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

Athena reporting incorrect element on import
by Kenneth Latham 20 Apr '15

20 Apr '15

Hi, I am having a number of issues with importing my data into Athema, the data that I collected was on the carbon K edge. As there is an issue with recording carbon (as it builds up on the mirrors), the synchrotron that I performed my measurments at (Australian Synchrotron) has developed software to perform a double normalization to remove these effects. The problem comes when importing the now normalized data into Athena. As it doesn't require normalization again, I select the norm(E) data type and the correct column for energy and response which produces the correct plot of the data. When I click OK it attempts to produce the other plots, sometimes it manages to make a k-space and R-space but q-space is never displayed and other times it only manages the energy plot. Additionally, the word element is lit up red and it has selected beryllium as the element on the L2 edge. Changing this to carbon does not seem to fix the problem as it reverts back to beryllium as soon as I leave the main page. Finally, when I go to peak fitting, any value added for peaks informs me that it is out of range. I have attached some normalized data. Any help with this would be greatly appreciated. Regards, Ken Latham

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Re: [Ifeffit] Problems installing demeter in Manjaro Linux
by Ramiro Moreira Toja 16 Apr '15

16 Apr '15

Bruce, force-installing with cpan did the trick, thanks! I still wonder if the apache/src thing may give me trouble some day. When installing the XMLRPC::Lite module, I hit on that again, but everything worked in the end. Thanks for your help (and for this great software, too!) Ramiro I'm not familiar with Manjaro. Are there package in its packaging system for those two perl modules? If so, just install them that way. If not, you could try running the cpan program and doing: force install Regexp::Assemble and force install XMLRPC::Lite Another option is to download those two packages from metacpan.org and install them by hand. As for the pgplot installation -- I believe I had to do the same thing the last time I built Ifeffit. Glad you figured it out! Good luck! Let us know if you run into other problems. B On 04/15/2015 09:40 PM, Ramiro Moreira Toja wrote: Hi, I'm using Manjaro 0.8.12 x64. I tried to install the demeter collection (following these instructions <https://bruceravel.github.io/demeter/pods/installation.pod.html>), but keep failing to do so. Also, I've checked to have installed all the reccomended packages, including apache and gnuplot. When installing PGPLOT, I've had to edit the configuration to use gif instead of png, because it kept failing to install. Once I did this, it went smoothly. I add this piece of information here hoping this helps to solve later problems. I'm having a little trouble installing dependencies. At the "sudo ./Build installdeps", it kept having trouble to find the apache/src. After a little Web search, it seems like I need to manually download the httpd sources, so I got them from here <http://apache.xfree.com.ar//httpd/httpd-2.4.12.tar.bz2>, but now it indicates I need Apache 1.3.0 version! If I do "perl Build.PL", I get: perl Build.PL Checking prerequisites... requires: ! Regexp::Assemble is not installed ! XMLRPC::Lite is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation So, I guess I'm having some more problems with the dependencies, apart from the Apache ones. What should be my next move to fix this? I've been even considering using a Ubuntu LiveUSB with persistence, just to get this working in a proven system, but really would like to get it working on my OS of choice. Thanks in advance Ramiro _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel ------------------------------------ bra...(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/ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Problems installing demeter in Manjaro Linux
by Ramiro Moreira Toja 16 Apr '15

16 Apr '15

Hi, I'm using Manjaro 0.8.12 x64. I tried to install the demeter collection (following these instructions <https://bruceravel.github.io/demeter/pods/installation.pod.html>), but keep failing to do so. Also, I've checked to have installed all the reccomended packages, including apache and gnuplot. When installing PGPLOT, I've had to edit the configuration to use gif instead of png, because it kept failing to install. Once I did this, it went smoothly. I add this piece of information here hoping this helps to solve later problems. I'm having a little trouble installing dependencies. At the "sudo ./Build installdeps", it kept having trouble to find the apache/src. After a little Web search, it seems like I need to manually download the httpd sources, so I got them from here <http://apache.xfree.com.ar//httpd/httpd-2.4.12.tar.bz2>, but now it indicates I need Apache 1.3.0 version! If I do "perl Build.PL", I get: perl Build.PL Checking prerequisites... requires: ! Regexp::Assemble is not installed ! XMLRPC::Lite is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation So, I guess I'm having some more problems with the dependencies, apart from the Apache ones. What should be my next move to fix this? I've been even considering using a Ubuntu LiveUSB with persistence, just to get this working in a proven system, but really would like to get it working on my OS of choice. Thanks in advance Ramiro

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FEFF calculation for two inequivalent absorbing sites
by Eugenio Paris 10 Apr '15

10 Apr '15

Hello everybody, I'm trying to make Co K-edge EXAFS fitting for the Co3O4 compound (*.cif file is attached). The nearest neighbour of Co is oxigen at about 1.93 Angstrom distance. Cobalt sits in two inequivalent sites in the unit cell. When I perform the FEFF calculation in Artemis for either one or the other site i get the same path with Reff = 1.93 and degeneracy = 4. So i wonder what is the correct way to take account of the presence of both sites. At the beginning i was thinking to put 2*amp as S0^2 parameter to take account for twice the coordination number. Then i tried to use the "Aggregate" option in Artemis. When I use this option i get exactly the same result, i.e. a SS path with Reff = 1.92 and degeneracy = 4... I was expecting to get twice the degeneracy.. (the margin and beta parameters are set to default) My question is: Why do i get the same path list when I do use the "Aggregate" pathfinder and when I don't? What is wrong in my interpretation? Thank you in advance! Sincerely, Eugenio

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error message by import
by Zimina, Anna (IKFT) 09 Apr '15

09 Apr '15

I get the following error message when I read the txt file with two columns of data (energy and intensity): "11:42:20: Use of uninitialized value $line in pattern match (m//) at C:/strawberry/perl/site/lib/Demeter/Files.pm line 188." Still the data can be read. What is the problem? Thanks in advance, Anna Zimina. ______________________________________________________________________________________ Karlsruhe Institute of Technology (KIT) Institute of Catalysis Research and Technology (IKFT) Dr. Anna Zimina Beamline scientist Hermann-von-Helmholtz-Platz 1 Building 345, Office 108 76344 Eggenstein-Leopoldshafen Phone: +49 721 608 28673 Fax: +49 721 608 26789 E-Mail anna.zimina(a)kit.edu<mailto:anna.zimina@kit.edu> [cid:image001.jpg@01D071F1.C77B7BC0]

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Atoms
by Zimina, Anna (IKFT) 08 Apr '15

08 Apr '15

In the last version Atoms is not present as a separate program. Is it correct? Mit freundlichen Grüßen, Anna Zimina ______________________________________________________________________________________ Karlsruhe Institute of Technology (KIT) Institut für Katalyseforschung und -technologie (IKFT) Dr. Anna Zimina Wissenschaftlerin Hermann-von-Helmholtz-Platz 1 Geb. 345 Zi. 108 76344 Eggenstein-Leopoldshafen Fon: +49 721 608 28673 Fax: +49 721 608 26789 E-Mail anna.zimina(a)kit.edu<mailto:anna.zimina@kit.edu> [cid:image001.jpg@01D071F0.3A2FB840]

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Evaluation of uncertainty using correlated Debye model + advices for the fitting of an hexagonal Co-foil
by Samy OuldChikh 07 Apr '15

07 Apr '15

Dear all, I would like to go beyond the fitting of the first shell for a cobalt metallic foil acquired at FAME beamlime (ESRF). It's not mandatory for the determination of So in this case, but I just would like to improve myself in EXAFS fitting. The cobalt foil has an hexagonal structure (P 63/mmc, a =b=2.507 A, c= 4.068 A) according to the supplier. The first 49 scattering paths calculated with FEFF were selected to cover the R range up to 5.1 A. This include multiple scattering paths. The parametrization of those scattering paths is as follow (.apj enclosed) : - Distances : 1) a spherical expansion term was used to describe distance variation in [hkl] direction (reff*alpha1) with l considered as "large" when compared to h,k (reff*alpha1) 2) another spherical expansion term was used to describe distance variation in pure [hk0] direction (reff*alpha2) 3) a rough average of two previous expansion terms for [hkl] direction when h,k are comparable to l (reff*(alpha2+alpha1)/2). - For modeling disorder, the correlated Debye model was used with 3 parameters dt, dt2, dt3 (t =293K): 1) [hkl] direction with l considered as "large" : debye(t,dt) 2) pure [hk0] direction: debye(t,dt2) 3) for [hkl] direction with h,k comparable to l : debye(t,(dt+dt2)/2) But does this choice of parametrization is really reasonable? It seems very rough to me but when I look at the fit results it looks ok. - Uncertainty on : 1) Distances : is it simply delta(r) = reff*delta(alpha) ? 2) Debye-Waller : I can't figure out how to relate the uncertainty computed for the Debye temperatures (dt, dt2) to the uncertainties of the debye-waller terms for each scattering paths. Although I spent some times trying to understand this paper, http://journals.aps.org/prb/pdf/10.1103/PhysRevB.20.4908, I can't write a simple relation at the end. Many thanks for your kind help, 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 ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Re: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED]
by Ravel, Bruce 06 Apr '15

06 Apr '15

Zhaoming, This conversation should be happening on the Ifeffit Mailing List. I did not notice that last night when I replied to your first email. Yet another reason not to answer email late at night! I continue to be sceptical of your claims. I have no problems with the data file you sent on either Windows or Linux once I correctly select the columns in the column selection dialog. Once imported, the default values for normalization are set as I expect and the data is interactive in the normal manner. Here are some hints about how to provide a useful bug report: http://bruceravel.github.io/demeter/pods/bugs.pod.html Please read it carefully. If there is more to this conversation, please use the mailing list. 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 ________________________________ From: ZHANG, Zhaoming [zzx(a)ansto.gov.au] Sent: Thursday, April 02, 2015 1:00 AM To: Ravel, Bruce Subject: RE: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED] Hi Bruce, Sorry, I did have to specify column 4 as energy, 7 as Io and 8 as It. The new version of Athena does read the .dat file in, but the default values for normalization are way wrong, and it doesn’t work by manually change them either. I’m happy to send you screen shots if necessary. Thanks again for your help. Zhaoming From: Ravel, Bruce [mailto:bravel@bnl.gov] Sent: Thursday, 2 April 2015 12:43 PM To: ZHANG, Zhaoming Subject: RE: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED] Zhaoming, I'm afraid I am sceptical of your story. I have no trouble reading this file and I don't believe that any change I've made since 0.9.20 would have affected this. Who knows, though. I'll take a lok on a windows machine when I get into work tomorrow morning. It's a rather awkward file. The first column is an index, not energy. That's one of my pet peeves -- just a ridiculous way to present the data and kind of mean-spirited to the user. When something is measured in energy, the first column should be energy. That means you have to explicitly select column 2 as the energy. Column 2 appears to be in keV, so you need to explicitly set that in the column selection dialog. Because column 1 was not the energy, Athena had no way of figuring that out. I have no idea which columns have data in them. 7 and 8 look rather like I0 and It. So you need to explicitly set your data columns, as well. I've attached a screenshot of the column selection dialog with all those settings. When data are presented as obfuscated as they are in this data file, it is not reasonable to expect that Athena will magically know how to disentangle everything without your help. You have to be responsible for knowing which columns to combine to turn your raw data into mu(E). B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov<mailto:bravel@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 ________________________________ From: ZHANG, Zhaoming [zzx(a)ansto.gov.au] Sent: Wednesday, April 01, 2015 7:34 PM To: Ravel, Bruce Subject: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED] Dear Bruce, I’ve encountered the same problem as Sander Bruun. My data were obtained from the Australian Synchrotron. In the past, I could read the .dat file (see attached example) directly into Athena. But it doesn’t work with the new version (0.9.20), and the beamline scientist doesn’t know why either. I would really appreciate if you could let me know what ‘fix’ we need! Thanks so much. Warm regards, Zhaoming

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Possible Error on 0.9.21
by Clark, Adam 01 Apr '15

01 Apr '15

Hi I have recently encountered an error in displaying the path geometry in the latest version of artemis, 0.9.21. When running feff and then selecting a path and viewing the geometry of this path an incorrect path is shown. This does not occur when using the same feff.inp file on the older 0.9.20 version. The problem is limited to the numbering and showing of the path geometry in the feff calculation window. Attached is the feff.inp, feff.txt files and a screenshot showing the produced feff.txt ‘show geometry for this path window’ for a selected @ O.1 @ path (instead showing the @ Zn.1 @ path) and ‘atoms and feff’ window showing the discrepancy in path numbering between the feff.txt file and feff window. Thanks Adam

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Artemis on Yosemite
by George Sterbinsky 26 Mar '15

26 Mar '15

Hello, When I attempt to open Artemis on OSX Yosemite (10.10.2) the error message copied below prints to the terminal. The initial image that indicates Artemis is opening does appear, although Artemis fails to open. Athena and Hephaestus open without error. Any suggestions as to how this could be resolved would be appreciated. Thanks, George $ artemis Can't locate Math/Round.pm in @INC (@INC contains: /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/ScatteringPath.pm line 44. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/ScatteringPath.pm line 44. Compilation failed in require at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter.pm line 306. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/UI/Artemis.pm line 26. Compilation failed in require at /opt/local/bin/artemis line 34. BEGIN failed--compilation aborted at /opt/local/bin/artemis line 34.

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