March 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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ifeffit and Mac OSX
by Matt Newville 04 Jul '04

04 Jul '04

Hi Raja, On Mon, 7 Oct 2002, rajasekaran swaminathan wrote: > Hi Matt, > > I tried again over the past few days to install the binary > installer on my mac (OS X.2). I couldn't find an attached aquaterm > / pgplot demo. The Aquaterm program opens, but I cannot see any > windows come out from that application. I mean, it is just like a > blank application. When I type ifeffit on Terminal app, it doesnt > recognise the presence of ifeffit in the ifeffitosx directory. i.e. > it says that the command is not found. The executable works > perfectly well on a Windows machine, and I was wondering whether > there are any such equivalents for a Macintosh machine. I also dont > think that the installer comes with athena/artemis/tkatoms etc.. Do > you have any other recommendations to resolve this issue? Also,if > it is possible, can I get a CD of these programs for a Macintosh > equivalent to an executable version for the Windows? > > I appreciate your help in this regard. I have used the binary installer once on a OS 10.1 system. It worked for me (after following the simple included instructions, of course) and plotting with Aquaterm did work. I haven't tried 10.2. I know the Mac binary installer does not include athena, artemis, or tkatoms. I believe it only provides the command-line ifeffit. I'm not sure I can answer many other questions about it. I don't know enough about it or 10.2 v. 10.1 issues to know how well it would work with 10.2. If the aquaterm/pgplot demos don't work, I'd guess it's a more serious problem and that the binary installer may not work. Is the Fink / X-Windows / PGPLOT installation procedure too big of a hassle? I know that can work, and that athena will work too. I also believe that the instructions are simpler for 10.2 than 10.1 (especially with respect to getting perl/Tk to work), but haven't tried this myself. I'm copying this message to the ifeffit mailing list, hoping that someone else may have better answers to these questions. How necessary is a complete binary installer for Mac OSX? Thanks, --Matt

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A question about the new Artemis version
by Stanislav Stoupin 31 Mar '04

31 Mar '04

Hello all I just upgraded to the newest horae-031 package It looks to me that the new Artemis version (0.7.001) doesn't have that nice button "use previous background" anymore. If I am not mistaken the button allowed to subtract background fitted previously. Am I? Is it somehow hidden in the new version? Thank you in advance Stanislav

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parameters in Athena's output files
by Bruce Ravel 23 Mar '04

23 Mar '04

Hi folks, Recently two separate people requested that Athena write a summary of the various parameters into the header of the column output files for mu(E), chi(k), and so on. That's a great idea and the next version of Athena will do this. In the interim, I wanted to point out a feature of Athena that some of you may not be familiar with. At the bottom of the Edit menu is a submenu called "Write a report." A report is a summary either of all groups or of the marked groups. There are three different output formats, but I suspect that most people will prefer the Excel spreadsheet format. Rather than explain it further, I'll leave you to give it go. The .xls file that gets written should be readable by any version of Excel as well as OpenOffice, Gnumeric, and Kspread. HTH B P.S. The final option in the "Edit->Write a report" menu is a peculiar output file that is of interest to folks who use Athena to process their data but who prefer XFit to Artemis for the analysis. -- 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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uncertainties
by mauro＠rulp.org 23 Mar '04

23 Mar '04

Maybe this is a "newbie" question, but I have noticed that in artemis's new version after the uncertainties there are values in round parentesis. What they mean? Thanks, Mauro.

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Confirmation
by jawad shah 23 Mar '04

23 Mar '04

Dear Sir, Is i am registered on your web side. With best regards Jawad __________________________________ Do you Yahoo!? Yahoo! Mail - More reliable, more storage, less spam http://mail.yahoo.com

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Re: Athena Suggestions
by Bruce Ravel 22 Mar '04

22 Mar '04

Dave, I hope you do not mind that I am answering via the mailing list. The answer I have planned will be something that I think others will find useful. On Saturday 20 March 2004 03:30 pm, Barton, David (DG) wrote: > LOCATION OF Eo > -Attached is two Ga XAFS spectra in an Athena file project. Look > closely at the chosen Eo positions, I think you would agree that the > choice is not near the maximum of the first derivative. These data > sets both have a fairly reasonable signal/noise so that shouldn't be > the source of the error. > > Athena Report of Eo: > --Ga_035 (10372.6 eV) and Ga_32-8 (10374.1 eV) > ==Eo difference = 1.5 eV > Using another plotting program: > --Ga_035 (10373.3 eV) and Ga_32-8 (10373.5 eV) > ==Eo difference = 0.2 eV > > I understand that using the maximum in the first derivative is just > an approximation of the Fermi Energy so the absolute value may not > be so meaningful. However, we often use relative changes in the > position of Eo as an indication of structural changes in our > catalytic materials, so it would be helpful if Ifeffit was slightly > more robust and precise in choosing the Eo value. Maybe you could > consider incorporating a "smoothing" parameter which would help > reduce the noise in the first derivative or some other algorithm > which makes a better choice in the presence of some noise in the > data. For the sake of everyone else, I'll mention that the data Dave sent me had a slightly ambiguous e0 because the peaks in the first derivative were split into two peaks about the same height and about 1/2 volt apart. In one case, Ifeffit's algorithm for identifying the peak came up with a point a bit to the left of the two peaks and the other time a bit to the right. In neither case did Ifeffit (and hence Athena) pick one of the points at the peak. These choices to the left and right of the peaks result in the unphysically large energy separation that Dave is asking about. My initial response to questions like this is that it is rarely wise to blindly trust a program -- ours or anyone else's -- to do the right thing all the time. Just because we get one spectrum right or someone else gets another spectrum right is not sufficient reason to always trust any program. If you need it to be right, check and make sure it is right. That was fine advice -- possibly even tautological. But it wasn't very practical. The software really should work hard to get it right as often as possible. You suggest smoothing. That would probably work pretty well in this case. Indeed, it woul probably result in choosing a value between the two peaks. That's closer to correct and would probably at least be more reproducible between spectra than what happened with your data. But it would not be a panacea. Look at Zr 0+ some time. The maximum in the first derivative is more than 10 volts above the Fermi energy. Smoothing would not fix the "maximum in the first derivative" algorithm in that situation. So even with a more robust algorithm, you would be well served to be sceptical. I think the solution to your problem is to be a bit more hands-on and to make use of more of Athena's features. I typically use Athena's preprocessing features to handle ensembles of related data. The details of what you might do vary from situation to situation, but here is the outline: 1. Import one scan. This is going to be your "standard" against which the rest will be compared, so it should be a trustworthy one. Calibrate it by hand using the Calibration option in the Data menu. Play around with the background removal and FT parameters until you are reasonably happy with the data processing. 2. Use the "Open many files" option in the Files menu to import several more of the data files in that ensemble of related data files. 3. When the column selection dialog comes up, make sure that the columns are properly selected. Before hitting the OK button, hit the button that says "Set preprocessing parameters". This will expand the column selection dialog, showing a new menu and bunch of checkbuttons. 4. From the menu labeled "Standard" select the first data file that you read in. This will activate all the checkbuttons below. Now select the buttons for "Align to the standard" and "Set parameters to the standard". 5. Now click the OK button. As each data file is imported, it will be aligned and the parameters, including e0, the background parameters, and the FT parameters, will all be set to the values you settled on for the first data set. Magic!! If all went well, then each data set will be calibrated the same way as the first one and the background and FT parameters will be well set. The caveat is that the automated alignment does not always work well. A quick plot will let you know if it failed and you need to go back and align by hand. But with data that is low noise and similar, it tends to work ok. Depending on your data set and what you are aiming to do, you may need to do some variation of what I described above. Of course, a change in Ifeffit's algorithm might still be in order. But, in any case, I encourage you to resolve your e0 problems by explicitly examining one data file and using preprocessing to make the rest consistent with the first. HTH, 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] beeps?
by SCalvin100＠aol.com 18 Mar '04

18 Mar '04

It beeps for me on Windows XP, although it's pretty subtle (more a burp than a beep). --Scott Calvin Sarah Lawrence College

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beeps?
by Peter Southon 18 Mar '04

18 Mar '04

>When this happens, is anything written to the screen? Does Artemis beep and >tell you to look at the ARTEMIS.TRAP file? If either is the case, I will >need to see what they say. Bruce, did you say Artemis beeps on errors? It doesn't seem to do that on my WinXP machine. I know its a simple thing (I have a simple mind), but it would be a great prompt to look at artemis.trap. Is there a sound problem with porting to Windows? Cheers, Peter Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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Ins: [Ifeffit] configurational average-tkatoms separate
by ALAM Sher 17 Mar '04

17 Mar '04

Hi Matt and Bruce, Prof. Matsuura, Matt is right, configurational average in feff8 is not reliable. However if you use as Matt suggest, and average even by looking you can see that results as quite OK. For example in one case Tl-1234, there are two Cu sites, and when one generates the XANES with both Cu1 and Cu2 as core, the average of these agree with experimental result...... For Bruce, just a little request, I prefer that Tkatoms is distributed as a separate package, at least there should be a choice so that if one wants to use only Tkatoms one can.... thanks sher > Dear Prof Matsuura, > > Feff8 does claim to allow configurational averages for EXAFS. > Unfortunately, the results with CFAVERAGE are clearly wrong even in > simple test cases. At the most basic level, in order to describe a > configurational averaged environment, fractional degeneracies would > be necessary. The feffnnn.dat files *never* report fractional > degeneracy, even when using CFAVERAGE. This should immediately make > you very suspicious that something is not right. > > I recommend not using the CFAVERAGE card, and instead making > separate feff runs for each candidate central atom, and then > averaging these sets of calculations, weighted by the fraction for > each candidate central atom. It's unfortunate that the tools for > modeling EXAFS of disordered crystals are so crude... there's > probably a lot of room for improvement in this area! > > Hope that helps, > > --Matt > > On Tue, 16 Mar 2004, Makoto Matsuura wrote: > > > 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 > > > > ****************************************** > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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