=head1 ARTEMIS: ATOMS, The Crystallographic Front End to FEFF

B<ARTEMIS> - B<ATOMS>, The Crystallographic Front End to B<FEFF>


The purpose of B<Atoms> is to generate a C<feff.inp> file from
crystallographic data.  The hard part of making a C<feff.inp> file is
creating the long list of atomic coordinates.  B<Atoms> thus makes the
hard part of running B<Feff> easy, at least for crystalline matrials.

This page can be used to create input data for B<Atoms> from scratch.
It will also be used to display crystallography data imported from an
C<atoms.inp> file or a CIF file.  To import an C<atoms.inp> file or
CIF file, use the normal file import dialog.

=head2 The title box

At the top is a text box for entering title lines identifying the
crystallographic data.  These lines will be written to the C<feff.inp>
file and to the top of the B<Feff> interpretation page.  This is a
good place to cite the literature reference or to provide other
important information about the crystal.

=head2 Crystal parameters

To the left side of the page are entry boxes for entering space group,
lattice constants, and lattice angles of the crystal.  A space group
must always be provided.  B<Atoms> is very flexible about how the
space group symbol is entered.  You can use the Hermann-Maguin or
Scheonflies symbols or the index of the space group from the
International Tables.  The algorithm that interprets the symbol is
insensitive to white space and capitalization -- C<P m -3 m> and
C<PM-3M>  are interpreted the same.  For complete details about how
the symbols are interpreted, see the B<Atoms> docuemntation on Bruce's
web site.

Lattice constants are entered in units of Angstroms, angles are
entered as decimal numbers in degrees (and not in arc minutes --
i.e. 89 and a half degrees is entered as 89.5 rather than 89'30").
Many space groups have symmetries that make some lattice angles and
constants the same.  In those situations, it is only necesary to fill
in the essential values.  For instance, a cubic space group only
requires a value for the C<a> constant.  B<Atoms> will know to set the
other lattice constants the same and to set the angles to 90 degrees.
For lower symmetry groups, you must provide all the necessary
information.

Below the lattice constants are entry boxes for C<Rmax> and the shift
vector and a menu for selecting the absorption edge of the B<Feff>
calculation.  C<Rmax> is the radial extent of the cluster that will be
written to the C<feff.inp> file.  Some space groups are given in the
International Tables with two different origins -- i.e. the origin is
placed at sites with two different point symmetries.  The fractional
coordinates of the sites are different for the two different settings
of the crystal.  In those cases, B<Atoms> requires that you use a
particular one of the two choices.  If your input data has used the
other origin choice, it should be fairly obvious.  In that case,
coordination numbers and distances to the coordination shells will
usually be obviously wrong.  When you use one of the space groups for
which two origin choices exist, B<Artemis> will issue a warning.  If
you suspect that the wrong origin choice has been used, insert the
values for the shift vector that were reported in the warning message.

On occassion, crystals are reported in the literature using origins
other than the standard one used in the International Tables.  A
famous example is germanium oxide.  Here is the crystal data for GeO2:

   title GeO2 (hexagonal)
   space p 32 2 1
   a=4.98502       c=5.64800
   rmax=6.0        core=Ge
   shift   0 0 0.66667
   atoms
     Ge    0.4513  0.0     0.0
     O     0.3969  0.3021  0.0909

For some reason, the crystallography reference for this material uses
an origin that is shifted by 2/3 in the z direction relative to the
origin used in the International Tables.  To get B<Atoms> to compute
this structure correctly, the shift vector given above must be used.

=head2 The atoms list

To the right side of the page is the list of unique crystallographic
sites.  As new sites are created, they are inserted into the list.
The sites are not edited directly, instead the editing area at the
bottom of the screen is used and the list of all sites is displayed
here.  This works much the same as the Guess, Def, Set page.

To edit a site, left-click on its entry in the list.  It's element
symbols, coordinates, and site tag will be displayed in the edit
area.  A right click on a site in the list will post a context menu
with several functions that can be perfromed on that site.  You can
re-order the list using the "Move" menu item.  A site can be copied
and the copy added to the list using the "Copy" menu item.  The
"Discard" menu item completely removes the site from the list.  The
list supports extended selection.  When many sites are selected
(i.e. highlighted in yellow), the "Discard" menu item will work on all
the selected sites.

Sites can also be reordered using the keyboard.  C<Alt-k> and C<Alt-j>
can be used to move the selected site up or down in the list. 

=head2 The edit area

At the bottom of the page is the collection of widgets used to
actually create and edit unique crystallographic sites.  The element
box is used to insert the two-letter element symbol for the site.  The
site will not be created if this is not a valid symbol.  The tag can
be any 10-letter string used to identify the site.  The tag is used to
differentiate sites that contain the same element.

The boxes for the C<x>, C<y>, and C<z> coordinates can be filled with
floating point numbers or simple fractions.  That is, C<0.5> and
C<1/2> are both acceptable.  These coordinates are fractional
positions in the unit cell and are not Cartesian coordinates.

Once you have created all sites in your crystal, click the "Run Atoms"
button.  This will process the crystallographic data, create the
C<feff.inp> file, display the C<feff.inp> page.



=head2 Atoms template files

The C<feff.inp> data that is generated when the "Run Atoms" button is
pressed is determined by the contents of a special template file.
B<Artemis> is distributed with a number of template files serving
different purposes.  The structure of the C<feff.inp> data is set by
the value of the "atoms->template" preference.  The default value is
"feff", which tells B<Artemis> to use the template file suitable for
running B<Feff6>.

If you want to run some other version of B<Feff>, you should set the
"atoms->template" preference variable to the appropriate value.
Templates are provided with B<Artemis> for writing B<Feff7> and
B<Feff8> input files.  B<Feff8> input files can be written which are
suitable for XANES or non-self-consistent EXAFS calculations.

Sometimes, it is useful to modify template files for writing out
specialized C<feff.inp> data.  If these modified template files are
placed in C<~/.horae/atp/> (unix) or C<C:Program
Files\Ifeffit\horae\atp> (windows), B<Artemis> will be able to find them.



=head2 Final note

A full explanation of how the B<Atoms> algorithms works is beyond the
scope of this document page.


=over 5

=item

L<Back to the main document|artemis>

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