January 2018 - Ifeffit - millenia.cars.aps.anl.gov

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.) >

5 7

XAFS short course in BNL: Nov 1-3, 2017
by Anatoly Frenkel 09 Feb '18

09 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

Autosave; problem with Athena crashing on mac
by Astrid Avellan 16 Jan '18

16 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