NAME¶
Xray::Absorption - X-ray absorption data for the elements
SYNOPSIS¶
use Xray::Absorption;
Xray::Absorption -> load("mcmaster");
$xsec = Xray::Absorption->cross_section('Cu', 9000);
This example returns the cross section of Copper at 9000 eV using the McMaster
tables.
DESCRIPTION¶
This module supports access to X-ray absorption data. It is designed to be a
transparent interface to absorption data from a variety of sources. Currently,
the only sources of data are the 1969 McMaster tables, the 1999 Elam tables,
the 1993 Henke tables, and the 1995 Chantler tables. The Brennan-Cowen
implementation of the Cromer-Liberman tables is available as a drop-on-top
addition to this package. More resources can be added easily.
Information used to compute the mass energy-absorption coefficient is taken from
the tabulations of Hubbell and Seltzer:
http://physics.nist.gov/PhysRefData/XrayMassCoef/cover.html
Because this is an object-oriented approach to X-ray absorption data, you must
call subroutines as class methods rather than as subroutines:
$xsec = Xray::Absorption->cross_section('Cu', 9000);
is correct, but
$xsec = Xray::Absorption::cross_section('Cu', 9000);
is incorrect. Using class methods rather than a function oriented approach
allows the user of the "Xray::Absorption" module to
hot
swap absorption data resources. For example
foreach $resource (Xray::Absorption->available) {
Xray::Absorption->load($resource);
print $resource, " : ",
Xray::Absorption->cross_section('Cu', 9000), $/;
};
compares the cross section of copper at 9 keV as calculated from the all
available data resources.
It is necessary to initialize "Xray::Absorption" to use a particular
database by invoking the "load" method. This method establishes and
changes inheritance.
METHODS¶
- "current_resource"
- Example:
$this = Xray::Absorption -> current_resource;
Identifies the currently selected resource.
- "in_resource"
- Example:
$is_there = Xray::Absorption -> in_resource($elem);
Returns true if $elem is tabulated in the current resource. $elem can be a
two letter symbol, the full name of the element, or a Z number.
- "get_energy"
- Example:
$energy = $energy = Xray::Absorption -> get_energy($elem, $edge);
Returns the edge energy for $elem. $edge is one of K, L1, L2, L3, M1, etc.
$edge may also be the Siegbahn or IUPAC symbol for a fluorescence line.
Some data resources provide more lines than others. Some may provide no
lines at all. See the documentation for each resource for which lines are
available. When either $elem or $edge is an unrecognized symbol, this
method returns 0.
- "next_energy"
- Example:
$next = Xray::Absorption -> next_energy($elem, $edge, @list);
Given a list of atomic symbols @list, return a list containing the element
symbol, edge symbol, and energy in eV of the next highest edge energy
after the $edge edge of $elem. This returns an empty list if the any
argument is unrecognizable.
- "cross_section"
- Examples:
$xsec = Xray::Absorption -> cross_section($elem, $en, $mode);
@xsec = Xray::Absorption -> cross_section($elem, \@en, $mode);
In scalar context, return the cross section in barns/atom of $elem at
$energy. In list context, return a list of cross-sections given a
reference to a list of energies. For some data resources, list context may
be significantly faster than repeated calls in scalar context, i.e. this
@xsec = Xray::Absorption -> cross_section($elem, \@en, $mode);
foreach (0 .. $#en) {
... do something with energy $xsec[$_] ...
};
will be way faster than
foreach (@en) {
$xsec = Xray::Absorption -> cross_section($elem, $en, $mode);
... do something with $xsec ...
};
The optional $mode argument tells this method what kind of data to return.
The default for all data resources is to return the cross section, however
each resource has several other option. For example, the McMaster tables
offer along with the absorption cross section, the coherent scattering,
the incoherent scattering, or the sum of the three contributions. The
allowed values for $mode depend on the data contained in the absorption
resource currently loaded, but the default is always to return the
photoelectron cross section, or the full cross section if the coherent and
incoherent scattering portions are included in the resource. See the
documentation for the individual resource modules. If $mode is not given
or is given incorrectly, the full cross section is returned.
If an energy is requested which is right on an edge, all data resources
assume that you want the cross-section just above the edge. The
granularity of the comparison between the requested energy and the edge
energy is 1 milivolt, so if you want a cross-section just below an edge,
you should request an energy that is more than 1 milivolt less than the
value returned by "get_energy".
- "data_available"
- Example:
$is_there = Xray::Absorption -> data_available($elem, $edge);
Returns true if the selected resource contains sufficient data for handling
the specified element in the energy range around the specified edge.
Returns false otherwise.
- "available"
- Example:
@list = Xray::Absorption -> available;
Returns a list of all available data resource.
- "scattering"
- Example:
@list = Xray::Absorption -> scattering;
Returns a list of all available data resource which contain anomalous
scattering functions.
- "verbose"
- Example:
@list = Xray::Absorption -> verbose($arg);
Turn verbose operation on or off. If $arg evaluates to true, then warning
messages will be printed to standard error. If $arg evaluates to false,
then methods will silently return 0 when they encounter problems.
- "get_atomic_weight"
- Example:
$value = Xray::Absorption -> get_atomic_weight($elem);
Return the atomic weight of $elem.
- "get_density"
- Example:
$value = Xray::Absorption -> get_density($elem);
Return the specific gravity of the pure material of $elem.
- "get_conversion"
- Example:
$value = Xray::Absorption -> get_conversion($elem);
Return the factor for converting between barns/atom and cm squared/gram for
$elem.
- "get_Siegbahn"
- Example:
$symbol = Xray::Absorption -> get_Siegbahn($sym);
Return the short Siegbahn symbol for an x-ray fluorescence line. Thus
"Ka1", "Kalpha1", and "K-L3" all return
"Ka1". The case of the input symbol does not matter and the
symbol is returned capitalized. White space and underscores will be
removed from the input symbol. The symbol "lb2,15" is translated
to "lb2". This returns 0 is $sym is not a recognizable symbol
for a line.
- "get_Siegbahn_full"
- Example:
$symbol = Xray::Absorption -> get_Siegbahn_full($sym);
Return the full Siegbahn symbol for an x-ray fluorescence line. Thus
"Ka1", "Kalpha1", and "K-L3" all return
"Kalpha1". The case of the input symbol does not matter and the
symbol is returned capitalized. White space and underscores will be
removed from the input symbol. This returns 0 is $sym is not a
recognizable symbol for a line.
- "get_IUPAC"
- Example:
$symbol = Xray::Absorption -> get_IUPAC($sym);
Return the IUPAC symbol for an x-ray fluorescence line. Thus
"Ka1", "Kalpha1", and "K-L3" all return
"K-L3". The case of the input symbol does not matter and the
symbol is returned in all capitals. White space and underscores will be
removed from the input symbol. This returns 0 is $sym is not a
recognizable symbol for a line.
- "get_gamma"
- Example:
$symbol = Xray::Absorption -> get_gamma($sym, $edge);
Return an approximation of the core-hole lifetime for the given atomic
symbol and edge. This follows Feff very closely. In fact the data used is
swiped from the setgam subroutine in Feff, which is in turn swiped from K.
Rahkonen and K. Krause, Atomic Data and Nuclear Data Tables, Vol 14,
Number 2, 1974. The values given by this routine are a bit different from
those given by Feff since a different interpolation is used. For O and P
edges a value of 0.1 is returned, as in Feff. If the arguments are not
interpretable, a value of 0 is returned.
- "get_one_minus_g"
- Example:
$symbol = Xray::Absorption -> get_g($sym, $energy);
Return an approximation of the factor required to translate tabulated
cross-section data to the mass energy-absorption coefficient, as described
by Hubbell at http://physics.nist.gov/PhysRefData/XrayMassCoef/cover.html.
This term, returned as "1-g" relates the the mass attenuation
coefficient, "mu/rho", to the mass energy-absorption
coefficient, "mu_en/rho", as
mu_en/rho = (1-g) * mu_tr/rho
where the mass energy-transfer coefficient, "mu_tr", is the sum of
the photoabsorption and incoherent cross-sections. (At the energies at
which this module is applicable, other cross-sections such as pair
production can be ignored.)
So, to use this factor, compute the sum of the photoabsorption and
incoherent cross-sections at some energy and multiply by the number this
method returns.
The importance of this term depends on energy and on element. For nitrogen,
for example, this term becomes increasingly important above 10 keV. For
argon, it is near unity up to about 30 keV.
No great care is taken to interpolate correctly around absorption edges.
That should be considered a bug.
This method returns 1 whenever it's imput data is confusing. That seems
safest.
SYMBOLS FOR FLUORESCENCE LINES¶
To specify fluorescence lines, Siegbahn or IUPAC symbols may be used. methods
are provided for converting between these notations. The Siegbahn notations
can be in the short or full forms. Here is a table of all recognized symbols:
Full Siegbahn Short Siegbahn IUPAC
-------------------------------------------------
Kalpha1 Ka1 K-L3
Kalpha2 Ka2 K-L2
Kalpha3 Ka3 K-L1
Kbeta1 Kb1 K-M3
Kbeta2 Kb2 K-N2,3
Kbeta3 Kb3 K-M2
Kbeta4 Kb4 K-N4,5
Kbeta5 Kb5 K-M4,5
Lalpha1 La1 L3-M5
Lalpha2 La2 L3-M4
Lbeta1 Lb1 L2-M4
Lbeta2 Lb2 L3-N4,5
Lbeta3 Lb3 L1-M3
Lbeta4 Lb4 L1-M2
Lbeta5 Lb5 L3-O4,5
Lbeta6 Lb6 L3-N1
Lgamma1 Lg1 L2-N4
Lgamma2 Lg2 L1-N2
Lgamma3 Lg3 L1-N3
Lgamma6 Lg6 L2-O4
Ll Ll L3-M1
Lnu Ln L2-M1
Malpha Ma M5-N6,7
Mbeta Mb M4-N6
Mgamma Mg M3-N5
Mzeta Mz M4,5-N6,7
In addition, the symbols "Lb2,15" and "Lbeta2,15" are
recognized as synonyms for "Lbeta2". The methods which interpret
these symbols will remove spaces and underscores from the input string. Thus
"K_alpha_1" and "K a 1" will both be recognized as
"Kalpha1". Since hyphens are part of the IUPAC notation,
"K-alpha-1" will not be recognized as "Kalpha1". Thus use
spaces or underscores if you want to make the Siegbahn notation more legible.
ABSORPTION DATA RESOURCES¶
Currently, "Xray::Absorption" has the McMaster, Elam, Henke, and
Chantler tables as its data resources. New resources may be added over time.
This section offers a few guidelines to anyone interested in supplying more
resources. It does not matter how the new resource calculates the cross
section. That is hidden behind the object-orientedness of the
"Xray::Absorption" module. It is essential that the new resource
take the namespace "Xray::Absorption::"
Resource, where
Resource is a descriptive name, like "McMaster" or
"Elam". It is essential that the new resource supply these methods
current_resource
in_resource
get_energy
next_energy
cross_section
and that they use the semantics described above. All other methods decribed in
the last section are defined in
Absorption.pm and do not need to be
redefined in the resource modules.
New resources are welcome to define new methods particular to that data resource
in addition to the 5 required methods.
UNITS¶
All energies returned by the methods of "Xray::Absorption" are in
electron volts. All cross sections are in units of barns per atom. A
conversion constant between that unit and cm squared per gram is supplied by
the "get_conversion" method. Atomic weights are in atomic units.
Densities are given as specific gravity (i.e. dimensionless).
BUGS AND THINGS TO DO¶
- •
- Check to be sure things are properly unloaded and overloaded when
switching resources.
- •
- Test for pathelogical cases, such as elements that don't exist, that have
Z's in the hundreds, energies that are very low or very high, and so
on.
- •
- It would be nice to implement the list that is used by the
"next_energy" method as a doubly linked list. In that way, a
"previous_energy" method would be trivial.
AUTHOR¶
Bruce Ravel <bravel@bnl.gov>
http://cars9.uchicago.edu/~ravel/software/
LICENCE AND COPYRIGHT¶
Copyright (c) 1999-2008 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.