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

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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Commercial MoS2 -- Correction
by dmc＠pdx.edu 11 Nov '04

11 Nov '04

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

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Commercial MoS2 fit
by dmc＠pdx.edu 11 Nov '04

11 Nov '04

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

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new versions of my codes
by Bruce Ravel 05 Nov '04

05 Nov '04

Hi! I just posted new source code tarballs of my codes at my web site and at SourceForge. A while back, there were some problems with a bug in the updater script for unix. If you have problems using the updater, either download and install the tarball by hand or grab the latest copy of the updater script and run it instead: http://leonardo.phys.washington.edu/~ravel/software/exafs/utilities/horae_u… The fixed updater script will be installed once you get the new tarball installed. An updater package for windows users will hopefully be available next week, assuming no serious bugs are found in the new codes. For Athena and Artemis, this is mostly a bug fix release, although a lot of bugs were fixed. Athena has one new feature, which is an indicator at the top of the list of data groups which tells you when your project has been modified and needs to be saved. Clicking on this indicator is the same as choosing "File->Save project". For those people following the development version of Artemis, along with a number of important bug fixes there are two major new features: 1. In the Fits menu, there is a menu item for saving a "full data" file. This file records the data, the fit, the residual, the background (if appropriate), and the window as columns in a single file. If chi(R) or chi(q) is saved, the FT parameters appropriate to the chosen fit are used for all the columns. 2. You can now revert your project to a previous fitting model by selecting that fit from the Data and Paths List and selecting the restore option from the Fits menu. Fit model restoration can also be done with the right-click menu on the list on the log viewer page. I'll be eager to hear how well this works for others. This is a pretty exciting release of the development version for me because I have now completed all the features I was planning to add in this round of development. I am going to take a break from adding major new features to Artemis for a while to give people a chance to find the bugs. I am also planning to release a windows executable of the development version within the next few weeks to allow some more people to try out all the new features. As always, let me know what problems you run into. 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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RE: [Ifeffit] Fitting Commercial Molybdenum Disulfide
by Kelly, Shelly D. 05 Nov '04

05 Nov '04

Hi Dan, Sigma2 can not be negative. It is the mean square displacement of the half path length. You can force it to be positive by using abs(ss) on the definition page for each path in the fit. Shelly > -----Original Message----- > From: dmc(a)pdx.edu [mailto:dmc@pdx.edu] > Sent: Thursday, November 04, 2004 10:19 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Fitting Commercial Molybdenum Disulfide > > Hi List, > > Here's my most recent data. I was able to look at the individual > paths > and changed my R-range to 2-4.5 angstroms on the first set of data, I set > the > second set of data to the same range, although 4 works better as a maximum > for > that set. The k-range on the second range had to be truncated though. > > Six paths are used for each fit, same parameters, except for amp (0.7 for > one > ~0.8 for the other). The seperate data sets still have a few parameters > that > are outside of the error bars of the other (ss2,ss3,ss4,alpha, > alpha2,alpha5). > What can I do to get these beamlines to agree? > > delr_# define alpha# * reff > all other parameters guessed. > ss for each path, only one e0 for all > > Thanks for the help, Dan > > > First Data set -- Full k-range works best, Full range used for fit. > Project title : Fitting merge 10_15_04.chi > > Guess parameters +/- uncertainties (initial guess): > e0 = 0.8686930 +/- 1.1038290 (guessed as 0.868694 > (1.103841)) > ss = 0.0041150 +/- 0.0004990 (guessed as 0.004115 > (0.000499)) > ss2 = 0.0044360 +/- 0.0004450 (guessed as 0.004436 > (0.000445)) > ss3 = 0.0243560 +/- 0.0201400 (guessed as 0.024368 > (0.020159)) > ss4 = -0.0065470 +/- 0.0047820 (guessed as -0.006545 > (0.004786)) > ss5 = -0.0016100 +/- 0.0050490 (guessed as -0.001611 > (0.005047)) > ss6 = 0.0059980 +/- 0.0139390 (guessed as 0.005996 > (0.013935)) > alpha = -0.0011360 +/- 0.0029380 (guessed as -0.001136 > (0.002938)) > alpha2 = 0.0071480 +/- 0.0019780 (guessed as 0.007148 > (0.001978)) > alpha3 = -0.0060900 +/- 0.0273580 (guessed as -0.006078 > (0.027378)) > alpha4 = -0.0198570 +/- 0.0154200 (guessed as -0.019851 > (0.015430)) > alpha5 = 0.1399050 +/- 0.0148530 (guessed as 0.139906 > (0.014848)) > alpha6 = 0.0199630 +/- 0.0268690 (guessed as 0.019961 > (0.026862)) > > Def parameters: > delr_1 = -0.0051820 > delr_2 = 0.0326180 > delr_3 = -0.0277930 > delr_4 = -0.0906110 > delr_5 = 0.6384270 > delr_6 = 0.0910950 > > Set parameters: > amp1 = .7 > > > Correlations between variables: > e0 and alpha --> 0.8170 > e0 and alpha2 --> 0.6726 > ss and ss2 --> 0.6591 > alpha and alpha2 --> 0.5516 > alpha5 and alpha6 --> -0.4856 > e0 and alpha3 --> 0.4083 > alpha3 and alpha4 --> 0.3588 > ss5 and ss6 --> -0.3581 > alpha and alpha3 --> 0.3100 > alpha2 and alpha3 --> 0.3045 > ss2 and alpha6 --> 0.2745 > e0 and ss3 --> 0.2649 > ss and ss3 --> 0.2627 > ss2 and ss3 --> 0.2626 > ss6 and alpha5 --> -0.2510 > All other correlations are below 0.25 > > > > > > > > > > > > Second Data Set -- Trucated k-range (2-13.5) > Project title : Fitting merge 10_15_04.chi > > Independent points = 25.270507813 > Number of variables = 14.000000000 > Chi-square = 1202.598221935 > Reduced Chi-square = 106.703108852 > R-factor = 0.057229121 > Measurement uncertainty (k) = 0.000827712 > Measurement uncertainty (R) = 0.022111003 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > amp = 0.7976070 +/- 0.1361170 (guessed as 0.776348 (0.139898)) > ss = 0.0037770 +/- 0.0015530 (guessed as 0.003589 > (0.001617)) > e0 = 0.5608430 +/- 1.8018380 (guessed as 0.642687 > (1.861307)) > alpha = -0.0061290 +/- 0.0049080 (guessed as -0.005966 > (0.005078)) > ss2 = 0.0029050 +/- 0.0009970 (guessed as 0.002686 > (0.001078)) > ss3 = 0.0075410 +/- 0.0094220 (guessed as 0.005992 > (0.008858)) > ss4 = -0.0110250 +/- 0.0035850 (guessed as -0.011776 > (0.004653)) > ss5 = -0.0042000 +/- 0.0078070 (guessed as -0.007610 > (0.005250)) > alpha2 = 0.0038110 +/- 0.0030450 (guessed as 0.003762 > (0.003187)) > alpha3 = -0.0037820 +/- 0.0145580 (guessed as 0.001200 > (0.015976)) > alpha4 = -0.0212550 +/- 0.0107080 (guessed as -0.011852 > (0.014417)) > alpha5 = 0.1151980 +/- 0.0236640 (guessed as 0.113430 > (0.014973)) > ss6 = 0.0028560 +/- 0.0166050 (guessed as -0.007250 > (0.003624)) > alpha6 = 0.0193530 +/- 0.0299640 (guessed as 0.001791 > (0.008195)) > > Def parameters: > delr_1 = -0.0279670 > delr_2 = 0.0173920 > delr_3 = -0.0172570 > delr_4 = -0.0969910 > delr_5 = 0.5256830 > delr_6 = 0.0883130 > > > Correlations between variables: > amp and ss --> 0.8382 > e0 and alpha --> 0.8048 > amp and ss2 --> 0.7964 > e0 and alpha2 --> 0.7533 > ss3 and alpha5 --> 0.7397 > ss5 and alpha4 --> -0.6999 > ss and ss2 --> 0.6591 > alpha and alpha2 --> 0.6159 > alpha5 and ss6 --> 0.6116 > ss5 and alpha3 --> -0.5790 > ss5 and alpha6 --> -0.5023 > ss3 and ss6 --> 0.4804 > alpha4 and alpha5 --> -0.4375 > e0 and alpha3 --> 0.4083 > ss4 and ss5 --> -0.4047 > ss3 and alpha4 --> -0.3972 > alpha5 and alpha6 --> 0.3827 > alpha3 and alpha6 --> 0.3498 > ss3 and ss5 --> -0.3278 > amp and ss3 --> 0.3209 > ss4 and ss6 --> 0.3181 > alpha and alpha3 --> 0.3100 > alpha2 and alpha3 --> 0.3045 > ss4 and alpha3 --> 0.2948 > amp and ss5 --> 0.2820 > ss2 and alpha6 --> 0.2745 > ss and ss3 --> 0.2627 > ss2 and ss3 --> 0.2626 > amp and alpha6 --> 0.2589 > alpha2 and alpha5 --> 0.2581 > All other correlations are below 0.25 > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Fitting Commercial Molybdenum Disulfide
by dmc＠pdx.edu 04 Nov '04

04 Nov '04

Hi Mailing list, I'm back at fitting commercial Molybdenum Disulfide to a Hexagonal p 63/m m c space group. Although my present fit is reasonable, thanks to the mailing list in August, I was hoping someone might have more suggestions to optimize it. Also, in order to better my fit, I still have seperate e0's, one for the first path, one for the remaining 2 paths. I haven't gotten a satisfactory physical explanation for this and I thought someone might have a good one. Also, the data on the same sample from two different beamlines seems to be somewhat different, namely the Reduced chi-square is very different (75.6 in one, 636.4 in the other). In both cases I use the first 3 single scattering paths. I may have included too much info, but better too much than too little. Thank You, Dan Carter Here are my parameters in both cases, values differ somewhat: Set: Amp = 0.7 guess: eO ~ 1.57 (1.52) (used for first path) guess: eO_1 ~ -4.77 (2.43) (used for remaining 2 paths) guess: ss ~ 0.0027 (0.000427) guess: alpha ~ -0.004 (0.003255) (positive for second fit) delr_1: alpha*reff First Fit: Project title : Fitting merge 10_15_04.chi Comment : Prepared by : Contact : Started : 11:49:36 on 22 October, 2004 This fit at : 11:10:57 on 28 October, 2004 Environment : Artemis 0.7.010 using Windows 2000, perl 5.006001, Tk 800.024, and Ifeffit 1.2.6 ============================================================ Independent points = 14.312500000 Number of variables = 4.000000000 Chi-square = 779.303886008 Reduced Chi-square = 75.568861674 R-factor = 0.041210572 Measurement uncertainty (k) = 0.000827712 Measurement uncertainty (R) = 0.022111003 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): e0_1 = -4.7737110 +/- 2.4268840 (guessed as -4.773687 (2.426889)) ss = 0.0027360 +/- 0.0004270 (guessed as 0.002736 (0.000427)) e0 = 1.5684690 +/- 1.5209160 (guessed as 1.568507 (1.520918)) alpha = -0.0040060 +/- 0.0032550 (guessed as -0.004006 (0.003255)) Def parameters: delr_1 = -0.0158980 Set parameters: amp = 0.7 Correlations between variables: e0_1 and alpha --> 0.8622 e0 and alpha --> 0.7870 e0_1 and e0 --> 0.7064 All other correlations are below 0.25 Project title : Fitting merge 10_15_04.chi Comment : Prepared by : Contact : Started : 11:49:36 on 22 October, 2004 This fit at : 11:10:57 on 28 October, 2004 Environment : Artemis 0.7.010 using Windows 2000, perl 5.006001, Tk 800.024, and Ifeffit 1.2.6 ============================================================ Independent points = 14.312500000 Number of variables = 4.000000000 Chi-square = 779.303886008 Reduced Chi-square = 75.568861674 R-factor = 0.041210572 Measurement uncertainty (k) = 0.000827712 Measurement uncertainty (R) = 0.022111003 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): e0_1 = -4.7737110 +/- 2.4268840 (guessed as -4.773687 (2.426889)) ss = 0.0027360 +/- 0.0004270 (guessed as 0.002736 (0.000427)) e0 = 1.5684690 +/- 1.5209160 (guessed as 1.568507 (1.520918)) alpha = -0.0040060 +/- 0.0032550 (guessed as -0.004006 (0.003255)) Def parameters: delr_1 = -0.0158980 Set parameters: amp = 0.7 Correlations between variables: e0_1 and alpha --> 0.8622 e0 and alpha --> 0.7870 e0_1 and e0 --> 0.7064 All other correlations are below 0.25 ===== Data set >>merge 6_17_04.chi<< ======================================== file: C:\Ifeffit\horae\stash\artemis.project.3\chi_data\merge 6_17_04.chi title lines: Athena data file -- Athena version 0.8.032 Saving merge 6_17_04 (group=merge) as chi(k) . Element=Mo Edge=K Background parameters . E0=20007.492 Eshift=0.000 Rbkg=1.000 . Standard=None . Kweight=2.0 Edge step=0.749 . Fixed step=no Flatten=yes . Pre-edge range: [ -150.000 : -75.000 ] . Normalization range: [ 150.000 : 895.199 ] . Spline range: [ 0.952 : 995.207 ] Clamps: None/Strong Foreward FT parameters . Kweight=2 Window=kaiser-bessel Phase correction=no . k-range: [ 2.000 : 16.100 ] dk=0.00 Backward FT parameters . R-range: [ 1.000 : 3.000 ] . dR=0.00 Window=kaiser-bessel Plotting parameters . Multiplier=1 Y-offset=0.000 . Merge in k space of: ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.101 (mos2_101) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.102 (mos2_102) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.103 (mos2_103) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.104 (mos2_104) k-range = 2.000 - 13.500 dk = 2.000 k-window = kaiser-bessel k-weight = 2 R-range = 1.000 - 3.000 dR = 0.100 R-window = kaiser-bessel fitting space = R background function = none phase correction = none R-factor for this data set = 0.74613 Second Fit: Project title : Fitting merge 10_15_04.chi Comment : Prepared by : Contact : Started : 11:49:36 on 22 October, 2004 This fit at : 11:23:36 on 28 October, 2004 Environment : Artemis 0.7.010 using Windows 2000, perl 5.006001, Tk 800.024, and Ifeffit 1.2.6 ============================================================ Independent points = 14.312500000 Number of variables = 4.000000000 Chi-square = 6562.747150466 Reduced Chi-square = 636.387602469 R-factor = 0.032979787 Measurement uncertainty (k) = 0.000181935 Measurement uncertainty (R) = 0.004860095 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): e0_1 = -4.0720090 +/- 1.9194040 (guessed as -4.773711 (2.426884)) ss = 0.0046360 +/- 0.0004110 (guessed as 0.002736 (0.000427)) e0 = 1.7659580 +/- 1.1543880 (guessed as 1.568469 (1.520916)) alpha = 0.0010900 +/- 0.0028430 (guessed as -0.004006 (0.003255)) Def parameters: delr_1 = 0.0043250 Set parameters: amp = 0.7 Correlations between variables: e0_1 and alpha --> 0.8416 e0 and alpha --> 0.8045 e0_1 and e0 --> 0.7141 All other correlations are below 0.25 ===== Data set >>merge 10_15_04.chi<< ======================================== file: C:\Ifeffit\horae\stash\artemis.project.3\chi_data\merge 10_15_04.chi title lines: Athena data file -- Athena version 0.8.032 Saving merge 6_17_04 (group=merge) as chi(k) . Element=Mo Edge=K Background parameters . E0=20007.492 Eshift=0.000 Rbkg=1.000 . Standard=None . Kweight=2.0 Edge step=0.749 . Fixed step=no Flatten=yes . Pre-edge range: [ -150.000 : -75.000 ] . Normalization range: [ 150.000 : 895.199 ] . Spline range: [ 0.952 : 995.207 ] Clamps: None/Strong Foreward FT parameters . Kweight=2 Window=kaiser-bessel Phase correction=no . k-range: [ 2.000 : 16.100 ] dk=0.00 Backward FT parameters . R-range: [ 1.000 : 3.000 ] . dR=0.00 Window=kaiser-bessel Plotting parameters . Multiplier=1 Y-offset=0.000 . Merge in k space of: ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.101 (mos2_101) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.102 (mos2_102) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.103 (mos2_103) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.104 (mos2_104) k-range = 2.000 - 13.500 dk = 2.000 k-window = kaiser-bessel k-weight = 2 R-range = 1.000 - 3.000 dR = 0.100 R-window = kaiser-bessel fitting space = R background function = none phase correction = none R-factor for this data set = 0.71585 Paths used to fit Both Data Sets, degen, s02 the same. other values different: F1 p 63/m m c: feff0001.dat .. feff = C:\Ifeffit\horae\stash\artemis.project.3\data0.feff2\feff0001.dat id = reff= 2.4135, nlegs= 2, path= Mo<->S label = r = 2.416130 degen = 6.000000 s02 = 0.700000 e0 = 1.765958 dr = 0.002630 ss2 = 0.004636 F1 p 63/m m c: feff0002.dat .. feff = C:\Ifeffit\horae\stash\artemis.project.3\data0.feff2\feff0002.dat id = reff= 3.1500, nlegs= 2, path= Mo<->Mo label = r = 3.153433 degen = 6.000000 s02 = 0.700000 e0 = -4.072009 dr = 0.003433 ss2 = 0.004636 F1 p 63/m m c: feff0003.dat .. feff = C:\Ifeffit\horae\stash\artemis.project.3\data0.feff2\feff0003.dat id = reff= 3.9683, nlegs= 2, path= Mo<->S label = r = 3.972625 degen = 6.000000 s02 = 0.700000 e0 = -4.072009 dr = 0.004325 ss2 = 0.004636

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IFEFFIT: Writing more than 16 arrays with write_data()
by Matt Newville 04 Nov '04

04 Nov '04

Hi Norbert, (Replying to the whole group this time....) On Wed, 3 Nov 2004, Norbert Weiher wrote: > Matt, > > I was just discussing with Bruce about exporting more than 15 sets with the > write_data() command. I am doing fits with lots of paths and like to have it > exported to one file... would it be difficult to increase the number of > arrays exportable by this command above 16 in IFEFFIT? It would not be difficult, and the current limit is definitely too low. I think it's a two line fix. But there will still be a finite limit of number of arrays. So: is 100 arrays enough? Do you need a fixed source kit or dll? And how quickly? This doesn't seem like a full release change to me. I haven't made any source changes to the stable distribution since July. So a question for Bruce and everyone else: Are there any other bug reports or suggestions for changes to the core? --Matt

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Problem exporting fit data with ARTEMIS
by Norbert Weiher 02 Nov '04

02 Nov '04

Dear Friends, I did a multi-dataset fit (9 data sets) and had the following problem: When trying to export all the fits to a single file (using save marked groups as), I got an empty file and artemis trapped a warning like the following. For sake of reproducing, I attached the file. My Tk version is the one which we should use (i.e. not the newest one) and saving just the experimental data in just the same fashion works... Any ideas why this happens? Regards, Norbert -- Error message follows -- Tk::Error: Can't call method "dispose" on unblessed reference at /usr/bin/artemi s line 7971. main::save_selected at /usr/bin/artemis line 7971 [\&main::save_selected,k] Tk callback for .menu1.menu.menu7 Tk::__ANON__ at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-multi/Tk.pm li ne 228 Tk::Menu::Invoke at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-multi/Tk/M enu.pm line 530 (command bound to event) main::__ANON__('Tk::Error: Can\'t call method "dispose" on unblessed ref erenc...') called at blib/lib/Tk.pm (autosplit into blib/lib/auto/Tk/Error.al) l ine 402 Tk::Error('MainWindow=HASH(0x953f240)','Can\'t call method "dispose" on unblessed reference at /usr/b...','main::save_selected at /usr/bin/artemis line 7971','[\&main::save_selected,k]','Tk callback for .menu1.menu.menu7','Tk::__ANO N__ at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thr...','Tk::Menu::Invoke at /u sr/lib/perl5/site_perl/5.8.0/i586-linux...','(command bound to event)') called a t /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-multi/Tk.pm line 340 eval {...} called at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-mu lti/Tk.pm line 340 Tk::MainLoop() called at /usr/bin/artemis line 1785 -- Dr. rer. nat. Norbert Weiher (weiher(a)chem.ethz.ch) Institute for Chemical and Bioengineering - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32

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RE: [Ifeffit] Artimis
by Chen, Yongsheng 02 Nov '04

02 Nov '04

Hi Matt, I did encounter that "No absorbing atom (ipot=0) defined" error sometimes, but I run Artemis only after I have feff calculations done. By the way, I use FEFF8. Thanks everybody for your kind help. I am afraid I can not do more test now since I am leaving tomorrow for Argonne for more XAFS experiments. Will check back if the problem remains after I have tried what you have suggested. Have a good weekend. Yongsheng > ---------- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Matt Newville > Reply To: XAFS Analysis using Ifeffit > Sent: Friday, October 22, 2004 2:20 PM > To: ravel(a)phys.washington.edu; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Artimis > > Hi, > > > On Friday 22 October 2004 4:38 pm, Chen, Yongsheng wrote: > > > Thanks for your advices. I did edit my Feff.inp in Word, but did not have > > > any problems with the old version. > > > > It is certainly possible to do so, but you MUST be careful to save the > > file as text. Because it is so easy to forget and just save in > > whatever format Word decides to use, I always discourage people from > > using Word for that purpose. > > Actually, Feff6 (and ifeffit) handle Unix and Windows line endings > just fine, but do have a harder time with Mac line-endings. I'm > not sure I know how to fix this: As far as I can tell it's at the > level of the fortran's read() statement. Sorry. > > One thing that confuses me is that Feff6 *should* have reported a > Feff 6L.02 > Fatal Error: No absorbing atom (ipot=0) defined > > which could have been used as a clue that something went wrong. > I don't know how artemis checks if a feff run went OK. > > > Hey Mac users! Could someone suggest a simple editor that Yongsheng, > > a new Mac user, should consider for the task of editing the kinds of > > text files that Feff and similar programs work with? > > TextEdit can save file with Unix-style line endings, especially if > you set the default to using 'Plain text' in the Preferences menu. > > BBedit is a popular and very good editor for Mac OS X. > > --Matt > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

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Re: [Ifeffit] choosing dk values
by Scott Calvin 01 Nov '04

01 Nov '04

Hi Mike, I would add to Matt's reply that it is sometimes quite important to realize that for a Hanning window and similar windows where there is a "sill" over which the window function goes from 0 to 1, the sill extends from kmin-dk/2 to kmin+dk/2 and from kmax-dk/2 to kmax+dk/2. This means that as you increase dk you actually sample more k-space, albeit in a suppressed way. Why is this important? Suppose you have something really screwy in your data at k=11.9 inverse angstroms...a second edge comes to mind as a possibility. You might then reasonably set kmax to 11 and think you're staying away from the problem. (Well, it might be messing up your background, but that's an issue for another day...) But suppose you make dk = 2. Now you are actually sampling data up to k = 12, which includes the really screwy bit. In some cases that can be a source of problems...it took me a long time to catch on to that particular wrinkle when I was starting out! Of course, with Artemis and Athena this is easy to catch, because you can plot the window function by checking the box marked "Window" (that Bruce is a clever dude). --Scott Calvin Sarah Lawrence College At 01:13 PM 11/1/2004 -0600, you wrote: >Hi Mike, > >On Mon, 1 Nov 2004, Michael A Groves wrote: > >> I'm doing some fitting with Artemis, and I noticed that, for >> different values of dk, I get better or worse fits. The only >> information I've gotten so far about dk was in the IFEFFIT >> documentation, and it basically said, "Don't mess with it." >> Can anyone give me more information on choosing a good dk value? >> Or, should I just stick with the default? >>

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choosing dk values
by Michael A Groves 01 Nov '04

01 Nov '04

Hi all, I'm doing some fitting with Artemis, and I noticed that, for different values of dk, I get better or worse fits. The only information I've gotten so far about dk was in the IFEFFIT documentation, and it basically said, "Don't mess with it." Can anyone give me more information on choosing a good dk value? Or, should I just stick with the default? Thanks, Mike Groves

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RE: [Ifeffit] Fitting Commercial Molybdenum Disulfide
by Kelly, Shelly D. 29 Oct '04

29 Oct '04

Hi Dan, I would suggest using one ezero with three different delr values for these three paths. You are introducting only one more variable. delr and ezero are correlated so by constraining delr you need more ezero values or vise versa. Shelly > -----Original Message----- > From: dmc(a)pdx.edu [mailto:dmc@pdx.edu] > Sent: Friday, October 29, 2004 10:25 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Fitting Commercial Molybdenum Disulfide > > > Mike & list, > > Where can I find a reasonable model for my delr terms, > if I do assume > that the bond angles are changing/there is no isotropic > expansion? Is there a > description somewhere in the archives that I could look at? > > Creating different sigma squared parameters for each > path did help the R- Factor somewhat, but not the reduced > chi. Here's some data: > > > Fit with seperate sigma's: > > Independent points = 14.312500000 > Number of variables = 6.000000000 > Chi-square = 5778.957783654 > Reduced Chi-square = 695.212966455 > R-factor = 0.029041008 > Measurement uncertainty (k) = 0.000181935 > Measurement uncertainty (R) = 0.004860095 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > e0_1 = -4.0347670 +/- 2.9998980 > (guessed as -4.072009 > (1.919404)) > ss = 0.0042860 +/- 0.0005990 > (guessed as 0.004636 > (0.000411)) > e0 = 1.6770760 +/- 1.3230290 > (guessed as 1.765958 > (1.154388)) > alpha = 0.0009180 +/- 0.0034050 > (guessed as 0.001090 > (0.002843)) > ss2 = 0.0048160 +/- 0.0006910 (0.0000) > ss3 = 0.0225310 +/- 0.0657250 (0.0000) > Def parameters: > delr_1 = 0.0036440 > Set parameters: > amp = 0.7 > > > Correlations between variables: > e0_1 and alpha --> 0.8542 > e0 and alpha --> 0.8470 > e0_1 and e0 --> 0.7407 > e0_1 and ss3 --> 0.7060 > alpha and ss3 --> 0.4715 > ss2 and ss3 --> -0.4214 > e0_1 and ss2 --> -0.3892 > e0 and ss3 --> 0.3772 > alpha and ss2 --> -0.2680 > All other correlations are below 0.25 > > > > > > > > > Fit without (original): > > > Independent points = 14.312500000 > Number of variables = 4.000000000 > Chi-square = 6562.747150128 > Reduced Chi-square = 636.387602437 > R-factor = 0.032979787 > Measurement uncertainty (k) = 0.000181935 > Measurement uncertainty (R) = 0.004860095 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > e0_1 = -4.0720130 +/- 1.9194050 > (guessed as -4.072009 > (1.919404)) > ss = 0.0046360 +/- 0.0004110 > (guessed as 0.004636 > (0.000411)) > e0 = 1.7659560 +/- 1.1543880 > (guessed as 1.765958 > (1.154388)) > alpha = 0.0010900 +/- 0.0028430 > (guessed as 0.001090 > (0.002843)) > > Def parameters: > delr_1 = 0.0043250 > > Set parameters: > amp = 0.7 > > > Correlations between variables: > e0_1 and alpha --> 0.8416 > e0 and alpha --> 0.8045 > e0_1 and e0 --> 0.7141 > All other correlations are below 0.25 > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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RE: [Ifeffit] Fitting Commercial Molybdenum Disulfide
by Kelly, Shelly D. 29 Oct '04

29 Oct '04

Hi Dan, Take a look at the fit in q-space with the model below. I suspect that you have left out important Multiple scattering paths that would cause a miss-fit to the data at low k values. To test for this, change the fit range to something like 4.0 1/Anstroms for k-min value, and try again. Shelly > -----Original Message----- > From: dmc(a)pdx.edu [mailto:dmc@pdx.edu] > Sent: Friday, October 29, 2004 11:03 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Fitting Commercial Molybdenum Disulfide > > > Hi Shelly, > > I seperated the delr's with different alpha terms, but > Mike seems to think > that this is assuming isotropic expansion that isn't there. > Also, the reduced > chi-square has gone up 150 or so. > > delr# define: alpha# * reff > > > Thanks for the help, Dan > > > Results with 1 eO and differing delr's: > > Independent points = 14.312500000 > Number of variables = 7.000000000 > Chi-square = 6186.771083042 > Reduced Chi-square = 846.054165202 > R-factor = 0.031090393 > Measurement uncertainty (k) = 0.000181935 > Measurement uncertainty (R) = 0.004860095 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > ss = 0.0042720 +/- 0.0006590 > (guessed as 0.004636 > (0.000411)) > e0 = 1.3293700 +/- 1.4673640 > (guessed as 1.765958 > (1.154388)) > alpha = -0.0001750 +/- 0.0040010 > (guessed as 0.001090 > (0.002843)) > ss2 = 0.0043180 +/- 0.0007370 (0.0000) > ss3 = 0.0072300 +/- 0.0164390 (0.0000) > alpha2 = 0.0076940 +/- 0.0027880 (0.0000) > alpha3 = -0.0512670 +/- 0.0232140 (0.0000) > > Def parameters: > delr_1 = -0.0006930 > delr_2 = 0.0305320 > delr_3 = -0.2034430 > > Set parameters: > amp = 0.7 > > > Correlations between variables: > e0 and alpha --> 0.8441 > ss3 and alpha2 --> 0.7651 > ss2 and alpha2 --> -0.6441 > e0 and alpha2 --> 0.5682 > ss2 and ss3 --> 0.4871 > alpha and alpha2 --> 0.4785 > ss3 and alpha3 --> 0.3825 > e0 and alpha3 --> -0.2743 > All other correlations are below 0.25 > > > > > > Original (2 e0s): > > > Independent points = 14.312500000 > Number of variables = 6.000000000 > Chi-square = 5778.957783654 > Reduced Chi-square = 695.212966455 > R-factor = 0.029041008 > Measurement uncertainty (k) = 0.000181935 > Measurement uncertainty (R) = 0.004860095 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > e0_1 = -4.0347670 +/- 2.9998980 > (guessed as -4.072009 > (1.919404)) > ss = 0.0042860 +/- 0.0005990 > (guessed as 0.004636 > (0.000411)) > e0 = 1.6770760 +/- 1.3230290 > (guessed as 1.765958 > (1.154388)) > alpha = 0.0009180 +/- 0.0034050 > (guessed as 0.001090 > (0.002843)) > ss2 = 0.0048160 +/- 0.0006910 (0.0000) > ss3 = 0.0225310 +/- 0.0657250 (0.0000) > > Def parameters: > delr_1 = 0.0036440 > > Set parameters: > amp = 0.7 > > > Correlations between variables: > e0_1 and alpha --> 0.8542 > e0 and alpha --> 0.8470 > e0_1 and e0 --> 0.7407 > e0_1 and ss3 --> 0.7060 > alpha and ss3 --> 0.4715 > ss2 and ss3 --> -0.4214 > e0_1 and ss2 --> -0.3892 > e0 and ss3 --> 0.3772 > alpha and ss2 --> -0.2680 > All other correlations are below 0.25 > > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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to Gael Poirier
by Bruce Ravel 27 Oct '04

27 Oct '04

Hi folks, Recently Gael Poirier has been having a problem using Athena with some XANES data. For whatever reason, when I send mail to Gael it gets bounced back. But he seems to receive mail from the mailing list. Go figure. Sorry for filling up people mail boxes, but I am using the list to send this along... B =============================================================== Gael, Thanks for sending the data. It is now clear what went wrong. I recently made a change in how Athena tries to detect xanes data, that is data that does not extend very far into the extended region. The advantage of identifying data that is xanes and not exafs is that Athena then does not have to do a background removal, which saves a little bit of time doing chores like alignment and normalization. Sadly, you have uncovered a bug. That happens. Your bug is that the kmax for the fourier transform gets set to when the data are imported as xanes. Then Athena mistakenly aborts when it sees this, even though no FT will be performed. Oops! Fortunately there is an easy work-around. When you import the data, explicitly import them as mu(E) rather than xanes(E). The only draw-back of doing so is that Athena will do a background removal every time you change the normalization parameters. That's not a big loss. Thanks for pointing this out. I will certainly fix this in the next release. -- 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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citing Artemis and Athena?
by k-kupiecki＠northwestern.edu 27 Oct '04

27 Oct '04

Hi everyone, I'm in the process of writing up my thesis and I've used Athena and Artemis quite a bit for the analysis of my SEXAFS data.... I was wondering what is the appropriate way to give references for this software and it's use? To my knowledge there are journal articles etc. regarding AUTOBK, FEFFIT, etc. Do I cite those? are there additional ways I should cite to give credit for Athena and Artemis too? Thanks for any suggestions you have! -Kristine Witkowski

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Re: Ifeffit Digest, Vol 20, Issue 22
by Michel Jaouen 25 Oct '04

25 Oct '04

>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. RE: Artimis (Matt Newville) > 2. RE: Artimis (Scott Calvin) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Sat, 23 Oct 2004 13:46:12 -0500 (CDT) >From: Matt Newville <newville(a)cars.uchicago.edu> >Subject: RE: [Ifeffit] Artimis >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Message-ID: <Pine.LNX.4.44.0410222107350.19561-100000@corvette> >Content-Type: TEXT/PLAIN; charset=US-ASCII > > >> I did encounter that "No absorbing atom (ipot=0) defined" error >> sometimes, but I run Artemis only after I have feff calculations >> done. > >I don't understand whether Feff ran to completion or not. Are you >saying that you made a successful run of Feff (including real >output files) but that Artemis still failed to read this >calculation? That seems pretty strange. > >> By the way, I use FEFF8. > >For Feff8, I believe you need to be much more careful about line >endings. It's not able to use Windows line-endings on unixes, for >example. > >But also: why would you use Feff8 for EXAFS analysis, as with >artemis?? Feff8 is a XANES code. As far as I know, it does not >give any improvements for EXAFS. > >--Matt > > > > > >------------------------------ > >Message: 2 >Date: Sun, 24 Oct 2004 11:23:03 -0400 >From: Scott Calvin <SCalvin(a)slc.edu> >Subject: RE: [Ifeffit] Artimis >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Cc: SCalvin(a)slc.edu >Message-ID: <a06010203bda178b3a7b7(a)[130.132.241.87]> >Content-Type: text/plain; charset="us-ascii" ; format="flowed" > >> >>But also: why would you use Feff8 for EXAFS analysis, as with >>artemis?? Feff8 is a XANES code. As far as I know, it does not >>give any improvements for EXAFS. > > >FEFF8 does give at least one improvement for EXAFS, which I've used >on occasion: the self-consistent field calculation can be used to >give an improved estimate of E0 prior to fitting. > >--Scott Calvin >Sarah Lawrence College > I agree with Scott: SCF calculation gives more reliable estimate of E0 because the Fermi level is more accurate. It makes that, when several atomic species are involved, you only need in principle one E0 for fitting (I have verified this point, at least for the case I'm presently working on). >------------------------------ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >End of Ifeffit Digest, Vol 20, Issue 22 >*************************************** -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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Re: Ifeffit Digest, Vol 20, Issue 22
by Michel Jaouen 25 Oct '04

25 Oct '04

Yongsheng, > > I did encounter that "No absorbing atom (ipot=0) defined" error >> sometimes, but I run Artemis only after I have feff calculations >> done. > >I don't understand whether Feff ran to completion or not. Are you >saying that you made a successful run of Feff (including real >output files) but that Artemis still failed to read this >calculation? That seems pretty strange. > >> By the way, I use FEFF8. > >For Feff8, I believe you need to be much more careful about line >endings. It's not able to use Windows line-endings on unixes, for >example. Artemis works fine for me (on a Mac) with feff8: just ask in the menu for Import feff calculation and choose the folder where is your feff8 calculation where you must have: feff.inp feffXXX.dat files files.dat paths.dat BUT ALL files must be Unix! Following Matt's advice, use BBEdit Lite (that's free or if you had some money buy BBEdit (the last vesrion is 8): that is really a very good Editor (the best for me) on Mac. Then open your files, check the option button and select Unix for Line Breaks. Best regards Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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RE: [Ifeffit] Artimis
by Chen, Yongsheng 23 Oct '04

23 Oct '04

Hi Bruce, Thanks for your advices. I did edit my Feff.inp in Word, but did not have any problems with the old version. I tried the cleaned up Feff.inp you sent me, it worked better in the sense that I could close Artemis after the warning appeared again, with my own version, I would have to use ForceQuit. I am a new mac user. I try to understand the message in the artemis.trap, although it's a text file, I do not understand too much. I sort of remember there is a notice about Perl version on some website. I have seen 'Perl' appearing in the trap file in many places, is this relative to the problem? Thanks for your help. Yongsheng > ---------- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Bruce Ravel > Reply To: ravel(a)phys.washington.edu;XAFS Analysis using Ifeffit > Sent: Friday, October 22, 2004 10:49 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Artimis > > <<File: feff.inp>><<File: ATT1852209.txt>> > On Friday 22 October 2004 12:30 pm, Chen, Yongsheng wrote: > > I installed the lastest version of Artemis, but met problems when trying to > > import FEFF calculations. The trap file and the feff input file are > > attached. The old version worked fine. I have a mac. > > Yongsheng, > > What is the history of the files you sent? The feff.inp file you > included in your email has a large number of non-printable chatracters > at the beginning of the file and all of the lines are terminated by > Macintosh end-of-line characters (that is, carriage return (ascii 13), > rather than line-feed (ascii 10)). Artemis currently makes no effort > to deal correctly with Mac EOL characters and Feff (as compiled on an > OSX, which is really a version of Unix under the hood) will not do so > either. Some quick tests suggested that is the case. > > So, there seems to be two problems with the feff.inp file you sent me > > 1. The junk characters at the beginning of the file. Those will > certainly confuse feff. > > 2. The end-ol-line characters. > > You can probably fix both by opening up the feff.inp file in any text > editor, stripping out the junk at the top of the file and explicitly > saving the file as a unix text file. I am sure that some of the Mac > users on the list can provide more details should you need it. > > I am suspicious that you might have edited the feff.inp file with a > word processor (such as MS Word). That is a very poor idea because it > can be hgard to avoid the situation where the word processor inserts > additional, not-for-display information in the file that neither > Artemis nor Feff will know how to deal with. If you create your > feff.inp files outside of Artemis, you must be careful not to do so in > a way that inserts additional stuff into the file. > > When I cleaned up the feff.inp file you sent, Artemis had no problem > with it. > > I suppose that another possibility is that the file became > "contaminated" after you tried it in Artemis but before I received > your email. If that is the case, it is really important that you fix > that and try submitting your question again. It is possible that you > are seeing some deeper problem in Artemis, but that I am focussing on > the ways in which the file became contaminated. That's a problem > because I am therefore not addressing the real issue. > > Attached is the cleaned up file, which works for me. > > Regards, > 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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Athena
by Gael Poirier 22 Oct '04

22 Oct '04

Hi Bruce, I have a problem with Athena version 0.8.032. When I select several opened groups as marked groups and plot them in E (using plot marked groups in E), it doesn't work and only the last opened spectrum appears in the graphic window. The program gives an error message:"ERROR:the minimum value of the forward fourier transform range exceeds the maximum value". However, I've tried with Athena 0.8.024 (IFEFFIT 1.2.5) and it worked very well. How can I plot all the groups in the same graphic window using Athena 0.8.032? Thank you very much Gael

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Artimis
by Chen, Yongsheng 22 Oct '04

22 Oct '04

Hi Bruce, I installed the lastest version of Artemis, but met problems when trying to import FEFF calculations. The trap file and the feff input file are attached. The old version worked fine. I have a mac. Thanks a lot. Yongsheng <<ARTEMIS.TRAP>> <<feff.inp>>

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RE : RE : [Ifeffit] Is artemis running on G5 Mac,
by POGER David 202545 21 Oct '04

21 Oct '04

Hello Thank you very much for your help Matt. Your advice was quite obvious in fact but I followed it to use horae_update properly. Thanks to that, I could see what was my first problem. I had an error about Aquaterm (the installation script couldn't find an Aquaterm library file (aquaterm.1.0.0.dylib I believe). So, I re-installed Aquaterm (the latest version found on SourceForge). And then, the installation was perfect, without any error anymore. And, here is now my second problem. When I open a project file (a '.chi' file) in Artemis, the program takes about 5s to try to open it (with the comment 'plotting in r space' at the bottom of the window), and then crashes down... I'm really sorry! Any other help or any idea? Thank you David > -----Message d'origine----- > De : ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] De la part de Matt Newville > Envoyé : jeudi 14 octobre 2004 23:54 > À : XAFS Analysis using Ifeffit > Objet : Re: RE : [Ifeffit] Is artemis running on G5 Mac, > > > On Thu, 14 Oct 2004, POGER David 202545 wrote: > > > I fear it doesn't work for me. I have untared the Horae-045.tar > > file in the Ifeffit directory. And when I type 'perl > > Makefile.PL', the installation script crashes and says 'Could > > not open /config/Config.mak file for reading'. The Greek gods > > may not be with me! I'll wait for the next tarball... Thanks a > > lot in adavance! > > This is probably still an issue with permissions, but I'm not sure > what you did exactly. It sounds like you tried to run horae_update > in the Applications/Ifeffit directory. If so, this probably won't > work, as you probably do NOT have write permissions to the > /Applications/Ifeffit directory, and horae_update creates a > folder (horae-045) to build the code it will install. > > Let me be more specific. Sorry if most of this is obvious! > 1. Open a Terminal > 2. move to your home directory: Type 'cd'. > 3. run horae_update with permission to write to the > /Library/Perl and /Applications/Ifeffit. Type > 'sudo horae_update'. When prompted for a password, > type the password for your user account (that is, > the same one you logged in as). > > 4. If you get a message that says 'command not found', then > read the message. > a) if the message begins 'bash: ... command not found' > then type '. /Applications/Ifeffit/bin/iff_init.sh' > Yes, that's a '.' followed by a space. > b) if the message begins 'tcsh: ... command not found' > then type 'source /Applications/Ifeffit/bin/iff_init.csh' > > Then do 'sudo horae_udate' again. > > If you already have the horae-045.tar.gz file, 'sudo horae_update' > is exactly the same as: > tar xvzf horae-045.tar.gz > cd horae-045 > perl Makefile.PL > sudo make install > > Once the installation is successful, you can remove the > 'horae-045' folder. > > --Matt > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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