=head1 ARTEMIS: Interpretation of the FEFF Calculation

B<ARTEMIS> - Interpretation of the B<FEFF> calculation

This page provides a concise overview of the B<Feff> calculation.  At
the top of the page is a summary of some of the statistics of the
calculation.  Below that is a chart showing the details of each path
from the calculation.  For each path, the degeneracy, the half path
length and the amplitude factor are shown.  The last column shows a
tokenized summary of the scattering path -- this allows you to see at
a glance which atoms were involved in the path.

The information and context menus available on this page allow you
organize, understand, and manipulate the paths in this B<Feff>
calculation.  Pretty much all functions involving the paths I<except>
writing math expressions for the path parameters are available on this
page.

=head2 The interpretation chart

The colors and fonts used in the chart convey information:

=over 4

=item B<Bold, black font>

These are paths that have been imported into the project and are
included in the fit.

=item B<Bold, brown font>

These are paths that have been imported into the project but are
excluded in the fit.

=item B<Normal, black text>

These are paths that have not been imported into the project but which
are available to be imported.

=item B<Normal, grey text>

These are paths that are unavailable for importation into the project.
These can be made available by re-running the B<Feff> calculation.
After the B<Feff> run, it is best to choose the "import no paths" to
avoid reimporting paths already in the project.  After that, these
paths will be written in normal, black text, indicating that they are
available for import.

=item B<Light brown background>

The light brown background is used to indicate single scattering paths.

=item B<Light blue background>

The light blue background is used to indicate collinear or nearly
collinear multiple scattering paths.

=back


=head2 Context menus

There are interesting and useful context menus on every part of this
page.  These menus are available by right clicking.

Right clicking anywhere in the text box at the top of the page will
pop up a menu with options for viewing files from the B<Feff>
calculation.

Right clicking in the interpretation chart will post a menu of options
relevant to the path on the line on which you clicked.  Each of the
four kinds of paths given by the four fonts described above has its
own menu.

For paths that are imported in the fit, the menu offers options for
plotting the path, displaying that path's page, including or excluding
the path in the fit, selecting or deselecting that path for plotting,
making that path the default for evaluation of def parameters after a
fit, displaying the text of the file containing the path, or
discarding the path.  The choices for including or excluding and for
selecting or deselecting depend on the state of that path in the Data
and Paths List. Also some options might be greyed out depending on the
state of that path.

For paths that have not been imported into the project, the context
menu allows you to import the path with the option of displaying its
page or leaving the display on the B<Feff> interpretation.  For paths
that are unavailable for import, a message saying so is posted when
one of those lines is right-clicked.

The interpretation chart allows for extended selection of lines in the
chart.  You can select additional paths by holding the control key
while clicking with the left mouse button.  Holding the shift key
while left clicking selects all line between the anchor (the one
outlined with a dashed line) and the one you click on.  You can also
click and drag to select all the lines you drag over.  When more than
one line is selected, the content of the context menu change to
reflect functionality that makes sense for many paths.  Extended
selection in the interpretation chart is therefore a good way of
including/excluding, selecting/deselecting, or plotting a large number
of paths.

The context menu that pops up when many lines are selected may be a
little surprising.  Its contents depend upon the state of the anchored
line, which in this case is the one that you right-click on to post
the menu.  The options in the context menu will be suitable to the
state of the anchored selection regardless of the states of the other
selected lines.  If you choose a menu item that does not make sense
for some of the selected lines, those lines will be ignored.

Here is a concrete example.  Suppose that you select a number of
lines, some of which are included in the fit and some of which have
not been imported in the fit.  If you then right click on one of the
included paths, you will get options appropriate to included paths.
If you then ask to plot the selected paths along with the data, the
included paths will be plotted and the imported paths will be
ignored.  If, instead, you click on one of the paths that has not been
imported yet, the context menu will give you the option of importing
the selected paths.  In that case, the paths that have already been
imported will be ignored.


=head2 Trouble shooting

On occassion you might see that lines in the B<Feff> interpretation
do not properly report on the contents of the path.  When this
happens, site tags are replaced by this string: C<E<lt>?E<gt>>.  There
are a couple common reasons you might see the C<E<lt>?E<gt>> tags:

=over 4

=item 1.

You have done some advanced voodoo with B<Feff>, editing the
C<files.dat> or C<paths.dat> files then rerunning the last module to
produce specialized output. 

=item 2.

You have discovered a bug in the algorithm B<Artemis> uses to harvest
information from the B<Feff> calculation.  IN that case, you should
send the C<feff.inp> file or the B<Artemis> project file to Bruce so
he can fix the problem.

=back


Note that the appearance of the C<E<lt>?E<gt>> tags is probably not an
indication that B<Feff> has misbehaved.  The B<Feff> calculation has
to run to completion and generate its normal output before this
problem can manifest itself.  The B<Feff> calculation is almost
certainly usable to analyze the data.  The B<Feff> interpretation page
is B<Artemis>'s attempt to organize information about the B<Feff>
calculation in some user-friendly format.  That this organizational
effort failed is not necessarily an indication that B<Feff> failed.

=over 5

=item

L<Back to the main document|artemis>

=back

