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

re:fits
by k-kupiecki＠northwestern.edu 15 Jan '05

15 Jan '05

Thank you Bruce and Shelley! I just wanted to thank Matt, Bruce and everyone involved with IFEFFIT/Artemis/Athena... it has been a Godsend.... I couldn't have stumbled on it at a better time (I'm frantically trying to analyze about 4 beamtimes worth of SEXAFS data for papers and my thesis and WINXAS wasn't really working out for me)!!!!! Does anyone have any suggestions for additional literature in regards to better understanding the quality of fits and the parameters involved?.... or perhaps know when we might be able to expect a updated version of the Artemis literature? (What is currently there has helped me sooo much that I've been checking for an update every couple of weeks hoping to get see sections 2.2-3.2..... ) Also.... I guess I've realized that only knowing IFEFFIT with Artemis I kinda take things for granted (like I didn't know that IFEFFIT was having problems, in certain cases since I had only been checking the "Results" and the error messages on the bottom of the window....) which meant I missed errors like this in the IFEFFIT (since I didn't notice anything unusual in the "Results"): ............ # Do the fit! ## fitting difference of Cov_0_06ML_bl1435_111703.chi and one or more paths ... ## === data set #1 of 1 feffit(1-8, group=data0_fit, chi=data0.chi, k=data0.k, kweight=2.00, rmin=1, rmax=4, kmin=2.5, kmax=15, dk=2, kwindow=kaiser-bessel, fit_space=R, do_bkg=no, data_set=1, data_total=1) feffit fitting 1 data sets fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... no uncertainties estimated! fit gave a warning message: too many fit iterations. try again with better guesses or a simpler problem. ............................................... I guess my question is.... is there anything else I should be looking for in the IFEFFIT printout that I might not otherwise notice by just using Artemis and looking at the error messages and "Results"? Thanks for the input! Sincerely, Kristine Witkowski Northwestern University

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Athena & Artemis in Windows
by Peter Southon 22 Dec '04

22 Dec '04

Hello Windows people A few days ago Shelly suggested that Athena and Artemis don't work when installed in the directory "C:/program files/ifeffit/". This has always worked for me using XP, though I wouldn't be surprised if it caused problems in some earlier versions of Windows. Regarding Poorani's question about TRAP files, I have found it useful to put a shortcut to "C:/program files/ifeffit/horae/stash/ARTEMIS.TRAP" on my desktop or wherever for easy access. Cheers, Peter >Date: Fri, 11 Jun 2004 08:36:32 -0500 >From: "Kelly, Shelly D." <SKelly(a)anl.gov> >Subject: RE: [Ifeffit] Running FEFF >To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> >Message-ID: <1C1577844A0BDF448E14E8CCB2F74424015A1B6D(a)ANLMAIL.anl.gov> >Content-Type: text/plain; charset="us-ascii" > >Hi Poorani, > >I believe that Athena and Artemis do not work properly when installed in >the C:/program files/ifeffit directory. The installation proceedures >say to specify C:/ifeffit instead. To fix if, but all of C:/program >files/ifeffit into the trash and then re-install. > >Shelly Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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RE: [Ifeffit] Using more than one E0
by Kelly, Shelly D. 14 Dec '04

14 Dec '04

Hi Guys, I wanted to add another comment about using multiple E0's. One of the best formulas that I have found involves assigning different atom types different E0's. This method seems to work well for M.S. paths. Here is an example of how it goes. I think that Daniel Haskel was the first to publish this type of E0 stuff. "Single and multiple scattering XAFS in BaZrO3: a comparison between theory and experiment" D. Haskel, B. Ravel, M. Newville and E. A. Stern Physica B 208&209 (1995) 151 Lets pretend that we have a copper oxide that we want to model. First shell Oxygen called O1, Second shell Cu called Cu1, Third shell Oxygen called O2. This method would use three E0's. One for the first shell oxygen atoms, Eo1. One for all the Cu atoms Ecu. and one for all other oxygen atoms Eo2. The Cu-O1 path has E0=Eo1. The Cu-Cu1 path has E0=Ecu. The Cu-O2 path has E0=Eo2. The Cu-O1-Cu-O1 path has E0=Eo1, (only scattering from O1 atom). The Cu-O1-Cu1-Cu path has E0=0.5*Eo1+0.5*Ecu. (scattering once from O1 and once from Cu1) ... And so forth and so on. Now if you set something like this up. You need to look at the results carefully and see if it works. Generally, scattering from an atom that has lost an electron due to an ionic bond will have a positive deltaE, and scattering from an atom that has gained an electron will have a negative deltaE. Of course this negative/positive deltaE is added to the alignment deltaE. If the values for Eo2 and Ecu are the same within the uncertainties of the measurement then you need to make them the same variable, so then you will only have two energy shifts, but you can still use it. This is most often the case as Matt mentioned but I always like to test it out. In addition, one electron transfer is about a shift by 6 eV, so if these values differ by more than say 10 eV something is not right. Since the shift is generally smallish, say 2 eV, your fit has to be really accurate to "see" these shifts. In particular they seem to be most important when you have all the deltaR values constrained in some way so that the error in deltaR is really really small. For example all deltaR values are related to unit cell parameters and atomic positions or and overall expansion term. HTH Shelly -----Original Message----- From: Wojciech Gawelda [mailto:wojciech.gawelda@epfl.ch] Sent: Thursday, May 27, 2004 1:18 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Using more than one E0 Hi everybody, I would like to address a couple of questions which are partially related to my recent struggles in fitting some EXAFS data. I'm trying to fit my data using several shells of different neighbors including a few single scattering paths and also so multiple scattering contributions (mainly collinear multiple scattering paths) all calculated with the help of FEFF 8.20. Now, I found once in the FEFFIT manual the following suggestion: one might consider using several different E0's for different paths in order to improve the fit. Ok, the explanation was based on some approximations coming from FEFF code which include incomplete core-hole shielding, lack of angular variations of the valence charge distribution and charge transfer between atoms in polar materials. My question is the following: does anyone of you have some experience with such procedure? And if yes, shall than distinguish between the first shell of nearest neighbors and the rest of the atoms in terms of their E0 corrections (using 2 parameters)? Or perhaps one can use separate E0's for each path? That's one thing... The second question concerns the background correction in Artemis: I was trying to find an easy explanation of what this procedure does during the fit but I guess I'm still somewhat confused...how one can judge whether the spline co-refinement does the right job? Some people on this mailing list underline that one should avoid high correlations between fitting parameters and background parameters in order to make sure that the fit is correct. But is it the only criterion? In some of my fits background line looks kind of constant over the entire R-range which was taken into the fit. Sometimes it becomes like a modulation peaking underneath some scattering paths...even if the background parameters don't correlate significantly with fitting parameters I have my doubts whether the result is trustful. Any hints about this procedure? Well, I'll greatly appreciate any comments and feedback from all you guys. I hope I'll be able to share some of my own soon :-) Cheers, Wojciech ********************************************************************* Wojciech Gawelda Laboratoire de Spectroscopie Ultrarapide (LSU) Institut des Sciences et Ingénierie Chimiques (ISIC), Faculté des Sciences de Base (SB-BSP) Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne-Dorigny, Switzerland Tel.: +41 (21) 693 0452 Fax.: +41 (21) 693 0422 E-mail: <mailto:wojciech.gawelda@epfl.ch> wojciech.gawelda(a)epfl.ch WWW: <http://lsu.epfl.ch> http://lsu.epfl.ch *********************************************************************

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horae-041 ...
by Bruce Ravel 31 Aug '04

31 Aug '04

.... is on SF and my web site. http://sourceforge.net/project/shownotes.php?release_id=264607 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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RE: [Ifeffit] Artemis fit results question
by Kelly, Shelly D. 31 Aug '04

31 Aug '04

Hi Timm, You can use an expression that will return only positive values for you variables. sigma2 = abs(ss) guess ss This will force the model to use a positive values for sigma2. You can also use a penalty factor to keep the value inbetween a given range of values. I believe that there is an example of that in the Artemis or Ifeffit manual. -Most often negative values is a strong indication that something in the model is not quite right. Be sure to look at your data and fits showing the individual contribution from each path in the real or imaginary part of the FT. A negative sigma2 value or a really small sigma2 value usually indicates one of two different things. 1) You have included too much noise in the FT which is randomly adding signal all over in R-space hence your sigma2 values are unrealistically small to compensate. To check for this case, reduce the k-max value in the FT of the data by 1 1/angstrom and see what happens in the fit. 2) The path type is not right. sigma2 is small because you actually need more electron density for that scattering path. Hence try a path with larger Z. Negative values for the degeneracy would indicate that the path length and/or atom type is not correct. Set the degeneracy, sigma2, and delr to some reasonable values then look at the real/imaginary part of the FT for the data, fit and the contribution from the path of interest. Look to see if the signal from the path of interest has a positive contribution to the data before you try to optimize the parameters. Here is my rule of thumb for reasonable sigma2 (units= angstroms2) values sigma2 = 0.001 to 0.003 for double bonds that do not participate in binding to another atom. i.e. for the axial oxygen atoms of a uranyl moiety, UO2. sigma2 = 0.003 to 0.008 for "normal" well ordered shells. Like for Cu metal. This is the usual range. sigma2= 0.009 to 0.015 for disordered shells that are rather weekly bound. i.e. for the equatorial oxygen atom of the uranyl. There is usually 4 to 6 of them and they are not well ordered. Some times these shells can be split into two shells given enough data range in k-space. sigma2=0.015 to 0.025 for really soft bonds like solutions or squishy metals (AgCl) Sigma2 values also depend on the distance. The rules given above are for 1st and 2nd shells of atoms. HTH Shelly -----Original Message----- From: Strathmann, Timothy J. Sent: Monday, August 30, 2004 3:42 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Artemis fit results question This may be a question related to Artemis or to EXAFS fitting in general for a relative newcomer. Over the past months, when I've fit EXAFS data using Artemis and feff-derived single-scattering paths, I sometimes end up with best fit values for 2nd-shell coordination numbers or sigma squared values that are negative. Do these values have any meaning, or do they most likely signify that the chosen paths are not appropriate for fitting the spectral region in question? Also, is there a way to constrain the parameters to only consider positive values. Thanks. Timm Strathmann

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two issues with horae-040
by Bruce Ravel 31 Aug '04

31 Aug '04

Hi, For those trying to use yesterday's source tarball, I noticed a serious issue last night. There is a bug in the build script. Building will fail during the "make" step of "perl Makefile.PL; make; make install". There is a simple work-around (type "make" a second time) but this problem breaks the horae_update script. Consequently, I will be releasing a new tarball today. It should be on SourceForge and my web site before noon (North American Eastern Standard Time -- same as New York City). Sorry for the inconvenience, thanks for your patience. 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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Artemis fit results question
by Timm Strathmann 30 Aug '04

30 Aug '04

This may be a question related to Artemis or to EXAFS fitting in general for a relative newcomer. Over the past months, when I've fit EXAFS data using Artemis and feff-derived single-scattering paths, I sometimes end up with best fit values for 2nd-shell coordination numbers or sigma squared values that are negative. Do these values have any meaning, or do they most likely signify that the chosen paths are not appropriate for fitting the spectral region in question? Also, is there a way to constrain the parameters to only consider positive values. Thanks. Timm Strathmann

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the development branch of Artemis
by Bruce Ravel 30 Aug '04

30 Aug '04

Hi! As I mentioned in my last email, today's source code release includes the new development branch of Artemis. As I said about a month ago, I am now maintaining a stable branch, which will usually only get bug fixes, and a development branch, which is where I will be working on new features. I put a few notes and a screenshot on my Artemis page: http://leonardo.phys.washington.edu/~ravel/software/exafs/aboutartemis.html scroll down to the middle of the page. There is a box labeled "Development Branch". I want to clarify how this is going to work: 1. The source tarball has both branches and both get built and installed. The development version gets installed as "diana". This allows you to try out the development version but still have the stable version to fall back on. 2. I don't intend to build Windows executables of the development version until it is almost ready for normal release. This is in part to save myself some work and in part to keep the development branch out of wide use until it has been much better tested. 3. The development version involves some changes to the project file format. It will read projects from the stable version, but some information will get lost in the other direction. 4. If you use the development version, you should anticipate that there will be problems and be prepared to submit good, clear, helpful bug reports. If you expect stable behavior, use the stable version. That said, I have been using the development version for my own analysis. It ain't perfect, but I am getting work done. Here are a few notes to get you started with the new features. You might want to go take a look at the screenshot on the Artemis web page. 1. The window is much larger now. This takes up more screen real estate, but the paths list is much taller. The blank area in the lower right hand corner will get filled with new plotting controls in the future. 2. Fits get added to the Data and Paths List as seen in the screen shot. Old fits are plotted just like anything else -- just select it and click a plot button. 3. Background functions and residuals can still be plotted, but they are no longer displayed in the Data and Paths List. Now to get a bkg or res plot, click the check buttons in the plot controls panel. Whenever you plot a fit, the background and residual functions from that fit will be plotted along with best fit function. 4. When you click on a fit entry, the main panel will display a tool for viewing and exploring the log files from the fits you have done. This is essentially the same as the log viewer that Stefano was asking about last week. There is a list of fits on the left side of the panel -- double-click and right-click are both useful. The main use of this page is to write little reports about parameters so you can compare your various fits. Fits are included into reports by selecting them from the list on the left and not by selecting them from the Data and Path List. 5. In many situations (plotting, saving files, etc) selecting the head of the fit branch means to use the most recent fit. Selecting both the head of the fit branch and the most recent fit is redundant, but should not cause any problems. 6. The fit entries in the Data and Paths List may behave a little surprisingly in the case of a multiple data set fit. Some things, like plotting, depend upon which data set the selected list item is under. Other things, like discarding a fit, will effect every data set. 7. In the upper right corner is a little box which tells you when you have modified your project and, therefore, might want to consider saving it. Keep an eye on that box and let me know if there are situations where it gets set incorrectly. 8. I have written some documentation for viewing inside Artemis. There are lots of buttons scattered around the program for displaying context appropriate documentation (you can see a couple in the screenshot). Feel free to read through this and suggest ways to improve upon it or even write some of it yourself! Lots of the documentation is still unwritten. Things that don't work correctly yet that I know about: 1. Saving fits to multi-column files certainly doesn't work. Saving individual fits to column data files should work. 2. Hiding individual or selected fits (see the Fit menu) is flaky. Things to remember about using the development branch: 1. You can always go back to the stable branch, they are installed side-by-side. 2. It's a development branch -- it's going to have lots of bugs. 3. I want to hear about your problems and your suggestions for new & better features. Have fun! 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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news and new releases
by Bruce Ravel 30 Aug '04

30 Aug '04

Hi folks, I just uploaded a new source code tarball of Athena, Artemis, and Hephaestus to SourceForge. This release includes several bug fixes from the last couple of months and a few new features. An updater for the Windows users should follow soon. Here are the release notes on SF: http://sourceforge.net/project/shownotes.php?release_id=264418 The highlights: 1. The first tarball with a version of the development branch. I'll discuss this more in another message to the mailing list later this afternoon. 2. You can now use CIF files for your crystallography data. I added funtionality to one of the libraries associated with Atoms to handle CIF files. This means than any program built off of those libraries automatically reads CIF files. The one caveat is that atoms and tkatoms will only read the first record in a multi-record CIF file. Extracting a later record requires some additional code at the level of the application rather than the library. Artemis will pop up a dialog for selecting from a multi-record CIF file. TkAtoms will not. You should consider the CIF functionality experimental. There are some tricky parts and I am not sure that my implementation will work in all situation. Please contact me in person or via the list if you have any trouble with CIF files. 3. A new look, a new utility, and several bug fixes in Hephaestus. 4. The horae_update script was updated to loop through the SF servers until it finds one that responds with the tarball. Special thanks this time to Dave Barton, my CIF implementation borrowed heavily from his handy cif2inp tool. Dave also made a number of good sugestions regarding Athena and Hephaestus. Also thanks to Tony Lanzirotti and Sean Luo, both of whom reported significant bugs that got fixed. 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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trying to start...
by Mauricio 30 Aug '04

30 Aug '04

Dear Ifeffit users, Sorry if it's an idiot question, but I'm in troubles when trying to work with my L3-Pb absorption data with Athena. I'm a beginner with the Ifeffit stuffs... Also, sorry if this report is not correctly posted, but I will try to give you the maximum information I can... Let's go. The data were taken at the Brazilian syncrotron laboratory, and the "important" data are in columns 3 (energy), 4 (Io) and 6 (It). The file is of the following form: "Data" "Hora" "Ponto X" "CION1(CURTA)" "CION3(Longa)" "CION2(Média)" "Det. D" "Translonga" "Transmédia" "Det. G" "Det. H" "Det. I" 04/02/04 12:32:51 12899.99 1671379 865008 1244452 0 0.658666 -0.363712 0 0 0 04/02/04 12:32:54 12901.16 1668799 863916 1242264 0 0.658384 -0.363215 0 0 0 04/02/04 12:32:57 12904.32 1661863 860550 1237862 0 0.658123 -0.363569 0 0 0 04/02/04 12:33:00 12905.99 1660709 860007 1237669 0 0.658059 -0.364045 0 0 0 04/02/04 12:33:03 12907.65 1656852 858657 1236381 0 0.657305 -0.364574 0 0 0 04/02/04 12:33:05 12909.82 1655818 858151 1236604 0 0.657270 -0.365344 0 0 0 04/02/04 12:33:08 12912.15 1655627 857952 1236890 0 0.657387 -0.365807 0 0 0 04/02/04 12:33:11 12913.82 1655763 858599 1238443 0 0.656715 -0.366308 0 0 0 When I try to open it, with the latest version (ifeffit-1.2.6) installed in a Windows XP computes, Athena says that the file has fewer than 10 data points. And the following message was trapped by Athena: Athena0.8.030warnC:\Arquivos de programas\Ifeffit\horae\stash\ATHENA.TRAPCODE(0x 3be700c) at athena line 1349 main::__ANON__('Use of uninitialized value in concatenation (.) or string at ath...') called at athena line 3658 main::read_raw('D:/meus documentos/LNLS/D04B-XAS 1832-03/data/B040006.DAT', '', undef, 'SCALAR(0x3a80b78)') called at athena line 3516 main::read_file(0) called at /PerlApp/Tk.pm line 340 eval {...} called at /PerlApp/Tk.pm line 340 Tk::MainLoop() called at athena line 1411 The files in the /examples/Athena folder open correctly. Do I need to "clean" the data, leaving only the desired columns, E, Io and It? Again, sorry if it's a dumb question and if the report is incomplete... Thank you in advance Mauricio ************************************** Maurício Antonio Pereira da Silva Departamento de Física Grupo de Dinâmica Molecular Universidade Federal de São Carlos - UFSCar Via Washington Luiz, km 235 Vila Monjolinho 13565-905 São Carlos - SP Brasil Tel: +55 (16) 33 51 82 22, ramal 262 Fax: +55 (16) 33 61 48 35 *************************************** --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com) Version: 6.0.742 / Virus Database: 495 - Release Date: 19/8/2004

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