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

A saving problem in newest Artemis version
by Aria 27 May '04

27 May '04

Hi folks, First, thank Bruce and Matt so much for their non-stopping work in updating those beautiful pieces of software. Somehow, another problem occurred to me after the auto-updating days ago. I am not sure if this only happened to me. Artemis so far has no problems in dealing with those project files which were created by the old versions. But when I tried to create a new project importing more than one FEFF calculations, after I saved and tried to reload it, Artemis simply failed to do so. The only FEFF path showed in the 'Data & Paths' panel is the first path in the first FEFF calculation. This is the message I copied from echo: Opening project zipfile C:/.../artemis60mT_C_100 ... Opening project zipfile artemis60mT_C_100 ... done! Doing intrp for CuOct ... Doing intrp for CuOct ... done! Artemis trapped a warning! Message dumped to C:\Program Files\Ifeffit\horae\stash\ARTEMIS.TRAP The artemis.trap files is shown as below: # Artemis 0.7.004 # This file created at 12:28:24 on 27 May, 2004 # using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.5 # IFEFFIT_DIR is C:\Program Files\Ifeffit # Workspace: C:\Program Files\Ifeffit\horae\stash\artemis.project.1\/ The following message was trapped by Artemis on a SIGWARN: Artemis0.7.004warnC:\Program Files\Ifeffit\horae\stash\ARTEMIS.TRAPCODE(0x3372680)C:\Program Files\Ifeffit\horae\stash\artemis.project.1\/ at artemis line 1551 main::__ANON__('Tk::Error: could not open C:\Program Files\Ifeffit\horae\stash\a...') called at blib\lib\Tk.pm (autosplit into blib\lib\auto\Tk\Error.al) line 402 Tk::Error('MainWindow=HASH(0x387c174)', 'could not open C:\Program Files\Ifeffit\horae\stash\artemis.proj...', '[\&main::dispatch_read_data]', '(menu invoke)') called at /PerlApp/Tk.pm line 340 eval {...} called at /PerlApp/Tk.pm line 340 Tk::MainLoop() called at artemis line 1695 When I click on the only path, another warning is trapped: # Artemis 0.7.004 # This file created at 12:39:51 on 27 May, 2004 # using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.5 # IFEFFIT_DIR is C:\Program Files\Ifeffit # Workspace: C:\Program Files\Ifeffit\horae\stash\artemis.project.1\/ The following message was trapped by Artemis on a SIGWARN: Artemis0.7.004warnC:\Program Files\Ifeffit\horae\stash\ARTEMIS.TRAPCODE(0x3372680)C:\Program Files\Ifeffit\horae\stash\artemis.project.1\/ at artemis line 1551 main::__ANON__('Use of uninitialized value in split at artemis line 5800, <PROJ>...') called at artemis line 5800 main::populate_path('data0.feff0.0') called at artemis line 2475 main::display_properties('Tk::Ev=SCALAR(0x3327260)', 'data0.feff0.0', 0, 'imagetext', 'body') called at /PerlApp/Tk/Widget.pm line 988 eval {...} called at /PerlApp/Tk/Widget.pm line 988 Tk::Widget::Callback('Tk::Tree=HASH(0x32d2c3c)', '-browsecmd', 'data0.feff0.0', 0, 'imagetext', 'body') called at /PerlApp/Tk/HList.pm line 181 Tk::HList::Button1('Tk::Tree=HASH(0x32d2c3c)') called at /PerlApp/Tk.pm line 340 eval {...} called at /PerlApp/Tk.pm line 340 Tk::MainLoop() called at artemis line 1695 I am not sure the information is enough. Hope it helps. Best regards, Aria

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RE: [Ifeffit] Autobk parameters
by Kelly, Shelly D. 26 May '04

26 May '04

Hi Stefano, > 1) I understand that energy calibration should be performed, and I > did so by using the atomic edge energy. I also understand that this > parameter could be fluctuating in the subsequent fitting. Any comment > on this procedure? I agree that all the energy shift stuff can be confusing. The important end result for Extended X-ray Absorption Fine Structure Analysis is to get the energy-grid of the data to match the energy-grid of the theory with the zero energy of the photo-electron somewhere on the absorption edge. In the process of doing this you may have more than one data set from the same sample with different energy-grids... Furthermore you may have more than one sample which may have different energy-grid from the other samples and the theory. Then to make things all the more complicated X-rays can change the oxidation state of metals in organic materials. So that the energy grid is supposed to be different and the data is useless. After all that, here are some answers. 1) Always measure a foil reference at the same time that you measure any EXAFS data. It is easy to do. Here is a reference for how to do it when your sample is too thick and you can not simply put the foil behind the It ion chamber. J L Cross and A I Frenkel. "Use of scattered radiation for absolute energy calibration." Rev. Sci. Instrum. 70: pp 38-40, 1998 2) Align each data scan: 2a) Without an energy reference. Align the data to one of the data sets (remember which one you used) so that the edges are all right on top of each other. Each sample has it's own energy-grid. 2b) By using the energy reference of the foil measured simultaneously with each scan. Align all the reference spectra to one of the reference spectra. Then shift each of the data sets that belong to the reference spectra by the same amount. Now each scan is independently aligned and you have an absolute energy reference for each scan. This is useful for XANES comparisons or if you suspect changes in the data while the measurement was taking place. The difference in energy from the reference to the data or from one data set to another is a real change and can be used to "say" stuff about the sample. 3) Check the alignment: Plot all the normalized xmu(E) data from the same sample in Athena, zoom in on the edge region -20 to 20 eV and take a good look. Hopefully they all line up. If there is a systematic change in the edge features? If so how much...less than 10 % (which is about the accuracy of the measurement). This means that you can most likely still use the data but that you have changes happening to your sample while the measurement was taking place and you should fix that next time. 4) Now the problem of alignment is somewhat smaller. All the data sets have the same energy grid if you used 2b...or all the data sets have there own energy grid if you used 2a. Now we need to align the data and the theory. To do this there are two steps. Choosing a zero energy of the photo-electron to define the k-grid in converting the data to chi(k), and then aligning the chi(k) data with the theory chi(k). 5) Choosing a Ezero in Athena: Pick any point that you like on the edge for Ezero in Athena. Plot the xmu data with the background and pre-edge and post-edge range. A circle on the plot shows the position of Ezero. Then right click The Ezero to set this energy to be the same value for all the data sets from this sample. Then plot the chi(k) data and see that the curves all look the same at low k-values. If not adjust Ezero a bit for the data sets that are different to get the chi(k) data to look the same. Then average the chi(k) data and write it out so that you can align it with the theory in Artemis. 6) Aligning data to theory: Read the data into Artemis. Read in what you think should work for a first shell feffxxxxx.dat file. Fit the data to the first shell. Plot the data and the theory in chi(k), take a look at the deltaE value from the fit. This value for deltaE is telling you how much the theory had to move to match-up with your choice of Ezero that you picked in step 5. If you think that the theory is correct and deltaE is larger than a few eV then you need to adjust your chi(k) data. But first write out what the theory should look like if you choose Ezero just right. 6b) Making a standard: In Artemis, set all the parameters to their best-fit values, except for deltaE. Set deltaE to zero and run the fit again. This is not really a fit. There are no parameters to optimize. Now the theory is showing you what the data should look like if you choose the perfect value for Ezero and the perfect background function in step 5. 7) Redo the background and energy choice: In Athena open up the chi(k).fit that was produced by step 6b. This is the "standard" that you can use to help get Ezero and the background correct. Then select individual scans taken from the sample and then open the standard menu and choose the theory chi(k) data. Right click on the standard to use the same standard for all data sets. Redo the background removal. Plot the chi(k) data and the standard. If they are different at low k you need to adjust Ezero so that they start at the same place. When you are done adjusting your choice for Ezero, plot the xmu(E) data and make sure that the circle that is your value for Ezero is on the edge. If it isn't, then the theory that you used to align the data doesn't work..and you need to start over in step 6. If the value is on the edge some where, right click on the Ezero choice and set its value for Ezero of all the scans. Then merge all the data in chi(k) and write it out for use in Artemis...as you did the first time making sure that all the scans have a similar bkg. 8) Redo the fit: Now the data and the theory are aligned and you can redo the fit varying all the parameters...deltaE in Artemis should be small..and the background should give a nice match at low-r values. Often this entire procedure is used at the end of your analysis to make a nice figure for publication. 9) Bonus of using an energy reference: If you used an energy reference measured simultaneously with the data sets then in the end you can simultaneously fit the different samples with only one deltaE in the fit for all of the samples. If you aligned each one independently then each data set should have it's own deltaE value..unless you have more information and can prove that they should be the same. HTH Shelly

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Autobk parameters
by Stefano Ciurli 26 May '04

26 May '04

Hi folks, guess what, another question... I would like to estimate the area of a small pre-edge peak in a Nickel spectrum. It is known that the area of this peak, compared to the XANES, is correlated to the degree of symmetry for the Ni(II) ion. I tried to use the peak fitting procedure implemented in Athena, but unsuccessfully. If I limit the fitting region to close to the pre-edge peak, and use either gaussian or lorentzian lineshape, the fitting is bad, really bad (shift of the fitted maximum, wrong linewidth). Maybe the peak is just too small. If I try to fit the entire XANES in addition to this small peak, I get very good fit for the XANES features, but negative intensities for the pre-edge peak. Any clues? Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

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[help] ifeffit -i = segmentation fault
by mauro＠rulp.org 26 May '04

26 May '04

Hi to all, I'm having big troubles with iFEFFIT. I have updated the systems (Linux GNU Debian/ Testing) and I realized that version 800.025 of perl-tk was automatically installed. After that, obviously, everything crashed with Artemis and friends. So I have downgraded perl-tk to 800.024 using a non standard debian package (because the standard one requires perl-base 5.6.1 and I'm working with perl-base 5.8.3) from here: http://snapshot.debian.net/cgi-bin/packages.cgi (I have used perl-tk_800.024-1.2_i386.deb) After that I decided to recompile everything... bad idea! ifeffit-1.2.5 recompiled fine (no errors appeared in the configure/make/make install process). *BUT* when I try to recompile horae-034 it crash on determining ifeffit version. In fact, if I run "ifeffit -i" it gives me: Segmentation fault (Killed, on another machine) I hope someone could help me because at the moment I can do nothing! :( Thanks, Mauro -- Mauro Rovezzi <mauro(a)rulp.org> - Physics student University of Rome "Tor Vergata", ESRF Beamline BM8 - GILDA

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athena 0.8.028, artemis 0.7.004, and hephaestus 0.02
by Bruce Ravel 25 May '04

25 May '04

Hi folks, I have just posted a new source code package for my codes on my web page and on SourceForge. You can now run the horae_update script. I have also assembled the contents of the Windows updater, which should be available in the next few days. When it is ready, the windows updater will notice and update you automatically. Along with many bug fixes and feature enhancements in Athena and Hephaestus, there are a large number of improvements in Artemis. As you all no doubt remember, there were quite a large number of serious bugs reported after the last release of Artemis. With the generous and patient help of several users I was able to understand and correct about two dozen problems leading to all sorts of misbehavior ranging from simple trap file generation to program crashes. I am guardedly optimistic that you will find the new release to be a significant improvement over the last in terms of stability and usability. Among the big new features of Artemis are: 1. An revamped Guess, Def, Set page with lots of new features. I'll be sending out an email later this afternoon explaining the new GDS page. 2. The ability to clone feff calculations. This will be very helpful for those of you doing multiple data set fits. This, too, will get its own email later today. 3. New ways of viewing the log file. 4. Expanded information about each path displayed on the paths page. and lots of minor enhancements. See the change log on my web site for the complete list. One caveat -- I once again made some changes to the format of the artemis project file. I will not be able to guarantee stability of the project file format for a long time to come. I'll make sure Artemis can read in project files from previous versions, but it is likely that any new version will write a project file that cannot be completely imported by older versions. That's just one more reason to stay up-to-date! Several people get an acknowledgement for their contributions to this release: David Barton, Gerrit Schmithals, Aria Yang, Scott Calvin, Peter Southon, and Dogan Paktunc all deserve a tip of the cap for excellent suggestions and useful bug reports. Shelly Kelly was amazingly generous with her time in the last few weeks helping me to debug the current version. She also helped me design the new GDS page and pushed me to add several of the other new features in the code. All of you should buy Shelly a beer the next time you see her -- I certainly will! As always, let me know what suggestions you have or problems you run into. Bruce -- 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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that didn't take long...
by Bruce Ravel 24 May '04

24 May '04

Hi, Once again a serious bug has cropped up in artemis within 24 hours of a new release. Sigh... I'm pretty good at the first 95% of making a new release, but I seem to suck at the last 5%! ;-( The problem this time is in trying to do the background corefinement. If you click on the "Fit background" button, the fit will run to completion but the log file will not be written. Fortunately, the fix is extremely simple. I will post a new source code tarball by the end of the day. I will also try to get a new executable built so that the windows updater can be updated. Until then, you should consider background corefinement to be broken. Thanks go to Gleb Pokrovski for pointing this out (as well as racing out to try the new version!). 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 horae library setup
by Paul Fons 24 May '04

24 May '04

I was going to roll my own version of the latest incarnation of horae, but I noticed the library structure and install location has changed (at least on os x). Can you elaborate on this (Matt or Bruce)? Better yet, is there a tar image of the source available for the mac os x version. Earlier I upgraded perl to 5.8.3 and then the older Tk broke so I was off on my own, so I was compiling everything myself, but now that the install is becoming more and more os x aware (thanks to Matt) it would seem to make sense to downgrade to Apple's older perl (which has prebinding enabled). Of course, now it only makes sense to get in sync with the official sources. Would it be possible to put up the sources on your web site Matt? Paul (an Italian (Elettra) for a ten days)

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graphics and fit
by Stefano Ciurli 22 May '04

22 May '04

Hello, just a thought: wouldn't it be nice to be able to read the feff.inp file directly into a simple molecular graphics program in order to see if the used coordinates contain any error? Maybe it is possible already and I am not aware of it. I understand that the program is mainly used by material scientists, but for us working with biological samples of metalloproteins it would be nice. Another suggestion: I know that Excurve is able to treat the histidine rings as a unity, and when performing the fit that program is able to maintain the ring rigid while fitting the distance between the metal and the imidazole ring of the histidine. How can I do that simply using your suite? Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

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a cautionary tale
by Peter Southon 21 May '04

21 May '04

Hello fellow Ifeffiters This a story about making feff.inp input files for FEFF. The more experienced readers of this list will probably be well aware of the issues involved, but I thought that relative newcomers such as myself might not know (which is why I'm posting this on the Ifefft list rather than the Feff list). In a nutshell, it is wise to create a large cluster of atoms to put into Feff (ie use a large Rmax in Atoms), but limit the number of paths with a reduced Rmax in Feff. I used Artemis/Atoms to make up a Feff input file (feff.inp) from crystallographic parameters, setting Rmax in Atoms to a relatively large value of 7.5 Å to create quite a large cluster of atoms. I then used FEFF to calculate scattering paths within the cluster, but first reduced the Rmax in feff.inp to 5.5 Å to limit the number of paths. So far so good. I then (for reasons too involved to discuss here) edited the feff.inp file to delete all atoms more than 5.5 Å from the centre, and ran Feff again. The results (judging from the relative amplitude values) were different, and in the case of some paths very different. Some intense paths changed in amplitude by a factor of 2 or greater, although I haven't looked at the finer details of the Feff results. The paths that changed the most were high-order multiple scattering paths, and surprisingly those paths did not involve atoms at the edges of the 5.5 Å radius. Now I'm sure that someone else can explain the reasons for this much better than I can, but I assume that the potentials for the atoms outside the 5.5 Å radius (which were neglected in the second calculations) significantly affect those inside the radius. I know that its always been my practice to perform the Feff calculation using only those atoms that I think are contributing to my spectrum, and I'm sure that others do the same. My advice is to use a larger cluster of atoms in Feff if you can - but as to how large I might leave that to someone else to comment. Regards, Peter PS - and four cheers to Bruce for improvements to Artemis, I can't wait for the Windows update. Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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horae 034 Debian packages
by Carlo U. Segre 21 May '04

21 May '04

Packages of the new horae are available for the unstable and stable distributions of Debian at # stable deb http://fermi.phys.iit.edu/debian/woody binary/ deb-src http://fermi.phys.iit.edu/debian/woody source/ # unstable deb http://fermi.phys.iit.edu/debian/sid binary/ deb-src http://fermi.phys.iit.edu/debian/sid source/ Please contact me if you have any problems installing them. 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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