April 2015 - Ifeffit - millenia.cars.aps.anl.gov

Bug report - autosave on mac
by Jean-Baptiste ABBE 16 Jul '15

16 Jul '15

Hi everybody, I wanted to report a really annoying problem for mac users. I’m running Athena on my laptop, on OSX 10.10 (Yosemite) with macports. I had to install also quartzX11 to be able to plot data (without it, it couldn’t find the DISPLAY value), but otherwise evrything went smoothly for a few days. Then the first bug occured. I wasn’t able anymore to select any point on the plotting area to do normalization, I had to set the value in the boxes instead. It was annoying, but I could manage that. But now I have a much more disturbing issue. Athena once crashed, (in the terminal, it was sait « Terminated 15 »), and every time I tried to launch it again, the same thing happens : 1) athena launch, a little bit longer than usual 2) a box appear to give me choice to recover data by importing it from autosave or not 3) I can’t select anaything and the rainbow wheel of death appears. After a few hours, nothing changes… and I have to terminate the programm manually. So I do some search on the internet and found thoses topics on the mailing list, and I tried thoses solutions : https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html> https://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04514.h… <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04514.html> I tried to find the autosave file : nothing I tried to uninstall and reinstall macports : nothing I tried to uninstall macports and install the demeter-devel : nothing In demeter-devel, i tried to modify the athena.demeter_config file, by changing the autosave prompt box value from true to false, and despite being admin on ma mac, I’m not able to change antything in the file. So nothing works at this moment. I will try again other solutions, but I will gladly accept any kind of help to solve my issues. Thank you ABBE J-Baptiste

4 7

Be EXAFS and publication
by Joshua Kas 08 Jul '15

08 Jul '15

Hi, This may be a long shot, but I was wondering if anyone is aware of EXAFS data on HCP Be. In particular we are looking for Debye-Waller Factors, so a publication would be great, but just data might work as well. Thanks, Josh Kas

2 1

Demeter Package for mac
by ebonturim＠usp.br 30 Apr '15

30 Apr '15

Hi everyone! I would like to know if the Demeter Package is already working into the mac (2015). Someone could use it? How do install the right way files? Thank you. Everton Bonturim

2 1

Re: [Ifeffit] energy resolution
by Lisa Bovenkamp 20 Apr '15

20 Apr '15

Hello all. I am getting confused with different comments how to determine the energy resolution of an XAS beamline. I think using peak fitting to determine the line width is a reasonable method. The basis of a XAS peak is the Voigt profile (a combination of a Lorenzian and Gaussian) The width of the Lorenzian equals the natural line width while the width of the Gaussian represents the experimental line width and some features Now here is question 1: What is the combination of the two profiles in the Athena peak fitting routine for the Pseudo-Voigt? Question 2: Is the sigma (Gaussian width) that delta E that represents the resolution - (E /delta E) ? Using a different program (Igor Pro) to determine the width gives different results because can only use a simple combination of Lorentz and Gauss (1:1). Thanks. Lisa

2 1

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

4 4

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

1 0

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

2 1

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

3 3

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]

3 6

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]

2 1