_ = read_xdi('/Users/DrPatridge/Desktop/2019-03-21/CaVO_50-40-10_vs_Zn.002') ^^^ File /Users/DrPatridge/.larch/init.lar, line 1 File "/xraylarch/share/larch/plugins/io/xdi.py", line 258, in read_xdi xdif = XDIFile(filename, labels=labels) File "/xraylarch/share/larch/plugins/io/xdi.py", line 124, in __init__ self.read(self.filename) File "/xraylarch/share/larch/plugins/io/xdi.py", line 165, in read mvals = tostrlist(xdi.meta_values, self.nmetadata) File "/xraylarch/share/larch/plugins/io/xdi.py", line 65, in Py3tostrlist return [str(i, 'ASCII') for i in (nitems*c_char_p).from_address(address)] File "/xraylarch/share/larch/plugins/io/xdi.py", line 65, in <listcomp> return [str(i, 'ASCII') for i in (nitems*c_char_p).from_address(address)] UnicodeDecodeError: ('ascii', b'3.1356369 \xc3\x85', 10, 11, 'ordinal not in range(128)’) Is this a plugin error or something else? I attached one of the files if anyone could test? I can open it in Athena. Thanks for any help, Chris ********************************************** Dr Christopher Patridge Associate Professor Dept of Chemistry SASE 315 716-829-8096 | patridgc(a)dyc.edu<mailto:patridgc@dyc.edu> www.dyc.edu<http://www.dyc.edu> Social: Twitter<http://www.twitter.com/drpatridgc> [cid:0a129c79-2c47-40b9-8a0d-22bf08b7005d@namprd14.prod.outlook.com]

2 1

Fwd: 64-bit Demeter not able to use on Windows computer
by Ravel, Bruce 28 Aug '19

28 Aug '19

Brittany, In your first post to the mailing list, you said you could not get the software to run on "a Windows computer". That you are looking for a 32 bit installer seems like extremely relevant information. I no longer have the capacity to build 32 bit versions of the installer, but I keep links to old versions available on the Demeter website. http://bruceravel.github.io/demeter/#old The most recent version for which a 32 bit installer exists is 0.9.25. Somewhat dated, but should still be useful. B PS: Please send email to the mailing list ifeffit(a)millenia.cars.aps.anl.gov and please do not send email directly to ifeffit-owner. Matt and I are the only ones who read mail sent to ifeffit-owner and we don't guarantee a response to email sent to that address. -------- Forwarded Message -------- Subject: 64-bit Demeter not able to use on Windows computer Date: Wed, 28 Aug 2019 09:10:17 -0400 From: Brittaney Courchesne <bcourchesne(a)laurentian.ca> To: ifeffit-owner(a)millenia.cars.aps.anl.gov Hi everyone, The 64-bit version of Demeter is not able to be used on my Windows computer I have, since it is a 32-bit version. Is there a way around this or does someone have the 32-bit version they can email me? I have tried disabling my firewall completely and trying to "allow" the programs through the firewall, and running as an administrator, but the 64-bit just doesn't seem to work. Thank you, Brittaney -- */Brittaney Courchesne, G.I.T./* MSc Geology Candidate Harquail School of Earth Sciences Laurentian University Sudbury, ON /bcourchesne(a)laurentian.ca <mailto:bcourchesne@laurentian.ca>/ -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 6BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

QFS fit for Am
by Daria Boglaienko 22 Aug '19

22 Aug '19

Hello, I have tried quick first shell fit for various compounds, but it does not work for Am. It does run fit for organic compound of Eu but it does not run fit for similar organic compound of Am. Please, let me know if there is something I can take into account. Thank you -Daria

3 2

Unable to use 64-bit Demeter on Windows computer
by Brittaney Courchesne 21 Aug '19

21 Aug '19

Hello, I am just sending this email to see if anyone has encountered the following problem: I downloaded the newest 64-bit version of Demeter on my Windows computer, and it downloaded successfully, but now when I double click on the program, a tiny window pops up for about 0.5 seconds and then disappears. I have tried redownloading twice. Thank you very much, Brittaney -- *Brittaney Courchesne, G.I.T.* MSc Geology Candidate Harquail School of Earth Sciences Laurentian University Sudbury, ON *bcourchesne(a)laurentian.ca <bcourchesne(a)laurentian.ca>*

3 3

Two analysts, one spectrum, similar outcome?
by Mike Massey 14 Aug '19

14 Aug '19

Hi Everyone, I'm curious, has anyone ever tried turning two analysts loose on the same unknown EXAFS spectrum to see if their fits come out with similar conclusions? If you have tried it, how did it work out? Were the conclusions indeed similar? If not, why not, and what did you end up doing about it? I was talking with a colleague today about our plans for data analysis, and we settled on this approach (since there are two interested parties willing to try to fit a series of unknown EXAFS datasets). The hope is, of course, that the two analysts will independently reach similar conclusions with similar fits and structural models, but to my mind that outcome is by no means guaranteed. Given the (presumably) wide variation in fitting customs and procedures, I can envision a scenario in which there are major differences. This got me wondering, "Has anyone tried this?" So I thought I'd ask. Your thoughts and experiences would be welcome. Thanks! Mike Massey

5 8

Installation of Demeter on Mac Issue
by Lyu, Yimeng 12 Aug '19

12 Aug '19

Hello everyone, I run into to some issues with installing Demeter to a Mac. After installation, warning messages as below show up. Sometimes Athena will quit and sometimes it opens and works just fine. I searched the email archives and apparently the solution is to replace the Template.pm with an older version file. However, I cannot download the attachment from the email thread http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/009382.html , as the attachment was encrypted. Can someone send me the Template.pm file so I can resolve this issue? Thanks in advance. —Yimeng 16:21:44: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 16:21:44: Name "Demeter::Templates::F" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 16:21:44: Name "Demeter::Templates::PT" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 16:21:44: Name "Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 16:21:44: Name "Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 16:21:44: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236.

2 2

PhD opportunities
by Silvia Ramos 12 Aug '19

12 Aug '19

Dear All, I would like to share information about two funded PhD positions to work on Frustrated Magnetic Materials at the University of Kent, in the United Kingdom (https://www.kent.ac.uk/scholarships/search/FN26EXPHYS02) One of them (with me) is to work on the determination of local structure. I thought it might be of interest to this community. I will be happy to answer any queries from interested candidates. Best regards, Silvia Ramos ============================ Dr. Silvia Ramos Senior Lecturer in Materials Physics Director of Graduate Studies Ingram 230b School of Physical Sciences University of Kent Canterbury CT2 7NH U.K. Phone: (0)1227 816023 e-mail: s.ramos-perez(a)kent.ac.uk<mailto:s.ramos-perez@kent.ac.uk>

1 0

XAFS short course in BNL Nov. 13-15
by Anatoly Frenkel 01 Aug '19

01 Aug '19

Dear subscribers: The info about the XAFS2019 short course at BNL is here: https://www.bnl.gov/xafs2019/ The application page is open. Best, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

1 0

Trouble with MacOS 10.14 Mojave
by christophe den auwer 26 Jul '19

26 Jul '19

Hi all, I have to re-install Demeter on my Mojave MacBook (version 10.14.5). X code version 10.2.1 Well it didn't totally worked out…. When I launch either Athena or Artemis, this is what I get (bellow). I also notice I have a new « opt » directory directly on the hard disk (this seems a strange location). Does anybody have an idea about that ? Thanks a lot for your help Christophe ------------------------------------------------------------------------------ Christophe Den Auwer Professeur Université Côte d’Azur Institut de Chimie de Nice Parc Valrose 06108 Nice, France christophe.denauwer(a)univ-cotedazur.fr ------------------------------------------------------------------------------

3 4

averaging data
by Danielle Brown 18 Jul '19

18 Jul '19

How do I average two data sets in Athena? Thanks! — Danielle Brown Office: CSE L180 Cell: 317-605-9311 IIT '20 - BS Physics IIT ID: A20417782 dbrown45(a)hawk.iit.edu d.e.brown93(a)gmail.com

3 2

Beamline scientist position at NSLS-II
by Stavitski, Eli 17 Jul '19

17 Jul '19

Dear all, Beamline scientist position for the Inner shell Spectroscopy beamline is now open at NSLS-II. To read the full posting and apply please go to https://jobs.bnl.gov/job/upton/inner-shell-spectroscopy-beamline-scientist/…. Thanks, Eli. __________________________________ Eli Stavitski, PhD, Physicist Inner Shell Spectroscopy (ISS) Lead Beamline Scientist National Synchrotron Light Source-II Bldg. 743, Brookhaven National Laboratory Upton, NY 11973-5000 631 344 8641 istavitski(a)bnl.gov<mailto:istavitski@bnl.gov>

1 0

Fitting in Wavelet transform space ?
by Samy Ould-Chikh 10 Jul '19

10 Jul '19

Dear colleagues, I have been using more and more wavelet transform in parallel of EXAFS fitting. In addition of the statistical parameters provided after the fit, I try also to compare the wavelet transform of experimental data against various structural models to choose the best. Absolutely nothing new here. After applying the wavelet transform to tens of structural model in a row which was bit long, I asked myself this question: Why can't we simply fit the experimental spectra in "wavelet space" instead of R space/k-space ? Does someone know about a code already doing it ? Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa Website: http://kcc.kaust.edu.sa/Pages/Home.aspx

2 1

Demeter installation macOS Mojave pgplot Build Fail
by Reddy, Aidan 09 Jul '19

09 Jul '19

Hi, I am trying to install Demeter on my mac and am encountering the following error during installation: ---> Building pgplot Error: Failed to build pgplot: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_graphics_pgplot/pgplot/main.log for details. Error: Follow https://guide.macports.org/#project.tickets to report a bug. Error: Processing of port demeter failed Any suggestions to resolve this issue? Thanks, Aidan Reddy

1 0

How to install Demeter on ubuntu 18.04
by William Del Net 08 Jul '19

08 Jul '19

Dear people I tried to install demeter on computer with ubuntu 18.04. I ve found the Deavd Hughes guide to demeter installation on Ubuntu 12.04 There are some differencies and I tried to follow everything. Well, everything seem to be installed, but when I run dathena, i have the following error message opd30@joconde:~/demeter$ ./bin/dathena Can't locate Demeter/Here.pm in @INC (you may need to install the Demeter::Here module) (@INC contains: /home/opd30/perl5/lib/perl5/5.26.1/x86_64-linux-gnu-thread-multi /home/opd30/perl5/lib/perl5/5.26.1 /home/opd30/perl5/lib/perl5/x86_64- linux-gnu-thread-multi /home/opd30/perl5/lib/perl5 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /home/opd30/perl5/lib/perl5/5.26.0 /home/opd30/perl5/lib/perl5/5.26.0/x86_64-linux-gnu-thread-multi /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at ./bin/dathena line 7. BEGIN failed--compilation aborted at ./bin/dathena line 7. Here.pm is located in~/demeter/lib/Demeter. And yes, it's not in @INC. My home directory is /home/opd30 Do you have a solution, or a guide to install properly demeter on Ubuntu 18.04 Thanks a lot william -- > DEL NET William ESRF CRG-FAME 71 avenue des Martyrs F-38043 GRENOBLE CEDEX 9 tel: +33 4 76 88 25 46 fax: +33 4 76 88 27 43

2 1

Inversion Degree
by Carlos Triana Estupinan 06 Jul '19

06 Jul '19

Dear All Dear I have EXAFS spectra for spinel Co3O4, and I have to determine the inversion degree X, or the cation distribution of Co at the octaedral and tetraedrical sites. The EXAFS fitting can be performed employing two clusters of atoms, one having the absorbing atom in tetrahedral site and one having the absorbing atom in octahedral site. However, I do not know how to exactly determine the fraction of cations in octahedral or tetraedral sites from fitting the spectra with two sites independently. Could you please tell me how exactly should I proced, can I define a EXAFS fitting parameter giving me the cation distribution of Co at the octaedral and tetraedrical sites. If so, how can I do it. Thanks and best regards, -- *Carlos Augusto Triana Estupiñan* * M.Sc. Sciences - **Physics* *Physicist* * Tel: +57 322 256-2309*

3 2

Postdoctoral position is available
by Anatoly Frenkel 03 Jul '19

03 Jul '19

Dear mailing list subscribers, There is an opening for a postdoctoral research associate position, described briefly below (for more details please contact me). A postdoc will investigate novel electromechanical materials using NSLS-II beamline facilities at Brookhaven National Laboratory, with primary technique being X-ray absorption fine structure. This position will be in Stony Brook University (located in close proximity to Brookhaven), under the supervision of Prof. Anatoly Frenkel. Responsibilities will include setting up new in situ operations for testing novel materials under applied electric field, developing and applying fast timing methods (such as modulation excitation spectroscopy), and collaborating with other participants of the NSF-BSF funded US-Israel collaboration. Annual trips to Israel for collaborative research will be required. Ph.D. in Physics, Chemistry or Materials Science, and strong knowledge of XAFS experiment, data analysis and modeling, documented in publications, are required. Three names of professional references are required with the applications that should include a cover letter describing relevant prior experience and interest in the position, and a CV with a list of publications. These materials should be emailed to anatoly.frenkel(a)stonybrook.edu with a subject line: XAFS postdoc position. ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

1 0

EXAFS from FEFF9 in ARTEMIS (ver 0.9.26)
by Manju 21 Jun '19

21 Jun '19

Hi I am analyzing my data in ARTEMIS (ver 0.9.26). I used the Rietveld refined parameters of XRD data into ATOMS interface and used that for path calculation. But the paths were not at same distances as indicated by .CIF file (in Vesta). I am having FEFF9 with me. So, I want to run EXAFS in FEFF9 and import the paths in ARTEMIS for fitting. Is it possible? Manju Junior Research Fellow Department of Basic and Applied Sciences Punjabi University, Patiala- 147 002 Punjab, India.

1 0

Multiple species with Artemis
by Mukundan, Vineetha 17 Jun '19

17 Jun '19

Hi All, A couple of questions. I was searching the previous threads to check if someone here had posted/explained an example with mixing parameters to find the % content of different constituents present in a sample with Artemis. This is for shell-by-shell fitting. Can Artemis fit multiple chemical species/phases to the experimental spectra simultaneously? OR fit the samples spectra measured at 2 different edges with one or two phase simultaneously? Don't know if I searched far enough. Apology if it has been discussed. In that case, could anyone please direct me to those threads. Thanks you, Vineetha

2 2

Re: [Ifeffit] Ifeffit Digest, Vol 196, Issue 1
by Mahima Makkar 17 Jun '19

17 Jun '19

Dear Sir, This mail is regarding the quotation that you have sent. Please change the address to Prof. Ranjani Viswanatha ICMS JNCASR, Jakkur PO 560064 Bangalore, INDIA. Mail id: rv(a)jncasr.ac.in Please refer the mail id as mentioned above and resend the quotation. Thanks and regards, Mahima On Thu, Jun 13, 2019 at 10:30 PM <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. Problem with Demeter installation on mac OS Mojave (Ga?lle Creff) > 2. Re: Problem with Demeter installation on mac OS Mojave > (Ravel, Bruce) > 3. Re: Problem with Demeter installation on mac OS Mojave > (Ga?lle Creff) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 12 Jun 2019 22:52:54 +0200 > From: Ga?lle Creff <gaelle.creff(a)unice.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Problem with Demeter installation on mac OS Mojave > Message-ID: <D0FD0963-0C63-4B93-9E99-E56654370D21(a)unice.fr> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > I have some troubles with the installation of Demeter on my mac (under OS > Mojave since this week end). > Athena crashed after the following message: > "21:48:34: Name "Demeter::Templates::T" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > 21:48:34: Name "Demeter::Templates::F" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::DS" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::PT" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::S" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::D" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. ? > > Artemis does not work either. > > Can someone help me? > > Thanks a lot. > Ga?lle > >

1 0

Problem with Demeter installation on mac OS Mojave
by Gaëlle Creff 13 Jun '19

13 Jun '19

Hi everyone, I have some troubles with the installation of Demeter on my mac (under OS Mojave since this week end). Athena crashed after the following message: "21:48:34: Name "Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::F" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::PT" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. » Artemis does not work either. Can someone help me? Thanks a lot. Gaëlle

3 3

Athena labels
by Stoll, Andreas (IAM) 24 May '19

24 May '19

Hi, Is it possible to change the x- and y-axes labels in the athena plots (energy against normalized xµE)? Greetings Andi

2 2

Postdoctoral position at SSRL in XAS of catalysts
by Bare, Simon R 20 May '19

20 May '19

There is an opening for a postdoctoral research associate positon in the fall of 2019 at Stanford Synchrotron Radiation Lightsource (SSRL) at SLAC National Lab. This postdoctoral position will involve using in-situ/in-operando synchrotron-based methods, primarily X-ray absorption spectroscopy (XAS), to study all aspects of catalysis. The focus of the project will be in developing advanced methods in data processing, data analysis and data modeling. The candidate will join a group at SSRL, under the guidance of Dr. Simon Bare, though the Consortium for Operando and Advanced Catalyst Characterization via Electronic Spectroscopy and Structure (Co-ACCESS); https://www-ssrl.slac.stanford.edu/content/science/chemistry-catalysis. Full details at: https://careers.slac.stanford.edu/sites/careers.slac.stanford.edu/files/Pos… Please send a letter with CV and list of publications, and names of two references, to the address below: Simon R Bare, email: simon.bare(a)slac.stanford.edu<mailto:simon.bare@slac.stanford.edu>

1 0

Two postdoctoral openings at SBU and BNL
by Anatoly Frenkel 20 May '19

20 May '19

Dear mailing list subscribers, There are two openings for postdoctoral research associate positions, described briefly below (for more details please contact me). Position 1: A postdoc will investigate novel electromechanical materials using NSLS-II beamline facilities at Brookhaven National Laboratory, with primary technique being X-ray absorption fine structure. This position will be in Stony Brook University (located in close proximity to Brookhaven), under the supervision of Prof. Anatoly Frenkel. Responsibilities will include setting up new in situ operations for testing novel materials under applied electric field, developing and applying fast timing methods (such as modulation excitation spectroscopy), and collaborating with other participants of the NSF-BSF funded US-Israel collaboration. Annual trips to Israel for collaborative research will be required. Ph.D. in Physics, Chemistry or Materials Science, and expert knowledge of XAFS experiment, data analysis and modeling, documented in publications, are required. Position 2: Catalysis Center for Chemical Innovations (CCEI), an Energy Frontier Research Center (EFRC) at the University of Delaware, is hiring a postdoctoral research associate to work with multiple teams of catalysis researchers of CCEI on XAFS projects. The postdoc will lead collaborative efforts by helping develop synchrotron-based projects, plan experiments, lead the visiting researchers in data collection, and work with CCEI groups on subsequent publications. This position will be supervised jointly by Profs. Anatoly Frenkel (Stony Brook U.) and Jingguang Chen (Columbia U.). The postdoc will be stationed at Brookhaven National Laboratory and travel several times a year to U. Delaware for collaborative meetings. The background is recent Ph.D. in Chemistry or Materials Science. Strong background in catalysis and XAFS measurements, data analysis and modeling are expected. Three names of professional references are required with the applications that should include a cover letter describing prior experience and interest in the position, and a CV with a list of publications. These materials should be emailed to anatoly.frenkel(a)stonybrook.edu with a subject line: XAFS postdoc position. ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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(no subject)
by Sameh Ibrahim Ahmed 20 May '19

20 May '19

Dear collegues I need the XAFS or XANES spectra for some material to use them in my analysis. Actually, I am not sure if there is a library for the XAFS spectra for different compounds available free online !. In fact, I need the spectra for the following elements and their oxides with different oxidation states as well 1- Ni 2- Fe 3- Mo 4- V 5- Co 6- Mn Thank you in advance for your help. Best regards -- سامح إبراهيم أحمد أستاذ مساعد الفيزياء جامعة عين شمس Sameh Ibrahim Ahmed Associate professor of Physics Ain-Shams University Abbassia-11588 Cairo-EGYPT email: sameh(a)sci.asu.edu.eg & sameh2977(a)gmail.com

2 1

Larch 0.9.43
by Matt Newville 02 May '19

02 May '19

Hi Folks, Larch 0.9.43 is now available, with installers for Windows, MacOS, and Linux at https://millenia.cars.aps.anl.gov/xraylarch/installation.html If you already have installed Larch, you should be able to update to the latest version with ~> conda update -c gsecars xraylarch from a terminal on Linux or Mac OSX. On Windows, you may have to specify the full path with something like: C:\Users\<YourName>\AppData\Local\Continuum\xraylarch\Scripts\conda.exe -c gsecars xraylarch If you have any trouble upgrading, you can simply remove the xraylarch installation folder and reinstall. If you would like to install Larch into a different Python environment, please read https://xraypy.github.io/xraylarch/installation.html Version 0.9.43 has several improvements to the XAS Viewer GUI application, including: - better handling of read/write cycles of multiple Athena project files. - better default normalization and better control over normalization, especially for XANES data. - improved PCA analysis (in part from the recent discussion here with Joselaine Cáceres Gonzalez), so that it now reports IND values to help determine the number of components and reports eigenvalues from simple matrix inversion (not SVD) so that they more closely match those in the XAFS literature. - addition of Partial Least Squares and LASSO regression analysis for selection and prediction of external quantities (valence, for example) based on training sets of XANES data with known values for these quantities. This machine-learning approach is based on work of M Dyar, et al in a series of papers over the past several years. I encourage and request anyone interested, and especially MacOS users, to try out the XAS Viewer app and let us know what needs improvement. For people interested in using Larch from Python, Version 0.9.43 includes a complete refactoring of the code to make Larch work better as a "normal" Python library. Specifically, the previous code organization with most of the real analysis code in "plugins" has been replaced with all code now placed within the main larch module, still organized by topic. This improves packaging -- `pip install xraylarch` can now work. This code reorganization also means that the python programmer can use more normal imports to get at the Larch library so that one can simply do >>> from larch.xafs import pre_edge, autobk, xftf We also fixed a serious and deep flaw that selected a matplotlib plotting library too early, making larch difficult to use with Jupyter, Spyder, or other Qt-based GUIs. This is now fixed, and import statements like the one above can be seamlessly used in Jupyter notebooks. I should note that the documentation and examples are definitely lagging behind the code especially regarding the most recent developments, but this will be worked on. If you having any questions, trouble, or suggestions on any part of Larch, please let us know. --Matt Newville

3 4

Pseudo Voigt crash Athena
by Lawley Craig Richard (PSI) 02 May '19

02 May '19

Dear Mailing list, I have run into an issue with the peak fitting section included in Athena. If I include a peak that is a Pseudo-Voigt and then save the project file. Upon trying to reopen the same project file, Athena becomes non responsive with the error message "PV is not yet implemented". The log file for the crash is as follows: Started at 2019-05-01T17:37:06 Win7Enterprise (64-bit) Service Pack 1 Service Pack 16176012102561 PATH is: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\c\bin;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\perl\site\bin;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\perl\bin;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\c\bin\gnuplot\bin DEMETER_BASE is: C:\Users\lawley_c\AppData\Roaming\DemeterPerl IFEFFIT_DIR is: C:\Users\lawley_c\AppData\Roaming\DemeterPerl\c\share\ifeffit\ perl version: v5.24.0 backend: ifeffit @INC: C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/site/lib C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/vendor/lib C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/lib . Demeter version 0.9.26 Can't call method "SetValue" on an undefined value at C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena/PeakFit.pm line 916. -------- Where lines 910-920 in the PeakFit.pm file readout as: 910 if ($result == wxID_NO) { 911 $::app->{main}->status("Not deleting lineshape."); 912 return 0; 913 }; 914 ## demolish the LineShape object, if it exists 915 $this->{'lineshape'.$n}->DEMOLISH if exists $this->{'lineshape'.$n}; 916 ## dig through the hierarchy of the StaticBox and Remove/Destroy each element 917 foreach my $s ($this->{'func'.$n}->GetChildren) { 918 foreach my $w ($s->GetSizer->GetChildren) { 919 $w->GetWindow->Destroy if defined($w->GetWindow); I couldnt find any previous thread regarding this issue. If anyone knows a solution or could link me to a pre existing thread I would much appreciate it. Thanks in advance Craig _______ Paul Scherrer Institut Craig Lawley OFLB/U109 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 5054 E-Mail: craig.lawley(a)psi.ch<mailto:craig.lawley@psi.ch> www.psi.ch<http://www.psi.ch/>

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Demeter Mac issues
by Elizabeth Tomaszewski 29 Apr '19

29 Apr '19

Hello all, Is anyone currently using the Demeter package on a Mac? I have followed the instructions given and have the package installed. However, when I try to open Athena through the terminal window, it gets stuck on the opening Athena image and the question box asking "Athena found an autosave file would you like to import it?" I can open Artemis and Hephaestus, but get the error message as follows: 12:29:30: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 563. This message is repeated five times. Only after opening and closing each software several times can I get them to run. Any suggestions as to: 1) how to make the Demeter package run more smoothly and 2) how to get Athena to open at all. Thank you for your assistance, Beth Tomaszewski -- Dr. E J Tomaszewski Postdoctoral Researcher Eberhard Karls Universitaet Tuebingen Center for Applied Geoscience (ZAG) Geomicrobiology Sigwartstrasse 10 72076 Tuebingen Germany

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Question about PCA
by Joselaine Cáceres gonzalez 25 Apr '19

25 Apr '19

Dear all, I performed PCA in a set of 11 XANES spectra and I was trying to use some of the functions and tests developed by Malinowski to extract the number of primary components. I found differences between eigenvalues calculated whit a matrix calculator and those calculated by ATHENA, but they are equivalent in some way since they explain the same amount of variance and when I calculate the IND function or Malinowski F-test I reach the same conclusions. To calculate the eigenvalues with the matrix calculator I first normalized my data matrix (step height normalization) with ATHENA, then I export the data to an Excel spreadsheet where I centered them: z=(value-mean)/standard_dev. Then I used SVD and Eigenvalue decomposition to find the eigenvalues and those obtained with SVD explain exactly the same amount of variance than those found with ATHENA but they are different. In all the calculation I did, I used the same amount of points 161, points in each spectrum in ATHENA and in the matrix calculator, exactly the same energy interval. I´d like to know if I am missing some step in the data pre-treatment that is prevented me to find the same eigenvalues obtained by ATHENA but also I´d like to know if I can straight forward use the values obtained with ATHENA to evaluate the functions proposed by Malinowski since these equations might be different depending if calculations are made using "covariance about the origin" or "correlation about the origin" and I am not sure what is the case. Thanks in advance! Best regards Joselaine

2 5

can't open Athena 0.9.26!
by m.rezaie 23 Apr '19

23 Apr '19

Hi, I upgraded my DEMETER to DEMETER 0.9.26 but I can't open it on my computer which is Win 7, 32 bit. How can I solve this problem? Best Regards Mahsa

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2019 APS/IIT Summer XAFS School
by Carlo Segre 18 Apr '19

18 Apr '19

Greetings: The 2019 APS/IIT Summer XAFS School will be held on the Illinois Tech Campus from July 7, 2019 to July 12, 2019. Please see the attached announcement for details and information on how to apply. Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org it helps to get the year right > On Apr 18, 2019, at 10:38 AM, grant bunker <bunker(a)agni.phys.iit.edu> wrote: > > Greetings, All - I would appreciate your help in the disseminating this announcement > > thanks - Grant > > <2019 XAFS summer school announcement.pdf>

1 0

Regarding FEFF9
by Manju 18 Apr '19

18 Apr '19

Hi I am trying to see the effect of crystal defects on XANES. Is there any way that I could create charged vacancy in feff.inp file, before importing it into FEFF9? Regards Manju Manju Junior Research Fellow Department of Basic and Applied Sciences Punjabi University, Patiala- 147 002 Punjab, India.

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LANL EXAFS Postdoc position
by Daniel Olive 17 Apr '19

17 Apr '19

Greetings all, Los Alamos National Laboratory has a postdoc position involving EXAFS for use in nuclear forensics/actinide research. The vacancy name is IRC72104, linked below, and contains additional information. https://lanl.jobs/jobs/?q=IRC72104 Please have a look and/or forward to those who may be interested. Best, Dan -- ------------ Daniel Olive Los Alamos National Laboratory MST-16: Nuclear Materials Science P.O. Box 1663 MS E574 Los Alamos, NM 87545 Chemical Sciences Division Lawrence Berkeley National Laboratory ------------

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Re: [Ifeffit] Demeter - Athena Warning, crashing
by Ravel, Bruce 16 Apr '19

16 Apr '19

Hi, The Demeter problem that presents itself with error messages like: 15:36:09: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. is one that comes up pretty often here on the mailing list. It is also a problem that is already solved on github, but I haven't made a new release in quite some time. The solution to this particular problem is shown here: https://github.com/bruceravel/demeter/blob/master/lib/Demeter.pm#L994-L996 You could simply edit the copy of Demeter.pm on your computer to have the three lines highlighted at that link. Or you could click the "Raw" button at the top of that page, then save the raw file in place of Demeter.pm on your computer. A bit more effort would be to remove the version of Text::Template that is on your computer and install an older version of Text::Template on your computer. This one should work: https://metacpan.org/release/MJD/Text-Template-1.46 The bottom line is that Demeter uses a perl module for which the documentation of a feature and its implementation used to agree and, at some point, stopped agreeing. The fix that I link to above addresses that problem, but the specific combination of Demeter and Text::Template that makes it onto some people computers expose this problem. Any of the solutions explained above should address this in the short term. Eventually I will make a new release and this problem will go away. Until then, hopefully people will find this email. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 6BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Demeter - Athena Warning, crashing
by natalia martin 16 Apr '19

16 Apr '19

Hi, I have just installed Demeter on my Mac and get the following error when trying to Launch ATHENA: 15:36:09: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::PT" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::F" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. I saw a previous post from Chris on the 2018-04-02 with a similar error ("Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 563, line 236.) which was solved by replacing the /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm With another template from p5.24. https://www.mail-archive.com/search?l=ifeffit@millenia.cars.aps.anl.gov&q=s… <https://www.mail-archive.com/search?l=ifeffit@millenia.cars.aps.anl.gov&q=s…> This solution does unfortunately now work for my case. Does anyone have an idea of how this error can be fixed? Best, Natalia

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job offers
by Kristina KVASHNINA 12 Apr '19

12 Apr '19

Dear Ifeffit Colleagues, There are two positions available at Rossendorf Beamline of ESRF, Grenoble, France. We are looking for a PhD student and a Postdoc to work on TOP project (Towards the bottom of the periodic table), funded by the European Research Council. Please could you share this with anyone who might be interested in applying? Thank you in advance! Kind regards, Kristina http://www.esrf.eu/files/live/sites/www/files/Jobs/giant/ROBL_Postdoc_4-1.p… http://www.esrf.eu/files/live/sites/www/files/Jobs/giant/ROBL_phd_student_2… -- Kristina Kvashnina Rossendorf Beamline (BM20) The European Synchrotron (ESRF) 71, avenue des Martyrs 38000 Grenoble, France tel +33(0)476882367 TOP group website https://www.hzdr.de/db/Cms?pNid=787

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Energy resolution issue [DLM=For-Official-Use-Only]
by JOHANNESSEN, Bernt 11 Apr '19

11 Apr '19

Hi there, I'm using a Demeter 0.9.26 download to display data in Athena. My raw data was converted into ascii readable format retaining a measured 0.25 eV step size through the XANES region. However, Athena seems to inexplicably change the plotted step size to 1.00 eV. I've reinstalled Demeter/Athena without any luck. I also have an older version of Athena (0.8.056) that can display the data with the correct / measured step size of 0.25 eV without any issues. Any idea why Demeter is messing up my energy resolution when I have not changed a single default parameter? Cheers, Bernt Dr. Bernt Johannessen Senior Scientist - XAS Australian Synchrotron Tel Email Web +61 3 8540 4240 berntj(a)ansto.gov.au<mailto:berntj@ansto.gov.au> www.ansto.gov.au<http://www.ansto.gov.au/> [fb]<https://protect-au.mimecast.com/s/0PdECwVLQmilZ0PocqY_I0?domain=facebook.com> [tw] <https://protect-au.mimecast.com/s/dwZYCxnMRvtEqmBZTYpBHF?domain=twitter.com> [ln] <http://www.linkedin.com/company/ansto> [yt] <http://www.youtube.com/user/ANSTOVideos> [ansto]

2 1

Import Error
by Clark Adam Hugh (PSI) 06 Apr '19

06 Apr '19

Dear Bruce and Lucy Thanks for your work around Lucy, it works perfectly but still doesn't explain the behavior I am observing. Bruce what other information would be useful to diagnose the problem I am currently having? I have attached two figures, one showing the import window with the setting I have been using, specifically that I am not using the rebin feature. The second figure shows the difference in the pre-edge region between importing the data with eV and keV units for the energy column to demonstrate clearly that resampling is occurring when importing with data that has an energy column of KeV. Many Thanks Adam Clark __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/129 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark(a)psi.ch -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Freitag, 5. April 2019 15:20 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 194, Issue 4 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. Data Import Bug (Athena 0.9.26) (Clark Adam Hugh (PSI)) 2. Re: Data Import Bug (Athena 0.9.26) (Ravel, Bruce) 3. Re: Data Import Bug (Athena 0.9.26) (Lucy M Mottram) ---------------------------------------------------------------------- Message: 1 Date: Fri, 5 Apr 2019 11:33:13 +0000 From: "Clark Adam Hugh (PSI)" <adam.clark(a)psi.ch> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Data Import Bug (Athena 0.9.26) Message-ID: <BDFF4FC62383D24DA3EF530480A33EA70B616536(a)MBX214.d.ethz.ch> Content-Type: text/plain; charset="us-ascii" Dear Mailing List I have recently come across a data import error when using Athena version 0.9.26. When importing data there appears to be a resampling which significantly reduces the resolution of the data. Attached is an example dataset with an energy step of 0.5 eV on the Cu K edge. When importing with Athena 0.9.26 this data is significantly resampled resulting in an energy resolution on the edge of 1.5 eV which can either be seen by plotting or by exporting and inspecting the datafile. Using version 0.9.25 resolves this issue entirely. The data itself appears to actually be visible correctly during the import process (the import tab shows the data listed correctly when choosing which columns to import). Is there a setting somewhere within Athena 0.9.26 that sets the default behavior to resample the imported data? Thanks Adam Clark __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/129 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark(a)psi.ch

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Can't open Athena project
by Antony Burnham 06 Apr '19

06 Apr '19

I'm having trouble opening my Athena project in Artemis. This contains two transmission spectra of zirconium phases. They plot just fine in Athena but when I try to import them in Artemis it doesn't recognise that there are any files at all in the project (except that one of the two spectra does display in the plot window). There's just a blank space in the left hand pane where the list of files usually appears. I don't have this problem with any of my fluorescence data from the same experiment. And when I have an Athena project with a mix of fluo and transmission spectra, only the former are listed in the import window. I attach the project and the two files that went into it, in the hope that someone can tell me what I (or the software) did wrong. Regards, Antony Burnham

3 2

Demeter crashing on WIndows
by mauricio.maps 05 Apr '19

05 Apr '19

Dear sirs I experienced a problem already reported on previous discussions, such as in: https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05069.html Following Bruce´s assumption that the antivirus must be the source of the crash of arthemis and athena, I disabled my free AVG antivirus and everything worked fine. With the antivirus on, it doesn´t work. Please, can anyone help me on how can I fix it? The log file is attached. Thank you for any help. <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

1 0

Data Import Bug (Athena 0.9.26)
by Clark Adam Hugh (PSI) 05 Apr '19

05 Apr '19

Dear Mailing List I have recently come across a data import error when using Athena version 0.9.26. When importing data there appears to be a resampling which significantly reduces the resolution of the data. Attached is an example dataset with an energy step of 0.5 eV on the Cu K edge. When importing with Athena 0.9.26 this data is significantly resampled resulting in an energy resolution on the edge of 1.5 eV which can either be seen by plotting or by exporting and inspecting the datafile. Using version 0.9.25 resolves this issue entirely. The data itself appears to actually be visible correctly during the import process (the import tab shows the data listed correctly when choosing which columns to import). Is there a setting somewhere within Athena 0.9.26 that sets the default behavior to resample the imported data? Thanks Adam Clark __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/129 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark(a)psi.ch

4 3

Export measured difference integrated areas
by Patridge, Christopher 04 Apr '19

04 Apr '19

Hello everyone, Is there an export option for the integrated areas found in difference spectra from Athena? It appears the only option is exporting the picture of plotted values? I was hoping to save a little from transcribing each value inside Athena. Thanks everyone, Chris ********************************************** Dr Christopher Patridge Assistant Professor Department of Chemistry SASE 315 D’Youville College 320 Porter Ave. Buffalo, NY 14201 716-829-8096 / 315-529-0501 patridgc(a)dyc.edu<mailto:patridgc@dyc.edu>

2 1

how to best implement fitting u (oxygen parameter) in an spinel
by Juan de la figuera 01 Apr '19

01 Apr '19

Dear all, I have a naive question. I have some mixed spinels, of which I want to fit among other parameters the oxygen parameter u which indicates the distortions around the oxygen anions, using only the single scattering paths. What would be the simplest way of fitting that? In the tests I did before using Artemis, I would start with the structure (usually with a cif file), using atoms/FEFF to calculate all the paths. But changing u changes the initial structure. One way I can think of is to apply a correction, obtained by hand, to deltaR on each O-M path. Of course, this is not a general solution but only good for a few paths. Am I missing something? Thanks in advance, Juan ---------------------------------------------------------------------------- Juan de la Figuera Instituto de Quimica Fisica "Rocasolano" c/ serrano, 119 Madrid, Spain 28006 Phone: +34 91 745 9517 http://surfmoss.iqfr.csic.es/ <http://surfmoss.iqfr.csic.es/surflab/people/juan-de-la-figuera> http://scholar.google.com/citations?user=GOiP624AAAAJ -----------------------------------------------------------------------------

2 1

Amplitude ratios greater than 100%
by Raj kumar 01 Apr '19

01 Apr '19

Dear All, With the attached CIF file, i have generated chi and other files. In turn, for some paths, i have found amplitude ratios are greater than 100% (even it is reaching few thousands % for some paths - chi file also attached with this email). I know, it is meaningless. I would like to know, why am i getting these weird ratios? What is wrong with the CIF file? Thanks, Raj

1 0

Demeter question and Larch
by Patridge, Christopher 27 Mar '19

27 Mar '19

Hi everyone, A Demeter question - Is the memory limit hard set in Athena? I know that I can change the 50 dataset limit, but can I increase the memory to handle more data as I have a relatively large set of spectra (~150)? I have installed and tested Larch, but I do not see an option to run difference spectra in Larch GUI unless I missed something? I am running windows virtualization (win 7 - 64 bit) Demeter if that affects the memory question. Thanks everyone, Chris ********************************************** Dr Christopher Patridge Assistant Professor Department of Chemistry SASE 315 D’Youville College 320 Porter Ave. Buffalo, NY 14201 716-829-8096 / 315-529-0501 patridgc(a)dyc.edu<mailto:patridgc@dyc.edu>

3 3

demeter on Mac 10.14.3 Mojave
by Ping, Yuan 18 Mar '19

18 Mar '19

Hello, I have a new mac laptop with Mac 10.14.3 Mojave and would like to install demeter in it. Following the steps in the website, everything worked ok during the installation. However, when I finally typed “athena” in the terminal, the following warning showed up. If I clicked OK, the Athena will just quit and gave a message “perl5.26 quit unexpectedly”. The same thing for Artemis. Hephaestus showed the same warning, but still works after clicking OK. Any clue to fix this problem? [cid:image001.png@01D4DDCA.F5FB5AD0] Thanks a lot! Yuan

1 0

Peaks in Background Subtraction in Athena
by Nathan Nakamura 18 Mar '19

18 Mar '19

Hello, I am working on some data processing of ZrO2 thin films collected in fluorescence mode, and had a question regarding the background subtraction in Athena. When I use the default values, I see a large negative spike in the background curve (shown in BGsubtract1.png). I can vary the spline clamps and other parameters to reduce this (BGsubtract1.copy), but it does not seem to have any significant effect on the final EXAFS (EXAFScompare.png). My question is, do large spikes/instabilities on the edge like this need to be accounted for, or are they ok as long as the background fit after the edge seems fine? My thought is that as long as the EXAFS is not significantly affected, it should be fine, but I do not have a good sense for how the presence of this peak may impact the background curve beyond the absorption edge. I have also attached the project file in Athena for reference. Thanks, -Nathan

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Question on XES in FEFF
by FonsPaul 18 Mar '19

18 Mar '19

I wrote a couple of days ago asking about XES calculations in FEFF9. But I didn't hear anything back so I am rephrasing the question with a little more detail. I am calculating XES for organic molecules and used the following input. CONTROL 1 1 1 1 1 1 EDGE K EXCHANGE 0 0 1.0 FMS 5.1 LDOS -30. 15. .1 PRINT 5 0 0 0 0 0 AFOLP 1.3 S02 1.0 SCF 4.5 0 30 .2 1 XES 8 0.05 0 The XES output is shown from what I understand in the xmu.dat file in the chi column, however plotting this data shows a curve that is not positive definite. As I don’t think there is such a thing as negative emission, this probably means that my understanding is less than complete. The FEFF manual is also not very helpful on this issue and says nothing about the XES emission output. On a related question, the Feff9 docs (http://monalisa.phys.washington.edu/feff/Docs/feff9/feff90/feff90_users_gui…) specify that the XES card has the following options: XES emin emax estep But the examples that come with JFEFF seem to show options that don’t make sense with this definition: BN crystal: XES -20 20 0.2 Cu: XES 8 0.07 0.0 GeCl4 (molecule): XES 8 0.05 0.0 It is hard to understand how an emax value of 0.05 or 0.07 makes any sense. Does anyone know that the correct definitions are? Perhaps the documentation should be updated as well.

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Larch - LCF error
by Lily Schacht 15 Mar '19

15 Mar '19

Hi, all. I’m attempting to perform LCF on a large number of noisey XANES scans. I normalized and rebinned the scans in Athena before importing into Larch using the GUI. When I try to fit a scan I get this error: Traceback (most recent call last): File "C:\Users\lilys\xraylarch\share\larch\plugins\xasgui\lincombo_panel.py", line 812, in onFitOne self.do_fit(form['group'], form) File "C:\Users\lilys\xraylarch\share\larch\plugins\xasgui\lincombo_panel.py", line 797, in do_fit self.parent.show_subframe('lcf_result', ResultFrame) AttributeError: 'SplitterWindow' object has no attribute 'show_subframe' I’ve tried exporting scans from Athena as .xmu and got the same error. Has anyone seen this before or have any advice? I’m using Larch 0.9.41 and Demeter 0.9.26. My guess is that this is a data format problem not a result of ugly data but for what it’s worth, I tried LCF in Athena and the program either crashed (assuming memory issue) or gave nonsensical results (maybe convergence issue). Thanks, Lily Schacht

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How to use Larch as function server
by ASAKURA, Hiroyuki 14 Mar '19

14 Mar '19

Dear all, I would like to use Larch as an external function server. I'm a Python novice, but if I understand correctly, the present server (larch -r) provides access to a Larch process controllable with xmlrpc from outside. However, I would like to do something like below to achieve looser coupling with my future code (maybe not in python). How can I do that? I appreciate any suggestion for my first step to go, though I guess it is a bit far from the Larch way. ### client.py (not a working code) from six.moves.xmlrpc_client import ServerProxy import os, json def main(): s = ServerProxy("http://127.0.0.1:4966/", allow_none = True) response = s.read_ascii(os.path.abspath("/path/to/xas/data")) # I expect a JSON or python dict with keys like "energy", "mu", etc. data = response response = s.pre_edge(data) # data is a JSON or python dict with keys like "energy", "mu", etc. if __name__ == '__main__': main() ### client.py end I guess one can write some sort of function wrapper, if one wants. ### server.py (not a working code) from six.moves.socketserver import ThreadingMixIn from six.moves.xmlrpc_server import SimpleXMLRPCServer, SimpleXMLRPCRequestHandler import json import larch from larch_plugins.xafs import find_e0, pre_edge, autobk from larch_plugins.io import read_ascii class LarchServer(ThreadingMixIn, SimpleXMLRPCServer): def __init__(self, *args, **kw): super().__init__(*args, **kw) self.larch = larch.Interpreter(with_plugins=True) self.larch.run_init_scripts() self.register_introspection_functions() class LarchRequestHandler(SimpleXMLRPCRequestHandler): def __init__(self, *args, **kw): super().__init__(*args, **kw) def _dispatch(self, method_name, args): return getattr(self, method_name)(*args) ### wrapper function to Larch function ### Do something nice to convert the file into processed data as JSON or a python dict def read_ascii(self, filepath): data = read_ascii(filepath, _larch=larch) # Return processed data as JSON, for example. return json.dumps(data) def main(): server = LarchServer( ("127.0.0.1", 4966), requestHandler = LarchRequestHandler, logRequests = None, allow_none = True ) server.serve_forever() if __name__ == '__main__': main() ### server.py end -- ASAKURA, Hiroyuki (Ph.D) Program-Specific Senior Lecturer (ESICB) T. Tanaka Lab., ESICB, Kyoto University, Japan asakura(a)moleng.kyoto-u.ac.jp http://www.moleng.kyoto-u.ac.jp/~moleng_04/asakura/

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XES calculations in Feff9.
by FonsPaul 07 Mar '19

07 Mar '19

I have been attempting to use Feff9 to calculate x-ray emission spectra. In short, it would appear that one only exchanges the XANES card with the XES card, however, there appears to be nothing in the documentation that clearly states where the output is directed or how it is labeled. The most logical output would be xmu.dat and the spectra is clearly different when the XANES card is swapped out with the XES card. The only column in the xmu.dat card that appears to make sense to be XES spectra would be the mu0 column as it is positive definite while the chi, column, for example, goes negative and appears to be an interference pattern. Can any one shed some light on this? Also while the documentation states that the XES card takes the form “XES emin emax estep”, the example for GeCl4 included with jfeff uses the options “XES 8 0.05 0.0” whereas the jfeff example file for XES of BN uses “XES -20 20 0.2”. While the second example makes sense, I don’t understand the meaning of the card values used for the GeCl4 molecule example. This is especially relevant as I wish to calculate XES for an epoxy polymer and I have no idea what the fields mean. Thanks for help on this in advance!

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Installation of Athena on Linux Ubuntu
by MOHAMED NAJI 07 Mar '19

07 Mar '19

Dear All, I would like to install Athena in my Linux Ubuntu 16.04 OS. Any idea on how to and if there is already a software develloped for Linux OS. I searched but didn't find it and I'm wondering if someone has already developed it. Thank you Mohamed Naji --

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Re: [Ifeffit] cant open Athena project
by fred.mosselmans＠diamond.ac.uk 07 Mar '19

07 Mar '19

Dear Antony, Your data type for these files is xanes, that won't give a chi set for artemis to read it in. You need to change the datatype to mu€ under the group tab in athena Cheers Fred Message: 1 Date: Thu, 7 Mar 2019 07:44:30 +0000 From: Antony Burnham <Antony.Burnham(a)anu.edu.au> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Can't open Athena project Message-ID: <MEAPR01MB4486896DFADAA39ADB94E966A24C0(a)MEAPR01MB4486.ausprd01.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" I'm having trouble opening my Athena project in Artemis. This contains two transmission spectra of zirconium phases. They plot just fine in Athena but when I try to import them in Artemis it doesn't recognise that there are any files at all in the project (except that one of the two spectra does display in the plot window). There's just a blank space in the left hand pane where the list of files usually appears. I don't have this problem with any of my fluorescence data from the same experiment. And when I have an Athena project with a mix of fluo and transmission spectra, only the former are listed in the import window. I attach the project and the two files that went into it, in the hope that someone can tell me what I (or the software) did wrong. Regards, Antony Burnham

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Error when first opening Athena on Mac
by Laura E Wasylenki 05 Mar '19

05 Mar '19

Hello, I’ve just attempted to install Demeter on a Mac running OS 10.13.6 (High Sierra). When I open Athena, the XAS processing window appears, but then a warning window appears on top of it that says “Demeter::Templates::D” used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm. I think a line number follows, but it is cut off. The warning contains several more lines that are identical to that one, except that D is replaced by other letters. When I dismiss the warning window by clicking “OK,” Athena and Perl just close down. Has anyone seen this, and does anyone know the solution? Thank you! —Laura ____________________________ Dr. Laura Wasylenki Associate Professor School of Earth and Sustainability Department of Chemistry & Biochemistry Northern Arizona University PO Box 5698, 700 S Osborne Drive Flagstaff, AZ 86011 laura.wasylenki(a)nau.edu<mailto:laura.wasylenki@nau.edu>

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Re: [Ifeffit] Ifeffit Digest, Vol 193, Issue 4
by Christopher Chantler 03 Mar '19

03 Mar '19

PS Simon, we are just around the corner [physics] and also link up with the Dementia work, so you might just drop across and have a chat / meeting! -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Monday, 4 March 2019 10:06:37 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 193, Issue 4 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. Re: Cu K edge XANES stds (Simon James) ---------------------------------------------------------------------- Message: 1 Date: Sun, 3 Mar 2019 23:06:19 +0000 From: Simon James <s.james(a)florey.edu.au> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Cu K edge XANES stds Message-ID: <A9A1ED50-AC0D-47F8-9D5D-2208001097E1(a)florey.edu.au> Content-Type: text/plain; charset="utf-8" Hi Drew, Thank you for your swift reply. Apologies for the delay in my response but I was dragged in to other matters. Appreciate the data and ref. Regarding the sanity check I have collected some spatially resolved Cu XANES ?maps? of cultured cells and some of the standards I collected during the run are horribly compromised for unclear reasons and I just wanted some clean data to reference while I work on cleaning up (to the degree possible) my standards. Thanks again. Cheers, Simon Simon James PhD Senior Research Officer NHMRC-ARC Dementia Research Development Fellow Melbourne Dementia Research Centre University of Melbourne The Florey Institute of Neuroscience and Mental Health Web: www.florey.edu.au<http://www.florey.edu.au> On 28 Feb 2019, at 2:51 am, Latta, Drew E <drew-latta(a)uiowa.edu<mailto:drew-latta@uiowa.edu>> wrote: Hi Simon, Since you are just looking for a sanity check (on what??) here are some Cu-S standards for you. They were published in DOI: 10.1021/es304736y. The Cu-cys sample is not a pure phase, but probably a mixture of cysteine/cystine. But it is likely mostly Cu(I). Further discussion is available in the SI of the paper above. The file is from an old, old version of Athena (0.8x)... hopefully it works for you. Best, Drew Latta ====================================== Drew E. Latta, Ph.D. Asst. Research Scientist The University of Iowa Civil and Environmental Engineering/IIHR 4105 Seamans Center Iowa City, IA 52242 Ph. 319-936-0034 email. drew-latta(a)uiowa.edu<mailto:drew-latta@uiowa.edu> ====================================== -----Original Message----- From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Simon James Sent: Tuesday, February 26, 2019 3:18 PM To: Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> Subject: [Ifeffit] Cu K edge XANES stds Hi mailing list, I am hoping someone is willing to share their Cu K-edge XANES spectra from biological Cu thiol complexes. I?m particularly interested in Cu(I/II)-GSH, Cu(I/II)-Cys or similar. I need a sanity check on some fluorescence data I am wrangling. Can anyone help? Best regards, Simon This mail was composed on the move via my phone. Apologies for any typos. Florey Institute of Neuroscience and a Mental Health Melbourne Brain Centre 30 Royal Pde Parkville, 3052 VIC _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit <Cu_Samples_athena.prj>_______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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Cu K edge XANES stds
by Simon James 03 Mar '19

03 Mar '19

Hi mailing list, I am hoping someone is willing to share their Cu K-edge XANES spectra from biological Cu thiol complexes. I’m particularly interested in Cu(I/II)-GSH, Cu(I/II)-Cys or similar. I need a sanity check on some fluorescence data I am wrangling. Can anyone help? Best regards, Simon This mail was composed on the move via my phone. Apologies for any typos. Florey Institute of Neuroscience and a Mental Health Melbourne Brain Centre 30 Royal Pde Parkville, 3052 VIC

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*****SPAM*****Creating EXAFS coefficient file for reverse monte carlo simulation
by tolga.ulucan＠metu.edu.tr 03 Mar '19

03 Mar '19

Hello everyone, I have synchrotron XRD and XAFS(L3 Tb edge) data on Al90Tb10 metallic glass alloy that i want to use them as constraints in a reverse monte carlo simulation(RMC_POT). RMC_POT manual says i need 2 files for XAFS. 1st chi(k)-k file which i exported from athena as normalized data and 2nd exafs coefficient file which i don't understand what it is or how to create it. I was wondering if anyone can help me on how to create this file or point me on a direction to get more info on this? Best wishes, Tolga Han Ulucan

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Data on Cd5H2(PO4)4·4H2O
by 1510405＠tongji.edu.cn 02 Mar '19

02 Mar '19

Hi all, I have acquired Cd L3-edge XANES spectra of my sample and some Cd standards for LCF analysis. However, I lack the spectra of Cd5H2(PO4)4·4H2O, which was important to my analysis. Therefore, I was wondering if anyone could share the Cd L3-edge XANES data of Cd5H2(PO4)4·4H2O with me? Best regards, Sicong Lei

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Can't load Iffeffit.dll
by Haas, de, W.B. 01 Mar '19

01 Mar '19

Dear mailing list, I recently started using Windows 10 Enterprise. However, now Athena, Artemis and Hephaestus don't launch (I see the the software icon but then it doesn't launch). I tried the suggestions made in an earlier thread but they didn't work for me: 1. Making sure there is permission to read and write in the location where Demeter is installed. 2. Making sure the antivirus software doesn't misidentify it as a threat. The CIT services of my university don't know how to solve this issue either. So I was wondering whether there were any other fixes known for this issue. The earlier thread: [Ifeffit] Problems Running Athena, Artemis and Hephaestus on P.C. with Windows 7 Enterprise Operating System May 2016 http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2016-May/008592.html Kind regards, Winfried de Haas

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Larch 0.9.42
by Matt Newville 26 Feb '19

26 Feb '19

Hi Folks, Larch 0.9.42 is now available, with installers for Windows, MacOS, and Linux at https://millenia.cars.aps.anl.gov/xraylarch/installation.html Version 0.9.42 fixes many problems, especially to the XAS Viewer GUI app which is now pretty close to a replacement for Athena but with better peak-fitting and with none of the limitations that were imposed by the outdated ifeffit library. For MacOSX, Version 0.9.42 can be installed with a standard Mac "pkg" installer file. If you have already installed Larch, you should be able to update to the latest version with conda update -c gsecars xraylarch on Windows, you may have to specify the full path with something like: C:\Users\<YourName>\AppData\Local\Continuum\xraylarch\Scripts\conda.exe -c gsecars xraylarch If you have any trouble upgrading, you can also simply remove the XrayLarch installation and reinstall using one the installers above. For Python programmers, Version 0.9.42 ends support for Python 2. No testing or packaging was done with Python 2 for this release, and going forward the master development branch will not work with Python 2. Please let us know if you having any questions, trouble, or suggestions. --Matt Newville

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Problem with using lincomb_fit function in the Larch
by Tayal, Akhil 26 Feb '19

26 Feb '19

Hello Matt, I could not be able to perform LCA using the lincomb_fit function in the Larch software. I am getting the error message from line number 80 in the lincombo_fitting.py script. I expect the function has some bug with reading the group values. It could not be even able to read the default array 'norm' nither any user-provided 'arrayname' such as 'flat or fpp.' Can you suggest any solution for it? Please find the data files and larch script I am using for this purpose. Thanks, Akhil

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Does anyone have XAS from Cu(I)-GSH and/or Cu(I)-cys
by Simon James 24 Feb '19

24 Feb '19

Hi mailing list, I am hoping someone can help me sanity check some XAS spectra I recorded. I have [Cu(I)cys], [Cu(I)GSH] spectra (recorded in fluorescence) and would be eternally grateful if anyone is prepared to share any of their data on these or similar compounds? I am really only interested in the edge but more data is always more data. Happy to discuss offline if preferred. Happy XAS'ing Best regards, Simon Simon James Senior Research Officer NHMRC-ARC Dementia Research Development Fellow Melbourne Dementia Research Centre University of Melbourne The Florey Institute of Neuroscience and Mental Health Office: +61 (3) 9035 6420 Mob: +61 (4) 3811 0982 Web: www.florey.edu.au<http://www.florey.edu.au> simon.james(a)florey.edu.au<mailto:simon.james@florey.edu.au>

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Hafnia standards
by Mukundan, Vineetha 21 Feb '19

21 Feb '19

Hi All, I am new to EXAFS data analysis and am working on Hafnia based dielectrics. So far, I have not measured reference standards of hafnia. I know my samples have monoclinic and orthorhombic phases. If anyone on this mailing list have these standards and don't mind sharing, please email me. Alternatively if there are ways to generate/simulate it (perhaps using FEFF and the corresponding .cif files), please let me know. Thank you, Vineetha

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XANES convolution method in FEFF9
by Ying Liu 20 Feb '19

20 Feb '19

Dear all. I am currently running FEFF9 on XANES calculation. However I could not figure out how FEFF transformed LDOS to the final xmu.dat. What function did LDOS data convoluted with to achieve xmu.dat? Looking forward to hearing any answer. Thank you. Ying Queen Mary University of London

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Re: [Ifeffit] questions: EXAFS
by Robert Gordon 19 Feb '19

19 Feb '19

Hi Vineetha, I advised during the course that students should use the ifeffit mailing list for questions post-school. An advantage of doing so is that one could receive assistance from any member of the community and not be at the mercy of the time constraints of any particular researcher. Another advantage is that someone more familiar with the type of problem you are studying might be able to offer more insight. I would like again to encourage you to make use of the mailing list. Other researchers may also see the problem with which you are dealing and it could help them too. Some general advice: Mixed phase samples can be problematic. If you know which two phases are present, you can simulate them separately and examine the local environments. If the near-neighbour environments are very similar, then some fitting can be done with reasonable results. You still need to keep in mind the resolution criteria for being able to resolve closely spaced paths. Looking at your O-scattering paths, not having seen your k-space data and range, I suspect you will not be able to resolve the splitting in the first shell, and so, would treat it as a single path (similar argument for Hf paths in 2nd shell). The starting model serves to give you amplitudes and phases for fitting. In that regard, whether you use monoclinic or orthorhombic starting model should not matter. Once fit, you would examine how well the fit result compares to either model. I would hope you also measured standard(s) of known composition and structure. Fitting such would help guide the fitting of your unknown. Model calculations can be done for your two suspected phases, including temperature effects with the DEBYE card in the FEFF input. A quick google search yielded this paper: https://ceramics.onlinelibrary.wiley.com/doi/abs/10.1111/j.1151-2916.1977.t… which gives a calculated Debye temp of 484K for monoclinic HfO2. You can check the literature further for other research on this material which may give an experimental value. With the model chi(k)'s, you can do linear combinations (manually) and see if you find some ratio that approaches agreement with your data. I don't see how to get the model chi(k) out of Artemis though. I even tried running the feff6 executable manually (with associated dll's) but it did not generate the chi.dat file I was expecting. I would suggest, if you wish to generate models and compare in this fashion, that you invest in a newer version of FEFF that does allow you to generate this output (i.e. get FEFF9). Other thoughts: XANES? Did you measure it for the unknown and standards? If so, are the two phases distinguishable? Background removal? Can you improve it to reduce the amplitude below 1 Angstrom? Always show the original data (merged ok), not simply the transforms when asking for help. That helps one assess the problem better. regards, Robert On 2019-02-19 9:43 a.m., Mukundan, Vineetha wrote: > > Hi Dr. Gordon, > > I am Vineetha and had met you at the EXAFS short course @ BNL in > November’18. I am trying to analyze a couple of my data on Hafnia and > am stuck. So I am seeking help with the following questions. Apology > in advance if it will some of your time. > > 1.I generated the scattering paths. See attached. It is safe to > discard the multiple scattering paths here. So I generated the plots > with Hf-O single scattering paths and Hf-Hf scattering paths. Clearly > it shows the first shell is mostly one or all of O1.1, O2.1 and O2.3 > paths. And the second shell is mostly influenced by Hf1.2, Hf1.3 and > Hf1.5. Am I correct in making this assumptions so far? IS there any > other way to figure out which paths are important or not important, > other than plotting them together with the data. > > 2.While fitting, I am really unsure how to set the parameters for each > path in my example. I am not sure how to set up the parameter when we > have multiple paths contributing to say first shell or second shell. > Also, I know using the Nyquist equation it is possible to figure out > the number of independent variables. I read up the ARTEMIS pages on > FeS2 example described but there the structure is cubic but my sample > is monoclinic. Here I am trying to fit only the monoclinic paths with > my data. > > 3.Also, I know my sample has monoclinic and orthorhombic structure. So > how does one go about generating the simulated EXAFS for a particular > structure on FEFF? say in my case the monoclinic and orthorhombic > ones. I have the .cif files for these 2. For figuring out the % amount > of monoclinic and orthorhombic phases in the sample, I am assuming I > will have to do a linear combination analysis. Am I correct? > > Any help in this regard will be really useful. > > Thank you, > > Vineetha > > *Vineetha Mukundan, PhD* > > Post-doc, Prof. Diebold’s Group > > Colleges of Nanoscale Science and Engineering > > SUNY Polytechnic Institute > > 257, Fuller Road > > Albany, NY 12203 USA > > CONFIDENTIALITY NOTICE > > The pages (including attachments) comprising this internet or > facsimile transmission contain CONFIDENTIAL information. This > information is intended for the sole and exclusive use by the > individual entity named as the recipient hereof and any further > disclosure or dissemination is prohibited. If you are not the > intended recipient, you are hereby notified that any disclosure, > copying, storage, distribution, or use of the contents of this > transmission is strictly prohibited and may be unlawful. If you have > received this transmission in error, please notify us immediately by > telephone or return e-mail, delete it from your mail system, and > destroy all copies in your possession. Thank you. >

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FEFF9 calculations of Tellurium Clusters
by Gentle, Cecilia M 14 Feb '19

14 Feb '19

Dear IFEFFIT Mailing List, I am running FEFF calculations using FEFF9. I am running these calculations on my department's cluster in parallel using a Linux machine Currently, I have run XANES calculations of CdTe and ZnTe at the K-edges of Zn, Cd and Te. I am calculating the XANES of various cluster sizes. I start with a cluster with a single coordination shell and build up to 7 coordination shells, running a XANES calculation with each cluster size. I have run these calculations for the K-edges of Cd, Te, and Zn. Unexpectedly, I receive an error for the Te K-Edge XANES calculation of ZnTe and CdTe for the cluster size of 2 coordination shells. The FEFF calculations run fine for a cluster with a single coordination shell and for clusters with 3 to 7 coordination shells. This is my first experience running FEFF. I have read through the FEFF manual, but I am having trouble interpreting the error message. I have the FEFF input file for Te K-Edge of a CdTe cluster with 2 coordination shells, and the resulting error message attached as a text files. Has anyone else experienced this before? If someone can point me to a section in the manual or another resource to help me understand the error, I would very much appreciate it. Thank you, Cecilia Gentle PhD Candidate University of Illinois

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EXAFS of solid-solution alloy
by Chongchong Mellon 08 Feb '19

08 Feb '19

Hi all, I have some problems in analyzing the EXAFS of solid-solution alloy, let us define as A0.5B0.5. I have searched the mailbox but cannot find similar discussion yet. So I post the question here and hope to get some suggestion from you. 1. A and B are immiscible metals from the phase diagram, which means that I couldn’t get the bulk A0.5B0.5 as a standard reference. In this case, how can I estimate the amp for the K-edge of A or B? 2. A and B are very near (atomic number B-A = 2) in the periodic table. So their lattice parameters are quite close to each other. In this case, when I tried to fit the 1st shell use A-A and A-B paths at the same time, the Happiness parameter becomes worse and the coordination number of A-B is not realistic (large errors!). If I fit with only the A-A path or A-B path, I get a good fit. However, atomic resolution STEM-EDX maps show the homogenous distribution of both A and B atoms. The A-A and A-B bond might have an equal ratio. In this case, how can I do the fitting? Thank you very much in advance! Sincerely, Chong

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Seeking a post-doctoral research in Environmental Chemistry at Carnegie Mellon University
by Gregory Lowry 08 Feb '19

08 Feb '19

Open Position Postdoctoral Researcher Civil and Environmental Engineering Carnegie Mellon University I am seeking a post-doctoral researcher in environmental chemistry. Candidates must have experience using synchrotron X-ray absorption spectroscopy for determining metal speciation in environmental samples (or similar matrices), and/or experience using synchrotron X-ray Fluorescence and XANES mapping (GeoPIXIE) to speciate metals in environmental or biological samples. Experience with mercury and/or arsenic geochemistry, and working knowledge of other characterization methods for metal-based nanoparticles (e.g. XRD, FTIR, XPS, ICP-MS, spICP-TOF-MS) are desirable. A demonstrated ability to publish research in high quality journals, meet deadlines, and write proposals is required. Effective English language oral and written communication are required. The candidate will interact with an interdisciplinary research team of faculty, post-docs, and Ph.D. students and with industry collaborators on a variety of projects including speciating Hg in matrices relevant to oil and gas exploration and metals speciation in plants. The successful candidate will be expected to design and conduct experiments in aqueous and non-aqueous matrices, collect and analyze synchrotron XAS spectra on samples containing mercury, arsenic, and other metals, prepare manuscripts and monthly research reports, assist in proposal writing, and present findings at national and international professional conferences. The position is for a minimum of one year, renewable depending on performance. Interested applicants should contact Prof. Greg Lowry glowry(a)cmu.edu. Please send a brief cover letter, curriculum vitae, a brief statement of research interests and the contact information for at least three references. Applications will be accepted until the position is filled. -- Gregory V. Lowry Walter J. Blenko, Sr. Professor of Civil & Environmental Engineering Deputy Director, Center for Environmental Implications of Nanotechnology Carnegie Mellon University, Pittsburgh, PA 15213

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Problem with running mback algorithm in the newer version of Larch
by Tayal, Akhil 08 Feb '19

08 Feb '19

Hello Matt, I found that while running the 'mback' algorithm there is an error in accessing f1_chantler database. Weirdly the commands work well for the older (0.9.35) version that happens to be installed on my old computer. But for the latest version (0.9.40), I simply could not able to generate the value of f1 and hence could not use the 'mback' algorithm. Do you have any suggestion to troubleshoot this issue on the latest version of the software? Also is there any inbuilt command to perform 'flattening algorithm' for normalization or one has to do it manually. Thanks, Akhil

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Post doctoral position at Pohang Accelerator Laboratory
by 이국승(에너지환경소재연구팀) 08 Feb '19

08 Feb '19

Dear all, A post-doctoral position is available at Pohang Accelerator Laboratory. Tasks will be development of electrocatalysts for fuel cells and/or water splitting and their XAFS analyses. Candidates should have a PhD degree in materials science, chemistry, chemical engineering, or other appropriate areas and should have experience in XAFS analysis and excellent writing and communication skills. Interested candidates please may contact Dr Kug-Seung Lee (lks3006(a)postech.ac.kr<mailto:lks3006@postech.ac.kr>) with your CV. Additioinal documents may be required, for example, letters of reference, representative publications, etc. Thank you. Kug-Seung Lee, Ph.D. Staff Scientist Manager, 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Researcher ID: http://www.researcherid.com/rid/D-7088-2011

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Larch 0.9.41
by Matt Newville 07 Feb '19

07 Feb '19

Hi Folks, Larch 0.9.41 is now available, with installers for Windows, MacOS, and Linux at https://millenia.cars.aps.anl.gov/xraylarch/installation.html If you have already installed Larch 0.9.39 or later, you should be able to update to the latest version with `conda update -c gsecars xraylarch`, Larch 0.9.41 is about six months in the making. There have been some important improvements in XAFS and XANES analysis, including improved MBACK algorithm (thanks Marco Alsina!) and many bugfixes and in the XAS Viewer GUI for pre-edge peak-fitting and linear combination analysis. Significant improvements have also been made X-ray microprobe analysis, including for XRF analysis as well as XRF and XRD mapping tools, including support for reconstructing X-ray fluorescence and diffraction tomography data. Larch now includes the very useful Dioptas GUI for XRD patterns from Clemens Prescher. At the very least, this can be used to view and calibrate X-ray diffraction data ("replace Fit2D") using pyFAI and related libraries from the folks at ESRF. For Python programmers: Version 0.9.41 makes a small but significant step toward making Larch a "more normal Python library", so that Python scripts using Larch as a library can avoid having to create and keep a running interpreter for many basic analysis steps, including interacting with the database of X-ray properties that includes data from Elam et al, Chantler, and so on. Version 0.9.41 works with Python 3.7, 3.6, and 2.7. The installers linked above are built with Anaconda Python 3.6. Most dependencies are also available as conda or pip packages for Python 3.7, and some are available with Python 2.7. This is the last version of Larch to be tested with Python 2.7. We will not deliberately break Python 2.7 until after 0.9.42 is released, at which point Larch will stop working with Python 2.7. We expect this to happen in two or three months. In the meantime, we will not intentionally break things for Python 2 but will no longer test or support Python 2. Please let us know if you having any questions or trouble. Cheers, --Matt Newville

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Problems Opening a larch saved athena Project in Athena
by Luis Carlos Colocho Hurtarte 05 Feb '19

05 Feb '19

Hi all, I have a some data from CLS, using the plug-in in Athena I could open most of them except a couple. I managed to open the rest using Larch (no Problem there), my interest is solely in saving them as .xmu/csv. Nevertheless when I saved in csv in Larch the axis order is inverted (X1 – Yn and Xn to Y1), also if I save them as an athena Project through larch and open it in Athena, the program crashes. Is this some kind of bug? The data plotted in Larch is fine, but the file is corrupted? Anyone experienced something like that passing from larch to Athena? Kind regards Luis -- Luis Carlos Colocho Hurtarte Lehrstuhl für Bodenkunde (Chair of Soil Science) Technische Universität München Emil-Ramann-Str. 2 85354 Freising Germany Telefon: +49 8161 71 -5266 Fax: +49 8161 71 -4466 http://www.soil-science.com

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Post Doctoral Position at Frei University Berlin/ Uni Bayreuth
by Ditty Dixon 05 Feb '19

05 Feb '19

*Dear All,* *As a part of joint German-Czech Research project "*Operando Fuel Cell" a* post-doctoral position is available for three years starting from 1st of April 2019 at *Universität Bayreuth/Frei University Berlin, Germany. The aim of the joint project with partners from Berlin and Prague is to obtain a more detailed insight into the complex reaction and degradation mechanisms in high temperature polymer electrolyte membrane fuel cells (HT-PEMFC). For this purpose, X-ray absorption spectroscopy (XAS) will be used during fuel cell operation in realistic working conditions. Your tasks will be: • Construction of testbench for HT-PEMFC tests • Design of a suitable in-situ cell for hard X-ray measurements at Pt L2 and L3 edges • Acquisition of beamtimes at BESSY and PETRA • In-operando XAS measurements at different Pt-based catalysts We are looking for a candidate with PhD, having experience in material characterization using spectroscopy techniques. Interested candidate may please contact Prof. Christina Roth (christina.roth(a)fu-berlin.de) or ( kerstin.soellner(a)uni-bayreuth.de) along with your CV. Thank You -- Dr. Ditty Dixon Ramanujan Faculty Electrochemical Power Source Division Central Electrochemical Research Institute (CSIR-CECRI) Karaikudi, India, 630003 Ph:00919400243084

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Plotting flattened feffit simulation results
by FonsPaul 28 Jan '19

28 Jan '19

Hi All, I have a rather simple question and a reply for either Larch or athena would be welcome. I have calculated a number of structures using DFT and have run feff on each of the appropriate sites and have then averaged the E(k) results. I have no problem reading in the data to athena, however, due to the lack of a pre-edge baseline, it is typically not possible to choose a reasonable “pre-edge” baseline so that I can plot the data for the different structures in “flattened” mode. The “post-edge” baseline works very well with the default values (as there is literally no noise in the spectra). My question is how can I induce athena to plot the E(k) data for the different structures in “flattened” mode. Ultimately, I will end up taking a Fourier transform into real space so I would also like to have a proper baseline so I can compare intensities as well. In effect, the data from feff9 is already normalized. Thanks for any suggestions!

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Job posting: Lead Beamline Scientist at NSLS-II, Brookhaven National Lab
by Matt Newville 27 Jan '19

27 Jan '19

Hi Folks, I was asked to forward this job posting: There is an opening for a Lead Beamline Scientist position at the National Synchrotron Light Source-II, Brookhaven National Laboratory. The candidate will assume leadership of the Inner-Shell Spectroscopy (ISS) Beamline, a high-flux, fast-scanning, damping wiggler spectroscopy beamline, with in-situ and operando instrumentation capabilities. The candidate will also be expected to develop an independent research program that utilizes the beamline capabilities. See https://jobs.bnl.gov/job/upton/lead-beamline-scientist-inner-shell-spectros… for details. --Matt

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Question about parameters of principle components analysis (PCA)
by 雷思聪 26 Jan '19

26 Jan '19

Hello, I see in many publications the indicator values (IND) numbers used to evaluate how many components are included, and SPOIL value used to evaluate quality of target transform in principle components analysis (PCA). However, they are obtained from PCA performed on SIXpack, rather than Athena (version 0.9.26). Hence, I wonder if I can get similar parameters after running of PCA in Athena? If not, how do I evaluate the PCA results? Thanks for your help!

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Larch flattening
by Kirill Lomachenko 25 Jan '19

25 Jan '19

Dear Matt, I have a question and a comment regarding Larch. I would appreciate if you could have a look. 1) The flattening algorithm for XAS in Larch works differently with respect to Athena when linear post-edge function is used for normalization. In Larch the normalized spectrum is always fitted by a parabola for flattening, no matter which function was used for normalization. It works fine when the post-edge function is also a parabola, but when it is a straight line, the resulting flattened spectrum does not stick to Y=1, as it is expected to do (and as it does in Athena). My question is: is it a bug or a feature? Just in case, I made some minor modifications in the pre_edge.py file that allow to get the same results as in Athena when linear post-edge is used. Maybe these corrections are a bit clumsy, but it seems to work. If anyone needs, I can share. 2) There is a typo in the larch web-manual in the description of the nnorm parameter of the pre_edge() function. It is stated that it is the number of terms in the fitting polynomial (i.e., 1+degree) whereas it seems that it is just its degree. So, nnorm=1 corresponds to a linear function and nnorm=2 to quadratic. In the gui help it is partially corrected, but the phrase "Default=3 (quadratic)" stays. It is not critical at all, but may be misleading for beginners... Using the possibility, I would like to thank you for all the great work you are doing on Larch. It really helps for large datasets! All the best, Kirill -- Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu

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Re: [Ifeffit] Dynamic XAFS Simulations?
by Gentle, Cecilia M 23 Jan '19

23 Jan '19

Dear Hunter, I also recommend you to join the mailing list for the ultrafast laser community: dyna(a)listes.epfl.ch [to subscribe: dyna-subscribe(a)listes.epfl.ch] Best, Cecilia Gentle PhD Candidate, Department of Chemistry University of Illinois at Urbana-Champaign https://www.vanderveen-lab.com/ -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, January 23, 2019 4:54 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 191, Issue 13 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. Dynamic XAFS Simulations? (Hunter Allison) 2. Re: Dynamic XAFS Simulations? (Robert Gordon) ---------------------------------------------------------------------- Message: 1 Date: Wed, 23 Jan 2019 13:26:21 -0800 From: Hunter Allison <hgalliso(a)uci.edu> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Dynamic XAFS Simulations? Message-ID: <CAH6J0e_vk1n4viX8H5A4vX=SRL0e5NQHmSZGEQ43wVxBzpwo5Q(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi, I'm a graduate student at the University of California, Irvine. Firstly, thank you for all the copious resources. It is a treasure trove of information and a beacon of light for someone just starting out. Let's begin with some brief background. In my research group, we intend to perform pump-probe spectroscopy with attosecond x-ray probes. The Professor says that we can use XAFS to study how the electrons move on these very short timescales. While the system is being setup and other experiments are being conducted, my Professor wants me to figure out how to do simulations of XAFS. This is a bit of a daunting order, since I've never simulated anything before and only have basic programming knowledge. The only direction I have is, "Try Google.". So, today, I've been "trying Google" and found my way to here. Since, I don't really know what I'm doing, I thought I try asking and finding out if anyone else does this sort of thing: How/where does one do simulations of dynamic XAFS? Where would I get started? (Please forgive me if this question has been answered somewhere else or if it seems profoundly dumb or too broad. I'm really just looking for some more direction. Perhaps, it could be that nobody does this and, in that case, I need to figure out how to model this myself. Wow! That thought seems daunting.) For example, let's say I want to find out how the x-ray adsorption of a carbon foil like Graphene would change on attosecond time scales as it's heated by a femtosecond laser and electrons move. Is there a program or code out there that people use to model this sort of thing?

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Dynamic XAFS Simulations?
by Hunter Allison 23 Jan '19

23 Jan '19

Hi, I'm a graduate student at the University of California, Irvine. Firstly, thank you for all the copious resources. It is a treasure trove of information and a beacon of light for someone just starting out. Let's begin with some brief background. In my research group, we intend to perform pump-probe spectroscopy with attosecond x-ray probes. The Professor says that we can use XAFS to study how the electrons move on these very short timescales. While the system is being setup and other experiments are being conducted, my Professor wants me to figure out how to do simulations of XAFS. This is a bit of a daunting order, since I've never simulated anything before and only have basic programming knowledge. The only direction I have is, "Try Google.". So, today, I've been "trying Google" and found my way to here. Since, I don't really know what I'm doing, I thought I try asking and finding out if anyone else does this sort of thing: How/where does one do simulations of dynamic XAFS? Where would I get started? (Please forgive me if this question has been answered somewhere else or if it seems profoundly dumb or too broad. I'm really just looking for some more direction. Perhaps, it could be that nobody does this and, in that case, I need to figure out how to model this myself. Wow! That thought seems daunting.) For example, let's say I want to find out how the x-ray adsorption of a carbon foil like Graphene would change on attosecond time scales as it's heated by a femtosecond laser and electrons move. Is there a program or code out there that people use to model this sort of thing?

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XAS data for Nickel Chloride
by Gill, Simerjeet 18 Jan '19

18 Jan '19

Hi, I am working with a molten salt system with Nickel Chloride as one of the components. If you have measured XAS data on anhydrous and hydrated Nickel Chloride at RT and elevated temperature, I would appreciate you sharing your data. Thanks in advance for your help! Simer Simerjeet K Gill, Materials Scientist, Nuclear Science and Technology Department, Brookhaven National Lab, Upton, NY 11973

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求助Athena软件32位电脑安装包，谢谢
by 2225295803 16 Jan '19

16 Jan '19

你好，我是天津大学马新宾课题组的硕士研究生袭雨杉，我的电脑是32位的，请问有32位的EXAFS分析软件Athena吗？可以发给我吗？谢谢

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Advice on using Athena for XANES LCF on spectra with a small edge step?
by Mike Massey 15 Jan '19

15 Jan '19

Hi All, Does anyone have advice for LCF of spectra with a small edge step? I've recently found myself with more and more issues fitting spectra like the one shown in the attached photo, where the spectrum is of good quality, but the fits end up not working out due to normalization (as far as I can tell). Sadly, I have so far ended up just throwing these fits out, but I'm hoping there is a better solution out there that someone might be able to recommend. One solution is "get more of the element of interest," as a beamline scientist recently told me. I'm just reluctant to really load it up in the data collection, because at 2 keV I get nervous about artifacts like self-absorption. Is there a better way? What am I missing? Thanks for your thoughts, Mike

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