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

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 29 Sep '20

29 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 18 Jun '20

18 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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