xray::absorption::shaltout(3pm) [debian man page]

Xray::Absorption::Shaltout(3pm) 			User Contributed Perl Documentation			   Xray::Absorption::Shaltout(3pm)

       "cross_section"
	   Example:

	      $xsec = Xray::Absorption -> cross_section($elem, $energy, $mode);

	      @xsec = Xray::Absorption -> cross_section($elem, @energy, $mode);

	   The $mode argument is different here than for the other resources.  The options are "xsec", "photo", "coherent" and "incoherent",
	   telling this method to return the full cross-section or just the photoelectric, coherent, or incoherent portions.

	   The values for all cross-sections are computed as log-log polynomials as described in the original paper by Shaltout et al.

NAME

       Xray::Absorption::Shaltout - Perl interface to the Shaltout tables

SYNOPSIS

	  use Xray::Absorption;
	  Xray::Absorption -> load("shaltout");

       See the documentation for Xray::Absorption for details.

DESCRIPTION

       This module is inherited by the Xray::Absorption module and provides access to the data contained in

	 Update of photoelectric absorption coefficients in the tables of McMaster
	 Abdallah Shaltout, Horst Ebel, and Robert Svagera
	 X-Ray Spectrometry(2006) vol. 35, p. 52-56

       The data is contained in a database file called shaltout.db which is generated at install time from a flat text database of the data which
       can be found at <http://www.ifp.tuwien.ac.at/forschung/abdallah.shaltout/> as explained in the reference.

       The required Chemistry::Elements module is available from CPAN in the miscellaneous modules section.

EDGE AND LINE ENERGIES

       The Shaltout data resource includes all K, L, M, and N edges but does not provide any of the line energies.  An minimal set of line
       energies is imported from the McMaster data resource.

BUGS AND THINGS TO DO

       This module has not be tested sufficiently.

AUTHOR

	 Bruce Ravel, bravel@bnl.gov
	 http://cars9.uchicago.edu/~ravel/software/Absorption/

perl v5.12.4							    2011-07-30					   Xray::Absorption::Shaltout(3pm)

Chemistry::Formula(3pm) 				User Contributed Perl Documentation				   Chemistry::Formula(3pm)

NAME

       Chemistry::Formula - Enumerate elements in a chemical formula

SYNOPSIS

	  use Chemistry::Formula qw(parse_formula);
	  parse_formula('Pb (H (TiO3)2 )2 U [(H2O)3]2', \%count);

       That is obviously not a real compound, but it demonstrates the capabilities of the routine.  This returns

	 %count = (
		   'O' => 18,
		   'H' => 14,
		   'Ti' => 4,
		   'U' => 1,
		   'Pb' => 1
		  );

DESCRIPTION

       This module provides a function which parses a string containing a chemical formula and returns the number of each element in the string.
       It can handle nested parentheses and square brackets and correctly computes stoichiometry given numbers outside the (possibly nested)
       parentheses.

       No effort is made to evaluate the chemical plausibility of the formula.	The example above parses just fine using this module, even though
       it is clearly not a viable compound.  Charge balancing, bond valence, and so on is beyond the scope of this module.

       Only one function is exported, "parse_formula".	This takes a string and a hash reference as its arguments and returns 0 or 1.

	   $ok = parse_formula('PbTiO3', \%count);

       If the formula was parsed without trouble, "parse_formula" returns 1. If there was any problem, it returns 0 and $count{error} is filled
       with a string describing the problem.  It throws an error afer the first error encountered without testing the rest of the string.

       If the formula was parsed correctly, the %count hash contains element symbols as its keys and the number of each element as its values.

       Here is an example of a program that reads a string from the command line and, for the formula unit described in the string, writes the
       weight and absorption in barns.

	   use Data::Dumper;
	   use Xray::Absorption;
	   use Chemistry::Formula qw(parse_formula);

	   parse_formula($ARGV[0], \%count);

	   print  Data::Dumper->Dump([\%count], [qw(*count)]);
	   my ($weight, $barns) = (0,0);
	   foreach my $k (keys(%$count)) {
	     $weight +=
	       Xray::Absorption -> get_atomic_weight($k) * $count{$k};
	     $barns  +=
	       Xray::Absorption -> cross_section($k, 9000) * $count{$k};
	   };
	   printf "This weighs %.3f amu and absorbs %.3f barns at 9 keV.
",
	     $weight, $barns;

       Pretty simple.

       The parser is not brilliant.  Here are the ground rules:

       1.  Element symbols must be first letter capitalized.

       2.  Whitespace is unimportant -- it will be removed from the string.  So will dollar signs, underscores, and curly braces (in an attempt to
	   handle TeX).  Also a sequence like this: '/sub 3/' will be converted to '3' (in an attempt to handle INSPEC).

       3.  Numbers can be integers or floating point numbers.  Things like 5, 0.5, 12.87, and .5 are all acceptible, as is exponential notation
	   like 1e-2.  Note that exponential notation must use a leading number to avoid confusion with element symbols.  That is, 1e-2 is ok, but
	   e-2 is not.

       4.  Uncapitalized symbols or unrecognized symbols will flag an error.

       5.  An error will be flagged if the number of open parens is different from the number of close parens.

       6.  An error will be flagged if any unusual symbols are found in the string.

ACKNOWLEDGMENTS

       This was written at the suggestion of Matt Newville, who tested early versions.

       The routine "matchingbrace" was swiped from the C::Scan module, which can be found on CPAN.  C::Scan is maintained by Hugo van der Sanden.

AUTHOR

       Bruce Ravel <bravel AT bnl DOT gov>

       http://cars9.uchicago.edu/~ravel/software/

       SVN repository: http://cars9.uchicago.edu/svn/libperlxray/

perl v5.12.4							    2011-07-30						   Chemistry::Formula(3pm)