.. Athena document is copyright 2016 Bruce Ravel and released under The Creative Commons Attribution-ShareAlike License http://creativecommons.org/licenses/by-sa/3.0/ Path interpretation =================== The hard part of using :demeter:`feff` effectively is keeping track of all the paths. The main tool :demeter:`demeter` offers for this is the path interpretation. .. code-block:: perl #!/usr/bin/perl use Demeter; my $feff = Demeter::Feff -> new(file => "feff/feff.inp"); $feff -> set(workspace => "feff/", screen => 0,); $feff -> potph $feff -> pathfinder; print $feff -> intrp; or, using the serialization file introduced in the last section, .. code-block:: perl #!/usr/bin/perl use Demeter; my $feff = Demeter::Feff -> new(yaml => "feff/feff.yaml"); print $feff -> intrp; Here is what gets printed out by the line with the ``intrp`` method: :: # Hg at site 15 in thymidine # This paths.dat file was written by Demeter 0.3.0 # The central atom is denoted by this token: <+> # Cluster size = 4.50000 Angstrom, containing 21 atoms # 23 paths were found # Forward scattering cutoff 25.00 # Distance fuzz = 0.0300 Angstroms # Angle fuzz = 3.0000 degrees # Suppressing eta: yes # ------------------------------------------------------------------------------- # degen Reff scattering path I legs type 0001 1 2.040 ---- <+> N16 <+> 2 2 single scattering 0002 2 2.923 ---- <+> C <+> 2 2 single scattering 0003 2 3.036 ---- <+> O <+> 2 2 single scattering 0004 4 3.171 ---- <+> C N16 <+> 1 3 obtuse triangle 0005 2 3.418 ---- <+> N16 C N16 <+> 0 4 dog-leg 0006 4 3.591 ---- <+> C O <+> 0 3 other double scattering 0007 4 3.676 ---- <+> O N16 <+> 0 3 other double scattering 0008 1 4.080 ---- <+> N16 <+> N16 <+> 1 4 rattle 0009 2 4.146 ---- <+> C O C <+> 0 4 dog-leg 0010 2 4.159 ---- <+> C C <+> 1 3 acute triangle 0011 1 4.191 ---- <+> N13 <+> 2 2 single scattering 0012 2 4.244 ---- <+> N13 C <+> 1 3 obtuse triangle 0013 2 4.258 ---- <+> O C O <+> 0 4 dog-leg 0014 1 4.263 ---- <+> C <+> 2 2 single scattering 0015 2 4.267 ---- <+> N13 N16 <+> 1 3 obtuse triangle 0016 2 4.301 ---- <+> C N16 C <+> 0 4 dog-leg 0017 1 4.297 ---- <+> C N13 C <+> 0 4 dog-leg 0018 2 4.317 ---- <+> N16 O N16 <+> 0 4 dog-leg 0019 2 4.314 ---- <+> C C <+> 1 3 obtuse triangle 0020 2 4.342 ---- <+> N16 C <+> 1 3 obtuse triangle 0021 1 4.343 ---- <+> N16 N13 N16 <+> 0 4 dog-leg 0022 1 4.364 ---- <+> C C C <+> 0 4 dog-leg 0023 1 4.420 ---- <+> N16 C N16 <+> 0 4 dog-leg This should be familiar to the :demeter:`artemis` user. The paths are presented in order of increasing half-path-length and each line provides an overview of the geometry of the path, starting with the degeneracy, the half-path-length, and a textual description of the atoms in the path. The line labeled *I* is the :quoted:`importance` of the path. This is an integer |nd| 0, 1, or 2 |nd| which :demeter:`demeter` assigns based on some heuristics for the likelihood that the path will contribute significantly to the fit. The high importance paths with value 2 are the single scattering and colinear multiple scattering paths. The mid importance paths tend to be short triangles. The configuration parameters :configparam:`Pathfinder,rank_high` and :configparam:`Pathfinder,rank_low` are used to determine the heuristic importance from the path ranking. The last column is a description of the shape of the path. The header contains some statistics about the cluster and the values of some of the relevant configuration parameters. As you will see in the next chapter, there is a way of obtaining a single lines from the path interpretation. Interpretaton output targets. ----------------------------- The ``intrp`` method can take an optional argument which is used to format the path interpretation. The argument can be either a string or `an anonymous hash `__. The string can be either ``latex`` or ``css``. With those, the path interpretation will be mark-up such that it can be inserted into a latex document using a LaTeX tabular environment or into an HTML document using CSS and span tags to format the text. This formatting works by inserting text at the beginning and ending of each line appropriate to the header or to the importance of the path. The anonymous hash option allows you to specify a different set of starting and ending tags for the lines in the interpretation. It looks like this: .. code-block:: perl my $formatting = {'comment' => $comment_start_tag, 'close' => $closing_tag, '1' => $mid_start_tag, '2' => $high_start_tag, '0' => $low_start_tag, }; $feff -> intrp($formatting); The command line ``intrp`` program that comes with :demeter:`demeter` colorizes the text on the screen by assigning ANSI color control sequences as the values of the anonymous hash.