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

Re: [Ifeffit] How to use Artemis with feff85L
by Bruce Ravel 12 Jan '18

12 Jan '18

Yes. But I am pretty busy these with my new beamline. "Beamline scientist" is my actual job. "Software guy" is a side project. So the software work gets done when it gets done. B On 01/12/2018 05:25 AM, José Carlos Conesa wrote: > Dear Bruce, > > Do you foresee that (in a not far future) Artemis may be adapted so that > it can use the results of feff8.5L? > > All the best, > > > El 12/09/2017 a las 19:11, Bruce Ravel escribió: >> >> Feff8L is not properly integrated into Artemis yet. Sorry. I have a >> new beamline these days. It's hard to find time to work on the software. >> >> This is on my to do list, but it's going to take a while. >> >> B >> >> >> On 09/12/2017 12:54 PM, José Carlos Conesa wrote: >>> Hi, >>> >>> I should like to use feff85L within Artemis (from Demeter 0.9.25), >>> just to check in my system whether selfconsistency has a role in >>> unifying E0 values (with feff 6, allowing different E0 for each >>> scatterer leads to E0 differences >10 eV, which seems too much to >>> me). I find that after loading the EXAFS data (from Athena) and a >>> model (a .cif file containing Cu, Ce and O atoms), if I click Run >>> Atoms and then Run Feff with feff6 as executable I get the usual set >>> of paths that allow me doing a fit of the data, but if I try to use >>> the feff85L.exe that comes with the Demeter software (by changing the >>> feff executable in the File/Edit preferences menu), after clicking >>> the Run Feff button (without including the SCF card) a bit of >>> computation happens and after finishing it the path list is empty. >>> >>> ¿Any idea of the possible reason why I get no path list? >>> >>> Thanks in advance >>> >> >> > -- 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/ 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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Some questions regarding running Larch code in Python
by Hanyu Zhang 09 Jan '18

09 Jan '18

Hello everyone, I'm trying to find radial distribution functions for materials with known concentrations of individual atoms by running Larch code through Python, but am having some difficulties with creating feffpaths: 1. I'm not quite understanding the feff.inp files stuff. Calling FeffRunner().run() with a input file that works with Atoms always throws the "rdinp not found exception". From what I'm understanding, feffrunner().run() calls the different modules to create a feffpath() group, but where are the rdinp, pot, xsph, etc codes/files? 2. Somewhat on the same line of thought, can someone give me an example of a valid feffNNNN.dat file to generate a feffpath() group? I went through feffdat.py and the parsing code in lines 88-102 (under __read()) looks like it only accepts very specific input formats. 3. What does "ipot" stand for in the "geom" variable? I understand that if I did pass in a valid file, I'd probably not have to know this, but I was just curious... Also, this might be a overly-general question, but is this the best way to approach the problem? The basic idea now is to get chi(k) values for a bunch of different paths/RDFs, and figure out which ones match experimental values the best. This is also the main reason I want to get past the Demeter GUI and Larch-specific interface: eventually I might throw the code on a supercomputer of some sort and have it crunch the numbers. The details still have to be worked out on my end, but I was wondering if there was a faster or better way to go about finding the RDF for compound materials with known concentrations of individual atoms. I've attached some of my Python code (with more specific versions of questions 1 and 2 inserted as comments) and the feff.inp file I've been testing with. (Simple file from http://cars9.uchicago.edu/~ newville/adb/search.html) I'm currently an undergrad exploring the field of XAFS, so sorry in advance if there is something obvious that I'm missing... Also, let me know if any clarifications are needed. Thank you for your time and sorry about the email being so long, Alice ---------- Hanyu (Alice) Zhang CWRU Class of 2018 | Engineering Physics major BS/MS program | Materials science *Minors:* Mathematics | Materials science *Honors societies:* National Society of Collegiate Scholars | Tau Beta Pi | Pi Mu Epsilon *Active Clubs:* Case Origami Circle | Case Rocket Team | CWRUbotix | Case Physics and Astronomy club | Math club

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data table for larch data group
by Bruce Ravel 22 Dec '17

22 Dec '17

Matt, If I read an ascii file with read_ascii() like so: a = read_ascii(file) The "a" group has a data attribute which contains the entire data table as a 2D array. It also has 1D arrays for each column from the data table. Those 1D arrays have attribute names taken from the column labels. If I do something to change the data table, is there a function that I can call that repopulates the 1D arrays with the columns of the altered data table? For example: a = read_ascii(file) a.data is, say, array<shape=(5,500)> a.data = a.data[:, (0 .. 10)] now a.data is, say, array<shape=(5,11)> a.repopulate_arrays() # <---- the thing i am looking for.... Now a.energy, a.i0, etc should be array<shape=(11,)> Hope that's clear. 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/ 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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looking for β-Mo2C standard
by woschangqiang＠126.com 13 Dec '17

13 Dec '17

Hello, dear everyone. I am analysing some data about Mo K edge, but lack of standards. I searched many websites and mailing list, and only found the data from Carlo Segre. I am still need the data of β-Mo2C. Can anyone help sent me a data copy, if you have β-Mo2C. Thank you very much. Best regards, Qiang CHANG UCAS

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Units for density in Athena's Booth self-absorption correction?
by John Christopher Lin 11 Dec '17

11 Dec '17

Dear XAFS community, I am trying to use the Booth algorithm to correct for self-absorption in Athena, and one of the input fields is for the density of the material. What units should be used for the density in that field? (I could not find the answer in Section 9.9 of the Athena documentation on self-absorption approximations.) Many thanks, John

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how to import this kind of XAFS data
by woschangqiang＠126.com 11 Dec '17

11 Dec '17

Dear Bruce Ravel, Matt Newville and Carlo Segre, I am sorry to reply late. Thanks very much for your time and detailed explanations. Qiang CHANG Unversity of Chinese Academy of Sciences

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Re: [Ifeffit] Ifeffit Digest, Vol 178, Issue 9
by Christopher Thomas Chantler 10 Dec '17

10 Dec '17

Dear all The two best tests of any self-absorption correction are 1. that the resulting curve looks like an absorption curve, and the slope is consistent with one above the edge and 2. the pixels in a two-dimensional detector are consistent with such a pixel-dependent correction without excessive fitting parameters. That is, the pixel geometry is corrected for. It is not trivial to do this with a single channel, pixel or spectrum. Chris -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS CIT, CCN President, 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, 11 December 2017 5:00:01 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 178, Issue 9 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. Units for density in Athena's Booth self-absorption correction? (John Christopher Lin) 2. Re: Units for density in Athena's Booth self-absorption correction? (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Sun, 10 Dec 2017 02:30:05 +0000 From: John Christopher Lin <jlin9(a)stanford.edu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Units for density in Athena's Booth self-absorption correction? Message-ID: <MWHPR02MB3358E7D14D4E058A9F44C79F8F360(a)MWHPR02MB3358.namprd02.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Dear XAFS community, I am trying to use the Booth algorithm to correct for self-absorption in Athena, and one of the input fields is for the density of the material. What units should be used for the density in that field? (I could not find the answer in Section 9.9 of the Athena documentation on self-absorption approximations.) Many thanks, John

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how to import this kind of XAFS data
by woschangqiang＠126.com 08 Dec '17

08 Dec '17

Hello, dear everyone. I downloaded a XAFS data about mettalic Ru from the website of ixs.iit.edu. There are 4 groups of information in the data, and each ranges between ~67800 with ~63000 in energy. So how to import the data to Athena, and how this kind of data was produced? Does anyone come across this situation? Thanks for your time and help in advance. Q. CHANG Unversity of Chinese of Academy of Sciences

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Hello
by Neama Imam 08 Dec '17

08 Dec '17

Dear Sir I am new user of Demeter, i would like to find he exact steps of Athena and Artemis. Best Regards Neama Imam : Post Doc. Position - XAFS beamline - Elettra-Sincrotrone Trieste S.C.p.A. Strada Statale 14, Km 163.5 Basovizza (Trieste), 34149 Trieste-Italia ( neama.imam(a)elettra.eu) and Lecturer : Atomic Energy Authority Nuclear Research Center Exp. Nuclear Phys. Dept. Solid State and Nanotechnology Lab. Cairo, Abou-Zabaal, Inshas , Egypt P.O. : 13759 Fax: 00-202-44520612 imam.eaea(a)gmail.com, nama_emam2018(a)yahoo.com

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Re: [Ifeffit] Demeter 0.9.26 launch faillure
by Kirill Lomachenko 06 Dec '17

06 Dec '17

Dear Kathy and Robert, great, it works! Thanks a lot Kirill

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