Graphical User Interfaces (GUI)#
Various programs are available that can read ORCA output files. Some programs that have proven specifically useful for ORCA output visualization are:
ChimeraX (For ChimeraX, the SEQCROW plugin is very useful. It can be downloaded from the
Tools/More Toolsmenu.)
With these you can visualize your geometry, the charges, plot orbital diagrams, spectra, etc.
Important
It might be necessary to include some extra printing for these programs (e.g., to generate orbital plots). In that case, use LARGEPRINT on the main input:
!HF DEF2-SVP LARGEPRINT
and a very detailed output file will be printed with the necessary information.
As Avogadro is the most commonly used and generally freely available option, we will further focus on the usage of the modified version as a GUI to ORCA. It 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.
Warning
Using other versions of Avogadro, e.g. Avogadro 2, may cause limited compatibility compared to the tailored version!
Avogaro as a GUI#
Drawing molecules#
After opening Avogadro, you will see its main main screen:
Figure: Avogadro's main screen.#
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
Elementand theAdjust hydrogenscan 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
Etool (the one with the green arrow poiting downwards) and thenStartto 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:
Figure: Creating ORCA inputs in Avogadro.#
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 Save output to a 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
Figure: Molecular orbital plot in Avogadro.#
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:
Figure: ESP plot in Avogadro.#
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 Vibrational frequencies), the vibrational modes can be animated after loading the file and the vibrational spectra can be plotted by selecting Plot Spectra:
Animation: Vibrational mode of formaldehyde.#