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

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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small update, unix only
by Bruce Ravel 10 Mar '04

10 Mar '04

Hi folks, I corrected a problem with yesterday's release that will only affect people using unix and perl 5.6 (or earlier). If you fall into that category, it will be clear because the package should install without a problem, but then Athena and/or Artemis will die without starting and issue an error about not being able to find the "longmess" function. I made a new tar ball and uploaded it to my web site and to SourceForge. There is only one small change in this release compared to the previous one and it will be completely transparent (I think!) for those using perl 5.8. There is *no need* to upgrade your perl installation just to run this release of my software. Of course, if anyone else runs into any problems, let me know. Thanks to Markus Janousch for an excellent bug report and for quickly testing the solution. B -- 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/

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new release of Athena and Artemis
by Bruce Ravel 09 Mar '04

09 Mar '04

Hi folks, I am announcing the release Athena 0.8.025 and Artemis 0.7.000. You can now run the Windows updater or the horae_update script on your unix machnies to install these new versions. Complete lists of changes can be found in the change logs on my web site. I have increased the minor version number of Artemis because of two significant new features. 1. Atoms is now incorporated into Artemis and there is a simple wrapper around Feff built into Artemis. You no longer need to run Atoms and Feff apart from Artemis. Instead, you now do these chores within Artemis and allow Artemis to organize and manage all of the output files from Feff. By default, Artemis assumes you will be using the version of feff6 that comes with Ifeffit (but that is configurable). 2. Artemis project files are now zip files which contain all data and feff files along with the description of the fitting model. This means that it is easy to share analysis projects with friends and to move analysis projects between computers. The project files are normal zip files that can be examined with PKZip, WinZip, StuffIt, ark, or File Roller. To explain these changes more fully, I have added a chapter to the draft document for Artemis. See chapter 5 in the PDF file at: http://leonardo.phys.washington.edu/~ravel/software/exafs/docs.html Please read this new chapter as it explains the features in full detail. As always, let me know about any bugs, questions, or suggestions. This is a significant new direction for Artemis, so I look forward to hearing about the issues that will, no doubt, come up. You can thank Adam Webb and Paul Fons for all the bugs that *aren't* in Artemis due to their excellent feedback on the new version. B -- ********* PLEASE NOTE MY NEW PHONE, FAX, & ROOM NUMBERS ****************** 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/

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athena 0.8.026 and artemis 0.7.001
by Bruce Ravel 09 Mar '04

09 Mar '04

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/

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Ins:[Ifeffit] Re: problems with the new version-solved
by ALAM Sher 09 Mar '04

09 Mar '04

Hi, Maybe this can be of help.... I had a problem with horae-030, which I solved.... Before when I installed horae-029 there were no problems. Please note that I am using Red Hat Linux The problem was that in directory Ifeffit under horae-030 there are files Group.pm and Path.pm, used respectively by athena and artemis....The version numbers of these did NOT coincide with those in the same files in directory /usr/lib/perl/perl_site/5. /Group.pm etc..... Thus I fixed the numbers in the above files and problem was solved..... Perhaps the problem can be conflicting verion numbers thanks sher > On Friday 05 March 2004 12:14 pm, Giuliana Aquilanti wrote: > > Hi Bruce, > > > > I am trying to get the new versions of Athena and Artemis. > > I cliccked on updater.exe but I continued having > > Athena 0.8.024 and Artemis 0.6.009. > > After I installed from zero ifeffit-1.2.5a.exe and the > > ifeffit_updater-1.1.exe but I have still the old versions. > > ...I don't understand.... > > Hi Giuliana, > > I don't think I understand either. If you have installed > ifeffit-1.2.5a.exe then the next time you run athena or artemis, the > installer should notice that you are not up to date. You certainly > are not -- I released Athena 0.8.025 and Artemis. 0.7.000 after Matt > released ifeffit-1.2.5a.exe. I was counting on the updater to do its > thing. > > However, if you are behind a firewall (which is, as I recall, the case > at ESRF), the firewall may obstruct the updater program. > > I don't know the solution to that problem, but I have taken the > liberty of CCing this to the mailing list. Perhaps someone else will > have some wisdom to share.... > > B > > > -- > 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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Re: problems with the new version
by Bruce Ravel 05 Mar '04

05 Mar '04

On Friday 05 March 2004 12:14 pm, Giuliana Aquilanti wrote: > Hi Bruce, > > I am trying to get the new versions of Athena and Artemis. > I cliccked on updater.exe but I continued having > Athena 0.8.024 and Artemis 0.6.009. > After I installed from zero ifeffit-1.2.5a.exe and the > ifeffit_updater-1.1.exe but I have still the old versions. > ...I don't understand.... Hi Giuliana, I don't think I understand either. If you have installed ifeffit-1.2.5a.exe then the next time you run athena or artemis, the installer should notice that you are not up to date. You certainly are not -- I released Athena 0.8.025 and Artemis. 0.7.000 after Matt released ifeffit-1.2.5a.exe. I was counting on the updater to do its thing. However, if you are behind a firewall (which is, as I recall, the case at ESRF), the firewall may obstruct the updater program. I don't know the solution to that problem, but I have taken the liberty of CCing this to the mailing list. Perhaps someone else will have some wisdom to share.... B -- 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/

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Chi^2-Map question
by Norbert Weiher 04 Mar '04

04 Mar '04

Dear Friends, maybe some of you remember that I was implementing a chi^2 mapping algorithm using the IFEFFIT library. This is working now, and for the data analysis of the maps I would like to ask your opinion on the following problem: I want to check with chi^2 maps if I can separate 2 shells, e.g. if a peak is comprising two O shells or only one. For this I take the one-shell fit, half the coordination number and then vary the distance of the shells against each other (all other values taking from the best single shell fit). If I find two contributions, I should see 2 mirror-symmetric minima centered at the corresponding DR values, e.g. (0,-0.1) and (-0.1,0) if I work with the same reference. These minima are separated by a saddle point which is more or less pronounced. In the case of some Fe complexes I simulated, it is clearly visible, while for my gold oxides, it is hardly seen but still there. If I take a system where I know there IS only one shell (e.g. Au metal) and do the map, I find no saddle point and correspondingly no 2 minima. Does anyone know a relation between the height of a saddle point and the physical significance of the map? I would be glad to learn more about, but the statistic books I know don't deal with such a problem (and I am chemist and not a mathematician)... If you need an example, I can send you two slides of a recent talk which explain this problem more in detail - just drop me a mail. Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (weiher(a)chem.ethz.ch) Institute for Chemical and Bioengineering - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32

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