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

sorting files in Athena
by Zajac, Dariusz 22 Feb '08

22 Feb '08

Hi, I can not find one small thing - sorting files in Athena - it makes me crazy ;) I work with QEXAFS data - usualy few tens of files or even more. Files are named in such way: "file_name"rXX.fio where XX is next file number (1, 2, 3, ... ,10, 11, 12, ... , 20, 21, etc.). I use Iffefit under Win XP, and every time when I open (import) more files I have them in such order: 1, 11, 12, 13, ... , 19, 2, 20, 21, 22, ... , 29, 3, 30, 31 ... etc. So, my question is if there is some "hidden" way to sort automatically files during importing or in the menue. Do you know something about? Is the sorting lexigraphical (from Windows)? another problem which apears, is the limitation of the memmory... thanks for answer and greetings kicaj ------------------------------------------------------------------------ Zajac Dariusz A. Deutsches Elektronen-Synchrotron -Hasylab phone: +49-40-8998-2932 Notkestr. 85 fax: +49-40-8998-2787 22607 Hamburg e-mail: Germany ------------------------------------------------------------------------

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Re: [Ifeffit] problem with feff.inp
by Matt Newville 21 Feb '08

21 Feb '08

It looks like the SCF calculation is having a hard time with the new potential. The input file you sent only has atoms out to 2.48 Ang (though perhaps you truncated it when posting???), but the SCF 4 0 30 0.2 1 in your feff.inp means to make a self-consistent potential out to 4 Ang. Without any atoms out that far, I can imagine it would have problems. I think you'll probably need a larger cluster than a single shell for a reasonable XANES simulation. Hope that helps, --Matt

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problem with feeff.inp
by Sebastiano Cammelli 21 Feb '08

21 Feb '08

Dear I have some problem with a very easy simulation. Everytime I try to introduce a potential with more elements, for instance POTENTIALS 0 26 Fe 1 26 Fe 2 29 Cu the program stops the simulation with a message that I do not understand and that is attached to this mail. This 'weird' behavior does not happen with a monoatomic potential like POTENTIALS 0 26 Fe 1 26 Fe and in this second case everything works perfectly. I would be very glad if you will have any suggestion. Thank you in advance Sebastiano Cammelli

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problem with feff.inp
by Sebastiano Cammelli 21 Feb '08

21 Feb '08

Dear I have some problem with some very easy simulations with FEFF. Everytime I introduce a second element in the matrix in this way POTENTIALS 0 26 Fe 1 26 Fe 2 29 Cu the simulation does not work and it stops with a message that you can read in the attached document. But the program works perfectly with the monoatomic potential POTENTIALS 0 26 Fe 1 26 Fe I do not understand what there is written in the feff-message, so I will appreciate any suggestion. Thank you in advance for your precious help. Sebastiano Cammelli

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Background Subtraction
by Aimee Morey 07 Feb '08

07 Feb '08

Dear All, I don't know if I am just overlooking this feature in Athena, but I would like to view my pre- and post-edge lines for background subtraction along with my experimental data. Is this feature possible with this software and does anyone have a suggestion on how to do this? Any help would be greatly appreciated, Aimee -- Aimee M. Morey Graduate Assistant Department of Chemistry, U-3060 University of Connecticut 55 North Eagleville Rd Storrs, CT 06269-3060 Phone # (860) 486 - 6567 Fax # (860) 486 - 2981 "All you need is love, but a little chocolate now and then doesn't hurt" - Lucy van Pelt (Peanuts)

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Athena installation
by cserhati csaba 29 Jan '08

29 Jan '08

Dear All, I installed the horae66 package on SUSE Linux 10.2. Everything went well, Artemis and Hephaestus works, but when I try to use Athena, I get the following message: unknown color name "Helvetica -12 bold" at /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Tk/Submethods.pm line 37. which looks like true, since 'Helvetica -12 bold' is certainly not a color name. On the other hand I do not have any idea where to go from here. Could you help me out of this please. Regards! -- Cserháti Csaba

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Athena installation
by cserhati csaba 29 Jan '08

29 Jan '08

Dear Bruce, thanks for the fast response. Ihave checked, the perl/Tk version which I use is 804.028 and there is no problem in the athenarc with fonts or colours. I any case I copied it to the end of the mail. The funny thing is, that Artemis works well, so there should not be anything wrong with the perl or Tk. I am not sure for 100% of course. Anyway, thanks! Regards! Csaba # These variables determine the color palette used by Athena. All of the # default values are named colors from X11's rgb.txt file. You can use X11 # named colors, any other named colors that your system recognizes, or # hexadecimal triplets (i.e. "#0000FF" for blue and so on). [colors] marked=darkviolet foreground=black background=cornsilk3 inactivebackground=antiquewhite3 activebackground=cornsilk2 darkbackground=cornsilk3 background2=bisque3 activebackground2=bisque2 disabledforeground=grey50 highlightcolor=blue2 activehighlightcolor=blue3 requiresupdate=steelblue4 button=red4 activebutton=brown3 mbutton=darkviolet activembutton=mediumpurple current=indianred1 frozencurrent=palegreen2 hlist=white single=red4 # These are the fonts used by Athena. There is currently no way of # modifying these within the preferences dialog. You will have to edit the # athenarc file directly. [fonts] smbold=Helvetica 10 bold tiny=Helvetica 8 normal med=Helvetica 12 normal medit=Helvetica 12 italic bold=Helvetica 12 bold boldit=Helvetica 12 bold italic large=Helvetica 14 normal fixed=Courier 12 entry=Courier 10 entrybold=Courier 10 bold small=Helvetica 10 normal -- Cserháti Csaba

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Re: [Ifeffit] Artemis
by Bruce Ravel 23 Jan '08

23 Jan '08

On Sunday 06 January 2008 11:26:53 you wrote: > Is there a way to calculate or read feff7 or FEFF8 paths with the > last version of Artemis? I could not find this information on this page: > > http://cars9.uchicago.edu/~ravel/software/aboutartemis.html > > and this option is not listed in your to-do list. I suppose that > there is a good reason for it! > > Implementing the possibility to read at once several FEFF paths (for > example from the list.dat file) could be useful, I think. Alain, I am CCing this general interest question to the mailing list. Artemis does not actually have a preference for the version of feff that you use. Since Feff is run as an external process, all you need to do is configure Artemis to use your prefered version. * In the Edit menu, select "Edit preferences". * In the Atoms groups, change `template' to "feff7" or "feff8", as you wish. That will have the effect of changing what kind of feff.inp file atoms makes. * In the Feff group, change `feff_executable' to the version of feff you are using. If the executable is not in the execution path, you will need to enter the fully resolved path as the value for that configuration parameter. If you have run feff independently of Artemis and simply wish to import the feffNNNN.dat files, that should work with no regard to the version of Feff that you used. The format of the feffNNNN.dat file did not change between feff6 and feff8. If you are seeing some particular failure of Artemis, then you will need to show me what happens. Without providing enough information for me to reproduce the problem on my own computer, it is not reasonable to expect that I can solve a problem. HTH, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] Path updating in Artemis
by Silvio Levy 31 Dec '07

31 Dec '07

Dear Bruce, in fact this is the very first shortcoming I notice in Artemis. It's a terrific piece of software. And I'm writing to propose a workaround, which I hope would be quick to implement (in any case easier than any heuristic that may eventually solve the problem in Demeter). Just as you can export and import artemis.variables file, allowing batch control over the GDS list, I'd like to have the same for parameter assignments. See below for a suggested file format, taken directly from the "Path parameter math expressions" screen. The key is that upon rereading, paths would be identified by their number -- their order in the file would be irrelevant. Hence resyncing would require only three quick steps: exporting the parameters to a file, editing the "Path number" lines to coincide with the Interpretation column, and reading the file back in again! The export/import steps might appear under the Theory menu, like the corresponding operation under the GDS menu. What do you think? Silvio ****** [A missing line might leave the parameter value untouched, while a line with nothing after the colon would unset the corresponding value.] Path number: 1 Title: [C] % whatever appears in the Data & Paths list label: N: 1 SO2: amp delE0: enot delR: delr sigma^2: ss Ei: 3rd: 4th: Path number: 2 Title: [S] label:

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Re: [Ifeffit] Path updating in Artemis
by Silvio Levy 31 Dec '07

31 Dec '07

> Modify the feff.inp file, run feff, import paths, > parametrize them. Thanks Bruce. The problem here is "parametrize them". This is too tedious a process to carry out every time two paths switch places. So I've been discarding and rereading only the paths that change numbers; still tedious, but doable. Incidentally, I have not been able to use "Export these path parameters / to selected paths" - it either does nothing or, worse, it exports the parameters to all paths. (Perhaps I don't understand the meaning of "selected" in this context.) Silvio

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