February 2005 - Ifeffit - millenia.cars.aps.anl.gov

Debye-Waller factors for metal oxides ?
by Ian James Drake 16 Apr '09

16 Apr '09

Hi, There is little discussion over the significance of fitted Debye-Waller factors (ss2) found for metal centers in metal oxides of heterogeneous catalysts. I am searching for a better way of determining how reasonable these values are in the fits I get. 1. Are phenomenological models like the correlated Debye model and Einstein model appropriate? It seems that Debye temperatures are hard to find for oxides. 2. Is there an equivalent value for ss2 in x-ray crystallography data that I can refer to for comparison in these materials? What should I look for in reviewing published x-ray crystallographic data? 3. Is the temperature dependence reported for the ss2 for some metals (like Cu and Al) similar to their respective oxides? For example, in Debye-Waller factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three between 25C and 300C. Would I expect a factor of three increase in crystalline zeolites (AlO4 structural units). 4. Specific to my work: I have studied Al containing oxides at temperatures between 25 and 300 C. I would like to quantify coordination changes by doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at temperature and I observe no change in the broadening of the data. Likewise, the fitting shows no sensitivity in the Debye-Waller factor. It is nearly constant at 0.001 A over the temperatures of interest. Since ss2 and the coordination number (CN) are correlated, I would like a way to bind the error on the fitted CN by modeling real physical changes in the Debye-Waller factors. Do you have any suggestions? Looking forward to your thoughts. Ian Drake Graduate Student UC Berkeley

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installation of horae in fedora2
by ynliu＠eps.mcgill.ca 22 Mar '05

22 Mar '05

Hello,all We finally succeeded in installing horae-048 in Fedora 2! It took us a long time to figure out why Tk could not be detected, but it turned out that the right version of Tk is the key. We found Tk-804.027 working in our Fedora2 system. The right order of installation is also important. We had to restart everything in installing horae after we set up Tk.If you are using this Tk-804.027, you don't need to look for unix folder as said on some web,just simply gunzip tar -xvf finename.tar (enter the new folder Tk-804.027) make make install(after this,you can make test if you want) And then the installation of horae will jsut go fluently following the instructions! To use athena or artemis, you need to enter the fold where athena.pl and artemis.pl are,and then "perl athena.pl". cheers Yanan ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Residual
by yetao＠chem.uga.edu 11 Mar '05

11 Mar '05

Hi, Is there anyone who can tell me how to view the residual in Artemis? Every time I checked the residual, only got the data curve. Best, Ye

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Re: uncertainties in "relative" values (Josh Kas)
by joshua jason kas 27 Feb '05

27 Feb '05

Hi Scott, if I understand correctly, the absolute uncertainties in the sizes are still large when you fit sizA and delta_size=(sizeB-sizeA), but I think that the uncertainty in the parameter delta_size showing the difference between the two could be very small, showing that there is a correlation between sizeA and sizeB. In order get this behavior I think you have to leave sizeA unconstrained when you do the multiple-dataset fit. If the uncertainty in delta_size is small, then the absolute uncertainties will be approximately sizeA +- ds_a, sizeB +- ds_a, more or less the same as before, but the uncertainty in sizeB given sizeA is much smaller sizeB = sizeA + delta_size +- dds. -Josh Kas > Hi Matt, > > I tried that, before realizing it didn't really do anything. > Performing a multi-dataset fit with two guessed variables, say size_A > and sizeA_v_sizeB, is of course completely equivalent to just having > the two sizes as guessed variables. And if size_A is set to some > arbitrary (but reasonable) value, sizeA_v_sizeB is equivalent to just > fitting size_B, and produces the "absolute" uncertainty again. This > would be different if the fit were truly multi-dataset in the sense > that we had parameters in common between samples, so that > constraining the size of A had some effect on the fit for B. But the > parameters that are in common, like S02, we constrained to a standard > rather than refining through a multi-dataset fit. > > I like your analogy to airline tickets...that is something like the > situation we seem to have. > > --Scott Calvin > Sarah Lawrence College > >> Hi Scott, >> >> Would it make sense to define a factor between the size of the >> two (or more) particles, say "sizeA_v_sizeB" and vary *that* in >> a fit of the two particles, keeping all the other things >> (k-weight, ranges, etc) the same for the two fits? That is, >> instead of asking "what is the size of particle A and what is >> the size of particle B?", ask "what is the size of particle A >> and how much bigger is particle B?". If you're observations are >> right, sizeA_v_sizeB should be statistically different from 1. >> >> --Matt >> >> PS: The price of airline tickets vary widely with many factors, >> but for any given flight, the price (starting "retail" price) of >> a first class ticket is always higher than a coach ticket. Of >> course, the coach ticket on some flights can easily be twice the >> price of a first class ticket on other flights. But everyone >> knows first class is always more expensive than coach. ;). > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 24, Issue 11 > *************************************** >

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[Fwd: FEFF Q]
by Bruce Ravel 27 Feb '05

27 Feb '05

Ryan, I am on vacation right now, so I have taken the liberty of forwarding your mail to the Ifeffit mailing list. Hopefully someone there will offer up an answer to your questions. Regards, B ---------------------------- Original Message ---------------------------- Subject: FEFF Q From: "R Tappero" <rtappero(a)udel.edu> Date: Fri, February 25, 2005 5:55 pm To: ravel(a)phys.washington.edu -------------------------------------------------------------------------- Hello Dr. Ravel, My name is Ryan Tappero and I am a graduate student in Dr. Sparks Env. Soil Chem research group. I am preparing for an XAFS experiment with M. Newville at APS. I read a recent paper (attached) where the authors used FEFF7 to generate theoretical phase and amplitude functions for cluster models (density functional theory/ DFT optimized structures). I am collaborating with one of my group members on this project, and he has completed the molecular orbital calcs for our proposed clusters. He has provided me with a set of coordinates for the optimized sorption complexes. I can not figure out how to input the x,y,z, coordinates into FEFF in order to generate the dominant scattering paths (for use with theoretical fitting of the XAFS data). Can you point me in the right direction? Sincere Thanks, Ryan Tappero Env. Soil Chem. U of DE, PLSC rtappero(a)udel.edu 410-996-9819 ravel <mailto:ravel@phys.washington.edu> @phys.washington.edu

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Postdoc position at HASYLAB
by Edmund Welter 15 Feb '05

15 Feb '05

Dear colleagues, at the Hamburger Synchrotron Strahlungslabor (HASYLAB) is a postdoc position in the XAFS business available. For more information please follow: http://www.desy.de/v2/docs/1107528217-e.pdf The main tasks of the succesfull applicant will be the operation of the X1 XAFS-beamline, to take care of the industrial XAFS users (This gives ample opportunities to use all the very nice programs which are topic of this list...) and last but not least HASYLAB strongly encourages postdocs to work in their own field of science. If you have questions about this mail or the available position please do not reply to the mailing list, but contact me directly instead. Best regards, Edmund Welter -- Dr. Edmund Welter HASYLAB at DESY e-mail : edmund.welter(a)desy.de Notkestr. 85 fon : (+49)-40-8998-4510 D-22603 HAMBURG fax : -2787 GERMANY secretary : -2304

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RE: About Cu2+ xafs
by Anatoly Frenkel 14 Feb '05

14 Feb '05

Dear Igor, Your problem is very interesting: the dependance of EXAFS analysis results on the FEFF model, and I am cc'ing my response to the group. Obviously, there does not exist a unique way to solve it. It is also true that it is important to know which set of results to choose because if you apply s02 to analyze your unknown compounds, whether it is 0.8 or 1.0 matters. There are several approaches that keep you from breaking your head trying to understand the underlying physics between SCF and nSCF and which of the two values of E0 are better . To choose which model is better, you have to approach it systematically by applying these models (SCF, nSCF and SS) to different systems where you know what debye waller factors should be (e.g., by performing temperature-dependent studies and comparing the resuls you obtained for DWF against those predicted by Einstein or Debye models. This has been done by many and it is a foolproof method. However, it is hard to do temperature dependent studies in solutions, and thus your options may be limited. You can also analyze pure Cu foil data measured in the same conditions at the same beamline, and obtian its S02 (it should be about 0.95 as I remember) and then impose it on your Cu2+ complex. However, this procedure does not allow the S02 in aqueous solutions to be slightly different than in the bulk Cu compounds, and we know that they may be different because the chemistry is strongly different, chemical potentials are discontinuous, and the argument of chemical transferrability of amplitudes and phases may not work. Also, it doesn't answer the question which FEFF calculation to prefer for the analysis of the complexes, but it helps a bit because it gives you some ballpark estimate what S02 should be. So, the first approach is to take S02 from Cu foil or Cu oxide data and impose it on the Cu in solution data. It may be a good start. By the way, in your case, both answers deviate by 10% from the average value: S02 = 0.9. That means, if you do not know which model is more reliable, pick 0.9 and your coordination numbers will be defined with 10% accuracy. It is a good accuracy in case of solutions. The second important question is what to do with E0 and distances. They do correlate, as your results show, and they should. However, the first nearest neighbor (equatorial) distances are identical between the two models. The second, axial, distances are different but overlap within the uncertainties. May be that one should be preferred that gives more realistic E0? Unfortunately, E0 is loosely defined in XAFS analysis (FEFF sets it at the muffin tin level) and it can be within 10-20 eV above Fermi energy. Since Fermi energy must be below 1s-3d transition energy, both of your results are, technically, legitimate. Unfortunately, there is no way to tell what should be the r_axial - partly, because it depends on pH and other factors, but it looks like both your models do give good agreement with expectations. What all these models have in common is that they are all based on theoretical calculations which means that they contain a black box and are hard to check experimentally. Some time ago, I adjusted FEFFIT to solve these problems by "bypassing" the black box part of them. I used an old-fashioned way of EXAFS analysis by using experimental standards instead of theoretical standards. For example, if you are certain that Cu2+ in aqueous solution is octahedrally coordinated, you can use this data set as experimental standard. If you extract the scattering amplitude and phase from this data set, the amplitude function will contain f(k) and S02 in it, and thus it spares you from trying obtaining it from the fit unambigously. Moreover, the phase function will have E0 and delta(k) informations in it as well, and if you align your standard and unknown in energy, the best results for delta r will be less model dependent if you relied on E0 obtained by FEFF. Here is a short paper where this method is explained in detail. http://pubweb.bnl.gov/people/frenkel/EXP-FEFF/thiols.pdf Regards, Anatoly Anatoly Frenkel Yeshiva University anatoly.frenkel(a)yu.edu -----Original Message----- From: Igor Frota de Vasconcelos [mailto:idevasco@nd.edu] Sent: Tuesday, February 08, 2005 9:39 AM To: Frenkel, Anatoly Subject: Re: About Cu2+ xafs Dear Dr. Frenkel, Thanks for your message! I will try put the whole story in a nut shell without leaving important details out! I am working with two different models for my hydrated Cu2+. The first one is a simple one with four water molecules on the equatorial plane, and two in the z axis. The four equatorial O's are 2 A away from the central Cu while the two axial O's are 2.29 A. I positioned the hydrogen atoms according to some molecular dynamics simulations of hydrated Cs and Pb (MD simulation of hydrated Cu2+ is harder because of the Jahn-Teller distortion). I also put eight water molecules in a second shell at 3.95 A to try to minimize truncation effects in the self-consistent calculation. I then used feff8.20 to calculate paths self-consistently (I will call this SCF) and not self-consistently (nSCF). The other model is the one you suggested in the mailing list (I'll call this one SS). The results using the latest linux based horae package are (the subscripts e and a denote equatorial and axial O's (I did not include results from multiple-scattering and hydrogen paths): 1) SCF: S02 = 0.9982900 +/- 0.0616710 E0 = -7.5800660 +/- 0.5694190 dr_e = -0.0443480 +/- 0.0034370 => r_e = 1.955652 +/- 0.0034370 ss_e = 0.0069170 +/- 0.0004820 dr_a = -0.0760780 +/- 0.0346330 => r_a = 2.213922 +/- 0.0346330 ss_a = 0.0320830 +/- 0.0076460 Reduced chi-square : 466.198889482 R-factor : 0.000652086 Measurement uncertainty (R) : 0.000306860 2) nSCF: S02 = 0.7977480 +/- 0.0758730 d_E0 = 1.1833490 +/- 0.8799960 dr_e = -0.0448740 +/- 0.0057950 => r_e = 1.955126 +/- 0.0057950 ss_e = 0.0051430 +/- 0.0008710 dr_a = -0.0107380 +/- 0.0451450 => r_a = 2.279262 +/- 0.0451450 ss_a = 0.0338300 +/- 0.0138210 Reduced chi-square : 2078.758619285 R-factor : 0.003396526 Measurement uncertainty (R) : 0.000306860 3) SS: S02 = 0.8082010 +/- 0.0866670 d_E0 = 1.1847890 +/- 1.6045490 dr_e = -0.0329940 +/- 0.0067630 => r_e = 1.957006 +/- 0.0067630 ss_e = 0.0049640 +/- 0.0008280 dr_a = -0.0959300 +/- 0.1364220 => r_a = 2.194070 +/- 0.1364220 ss_a = 0.0460070 +/- 0.0358600 The nSCF and SS results are very similar but some SS errors are significantly larger. Therefore I will base my comments and comparisons on the SCF and nSCF results. As you can see, the structural parameters are pretty much within error! S02 and d_E0 however, differ quite a lot. Although the d_E0 of 1.18 from the nSCF seems more reasonable than the -7.58 value from the SCF, the SCF fit is much better (lower reduced chi-square and R-factor). The S02 values are not within error. My problems are, then, two-folded: The first is a practical one: I don't know which S02 and d_E0 to pick and it is really bad because nailing them down (specially S02) is the whole purpose of the analysis of this standard. The second problem is of philosophical nature and more important than the first one because its clarification will provide the answer for the first problem and also some peace of mind. I do not understand why the E0 corrections (d_E0's) are so different. The fact that the correction obtained from SCF calculation is larger (and apparently worse) than that obtained from the nSCF calculation (absolute values) seems counter intuitive to me. The E0 value I picked for background subtraction is 8989 eV, and applying the corrections, I find an edge energy of 8990.1 eV and 8981.5 eV respectively. This second value falls in the pre-edge region, pretty much on the 1s-3d transition bump. Despite the evidences, I tend to trust the SCF's d_E0 value the most but would like to understand the physics (or lack of) behind the different feff calculations! I apologize if I bored you with unecessary details! Thank you very much for your attention and willingness to help! I really appreciate it! Best regards, Igor Anatoly Frenkel wrote: Dear Igor, I am getting back to your question now. It would help if I knew what E0 value you are getting. What is the value of s02 that you are obtaining? How are you modeling the Cu2+ standard compound? Are you using a bulk reference of a Cu-O bond (e.g., by using CuO oxide, or you are using a method in one of the IFEFFIT posts that I suggested (by using SS and OVERLAP cards)? If you tried one but not another, it is important that you compare them because the small clusters have all sort of truncation effects that cumulatively change photoelectron scattering amplitude and phase from those in the bulk. If both models produce similar FEFF paths for the first nearest Cu-O distance, it does not matter which one to choose in order to fit the standard compound. If they are different, use them separately when you fit the EXAFS data, and see which one gives you a more reasonable values of s02 and E0. I'll wait until I have a feedback from you because without knowing exactly what you are doing it is hard to give advice on what to do. From my experience with different Cu2+ complexes, these systems can be reliably analyzed. Let me know where you are getting stuck. Regards, Anatoly [Anatoly Frenkel] From: Igor Frota de Vasconcelos [mailto:idevasco@nd.edu] Sent: Wednesday, January 26, 2005 12:16 PM To: Frenkel, Anatoly Subject: About Cu2+ xafs Dear Dr. Frenkel, I am Igor Vasconcelos and I work under the supervision of Dr. Bruce Bunker at the University of Notre Dame's Physics department. I am currently working with some XAFS data on Cu(II) adsorbed on bacterial cell walls. I started out with (Cu(H2O)6)+2 standard to have a better feeling about the Cu+2 systems and to obtain a reliable estimate of S02 to use in the samples' fits. I am using SCF FEFF8.20 paths to fit the data and, although structural parameters make sense, I have exhausted my resources and still haven't understood a rather strange Eo value I am getting. I suspect it has to do with the way feff performs the calculations. I understand you have an extensive knowlegde on this system and I am hopeful you will be willing to provide me some help. I have followed recent posts in the ifeffit mailing list from you and I have two of your papers (Env. Science Tech. 1998 and 2000) on the subject as references. I would be very grateful if you would take the time to receive my question and answer it, in case you have the time and the inclination. I am looking forward to hearing from you. Thank you in advance for your attention, Igor -- IGOR F. VASCONCELOS Department of Physics University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556 USA phone: (1 574) 631 5650 fax: (1 574) 631 5952 e-mail: idevasco(a)nd.edu www.nd.edu/~idevasco -- IGOR F. VASCONCELOS Department of Physics University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556 USA phone: (1 574) 631 5650 fax: (1 574) 631 5952 e-mail: idevasco(a)nd.edu www.nd.edu/~idevasco

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Debye-Waller factors for metal oxides ?
by TAO,Ye 09 Feb '05

09 Feb '05

Dr.Rehr mentioned the calculation of DWs using spring constants with the equation-of-motion method(EM) and the recursion method(RM). I wonder if these two methods can be incorporated into ifeffit like Debye and Enstein model. I use EM to calculate the DWs for metal complex molecules, and they work pretty well for a preliminary analysis, but I have to input the calculated DW factors into Artemis one by one manually :-( Ye

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DW Factor follow up
by Ian James Drake 07 Feb '05

07 Feb '05

> Hi, > > Thank you for all this valuable information. > > Can I make a general statement in comparing the DW of metal and its crystalline oxide at a given >temperature? For example, I find the DW for Al metal to be 0.015A in the first scattering path >(Al-Al) at 25C (using correlated Debye model). However, the fitted value of the DW for Al oxide >in the first path (Al-O) was 0.001 A. In both fits, the CN was set to a constant since it is >known from other techniques. Can a general statement be made comparing relative magnitudes of >metal-metal DW and metal-oxygen DW-factors? > > Is there a good general resource for the Debye temperatures of metal oxides, like zeolite or >Al2O3? > > Thank you again for all your guidance. > > Ian Drake

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RE: [Ifeffit] Debye-Waller factors for metal oxides ?
by Kelly, Shelly D. 07 Feb '05

07 Feb '05

I agree with John Rehr. With a temperature dependent data set, the best model that I have found is to allow each atom pair to have a thermal and static disorder component. Sigma2 = debye(Temp,Td_O1) + stat_O1 (This example is for the first oxygen (O1) shell of the metal oxide) The static disorder component should be the same for all data sets from the same sample at the different temperatures. The thermal component should increase as the temperature increases. If you are lucky a Debye or Einstein model will work well enough. You will have to test both. In addition, the thermal change in sigma2 should be about the same for different samples that are closely related. (We could argue about this last point. The best thing to do is to test this constraint by first not imposing it and determine within the uncertainties in the measurement, if it is true. I have found that it usually is an okay constraint.) In the end, you simultaneously model the temperature dependence and the sample dependence spectra all together. You constrain the static disorder term to be independent of temperature, and you constrain the debye temperature to be independent of sample change. This should impose enough constraints on sigma2 values to accurately look at changes in coordination number. Of course the coordination numbers do not change as a function of temperature but only as a function of sample changes. HTH Shelly Shelly Kelly ---------------------------- skelly(a)anl.gov Bldg 203, RM E113 phone: (1) 630-252-7376 Argonne National Laboratory fax: (1) 630-252-9793 Argonne, IL 60439 www.mesg.anl.gov > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of John J. Rehr > Sent: Monday, February 07, 2005 10:07 AM > To: XAFS Analysis using Ifeffit > Cc: John J. Rehr > Subject: Re: [Ifeffit] Debye-Waller factors for metal oxides ? > > > > The lack of accurate Debye-Waller factors in complex materials, like > metal oxides, can be a real problem. In my view, simple phenomenological > methods like correlated Debye and Einstein models can't always be trusted. > > There is an alternative approach to fitting DW factors in such systems > which might be useful. The idea is to fit a few spring constants k_ij > between > the atoms, rather than the DW factors themselves, e.g., for the most > important > sites. This is efficient since the spring constants are temperture > independent. This has been tested by Rossner et al. using their Bayesian > approach [Rossner, H. H. and Krappe, H. J., (2004). Phys. Rev. B 70, > 104102] > The fitting is does via an analytical formula for the Debye-Waller factors > based on a fast recursion method [Poiarkova, A. V. & Rehr, J. J. (1998). > Phys. Rev. B 59, 948]. > > Of course, such an approach still misses contributions to the DW factors > due to structural disorder, which are addititive. > > J. Rehr > > > > On Sun, 6 Feb 2005, Ian James Drake wrote: > > > Hi, > > > > There is little discussion over the significance of fitted Debye-Waller > > factors (ss2) found for metal centers in metal oxides of heterogeneous > > catalysts. I am searching for a better way of determining how > reasonable > > these values are in the fits I get. > > > > 1. Are phenomenological models like the correlated Debye model and > Einstein > > model appropriate? It seems that Debye temperatures are hard to find for > > oxides. > > > > 2. Is there an equivalent value for ss2 in x-ray crystallography data > that I > > can refer to for comparison in these materials? What should I look for > in > > reviewing published x-ray crystallographic data? > > > > 3. Is the temperature dependence reported for the ss2 for some metals > (like > > Cu and Al) similar to their respective oxides? For example, in Debye- > Waller > > factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: > > Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three > > between 25C and 300C. Would I expect a factor of three increase in > > crystalline zeolites (AlO4 structural units). > > > > 4. Specific to my work: I have studied Al containing oxides at > temperatures > > between 25 and 300 C. I would like to quantify coordination changes > by > > doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at > temperature > > and I observe no change in the broadening of the data. Likewise, the > fitting > > shows no sensitivity in the Debye-Waller factor. It is nearly constant > at > > 0.001 A over the temperatures of interest. Since ss2 and the > coordination > > number (CN) are correlated, I would like a way to bind the error on the > > fitted CN by modeling real physical changes in the Debye-Waller factors. > Do > > you have any suggestions? > > > > Looking forward to your thoughts. > > > > Ian Drake > > Graduate Student > > UC Berkeley > > _______________________________________________ > > 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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