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

common mono crystals
by Bruce Ravel 01 Dec '04

01 Dec '04

Hi folks, One of my chores for today is to implement a utility in Athena for converting encoder readings in a raw data file into energy. This will make some of the data in the Lytle database a bit easier to use. One of the things that the user must specify is the d-spacing of the mono crystal. I want to provide a menu of common crystals. The orange book is kind enough to provide an exhaustive list -- but it's kind of overkill. Somehow I doubt if many people are using a sucrose 001 monochromator even though that d-spacing is given in the orange book ;-) (Really! It's on page 4-12!) I want to do an informal survey of what crystals the ifeffit crowd regularly uses. I am certainly going to include Si111, Si311, and Si200 in the list, so I don't need to hear from people who use those crystals. What others should go in the list? Beryl? Germanium? Graphite? Let me know.... Thanks, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Importing Athena data into Excel
by sej9＠cornell.edu 29 Nov '04

29 Nov '04

I can't remember how to import chi(r) data from a merged file in Athena into Excel. Sarah

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formula checking
by Peter Southon 22 Nov '04

22 Nov '04

Hello all, I've got a quick question about the checking of formulas. I mistakenly typed "//" instead of "/" into several 'def' commands in my model. Unfortunately it took me a long time to find the mistake, since it was a complex model and by some fluke the equation gave almost (but not quite) the expected value. Since "//" doesn't seem to be a valid Ifeffit operator, why didn't either Ifeffit or Artemis pick it up? Regards, Peter Peter Southon Postdoctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 7482

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Rbkg value in Athena
by Ann Liang 18 Nov '04

18 Nov '04

Hi Bruce, I am a little bit confused on what the Rbkg value should be when I do the background subtraction. I have read some previous posts which stated that Rbkg can be determined after the fit. However, I always think that the fit depends strongly on how the background being subtracted. How does the initial spline value affect the background subtraction? Should it be 1eV or 25 eV above the edge? I appreciate your help. Thanks, Ann

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Re: [Ifeffit] formula checking
by Scott Calvin 17 Nov '04

17 Nov '04

Hi Matt, Bruce, etc., I think Matt's suggestion is a very good one. In the past, I have occasionally run into problems where Ifeffit flags a problem but Artemis doesn't check for the particular flag. Since when I'm rolling along using Artemis I don't alsays inspect the Iffefit messages, I didn't realize anything funny has happened immediately...it wasn't until I realized the fit didn't make sense that I checked if Ifeffit had correctly identified a typo or whatever. I've always alerted Bruce when these things have come up, and he's incorporated them into new releases, but it would be very good if Ifeffit had a couple of generic warning flags that Artemis could grab on to and thus prominently alert the user that something went wrong... --Scott Calvin Sarah Lawrence College At 11:08 AM 11/17/2004 -0600, you wrote: >Hi Bruce, Peter, > >Ifeffit does print a warning message about a syntax error on using >'//'. But it's completely believable and forgivable that Artemis >doesn't catch this. > >Bruce, would it help if a flag was set indicating 'syntax error' >in addition to printing the warning message? That way you could >wrap each of the definitions with a perl function that did the >ifeffit command and check for syntax errors, doing something >sensible (popping up a warning dialog box, for example) on a >syntax error. That might be better than checking for '//' itself, >because it would detect other syntax errors as well. > >A flag meaning 'math error' (as on divide-by-zero or sqrt(-1)) >might be useful too, I suppose.... >

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Re: strange distance obtained using atoms
by Bruce Ravel 15 Nov '04

15 Nov '04

On Thursday 11 November 2004 9:11 am, Valmor Mastelaro wrote: > Bruce, I´m using the atoms program to obtain the feff.inp file for a PZT > compound. when I introduced the crystallographic informations on the atoms, > I obtained only one distance that is too short to be true, Ti-Zr = 0.483 > > I verify all the crystallographic parameters in the literature and they > seens to be correct. (Journal of Physics: condensed matter 10, 6251-6269 > (1998). Hi Valmor. I am taking the liberty of forwarding my answer to the Ifeffit mailing list as well as the feffusers list. Here is the Atoms input file that Valmor sent: space = R 3 c a = 5.78510 c = 14.2880 core = Ti edge = K rmax = 9.0 atoms ! elem x y z tag occ. Pb 0.00000 0.00000 0.27170 1.00000 Ti 0.00000 0.00000 0.03590 1.00000 Zr 0.00000 0.00000 0.00210 1.00000 O 0.16321 0.34281 0.08333 1.00000 Actually, the one very short atom was only the most obvious of a host of problems with this input data. Look also at the Zr/Ti coordination shell. There are far too many atoms and they are much too close (about 0.483 AA apart -- imagine that!) to one another. Reading the paper that he cited, I see that coordinates are given for the anion and cation positions by parameterized deviations from the symmetry positions of the space group. It's really a very clever paper -- the parameters of the structure are things like cation displacement and octahedral tilt. Very cool stuff, all of which is explained abstractly in Table 1. Then in Table 3, the authors give the actual values of the parameters for each of the anions and cations. Among the data in this table are the fractional occupancies of Zr and Ti along with separate displacement parameters for those two cations. Before I go on, you need to read this old entry to the Ifeffit mailing list: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2002-July/000092.html That entry actually answers your question about why Atoms isn't working as you anticipated, but I'll expand on a few points here. Feff (and therefore Atoms) presumes that you have one entire atoms at any given site. Feff does not allow you to fractionally occupy a location in space. This may be a shortcoming of Feff, but there are good reasons why Feff behaves that way. Since Feff does not know how to compute a cluster with fractional atoms, Atoms does attempt to write fractional atoms to the cluster. Thus, when you put *both* Ti and Zr in the atoms.inp file, Atoms put six of each in the unit cell. (This crystal has six formula units in each unit cell.) That's obviously incorrect. The paper you cite clearly states that the samples have between 13 and 40% Ti according to the stoichiometry Pb Zr_{1-x} Ti_x O_3. So it is simply incorrect to have both the Ti and Zr entries in your atoms input file. As I explain in the link above, you generally cannot solve a problem like this with a single Feff calculation. You simply must consider an analysis strategy which involves at least 2 and possibly many more Feff calculation. Are you doing EXAFS analysis? If so, then you should consider running Feff once without the Ti site and using the parameter given in the cited paper for the Zr site. Then run Feff again with the Zr site and using the parameters given for the Ti site. Then, when you do your analysis, you will need to multiply the amplitude terms for the paths from the Zr calculation by (to use the example of one end member) 0.87 and multiply the amplitudes of the paths from the Ti calculation by 0.13. Or are you doing XANES calculations? In that case, you will need to run many Feff calculations with the Ti and Zr sites randomly populated following the modle of the Au2O3 that I discuss in the link above. In any case, the bottom line that you have to remember when using Atoms and Feff is that these programs do not and cannot treat occupancy in the same manner as is discussed in a paper on Reitveld refinement. (That is true at least in the context of running a *single* Feff calculation.) You have to understand and think hard about how Atoms works and how Feff works and how they should be used for your specific analysis problem -- this is particularly true in a problem like this, which involves a rather complicated scheme for treating the relationship between stoichiometry and structure. Hope that helps, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Please accept my apology
by Firouzeh Tannazi 11 Nov '04

11 Nov '04

Dear Ifeffit Mailing-List Members; Please accept my apology for accidentally sending a personal message to the ifeffit mailing list. Best Regards, Firouzeh Tannazi.

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Thesis Correction
by Firouzeh Tannazi 11 Nov '04

11 Nov '04

Hi Dr. Bunker; Let me at first thank you very much for the corrections and edition that you have made on the dissertation. I just want to remind you those sections that need more corrections. First the Introduction section which is very disperse! As we have "Abstract" part and any chapter has introduction we may eliminate the introduction chapter and add its stuff to other introduction parts or if you think it is better to keep it, I really appreciate if you write it in the way that more emphasize will be on last part . The next part is section 2.6, "X-ray Fluorescence Spectroscopy" which I want to talk about the differences and similarities between that method and XAFS. Regards, Firouzeh.

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new update for Windows
by Matt Newville 11 Nov '04

11 Nov '04

Hi I just posted a new update to Ifeffit for Windows. This includes the recent changes to Athena, Artemis, and Hephaestus that Bruce mentioned recently (in http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-November/001487.html) It also includes a new base Ifeffit library (1.2.6a) that can now write up to 99 array columns to output files, to fix the bug that Borbert Weiher and Bruce pointed out. In addition, the default Ifeffit library now allows for 1024 paths. If you have trouble running this (say, on an older machine), there is also a version of ifeffit_10.dll that supports up to 256 paths under the 'build_setup\dlls\IFF1.2.6a_MPATHS256' folder. --Matt

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MoS2 fit
by Grant Bunker 11 Nov '04

11 Nov '04

I haven't played with these data or this analysis, but the difficulty in fitting the known structure may suggest a problem with the data. One experimental problem that springs to mind, since MoS2 is a layered structure, is whether there might be a preferred orientation in the sample particles, i.e. the particles might not be randomly oriented. Since the x-ray beam is polarized this could cause some serious weirdness in the XAFS fitting (if the polarization weren't explicitly considered). grant On Thu, 11 Nov 2004 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Commercial MoS2 fit (dmc(a)pdx.edu) > 2. Commercial MoS2 -- Correction (dmc(a)pdx.edu) > 3. Re: Commercial MoS2 -- Correction (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 11 Nov 2004 08:12:34 -0800 > From: dmc(a)pdx.edu > Subject: [Ifeffit] Commercial MoS2 fit > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <1100189554.41938f7244a49(a)webmail.pdx.edu> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi List, > > I have tried a variety of different things to get this fit to work. It > seems pretty decent now, although, for my two MS paths (4,5) I had to force the > sO^2's to be positive. In the process one of them is now zero. My > parameter 'amp' wants to be 0.5 so I had to set it to 0.7 because I know that > it shouldn't be as low as 1/2. Changing the k-weight doesn't seem to help. > Here's my Data: > > Thanks, Dan > > > > Project title : Fitting merge 10_15_04.chi > ============================================================ > > Independent points = 28.581054688 > Number of variables = 13.000000000 > Chi-square = 5995.284754934 > Reduced Chi-square = 384.780419245 > R-factor = 0.043668737 > Measurement uncertainty (k) = 0.000187262 > Measurement uncertainty (R) = 0.006509968 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > e0 = 0.8645560 +/- 1.2283680 (guessed as 0.864556 (1.228344)) > ss = 0.0041070 +/- 0.0005190 (guessed as 0.004107 (0.000519)) > ss2 = 0.0043590 +/- 0.0005200 (guessed as 0.004359 (0.000520)) > ss3 = 0.0217810 +/- 0.0333390 (guessed as 0.021781 (0.033341)) > ss4 = 0.0000000 +/- 0.0509500 (guessed as 0.000000 (0.050951)) > ss5 = 0.0000360 +/- 0.0063810 (guessed as 0.000036 (0.006382)) > ss6 = 0.0028730 +/- 0.0071340 (guessed as 0.002873 (0.007133)) > alpha = -0.0012530 +/- 0.0031940 (guessed as -0.001253 (0.003193)) > alpha2 = 0.0075160 +/- 0.0022250 (guessed as 0.007516 (0.002225)) > alpha3 = -0.0171580 +/- 0.0323200 (guessed as -0.017158 (0.032321)) > alpha4 = -0.0165410 +/- 0.1054840 (guessed as -0.016541 (0.105487)) > alpha5 = -0.0181860 +/- 0.0187940 (guessed as -0.018186 (0.018795)) > alpha6 = 0.0227330 +/- 0.0147690 (guessed as 0.022733 (0.014767)) > > Def parameters: > delr_1 = -0.0057180 > delr_2 = 0.0342980 > delr_3 = -0.0782970 > delr_4 = -0.0754820 > delr_5 = -0.0829880 > delr_6 = 0.1037370 > > Set parameters: > amp1 = .7 > > > Correlations between variables: > ss3 and alpha4 --> 0.8462 > e0 and alpha --> 0.8335 > ss4 and alpha3 --> -0.6693 > e0 and alpha2 --> 0.6159 > ss and ss2 --> 0.6114 > alpha5 and alpha6 --> -0.5959 > alpha4 and alpha5 --> -0.5821 > ss4 and ss5 --> -0.5505 > ss3 and alpha5 --> -0.5246 > alpha and alpha2 --> 0.5146 > ss5 and ss6 --> -0.4931 > ss2 and alpha5 --> 0.4681 > ss5 and alpha3 --> 0.3885 > ss6 and alpha6 --> 0.3700 > alpha2 and alpha5 --> 0.3208 > ss2 and alpha4 --> -0.2992 > ss4 and alpha5 --> 0.2955 > ss3 and ss4 --> 0.2923 > ss5 and alpha2 --> -0.2842 > e0 and alpha4 --> -0.2781 > ss2 and ss3 --> -0.2677 > alpha3 and alpha5 --> -0.2523 > All other correlations are below 0.25 > > > > ------------------------------ > > Message: 2 > Date: Thu, 11 Nov 2004 08:20:02 -0800 > From: dmc(a)pdx.edu > Subject: [Ifeffit] Commercial MoS2 -- Correction > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <1100190002.419391328eb1a(a)webmail.pdx.edu> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi List, > > It appears that changing the k-weight on my fit does improve the fit. > I still have the problem of forcing the sO^2's on the two MS paths to be > positive. Here's some new data with k-weight 3: > > Thanks, Dan > > Project title : Fitting merge 10_15_04.chi > ============================================================ > > Independent points = 28.581054688 > Number of variables = 13.000000000 > Chi-square = 1527.118835332 > Reduced Chi-square = 98.011262136 > R-factor = 0.025169471 > Measurement uncertainty (k) = 0.000185138 > Measurement uncertainty (R) = 0.081594539 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > e0 = 1.1335810 +/- 1.3393990 (guessed as 1.133581 (1.339426)) > ss = 0.0035870 +/- 0.0003110 (guessed as 0.003587 (0.000311)) > ss2 = 0.0042850 +/- 0.0002780 (guessed as 0.004285 (0.000278)) > ss3 = 0.0303100 +/- 0.0510420 (guessed as 0.030310 (0.051043)) > ss4 = 0.0000000 +/- 0.0303840 (guessed as 0.000000 (0.030385)) > ss5 = -0.0008090 +/- 0.0043530 (guessed as -0.000809 (0.004353)) > ss6 = 0.0059560 +/- 0.0089810 (guessed as 0.005956 (0.008981)) > alpha= -0.0006040 +/- 0.0023740 (guessed as -0.000604 (0.002374)) > alpha2= 0.0073900 +/- 0.0016520 (guessed as 0.007390 (0.001652)) > alpha3= -0.0167250 +/- 0.0535940 (guessed as -0.016725 (0.053595)) > alpha4= -0.0120340 +/- 0.0773040 (guessed as -0.012034 (0.077302)) > alpha5= -0.0216900 +/- 0.0127530 (guessed as -0.021690 (0.012751)) > alpha6= 0.0219980 +/- 0.0183950 (guessed as 0.021998 (0.018395)) > > Def parameters: > delr_1 = -0.0027560 > delr_2 = 0.0337230 > delr_3 = -0.0763210 > delr_4 = -0.0549150 > delr_5 = -0.0989780 > delr_6 = 0.1003830 > > Set parameters: > amp1 = .7 > > > Correlations between variables: > e0 and alpha --> 0.8490 > e0 and alpha2 --> 0.8006 > ss3 and alpha4 --> 0.7123 > alpha and alpha2 --> 0.6792 > ss4 and alpha5 --> 0.6298 > ss and ss2 --> 0.6114 > alpha5 and alpha6 --> -0.5959 > ss5 and alpha4 --> 0.5328 > ss3 and ss4 --> 0.5300 > ss5 and ss6 --> -0.4931 > ss4 and alpha3 --> -0.4617 > ss2 and alpha5 --> 0.3847 > ss6 and alpha6 --> 0.3700 > ss2 and alpha3 --> 0.3276 > ss4 and ss5 --> -0.2764 > alpha2 and alpha4 --> 0.2506 > All other correlations are below 0.25 > > > > > > ------------------------------ > > Message: 3 > Date: Thu, 11 Nov 2004 12:19:06 -0500 > From: Scott Calvin <scalvin(a)slc.edu> > Subject: Re: [Ifeffit] Commercial MoS2 -- Correction > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <3.0.1.32.20041111121906.00a657e0(a)mail.slc.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Dan, > > A couple of quick thoughts, that might also be helpful to people starting > out with EXAFS fitting. > > First of all, the good news is that changing the k-weight does not seem to > affect the values ifeffit finds for the parameters significantly (i.e. I > didn't see any that moved outside of their uncertainties). That's very > reassuring. The fact that the fit quality is noticeably better at k-wt 3 > suggests to me that you might try raising kmin a bit--maybe the k-wt 3 fit > works better because the fits are struggling at the low end of the k-range? > Sometimes it's hard to get the background to work right down at low k, and > it looks like you have plenty of data range based on the number of > independent points. > > Second, I don't like forcing S02 to 0.7 because 0.5 is too low very much. > An iffy sample or problems with normalization can both suppress S02 below > the nominally ideal value. Forcing the fit to adopt a higher S02 then just > has the effect of screwing up correlated variables, like the Debye-Waller > factors. I'd look for explanations for the low S02 rather than just > disallowing it. (I certainly have set S02 in some of my published work, but > those were cases of complex fits where it seemed to be a false minimum, > rather than a sample or normalization error.) > > Finally, I'd try some "reasonable" constraints on your MS paths. If they > are triangle paths, it is not possible to come up with a rigorous formula > for how to write the debye-waller factors and alpha's for MS paths in terms > of the direct scattering paths, because you don't know for sure how the > motions of nearby atoms correlate. But in my experience, which is mainly > with metals and transition metal oxides, fits are generally not > particularly sensitive to the details of MS path constraint strategies. > Here's a constraint strategy of medium complexity that I teach my > undergrads that you can try: > > Def the alpha's of the MS paths to be the average of the alpha's for the > direct scattering paths that make them up, weighted by the length of the > segment. It's quite probable in a material such as yours that some segment > will be a S-S path which you don't have available as a direct scattering > path. Maybe just leave that piece out of the average. > > Def the ss's of the MS paths to be the sum of the ss's for the direct > scattering paths that make them up, divided by 4. Why divided by 4? Because > the ss for a half-path is rigorously equal to 1/4 the ss for a whole path. > Why add them? If the ss of each segment is truly uncorrelated, then adding > them is statistically proper. Of course, this is a truly awful > approximation in some cases, notably as the paths come closer to being > focused (i.e. one of the angles of the triangle becomes large). In cases > where the biggest angle in the triangle is more than about 140 degrees, I > just treat it as a focused path, but I doubt that's true for your two MS's. > > Please understand that this constraint scheme is fairly arbitrary! When > working with a new material, I suggest trying a constraint scheme like > this, and then seeing how sensitive the fit is to this constraint. For > example, multiply all the ss's of the MS's paths by 2 and see how stable > the fit is. Go back to allowing the alpha for the MS paths to vary freely > and see again if the fit is stable. This kind of probing will tell you > whether the MS paths are something that have to be carefully considered, or > if they are just a small correction to your fit that should be included but > don't have to be included particularly carefully. It is my experience that > the latter is often the case, but you have to find out for yourself on this > material. > > --Scott Calvin > Sarah Lawrence College > > At 08:20 AM 11/11/2004 -0800, you wrote: > >Hi List, > > > > It appears that changing the k-weight on my fit does improve the fit. > >I still have the problem of forcing the sO^2's on the two MS paths to be > >positive. Here's some new data with k-weight 3: > >> > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 21, Issue 8 > ************************************** >

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