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

[Ifeffit] Re: from I.Demchenko (PhD student at the Institute of Physics PAS)
by Bruce Ravel 07 Apr '04

07 Apr '04

Hi Iraida, I hope you don't mind that I CC my reply to the ifeffit mailing list. I have some suggestions for you, but I thought it might be helpful to you to see if anyone else has anything to contribute. (The attachments to Iraida's email included a couple of screenshots showing the plotting window with a very good-loooking fit. She also sent the artemis log file showing many of the numbers she quotes below.) On Tuesday 06 April 2004 12:12 pm, Iraida Demchenko wrote: > I have a problem with fitting of my data for 0.5 microns of Ge on > Si(001) substrate (grown by MBE). The spectrum for K-edge of Ge was > collected by TY mode. This sample is a standard for my next > fitting. >From this fitting (for 1 shell) I want to draw > So^2... But, if I apply a "trick" with k-weight determination as 1 > and So^2 value changing from 0.7 to 1.1 and repetition of this > operation for k^1, k^2, k^3, I get three parallel lines for > sigma^2(Ge-Ge) as function of So^2 :(. They aren't crossed in this > area. This is kind of surprising to me. I have used the three-lines trick many times and have never seen the situation of three parallel lines. I am a little confused how that is even possible. One might expect this trick to do strange things in the case of a first shell that is not well separated from higher shells, but my memory of Ge is that the first shell is well separated. Another situation that might lead to trouble is if strain induced by the substrate splits the first shell into two well-separated peaks. However, that does not seem to be the case for you either. 1/2 micron is (I think) thick enough so that the film should be bulk-like. Sadly, I am stumped. Has anyone else ever seen this? > On the other hand, I tried to fit my data (3 shells, k-w=2; dk=2; > Hanning; k(3.5-12.3)) and I've obtained: reduced chi-square=10.33; > R-factor=0.011; So^2=1.22 +/- 0.34; dr_1=0.0107+/-0.006; > sigma^2_1shell=0.0037+/-0.0019; sigma^2_2=0.0068+/-0.0033; > sigma^2_5=0.0096+/-0.0041(3 shell) (of course, that errors were > recalculated(following FEFFIT, p.44). I doubt about the obtained > value for So^2=1.22 +/-0.34. Within the error, of course, I can say, > that this value is in the range from 0.6 to1. But, the correlations > between variables are: amp (So^2) and sigma2_1: 0.916 :(; amp and > sigma^2_2: 0.498; amp and sigma^2_5: 0.49; sigma^2_1 and sigma^2_2: > 0.47; sigma^2_1 and sigma^2_5: 0.45.....all other correlations are > below 0.25. In the attachment there is a log file for this fitting, > as you can see sigma^2_3 is -0.0055+/-0.016 :(. > > Are there any other ways to determine our So^2? Or these actual results > (So^2=1.22) we can consider as good? What do You think about this fit? First, as you say, your value for S02 is not unreasonable in that the error bar covers a value that one might expect. Still, you are right that 1.22 is an oddly large best fit value and suggests that something else might be happening in the data. Second, I wouldn't be so concerned about the high correlation between S02 and sigma^2. It's normal. Here is a nice short piece by Matt about correlations: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-February/000713.html The rest of thread might be of interest to you, as well. At another point in that thread, there is some discussion of how the normalization is done. Have you examined that carefully? If the post-edge line intersects E0 at an oddly low value, then the edge-step used in the normalization might be rather too small. This is certainly a possibility in fluorescence data where the region after the edge sometimes sweeps upward. In that case, the normalization range is such that the regressed post-edge line can be below the data near E0. I explained this in some more detail at http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-February/000711.html That could be the cause of a best-fit S02 that is larger than 1, That's my best guess, given that I have not seen the mu(E) data, for what is happening. I was bit confused by thing about sigma^2_3. I saw in the log file that it was, as you said, negative. But none of the sigma^2 values for the paths were negative. It wasn't clear how that sigma^2 value was being used. Hope that helps, B P.S. I could tell from the log file that you sent me that you are using a *very* old version of Artemis and presumably of ifeffit as well. You may want to download the latest ifeffit installation package from http://cars9.uchicago.edu/ifeffit/download.html and then let the automatic updater bring your computer completely up to date. -- 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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simultaneous fitting of multiple data sets in ifeffit
by Stanislav Stoupin 05 Apr '04

05 Apr '04

Hello! First of all I would like to thank Bruce for answering my questions. As a beginner I very much appreciate your help. Now I am trying to compare my results using two possible ways of doing EXAFS analysis : 1. Artemis 2. ifeffit command line (loading input files) Here is my question: When I use ifeffit commands it is not clear to me how to assing different kmin/kmax (rmin/rmax) values to different data sets in a multiple data set fit. My current understanding of the problem is as follows: As ifeffit documentation says all variables are global. At the same time ifeffit tries to evaluate all parameters of feffit() command first and does the fit only after determination of kmin kmax rmin rmax. What happens is that the last given values are assigned to these variables. Could somebody show me an example of a script that allows to assing different values of kmin kmax rmin and rmax for different data sets? Stanislav

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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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