November 2006 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] OS X: (was: new release (061) of my codes)
by Matt Newville 29 Nov '06

29 Nov '06

Bruce, everyone Mac-interested: I believe many of the problems that have been seen come from the idea that one can install the binary, and then expect upgrading from source to work. I believe this will always be fragile: Mac OS X does not come with an installed compiler for C or Fortran (they are available). For these machines, the standard 'perl Makefile.PL' will fail. Whether this is the cause of the recent problems is a separate question. The way I see it, there are two ways to go here: A) assume that Mac is "just-another-version-of-Unix" so that installations and upgrading from source should work. B) assume that Mac is as special as Windows, and that ALL installations and upgrades need an actual installer or a simple, foolproof upgrade mechanism that involves no users typing at a terminal. An "upgrade" could simply consist of a zip file of new files, but we'd need a program (like exists for Windows) that did this upgrading semi-automatically. If the perl upgrades were "pure perl" and did not include a compilation, it could probably be made to work more reliably. But I don't quite see that as the right solution, because it still expects upgrades to happen with a different model than the original installation. Personally, I'm not thrilled about having to support option A. Option B means that someone will have to do the work of making and testing binary installers and upgrades. It will probably mean having to stick close to Mac OS X upgrade cycle. But I think we need a consensus on this. Any opinions? --Matt

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Re: horae 062 on Mac OS X
by Michel Jaouen 28 Nov '06

28 Nov '06

Dear all, I have just installed on my Mac (ppc 2x1.8 GHz) OS X 10.4.8 the last version made by Paul Fons (thanks Paul for your so nice job), ie horae 062. As it has been posted, I have to be the owner of the applications to suppress the Apple Script stuff previously reported by Stephano. All run smoothly excepted for TkAtoms that never starts! I have tried to launch it by hands in the terminal (X11) but it fails too. I see it tries to start the Applet, but nothing happens (and no error message!). A little bit annoying because I use TkAtoms quite often for feff8 runs. The only point I see in the Console is the following: XFree86 Version 4.4.0 / X Window System (protocol Version 11, revision 0, vendor release 6600) [DRI] screen 0 installation complete Screen 0 added: 1280x1024 @ (0,0) Could not init font path element /usr/X11R6/lib/X11/fonts/CID/, removing from list! Quitting XDarwin... But I'm note sure it is related to the problem. Any hints for a solution is welcomed. 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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new release of the horae source code
by Bruce Ravel 27 Nov '06

27 Nov '06

Hi folks, I just made a new release of the source code for Athena, Artemis, and Hephaestus. This includes small changes to Artemis and Hephaestus and several new features and bug fixes for Athena. For details, please see http://cars9.uchicago.edu/iffwiki/HoraeVersion063 Athena includes several nice usability improvements, including a new way of specifying k-weightings for chi(k) plots and Fourier transforms that works very similarly to the plotting k-weight in Artemis. An updater for the windows users should be available before too long. We will make an announcement when it is available. I wanted to get the source tarball out the door for the benefit of Jeff and the other elves working on the MacTel package. When they smooth out the rough patches in the MacTel distribution, I'd like them to be using the latest codes. Enjoy! B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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Coordination number
by Juan Antonio Maciá Agulló 23 Nov '06

23 Nov '06

Hi all, I have a simple question but I am afraid it is polemic. Why people always calculate coordination numbers and bond distances and how? I have an e-mail where Bruce described perfectly how to calculate the coordiantion number for the first shell. But,...if I have bimetallic catalysts or/and a mixture of structures with several close paths (similar Reff), then coordination number is an average number? I am not very sure how to calculate them in Artemis with SO2 and standards. 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

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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