xray::fluorescenceexafs(3pm) [debian man page]
Xray::FluorescenceEXAFS(3pm) User Contributed Perl Documentation Xray::FluorescenceEXAFS(3pm) NAME
Ifeffit::Demeter::FluorescenceEXAFS - Corrections for fluorescence EXAFS data DESCRIPTION
This provides class methods for computing corrections to fluorescence EXAFS data due to normalization, I0, and self-absorption effects. The corrections are computed from x-ray absorption coefficients provided by the Xray::Absorption package. METHODS
Note that the values returned for all methods depend on the data resource used. See Xray::Absorption. "mcmaster" This is called "mcmaster" for historical reasons. It calculates the normalization correcion for a given element. $sigma_mm = Xray::FluorescenceEXAFS->mcmaster($element, $edge); It takes the central atoms tag and the alphanumeric edge symbol as arguments and returns the normalization correction in units of Angstrom squared. "normalization" and "edgestep" are aliases for this method. "i0" This calculates the correcion due to the I0 fill gases in a fluorescence experiment. $gases = {nitrogen=>$nitrogen, argon=>$argon, krypton=>$krypton}; $sigma_i0 = Xray::FluorescenceEXAFS->i_zero($central, $edge, $gases); It takes the central atoms tag, the alphanumeric edge symbol, and a reference to a hash containing the volume percentages of the three gases as arguments. It assumes that any remaining volume is filled with helium and it correctly accounts for the fact that nitrogen is a diatom. It returns the I0 correction in units of Angstrom squared. "i_zero" and "izero" are aliases for this method. "self" This calculates the correcion due to self-absorption fluorescence experiment. It assumes that the sample is infinately thick and that the entry and exit angles of the photons are the same. $contents = {Y=>1, Ba=>2, Cu=>3, O=>7}; ($amp_i0, $sigma_i0) = Xray::FluorescenceEXAFS->self($central, $edge, $contents); It takes the central atoms tag, the alphanumeric edge symbol, and a reference to a hash which counts the atoms in the unit cell. It returns a list whose zeroth element is the multiplicative amplitude correction and whose first element is the sigma^2 correction in units of Angstrom squared. "overabsorption" is an aliases for this method. BUGS AND LIMITATIONS
o Fourth cumulant corrections are not calculated. o Geometry and thickness effects are not included in the self absorption calculation Please report problems to Bruce Ravel (bravel AT bnl DOT gov) Patches are welcome. AUTHOR
Bruce Ravel (bravel AT bnl DOT gov) http://cars9.uchicago.edu/~ravel/software/ LICENCE AND COPYRIGHT
Copyright (c) 2006-2008 Bruce Ravel (bravel AT bnl DOT gov). All rights reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See perlartistic. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. perl v5.12.4 2011-07-30 Xray::FluorescenceEXAFS(3pm)
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Xray::Scattering::WaasKirf(3pm) User Contributed Perl Documentation Xray::Scattering::WaasKirf(3pm) NAME
Xray::Scattering::WassKirf - Perl interface to the Waaskirf-Kirfel tables SYNOPSIS
use Xray::Scattering; Xray::Scattering->load('WaasKirf'); $fnot = Xray::Scattering->get_f($symb, $d); DESCRIPTION
This module provides a functional interface to the Waasmaier-Kirfel tables of coefficients for calculating the Thomson (kinematical) scattering factors of the elements and common valence states. The coefficients are stored externally in the waaskirf.db database file. The coefficients are for an Aikman expansion, which is of this form: 5 f0 = sum [ ai*exp(-bi*s^2) ] + c i=1 Thus there are 11 coefficients for each of the 211 tabulated element/valence symbols. "s" is "sin(theta)/lambda". "(lambda*s)/2pi" is the momentum transfer. "s" is simply related to the crystal d-spacing by "s=1/2d". The reference for these tables is "New Analytical Scattering Factor Functions for Free Atoms and Ions for Free Atoms and Ions", D. Waasmaier & A. Kirfel, Acta Cryst.(1995) A51, pp. 416-413. [doi:10.1107/S0108767394013292] These data, computed for neutral atoms and ions, are valid for the full range of sin(theta)/lambda from 0.0 to 6.0 A-1. The actual data used in the W-K Aikman expansion can be found in a few places on the web. Here is where I obtained the file used with this module: http://ftp.esrf.fr/pub/scisoft/xop/DabaxFiles/f0_WaasKirf.dat METHODS
"get_f" This function calculates the Thomson scattering for a given symbol and d-spacing. The Thomson scattering depends only on the momentum transfer. The d-spacing of the scattering planes is a closely related quantity and is easily calculated from the crystal structure, see Xtal.pm. $symb = "Ce3+"; $fnot = Xray::Scattering->get_f($symb, $d); If the symbol cannot be found in the table, "get_f" returns 0. It also returns 0 when $symbol consists of whitespace or is "null" or "nu". If $symbol is a number or the name of an element, then it assumes you want the Thomson scattering for the neutral element. The absolute value of $d_spacing is used by this function. If you ask for a valence state that is not in the table but for an element whose 0+ state is in the table, this method returns the scattering factor for the 0 valent atom. "get_coefficients" This returns the 11 element list containing the coefficients for the given symbol. @coefs = Xray::Scattering->get_coefficients($symb) This returns a1,b1,a2,b2,a3,b3,a4,b4,c. If you ask for a valence state that is not in the table but for an element whose 0+ state is in the table, this method returns the coefficients for the 0 valent atom. "has" This is a test of whether a given symbol is tabulated in the Waasmaier-Kirfel table. It returns the symbol itself if found in the table or 0 if it is not in the table. $symb = "Ce3+"; $is_tabulated = Xray::Scattering->has($symb); ELEMENTS AND VALENCE STATES
The following is a list of symbols for the tabulated elements and valence states. The final two are ways of refering to an empty site (i.e. a null or blank atom). H H1- He Li Li1+ Be Be2+ B C Cval N O O1- O2- F F1- Ne Na Na1+ Mg Mg2+ Al Al3+ Si Siva Si4+ P S Cl Cl1- Ar K K1+ Ca Ca2+ Sc Sc3+ Ti Ti2+ Ti3+ Ti4+ V V2+ V3+ V5+ Cr Cr2+ Cr3+ Mn Mn2+ Mn3+ Mn4+ Fe Fe2+ Fe3+ Co Co2+ Co3+ Ni Ni2+ Ni3+ Cu Cu1+ Cu2+ Zn Zn2+ Ga Ga3+ Ge Ge4+ As Se Br Br1- Kr Rb Rb1+ Sr Sr2+ Y Zr Zr4+ Nb Nb3+ Nb5+ Mo Mo3+ Mo5+ Mo6+ Tc Ru Ru3+ Ru4+ Rh Rh3+ Rh4+ Pd Pd2+ Pd4+ Ag Ag1+ Ag2+ Cd Cd2+ In In3+ Sn Sn2+ Sn4+ Sb Sb3+ Sb5+ Te I I1- Xe Cs Cs1+ Ba Ba2+ La La3+ Ce Ce3+ Ce4+ Pr Pr3+ Pr4+ Nd Nd3+ Pm Pm3+ Sm Sm3+ Eu Eu2+ Eu3+ Gd Gd3+ Tb Tb3+ Dy Dy3+ Ho Ho3+ Er Er3+ Tm Tm3+ Yb Yb2+ Yb3+ Lu Lu3+ Hf Hf4+ Ta Ta5+ W W6+ Re Os Os4+ Ir Ir3+ Ir4+ Pt Pt2+ Pt4+ Au Au1+ Au3+ Hg Hg1+ Hg2+ Tl Tl1+ Tl3+ Pb Pb2+ Pb4+ Bi Bi3+ Bi5+ Po At Rn Fr Ra Ra2+ Ac Ac3+ Th Th4+ Pa U U3+ U4+ U6+ Np Np3+ Np4+ Np6+ Pu Pu3+ Pu4+ Pu6+ Am Cm Bk Cf ' ' Nu AUTHOR
Bruce Ravel, bravel AT bnl DOT gov http://cars9.uchicago.edu/~ravel/software/exafs/ perl v5.12.4 2011-07-30 Xray::Scattering::WaasKirf(3pm)