.. _toc-tool-atom-plot:

.. module:: sisl_toolbox.siesta.atom


Plotting `atom` output
======================

Suggestions and improvements to this utility is most welcome!

Creating pseudopotentials using `atom`_ will often require users to
post-analyze the output of the program.

Here we aid this visualization process by adding a command line interface
for plotting details of the output via a simple command.


Command line tool
-----------------

It may be called using

.. code-block:: console

   stoolbox atom-plot <atom-output-directory>

which by default will create 4 plots.

.. image:: atom_plot_output.png
   :align: center
   :width: 500
   :alt: Default `stoolbox atom-plot` output


It mimicks the shell commands provided by `atom`_ for plotting with some additional details.

By default the program will output details regarding the core-charge and valence charge
overlap (use full for determining whether core-corrections should be used).


.. code-block:: console

   Total charge in atom: 82.00213
   Core-correction r_pc [2.0, 1.5, 1]: [0.8656676967, 0.9330918445, 1.0573356051] Bohr

Here it is for lead and the first line gives the total charge in the atom calculation.
Note that the deviation stems from the different integration schemes used in the toolbox
and in `atom`_.
The 2nd line prints details about the where the core charge is some factor larger than
the pseudo potential valence charge. In this case it prints the radii :math:`r_i` where
:math:`\rho_{\mathrm{core}}(r_i)/\rho_{\mathrm{valence}}(r_i)` equals :math:`2`, :math:`1.5` and :math:`1`.

The full overlap is printed in the title of the charge plot. It is calculated as:

.. math::

   \mathcal O = \int \mathrm{min}(\rho_{\mathrm{core}}(r), \rho_{\mathrm{valence}}(r)) \mathrm dr


Input generation
----------------

The tool can also be used to generate the input files for `atom`_. While it is possible to read
input files from ``INP`` files, one may also define a specific `Atom` object which
will be used to generate the input file.


.. code-block::

   from sisl import *
   from sisl_toolbox.siesta.atom import *

   s = AtomicOrbital(n=5, l=0, q0=1., R=2.4)
   p = AtomicOrbital(n=5, l=1, q0=0., R=1.6)
   d = AtomicOrbital(n=4, l=2, q0=10., R=1.4)
   f = AtomicOrbital(n=4, l=3, q0=0., R=2.)

   Ag = Atom("Ag", orbitals=[s, p, d, f])

   atom_input = AtomInput(Ag, rcore=2., xc="pb", flavor="tm2")

   # write the INP file in current directory
   atom_input.pg()



.. autosummary::
   :toctree: ../generated/

   AtomInput