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

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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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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EXAFS sample prep
by Kelly, Shelly D. 02 Feb '05

02 Feb '05

Hi Ritika, I hope you do not mind, I'm sending this to the Ifeffit mailing list since others might be interested as well. This email message is about how to prepare an EXAFS sample. We are talking about measuring a Ti-edge from some sample in solution. But any edge and any sample in any matrix will also work just file. You want to set-up your sample so that you have a lot of Ti atoms in the path of the x-ray beam. This is because the EXAFS signal comes from the adsorption from the Ti atoms. Hence more Ti atoms give more adsorption events resulting in a smaller statistical error in the EXAFS spectra. BUT..... In transmission mode the EXAFS signal comes measuring the number of x-rays incident on the sample and transmitted through the sample. If all the x-rays are adsorbed by the Ti atoms in the sample then you do not have any transmitted x-ray signal. Hence you get really noise data because you have no statistically significantly transmitted x-ray signal. So you need your sample to be thin so that a lot of the x-rays pass through the sample such that you have something to measure. In fluorescence mode the EXAFS signal comes from the x-rays emitted by the Ti atoms as the core hole is re-filled. These emitted x-rays need to escape the sample without being re-adsorbed by the sample. Hence the sample needs to be dilute for fluorescence mode measurements. When you make a measurement in fluorescence mode it is always best to collect the transmitted x-ray signal as well. Then you can make a comparison to see if "self adsorption effects" are small. Transmission measurements typically have better signal to noise ratio than fluorescence measurements. So if you can, make your measurements in transmission mode. You can use Tkatoms or Artemis to calculate the best sample thickness and the best concentration to use for the measurements and which EXAFS mode will work best for your samples. >From the components of your sample you can calculate the thickness of the sample that will give 2.5 adsorption lengths. The transmitted x-ray intensity is given by the incident x-ray intensity multiplied by the exponential of the absorption coefficient times the sample thickness. I = I0 * exp(-mu(E) * x) Where I is the transmitted x-ray intensity I0 is the initial x-ray intensity Mu(E) is the absorption coefficient = weighted sum of absorption coefficient from each atom in the beam. X is the thickness of the sample. IF mu(E) * x = 2.5 then the percent of transmitted x-rays is about 10% of the incident x-ray intensity. This is just enough at NSLS where the incident x-ray intensity will be about 10^6 x-rays per second. This means that 10^4 x-rays per second will hit your transmitted Ion chamber. You want to make the transmitted ion chamber adsorb all (99%) of theses x-rays. Then your statistical error in the measurement will be 1/sqrt(N) or 1/sqrt(10^4) or 1%. You need to have at least this many x-rays to measure. At the beam line you measure the total absorption edge. The EXAFS signal, if you are lucky, makes up about 10% of the absorption edge. Hence you need to have a statistical error of no more than 1% to make a measurement. If you can make the sample thinner then you do even better. Now for the other problem: You want to get as many Ti atoms into the sample with a total sample thickness of 2.5 absorption lengths. To do this part you need to calculate the absorption of just the Ti atoms in the sample. I call this delta_mu(E). If you can get the delta_mu(E) * x to be between 0.1 and 1.0 with the total absorption of the sample below 2.5 then you can make the measurement in transmission mode. This means that between 10% and 70% of the absorption in the sample will be due to the Ti atoms. This is enough to get a good transmission signal. If you adsorption from the Ti atoms in the sample is between 1% and 10% then you will hope to make the measurement in fluorescence mode. Now for the practical part: Say you have a solution with 1% Ti-stuff in water by NUMBER of atoms. If you usually work by weight then you need to convert to number for this calculation. Take the feff.inp file for Ti-stuff. Look at the top of the file. You should find total_mu(E) (absorption of the entire sample at the Ti edge), and delta_mu(E) (absorption of Ti atoms at the Ti-edge). Then use Hephaestus to calculate the total_mu(E) for water at the Ti edge energy. To get the total absorption you need to calculate the weighted average for water and Ti-stuff. See how thick you can make your sample and satisfy the criteria for less than a total absorption length of 2.5. (99%_by_number_water_atoms * total_mu(E)_for_water + 1%_by_number_Ti-stuff * total_mu(E)_for_Ti-stuff ) * sample_thickness = 2.5 Once you have that thickness then you can see what the absorption for just the Ti atoms is. 1%_by_number_Ti-Stuff*delta_mu(E)_for_Ti * sample_thickness = absorption_length_for_Ti And then you can figure out if you have a fluorescence or transmission experiment. Absorption_length = 0.1 to 1.0 you have transmission. Absorption_length=0.01 to 0.1 you have fluorescence. Usually you have to go around and around with this sort of calculation to optimize the conditions for the measurements. Hope that Helps Shelly

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RE: [Ifeffit] Two edge problem (in the same scan)
by Kelly, Shelly D. 26 Jan '05

26 Jan '05

> -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel > Sent: Wednesday, January 26, 2005 1:30 PM > To: asg2(a)lehigh.edu; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Two edge problem (in the same scan) > > > Hello everybody, > > I have a question/problem. Last year during the EXAFS course at NSLS, I > > had requested Bruce if it is possible to analyze the data with two > > edges. For example, I have the data for As and Se K-edges, which I > > collect in the same scan. In WinXAS program, I can section the edges and > > analyze them separately. At that time, the program was not able to > > perform these edges or the sectioning. Have we reached this possibility. > > I tried again using the latest updated Athena, but it seems not to be > > working. Can you please tell me whether the sectioning or dealing with > > two edges in the same spectra can be done > > I don't unfderstand why "sectioning" is necessary. What precludes you > from reading the data set a second time and setting e0 to be appropriate > for the second edge? Then your pre- and post-edge lines will be made > using the second e0 and everything else should just follow normally. > > I understand that Athena does not have a way to specify the second edge in > the column selection dialog, but that seems to me like an inconvenience > more than a real limitation. It is an inconvenience because you then have > to specify the second e0 by hand rather than have Athena's magic find it > for you, but is that really so hard? > > B > [Kelly, Shelly D.] Another feature that I have found useful for data with multiple edges is the truncate function. Once you read the data set into Arthena. Make a copy of the data set. Choose your e-zero for each data set. And then truncate the data sets to the "normal" range. This will help with some of the automatic presets, which use the full data range by default, and can give you a very scary initial background function. SK

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Two edge problem (in the same scan)
by Ashtosh Ganjoo 26 Jan '05

26 Jan '05

Hello everybody, I have a question/problem. Last year during the EXAFS course at NSLS, I had requested Bruce if it is possible to analyze the data with two edges. For example, I have the data for As and Se K-edges, which I collect in the same scan. In WinXAS program, I can section the edges and analyze them separately. At that time, the program was not able to perform these edges or the sectioning. Have we reached this possibility. I tried again using the latest updated Athena, but it seems not to be working. Can you please tell me whether the sectioning or dealing with two edges in the same spectra can be done Ashtosh

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[DATA-REQUEST] Platinum standards
by MauRo 24 Jan '05

24 Jan '05

Hi to all, I'm looking forward for some EXAFS (transmission or fluorescence) spectra of Platinum oxide and Platinum carbide at L_III and/or L_I edge. Is there anyone who has taken this data and is so kind to send them to me? Thanks, Mauro

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Increase NOVP error message meaning
by Paul Fons 23 Jan '05

23 Jan '05

I am trying to run feff on some chalcogenide structures that have rather nearest-neighbor long bond lengths, e.g. > Bond search from target site: Te1 > ...found 6 atoms within 0.00 - 3.20 A of this site > > ------------------------ > dist [Å] atoms > ------------------------ > 1. 3.0488 6 > ------------------------ > Bond search complete When I use this structure in feff82, I get the rather mysterious error INCREASE NOVP: > > 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 > free atom potential and density for atom type 3 > 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 > overlapped potential and density for unique potential 3 > muffin tin radii and interstitial parameters > tell authors to INCREASE NOVP Being an experimentalist, I did increase novp until the previous error message stopped, however this resulted in a core dump: > 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 > free atom potential and density for atom type 3 > 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 > overlapped potential and density for unique potential 3 > muffin tin radii and interstitial parameters > iph, rnrm(iph)*bohr, rmt(iph)*bohr, folp(iph) > 0 1.76126E+00 1.74898E+00 1.01667E+00 > 1 1.71891E+00 1.63874E+00 1.12886E+00 > 2 1.35785E+00 8.69242E-01 1.15000E+00 > 3 1.78418E+00 1.76792E+00 1.02193E+00 > mu_old= nan > 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 > Segmentation fault (core dumped) When running the equivalent file in feff6, I get the > 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 > free atom potential and density for atom type 3 > overlapped potential and density for unique potential 0 > overlapped potential and density for unique potential 1 > overlapped potential and density for unique potential 2 > overlapped potential and density for unique potential 3 > 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. > phase shifts for unique potential 3 > 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 This message seems similar to the troubleshooting section in feff8 for which it states: • Non-physical, widely spaced distributions of atoms. Symptoms of this common problem are very large muffin-tin radii (see the header of any ‘.dat’ file) and possibly a failure of the phase-shift program to converge. This gives error message hard test fails in fovrg. How to I avoid this problem (obviously the crystal structure is a given!). I tried the INTERSTITIAL card, but to no avail. Any suggestions are welcome. 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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Windows update for athena/artemis
by Matt Newville 18 Jan '05

18 Jan '05

Hi, I've built a Windows update file to upgrade to the latest versions of Athena and Artemis. Since Bruce is off-line for a while and since there is no easy way for us to make these executables, there is not much we'll be able to do if there is a problem with this version. Because of this, I am NOT releasing this as a normal update yet, but would like the braver of you to download and install this update by hand and give the new versions of Athena and Artemis a test drive. The update file is at http://cars9.uchicago.edu/ifeffit/updates/ifup_013.zip which is just a simple zip file that can be unpacked in your Ifeffit folder. (Probably C:/Program Files/Ifeffit). If you're willing to try these versions, please let me know how it goes. I'll wait until I hear some positive responses before I make a general update release that would automatically update everyone to these versions. Thanks, --Matt

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