August 2008 - Ifeffit - millenia.cars.aps.anl.gov

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

16 Apr '09

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

9 21

New Method for Normalization?
by Barton, David (DG) 30 Mar '09

30 Mar '09

XANES Aficionados, I know most users on this list are hard-core EXAFS analysts, but some of us use XANES analysis to decipher mixed phases or use it to get structural clues when data quality isn't sufficient for EXAFS analysis. Anyway, I have a question for those interested in quantitative analysis of XANES or those that are willing to offer an opinion on methods to normalize raw spectra to get reliable, repeatable comparisons of near-edge features. Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below: J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines? Dave _________________________________ David Barton The Dow Chemical Company

12 22

Ifeffit Ok on BlueWhite64, ...
by Chachi Rojas 03 Feb '09

03 Feb '09

Hi Matt Ifeffit run perfectely (thanks Matt) after installed by your scripts on RC1. Now, a question for Bruce try to install horae-065, but, error message is below: ---------- === The Ifeffit wrapper, Athena, Artemis, and Hephaestus === This is linux. Checking dependencies ... Tk is not installed. Download the latest from http://search.cpan.org/search?module=Tk Failed dependencies. Not installing athena and artemis. ------ Tk modules (version 8.4.15) were installed on /usr, but perl Makefile.PL it does not recognize Some idea Ch. > Date: Wed, 22 Aug 2007 15:56:26 -0500 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: [Ifeffit] Ifeffit and gfortran (was: iffefit compile on > BlueWhite64) > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0708221356y37280877v86ac576fe9b6b96c(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Chachi, all > > I believe I have a source kit that will build correctly for you using > gfortran. I've tested on three different generations of Fedora/Redhat > linux systems, one with only g77, one with only gfortran, and one with > both, and the installation now works on all of them. > > Please try > http://cars9.uchicago.edu/~ifeffit/src/ifeffit-1.2.10_rc1.tar.gz > > With this tar ball, you will need to install pgplot: > tar xvzf ifeffit-1.2.10_rc1.tar.gz > cd ifeffit-1.2.10 > sh PGPLOT_install > ./configure > make > make install > > (doing the two 'install steps' with sufficient privilege). Again, you > need to install PGPLOT with the provided script. Both the PGPLOT and > Ifeffit installations will use gfortran if available, and g77 if > gfortran is not available. I think it would not be too difficult to > attempt to use Intel's ifort compiler or g95, though I do not know > that it's needed-- all linux distribution come with gcc so have > easy-to-use packages for gfortran (and, for "legacy", g77). > > I did get horae-065 and the python wrappers to build with no trouble > (once the Tk modules were installed) on all systems, though I haven't > done much more than trivial testing. > > Since I tested only on a few linux boxes, I'd be interested in hearing > reports for other systems. > > I'll wait a few days (or more) to hear reports before uploading this > as ifeffit-1.2.10. > > --Matt >

8 9

export from large Athena projects
by shiryaev＠crys.ras.ru 19 Sep '08

19 Sep '08

Hi, It seems that there is a problem in exporting normalised data files from large (i.e. >10 curves) Athena projects: Exported data are cut in energy. When one exports the files one by one, this problem does not occurs. All the best, Andrei

6 8

lanthanides convergence
by Eugenio Otal 02 Sep '08

02 Sep '08

Bruce, I am running feff to model XANES of Erbium doped ZnO. I have a big problem to find the convergence of FMS in this kind of systems. I increased the atoms number in feff code to nclusx=500 and still have not found convergence. Should I increase the nclusx to a bigger number?, is there a limit for this number independent from the computer RAM or I do have another chance?. Thanks for your time and patience. 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Eugenio H. Otal CINSO - CONICET - CITEFA eotal(a)citefa.gov.ar eugenioh(a)gmail.com 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

2 2

Problem reproducing spectrum for Ti complex
by Janine GRATTAGE 29 Aug '08

29 Aug '08

Dear IFEFFIT mailing list, I have been trying to reproduce the XANES spectrum of a titanium compound (titanium phthalocyanine dichloride) using FEFF 8.4. The overall shape is reproduced reasonably well, but I wanted to ask the mailing list users if they have any ideas as to how to improve the details such as the pre-edge (to give two distinct peaks) and peak positions over the absorption edge. I have attached a file showing the experimental spectrum, two FEFF input files and the corresponding XMU output files. These two files have the same atomic co-ordinates for the molecule, but one has 'standard' broadening and the Fermi level has been shifted by -1eV (geom1) where the other has reduced experimental broadening (-3) a shifted Fermi level, and smaller step size (geom1acc). I have tried changing the geometry of the molecule by moving one or both of the Cl atoms, and by trying a flat molecular geometry rather than the 'umbrella' shape in the attached files, but the spectra attached are the best match to experiment. Any help or suggestions on improvements would be greatly appreciated. Best regards and thanks in advance, Janine Grattage -- Dr Janine GRATTAGE Postdoctoral Fellow, ID26 European Synchrotron Radiation Facility (ESRF) Sector 26, BP 220 6, rue Jules Horowitz, 38043 Grenoble, Cedex 9, FRANCE Tel: +33(0)4 38 88 19 30 Email: janine.grattage(a)esrf.fr TITLE TiPcCl2 molecule Geom1acc CONTROL 1 1 1 1 1 1 PRINT 5 0 0 0 0 0 FMS 8.0 1 *1 appropriate for molecules (wiki) MULTIPOLE 2 *Dipole and quadrupole EXCHANGE 0 1. -3. *Dirac Hara, -1eV Fermi level shift, -3 broadening SCF 4 *includes second coordination shell XANES 6.0 0.03 0.001 AFOLP 1.2 CRITERION 0 0 RPATH 0.1 * emin emax eimag LDOS -20 20 0.2 POTENTIALS *absorbing atom is the Ti *ipot z tag 0 22 Ti 1 6 C 2 7 N 3 1 H 4 17 Cl ATOMS *xmod ymod zmod ipot 0 0 0 0 2.11844236 -0.00045764 -0.28362660 2 0.00049691 2.11838749 -0.28403609 2 -2.11834820 0.00044201 -0.28432911 2 -0.00040276 -2.11840312 -0.28391961 2 2.50033703 2.49920371 -0.37080272 2 -2.49915235 2.50026531 -0.37163159 2 -2.50021397 -2.49922414 -0.37149421 2 2.49927541 -2.50028574 -0.37066535 2 2.92077159 1.14863904 -0.35919200 1 -1.14858929 2.92070211 -0.35991542 1 -2.92065235 -1.14865884 -0.36009724 1 1.14870854 -2.92072190 -0.35937383 1 2.92028351 -1.14989912 -0.35912883 1 1.14994884 2.92021403 -0.35953433 1 -2.92016426 1.14987932 -0.36016040 1 -1.14982959 -2.92023383 -0.35975490 1 4.24012097 0.69267038 -0.46786156 1 -0.69260556 4.24003046 -0.46877686 1 -4.23996562 -0.69269616 -0.46922925 1 0.69276092 -4.24005624 -0.46831395 1 4.23982641 -0.69449678 -0.46782344 1 0.69456158 4.23973590 -0.46854687 1 -4.23967106 0.69447100 -0.46926736 1 -0.69440621 -4.23976169 -0.46854393 1 5.42180506 1.42299661 -0.58110099 1 -1.42291609 5.42169266 -0.58234553 1 -5.42161213 -1.42302863 -0.58282014 1 1.42310907 -5.42172466 -0.58157559 1 5.42120023 -1.42533102 -0.58102274 1 1.42541150 5.42108783 -0.58187330 1 -5.42100730 1.42529900 -0.58289838 1 -1.42521852 -5.42111985 -0.58204782 1 6.62671213 0.70509648 -0.69117255 1 -0.70500071 6.62657845 -0.69255053 1 -6.62648265 -0.70513457 -0.69333050 1 0.70523027 -6.62661650 -0.69195251 1 6.62641208 -0.70794872 -0.69113373 1 0.70804448 6.62627840 -0.69231626 1 -6.62618259 0.70791063 -0.69336932 1 -0.70781492 -6.62631646 -0.69218678 1 5.41276801 2.50322415 -0.58475924 3 -2.50314311 5.41265491 -0.58615139 3 -5.41257388 -2.50325637 -0.58641595 3 2.50333729 -5.41268710 -0.58502379 3 5.41170441 -2.50555482 -0.58462164 3 2.50563579 5.41159131 -0.58532097 3 -5.41151028 2.50552260 -0.58655354 3 -2.50544161 -5.41162354 -0.58585421 3 7.56137780 1.23956000 -0.77936602 3 7.56085067 -1.24281398 -0.77929784 3 -7.56059192 1.24277103 -0.78187250 3 -7.56111904 -1.23960294 -0.78180432 3 -1.23945199 7.56122707 -0.78099842 3 1.24292195 7.56069994 -0.78058687 3 1.23971085 -7.56126996 -0.78017192 3 -1.24266309 -7.56074286 -0.78058347 3 0.00040523 -0.00006766 -2.45005490 4 -0.00040584 0.00006782 2.45002706 4 END # TiPcCl2 molecule Geom1acc Feff 8.40 # POT SCF 30 4.0000 0, core-hole, AFOLP (folp(0)= 1.200) # Abs Z=22 Rmt= 1.437 Rnm= 1.537 K shell # Pot 1 Z= 6 Rmt= 0.840 Rnm= 0.996 # Pot 2 Z= 7 Rmt= 0.885 Rnm= 1.008 # Pot 3 Z= 1 Rmt= 0.789 Rnm= 0.909 # Pot 4 Z=17 Rmt= 1.538 Rnm= 1.686 # Gam_ch=9.030E-01 H-L exch Vi=-3.000E+00 Vr= 1.000E+00 # Mu=-1.040E+01 kf=2.632E+00 Vint=-1.880E+01 Rs_int= 1.378 # FMS rfms= 8.0000 # PATH Rmax= 0.100, Keep_limit= 0.00, Heap_limit 0.00 Pwcrit= 0.00% # S02=1.000 Global_sig2= 0.00000 # file sig2 tot cw amp ratio deg nlegs reff inp sig2 # 0/ 0 paths used # xsedge+ 50, used to normalize mu 4.8609E-04 # ----------------------------------------------------------------------- # omega e k mu mu0 chi @# 4966.250 -12.512 -0.540 9.13165E-04 3.37112E-03 -2.45795E-03 4966.484 -12.279 -0.480 1.06274E-03 4.18380E-03 -3.12106E-03 4966.689 -12.074 -0.420 1.27282E-03 5.35021E-03 -4.07739E-03 4966.868 -11.895 -0.360 1.58625E-03 7.11910E-03 -5.53285E-03 4967.019 -11.744 -0.300 2.09217E-03 1.00069E-02 -7.91471E-03 4967.142 -11.621 -0.240 3.00252E-03 1.52351E-02 -1.22326E-02 4967.238 -11.525 -0.180 4.92381E-03 2.62777E-02 -2.13539E-02 4967.307 -11.456 -0.120 1.00982E-02 5.59015E-02 -4.58033E-02 4967.348 -11.415 -0.060 2.70590E-02 1.52513E-01 -1.25454E-01 4967.351 -11.412 -0.051 3.08226E-02 1.73905E-01 -1.43082E-01 4967.361 -11.402 0.000 4.35361E-02 2.46060E-01 -2.02524E-01 4967.365 -11.398 0.030 4.81925E-02 2.72502E-01 -2.24310E-01 4967.375 -11.388 0.060 5.99908E-02 3.39822E-01 -2.79831E-01 4967.392 -11.371 0.090 7.06798E-02 4.01939E-01 -3.31259E-01 4967.416 -11.347 0.120 7.66663E-02 4.38394E-01 -3.61727E-01 4967.447 -11.316 0.150 7.97483E-02 4.59111E-01 -3.79362E-01 4967.485 -11.278 0.180 8.14520E-02 4.72336E-01 -3.90884E-01 4967.529 -11.233 0.210 8.25377E-02 4.81982E-01 -3.99444E-01 4967.581 -11.182 0.240 8.33826E-02 4.89861E-01 -4.06478E-01 4967.639 -11.124 0.270 8.41397E-02 4.96841E-01 -4.12701E-01 4967.704 -11.059 0.300 8.48985E-02 5.03368E-01 -4.18469E-01 4967.776 -10.987 0.330 8.56237E-02 5.09640E-01 -4.24016E-01 4967.855 -10.908 0.360 8.62149E-02 5.15699E-01 -4.29484E-01 4967.941 -10.822 0.390 8.67731E-02 5.21557E-01 -4.34784E-01 4968.034 -10.729 0.420 8.78023E-02 5.27174E-01 -4.39371E-01 4968.133 -10.630 0.450 9.10340E-02 5.32553E-01 -4.41519E-01 4968.239 -10.524 0.480 1.04529E-01 5.37749E-01 -4.33220E-01 4968.352 -10.411 0.510 1.23575E-01 5.42866E-01 -4.19290E-01 4968.472 -10.291 0.540 1.10145E-01 5.48027E-01 -4.37883E-01 4968.599 -10.164 0.570 1.15424E-01 5.53380E-01 -4.37956E-01 4968.733 -10.030 0.600 1.29776E-01 5.59004E-01 -4.29228E-01 4968.874 -9.889 0.630 1.40253E-01 5.64967E-01 -4.24714E-01 4969.021 -9.742 0.660 1.30116E-01 5.71309E-01 -4.41194E-01 4969.175 -9.588 0.690 1.02880E-01 5.78006E-01 -4.75126E-01 4969.337 -9.426 0.720 7.82317E-02 5.85054E-01 -5.06823E-01 4969.505 -9.258 0.750 6.27424E-02 5.92438E-01 -5.29696E-01 4969.679 -9.084 0.780 5.40260E-02 6.00135E-01 -5.46109E-01 4969.861 -8.902 0.810 4.93417E-02 6.08094E-01 -5.58753E-01 4970.050 -8.713 0.840 4.72836E-02 6.16308E-01 -5.69025E-01 4970.245 -8.518 0.870 4.73852E-02 6.24726E-01 -5.77341E-01 4970.448 -8.315 0.900 5.02215E-02 6.33358E-01 -5.83136E-01 4970.657 -8.106 0.930 5.67812E-02 6.42152E-01 -5.85370E-01 4970.873 -7.890 0.960 6.13993E-02 6.51085E-01 -5.89686E-01 4971.096 -7.667 0.990 5.66943E-02 6.60139E-01 -6.03445E-01 4971.325 -7.438 1.020 6.16275E-02 6.69310E-01 -6.07683E-01 4971.562 -7.201 1.050 7.15826E-02 6.78561E-01 -6.06979E-01 4971.805 -6.958 1.080 6.00972E-02 6.87872E-01 -6.27775E-01 4972.056 -6.707 1.110 6.50374E-02 6.97223E-01 -6.32185E-01 4972.313 -6.450 1.140 7.38111E-02 7.06611E-01 -6.32800E-01 4972.577 -6.186 1.170 8.62661E-02 7.16016E-01 -6.29750E-01 4972.848 -5.915 1.200 1.03456E-01 7.25401E-01 -6.21944E-01 4973.126 -5.637 1.230 1.26524E-01 7.34746E-01 -6.08222E-01 4973.410 -5.353 1.260 1.54971E-01 7.44066E-01 -5.89095E-01 4973.702 -5.061 1.290 1.82740E-01 7.53341E-01 -5.70601E-01 4974.000 -4.763 1.320 2.00380E-01 7.62518E-01 -5.62138E-01 4974.305 -4.458 1.350 2.11141E-01 7.71629E-01 -5.60487E-01 4974.617 -4.146 1.380 2.30273E-01 7.80636E-01 -5.50363E-01 4974.936 -3.827 1.410 2.66899E-01 7.89521E-01 -5.22623E-01 4975.262 -3.501 1.440 3.21552E-01 7.98299E-01 -4.76747E-01 4975.594 -3.169 1.470 3.88177E-01 8.06915E-01 -4.18738E-01 4975.934 -2.829 1.500 4.53793E-01 8.15386E-01 -3.61592E-01 4976.280 -2.483 1.530 5.03101E-01 8.23710E-01 -3.20609E-01 4976.633 -2.130 1.560 5.32723E-01 8.31850E-01 -2.99127E-01 4976.993 -1.769 1.590 5.66560E-01 8.39805E-01 -2.73245E-01 4977.360 -1.403 1.620 6.34775E-01 8.47573E-01 -2.12798E-01 4977.734 -1.029 1.650 6.84473E-01 8.55136E-01 -1.70663E-01 4978.115 -0.648 1.680 6.71745E-01 8.62493E-01 -1.90748E-01 4978.502 -0.261 1.710 7.03172E-01 8.69644E-01 -1.66472E-01 4978.897 0.134 1.740 7.94749E-01 8.76587E-01 -8.18378E-02 4979.298 0.535 1.770 8.38553E-01 8.83285E-01 -4.47320E-02 4979.706 0.943 1.800 8.11564E-01 8.89757E-01 -7.81934E-02 4980.121 1.358 1.830 8.36275E-01 8.96019E-01 -5.97439E-02 4980.542 1.780 1.860 9.16563E-01 9.02018E-01 1.45451E-02 4980.971 2.208 1.890 1.00872E+00 9.07788E-01 1.00932E-01 4981.407 2.644 1.920 1.08114E+00 9.13312E-01 1.67828E-01 4981.849 3.086 1.950 1.11955E+00 9.18608E-01 2.00945E-01 4982.298 3.535 1.980 1.13308E+00 9.23657E-01 2.09423E-01 4982.754 3.991 2.010 1.14273E+00 9.28461E-01 2.14271E-01 4983.217 4.454 2.040 1.15283E+00 9.33035E-01 2.19790E-01 4983.687 4.924 2.070 1.15849E+00 9.37346E-01 2.21143E-01 4984.163 5.401 2.100 1.16452E+00 9.41447E-01 2.23068E-01 4984.647 5.884 2.130 1.18412E+00 9.45303E-01 2.38817E-01 4985.137 6.374 2.160 1.21498E+00 9.48932E-01 2.66044E-01 4985.634 6.872 2.190 1.24240E+00 9.52334E-01 2.90069E-01 4986.139 7.376 2.220 1.25155E+00 9.55511E-01 2.96036E-01 4986.649 7.887 2.250 1.23876E+00 9.58461E-01 2.80303E-01 4987.167 8.404 2.280 1.21617E+00 9.61204E-01 2.54969E-01 4987.692 8.929 2.310 1.20218E+00 9.63742E-01 2.38437E-01 4988.223 9.460 2.340 1.21246E+00 9.66074E-01 2.46388E-01 4988.762 9.999 2.370 1.25770E+00 9.68220E-01 2.89477E-01 4989.307 10.544 2.400 1.32791E+00 9.70161E-01 3.57749E-01 4989.859 11.096 2.430 1.38130E+00 9.71917E-01 4.09379E-01 4990.418 11.655 2.460 1.38220E+00 9.73507E-01 4.08696E-01 4990.984 12.221 2.490 1.34139E+00 9.74933E-01 3.66459E-01 4991.556 12.793 2.520 1.29626E+00 9.76174E-01 3.20089E-01 4992.136 13.373 2.550 1.27334E+00 9.77270E-01 2.96074E-01 4992.722 13.959 2.580 1.27044E+00 9.78222E-01 2.92220E-01 4993.315 14.552 2.610 1.26795E+00 9.79029E-01 2.88916E-01 4993.915 15.153 2.640 1.25051E+00 9.79692E-01 2.70818E-01 4994.522 15.759 2.670 1.21688E+00 9.80191E-01 2.36689E-01 TITLE TiPcCl2 molecule Geom1 CONTROL 1 1 1 1 1 1 PRINT 5 0 0 0 0 0 FMS 8.0 1 *1 appropriate for molecules (wiki) MULTIPOLE 2 *Dipole and quadrupole EXCHANGE 0 1 *Dirac Hara, -1eV Fermi level shift SCF 4 *includes second coordination shell XANES 6.0 0.05 0.01 AFOLP 1.2 CRITERION 0 0 *use all paths *RPATH 0.1 * emin emax eimag LDOS -20 20 0.2 POTENTIALS *absorbing atom is the Ti *ipot z tag 0 22 Ti 1 6 C 2 7 N 3 1 H 4 17 Cl ATOMS *xmod ymod zmod ipot 0 0 0 0 2.11844236 -0.00045764 -0.28362660 2 0.00049691 2.11838749 -0.28403609 2 -2.11834820 0.00044201 -0.28432911 2 -0.00040276 -2.11840312 -0.28391961 2 2.50033703 2.49920371 -0.37080272 2 -2.49915235 2.50026531 -0.37163159 2 -2.50021397 -2.49922414 -0.37149421 2 2.49927541 -2.50028574 -0.37066535 2 2.92077159 1.14863904 -0.35919200 1 -1.14858929 2.92070211 -0.35991542 1 -2.92065235 -1.14865884 -0.36009724 1 1.14870854 -2.92072190 -0.35937383 1 2.92028351 -1.14989912 -0.35912883 1 1.14994884 2.92021403 -0.35953433 1 -2.92016426 1.14987932 -0.36016040 1 -1.14982959 -2.92023383 -0.35975490 1 4.24012097 0.69267038 -0.46786156 1 -0.69260556 4.24003046 -0.46877686 1 -4.23996562 -0.69269616 -0.46922925 1 0.69276092 -4.24005624 -0.46831395 1 4.23982641 -0.69449678 -0.46782344 1 0.69456158 4.23973590 -0.46854687 1 -4.23967106 0.69447100 -0.46926736 1 -0.69440621 -4.23976169 -0.46854393 1 5.42180506 1.42299661 -0.58110099 1 -1.42291609 5.42169266 -0.58234553 1 -5.42161213 -1.42302863 -0.58282014 1 1.42310907 -5.42172466 -0.58157559 1 5.42120023 -1.42533102 -0.58102274 1 1.42541150 5.42108783 -0.58187330 1 -5.42100730 1.42529900 -0.58289838 1 -1.42521852 -5.42111985 -0.58204782 1 6.62671213 0.70509648 -0.69117255 1 -0.70500071 6.62657845 -0.69255053 1 -6.62648265 -0.70513457 -0.69333050 1 0.70523027 -6.62661650 -0.69195251 1 6.62641208 -0.70794872 -0.69113373 1 0.70804448 6.62627840 -0.69231626 1 -6.62618259 0.70791063 -0.69336932 1 -0.70781492 -6.62631646 -0.69218678 1 5.41276801 2.50322415 -0.58475924 3 -2.50314311 5.41265491 -0.58615139 3 -5.41257388 -2.50325637 -0.58641595 3 2.50333729 -5.41268710 -0.58502379 3 5.41170441 -2.50555482 -0.58462164 3 2.50563579 5.41159131 -0.58532097 3 -5.41151028 2.50552260 -0.58655354 3 -2.50544161 -5.41162354 -0.58585421 3 7.56137780 1.23956000 -0.77936602 3 7.56085067 -1.24281398 -0.77929784 3 -7.56059192 1.24277103 -0.78187250 3 -7.56111904 -1.23960294 -0.78180432 3 -1.23945199 7.56122707 -0.78099842 3 1.24292195 7.56069994 -0.78058687 3 1.23971085 -7.56126996 -0.78017192 3 -1.24266309 -7.56074286 -0.78058347 3 0.00040523 -0.00006766 -2.45005490 4 -0.00040584 0.00006782 2.45002706 4 END # TiPcCl2 molecule (positions calculated from ADF) Feff 8.40 # POT SCF 30 4.0000 0, core-hole, AFOLP (folp(0)= 1.200) # Abs Z=22 Rmt= 1.437 Rnm= 1.537 K shell # Pot 1 Z= 6 Rmt= 0.840 Rnm= 0.996 # Pot 2 Z= 7 Rmt= 0.885 Rnm= 1.008 # Pot 3 Z= 1 Rmt= 0.789 Rnm= 0.909 # Pot 4 Z=17 Rmt= 1.538 Rnm= 1.686 # Gam_ch=9.030E-01 H-L exch Vi= 0.000E+00 Vr= 1.000E+00 # Mu=-1.040E+01 kf=2.632E+00 Vint=-1.880E+01 Rs_int= 1.378 # FMS rfms= 8.0000 # PATH Rmax=-1.000, Keep_limit= 0.00, Heap_limit 0.00 Pwcrit= 0.00% # S02=1.000 Global_sig2= 0.00000 # file sig2 tot cw amp ratio deg nlegs reff inp sig2 # 0/ 0 paths used # xsedge+ 50, used to normalize mu 4.6992E-04 # ----------------------------------------------------------------------- # omega e k mu mu0 chi @# 4964.275 -14.488 -0.900 1.44077E-02 3.21565E-02 -1.77488E-02 4964.923 -13.840 -0.800 1.61993E-02 3.95010E-02 -2.33017E-02 4965.495 -13.268 -0.700 1.84771E-02 4.97434E-02 -3.12663E-02 4965.990 -12.773 -0.600 2.15278E-02 6.45932E-02 -4.30654E-02 4966.409 -12.354 -0.500 2.58451E-02 8.69527E-02 -6.11076E-02 4966.752 -12.011 -0.400 3.21686E-02 1.21157E-01 -8.89880E-02 4967.019 -11.744 -0.300 4.10037E-02 1.70217E-01 -1.29214E-01 4967.209 -11.554 -0.200 5.09103E-02 2.25913E-01 -1.75002E-01 4967.323 -11.440 -0.100 5.83015E-02 2.67539E-01 -2.09238E-01 4967.351 -11.412 -0.051 6.02274E-02 2.78296E-01 -2.18069E-01 4967.361 -11.402 0.000 6.09319E-02 2.82145E-01 -2.21213E-01 4967.371 -11.392 0.050 6.15821E-02 2.85805E-01 -2.24223E-01 4967.400 -11.363 0.100 6.35112E-02 2.96793E-01 -2.33281E-01 4967.447 -11.316 0.150 6.67307E-02 3.14931E-01 -2.48200E-01 4967.514 -11.249 0.200 7.10829E-02 3.39349E-01 -2.68267E-01 4967.600 -11.163 0.250 7.62645E-02 3.68148E-01 -2.91884E-01 4967.704 -11.059 0.300 8.19260E-02 3.98629E-01 -3.16703E-01 4967.828 -10.935 0.350 8.77714E-02 4.28185E-01 -3.40413E-01 4967.971 -10.792 0.400 9.37945E-02 4.55258E-01 -3.61463E-01 4968.133 -10.630 0.450 1.00145E-01 4.79354E-01 -3.79209E-01 4968.314 -10.449 0.500 1.06691E-01 5.00709E-01 -3.94018E-01 4968.514 -10.249 0.550 1.12394E-01 5.19879E-01 -4.07485E-01 4968.733 -10.030 0.600 1.15591E-01 5.37511E-01 -4.21920E-01 4968.971 -9.792 0.650 1.13910E-01 5.54177E-01 -4.40267E-01 4969.228 -9.535 0.700 1.06198E-01 5.70351E-01 -4.64152E-01 4969.505 -9.258 0.750 9.61631E-02 5.86343E-01 -4.90179E-01 4969.800 -8.963 0.800 8.86382E-02 6.02345E-01 -5.13707E-01 4970.114 -8.649 0.850 8.55330E-02 6.18458E-01 -5.32925E-01 4970.448 -8.315 0.900 8.67318E-02 6.34730E-01 -5.47998E-01 4970.800 -7.963 0.950 9.08250E-02 6.51152E-01 -5.60327E-01 4971.171 -7.592 1.000 9.64994E-02 6.67694E-01 -5.71195E-01 4971.562 -7.201 1.050 1.03277E-01 6.84334E-01 -5.81056E-01 4971.972 -6.791 1.100 1.11508E-01 7.01012E-01 -5.89504E-01 4972.400 -6.363 1.150 1.27017E-01 7.17678E-01 -5.90661E-01 4972.848 -5.915 1.200 1.51783E-01 7.34259E-01 -5.82476E-01 4973.315 -5.448 1.250 1.85121E-01 7.50729E-01 -5.65608E-01 4973.800 -4.963 1.300 2.22060E-01 7.66999E-01 -5.44939E-01 4974.305 -4.458 1.350 2.60104E-01 7.83015E-01 -5.22911E-01 4974.829 -3.934 1.400 3.10517E-01 7.98732E-01 -4.88216E-01 4975.372 -3.391 1.450 3.82202E-01 8.14085E-01 -4.31883E-01 4975.934 -2.829 1.500 4.63881E-01 8.29030E-01 -3.65149E-01 4976.515 -2.248 1.550 5.37065E-01 8.43501E-01 -3.06436E-01 4977.115 -1.648 1.600 6.07253E-01 8.57469E-01 -2.50216E-01 4977.734 -1.029 1.650 6.73937E-01 8.70893E-01 -1.96956E-01 4978.372 -0.391 1.700 7.30804E-01 8.83727E-01 -1.52923E-01 4979.030 0.267 1.750 8.02516E-01 8.95956E-01 -9.34395E-02 4979.706 0.943 1.800 8.54202E-01 9.07537E-01 -5.33342E-02 4980.401 1.638 1.850 9.26242E-01 9.18471E-01 7.77126E-03 4981.115 2.353 1.900 1.02684E+00 9.28720E-01 9.81182E-02 4981.849 3.086 1.950 1.10155E+00 9.38305E-01 1.63246E-01 4982.601 3.838 2.000 1.13866E+00 9.47198E-01 1.91459E-01 4983.373 4.610 2.050 1.16173E+00 9.55400E-01 2.06331E-01 4984.163 5.401 2.100 1.18362E+00 9.62930E-01 2.20694E-01 4984.973 6.210 2.150 1.21605E+00 9.69805E-01 2.46241E-01 4985.802 7.039 2.200 1.24599E+00 9.76015E-01 2.69973E-01 4986.649 7.887 2.250 1.25003E+00 9.81596E-01 2.68433E-01 4987.516 8.753 2.300 1.24364E+00 9.86570E-01 2.57068E-01 4988.402 9.639 2.350 1.26862E+00 9.90955E-01 2.77669E-01 4989.307 10.544 2.400 1.33164E+00 9.94768E-01 3.36871E-01 4990.231 11.468 2.450 1.36605E+00 9.98067E-01 3.67984E-01 4991.174 12.411 2.500 1.33716E+00 1.00084E+00 3.36318E-01 4992.136 13.373 2.550 1.30098E+00 1.00317E+00 2.97807E-01 4993.117 14.354 2.600 1.28188E+00 1.00505E+00 2.76824E-01 4994.117 15.354 2.650 1.24913E+00 1.00652E+00 2.42606E-01 4995.136 16.373 2.700 1.19116E+00 1.00762E+00 1.83538E-01 4996.174 17.412 2.750 1.12334E+00 1.00839E+00 1.14945E-01 4997.232 18.469 2.800 1.05879E+00 1.00886E+00 4.99339E-02 4998.308 19.545 2.850 1.00361E+00 1.00905E+00 -5.44234E-03 4999.403 20.640 2.900 9.66190E-01 1.00899E+00 -4.28024E-02 5000.518 21.755 2.950 9.53894E-01 1.00874E+00 -5.48451E-02 5001.651 22.888 3.000 9.61104E-01 1.00831E+00 -4.72049E-02 5002.804 24.041 3.050 9.70657E-01 1.00771E+00 -3.70537E-02 5003.975 25.212 3.100 9.65699E-01 1.00699E+00 -4.12896E-02 5005.166 26.403 3.150 9.43779E-01 1.00616E+00 -6.23849E-02 5006.376 27.613 3.200 9.12270E-01 1.00527E+00 -9.29971E-02 5007.604 28.841 3.250 8.79909E-01 1.00430E+00 -1.24395E-01 5008.852 30.089 3.300 8.53592E-01 1.00330E+00 -1.49707E-01 5010.119 31.356 3.350 8.37319E-01 1.00228E+00 -1.64962E-01 5011.405 32.642 3.400 8.32342E-01 1.00126E+00 -1.68915E-01 5012.710 33.947 3.450 8.37897E-01 1.00024E+00 -1.62341E-01 5014.034 35.271 3.500 8.52224E-01 9.99254E-01 -1.47030E-01 5015.377 36.614 3.550 8.73066E-01 9.98292E-01 -1.25226E-01 5016.739 37.976 3.600 8.98424E-01 9.97383E-01 -9.89589E-02 5018.120 39.357 3.650 9.25999E-01 9.96535E-01 -7.05367E-02 5019.520 40.757 3.700 9.53423E-01 9.95731E-01 -4.23079E-02 5020.939 42.176 3.750 9.78294E-01 9.94988E-01 -1.66939E-02 5022.378 43.615 3.800 9.98847E-01 9.94307E-01 4.53986E-03 5023.835 45.072 3.850 1.01451E+00 9.93705E-01 2.08018E-02 5025.311 46.548 3.900 1.02568E+00 9.93184E-01 3.25003E-02 5026.807 48.044 3.950 1.03332E+00 9.92711E-01 4.06132E-02 5028.321 49.558 4.000 1.03851E+00 9.92313E-01 4.61965E-02 5029.855 51.092 4.050 1.04223E+00 9.91980E-01 5.02542E-02 5031.407 52.644 4.100 1.04512E+00 9.91711E-01 5.34115E-02 5032.979 54.216 4.150 1.04746E+00 9.91501E-01 5.59600E-02 5034.570 55.807 4.200 1.04937E+00 9.91335E-01 5.80315E-02 5036.179 57.416 4.250 1.05095E+00 9.91211E-01 5.97411E-02 5037.808 59.045 4.300 1.05246E+00 9.91143E-01 6.13166E-02 5039.456 60.693 4.350 1.05412E+00 9.91101E-01 6.30208E-02 5041.123 62.360 4.400 1.05575E+00 9.91083E-01 6.46637E-02 5042.809 64.046 4.450 1.05588E+00 9.91095E-01 6.47840E-02

2 1

Comparison of "amp" between Feff8.40 and feff6 - Curved waves or Plane waves?
by Ying Zou 29 Aug '08

29 Aug '08

Dear all, Nice to get so prompt response from Bruce and Scott, thanks for their effort to make this list vital! Looks like "amp" is a factor which can be reduced. Then there is a question: how would all paths be sorted? by Reff or by "amp"? More techically related another question is then: can FEFFIT and FEFF work seamless together on this? Is there any presumption in FEFFIT (or more explicityly, ARTEMIS/ATHENA) which assumes all the paths have been sorted by descending "amp" down from 100% with ascending REFF? The background story behind this: using the same structural model (thanks Bruce!), I tried to fit either use paths from FEFF840 or from FEFF6. The fitting with FEFF6 paths does a quite good job, giving a R_factor~1%, reduced chi square~ 90. Yet the one with FEFF840 paths terminates abnormally because two parameters cannot be determined. Attached please find two ARTEMIS project files. And appreciate for comments! Ying Ying Zou Research Assoc., Dr. Phys. Physics Department, UWM

2 1

Re: [Ifeffit] Comparison of "amp" between Feff8.40 and feff6 - Curved waves or Plane waves?
by Ying Zou 29 Aug '08

29 Aug '08

Dear all, While I am calculating FEFF path through Feff8.40 using the "feff8.inp" as attached, I notice that the value of "amp" shown on "FEFF interpretation page" for some paths goes over 100%. For example, path 14 has a Reff=3.9317 far away from first shell, yet it has an "amp"=169.913. On the contrary, if I do the same in Artemis through embedded Feff6.0(using "feff6.inp"), none of paths has an "amp" over 100%. I am guessing this could be all right because Feff8 is using curved waves Feff6 instead plane waves. Any comments on this would be greatly appreciated! Ying Ying Zou Research Assoc., Dr.Phys. Physics Department, UWM =======================feff8.inp======================================= * This feff.inp file generated by ATOMS, version 2.50 * ATOMS written by and copyright (c) Bruce Ravel, 1992-1999 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu = 5194.4 cm^-1, delta mu = 761.6 cm^-1 * specific gravity = 7.942, cluster contains 25 atoms. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * mcmaster corrections: 0.00093 ang^2 and 0.165E-05 ang^4 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE Perovskite: PbTiO3 EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 3 * r_scf [ l_scf n_scf ca ] SCF 3.88586 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 0 0 0 EXAFS RPATH 7.77172 * kmax [ delta_k delta_e ] *XANES 4.0 0.07 0.5 * r_fms [ l_fms ] *FMS 3.88586 ******** * *RPATH 0.10000 * emin emax resolution *LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 22 Ti -1 -1 0 1 8 O -1 -1 3 2 82 Pb -1 -1 1 3 22 Ti -1 -1 1 ATOMS 0.00000 0.00000 0.00000 0 Ti 0.00000 0.00000 0.00000 -1.76630 1 Oapical 1.76630 1.95250 0.00000 0.32417 1 Oplanar 1.97923 0.00000 -1.95250 0.32417 1 Oplanar 1.97923 -1.95250 0.00000 0.32417 1 Oplanar 1.97923 0.00000 1.95250 0.32417 1 Oplanar 1.97923 0.00000 0.00000 2.38970 1 Oapical 2.38970 -1.95250 -1.95250 1.91592 2 Pb 3.36084 1.95250 -1.95250 1.91592 2 Pb 3.36084 -1.95250 1.95250 1.91592 2 Pb 3.36084 1.95250 1.95250 1.91592 2 Pb 3.36084 1.95250 -1.95250 -2.24008 2 Pb 3.55563 -1.95250 1.95250 -2.24008 2 Pb 3.55563 -1.95250 -1.95250 -2.24008 2 Pb 3.55563 1.95250 1.95250 -2.24008 2 Pb 3.55563 -3.90500 0.00000 0.00000 3 Ti 3.90500 0.00000 3.90500 0.00000 3 Ti 3.90500 3.90500 0.00000 0.00000 3 Ti 3.90500 0.00000 -3.90500 0.00000 3 Ti 3.90500 0.00000 0.00000 4.15600 3 Ti 4.15600 0.00000 0.00000 -4.15600 3 Ti 4.15600 3.90500 0.00000 -1.76630 1 Oapical 4.28589 0.00000 -3.90500 -1.76630 1 Oapical 4.28589 -3.90500 0.00000 -1.76630 1 Oapical 4.28589 0.00000 3.90500 -1.76630 1 Oapical 4.28589 END ============================================================================ ========================feff6.inp========================================== * This feff6 input file was generated by Artemis 0.8.011 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu*x=1: 2.06 microns, unit edge step: 13.38 microns * specific gravity = 7.942 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * Normalization correction: 0.00048 ang^2 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * ----------------------------------------------------------------- * The following crystallographic data were used: * * title Pb Ti O3 * title Glazer A M * title # Powder profile refinement of lead zirconate titanate at several temperatures. * title # II. Pure PbTiO3 * title # Locality: synthetic * title # Sample: T = 25 C * space = P 4 m m * a = 3.9050 b = 3.9050 c = 4.1560 * alpha = 90.0 beta = 90.0 gamma = 90.0 * core = Ti edge = K * atoms * ! elem x y z tag occ * Pb 0.00000 0.00000 0.00000 Pb 1.00000 * Ti 0.50000 0.50000 0.53900 Ti 1.00000 * O 0.50000 0.50000 0.11400 Oapical 1.00000 * O 0.50000 0.00000 0.61700 Oplanar 1.00000 * ----------------------------------------------------------------- TITLE Pb Ti O3 TITLE Glazer A M TITLE # Powder profile refinement of lead zirconate titanate at several temperatures. TITLE # II. Pure PbTiO3 TITLE # Locality: synthetic TITLE # Sample: T = 25 C HOLE 1 1.0 * Ti K edge (4966.0 eV), second number is S0^2 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 RMAX 4.29550 *CRITERIA curved plane *DEBYE temp debye-temp NLEG 4 POTENTIALS * ipot Z element 0 22 Ti 1 82 Pb 2 22 Ti 3 8 O ATOMS * this list contains 25 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Ti 0.00000 0.00000 0.00000 -1.76630 3 Oapical_1 1.76630 1.95250 0.00000 0.32417 3 Oplanar_1 1.97923 -1.95250 0.00000 0.32417 3 Oplanar_1 1.97923 0.00000 1.95250 0.32417 3 Oplanar_1 1.97923 0.00000 -1.95250 0.32417 3 Oplanar_1 1.97923 0.00000 0.00000 2.38970 3 Oapical_2 2.38970 1.95250 1.95250 1.91592 1 Pb_1 3.36084 -1.95250 1.95250 1.91592 1 Pb_1 3.36084 1.95250 -1.95250 1.91592 1 Pb_1 3.36084 -1.95250 -1.95250 1.91592 1 Pb_1 3.36084 1.95250 1.95250 -2.24008 1 Pb_2 3.55563 -1.95250 1.95250 -2.24008 1 Pb_2 3.55563 1.95250 -1.95250 -2.24008 1 Pb_2 3.55563 -1.95250 -1.95250 -2.24008 1 Pb_2 3.55563 3.90500 0.00000 0.00000 2 Ti_1 3.90500 -3.90500 0.00000 0.00000 2 Ti_1 3.90500 0.00000 3.90500 0.00000 2 Ti_1 3.90500 0.00000 -3.90500 0.00000 2 Ti_1 3.90500 0.00000 0.00000 4.15600 2 Ti_2 4.15600 0.00000 0.00000 -4.15600 2 Ti_2 4.15600 3.90500 0.00000 -1.76630 3 Oapical_3 4.28589 -3.90500 0.00000 -1.76630 3 Oapical_3 4.28589 0.00000 3.90500 -1.76630 3 Oapical_3 4.28589 0.00000 -3.90500 -1.76630 3 Oapical_3 4.28589 END ========================================================================

4 3

Re: [Ifeffit] charge transfer by SCF in FEFF8 and simulation for charge disproportionation
by Ying Zou 28 Aug '08

28 Aug '08

Dear all, I am doing a SCF calculation by Feff8.40 for a model compound PbTiO3. However, the obtained charge transfer deviates far away from its well-known formal oxidation state. According to common electron negativity data, the oxidation state would be: Pb 2+ Ti 4+ O 2- The SCF run gave out charge transfer for those atoms as following: Pb 0.717 Ti 0.181 O -0.300 After I read through the existing threads on charge transfer in this list, I know that transfered charge FEFF gives out is just a portion of general formal oxidation state. Can we undderstand that this is just ionic portion for entire bonding? Such as for oxygen, "-0.300" is ionic bonding, while the rest of valency (-1.700) exists as covalent bonding, which doesn't have apparent charge transfer by definition. Another related question is then: is there any way in FEFF to take into account this "covalence" part? (maybe deriving from overlapping area of mufftin-potential?) I think this may be crucial for a self-consistent analysis of charge disproportionation. Any comments on this would be greatly appreciated. Attached please see"atom.inp" and "feff.inp". Thanks so much! Ying Ying Zou Research associate,Dr. Phys. Physics Department, UWM ***************atoms.inp*********************************** ! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = Perovskite: PbTiO3 space = p 4 m m a = 3.9050 b = 3.9050 c = 4.1560 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ti edge = K rmax = 4.2950 atoms ! elem x y z tag occ. Pb 0.00000 0.00000 0.00000 Pb 1.00000 Ti 0.50000 0.50000 0.53900 Ti 1.00000 O 0.50000 0.50000 0.11400 Oapical 1.00000 O 0.50000 0.00000 0.61700 Oplanar 1.00000 ****************************************************************** ************feff.inp*************************************** * This feff.inp file generated by ATOMS, version 2.50 * ATOMS written by and copyright (c) Bruce Ravel, 1992-1999 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu = 5194.4 cm^-1, delta mu = 761.6 cm^-1 * specific gravity = 7.942, cluster contains 25 atoms. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * mcmaster corrections: 0.00093 ang^2 and 0.165E-05 ang^4 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE Perovskite: PbTiO3 EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 3 * r_scf [ l_scf n_scf ca ] SCF 3.88586 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 0 0 0 EXAFS RPATH 7.77172 * kmax [ delta_k delta_e ] *XANES 4.0 0.07 0.5 * r_fms [ l_fms ] *FMS 3.88586 ******** * *RPATH 0.10000 * emin emax resolution *LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 22 Ti -1 -1 0 1 8 O -1 -1 3 2 82 Pb -1 -1 1 3 22 Ti -1 -1 1 ATOMS 0.00000 0.00000 0.00000 0 Ti 0.00000 0.00000 0.00000 -1.76630 1 Oapical 1.76630 1.95250 0.00000 0.32417 1 Oplanar 1.97923 0.00000 -1.95250 0.32417 1 Oplanar 1.97923 -1.95250 0.00000 0.32417 1 Oplanar 1.97923 0.00000 1.95250 0.32417 1 Oplanar 1.97923 0.00000 0.00000 2.38970 1 Oapical 2.38970 -1.95250 -1.95250 1.91592 2 Pb 3.36084 1.95250 -1.95250 1.91592 2 Pb 3.36084 -1.95250 1.95250 1.91592 2 Pb 3.36084 1.95250 1.95250 1.91592 2 Pb 3.36084 1.95250 -1.95250 -2.24008 2 Pb 3.55563 -1.95250 1.95250 -2.24008 2 Pb 3.55563 -1.95250 -1.95250 -2.24008 2 Pb 3.55563 1.95250 1.95250 -2.24008 2 Pb 3.55563 -3.90500 0.00000 0.00000 3 Ti 3.90500 0.00000 3.90500 0.00000 3 Ti 3.90500 3.90500 0.00000 0.00000 3 Ti 3.90500 0.00000 -3.90500 0.00000 3 Ti 3.90500 0.00000 0.00000 4.15600 3 Ti 4.15600 0.00000 0.00000 -4.15600 3 Ti 4.15600 3.90500 0.00000 -1.76630 1 Oapical 4.28589 0.00000 -3.90500 -1.76630 1 Oapical 4.28589 -3.90500 0.00000 -1.76630 1 Oapical 4.28589 0.00000 3.90500 -1.76630 1 Oapical 4.28589 END *******************************************************************

2 1

Re: [Ifeffit] Quick question about atoms.exe and .cif files
by Bruce Ravel 26 Aug '08

26 Aug '08

On Tuesday 26 August 2008 01:44:03 you wrote: > Hi Bruce, > > I have atoms running well, but whenever I input a simple diamond > structure .cif file (like the attached silicon.cif file), I get the wrong > structure. I've tried everything that I could think of, but it doesn't > work. I'm not sure if it is something I'm doing wrong, or something > intrinsic in the .cif file. I'm currently running the command line program > with the command "atoms.exe -u -o "silicon.inf" "Silicon.cif"", with the > files being appropriately loaded. If you get the chance could you tell me > if it is an easy problem that I can quickly fix (and the solution), or if > it is something more in depth: I'd appreciate it. > > Zak I am forwarding this question to the Ifeffit mailing list. This is the sort of question for which that forum was created. Please make use of it. http://cars9.uchicago.edu/iffwiki/BruceRavel/FormLetters/HelpRequest As the warning message says, "F d -3 m" is one of those space groups in the International Tables that offers two choices for the position of the origin. There is no way to correct that from the command line, so your two options are: 1. Use Artemis to generate your unit cell file and apply the shift vector given in the warning message or 2. Edit the cif file to put the Si atom at (1/8,1/8,1/8) B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

1 0