Demeter

Description Perl tools for X-ray Absorption Spectroscopy
Demeter > Perl Modules > Demeter::Tools
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NAME

Demeter::Tools - Utility methods for the Demeter class

VERSION

This documentation refers to Demeter version 0.9.26.

DESCRIPTION

This module contains a number of methods that work better (in Bruce's opinion) as class methods than as object methods.

METHODS

simpleGDS

This is syntactic sugar for the GDS object constructor. The following are equivalent:

  $gdsobject = Demeter::GDS ->
                  new(type    => 'guess',
                      name    => 'alpha',
                      mathexp => 0,
                     );
  #
  $gdsobject = $demeter_object -> simpleGDS("guess alpha = 0");

The text string that is the argument for this wrapper is parsed identically to how a guess parameter in a feffit.inp file is parsed.

distance

This returns the Cartesian distance between two points.

   my $d = distance(@point1, @point2);

Each of the arrays passed to this function must be exactly three elements long and are assumed to contain the x, y, and z Cartesian coordinates, in that order.

now

This returns a string with the current date and time in a convenient, human-readable format.

   print "The time is: ", $demeter_object -> now, $/;
howlong

This returns a string used for indicating an amount of elapsed time. The argument is a DataTime object made at the beginning of the event whose elapsed time is being measured.

   my $start = DateTime->now( time_zone => 'floating' );
   #  ... do something
   my $text = Demeter->howlong($start);

returns

   That took NN seconds.

It can be customized:

   my $text = Demeter->howlong($start, "Your fit");

returns

   Your fit took NN seconds.

For something longer than a minute, it would return

   Your fit took MM minutes and NN seconds.
environment

This returns a string showing the version numbers of Demeter and perl, and the identifier string for your operating system.

   print "You are running: ", $demeter_object -> environment, $/;
who

This makes a halfhearted attempt to figure out who you are. On a unix machine, it returns a concatination of the USER and HOST environment variables. On Windows it currently returns the fairly stupid "you@your.computer".

   print "You are: ", $demeter_object -> who, $/;
check_parens

Return 0 if a string has matching round braces (parentheses). A positive (negative) return value indicates the number of excess open (close) round braces. This can be used a boolean check on a string.

  $is_mismatched = $demeter_object->check_parens($string);

This only matches round braces. It ignores square, curly, or angle braces, none of which serve a purpose in Ifeffit math expressions.

is_windows

Return true if running on a Windows machine.

  my $is_win = $demeter_object -> is_windows;
is_osx

Return true if running on a Macintosh OSX machine.

  my $is_mac = $demeter_object -> is_osx;
halflength

Given a list of references to arrays -- each of which contains the x, y, and z coordinates of an atom -- return the half length of the path. The half length is the sum of the individual legs divided by 2. The first item in the list is assumed to the absorber at and is tacked onto the end of the list to close the path.

  my $hl = $demeter_object ->
         halflength(\@coords1, \@coords2, ... \@coordsN);
euclid

Return the greatest common denominator of two numbers.

  my $gcd = $demeter_object->euclid(1071, 462);
  ## $gcd is 21

This is used by Demeter::Atoms to determine stoichiometry for the feff8 input file's potentials list.

fract

Returns a fraction of rational numbers given an input float,using 5 significant digits beyond the decimal.

  my $frac = $demeter_object -> fract(0.5);
  ## will print as "1/2"
slurp

Slurp a file into a scalar.

  my $string = $demeter_object -> slurp('/path/to/file');
write_file

Dump a string into a file.

  $demeter_object -> write_file($file, $string);
randomstring

Return a rendom character string using random numbers from Math::Random

  $string = Demeter->randomstring($length);

The resulting string will be $length characters long. If not specified, it will be 6 characters long.

Dump

This is just a wrapper around Data::Dump::Color, Data::Dump or Data::Dumper, whichever is installed. Pass it a reference and it will be pretty-printed;

  print $any_object -> Dump(\@some_array);
trace

Print an ANSI-colorized stack trace to STDOUT from any location.

  $any_object -> trace;
pjoin

Write stuff to the screen in an ugly but easy to read manner.

  Demeter->pjoin($this, $that, @and_the_other);
unistrip

Remove non-ASCII characters from a string. This simple, blunt hammer is used to save just the text without the coloration from Athena's status bar buffer.

  my $no_utf = Demeter->unistrip($text);
Touch

This is a wrapper around the touch method from File::Touch.

  Demeter->Touch($some_file);
feffdocversion

This method attempts to determine the appropriate version of the Feff document to show. If the version is not specified, it will be determined from the value of the feff->feff-executable configuration parameter.

  $version = Demeter->feffdocversion;

The only two options currently supported are 6 and 9.

feffdoc

This returns the URL of the main page of the Feff documentation for either version 6 or 9, depending on which is requested or determined via the feffdocversion method.

  $url = Demeter->feffdoc;
feffcardpage

This returns the URL for the page documenting a specific card in the Feff6 or Feff9 input file.

  $url = Demeter->feffcardpage($card, $version);

Specifying the Feff version is optional. If not specified, it will use the value returned by the feffdocversion method.

CONFIGURATION AND ENVIRONMENT

See Demeter::Config for a description of the configuration system.

DEPENDENCIES

The dependencies of the Demeter system are listed in the Build.PL file.

BUGS AND LIMITATIONS

Please report problems to the Ifeffit Mailing List (http://cars9.uchicago.edu/mailman/listinfo/ifeffit/)

Patches are welcome.

AUTHOR

The euclid method was swiped from Math::Numbers by David Moreno Garza and is Copyright (C) 2007 and is licensed like Perl itself.

Bruce Ravel (http://bruceravel.github.io/home)

http://bruceravel.github.io/demeter/

LICENCE AND COPYRIGHT

Copyright (c) 2006-2018 Bruce Ravel (http://bruceravel.github.io/home). All rights reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See perlgpl.

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.

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