.. _GUI:

Using Avogadro as a GUI
=======================

The Avogadro software is a free GUI that can be use to set up you geometries and even analyze ORCA outputs, and the ORCA team has developed their own version that can be downloaded from the `ORCA forum`_. There you can find a windows installer, that can be used also by Linux users with `Wine <https://www.winehq.org/>`_.

.. _`ORCA forum`: https://orcaforum.kofo.mpg.de

Drawing molecules
-----------------

After opening the program, you will see its main main screen:

   .. image:: avogadro_main.png

* Using the **pencil** tool, you can draw you molecule using the left click to create and right click to delete atoms.
* The atom type is selected under "Element" and the "Adjust hydrogens" can automatically fix the valence of you molecule.
* The **blue star** can be used to rotate the molecule and the **glove** to move atoms.
* After drawing you guess structure, click on the **"E"** tool (the one with the green arrow poiting downwards) and then "Start" to run a simple molecular mechanics optimization.

You can save you geometry as a .xyz file or directly use Control+C to copy the xyz data and paste it on a text editor.

Creating inputs
---------------

After drawing a molecule, you can use Avogadro to make simple ORCA inputs. Click on "Extensions", select "Orca" and "Generate Orca Inputs..." to open a new window:

   .. image:: avogadro_input.png

where you can choose the options you need and "Generate..." the input. If you want to generate orbital plots, you should add LARGEPRINT on the main input.

Visualizing output
------------------

Orbital plots
.............

If you run a calculation using !LARGEPRINT on the main input and :ref:`output_to_file`, you can visualize the orbitals by opening the `basename.out` file in Avogadro. Then select the orbital you want on the right panel to get something like

   .. image:: avogadro_orbital.png

for the HOMO of formaldehyde. Higher quality images can be generated by changing the "Quality" option or on the "Configure" button next to it.

.. hint::

   If the orbital image is not immediately available, click on "Render" to produce the image.

Density Plots
.............

After loading an output file, you can also go to "Extensions" and click "Create Surfaces...". A new window will appear were you can select the "Surface Type" and "Color by" to make this density plots with the electrostatic potential on the surface:

   .. image:: avogadro_density.png

Here blue means positive charge and red negative charge. You can also change the resolution of these surfaces at will.

Vibrational modes and IR
........................

In case your output has a frequency calculation on it (see :ref:`vibfreq`), the vibrational modes can be animated after loading the file and the vibrational spectra can be plotted by selecting "Plot Spectra":

   .. image:: form_vib.gif
      :align: center

.. note::

   Similar functionalities are available with the `Chemcraft <https://chemcraftprog.com>`_ and `Gabedit <https://sites.google.com/site/allouchear/Home/gabedit/download>`_ softwares as well.