August 2013 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 04 Dec '14

04 Dec '14

Hello, I had posted a comment/question a few months back when I had initially installed Mountain Lion on my mac regarding iXAFS compatibility with XQuartz and the new OS not supporting X11 anymore. Since then I have received a few comments back and I found one solution to be the best. This was originally sent by Tsu-Chien Weng from SSRL (tsuchien(a)slac.stanford.edu) Please find the following solution below. Once you install XQuartz the rest will be done in the Terminal.app. This is a one time solution and I havent had any trouble thus far with the program. Hope this works as well for everyone else as it did for me. 1. Install XQuartz from <http://xquartz.macosforge.org/landing/> 2. open Terminal.app 3. cd /Applications/Utilities 4. sudo mkdir X11.app 5. cd X11.app 6. sudo ln -s ../XQuartz.app/Contents Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

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Artemis Bug -- Path Like Object
by mattie.peck＠huskers.unl.edu 30 Aug '13

30 Aug '13

Hey Everyone, I've found another bug in Artemis. When I try to add a path like object to the paths list the program crashes. I've attached the log file and copied the text of it below. I'm using the newest version of Artemis 0.9.18.2 and running Windows XP. Thanks, Mattie Peck LOG FILE TEXT BELOW: Started at 2013-08-30T11:27:21 WinXP/.NetMedia Center Edition Service Pack 3 Service Pack 35126002302561 PATH: C:\GPIB_32\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\Program Files\QuickTime\QTSystem\;C:\strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin;C:\GPIB_32\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Zone Labs\ZoneAlarm\MailFrontier;C:\Program Files\Microsoft SQL Server\90\Tools\binn\;C:\Program Files\QuickTime\QTSystem\;C:\FullProf_Suite perl version: v5.12.3 @INC: C:/strawberry/perl/site/lib C:/strawberry/perl/vendor/lib C:/strawberry/perl/lib . Can't locate object method "pathfinder_index" via package "Demeter::SSPath" at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Path.pm line 254.

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Artemis Bug
by mattie.peck＠huskers.unl.edu 29 Aug '13

29 Aug '13

Hello, I've got another bug I think. Like I said I'm using the new version of Artemis to open old .apj files and I've noticed that the path information isn't importing correctly. I have opened several .apj files and this problem happens with all of them. I have attached the .apj file and a pdf with screen shots pointing out the discrepancies. I have the latest version of demeter 0.9.18 and I am running Windows XP. Thanks for the help. Sincerely, Mattie Peck

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Artemis Crash
by mattie.peck＠huskers.unl.edu 28 Aug '13

28 Aug '13

Hello, I'm using the new version of Artemis to open old .apj files and when I try to run a fit the program completely shuts down. It allows me to start Artemis and load plots but as soon as I click the "fit" button it crashes. I have attached the .apj file and the dartemis log file and I have copied the text from the log file below. I have the latest version of demeter 0.9.18 and I am running Windows XP. Thanks for the help. Sincerely, Mattie Peck LOG FILE CONTENTS BELOW: Started at 2013-08-28T14:18:37 WinXP/.NetMedia Center Edition Service Pack 3 Service Pack 35126002302561 PATH: C:\GPIB_32\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\Program Files\QuickTime\QTSystem\;C:\strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin;C:\GPIB_32\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Zone Labs\ZoneAlarm\MailFrontier;C:\Program Files\Microsoft SQL Server\90\Tools\binn\;C:\Program Files\QuickTime\QTSystem\;C:\FullProf_Suite perl version: v5.12.3 @INC: C:/strawberry/perl/site/lib C:/strawberry/perl/vendor/lib C:/strawberry/perl/lib . At line 55 of file rdffdt.f (unit = 1, file = 'fort.1') Fortran runtime error: End of file

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a caveat for Demeter 0.9.18 and Athena project files
by Bruce Ravel 27 Aug '13

27 Aug '13

Hi everyone, There is one feature of the new version of Athena that requires some explanation. I discovered a programming error in Athena that has existed for a long time and which made it difficult to add new features to Athena. In order to accommodate three features in this release (as well as future improvements), I had to make a change to the contents of the Athena project file and a corresponding change to how Athena reads them. The result of this is that a project file written by version 0.9.18 cannot be read by earlier versions of Athena. To manage a situation where you need to send a project file to someone who has not yet upgraded to 0.9.18, it is possible to explicitly ask Athena to write a project file that is backwards compatible. This is done by checking the "Backwards compatibility" check button in the File menu, as shown in the attached screenshot. Check that button, then re-save the project file. Athena project files exported this way will lose a small amount of information, but they will be imported without trouble by earlier versions of Athena. I apologize in advance for any confusion. I would not have made this decision were I not convinced that the new functionality was worth the potential confusion. Regards, B PS: For the technical-minded, I'll explain the situation in more detail. The change involves dropping the use of this Perl module: https://metacpan.org/module/MooseX::StrictConstructor I had been using that module to restrict the creation of new attributes for the objects that contain a data group. The effect of that module is to terminate the program when it encounters an unknown attribute. I don't quite recall why I decided that was the preferred behavior, but it has been in place since the early releases of Demeter. In 0.9.18 I needed to add three new attributes: an uncertainty in energy shift after aligning, a normalization parameter that is in Larch but not Ifeffit, and a flag related to processing dispersive XAS data. As I integrate Larch into Demeter, there will be more new Data attributes. Having made this change for this release, I do not anticipate a similar problem in the future. So, I had to bite the bullet and make this change that affects backwards compatibility. The check button for backwards compatible project files simply filters out the three new attributes before writing the project file, hence the small amount of information loss. -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Demeter 0.9.18
by Bruce Ravel 27 Aug '13

27 Aug '13

Hi everyone, I just tagged release 0.9.18 of Demeter on github and posted a new Windows updater package. This is, by any measure, a big update. The list of new features and fixed bugs is quite lengthy -- here's the complete list: http://bruceravel.github.io/demeter/Changes.html#sec-1.1 There's a lot of great new stuff in Athena and Artemis, including a lot of fulfilled feature requests. Please check it out! I have also updated both Users' Guides to reflect many of these new features. The Users' Guides can be found at Demeter's home page: http://bruceravel.github.io/demeter/ For the Windows users, I have added a item to the Start Menu that opens the folder containing the log files that are written when one of the programs runs into a problem. Hopefully that will make it easier and more convenient to find them and include them in bug reports. Cheers, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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amorphous metal alloys EXAFS spectra to be fitted with Artemis
by "Piotr J. Bardziński" 25 Aug '13

25 Aug '13

Dear Sir or Madam, I got a normalized Fe K-edge EXAFS spectrum for my amorphous 7-component alloy sample, for which I know its atomic percent composition. I need to find out the interatomic distances between the Fe and the other atoms present in the alloy (identify the peaks in R-space) as well as how many atoms of each element is surrounding the absorbing iron atom (coordination number). To meet my goal, I think I need to fit the R-space Fourier transform of my EXAFS spectrum in a program like Artemis. Unfortunately, I haven`t found any tutorial discussing how to deal with amorphous sample with unknown organization of the atoms. When you are about to prepare an atomic model in Artemis for fitting, you need to build a model with an initial interatomic distances, atomic coordination number, etc, but all that is obviously unknown to me. I know nothing about the short range order in my material and I want to learn it from the experiment itself (note that itcan be and most probably is different from the one present in crystalline structures). So, my question is, could somebody tell me how to deal with such system using the Artemis, what type of initial models for fitting should be prepared? All of your help will be greatly appreciated. Best regards, Piotr Bardziński,

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Recommendations for DFT/computational chemistry software?
by Scott Calvin 22 Aug '13

22 Aug '13

Hi all, I know many of you use DFT calculations to help model EXAFS data for molecular compounds. Do you have recommendations for good computational chemistry packages, commercial or otherwise, to use for that purpose? --Scott Calvin Sarah Lawrence College

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Lecture/tutorials required on FeFF 9.x
by S. Gautam 22 Aug '13

22 Aug '13

Dear All, I have been trying to find out some lectures/tutorials on FeFF 9.x (J.J. Rehr) to deliver my XAFS users, other than it's UserGuide as available on the website. If someone has made for their users, it would help me to deliver with acknowledging you. thanks in advance sincerely Sanjeev ----- Dr. Sanjeev Gautam KIST -PAL , South Korea -------------- http://orcid.org/0000-0003-3123-9906 -----

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(D) Atoms crashing while running feff
by Matt Frith 18 Aug '13

18 Aug '13

Dear All, I have been trying to run a feff calculation on FeAl2O4 with Fe as the absorbing atom. Every time I attempt the calculation in Artemis crashes. Atoms also crashes if it is run independently. The dartemis and datoms log files both read: "At line 90 of file istprm.f Fortran runtime error: End of file Can't close(GLOB(0x931c6cc)) filehandle: '' at C:/strawberry/perl/site/lib/Demeter/Feff.pm line 1015" Can someone please tell me what I need to edit to solve this problem? Can editing something on the input file fix this problem? The cif file and datoms log file for the problem are attached. Problem occurred on Win 7 32bit computer. Thank you for your time. Sincerely, Matt Frith Graduate Student Princeton University

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