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

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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Random behaviour Artemis 0.7.001
by mauro＠rulp.org 17 Mar '04

17 Mar '04

Hi to all, I'm a new ifeffit user (I started using this software in october '03). My environment: Linux Debian/GNU, perl 5.008003, Tk 800.024 and Ifeffit 1.2.5 First of all, I would like to express my congratulations to the authors and thanks them all for their work. I updated the new versions last week and I appreciate the new more user friendly layout. But I found some strange behaviour with Artemis. 1. When Artemis starts, I receive this message: Use of uninitialized value in join or string at /usr/local/bin/artemis line 1236 2. Sometimes I save a project and when I reopen it doesn't found the datafiles (obviously I didn't modify the file names). 3. Sometimes the fit have no-sense values so I have to save the project, rerun Artemis, and with the same parameters I obtain good fit. It seems like after a certain number of fits the software starts to fail. I would like to know if someone have noticed the same behaviour. The problem is that points 2,3 are random. Thanks, Mauro

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Re: problems with the new version
by Peter Southon 17 Mar '04

17 Mar '04

Hello Matt, I'm having similar problems with the updater as those described a few days ago, but the fix that you posted didn't work for me. I've copied in the new .ini file (which I figure just re-sets the date stamp). This pursuades the updater to run, but after processing for a few seconds (and I'm sure it does send an internet message) it flashes up a TK screen for a split second then closes/crashes, then the main program runs. I can't figure out how to extract an error message from the updater. This is a new installation - putting ifeffit onto my home computer (WinXP), using an old-ish install file from cd (ifeffit 1.2.4) and updater 1.1. I'm rather avioding downloading anything that I don't have to as my connection here is rather slow... Hope you can help!! Cheers, Peter > Hi Bruce, Giuliana, > > There have been a couple other reports like this, but they always > seem to go away eventually. I doubt the firewall is an issue (if you > can download a zip file from a web page on your computer, the > updater will work.. if you can't download a zip file, the updater > should let you know this). > > I've just added a FAQ entry about this: > > http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=show&file=faq02.008.htp > > The upshot is that I'd suggest replacing the file > C:\Program Files\Ifeffit\updates\updater.ini > > with > http://cars9.uchicago.edu/ifeffit/updates/updater.ini > > and editing (notepad,wordpad,...) and the file > C:\Program Files\Ifeffit\updates\updater.dat > > to read '005'. (Just three numbers, on one line). Then, re-running > athena, artemis, etc should immediately tell you that there are > updates available, and download and install them. If you have > problems, please note whether > a) ifup_006.zip gets downloaded (the progress bar in the > lower right corner of the updater GUI should shows the > download progress). > b) whether the main GUI panel lists any files being unpacked. > > Hope that helps, > > --Matt > > Peter Southon Research Fellow School of Chemistry University of Sydney Australia ------------------------------------------------- This mail sent through IMP: www-mail.usyd.edu.au

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configurational average
by Makoto Matsuura 16 Mar '04

16 Mar '04

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 ******************************************

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Bug in Atoms
by Schmithals 16 Mar '04

16 Mar '04

Hello, I have attached an atoms.inp file that causes problems when used with Artemis. Both, Atoms run from within Athena as well as TkAtoms generate a feff.inp file with a wrong POTENTIALS-Card. Subsequently, FEFF will refuse to run, saying that potential number 1 is not used. I tried the same procedure with an older atoms.exe and had no problems. Another bug: TkAtoms allows only to open the space group browser only once. Every further click on "Browse space groups" will have no effect. I use Windows 2000 Pro. Regards, Gerrit

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Debian versions of horae-031
by Carlo U. Segre 16 Mar '04

16 Mar '04

Hello All: For those of you interested in Debian Linux packages, I have just completed a complete restructuring of the horae and ifeffit packages. This includes individually packageing the CPAN modules that are used in horae. The "unstable/sid" packages are already up and available and I should have the "stable/woody" versions posted by Tuesday midmorning. Please let me know of any bugs that you might find so that I can make the packages work. To get the packages, place the following lines in your /etc/apt/sources.list file: deb http://fermi.phys.iit.edu/debian/woody binary/ deb-src http://fermi.phys.iit.edu/debian/woody source/ deb http://fermi.phys.iit.edu/debian/sid binary/ deb-src http://fermi.phys.iit.edu/debian/sid source/ for the two distributions. Now that I have the new framework and a cleaner structure, it will be easier for me to keep current with Bruce's releases. 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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Athena quirk
by Dave Baker 16 Mar '04

16 Mar '04

Bruce, I have recently updated my Ifeffit package to the current versions (Ifeffit 1.2.5 and Athena 0.8.026) under Win2k Pro, and I have noticed something that is a bit irritating. My situation is this: I have a project open in Athena, but decide to refresh or rename that project file to something different from within Windows explorer. I expected to only have to close the project file within Athena but keep Athena itself running. This is not the case, however, as Athena does not "let go" of the file until it is completely closed. After closing, I can rename the project file without difficulty, but then I must restart Athena from square one. Is this normal behavior? Does anyone else see this behavior? Thanks in advance for your help. -Dave Baker

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