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

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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Re: [Ifeffit] Help with Ag and Pd
by huangwei＠UDel.Edu 24 Oct '06

24 Oct '06

Dear Matt, Many thanks. I download the Ag foil reference and Pd reference. And they are exactly what I want. Thank you very much! Wei

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Help with Ag and Pd
by huangwei＠UDel.Edu 23 Oct '06

23 Oct '06

Dear all feff members, I am a new member here. I have some problems with my Pd-Ag bimetallic samples. I cannot get good EXAFS signals for both Pd and Ag. Can somebody share a good Ag foil and Pd foil reference with me (transmition)? Thank you very much! Wei

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Re: still the spike
by Silvio Levy 19 Oct '06

19 Oct '06

Dear Bruce, OK, I hear you. I'll stop obsessing about the spike and only show chi*k^2 plots in my thesis :-) More seriously -- Your answer helps put things into perspective, and the comparison between the FFT with k-range starting at 0 and 1 is instructive. It's worth noting, however, that in R space there is a hump from R=1 to R=1.4 that (to my knowledge) has no physical explanation, and which is more pronounced when the FT is taken starting at k=0. Should I not worry about this either? Thanks Silvio

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still the spike
by Silvio Levy 19 Oct '06

19 Oct '06

Dear Shelly, Dear Bruce Thanks for both your answers. Going through Shelly's slides was a nice refresher course. Bruce, ok, I see why normalization is not affected. However.... The data were already correctly aligned. I've now explicitly tied the data to the standard, using the Data menu, and the auto-align shift was only 0.02 eV. So this had no effect on the spike. Setting the lower bound of the spline range to 0 mainly shifts the position of the spike to near k=0, and so hides it somewhat when we multiply chi by a power of k. But it's still visible in E space (a large negative peak in the spline). Setting a spine clamp at the low end changes things slightly but not qualitatively. Changing E0 would seem to be a reasonable step. After all, there is no reason why k=0 should coincide exactly with the first inflection point on the edge!! But again, all attempts, for Eshift varying from -5 to 10eV, make no qualitative difference. All other tweaks I've tried also maintain the spike, or else distort the spline so much as to introduce other errors. For comparison, I took the first curve (labeled 0.12) in project AuChloride_LCF_example.prj from Scott's talk. There is something of a sharp departure between the spline and the data visible in E space, as in my case. But the plot in k space -- even of chi itself without multiplying a power of k -- is nice and smooth. All this is in http://www.msri.org/~levy/files/example.prj which contains only one group from me and one from Scott. Would you be willing to take a closer look? I'd not be asking except that I'm completely stumped. My data seem perfectly normal. Thanks again, Silvio

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