March 2004 - Ifeffit - millenia.cars.aps.anl.gov

Random behaviour Artemis 0.7.001
by mauro＠rulp.org 17 Mar '04

17 Mar '04

Hi to all, I'm a new ifeffit user (I started using this software in october '03). My environment: Linux Debian/GNU, perl 5.008003, Tk 800.024 and Ifeffit 1.2.5 First of all, I would like to express my congratulations to the authors and thanks them all for their work. I updated the new versions last week and I appreciate the new more user friendly layout. But I found some strange behaviour with Artemis. 1. When Artemis starts, I receive this message: Use of uninitialized value in join or string at /usr/local/bin/artemis line 1236 2. Sometimes I save a project and when I reopen it doesn't found the datafiles (obviously I didn't modify the file names). 3. Sometimes the fit have no-sense values so I have to save the project, rerun Artemis, and with the same parameters I obtain good fit. It seems like after a certain number of fits the software starts to fail. I would like to know if someone have noticed the same behaviour. The problem is that points 2,3 are random. Thanks, Mauro

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Re: problems with the new version
by Peter Southon 17 Mar '04

17 Mar '04

Hello Matt, I'm having similar problems with the updater as those described a few days ago, but the fix that you posted didn't work for me. I've copied in the new .ini file (which I figure just re-sets the date stamp). This pursuades the updater to run, but after processing for a few seconds (and I'm sure it does send an internet message) it flashes up a TK screen for a split second then closes/crashes, then the main program runs. I can't figure out how to extract an error message from the updater. This is a new installation - putting ifeffit onto my home computer (WinXP), using an old-ish install file from cd (ifeffit 1.2.4) and updater 1.1. I'm rather avioding downloading anything that I don't have to as my connection here is rather slow... Hope you can help!! Cheers, Peter > Hi Bruce, Giuliana, > > There have been a couple other reports like this, but they always > seem to go away eventually. I doubt the firewall is an issue (if you > can download a zip file from a web page on your computer, the > updater will work.. if you can't download a zip file, the updater > should let you know this). > > I've just added a FAQ entry about this: > > http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=show&file=faq02.008.htp > > The upshot is that I'd suggest replacing the file > C:\Program Files\Ifeffit\updates\updater.ini > > with > http://cars9.uchicago.edu/ifeffit/updates/updater.ini > > and editing (notepad,wordpad,...) and the file > C:\Program Files\Ifeffit\updates\updater.dat > > to read '005'. (Just three numbers, on one line). Then, re-running > athena, artemis, etc should immediately tell you that there are > updates available, and download and install them. If you have > problems, please note whether > a) ifup_006.zip gets downloaded (the progress bar in the > lower right corner of the updater GUI should shows the > download progress). > b) whether the main GUI panel lists any files being unpacked. > > Hope that helps, > > --Matt > > Peter Southon Research Fellow School of Chemistry University of Sydney Australia ------------------------------------------------- This mail sent through IMP: www-mail.usyd.edu.au

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configurational average
by Makoto Matsuura 16 Mar '04

16 Mar '04

My question is how the path files (feffxxx.dat) are defined when "configurational average" is used in feff calculation. And how we apply path data avaraged configurationally to the fitting calculation. For example in case of CaCu5 structure two Cu sites are there, i.e. 3g and 2c site. If we use control card of "CFAVERAGE" in feff calculation with setting Cu 3g as a core. Then configurational average will be done over the 2c sites. The below shows the two log files of feff8 ( list.log ) in the case of the configurationally averaged (core Cu 3g site) and without configurationally averaged. I calculate Fourier transform (RSF) using each path (feffxxxx.dat) deduced by feff calculation applying configurationally averaged and compared with that of the total one. I fail to coincide sum of RSF's for each path with the total RSF. I like to know the reason of it. Next question is how we use the paths (feffxxxx.dat) in the feffit calculation when we use "configurational average" in feff calculation. Can we use the feffxxxx.dat files as it is for the feffit? list of list.log when configurationally average card is used. //////////////////////////////////////////////////////////////////////////// /////////////////////////////////// Cu K-edge for Cu 3g of CaCu5:output for feff8 absorber Feff 8.10 Cu configurational avaraged with Cu2c site DEBYE temp =300K at 20K Abs Z=28 Rmt= 1.347 Rnm= 1.394 K shell Pot 1 Z=28 Rmt= 1.354 Rnm= 1.403 Pot 2 Z=57 Rmt= 1.773 Rnm= 1.830 Gam_ch=1.576E+00 H-L exch Mu=-1.168E+01 kf=1.918E+00 Vint=-2.026E+01 Rs_int= 1.891 ----------------------------------------------------------------------- pathindex sig2 amp ratio deg nlegs r effective 1 0.00000 100.000 2.000 2 2.4634 2 0.00000 93.844 2.000 2 3.2025 3 0.00000 16.979 1.000 2 3.9873 4 0.00000 13.047 8.000 3 4.2800 5 0.00000 55.603 4.000 2 4.3163 6 0.00000 44.329 4.000 2 4.7095 7 0.00000 36.814 2.000 2 4.7769 8 0.00000 19.574 8.000 3 4.8182 9 0.00000 8.950 8.000 3 4.8369 10 0.00000 4.441 2.000 4 4.9269 11 0.00000 3.423 4.000 4 4.9268 12 0.00000 8.603 4.000 3 5.0671 13 0.00000 13.297 8.000 3 5.2064 14 0.00000 11.402 8.000 3 5.5573 15 0.00000 27.903 4.000 2 5.5851 16 0.00000 3.001 8.000 4 5.6659 17 0.00000 31.325 8.000 3 5.8408 18 0.00000 23.977 4.000 2 5.8943 19 0.00000 8.327 4.000 4 6.0965 20 0.00000 25.802 8.000 3 6.1496 list of list.log without using configurational average //////////////////////////////////////////////////////////////////////////// ////////// Cu K-edge for Cu 3g of CaCu5:output for feff8 absorber Feff 8.10 Cu No configurational avaraged DEBYE temp =180K at 20K Abs Z=28 Rmt= 1.347 Rnm= 1.394 K shell Pot 1 Z=28 Rmt= 1.354 Rnm= 1.403 Pot 2 Z=57 Rmt= 1.773 Rnm= 1.830 Gam_ch=1.576E+00 H-L exch Mu=-1.168E+01 kf=1.918E+00 Vint=-2.026E+01 Rs_int= 1.891 ----------------------------------------------------------------------- pathindex sig2 amp ratio deg nlegs r effective 1 0.00000 100.000 4.000 2 2.4634 2 0.00000 96.591 4.000 2 2.5063 3 0.00000 93.844 4.000 2 3.2025 4 0.00000 14.579 16.000 3 3.7165 5 0.00000 16.979 2.000 2 3.9873 6 0.00000 13.047 16.000 3 4.2800 7 0.00000 55.603 8.000 2 4.3163 8 0.00000 27.399 4.000 2 4.3410 9 0.00000 8.758 16.000 3 4.4556 10 0.00000 12.606 16.000 3 4.6430 11 0.00000 12.963 16.000 3 4.6430 12 0.00000 6.132 8.000 3 4.6767 13 0.00000 44.329 8.000 2 4.7095 14 0.00000 36.814 4.000 2 4.7769 15 0.00000 19.574 16.000 3 4.8182 16 0.00000 8.950 16.000 3 4.8369 17 0.00000 10.192 4.000 3 4.9269 18 0.00000 9.147 4.000 4 4.9269 19 0.00000 4.441 4.000 4 4.9269 20 0.00000 3.423 8.000 4 4.9268 ****************************************** Miyagi National College of Technology Prof. Makoto Matsuura email: matsuura(a)miyagi-ct.ac.jp TEL&FAX 022-381-0270 ******************************************

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Bug in Atoms
by Schmithals 16 Mar '04

16 Mar '04

Hello, I have attached an atoms.inp file that causes problems when used with Artemis. Both, Atoms run from within Athena as well as TkAtoms generate a feff.inp file with a wrong POTENTIALS-Card. Subsequently, FEFF will refuse to run, saying that potential number 1 is not used. I tried the same procedure with an older atoms.exe and had no problems. Another bug: TkAtoms allows only to open the space group browser only once. Every further click on "Browse space groups" will have no effect. I use Windows 2000 Pro. Regards, Gerrit

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Debian versions of horae-031
by Carlo U. Segre 16 Mar '04

16 Mar '04

Hello All: For those of you interested in Debian Linux packages, I have just completed a complete restructuring of the horae and ifeffit packages. This includes individually packageing the CPAN modules that are used in horae. The "unstable/sid" packages are already up and available and I should have the "stable/woody" versions posted by Tuesday midmorning. Please let me know of any bugs that you might find so that I can make the packages work. To get the packages, place the following lines in your /etc/apt/sources.list file: deb http://fermi.phys.iit.edu/debian/woody binary/ deb-src http://fermi.phys.iit.edu/debian/woody source/ deb http://fermi.phys.iit.edu/debian/sid binary/ deb-src http://fermi.phys.iit.edu/debian/sid source/ for the two distributions. Now that I have the new framework and a cleaner structure, it will be easier for me to keep current with Bruce's releases. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)agni.phys.iit.edu http://www.iit.edu/~segre

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Athena quirk
by Dave Baker 16 Mar '04

16 Mar '04

Bruce, I have recently updated my Ifeffit package to the current versions (Ifeffit 1.2.5 and Athena 0.8.026) under Win2k Pro, and I have noticed something that is a bit irritating. My situation is this: I have a project open in Athena, but decide to refresh or rename that project file to something different from within Windows explorer. I expected to only have to close the project file within Athena but keep Athena itself running. This is not the case, however, as Athena does not "let go" of the file until it is completely closed. After closing, I can rename the project file without difficulty, but then I must restart Athena from square one. Is this normal behavior? Does anyone else see this behavior? Thanks in advance for your help. -Dave Baker

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Re: [Ifeffit] Bugs in new versions of Athena and Artemis
by Schmithals 11 Mar '04

11 Mar '04

Bruce, thanks for the comprehensive response to my questions. > You can edit the titles on the data page to put your own information > in the header written to the data chi(x) files. But I see your point > and will include that in the next release. Concerning Athena I see how to work around the problems. Putting parameter-information in the project title is indeed a help. But usually the parameters will change often so an automated writing to the exported files would be better. I would therefore appreciate this function in a future release. I will now concentrate on Artemis. I did again a new full installation of Ifeffit and set up the example files again, carefully looking at the error messages. (BTW: Initially the FEFF-executable is set to feff6, it is necessary to switch to feff6l by hand). > 1. Did you do anything to the folders or files under > C:\Program Files\Ifeffit\horae\stash\artemis.project.0\ > while Artemis was still running? I did never edit any file in the \horae\ .. folders but before deleting the old installation I had a look there and found around 20 folders called "artemis.project.0", "artemis.project.1" etc. After the new installation the "artemis.project.0" was removed each time not cluttering up the folder. Could there be a relation to the errors? > The basic flowchart for an Artemis 0.7 project is this: (1) import > data, (2) import or create atoms data, (3) run atoms, (4) check the > feff.inp data and run feff, (5) set up your fitting model, (6) hit the > big green button. I set up the project file in the order you described: and indeed everything works normal ! I therefore tried to reverse the order: first load in a feff-calculation, play with it and afterward load a data-file. The project file went corrupt again (error messages in ARTEMIS.TRAP). I tried it a few times in the "wrong order", some times it went OK. After a while I figured out what the problem might be: When I load the data file (for the first time) via the dialog Data | Change Data File problems will occur (which I usually did despite the fact the the dialog was built to CHANGE an existing data file - I was just confused about the variety of ways to load in a data file). When I first load in the data file via File | Open data file or project it will be OK. Does that make sense? I am sorry but the errors are not always reproducible and I did my best to figure out a possible scheme. I included a corrupted and a good file but they seemed pretty equal. When I load in the corrupted file a second time everything will be okay, probably only the copy in the stash-folder gets corrupt? I summarize: when I follow the correct order I could not find any errors so far. All the different error messages I had might be related to a wrong loading procedure. > (1) Completely delete the feff calculation from the project using the > discard option in the Feff menu and then start over again Do you think it is risky to delete the FEFF-calculation in the Zip-file manually? HTH, Gerrit

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Re: [Ifeffit] Bugs in new versions of Athena and Artemis
by Stanislav Stoupin 11 Mar '04

11 Mar '04

> Date: Thu, 11 Mar 2004 10:20:42 -0500 > From: Bruce Ravel <ravel(a)phys.washington.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Bugs in new versions of Athena and Artemis > > > Gerrit > > I am looking into each of your points about artemis. I have not seen > any of these behaviors on my linux machine, so I booted up the Windows > 2K virtual machine and am checking them out. > > Just to keep my thoughts organized, I am going to address each of your > points in separate emails as I get to them. > > > - Having multiple FEFF-Calculations in one file is not possible: > > 'Co Hexa Cubic.apj' is a project where I imported two different atoms > > calculations (first hexagonal cobalt, second cubic cobalt) and ran FEFF. > > But only the second calculation can be displayed. And when looking at > > the project file there exists only one FEFF-calculation despite two > > trees in the Artemis program. It seems as if the first calculation has > > been overwritten. > > I concur that the project file you sent is flawed. There is certainly > only one feff calculation in the file. > > However, I cannot reproduce this problem on my computer. When I > import two atoms.inp file and run atoms then feff in any order, I end > up with two usable feff calculation. When I save the project and > reopen the project, I still have two usable feff calculations. > > Apparently something went wrong as you were doing this, but I don't > yet have enough information to track down the problem. > It seems similar to the problem that I had but it was with the previous version of Artemis which I still use I have seen this kind of behavior both on my Linux machine (Debian (woody) - Artemis 0.6.010) and my Windows machine (windows 2000 - Artemis 0.6.008) I think that my project file was flawed somehow To be more precise I can describe my problem as follows: I used the same project file as a standard and all other projects were based on it. Every new project I created was a modification of that standard.The standard contained two data groups there were three Feff calculations assigned to the first group of data: FEFF(1) FEFF(2) FEFF(5) and two Feff calculations assigned to the second one: FEFF(3) FEFF(4) Every time I modified the standard and saved as a new project file this new project file did not contain FEFF(5) when reopened ( not only the FEFF(5) paths but the whole tree) If I modify the reopened project by addition of this FEFF(5) and then save the project again the problem is gone I was unable to reproduce the problem. Therefore, I suggested the bug was in the project file that I used as a standard. The solution to the problem was that I have created another standard from scratch and I never had this problem again Stanislav

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Bugs in new versions of Athena and Artemis
by Schmithals 11 Mar '04

11 Mar '04

Hello, I just installed the new update so now I have Athena 0.8.026 and Artemis 0.7.001. First I would like to say that I like the new features, particularly the possiblity to run Atoms and FEFF within Artemis and the fact that all files are included in one zip-file. However, I noticed some major bugs on my Windows 2000 machine (although I do not want to exlude the possibility of wrong handling). I attached some example files as a zip archive. Athena: - I usually read in a rather large number of chi(k) data-files. It then happens often that a few of the created groups will not be displayed: when I mark/select such a group and press a purple/red button it might for example plot correctly for E, R and q; but in k-space it will simply give a message to the Echo Area ( .. plotting in k-space .. done! ) but the resulting graph will be blank. This behaviour generally occurs when the number of data-files is around 150 but I also observed it with less files. I am sure that the files to import are corrupt as they behave well when I read them in separately. - When I close the graph window the main athena program will crash. I remember that this behaviour has been discussed earlier. - While loading (and saving) of projects with many data groups is reasonably fast, closing such a project requires an extremely long time. Is that a normal behaviour? Artemis: The behaviour of Artemis on my machine makes its use almost impossible: - Data file can not be read in: When I read in a datafile (Data | Change data file) Athena will correcly show up a dialog and display the data in k-space in the graph window. Any subsequent click on k, R or q-buttons will give the error message: "You have not yet loaded data ...". I am not be able to save the datafile, instead an error message will occur "You cannot write the artemis description file". I tried it with my own data (exp005_absW.chi) and with an example file (cu010k.chi). If I first set up a FEFF calculation and afterwards import a data file I am able to plot the data file in k-space but in R-space it will only show a horizontal line. When fitting always a warning message will appear: "There are errors in your math expressions ...". "Co Cubic 3.apj" is an example of such a file. As you can see, the folder chi_data in the zip-file contains no data. - Having multiple FEFF-Calculations in one file is not possible: 'Co Hexa Cubic.apj' is a project where I imported two different atoms calculations (first hexagonal cobalt, second cubic cobalt) and ran FEFF. But only the second calculation can be displayed. And when looking at the project file there exists only one FEFF-calculation despite two trees in the Artemis program. It seems as if the first calculation has been overwritten. - Previous FEFF paths are not removed from Zip file 'Co Cubic 1.apj' is a project where I first set the cluster size to 8 and then ran Atoms and FEFF and imported all paths. I then set the cluster size to 4 and did the procedure again. The second time the same number of paths will be imported as in the first case although there should only exist a fraction of them. This problem can only be solved by deleting first all paths in the zip-file manually (which I do using a zip-program) and then run FEFF again. - Making 'Sum of paths (no fit)' produces no output (when no data file is loaded). In 'Co Cubic 2.apj' I set up an Atoms page and ran the FEFF calculation. When choosing 'Sum of paths (no fit)' | all paths from the menu it will indicate a correct calculation but when trying to plot the fit it will fail. I wonder if the described behaviour depends on Windows or on my particular computer. I tried a completely new installation which did not improve the situation. After complaining so much I would still like to propose a new feature: after processing data with Athena I export the chi(R)/chi(q) data to use it in a data analysis program with enhanced graphing capabilities. I would really appreciate if the used parameters would be written at the beginning of the exported datafile as it is quite difficult to keep track of all these options. I hope my remarks are helpful. Regards, Gerrit

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Ins:-simple suggestion when you make new releases
by ALAM Sher 11 Mar '04

11 Mar '04

Hi Bruce, I was able to find the longmess problem and in one solution did a version change [which you did not like] because I use both versions of perl 5.5 and perl 5.8 and several versions of red hat 7.2,7.3, 8 and 9....However most people are using single perl and linux operating systems. Thus I suggest that like you did with Tk let us know ahead of time for which perl version the programs are tested. The other thing that is not clear to me is that if you say for example that programs require perl xyz or later, do you actually check that they run under the allowed versions? before releasing...... thanks sher > > Hi folks, > > New versions of Athena and Artemis are now ready. The windows and > unix updater programs will now grab and install these updates. > > This release addresses many bugs that were found in the previous > release. There are also a couple of nice things for the Windows > users. I recently upgraded by license for the PerlApp program, which > is the program which builds the Windows executables from the perl > source code. The new version of PerlApp has the very nice feature of > generating *much* smaller executables -- Athena is about 2 megs as > compared to about 5 megs from the previous version of PerlApp. > > There are two big new features in this release. > > 1. Athena now has an interface for doing linear combination fits of > standard XANES spectra to an unknown. Look in the Analysis menu. > > 2. Both Athena and Artemis have a new mechanism for trapping certain > kinds of errors and writing files that can be included in a bug > report. If a certain class of problem gets tripped while you are > using one of the codes, the program will beep and you will see a > message like this in the echo area: > > Artemis trapped a warning! Message dumped to C:\Program > Files\Ifeffit\horae\ARTEMIS.TRAP > > If you decide to send me a bug report regarding whatever lead to > the error, you should include the specified file along with your > bug report. The trap file may look cryptic, but it will probably > help me a lot in solving the problem. > > Update and enjoy! > B > > P.S. Big thanks this time for excellent bug reports from Peter > Southon, Peter Pfalzer, and valient beta tester Adam Webb. > Thanks also to Simon Bare for his help with the linear > combination interface. > > > > -- > Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu > Code 6134, Building 3, Room 405 > Naval Research Laboratory phone: (1) 202 767 2268 > Washington DC 20375, USA fax: (1) 202 767 4642 > > NRL Synchrotron Radiation Consortium (NRL-SRC) > Beamlines X11a, X11b, X23b > National Synchrotron Light Source > Brookhaven National Laboratory, Upton, NY 11973 > > My homepage: http://feff.phys.washington.edu/~ravel > EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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