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

XAFS short course in BNL: Nov 1-3, 2017
by Anatoly Frenkel 08 Feb '18

08 Feb '18

Dear subscribers: Please share with your group members or others, who may be interested, the following information about the short course on XAFS spectroscopy: Title: *Data Analysis and Modeling of XANES and EXAFS Spectra. Applications to Nanomaterials* Dates: *November 1-3, 2017* Location: *Brookhaven National Laboratory* The course is open for applications at this web site: https://www.bnl.gov/exafs2017/ <https://mail.bnl.gov/OWA/redir.aspx?C=Cs5LzjKsiYS2QXnknBXt0VXGF6SSe4a5Kclqc…> The course will be useful for those scientists who are familiar with the foundations of XAFS experiment, theory and data analysis, and seek training in advanced methods. The course will include lectures, software demonstrations, and data analysis sessions. The emphasis will be on applications of XAFS to nanomaterials but we will welcome all participants who are interested in modern analysis methods. The course instructors will use examples from their research during presentations. The topics covered will include: -Theory of XANES, -XANES data analysis, -Structural refinement using XANES, with emphasis on the following methods: -Molecular dynamics, -Reverse Monte Carlo. -Machine Learning methods During the data analysis practicum on November 3, participants will get an opportunity to work with research projects with the help of the course instructors. The course is co-sponsored by BNL and Synchrotron Catalysis Consortium (SCC). 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 -------------------------------------------------------------------

4 7

larch warning that I don't understand
by Ravel, Bruce 07 Feb '18

07 Feb '18

Matt, When Larch starts, what is meant by warnings like this: No handlers could be found for logger "pyFAI.opencl.common" or No handlers could be found for logger "pyFAI.gui.matplotlib" The first one went away by installing python's opencl interface -- a rather sizable prerequisite! I haven't figured out how to make the second one happy. Thanks, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter

4 4

Demeter Mac install on High Sierra
by Alexandre Simionovici 04 Feb '18

04 Feb '18

Hi guyz, Trying to install Demeter on a Mac thru the Macports command: sudo port install xorg-server demeter neither demeter nor xorg-server is known ! Macs nowadays have XQuartz as X11 window manager so xorg is not needed but what about Zeus' wife ? Has someone managed to install it on High Sierra or even Sierra ? TIA, Alex -- _____________________________________________________________________ | Pr. Alexandre Simionovici | |Institut des Sciences de la Terre, UGA/CNRS tel. +33-(0)4.76.63.51.96 | |Observatoire des Sciences de l'Univers de Grenoble fax. +33-(0)4.76.51.40.58| |UMR 5275, Maison des Géosciences, alexandre.simionovici(a)univ-grenoble-alpes.fr| |CS 40700, 38058 Grenoble Cedex 9, FRANCE | |------------------------------------------------------------------------------------------------------------------|

1 0

Autosave; problem with Athena crashing on mac
by Astrid Avellan 15 Jan '18

15 Jan '18

All, I recently updated my mac OSX and had to change for iXAFS on my OSX 10.8 to the demeter servers on 10.12 It was runing fine, untill Athena crashed. When I was trying to restart it, it was frozen, asking me if I want to open the autosave file, but no being able to click anywhere. All the posts online says that you want to find the file athena.autosave in your Mac in the folder $home/.horae/stash The trick is that you CANNOT see these folders by default in your Mac. To show the hidden folders in your system, you have to type into your terminal $ defaults write com.apple.finder AppleShowAllFiles YES killall Finder Once you have done that, you can find the .horae folder ONLY manually in $home/.horae/stash. A search in your folder finder will NOT work. I deleted the Athena.autosave folder, AND open the Demeter.ini file (in $home/.horae/downloads) and chance “autosave=true” for “autosave=false”. Once you are done, you can hide the folders again by typing $ defaults write com.apple.finder AppleShowAllFiles NO killall Finder Now, everything is running smoothly. But I don’t have any autosave : I autosave myself regularly! Enjoy a long life with Athena! Best Astrid

1 0

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

12 Jan '18

Jose, I am unclear what you are sad about. The version of Feff has little to do with the quality of the analysis. See our recent paper: https://doi.org/10.1107/S1600577517011651 It is true that feff8l would simplify and streamline the code, making it easier to write and maintain. That's a bit incentive /for/ /me/ to do that work. But I think you are overstating the impact on the analysis you and others do with Artemis. B On 01/12/2018 07:15 AM, José Carlos Conesa wrote: > OK Bruce, I understand. (Sigh) > > Good luck in your actual job. > > JC > > > El 12/01/2018 a las 12:35, Bruce Ravel escribió: >> >> 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/

1 0

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/

1 0

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

2 2

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/

2 2

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

1 0

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

2 2