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

possible bug in Atoms
by Matt Frith 17 Apr '14

17 Apr '14

Dear All, I think I may have found a possible bug with the stand-alone version of (D) Atoms. If I generate an inp file in atoms, save it and then try and run feff on it later, Atoms crashes without attempting the calculation. However, if I load that same input file in (D)Artemis it will run feff without crashing. Stand-alone atoms will also fail if I generate the input file in Artemis, save it and then try and later open it using Atoms. Only Atoms or Artemis is open at a time, This problem is occurring on both 32 and 64 bit Windows 7 computers running the current (0.9.18.2) package. The problem occurred using 0.9.17 also. Any ideas of why I am all of a sudden having this issue when it has not been a problem before? The cif file, inp file, and atoms log file are all attached. Sincerely, Matt Frith

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Artemis Feature Request
by Shelly Kelly 16 Apr '14

16 Apr '14

Bruce: Does Artemis have the ability to save the path list information in a format similar to the old intrp.dat file to disk? Seems like this feature could go on the "export" button on the Atoms tab. Or it might also belong on the "Save calc" on the Paths tab. This button gave me a feff.yaml file that I don't know how to open, maybe it is in there? Thank-you for considering this suggestion. Shelly

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reporting a problem
by Ronald A. Quinlan 16 Apr '14

16 Apr '14

To whom it may concern: I recently downloaded the new Demeter (Athena). However, every time I attempt to do a LCF the system closes. I have installed Xcode and Line Command Tools for my operating systems (OS X 10.8.5). Any advice would be appreciated. RAQ

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wavelet transforms for EXAFS
by Matt Newville 14 Apr '14

14 Apr '14

Hi Folks, It's been on my To-Do list for many years, and was one of the arguments for needing to be able to handle multi-dimensional arrays for EXAFS analysis. So I'm happy to say that the Continuous Cauchy Wavelet transform of Munuz, Argoul, and Farges (from American Mineralogist 2003) is now (only ten years late) available in Larch. See http://xraypy.github.io/xraylarch/xafs/wavelets.html for an example. The code (see https://github.com/xraypy/xraylarch/blob/master/plugins/xafs/cauchy_wavelet… ) is adopted from the matlab code of M Munoz and F Farges, and that publication should be used as the citation for this routine. I know there are other implementations of wavelet transforms for EXAFS.... suggestions for changes or additions are welcome, as is additional code. The ability to actually fit data in wavelet space is not yet implemented. This was sort of planned for, and so shouldn't be too difficult to do. If anyone is interested in trying to fit EXAFS data in wavelet space, please let me know. I try to avoid too many announcements about why you should be using Larch instead of Ifeffit, but this is a clear case of something that was impossible in Ifeffit, but added as a single file of code (less than 150 lines, including code documentation) to Larch. --Matt

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Demeter: Problem closing communication to gnuplot
by George Sterbinsky 13 Apr '14

13 Apr '14

Hello, I am trying to learn to use Demeter following The Demeter Programmer Guide. When I attempt to run the first example script in the importing data section I get the following error message: Graphics::GnuplotIF (object 1): problem closing communication to gnuplot I also see the plot window flash open and then closed on my screen. I am using perl 5.16.1 on mac OSX 10.8.5. If anyone can provide any suggestions as to how I might correct this please let me know. Thank you, George

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Athena Ubuntu 12.04 LTS
by David Pickup 10 Apr '14

10 Apr '14

Hello, I'm running Athena (Demeter 0.9.20) with Ubuntu 12.04 LTS. Every time I go to the 'align data' window (with data open), Athena closes and the following message appears in the terminal: Usage: Wx::ComboBox::GetClientData(THIS, n) at /home/dave/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/Align.pm line 161, <F> line 1. Any suggestions on how to fix this problem. Thanks, Dave -- ----------------------------------------------------- Dr Dave Pickup School of Physical Sciences Ingram Building University of Kent Canterbury CT2 7NH Tel. 01227 823276 Fax. 01227 827558

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Dafs - DIFFKK
by Alessandro Lisboa 10 Apr '14

10 Apr '14

Dear, My name is Alessandro Lisboa. I am a phd student of physics in Brazil - University of Brasilia. In the last February was held the first experiment DAFS in the Laboratório Nacional de Luz Síncrotron of Brazil. I performed this experiment and now I'm trying to analyze the data. I am having difficulty to establishing a procedure for analysis. I've read many things about. I tried to generate the diffkk.inp but I can not get result. I do not know what I'm doing wrong. I ask, please, help me with a procedure to analyze. For example, what is the sequence of files that need to create and run? I would be eternally grateful for your help. Regards, Alessandro Lisboa -- ----- *M.Sc. Alessandro F. Lisboa MoreiraPh.D. Student Complex Fluids GroupUniversidade de Brasília (UnB) - Instituto de FísicaBrasília/DF (Brazil)*

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Larch: problems importing feff paths
by Johan Nilsson 09 Apr '14

09 Apr '14

Hello, I'm experimenting a bit with exafs fitting in Larch but I've come across a problem when I try to import my feff paths. Basically what happens is: $ larch Larch 0.9.22 (12-Dec-2013) M. Newville, T. Trainor using python 2.7.5, numpy 1.7.1, wx-enabled, wx version 2.8.12.1 larch> path = feffpath('feff0001.dat') file <stdin>, line 0 IndexError: list index out of range path = feffpath('feff0001.dat') ^^^ larch> I don't know if this is an issue with my input file to feff or if this is some sort of bug in Larch. I wrote the feff.inp from scratch using a template and the structure is supposed to be bulk PdO. I've attached my feff.inp and feff0001.dat if someone wants to try and reproduce the problem. I tried another set of paths that was calculated for FeO using an input file from webatoms and those appear to import without issues. I've attached those as well in a zip if someone wants to compare the two sets. I'm running Ubuntu 13.10 on my PC. Best regards, Johan

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D-Atoms program, common positions and occupancies
by Moneeb Shatnawi 09 Apr '14

09 Apr '14

Dear Robert Gordon, Hello, Thank you so much for the reply. Yes, it turned out that I was using a relaxed model of CdSe where I should have changed the space group accordingly. When I replaced the input file with the correct one, everything went fine with no error messages, I appreciate your help, Moneeb

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my backlog of Demeter chores
by Bruce Ravel 08 Apr '14

08 Apr '14

Hi everyone, For the last couple of weeks, I have been having trouble finding time to address the bugs that have been reported. Moneed Shatnawi, Alexander Britz, Matt Frith, Mengling Stuckman, Alison Tebo, and Thomas Huthwelker have all asked reasonable questions about actual issues with the software. I am writing today to assure them that they are on my mind, but there haven't been enough hours in the day or days in the week recently for me to address the problems. But I will! Soon, I hope. 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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