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

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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back to work....
by Bruce Ravel 10 Mar '05

10 Mar '05

Hi everyone! I am back from vacation and (on March 7th) started my new position here in Argonne's Environmental Research Division. I had a splendid vacation and am very excited about my new position. For those of you who are APS users, I'll be spending a good fraction of my time at sector 10 (MR-CAT). Stop by and say hi -- especially those of you that I have met in person! I have to confess that I have not been following the discussions on the mailing list very closely in the last several weeks, but I see that there have been a number of bug reports and other problems that people have encountered with the software. I am still settling into my new job and my new home, but I hope to get back to work on the codes real soon. And I will certainly resume active participation in the discussions on the list. Regards, Bruce -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Environmental Research Division, Bldg 203, Room E165 Argonne National Laboratory phone: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Re: [Ifeffit] Athena Chi file created, but nothing there
by Adam Webb 08 Mar '05

08 Mar '05

Dan, I think the problem was when you first imported the data. When you import the data, Athena tries to figure out what type it is. In your case the first file is very short and Athena probably selected XANES data. This disables the k,q etc since they don't apply. Re-import your data but be sure to select mu(E) as the Data Type in the import window. The rest of your problems should go away. Cheers, Adam > Dear mailing list -- > > I'm having difficulty creating a chi file. First off I cannot > plot my data files in k, q , etc. The files can only be plotted in E > or merged and plotted in k, q, etc. > > Second, when I go to the file menu to create a chi(k) from the > marked original text file, Athena won't let me. That is to say the > only option is create to Save Mu(E) and when I do that a file is > created with nothing in it. > > When I merge 2 data files and create a chi(k) file from that, > again, a file is created and named, but nothing is there. Is there > something wrong with my data files? I don't see any error messages. > Let me know if you need more info. > > I'll also attach my athena file. > > Thanks, Dan ------------------------------------------------------ M. Adam Webb Ph.D., MCIC Alberta Synchrotron Institute (http://www.asi-cls.ca/) 8308 - 114 Street, Suite 2080 Edmonton, Alberta, T6G 2E1, Canada Phone: (780)492-5464 Fax: (780)492-6160 Email: adam.webb(a)asi-cls.ca

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Athena Chi file created, but nothing there
by Daniel Carter 04 Mar '05

04 Mar '05

Dear mailing list -- I'm having difficulty creating a chi file. First off I cannot plot my data files in k, q , etc. The files can only be plotted in E or merged and plotted in k, q, etc. Second, when I go to the file menu to create a chi(k) from the marked original text file, Athena won't let me. That is to say the only option is create to Save Mu(E) and when I do that a file is created with nothing in it. When I merge 2 data files and create a chi(k) file from that, again, a file is created and named, but nothing is there. Is there something wrong with my data files? I don't see any error messages. Let me know if you need more info. I'll also attach my athena file. Thanks, Dan

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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 13 Feb '05

13 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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