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

Re: [Ifeffit] Artemis
by Juan Antonio Macia Agullo 10 Nov '06

10 Nov '06

OK, good answer Scott. My fits have lower values of R-factor but when I depict them in k-space they do not fit quite well to the experimental data due to the short range of R space chosen, of course if I increase range of R then I hope fits in k space will look better. When I talked about distant paths I mean paths contributing to other shells. I will consider MS but with simple constraints. Thank you very much Best regards, JA

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Re: [Ifeffit] Artemis
by Juan Antonio Macia Agullo 10 Nov '06

10 Nov '06

Thanks a lot Scott, I will do it. Sorry, but I do not understand what you mean with the sentence "in a physically reasonable way: delr might need to be scaled by reff". Could I use the same delR for all single scattering paths (even distant paths)? In principle, I am not going to consider MS paths. I hope fits increasing R-range will improve very much fits in k-space because now they are not very good. Best regards, JA ---- Mensaje Original ---- > Hi Juan, > > The same S02 should be OK; that's generally thought to be chemically > transferable. > > Unless I'm misunderstanding something about your system, there is no > physical basis to justify the same delr. Think about it: why would > both phases show the same difference in bond length between the model > and the actual structure? > > Using the same sigma2 is also problematic; it seems unlikely that the > disorder and vibrational spectrum is the same in the two cases. > > deltaE0, to first approximation, may be the same. In both phases the > valence of the absorbing atom is the same (i.e. 0), so assuming the > same E0 is not unreasonable. > > To my mind, therefore, you need at least 6 parameters (plus whatever > else you're using; e.g. the fraction of each phase present). > > So I'll use this opportunity to beat one of my favorite drums: why > not try a multishell fit? It sounds to me like you have phases that > are likely to be fairly crystalline. If your data is decent, you may > be able to extend your fit out to several coordination shells without > adding many new free parameters. (You have to do this in a physically > reasonable way: delr might need to be scaled by reff, etc.) This > might be a net gain in degrees of freedom, and also might reduce > uncertainties in some of the fitted variables by reducing correlations. > > --Scott Calvin > Sarah Lawrence College > > At 03:25 AM 11/9/2006, you wrote: > > > >Hi people!! > > > >I was fitting with Artemis bimetallic catalysts with two different > >structures: > >platinum structure plus an intermetallic compound structure. As I only use a > >small range of R space (1st shell) for fitting, I have a small number of > >independents points and I used an appropriate number of variables. The > >question is: I used the same values of SO2, delR, sigma^2 and > >deltaE0 for both > >structures, is that ok? or maybe I have to increase until 8 the number of > >variables? > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Artemis
by Juan Antonio Macia Agullo 09 Nov '06

09 Nov '06

Hi people!! I was fitting with Artemis bimetallic catalysts with two different structures: platinum structure plus an intermetallic compound structure. As I only use a small range of R space (1st shell) for fitting, I have a small number of independents points and I used an appropriate number of variables. The question is: I used the same values of SO2, delR, sigma^2 and deltaE0 for both structures, is that ok? or maybe I have to increase until 8 the number of variables? Thank you very much Best regards, JA

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Re: [Ifeffit] Node in chi(k) envelope for a single shell
by Silvio Levy 06 Nov '06

06 Nov '06

Thanks to all who replied and for the references proved by Bruce Ravel and Wayne Lukens. What a beautiful explanation. Best wishes, Silvio

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Node in chi(k) envelope for a single shell
by levy＠msri.org 06 Nov '06

06 Nov '06

Dear List, I have noticed in several fits that Artemis -- i.e., feff -- reports for a SINGLE shell (with absorber = scatterer = Hg, edge = L3) an almost-node in the envelope of chi(k) around 6 inverse angstroms. See the image at http://pjm.math.berkeley.edu/users/levy/files/HgNode.gif and the FEFF output after my signature. I've done my best to account for this behavior, but I simply don't have a physical intuition for why the F(k) factor should dip to zero or almost zero. Note that this is not a beat caused by two similar frequencies being added; the Fourier transform does of course show two peaks -- which is how my curiosity was aroused -- but the example figure comes from a SINGLE path, with 12 identical scatterers all at the same distance from the absorber. Looking forward to your two cents... Silvio Metacinnabar from CSDWeb, HgS Niculescu et al. 1970 Feff 6L.02 potph 4.12 Abs Z=80 Rmt= 1.327 Rnm= 1.667 LIII shell Pot 1 Z=16 Rmt= 1.218 Rnm= 1.515 Pot 2 Z=80 Rmt= 1.310 Rnm= 1.624 Gam_ch=5.000E+00 H-L exch Mu=-2.727E+00 kf=1.809E+00 Vint=-1.519E+01 Rs_int= 2.005 Path 2 icalc 2 Feff 6L.02 genfmt 1.4\4 ------------------------------------------------------------------------------\- 2 12.000 4.1366 2.9707 -2.72701 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# 0.0000 0.0000 0.0000 0 80 Hg absorbing atom 0.0000 -2.9250 -2.9250 2 80 Hg k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# 0.000 5.8876E+00 0.0000E+00 -5.3100E+00 0.1085E+01 5.5410E+00 1.8179E+00 0.200 5.8828E+00 6.5887E-02 -6.9020E+00 0.1085E+01 5.5726E+00 1.8284E+00 0.400 5.8685E+00 1.3063E-01 -8.3679E+00 0.1084E+01 5.6628E+00 1.8594E+00 0.600 5.8452E+00 1.9388E-01 -9.7059E+00 0.1082E+01 5.7987E+00 1.9101E+00 0.800 5.8135E+00 2.5592E-01 -1.0913E+01 0.1079E+01 5.9607E+00 1.9793E+00 1.000 5.7742E+00 3.1673E-01 -1.1989E+01 0.1077E+01 6.1257E+00 2.0656E+00 1.200 5.7279E+00 3.7510E-01 -1.2932E+01 0.1075E+01 6.2715E+00 2.1679E+00 1.400 5.6750E+00 4.2855E-01 -1.3742E+01 0.1074E+01 6.3832E+00 2.2854E+00 1.600 5.6157E+00 4.7354E-01 -1.4416E+01 0.1075E+01 6.4589E+00 2.4174E+00 1.800 5.5491E+00 5.0618E-01 -1.4949E+01 0.1076E+01 6.5142E+00 2.5639E+00 2.000 5.4733E+00 5.2301E-01 -1.5329E+01 0.1077E+01 6.5837E+00 2.7250E+00 2.200 5.3844E+00 5.2240E-01 -1.5543E+01 0.1078E+01 6.7192E+00 2.9013E+00 2.400 5.2972E+00 5.4699E-01 -1.5605E+01 0.1190E+01 4.9983E+00 3.0942E+00 2.600 5.3179E+00 5.7289E-01 -1.5987E+01 0.1239E+01 4.3905E+00 3.2252E+00 2.800 5.3348E+00 5.8762E-01 -1.6217E+01 0.1258E+01 4.1537E+00 3.3638E+00 3.000 5.3246E+00 5.9586E-01 -1.6383E+01 0.1257E+01 4.0743E+00 3.5096E+00 3.200 5.3065E+00 6.1650E-01 -1.6474E+01 0.1250E+01 4.0802E+00 3.6618E+00 3.400 5.2733E+00 6.3374E-01 -1.6567E+01 0.1239E+01 4.1398E+00 3.8197E+00 3.600 5.2309E+00 6.4470E-01 -1.6663E+01 0.1226E+01 4.2364E+00 3.9827E+00 3.800 5.1752E+00 6.3603E-01 -1.6766E+01 0.1212E+01 4.3604E+00 4.1501E+00 4.000 5.1090E+00 6.0562E-01 -1.6883E+01 0.1198E+01 4.5058E+00 4.3214E+00 4.200 5.0331E+00 5.5941E-01 -1.6984E+01 0.1183E+01 4.6683E+00 4.4959E+00 4.400 4.9489E+00 4.9872E-01 -1.7115E+01 0.1168E+01 4.8452E+00 4.6734E+00 4.600 4.8588E+00 4.2625E-01 -1.7230E+01 0.1154E+01 5.0343E+00 4.8533E+00 4.800 4.7653E+00 3.5048E-01 -1.7327E+01 0.1139E+01 5.2341E+00 5.0355E+00 5.000 4.6691E+00 2.7395E-01 -1.7453E+01 0.1125E+01 5.4434E+00 5.2195E+00 5.200 4.5722E+00 1.9793E-01 -1.7590E+01 0.1110E+01 5.6610E+00 5.4051E+00 5.400 4.4760E+00 1.3243E-01 -1.7866E+01 0.1096E+01 5.8864E+00 5.5922E+00 5.600 4.3817E+00 8.0754E-02 -1.8387E+01 0.1083E+01 6.1187E+00 5.7805E+00 5.800 4.2890E+00 7.7722E-02 -1.9408E+01 0.1070E+01 6.3576E+00 5.9699E+00 6.000 4.1996E+00 1.2225E-01 -1.9952E+01 0.1058E+01 6.6024E+00 6.1603E+00 6.500 3.9822E+00 2.6906E-01 -2.0350E+01 0.1031E+01 7.2385E+00 6.6398E+00 7.000 3.7681E+00 3.8170E-01 -2.0473E+01 0.1010E+01 7.9052E+00 7.1233E+00 7.500 3.5495E+00 4.3899E-01 -2.0529E+01 0.9919E+00 8.5988E+00 7.6098E+00 8.000 3.3245E+00 4.4840E-01 -2.0549E+01 0.9763E+00 9.3169E+00 8.0987E+00 8.500 3.1062E+00 4.3705E-01 -2.0526E+01 0.9613E+00 1.0057E+01 8.5893E+00 9.000 2.8953E+00 4.1495E-01 -2.0476E+01 0.9480E+00 1.0818E+01 9.0814E+00 9.500 2.6939E+00 3.9247E-01 -2.0391E+01 0.9367E+00 1.1598E+01 9.5746E+00 10.000 2.4999E+00 3.7170E-01 -2.0271E+01 0.9291E+00 1.2396E+01 1.0069E+01 11.000 2.1169E+00 3.6890E-01 -1.9990E+01 0.9196E+00 1.4041E+01 1.1059E+01 12.000 1.7611E+00 4.1306E-01 -1.9816E+01 0.9119E+00 1.5747E+01 1.2052E+01 13.000 1.4328E+00 4.6749E-01 -1.9744E+01 0.9072E+00 1.7507E+01 1.3046E+01 14.000 1.1169E+00 5.1022E-01 -1.9760E+01 0.9054E+00 1.9317E+01 1.4041E+01 15.000 8.2534E-01 5.3666E-01 -1.9821E+01 0.9032E+00 2.1172E+01 1.5037E+01 16.000 5.5314E-01 5.4489E-01 -1.9903E+01 0.9025E+00 2.3070E+01 1.6034E+01 17.000 2.9163E-01 5.3763E-01 -2.0012E+01 0.9015E+00 2.5007E+01 1.7031E+01 18.000 4.7223E-02 5.2008E-01 -2.0124E+01 0.8986E+00 2.6981E+01 1.8029E+01 19.000 -1.8906E-01 4.9327E-01 -2.0255E+01 0.8968E+00 2.8989E+01 1.9027E+01 20.000 -4.1335E-01 4.6035E-01 -2.0384E+01 0.8947E+00 3.1029E+01 2.0025E+01

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CuCl (final thought)
by Denis Testemale 02 Nov '06

02 Nov '06

Hello again. This is my final statement (I hope) concerning CuCl! Marco, it seems to me that your data (as well as the data from the 4th reference you mention, Takaoka et al., Chemosphere, 2005) is contaminated by Cu(II). CuCl being highly sensitive to air (and to light as well), Cu(I) is quickly oxydised. The large peak between 8990 and 9000eV in the spectrum corresponds to the white line of Cu(II). And since this white line is larger than Cu(I)'s one, you obtain this too small pre-edge. Hope that can help. Thanks again. Cheers. denis 2006/10/31, ifeffit-request(a)millenia.cars.aps.anl.gov < ifeffit-request(a)millenia.cars.aps.anl.gov>: > > 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. CuCl: thanks! (Denis Testemale) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 31 Oct 2006 09:52:29 +1030 > From: "Denis Testemale" <denis.testemale(a)gmail.com> > Subject: [Ifeffit] CuCl: thanks! > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <4ba19e1a0610301522k7d3a1fcbyb1459cf21fc10851(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Many thanks for the exhaustive and quick answers. There is still this > doubt > about the XANES shape, but at least I have some more references to deal > with > it. > Cheers. > denis > > > > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Ifeffit digest..." > > > > > > Today's Topics: > > > > 1. CuCl(solid) spectra? (Denis Testemale) > > 2. Re: CuCl(solid) spectra? (Marco A. Alsina) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 30 Oct 2006 11:39:40 +1030 > > From: "Denis Testemale" <denis.testemale(a)gmail.com> > > Subject: [Ifeffit] CuCl(solid) spectra? > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Message-ID: > > <4ba19e1a0610291709m1ae4315bx3c16d146a84fd06b(a)mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > G'day! > > > > I'm looking for a spectrum of CuCl (solid), or a reference where I can > see > > one. I'm more interested in the XANES than the EXAFS region. I've found > > Rumpf et al., Journal of Solid State Chemistry, 163, 158 (2002), but > what > > puzzles me is that the spectra in the Farrel Lytle database are somewhat > > different with a stronger whiteline. Only the spectrum at 77K (from FL > > database) does not have this white line, but its poor definition does > not > > make me feel confident. > > Thanks in advance. > > Denis > > > > -- > > Denis Testemale > > School of Earth and Environmental Sciences, Adelaide University > > and > > South Australian Museum > > North Terrace > > 5000 Adelaide > > ph: +61 8 8207 7659 > >

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CuCl: thanks!
by Denis Testemale 30 Oct '06

30 Oct '06

Many thanks for the exhaustive and quick answers. There is still this doubt about the XANES shape, but at least I have some more references to deal with it. Cheers. denis > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. CuCl(solid) spectra? (Denis Testemale) > 2. Re: CuCl(solid) spectra? (Marco A. Alsina) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Oct 2006 11:39:40 +1030 > From: "Denis Testemale" <denis.testemale(a)gmail.com> > Subject: [Ifeffit] CuCl(solid) spectra? > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <4ba19e1a0610291709m1ae4315bx3c16d146a84fd06b(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > G'day! > > I'm looking for a spectrum of CuCl (solid), or a reference where I can see > one. I'm more interested in the XANES than the EXAFS region. I've found > Rumpf et al., Journal of Solid State Chemistry, 163, 158 (2002), but what > puzzles me is that the spectra in the Farrel Lytle database are somewhat > different with a stronger whiteline. Only the spectrum at 77K (from FL > database) does not have this white line, but its poor definition does not > make me feel confident. > Thanks in advance. > Denis > > -- > Denis Testemale > School of Earth and Environmental Sciences, Adelaide University > and > South Australian Museum > North Terrace > 5000 Adelaide > ph: +61 8 8207 7659 >

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CuCl(solid) spectra?
by Denis Testemale 30 Oct '06

30 Oct '06

G'day! I'm looking for a spectrum of CuCl (solid), or a reference where I can see one. I'm more interested in the XANES than the EXAFS region. I've found Rumpf et al., Journal of Solid State Chemistry, 163, 158 (2002), but what puzzles me is that the spectra in the Farrel Lytle database are somewhat different with a stronger whiteline. Only the spectrum at 77K (from FL database) does not have this white line, but its poor definition does not make me feel confident. Thanks in advance. Denis -- Denis Testemale School of Earth and Environmental Sciences, Adelaide University and South Australian Museum North Terrace 5000 Adelaide ph: +61 8 8207 7659

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compiling horae-062a on AMD64
by crojasa＠unmsm.edu.pe 29 Oct '06

29 Oct '06

Hello List I trying install horae-062a on my Slamd64 11.0 ( AMD64 3200+), but it appears a following error; ...... /usr/bin/perl5.8.8 chantler2st.PL chantler.db Can't locate Chemistry/Elements.pm in @INC (@INC contains: /usr/lib/perl5/5.8.8/x86_64-linux /usr/lib/perl5/5.8.8 /usr/lib/perl5/site_perl/5.8.8/x86_64-linux /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl .) at chantler2st.PL line 40. BEGIN failed--compilation aborted at chantler2st.PL line 40. make[1]: *** [chantler.db] Error 2 make[1]: Leaving directory `/usr/local/src/horae-062a/Absorption' make: *** [subdirs] Error 2 Some idea for this error, Either it cannot install Gifefiit. PGplot - Ok Ifeffit - Ok Tk - 95% ok (according to test) Thanks Chachi Rojas Ayala GMC FCF UNMSM Claro:01-97489347 email:crojasa@unmsm.edu.pe

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Artemis import error
by Richard Mayes 25 Oct '06

25 Oct '06

Bruce and all, I'm having trouble importing an Athena project file into Artemis. When I try to import a particular set of data into Artemis as an Athena project file, Artemis keeps giving the errors "Use of uninitialized value in...at artemis line 11223." (where the ... is either hash element or method). I have attached a screenshot (.jpg) of the error message and the offending data as an Athena project file. I can open the rest of my data in Artemis with no problems, even from a file with this data in it, but when I try to open this set of data, it won't work. Any ideas on what the problem is? Rich Mayes

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