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

Problems with atoms
by Dominik Samuelis 09 Mar '07

09 Mar '07

Hi, we are trying to create a feff.inp file for the octahedral core of the monoclinic beta-Ga2O3 structure. If we enter '12' as space group, there are some atoms missing. However, if we use the symbolic 'c 2/m', everything is fine. This occurs with TkAtoms, as well as with the Atoms implementation in Artemis 0.8.007. I haven't tried Webatoms yet, but I assume it'll be the same. The .cif-file for b-Ga2O3 is included. Any clues ? Cheers, dominik First octahedron with 'c 2/m' as space group index: [...] ATOMS * this list contains 16 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Ga2 0.00000 0 -1.93032 0.00000 0.14228 2 O3 1.93556 1 0.06926 1.51855 -1.20114 2 O1 1.93740 2 0.06926 -1.51855 -1.20114 2 O1 1.93740 3 1.99294 0.00000 0.22127 2 O2 2.00519 4 0.17363 1.51855 1.40203 2 O2 2.07409 5 0.17363 -1.51855 1.40203 2 O2 2.07409 6 0.00000 3.03710 0.00000 1 Ga2 3.03710 7 [...] END The same, with '12' as space group index. Please note the missing O2 in the first octahedron. There are also some other missing atoms: [...] ATOMS * this list contains 12 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Ga2 0.00000 0 -1.93032 0.00000 0.14228 2 O3 1.93556 1 0.06926 1.51855 -1.20114 2 O1 1.93740 2 0.06926 -1.51855 -1.20114 2 O1 1.93740 3 0.17363 1.51855 1.40203 2 O2 2.07409 4 0.17363 -1.51855 1.40203 2 O2 2.07409 5 0.00000 3.03710 0.00000 1 Ga2 3.03710 6 [...] END -- Dipl.-Ing. Dominik Samuelis samuelis(a)pc.rwth-aachen.de Physikalische Chemie I RWTH Aachen University Phone: +49-241-80-94840 Fax: +49-241-80-92128 Landoltweg 2 52056 Aachen Germany data_83645-ICSD _audit_creation_date 107-01-11 _audit_creation_method 'generated by RETRIEVE 2.0' _database_code_ICSD 83645 _chemical_name_systematic 'Gallium oxide - $-beta' _chemical_formula_structural 'Ga2 O3' _chemical_formula_sum 'Ga2 O3' _publ_section_title 'A reinvestigation of $-beta-gallium oxide' loop_ _publ_author_name 'Ahman, J' 'Svensson, G' 'Albertsson, J' _journal_name_full 'Acta Crystallographica C (39,1983-)' _journal_coden_ASTM ACSCEE _journal_volume 52 _journal_year 1996 _journal_page_first 1336 _journal_page_last 1338 _cell_length_a 12.214(3) _cell_length_b 3.0371(9) _cell_length_c 5.7981(9) _cell_angle_alpha 90 _cell_angle_beta 103.83(2) _cell_angle_gamma 90 _cell_volume 208.8 _cell_formula_units_Z 4 _symmetry_space_group_name_H-M 'C 1 2/m 1' _symmetry_Int_Tables_number 12 _symmetry_cell_setting monoclinic loop_ _symmetry_equiv_pos_as_xyz 'x,y,z' 'x,-y,z' '-x,-y,-z' '-x,y,-z' '1/2+x,1/2+y,z' '1/2+x,1/2-y,z' '1/2-x,1/2-y,-z' '1/2-x,1/2+y,-z' loop_ _atom_type_symbol _atom_type_oxidation_number Ga3+ 3.000 O2- -2.000 loop_ _atom_site_label _atom_site_type_symbol _atom_site_symmetry_multiplicity _atom_site_Wyckoff_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy _atom_site_attached_hydrogens _atom_site_calc_flag Ga1 Ga3+ 4 i 0.09050(2) 0. 0.79460(5) 1. 0 d Ga2 Ga3+ 4 i 0.15866(2) 0.5 0.31402(5) 1. 0 d O1 O2- 4 i 0.1645(2) 0. 0.1098(3) 1. 0 d O2 O2- 4 i 0.1733(2) 0. 0.5632(4) 1. 0 d O3 O2- 4 i -0.0041(2) 0.5 0.2566(3) 1. 0 d _refine_ls_R_factor_all 0.022

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Re: [Ifeffit] Atoms error message
by Bruce Ravel 08 Mar '07

08 Mar '07

On Wednesday 07 March 2007 08:58, Øystein Prytz wrote: > Hello! > > I recently installed Ifeffit on my WinXp machine in order to run the > Atoms program locally. However, when I try to run it, I get the > following error message: > > M:\>atoms > can't open \share\perl\Xray\space_groups.db: No such file or directory > at /PerlA > pp/Xray/Xtal.pm line 116 > BEGIN failed--compilation aborted at atoms line 44. > > which is weird, since there is a directory > > C:\Program Files\Ifeffit\share\perl\Xray\ > > which contains the space_groups.db file. Do you have any suggestions as > to what might be wrong? Hi Øystein, I am CCing my answer to the Ifeffit mailing list. It's not so weird. The icons and Start menu entries that Ifeffit installs do not point directly at the executables. Rather they point at BAT files that set some environment variables, then run the executables. If you want to run any of the programs from the DOS command line, you need to set those environment variables i some other way. When I build my codes, I start by running a BAT file with these lines: SET IFEFFIT_DIR=C:\Program Files\Ifeffit SET PATH=%PATH%;%IFEFFIT_DIR% SET PGPLOT_DIR=%IFEFFIT_DIR%\bin SET PGPLOT_DEV=/GW Without those set, you will not be able to run the codes successfully from the command line. > PS: it seems the WebAtoms page is malfunctioning, I get a "HTTP 500 > Internal server error". Yup. That was discssed on the Ifeffit mailing list starting here: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2007-January/002858.html and continuing as the first few messages in February: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2007-February/thread.html See the whole thread for the discussion and work-around. It seems as though the simplest work-around is to delete the stuff in the titles box. Fixing this is on my list of things to do, but it hasn't happened yet. 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/exafs/

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Re: [Ifeffit] Ifeffit on Windows Vista
by Bruce Ravel 08 Mar '07

08 Mar '07

On Monday 05 March 2007 12:28, Francesc Sepulcre wrote: > Dear Bruce, > > Is just to know if is possible to install ifeffit (Artemis, Athena,...) on > Windows Vista. If yes, please, let me know how to do this, because Im > trying to install version 1.2.9 but doesnt works. > > Please, excuse me if this is not the correct way to ask about this problem. Hi Francesc, I am forwarding my response to the Ifeffit mailing list (which is the best forum for questions of this sort.) To join, go to: http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ I am not in a position to comment. I don't have a Vista machine of my own. Nor does Matt, as far as I know. So we certainly have not yet tested the software on Vista. Is anyone on the list using Vista yet? Any hints for Francesc about getting the installer to work? Francesc, perhaps if you could give us some more information about how it fails -- screenshots, transcriptions of error messages, something that gives a clue as to what the problem is -- someone may be able to make a useful suggestion. 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/exafs/

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Using parameters in Artemis
by David Weedon 08 Mar '07

08 Mar '07

Hi All, I am new to Artemis so these questions are very basic - but never-the-less confusing to me. I learnt a lot by using Scott Calvin's ZnO example but ran into trouble when I got to Fit 3. In the Journal entry we are asked to click "Guess, Def, Set", then click "new" and enter DelScale = 0. After I hit the "Guess" button I cannot find the parameter "dr" on the list. Am I correct in assuming that "dr" is some kind of reserved parameter name that should not be used in equations? Which leads me to ask several questions (probably silly questions)??? QUESTIONS: 1 I presume all the parameters like "amp, deg, delr, ss2 and enot" relate to the obvious parameters in the EXAFS eqn. Assigning numerical values makes sense but what is going on when we create mathematical functions?? Is there a list of functions that we can model here? Is it somewhere in the software? 2 What are we doing when we make our own parameters? Are they a mixture of parameters from the EXAFS equation that we wish to evaluate in the fit, and if so why? 3 The parameter "amp" is defined as the relative importance of the path and is assigned a value eg. 100 or 30, is this some form of percentage of this path to the first (major) path? Thanks, Dave Dr Dave Weedon Research Fellow - ACeSSS, (Applied Centre for Structural and Synchrotron Studies) Division of Information Technology, Engineering and the Environment, University of South Australia, Mawson Lakes, Adelaide, South Australia, 5095 Phone: +61 8 8302 3096 Email: david.weedon(a)unisa.edu.au

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Re: [Ifeffit] Ifeffit on Windows Vista
by Bruce Ravel 07 Mar '07

07 Mar '07

On Monday 05 March 2007 12:28, Francesc Sepulcre wrote: > Dear Bruce, > > Is just to know if is possible to install ifeffit (Artemis, Athena,...) on > Windows Vista. If yes, please, let me know how to do this, because Im > trying to install version 1.2.9 but doesnt works. > > Please, excuse me if this is not the correct way to ask about this problem. Hi Francesc, I am forwarding my response to the Ifeffit mailing list (which is the best forum for questions of this sort.) To join, go to: http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ I am not in a position to comment. I don't have a Vista machine of my own. Nor does Matt, as far as I know. So we certainly have not yet tested the software on Vista. Is anyone on the list using Vista yet? Any hints for Francesc about getting the installer to work? Francesc, perhaps if you could give us some more information about how it fails -- screenshots, transcriptions of error messages, something that gives a clue as to what the problem is -- someone may be able to make a useful suggestion. 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/exafs/

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EuL3-edge-XANES (from one of Bruce's courses)
by Joel Brugger 05 Mar '07

05 Mar '07

Hi, Looking at the notes from one of Bruce Ravel¹s 2000 EXAFS courses, I noticed that you used EuTiO3 as an example. My understanding is that this is a Eu++ compound; yet the resonance peak in the XANES spectrum occurs spot on where I would expect Eu+++ to be, around 6982 eV. As the table below shows (from Rakovan, J., Newville, M., and Sutton, S. (2001) Evidence of heterovalent europium in zoned Llallagua apatite using wavelength dispersive XANES. American Mineralogist, 86, 697-700), the location of the Eu++ resonance peak does not seem to vary much from compound to compound. I¹m also joining a figure showing the XANES L3 Eu spectra of EuTiO3 together with other compounds. The Std spectra shown for comparison are for mixtures of Eu2O3, W, and WO3 cooked at 1200C in an inert atmosphere, and prepared so that sample StdB has 20% Eu++, and sample stdC 50% Eu++ (the final product is a mixture of EuWO4 and Eu2(WO4)2). The growing peak at 6974 corresponds to Eu++. Any thought about this discrepancy? Where are the data published? Thanks in advance for you help, All the best as ever, JOEL Ps I cc¹d to Bruce Ravel¹s email address as I don¹t think that the list takes attachments or embedded figures... Rakovan, J., Newville, M., and Sutton, S. (2001) Evidence of heterovalent europium in zoned Llallagua apatite using wavelength dispersive XANES. American Mineralogist, 86, 697-700.

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Re: [Ifeffit] Fwd: Re: why ss_2 is negative?
by hw26＠njit.edu 04 Mar '07

04 Mar '07

Dear all, Thanks million for your great advice for my EXAFS modeling! It helps me understand more about EXAFS and I really appreciate it! But I still have some questions to consult you. I took your suggestion and have the amp and e0 the same for each path. In addition, I fixed the number axial U-O as 2. For the equatorial ligand, since the total coordination number is between 4 and 6, I guess the number of U-F as 2(that is n1), and def the number of U-O as (5-n1)(that is n2). Then I did the fit. The result showed the ss_2 is still negative. So I set the ss_2 as 0.003, did the fitting again. I don't know if it is ok to fix the ss_2=0.003. It seems the dr_1 change a lot. In addition, I tried to do fitting in Kw=2 in stead of Kw=3. At this time, the ss_2 is positive, and from my understanding, it seems the modeling is more resonable for dr_1 and dr_2, but the R-factor is 0.023, a little bit larger than 0.02. How can I decide which one I should use, the Kw=3 or Kw=2? Is there anything I can do to improve the modeling? The attached is my modeling. I am sorry to put attachment in the email that my bother you. Best regards! Hao > Hao, > > A few more comments: > > 1. It is well advised for anyone starting to look at uranyl compounds > with XAS to read Shelly's various publications on that topic. > Geochem. Cosmo. Acta, 66(22) 3875-3891, (2002) is particularly > useful. Google scholar can help you locate more of her papers. > > 2. I am the first to admit that Artemis and Ifeffit are difficult > tools for the beginning exafs practitioner. These tools try to > provide a usable face to a difficult problem. Ifeffit was written > with enough flexibility and power to allow the so-called experts > to do the analysis they want to do. That means that Artemis has > enough freedom to allow the unsuspecting user to do ill-advised > things. > > You really need to think about what each of the parameters means. > For example, just because Artemis allows you to float e0 freely > for each path does not mean that doing so is a good idea. There > are situations where it is a very good idea to have more than one > e0 parameter in your fit, but I suspect that yours is not one of > them. Consequently, you should consider constraining all your > paths to have the same e0. > > What do I mean by "constrain"? Well, on the Guess,Def,Set page, > you can define a single e0 parameter as a guess parameter, then > use that parameter on each of the path pages. In that way, you > will have one floating parameter in your fit that is used to > describe the e0 of all your parameters. > > Similarly, you should think hard about the numbers of each kind of > path. A uranyl moiety is unlikely to have more or less than 2 > uranyl ligands. The uranyl bond is very strong, consequently it > is energetically unfavorable in a uranyl for those two bonds to be > over- or under-filled. Consequently, you can consider setting the > number of yl oxygens to 2. Furthermore, the equatorial plane is > likely to have between 4 and 6 oxygens, so you should think of > ways to constrain the total number of equatorial oxygens to be > something reasonable. Since the coordination number is highly > correlated with sigma^2 in a statistical sense, thinking well > about coordination number should help address your original > question. > > 3. Scott has made a very nice Artemis tutorial which can be found at > http://cars9.uchicago.edu/iffwiki/HoraeSoftware#contrib > It comes in the form of a series of Artemis projects. Newcomers > benefit by working through his tutorial before trying to analyse > their own data with Artemis. > > 4. The Ifeffit web site, my home page, and especialy http://xafs.org > are all filled with useful information for the XAS novice. If you > haven't already looked through the resources on those sites, you > really should budget some time to do so. > > > HTH, > 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/ > > _______________________________________________ > 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] EXAFS analysis with FEFF
by Bruce Ravel 27 Feb '07

27 Feb '07

Hi Gemma, I am not sure that I have the whole answer for you. I too have had trouble at times getting feff8 to run with hydrogen atoms in the cluster. I am CCing my response to the mailing lists for Feff and Ifeffit in hopes that someone else might have some more wisdom for you. The feff.inp file you sent me is appended to the end of this email, in case any of the brains on the mailing lists need to see it. On Tuesday 27 February 2007 11:27, Gemma GUILERA wrote: > I am currently running FEFF8.2 for one of my systems which include some H > atoms (as hydrides). These are actually very important in the structure and > I want to consider them in the run. > For this I used the FOLP function in POT with an overlapping value of 0.8 > for H as suggested in the manual. Also, since I think that the AFOLP card > gets deactivated, I also added these cards for the rest of the potentials > keeping them at 1.15. > I obviously do something completely wrong because the program stops and > appears an error message of the type: > > FOLP for POTENTIAL type 0 is too big. > Reduce overlap using FOLP and rerun. > > I do not understand what I need to do, because the potential 0 is not the > one I am modifying with respect to the default values. > I would really appreciate if you could have a look at the feff.inp file and > tell me what did I do wrongly...and sorry for wasting your time. Well, my understanding is that Feff's various overlapping methods do have effects that are not restricted to the ipots that you are explicitly modifying. That is, if you restrain the size of one muffin tin, other muffin tins can get a bit bigger or smaller to compensate. It depends on the geometry and how the atom you are modifying is represented in the cluster. My first thought is that you need to play around with the FOLP value for the absorber. Try smaller values to see if you can get Feff to run to completion. My second thought is to abandon the FOLP keywords and try using AFOLP. Another thought is that you may need to use a larger cluster. Some atom types -- B for example -- have few representatives in your cluster and so their muffin tin radii might be improperly constrained. Does anyone else have any good suggestions for Gemma? B TITLE FeBH6Fe complex 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 2.90160 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 0 0 0 FOLP 0 1.15 FOLP 1 0.8 !Use 0.8 muffin-tin radii overlapping factor for H FOLP 2 1.15 FOLP 3 1.15 FOLP 4 1.15 FOLP 5 1.15 EXAFS RPATH 6 * kmax [ delta_k delta_e ] *XANES 4.0 0.07 0.5 * r_fms [ l_fms ] *FMS 2.90160 0 * *RPATH 0.10000 * emin emax resolution *LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 26 Fe -1 -1 0 1 1 H -1 -1 6 2 5 B -1 -1 1 3 15 P -1 -1 6 4 6 C -1 -1 46 5 26 Fe -1 -1 2 ATOMS 0.00000 0.00000 0.00000 0 Fe1 0.00000 -0.71680 -1.08741 -0.20797 1 H42 1.31891 -1.33000 0.40717 0.04190 1 H41 1.39156 -0.20933 -0.03121 -1.56977 1 H40 1.58398 -1.50973 -0.47766 -1.07196 2 B1 1.91221 0.07929 -0.26849 2.16349 3 P3 2.18152 0.78129 2.03650 0.10939 3 P2 2.18397 2.03623 -0.76920 -0.20440 3 P1 2.18625 -2.30265 0.13209 -1.93594 1 H42 3.01123 -2.81012 -0.92412 -0.57414 1 H40 3.01338 -1.68946 -1.36249 -2.18581 1 H41 3.08033 3.15055 -0.21476 1.16774 4 C22 3.36686 0.19242 -2.02477 2.69082 4 C25 3.37301 2.87884 -0.31857 -1.75462 4 C13 3.38643 1.52559 0.58481 2.96848 4 C24 3.38840 2.32803 2.20201 1.14003 4 C49 3.40121 -0.35734 3.30346 0.81773 4 C37 3.42188 1.28771 2.89227 -1.43362 4 C43 3.47544 2.68114 0.97735 2.02827 4 C23 3.50109 -1.29194 0.30124 3.24246 4 C31 3.50334 2.42741 -2.57443 -0.17395 4 C1 3.54263 1.08472 2.33572 -2.68697 4 C48 3.72183 -2.31005 1.13130 2.75352 4 C36 3.76803 -3.01946 -0.95533 -2.14391 5 Fe1 3.82441 -0.91239 -2.83347 2.42108 4 C26 3.83701 1.44841 -3.56032 -0.07829 4 C3 3.84446 2.35340 -0.84952 -2.93358 4 C15 3.85565 -1.36594 3.79736 -0.00896 4 C38 4.03557 -0.32880 3.71800 2.14367 4 C42 4.30429 1.32048 -2.62656 3.24943 4 C30 4.38193 3.96885 0.55229 -1.84177 4 C21 4.41009 1.89033 4.15594 -1.34798 4 C44 4.76049 -1.27608 0.01031 4.60350 4 C32 4.77710 3.77855 -2.96794 -0.18652 4 C11 4.80842 3.85573 1.40280 2.91662 4 C50 5.03400 -4.10418 -3.29104 0.54306 4 C48 5.28868 -3.80075 -2.99182 -2.25330 3 P2 5.33611 -3.09875 -0.68684 -4.30740 3 P3 5.35048 -2.10707 1.87815 -4.56499 4 C26 5.36715 -0.70940 -2.08663 -4.89743 4 C36 5.37049 -5.05569 -0.18613 -1.93951 3 P1 5.41815 -5.37286 -0.10580 0.78966 4 C15 5.43161 -1.65351 -4.75268 -2.13495 4 C38 5.46627 -4.46787 2.60499 -2.06562 4 C3 5.56908 -1.72752 -1.25656 -5.38637 4 C31 5.79450 -4.30717 -3.84760 -0.71029 4 C43 5.81895 -2.66211 -4.25879 -2.96164 4 C37 5.83056 -3.21187 1.06944 -4.83473 4 C25 5.90207 -5.89830 -0.63676 -0.38929 4 C13 5.94533 END -- 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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Re: [Ifeffit] Ifeffit Digest, Vol 48, Issue 14
by Roque, J (Josep) 27 Feb '07

27 Feb '07

The statement "Feff 6.02L doesn't work" is false also in Josep's computer. It works correctly.. Thanks. J. -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 26 February 2007 18:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 48, Issue 14 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: E0 for bulk crystals and nanoparticles (Leandro Araujo) 2. Fwd: Re: E0 for bulk crystals and nanoparticles (Bruce Ravel) 3. FEFF 6L.02 (Roque, J (Josep)) 4. Re: FEFF 6L.02 (Bruce Ravel) 5. Re: FEFF 6L.02 (Anatoly Frenkel) ---------------------------------------------------------------------- Message: 1 Date: Mon, 26 Feb 2007 14:52:10 +1100 From: "Leandro Araujo" <leandrolangie(a)gmail.com> Subject: Re: [Ifeffit] E0 for bulk crystals and nanoparticles To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <5f59b3760702251952y535fae5axb9fd91d63789564f(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anatoly and Scott, thanks for the quick and valuable answers! Sorry I didn't specify the system in more detail; this is a point that Matt always stresses when replying messages in this list (i.e., there is no "one fits all" answer, so a detailed description of the system is needed) and by now I should have assimilated it already... Anyway, I see no changes whatsoever in the XANES spectra of the T-dep measurements, so I think it will be worth the try. Since I'm dealing with Ge NCs buried about 1micron deep into a SiO2 matrix, I reckon effects like hydrogen chemisorption, charge exchange with support, ligand desorption and oxidation will not take place, specially at such low T's. Thanks once more for the help, Leandro ------------------------------ Message: 2 Date: Mon, 26 Feb 2007 09:04:16 -0600 From: Bruce Ravel <bravel(a)anl.gov> Subject: [Ifeffit] Fwd: Re: E0 for bulk crystals and nanoparticles To: XAFS Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200702260904.16718.bravel(a)anl.gov> Content-Type: Text/Plain; charset="iso-8859-15" On Sunday 25 February 2007 20:44, Leandro Araujo wrote: > I don't know if it is just me, but in my short time working with EXAFS > I got the strong impression that it is very easy to fall into the > temptation of sophistry to get to the "expected" results from a fit. That is very well put. I hope everyone reading the list today appreciates your wise words. > In this respect, I consider the mailing list an invaluable resource to > help overcoming such a temptation. That's great -- thanks. Kind words go a long way with those of us who invest time on the mailing list. As for your question -- I really liked Scott's point about looking at the XANES as a clue about whether e0 should be changing in the EXAFS. Use all the information (spectroscopic or otherwise) available to you. 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/exafs/ ------------------------------ Message: 3 Date: Mon, 26 Feb 2007 16:29:49 -0000 From: "Roque, J $Josep$" <josep.roque(a)diamond.ac.uk> Subject: [Ifeffit] FEFF 6L.02 To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <DC69C90BD4A39249BF59689B2E06427803B04E42(a)exchange33.fed.cclrc.ac.uk> Content-Type: text/plain; charset="us-ascii" I am trying to run FEFF 6L.02 from version of IFEFFIT 1.2.9 on a Windows platform but it doesn't seems to work.. How can I fix this problem?? Cheers Dr Josep Roque Post Doctoral Research Associate: Microfocus Spectroscopy (I18) Diamond Light Source Ltd Diamond House Chilton Didcot Oxfordshire OX11 0DE Tel: 01235 778735 Email: josep.roque(a)diamond.ac.uk

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FEFF 6L.02
by Roque, J (Josep) 26 Feb '07

26 Feb '07

I am trying to run FEFF 6L.02 from version of IFEFFIT 1.2.9 on a Windows platform but it doesn't seems to work.. How can I fix this problem?? Cheers Dr Josep Roque Post Doctoral Research Associate: Microfocus Spectroscopy (I18) Diamond Light Source Ltd Diamond House Chilton Didcot Oxfordshire OX11 0DE Tel: 01235 778735 Email: josep.roque(a)diamond.ac.uk

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