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

Small clusters in Feff
by Kelly, Shelly D. 07 Oct '05

07 Oct '05

Hi EXAFS friends, I was reading a paper this morning where the authors used a small hydrated cluster in Feff8.2. The cluster has a metal center surrounded by one shell of oxygen atoms. All feff paths in the calculation were used in the model fits. No mention was made in the manuscript of the muffin tin radii used in the Feff8.2 calculation based on this small cluster, hence I assume that these authors were unaware of the potential pit falls in doing so. Using feff7, I have run a comparison of the calculated signal from a bounded and unbounded shell of atoms at the same distance. I found that the unbounded shell of atoms has a muffin tin radii that is really big because it is not bounded by any other atoms giving rise to an error in the calculated signal from these atoms. Has anyone run this experiment with Feff8.2? I have always used the metal-oxide crystal structure in my modeling of hydrated metal ions and have found reasonable agreement with chemical speciation calculations. I believe that the non-expert users of Feff, find it difficult to remember not to use the exact model within Feff because of this "feature". Is there any discussion of adding a hydration sphere option into Feff? I look forward to your comments. Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60440

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new tip of the week
by Bruce Ravel 07 Oct '05

07 Oct '05

Hi, The Tip Of The Week took last week off to go visit my mom ;-) This week's is about "Selecting paths to plot automatically after a fit" in Artemis. http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek Enjoy! B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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delR versus thermal expansion A and first cumulant C1*
by Leandro Langie Araujo 05 Oct '05

05 Oct '05

Dear all, I’m writing because I’ve been trying to analyze some thermal dependent EXAFS data for the first shell of a c-Ge sample and ended up in a conceptual confusion. If any of you could give me some help on this I’d be very grateful. Whenever we fit an EXAFS spectrum with Artemis/IFEFFIT, we get a /delR/ value. As far as my (very) limited comprehension goes, /delR/ is the difference between the theoretical (FEFF8) bond length, /R0/, and the result of the best fit to my data, /R/, which gives the experimental bond length. So, this should be the /first cumulant/ of my distance distribution, right? The net linear thermal expansion /A/ (as defined by Anatoly Frenkel and John Rehr in [PRB48, 585, 1993]) from an one-dimensional model seems to have been considered as equal to the temperature variation of the /delR/ values by several people, including Matt Newville (on his thesis). Following this approach, it is possible to relate the EXAFS cumulants (/delR/, /ss/, /C3/ and /C4/) of the distance distribution with the constants of an one-dimensional anharmonic effective potential, following a correlated Einstein model. I was going through this path... … when I came across some papers (P. Fornasini and G. Dalba in [PRL82, 4240, 1999; PRB70, 174301, 2004] and E. A. Stern in [J.Phys.IV 7, C2-137,1997]) where an issue is raised; it is said that the thermal evolution of the first cumulant /C1/* of the real distance distribution in a crystal (which was said to be equivalent to /delR/) is NOT equal to /A/, because in a crystal there are vibrations perpendicular to the bond direction which are not considered in the one-dimensional model. It is argued that the temperature dependence of these vibrations perpendicular to the bond direction give raise to a positive shift of the minimum of the effective pair potential, while the net thermal expansion /A/ accounts only for changes due to the asymmetry of the potential. So, the main questions hammering my head are: - does /delR/ include any contribution from vibrations perpendicular to the bond direction? Can really /delR/ and /C1/* be the same quantity? - is the thermal evolution of /delR/ equal to the net thermal expansion /A/? Or should some correction for perpendicular vibrations be added to relate both quantities? Sorry if I made it too long, but it was something hard to express in a few words… Any help will be greatly appreciated. Cheers, Leandro

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R-factor and reduced chi square
by OWEN N LI 05 Oct '05

05 Oct '05

Hi, I understand R-factor and reduced chi square are statistical ways to see if the model is reasonable (R-factor) and if one model is better than the others (reduced chi square). But how much should I read into it? I have model A and B, I believe A is more theoretical sound than B. but when I fit them using IFEFFIT, the R-factor and reduced chi square of B is slightly better than A (B: 0.03, 28; A: 0.04, 33). What does that tell me? Is my assumption incorrect? Or are they more or less the same? Owen

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RE: [Ifeffit] New Method for Normalization?
by Barton, David (DG) 04 Oct '05

04 Oct '05

Bruce, You mentioned: > Isn't Ifeffit's Cromer-Liberman normalization scheme > substantially similar to the method presented in that paper? > When I use the Cromer-Liberman background subtraction routine in Athena the Normalized data is not flattened. Normalized, but not *flattened* data results in a skewed XANES region which is affected by the amount of curvature in the background. If I choose "Flatten" in Athena, it is my understanding that it applies a linear pre-edge and 2nd order polynomial post-edge regardless of which background was chosen (Autobk or CLNorm). The Clnorm background does appear to "flatten" the chi(k) data which can be useful for EXAFS analysis, but it doesn't flatten the mu(E) data. When one attempts to analyze XANES data it is preferred to have the entire post-edge "flattened" in mu(E) space so that the background curvature is eliminated from the dataset. Ultimately, as Matt stated, it would be nice to be able to combine a Victoreen and CLNorm background to get a reasonably "flattened" mu(E) function. I would also suggest adding the ability to independently set the pre-edge and post-edge functions (n'th order polynomial, Victoreen, CLNorm, or MBACK??) for Normalization and Flattening. These choices would be separate from the choice of background removal method to get chi(k) (Autobk or CLNorm). Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Bruce Ravel > Sent: Thursday, September 29, 2005 5:20 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] New Method for Normalization? > > > On Thursday 29 September 2005 15:48, Barton, David (DG) wrote: > > Has anyone considered using the methods of Penner-Hahn to normalize > > their data to get reliable intensities of near-edge features? The > > reference to their method of normalization is below: > > > > J. Synchrotron Rad. (2005). 12, 506-510 > [doi:10.1107/S0909049504034193] > > "A method for normalization of X-ray absorption spectra" > T.-C. Weng, > > G. S. Waldo and J. E. Penner-Hahn > > > > It is my understanding the Ifeffit uses a linear function to remove > > the pre-edge and a quadratic for the post-edge and that the > Athena's > > flatten is a subtraction of these functions. This is an excellent > > method under most scenarios since the background is usually fairly > > smooth and can be well approximated by a quadratic equation. > > Personally, I have had only a few rare cases where the quadratic > > function on the post-edge was not sufficient to reliably > normalize the > > data and in those cases a third-order polynomial was > sufficient. Does > > anyone else have an opinion on using alternative normalization > > routines? > > Isn't Ifeffit's Cromer-Liberman normalization scheme > substantially similar to the method presented in that paper? > > B > > > -- > Bruce Ravel ---------------------------------------------- > bravel(a)anl.gov > > Molecular Environmental Science Group, Building 203, Room > E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, > Room B007 > > Argonne National Laboratory phone and voice mail: > (1) 630 252 5033 > Argonne IL 60439, USA fax: > (1) 630 252 9793 > > My homepage: http://cars9.uchicago.edu/~ravel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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RE: [Ifeffit] R-factor and reduced chi square
by Kelly, Shelly D. 04 Oct '05

04 Oct '05

Hi Owen, A test for a significant change in the reduced chi square (RCS). [(RCS1)^2/(RCS2)^2] - 1 greater than 2 * sqrt ( 2 / degrees of freedom) If you can not read that, I have this published in J. Phys Chem B, V105 no27 year (2001). You can down load that paper from my web page www.mesg.anl.gov. I guess it is a reasonable test:). For most model fits a change by a factor of 2 is needed to be statistically significant. Good luck Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60440 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of OWEN N LI > Sent: Tuesday, October 04, 2005 1:08 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] R-factor and reduced chi square > > Hi, > I understand R-factor and reduced chi square are statistical ways to > see if the model is reasonable (R-factor) and if one model is better > than the others (reduced chi square). But how much should I read into it? > > I have model A and B, I believe A is more theoretical sound than B. > but when I fit them using IFEFFIT, the R-factor and reduced chi square > of B is slightly better than A (B: 0.03, 28; A: 0.04, 33). What does > that tell me? Is my assumption incorrect? Or are they more or less the > same? > > Owen > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Muffin tin radius adjustment?
by Paul Fons 03 Oct '05

03 Oct '05

I am trying to analyze some XAFS data on a Sb-Te compound and when I run feff(6) I get errors regarding the coordination number being too small implying the muffin tin radius is too big. In this material the first nearest neighbor bond length is about 3 angstroms (slightly more or less depending on the site). I assume this is related to the cause of the problem. Any suggestions as to how to fix/avoid this sort of problem? feff6 output is pasted below. Interestingly enough, feff8 does not output any error messages and the sum of the paths looks identical (at least at first glance). Is this a false error message or (more likely) has feff8 become more intelligent with regards to defining the muffin tin radius? Feff6 output Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 muffin tin radii and interstitial parameters phase shifts for unique potential 0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 2 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. Preparing plane wave scattering amplitudes... nncrit in prcrit 9 Searching for paths... WARNING in PATHS Module: rmax > distance to most distant atom. Some paths may be missing. rmax, ratx 15.50000 15.40291 Rmax 15.5000 keep and heap limits 0.0000000 0.0000000 Preparing neighbor table Feff8 output Calculating potentials ... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 initial state energy overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 muffin tin radii and interstitial parameters iph, rnrm(iph)*bohr, rmt(iph)*bohr, folp(iph) 0 1.79879E+00 1.71274E+00 1.13279E+00 1 1.81342E+00 1.72495E+00 1.13595E+00 2 1.83703E+00 1.74437E+00 1.14149E+00 mu_old= -0.508 Done with module 1: potentials. Calculating LDOS ... LDOS calculation for specified grid Calculating energy and space dependent l-DOS. It takes time ... potential type 0 potential type 1 potential type 2 Calculating chi and rho... 0 Calculating chi and rho... 1 Calculating chi and rho... 2 Done with LDOS. Calculating cross-section and phases... absorption cross section phase shifts for unique potential 0 phase shifts for unique potential 1 phase shifts for unique potential 2 Done with module 2: cross-section and phases... Done with module 3: FMS. Preparing plane wave scattering amplitudes... Searching for paths... WARNING: rmax > distance to most distant atom. Some paths may be missing. rmax, ratx 1.55000E+01 0.00000E+00 Rmax 15.5000 keep and heap limits 0.0000000 0.0000000 Preparing neighbor table Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８茨城県つくば市東１−１−1 つくば中央第４近接場光応用工学センターポール・フォンス主任研究官

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Runner.exe Network Error
by Barton, David (DG) 28 Sep '05

28 Sep '05

Bruce and Matt, I am running the Ifeffit 1.2.8 on a Win2000 box and I having several issues with the startup of Athena/Artemis when I am not connected to a network. First thing is that all programs run fine when I am connected to the internet. So the obvious workaround for me is to just make sure that I have an open network connection before running Athena/Artemis. However, it would be nice if the auto-update feature in "Runner.exe" would still let me run Athena/Artemis when I wasn't connected to the network, basically just ignore looking for an update when I don't have a network connection. The errors that I get in the Runner.exe.log are below. There are two different cases shown. The first set of errors are when I have a connection to my local network, but have not yet logged onto the firewall that lets me out onto the internet. The second set of errors comes up when I unplug the network connection completely. Hope these help. NETWORK CONNECTION NO INTERNET CONNECTION ----------------------------------------- Traceback (most recent call last): File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 299, in read_web_version File "urllib.pyc", line 76, in urlopen File "urllib.pyc", line 181, in open File "urllib.pyc", line 306, in open_http File "urllib.pyc", line 319, in http_error File "urllib.pyc", line 565, in http_error_302 File "urllib.pyc", line 580, in redirect_internal File "urllib.pyc", line 181, in open File "urllib.pyc", line 306, in open_http File "urllib.pyc", line 319, in http_error File "urllib.pyc", line 616, in http_error_401 File "urllib.pyc", line 624, in retry_http_basic_auth File "urllib.pyc", line 650, in get_user_passwd File "urllib.pyc", line 658, in prompt_user_passwd NO NETWORK CONNECTION -------------------------------------- File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 302, in read_web_version Dave _________________________________ David Barton The Dow Chemical Company

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getting chi(r) information out of command line IFEFFIT
by Sean X. Luo 28 Sep '05

28 Sep '05

Hello all. It's been a while since I've written on the mailing list about this project, but it's come up that I need everyone's general input. Just a brief overview of the project: I am working with Scott Calvin to simultaneously fit 12 data sets in the command line of IFEFFIT, and I need to somehow get the chi(r) information for the fit out of the command line. I've tried around with the "show" command and the different permutations possible with that, but whenever I type in "show(fit.r, fit.chir_real)" (which is our guess right now on how to get the information I need out of the command line), it gives me the error that the arrays fit.r and fit.chir_real does not exist, or something along those lines. Does anyone else have any idea on how to run this? Thanks in advance, - Sean.

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RE: [Ifeffit] Fe oxide
by Kelly, Shelly D. 26 Sep '05

26 Sep '05

Hi Juro, I had some fun playing with this project file. I hope you don't mind. Here is a list of suggestions. 1st: Don't use the paths that are less than 0.1 Angstroms apart. 1st-b: If you don't know the CN set it to ONE and then vary just the amplitude. There is a degen box multiplied by a amp box. Degen should be one. 2st: set the values for CN, and s2, while letting delr vary 3rd. Let the CN and delr vary. You will find that the Fe path around 3 Ansgroms isn't needed. 4th. Make sure your fit range and data ranges are appropriate. 5th. Add as much constraints as you think is reasonable. First Oxygen coordination number should be 6 or 4 total. I thought 6 worked well. 6th. Fit the data with k-weight of 1,2, and 3, to get the uncertainties smaller. Take a look at the project file. I think that this model or one like it might work. You need a separate S02 value from the Amp value. Amp should be S02*Amp. I didn't add a S02 part. You should get that from a known standard measured on the same beamline. S02 should be between 0.70 and 1.0. So the CN reported are likely a bit too big. Good luck, Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60440 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Juraj Majzlan > Sent: Monday, September 26, 2005 8:46 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Fe oxide > > Hello, > > I am trying to fit an EXAFS spectrum of an X-ray amorphous > Fe precipitate. In a model (goethite), there are Fe atoms > at 3.02, 3.29, and 3.45 A. Fitting the two most distant > shells of iron gives strange results. Fitting them > simultaneously gives very high amplitudes (32, -66) which > cancel each other (fig. 1) and produce a beautiful and > unreasonable fit (fig. 2). > > Fitting them separate gives small ('reasonable') > amplitudes, but the distance (dr) have very high > uncertainties, e.g., dr = 0.12 +- 20.3. > > Can I expect to resolve these three Fe shells or is it > asking too much? > > I am also attaching the Artemis file, but will appreciate > any comments and suggestions. > > Juro Majzlan > > > ---------------------------------- > Juraj Majzlan > Institute of Mineralogy and Petrology > Albert-Ludwig-University of Freiburg > Albertstrasse 23b > Freiburg, D-79104, Germany > telephone +49-761-203-6416 > fax +49-761-203-6407 > http://www.minpet.uni-freiburg.de/sites/personen/majzlan.html

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