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Re: [Ifeffit] third cumulant and radial distribution function
by Matt Newville 14 Jul '08

14 Jul '08

Hi Chiara, On Sat, Jul 12, 2008 at 2:58 PM, chiara maurizio <maurizio(a)esrf.fr> wrote: > matt, > > I have a problem with an exafs analysis: > from the exafs analysis (with feffit2.98) of the first shell of a disordered > system > I get the first three cumulants. > now, I wander how can reconstruct from them the radial distribution function > which is the best solution? I have tried with the skew-normal distribution, > but for the high skewness (ratio of third cumulant to sigma3) > values I get - that is around 2.5 - it is not well defined. > Do you have a suggestion? > Thanks, Hmm, you mean you get a number for "third" that is 2.5 times the number for "sigma2"? That seems huge. I think that may mean that the pair distribution function is so skewed that the cumulant expansion out to third order may not be complete enough to be useful (some say at this point that the cumulant expansion "breaks down", but as it is a simple measure of the moments of a distribution, it seems to me that it is always valid, but not necessarily useful). When the higher order cumulants become large, a histogram approach might be more meaningful. To do this, you can make a series of paths at 0.1Ang spacing (as an example), around your expected bond length, assign each of them a sigma2 value (perhaps a variable that is constrained for all paths to be the same) and a relative amplitude for each path that follows some arbitrary distribution function. Then you can have the fitting adjust the amplitude parameters for the distribution function. In this way, nearly arbitrary distribution functions can be modeled, though with some effort. Is that a reasonable approach for your situation? If not, can you give some more details for this system? --Matt

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The question about ELNES simulation for alumina
by GFE 14 Jul '08

14 Jul '08

Hi all users, I am one of FEFF8 users and calculating ELNES Al-L3 edges for gamma-alumina. Upon calculating ELNES I have problems, since two different crystallographic sites exist in the structure and contain vacancies with respect to SOF values. As I read the article about vacancies here, at first I transformed coordinations of atoms in P1 group and removed atoms with respect to the SOF value. Then I generated input files and simulated ELNES for two different crystallographic sites. But here I am not sure if I should just average two spectra or use proper weighting factor(maybe Wyckhoff number?). Because I can not easily get the reference spectra, it is not easy to decide it with appropriate reasons. I attach my input file. If anyone can help me, please give me advices. * This feff8 input file was generated by Artemis 0.8.011 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE Alumina TITLE Aluminium Oxide (2.67/4) - Gamma TITLE (Al2 O3)1.333 TITLE Al2.666 O3.999 TITLE Gutierrez, G.;Taga, A.;Johansson, B. TITLE Physical Review, Serie 3. B - Condensed Matter (18,1978-) TITLE Theoretical structure determination of gamma-(Al2 O3) * Al L3 edge energy = 72.50 eV EDGE L3 S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 1 1 1 1 1 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 0 0.4 *** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 4.0 ELNES 5.0 0.05 0.05 # calculate elnes. 200 1 0 # beam energy in keV 2 0.0 # collection semiangle, convergence semiangle (in mrad) 50 3 # q-integration mesh : radial size, angular size 0.0 0.0 # position of the detector (x,y angle in mrad) *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 5.5 0 *** for EXAFS: RMAX 6.0 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 13 Al 3 3 0.01 1 13 Al 3 3 1.99 2 8 O 2 2 3 ATOMS * this list contains 107 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Al1_1 0.00000 0 1.02531 1.02531 1.02531 2 O1_1 1.77589 1 -1.02531 -1.02531 1.02531 2 O1_7 1.77589 2 -1.02531 1.02531 -1.02531 2 O1_10 1.77589 3 1.02531 -1.02531 -1.02531 2 O1_16 1.77589 4 2.95763 0.98587 0.98587 1 Al2_15 3.26978 5 0.98587 2.95763 0.98587 1 Al2_12 3.26978 6 -2.95763 -0.98587 0.98587 1 Al2_9 3.26978 7 -0.98587 -2.95763 0.98587 1 Al2_14 3.26978 8 -0.98587 -0.98587 2.95763 1 Al2_4 3.26978 9 -2.95763 0.98587 -0.98587 1 Al2_8 3.26978 10 2.95763 -0.98587 -0.98587 1 Al2_2 3.26978 11 0.98587 -2.95763 -0.98587 1 Al2_5 3.26978 12 -0.98587 0.98587 -2.95763 1 Al2_13 3.26978 13 -2.99706 0.94644 0.94644 2 O1_22 3.28236 14 -0.94644 2.99706 0.94644 2 O1_17 3.28236 15 2.99706 -0.94644 0.94644 2 O1_20 3.28236 16 0.94644 -2.99706 0.94644 2 O1_23 3.28236 17 -0.94644 0.94644 2.99706 2 O1_27 3.28236 18 0.94644 -0.94644 2.99706 2 O1_29 3.28236 19 2.99706 0.94644 -0.94644 2 O1_25 3.28236 20 0.94644 2.99706 -0.94644 2 O1_30 3.28236 21 -2.99706 -0.94644 -0.94644 2 O1_31 3.28236 22 -0.94644 -2.99706 -0.94644 2 O1_28 3.28236 23 0.94644 0.94644 -2.99706 2 O1_24 3.28236 24 -0.94644 -0.94644 -2.99706 2 O1_18 3.28236 25 -1.97175 1.97175 1.97175 1 Al1_5 3.41517 26 1.97175 -1.97175 1.97175 1 Al1_8 3.41517 27 1.97175 1.97175 -1.97175 1 Al1_7 3.41517 28 -1.97175 -1.97175 -1.97175 1 Al1_6 3.41517 29 2.91819 2.91819 1.02531 2 O1_6 4.25240 30 -2.91819 -2.91819 1.02531 2 O1_4 4.25240 31 2.91819 1.02531 2.91819 2 O1_12 4.25240 32 1.02531 2.91819 2.91819 2 O1_15 4.25240 33 -2.91819 -1.02531 2.91819 2 O1_14 4.25240 34 -1.02531 -2.91819 2.91819 2 O1_9 4.25240 35 -2.91819 2.91819 -1.02531 2 O1_13 4.25240 36 2.91819 -2.91819 -1.02531 2 O1_11 4.25240 37 -2.91819 1.02531 -2.91819 2 O1_3 4.25240 38 -1.02531 2.91819 -2.91819 2 O1_8 4.25240 39 2.91819 -1.02531 -2.91819 2 O1_5 4.25240 40 1.02531 -2.91819 -2.91819 2 O1_2 4.25240 41 4.88994 0.94644 0.94644 2 O1_22 5.06981 42 0.94644 4.88994 0.94644 2 O1_23 5.06981 43 -4.88994 -0.94644 0.94644 2 O1_20 5.06981 44 -0.94644 -4.88994 0.94644 2 O1_17 5.06981 45 0.94644 0.94644 4.88994 2 O1_24 5.06981 46 -0.94644 -0.94644 4.88994 2 O1_18 5.06981 47 -4.88994 0.94644 -0.94644 2 O1_25 5.06981 48 -0.94644 4.88994 -0.94644 2 O1_28 5.06981 49 4.88994 -0.94644 -0.94644 2 O1_31 5.06981 50 0.94644 -4.88994 -0.94644 2 O1_30 5.06981 51 -0.94644 0.94644 -4.88994 2 O1_27 5.06981 52 0.94644 -0.94644 -4.88994 2 O1_29 5.06981 53 -4.92938 0.98587 0.98587 1 Al2_15 5.12276 54 -0.98587 4.92938 0.98587 1 Al2_14 5.12276 55 4.92938 -0.98587 0.98587 1 Al2_9 5.12276 56 0.98587 -4.92938 0.98587 1 Al2_12 5.12276 57 2.95763 2.95763 2.95763 1 Al2_1 5.12277 58 -2.95763 -2.95763 2.95763 1 Al2_7 5.12277 59 -0.98587 0.98587 4.92938 1 Al2_13 5.12276 60 4.92938 0.98587 -0.98587 1 Al2_8 5.12276 61 0.98587 4.92938 -0.98587 1 Al2_5 5.12276 62 -4.92938 -0.98587 -0.98587 1 Al2_2 5.12276 63 -2.95763 2.95763 -2.95763 1 Al2_10 5.12277 64 2.95763 -2.95763 -2.95763 1 Al2_16 5.12277 65 -0.98587 -0.98587 -4.92938 1 Al2_4 5.12276 66 -2.99706 2.99706 2.99706 2 O1_32 5.19106 67 2.99706 -2.99706 2.99706 2 O1_26 5.19106 68 2.99706 2.99706 -2.99706 2 O1_19 5.19106 69 -2.99706 -2.99706 -2.99706 2 O1_21 5.19106 70 3.94350 3.94350 0.00000 1 Al1_4 5.57695 71 -3.94350 3.94350 0.00000 1 Al1_4 5.57695 72 3.94350 -3.94350 0.00000 1 Al1_4 5.57695 73 -3.94350 -3.94350 0.00000 1 Al1_4 5.57695 74 3.94350 0.00000 3.94350 1 Al1_3 5.57695 75 -3.94350 0.00000 3.94350 1 Al1_3 5.57695 76 0.00000 3.94350 3.94350 1 Al1_2 5.57695 77 0.00000 -3.94350 3.94350 1 Al1_2 5.57695 78 3.94350 0.00000 -3.94350 1 Al1_3 5.57695 79 -3.94350 0.00000 -3.94350 1 Al1_3 5.57695 80 0.00000 3.94350 -3.94350 1 Al1_2 5.57695 81 0.00000 -3.94350 -3.94350 1 Al1_2 5.57695 82 -4.96881 2.91819 1.02531 2 O1_6 5.85288 83 -2.91819 4.96881 1.02531 2 O1_4 5.85288 84 4.96881 -2.91819 1.02531 2 O1_4 5.85288 85 2.91819 -4.96881 1.02531 2 O1_6 5.85288 86 -4.96881 1.02531 2.91819 2 O1_12 5.85288 87 -1.02531 4.96881 2.91819 2 O1_9 5.85288 88 4.96881 -1.02531 2.91819 2 O1_14 5.85288 89 1.02531 -4.96881 2.91819 2 O1_15 5.85288 90 -2.91819 1.02531 4.96881 2 O1_3 5.85288 91 -1.02531 2.91819 4.96881 2 O1_8 5.85288 92 2.91819 -1.02531 4.96881 2 O1_5 5.85288 93 1.02531 -2.91819 4.96881 2 O1_2 5.85288 94 4.96881 2.91819 -1.02531 2 O1_13 5.85288 95 2.91819 4.96881 -1.02531 2 O1_11 5.85288 96 -4.96881 -2.91819 -1.02531 2 O1_11 5.85288 97 -2.91819 -4.96881 -1.02531 2 O1_13 5.85288 98 4.96881 1.02531 -2.91819 2 O1_3 5.85288 99 1.02531 4.96881 -2.91819 2 O1_2 5.85288 100 -4.96881 -1.02531 -2.91819 2 O1_5 5.85288 101 -1.02531 -4.96881 -2.91819 2 O1_8 5.85288 102 2.91819 1.02531 -4.96881 2 O1_12 5.85288 103 1.02531 2.91819 -4.96881 2 O1_15 5.85288 104 -2.91819 -1.02531 -4.96881 2 O1_14 5.85288 105 -1.02531 -2.91819 -4.96881 2 O1_9 5.85288 106 END * This feff8 input file was generated by Artemis 0.8.011 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE Alumina TITLE Aluminium Oxide (2.67/4) - Gamma TITLE (Al2 O3)1.333 TITLE Al2.666 O3.999 TITLE Gutierrez, G.;Taga, A.;Johansson, B. TITLE Physical Review, Serie 3. B - Condensed Matter (18,1978-) TITLE Theoretical structure determination of gamma-(Al2 O3) * Al L3 edge energy = 72.50 eV EDGE L3 S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 1 1 1 1 1 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 0 0.4 *** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 4.0 ELNES 5.0 0.05 0.05 # calculate elnes. 200 1 0 # beam energy in keV 2 0.0 # collection semiangle, convergence semiangle (in mrad) 50 3 # q-integration mesh : radial size, angular size 0.0 0.0 # position of the detector (x,y angle in mrad) *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 5.5 0 *** Energy grid over which to calculate *** DOS functions *** for EXAFS: RMAX 6.0 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 13 Al 3 3 0.01 1 13 Al 3 3 1.99 2 8 O 2 2 3 ATOMS * this list contains 106 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Al2_1 0.00000 0 1.93232 0.03943 0.03943 2 O1_32 1.93312 1 0.03943 1.93232 0.03943 2 O1_26 1.93312 2 0.03943 0.03943 1.93232 2 O1_19 1.93312 3 -1.93232 -0.03943 -0.03943 2 O1_15 1.93312 4 -0.03943 -1.93232 -0.03943 2 O1_12 1.93312 5 -0.03943 -0.03943 -1.93232 2 O1_6 1.93312 6 1.97175 1.97175 0.00000 1 Al2_7 2.78848 7 1.97175 0.00000 1.97175 1 Al2_10 2.78848 8 0.00000 1.97175 1.97175 1 Al2_16 2.78848 9 -1.97175 0.00000 -1.97175 1 Al2_12 2.78848 10 0.00000 -1.97175 -1.97175 1 Al2_15 2.78848 11 -2.95763 0.98587 0.98587 1 Al1_2 3.26978 12 0.98587 -2.95763 0.98587 1 Al1_3 3.26978 13 -0.98587 -0.98587 2.95763 1 Al1_7 3.26978 14 -0.98587 2.95763 -0.98587 1 Al1_8 3.26978 15 2.95763 -0.98587 -0.98587 1 Al1_5 3.26978 16 0.98587 0.98587 -2.95763 1 Al1_4 3.26978 17 1.93232 1.93232 1.93232 2 O1_21 3.34688 18 -1.93232 -1.93232 -1.93232 2 O1_1 3.34688 19 -2.01119 -2.01119 1.93232 2 O1_24 3.43855 20 -1.93232 2.01119 2.01119 2 O1_2 3.43855 21 2.01119 -1.93232 2.01119 2 O1_3 3.43855 22 2.01119 2.01119 -1.93232 2 O1_4 3.43855 23 -2.01119 1.93232 -2.01119 2 O1_23 3.43855 24 1.93232 -2.01119 -2.01119 2 O1_22 3.43855 25 -3.90407 -2.01119 0.03943 2 O1_27 4.39183 26 -2.01119 -3.90407 0.03943 2 O1_29 4.39183 27 -0.03943 3.90407 2.01119 2 O1_5 4.39183 28 3.90407 -0.03943 2.01119 2 O1_8 4.39183 29 -0.03943 2.01119 3.90407 2 O1_11 4.39183 30 2.01119 -0.03943 3.90407 2 O1_13 4.39183 31 3.90407 2.01119 -0.03943 2 O1_9 4.39183 32 2.01119 3.90407 -0.03943 2 O1_14 4.39183 33 -3.90407 0.03943 -2.01119 2 O1_17 4.39183 34 0.03943 -3.90407 -2.01119 2 O1_20 4.39183 35 -2.01119 0.03943 -3.90407 2 O1_30 4.39183 36 0.03943 -2.01119 -3.90407 2 O1_25 4.39183 37 -2.01119 3.98293 0.03943 2 O1_29 4.46208 38 3.98293 -2.01119 0.03943 2 O1_27 4.46208 39 -3.98293 -0.03943 2.01119 2 O1_8 4.46208 40 -0.03943 -3.98293 2.01119 2 O1_5 4.46208 41 -2.01119 0.03943 3.98293 2 O1_30 4.46208 42 0.03943 -2.01119 3.98293 2 O1_25 4.46208 43 -3.98293 2.01119 -0.03943 2 O1_9 4.46208 44 2.01119 -3.98293 -0.03943 2 O1_14 4.46208 45 3.98293 0.03943 -2.01119 2 O1_17 4.46208 46 0.03943 3.98293 -2.01119 2 O1_20 4.46208 47 -0.03943 2.01119 -3.98293 2 O1_11 4.46208 48 2.01119 -0.03943 -3.98293 2 O1_13 4.46208 49 3.94350 -1.97175 1.97175 1 Al2_13 4.82978 50 -3.94350 -1.97175 1.97175 1 Al2_13 4.82978 51 -1.97175 1.97175 3.94350 1 Al2_5 4.82978 52 1.97175 -1.97175 3.94350 1 Al2_8 4.82978 53 3.94350 1.97175 -1.97175 1 Al2_14 4.82978 54 -3.94350 1.97175 -1.97175 1 Al2_14 4.82978 55 1.97175 3.94350 -1.97175 1 Al2_9 4.82978 56 1.97175 -3.94350 -1.97175 1 Al2_9 4.82978 57 -1.97175 1.97175 -3.94350 1 Al2_5 4.82978 58 1.97175 -1.97175 -3.94350 1 Al2_8 4.82978 59 4.92938 0.98587 0.98587 1 Al1_2 5.12276 60 0.98587 4.92938 0.98587 1 Al1_3 5.12276 61 2.95763 2.95763 2.95763 1 Al1_6 5.12277 62 0.98587 0.98587 4.92938 1 Al1_4 5.12276 63 -4.92938 -0.98587 -0.98587 1 Al1_5 5.12276 64 -0.98587 -4.92938 -0.98587 1 Al1_8 5.12276 65 -2.95763 -2.95763 -2.95763 1 Al1_1 5.12277 66 -0.98587 -0.98587 -4.92938 1 Al1_7 5.12276 67 3.94350 3.94350 0.00000 1 Al2_4 5.57695 68 -3.94350 3.94350 0.00000 1 Al2_4 5.57695 69 3.94350 -3.94350 0.00000 1 Al2_4 5.57695 70 -3.94350 -3.94350 0.00000 1 Al2_4 5.57695 71 0.00000 3.94350 3.94350 1 Al2_2 5.57695 72 0.00000 -3.94350 3.94350 1 Al2_2 5.57695 73 0.00000 3.94350 -3.94350 1 Al2_2 5.57695 74 0.00000 -3.94350 -3.94350 1 Al2_2 5.57695 75 -3.90407 -3.90407 1.93232 2 O1_18 5.84956 76 -1.93232 3.90407 3.90407 2 O1_16 5.84956 77 3.90407 -1.93232 3.90407 2 O1_10 5.84956 78 3.90407 3.90407 -1.93232 2 O1_7 5.84956 79 -3.90407 1.93232 -3.90407 2 O1_28 5.84956 80 1.93232 -3.90407 -3.90407 2 O1_31 5.84956 81 -3.90407 3.98293 1.93232 2 O1_18 5.90249 82 3.98293 -3.90407 1.93232 2 O1_18 5.90249 83 -3.98293 -1.93232 3.90407 2 O1_10 5.90249 84 -1.93232 -3.98293 3.90407 2 O1_16 5.90249 85 -3.90407 1.93232 3.98293 2 O1_28 5.90249 86 1.93232 -3.90407 3.98293 2 O1_31 5.90249 87 -3.98293 3.90407 -1.93232 2 O1_7 5.90249 88 3.90407 -3.98293 -1.93232 2 O1_7 5.90249 89 3.98293 1.93232 -3.90407 2 O1_28 5.90249 90 1.93232 3.98293 -3.90407 2 O1_31 5.90249 91 -1.93232 3.90407 -3.98293 2 O1_16 5.90249 92 3.90407 -1.93232 -3.98293 2 O1_10 5.90249 93 -5.95468 0.03943 0.03943 2 O1_32 5.95494 94 0.03943 -5.95468 0.03943 2 O1_26 5.95494 95 3.98293 3.98293 1.93232 2 O1_18 5.95494 96 3.98293 1.93232 3.98293 2 O1_28 5.95494 97 1.93232 3.98293 3.98293 2 O1_31 5.95494 98 -0.03943 -0.03943 5.95468 2 O1_6 5.95494 99 -0.03943 5.95468 -0.03943 2 O1_12 5.95494 100 5.95468 -0.03943 -0.03943 2 O1_15 5.95494 101 -3.98293 -3.98293 -1.93232 2 O1_7 5.95494 102 -3.98293 -1.93232 -3.98293 2 O1_10 5.95494 103 -1.93232 -3.98293 -3.98293 2 O1_16 5.95494 104 0.03943 0.03943 -5.95468 2 O1_19 5.95494 105 END

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Re: [Ifeffit] Pre-edge reproduction in FEFF8
by joshua jason kas 10 Jul '08

10 Jul '08

Hi Janine, I think there could be two issues here, 1) The feff fermi level is not highly accurate, so you should set it using the output of your DFT calculation. This can be done by setting the vr argument to the EXCHANGE card in feff. Note that a positive value of vr shifts the fermi level by -vr. 2) A second pre-edge peak shows up if you use a slightly distorted geometry, which suggests that vibrational distortion will have an effect due to symmetry breaking. Note that the second peak does not appear in the spectrum unless the fermi level is shifted down by about an eV, so maybe extra peaks in the other systems are getting cut off due to an overestimated fermi level. Cheers, Josh Kas On Wed, 9 Jul 2008, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > 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. Pre-edge reproduction in FEFF8 for Cobalt molecules > (Janine GRATTAGE) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 09 Jul 2008 15:07:56 +0200 > From: Janine GRATTAGE <janine.grattage(a)esrf.fr> > Subject: [Ifeffit] Pre-edge reproduction in FEFF8 for Cobalt molecules > To: Ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <4874B82C.5040607(a)esrf.fr> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I am studying the K edge XANES of a series of cobalt containing > molecules and I am having trouble reproducing the pre-edge features > using FEFF8.4. For all three "acac" molecules I studied (which have > different acetylacetonate ligand arrangements on the Co atom), the > experimental pre-edges show two or three features of varying > intensities, but the FEFF calculated pre-edge is identical for each > molecule. I have tried for one of the molecules, Co(acac)2, to use both > the dipole contribution only, and both the dipolar and quadrupole > components in the calculations, by using the card MULTIPOLE 0 and > MULTIPOLE 2 - two figures are attached. > > For the input file (attached also) the atomic coordinates were > calculated by using a density functional theory minimised molecular > geometry using ADF. Any suggestions as to how to improve the pre-edges > (i.e. show more than one feature, and vary for the different molecules) > would be welcome! > > Thank you in advance, > > Dr. Janine Grattage > Postdoc, ESRF. >

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linear combination fitting
by heavy Deez 10 Jul '08

10 Jul '08

Hi All I have a metal that (i think) has two briding oxo ligands. When I add an lewis acid it looks as though some fraction of the bridging oxo ligands are accepting the acid. Using artemis (I'm using the windows version) can I have two models (A: a metal with two briding oxos and B: a metal with one oxygen path and one lewis acid path) and try to fit a combination of those two models to the data? Dave

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Pre-edge reproduction in FEFF8 for Cobalt molecules
by Janine GRATTAGE 09 Jul '08

09 Jul '08

Dear all, I am studying the K edge XANES of a series of cobalt containing molecules and I am having trouble reproducing the pre-edge features using FEFF8.4. For all three "acac" molecules I studied (which have different acetylacetonate ligand arrangements on the Co atom), the experimental pre-edges show two or three features of varying intensities, but the FEFF calculated pre-edge is identical for each molecule. I have tried for one of the molecules, Co(acac)2, to use both the dipole contribution only, and both the dipolar and quadrupole components in the calculations, by using the card MULTIPOLE 0 and MULTIPOLE 2 - two figures are attached. For the input file (attached also) the atomic coordinates were calculated by using a density functional theory minimised molecular geometry using ADF. Any suggestions as to how to improve the pre-edges (i.e. show more than one feature, and vary for the different molecules) would be welcome! Thank you in advance, Dr. Janine Grattage Postdoc, ESRF. TITLE Co(acac)2 molecule (positions calculated from ADF) CONTROL 1 1 1 1 1 1 PRINT 5 0 0 0 0 0 FMS 8.0 1 MULTIPOLE 2 *Dipole and quadrupole EXCHANGE 0 SCF 4 XANES 6.0 0.05 0.2 AFOLP 1.2 CRITERION 0 0 RPATH 0.1 POTENTIALS *absorbing atom is the Co *ipot z tag 0 27 Co 1 6 C 2 8 O 3 1 H * emin emax eimag LDOS -20 20 0.2 ATOMS *xmod ymod zmod ipot 0 0 0 0 1.215218816280 -0.309100252578 -1.431324718 2 -0.217607039789 -1.897944380700 -0.005357055 2 -1.228393340190 0.284283035201 1.425208450 2 0.217607039789 1.897944380700 -0.005357055 2 1.228393340190 -0.284283035201 1.425208450 2 -1.215218816280 0.309100252578 -1.431324718 2 2.461554037210 -0.585442644025 1.249179175 1 2.449973875140 -0.607258629432 -1.261471366 1 3.077724186530 -0.747390649788 -0.007702405 1 -2.449973875140 0.607258629432 -1.261471366 1 -2.461554037210 0.585442644025 1.249179175 1 -3.077724186530 0.747390649788 -0.007702405 1 -3.333677165250 0.784913309065 2.503472842 1 -3.310505519850 0.828566491764 -2.520100777 1 3.310505519850 -0.828566491764 -2.520100777 1 3.333677165250 -0.784913309065 2.503472842 1 0.744861056140 2.158346265240 -0.765559633 3 4.127503029710 -1.002325583410 -0.010329201 3 -4.127503029710 1.002325583410 -0.010329201 3 -2.732128568660 0.630329148613 3.388286366 3 -4.148148502600 0.074161680964 2.492221519 3 -3.731734858880 1.789989812830 2.508888827 3 -2.700857258570 0.689131080622 -3.401882342 3 -3.708408276140 1.833684861860 -2.511824379 3 -4.125108300580 0.117927411672 -2.528611312 3 4.125108300580 -0.117927411672 -2.528611312 3 2.700857258570 -0.689131080622 -3.401882324 3 3.708408276140 -1.833684861860 -2.511824379 3 3.731734858880 -1.789989812830 2.508888827 3 2.732128568660 -0.630329148613 3.388286366 3 4.148148502600 -0.074161680964 2.492221519 3 0.658191656841 2.172714999380 0.803408304 3 -0.658191656841 -2.172714999380 0.803408304 3 -0.744861056140 -2.158346265240 -0.765559633 3 END

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Questions on EXAFS
by Rajasekaran S 08 Jul '08

08 Jul '08

I have a couple of questions on the use of EXAFS: 1. How sensitive is EXAFS/XANES in determining ~ couple of ppm (up to 100ppm) of halogen content in solid content? 2. Also, are there lab-scale EXAFS/XANES equipments available towards this? Anyone working on lab-scale equipments? Thanks Raja

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reply to: RMULTIPLIER-Card (edge shifts/bond lengths)
by grant bunker 05 Jul '08

05 Jul '08

RE the effect of bond length on edges: this physical effect is normal and has been known for many decades. Although the XANES is a composite of mu_zero, single scattering, and multiple scattering, there is an underlying simple effect of bond length. Broad features on K-edges (which are dominated by mu_zero and single scattering) shift approximately as delta E ~ k^2 ~ 1/r^2, where r is the average nearest neighbor bond length, simply from the phase advance in the single scattering component. The phases of the higher frequency oscillations from multiple scattering advance more rapidly when the bond length is increased. L edges are a bit different because there are often bound states near the fermi level that have to be accounted for. I studied this in my thesis quite a while ago (gb thesis 1984) in the pre-FEFF era. Theoretically, by freezing the charge densities of the atoms, changing the bond lengths (and other geometrical parameters), and then calculating the XANES in both single scattering and multiple scattering approximations shows that it is primarily a geometrical effect, for the reason I outlined above. It also is in accord with experiment as I showed with Mn oxides. A basic introduction can be found here: http://gbxafs.iit.edu/training/XANES_intro.pdf grant bunker On Jun 23, 2008, at 9:34 AM, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > 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. RMULTIPLIER-Card (s440697(a)stud.uni-goettingen.de) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 23 Jun 2008 16:33:50 +0200 (CEST) > From: s440697(a)stud.uni-goettingen.de > Subject: [Ifeffit] RMULTIPLIER-Card > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <53054.134.76.41.165.1214231630.squirrel(a)webmail.stud.uni-goettingen.de > > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > I have a question concerning the RMULTIPLIER-Card in XANES- > Calculations. I > made some calculations with different rmult values (1.00, 1.01, 1.05, > 1.10) and found a shift of the absorption-edge or rather the slope > of the > peak. I attached the diagram of this calculation (Sulfur-K-edge of > gypsum). > > My question is, what could be a physical reason for this behaviour? > With > this Parameter one change the interatomic disctances. Hence the > interference phenomena and the curve progression should be change, > too. Is > this right? > > > > Thanks for your help. > > Have a nice day, > Eckhard > > PS: the same behaviour occurs in a inverse sense for rmult < 1 > > --------------------------------- > Eckhard Bosman > e.bosman(a)stud.uni-goettingen.de > +49 (0)551-39-14441 > Raum: E0.104 > Institut f?r R?ntgenphysik > Friedrich-Hund-Platz 1 > 37077 G?ttingen > Germany >

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Re: [Ifeffit] Ifeffit Digest, Vol 64, Issue 12
by joshua jason kas 23 Jun '08

23 Jun '08

Hi Eckhard, You are right that the curves change because of quantum interference due to scattering of the photoelectron with it's neighbors. Also the edge can shift because you are performing an expansion of the system which will change the potentials, DOS, and fermi level. Cheers, Josh Kas On Mon, 23 Jun 2008, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > 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. RMULTIPLIER-Card (s440697(a)stud.uni-goettingen.de) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 23 Jun 2008 16:33:50 +0200 (CEST) > From: s440697(a)stud.uni-goettingen.de > Subject: [Ifeffit] RMULTIPLIER-Card > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <53054.134.76.41.165.1214231630.squirrel(a)webmail.stud.uni-goettingen.de> > > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > I have a question concerning the RMULTIPLIER-Card in XANES-Calculations. I > made some calculations with different rmult values (1.00, 1.01, 1.05, > 1.10) and found a shift of the absorption-edge or rather the slope of the > peak. I attached the diagram of this calculation (Sulfur-K-edge of > gypsum). > > My question is, what could be a physical reason for this behaviour? With > this Parameter one change the interatomic disctances. Hence the > interference phenomena and the curve progression should be change, too. Is > this right? > > > > Thanks for your help. > > Have a nice day, > Eckhard > > PS: the same behaviour occurs in a inverse sense for rmult < 1 > > --------------------------------- > Eckhard Bosman > e.bosman(a)stud.uni-goettingen.de > +49 (0)551-39-14441 > Raum: E0.104 > Institut f?r R?ntgenphysik > Friedrich-Hund-Platz 1 > 37077 G?ttingen > Germany >

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RMULTIPLIER-Card
by s440697＠stud.uni-goettingen.de 23 Jun '08

23 Jun '08

Hi, I have a question concerning the RMULTIPLIER-Card in XANES-Calculations. I made some calculations with different rmult values (1.00, 1.01, 1.05, 1.10) and found a shift of the absorption-edge or rather the slope of the peak. I attached the diagram of this calculation (Sulfur-K-edge of gypsum). My question is, what could be a physical reason for this behaviour? With this Parameter one change the interatomic disctances. Hence the interference phenomena and the curve progression should be change, too. Is this right? Thanks for your help. Have a nice day, Eckhard PS: the same behaviour occurs in a inverse sense for rmult < 1 --------------------------------- Eckhard Bosman e.bosman(a)stud.uni-goettingen.de +49 (0)551-39-14441 Raum: E0.104 Institut für Röntgenphysik Friedrich-Hund-Platz 1 37077 Göttingen Germany

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Re: [Ifeffit] FMS + SCF Card
by joshua jason kas 19 Jun '08

19 Jun '08

> Hello, > I have some questions concerning the FMS and SCF Card in XANES-Calculations. > > I have always used the same value for lfms1 (SCF-Card) and lfms2 > (FMS-Card). Does it make sense to use different values in the same > feff.inp (for example lfms1 = 0 and lfms2 = 1)? I don't think so. > > There is the lfms2 parameter in the FMS-Card and the description in the > FEFF manual for lfms2 = 0 (appropriate for solids): "With the default > value of 0, the FMS is calculated for a cluster of size rfms around each > representative unique potential." My question is, what does it mean "each > representative unique potential"? Every potential, which is defined in the > POTENTIAL Card? I.e. with 4 potentials in the POTENTIAL Card, the FMS is > done for each of these 4 potentials? Or does it mean, the FMS is done for > really every potential of every atom? Hi Eckhard, The SCF with lfms1 = 0, works in the following manner. 1) Representative atoms are chosen for each potential type defined in the POTENTIAL card. These are chosen to be the closest atoms of that type to the absorbing atom. 2) FMS is performed for each representative atom (including the absorber) with FMS radius measured from that representative atom. So, to answer your questions, 1) lfms2 does not do anything unless you set the second value of the PRINT card to 3 or greater, and then it only changes the way that the Mulliken counts and the output in ratio.dat are calculated, not xmu.dat (the final spectrum). 2) With 4 potentials in the POTENTIAL Card, the FMS is done for each of these 4 potentials NOT for each atom in the cluster. The density of states is then calculated inside the norman radius centered about each of the representative atoms, and is assumed to be the same for all other atoms of that type. Cheers, Josh Kas > > Thanks for your help and time. > > sincerely yours, > Eckhard > > > > --------------------------------- > Eckhard Bosman > e.bosman(a)stud.uni-goettingen.de > +49 (0)551-39-14441 > Raum: E0.104 > Institut f?r R?ntgenphysik > Friedrich-Hund-Platz 1 > 37077 G?ttingen > Germany > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 64, Issue 10 > *************************************** >

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