Visualization
Visualizing data from Octopus output
Every given number of time iterations, or after ground-state calculations, some of the functions that characterise the system may be written to disk so that they may be analized. Files are written within static/ output directory after the self-consistent field, or within td.x/ directories, during evolution, where “x” stands for the iteration number at which each write is done.
The function that you want to plot is selected by the Output variable and the output format is chosen by the OutputFormat.
Postopus
In recent years, a new, python based, framework has been created to analyze the results of Octopus calculations. Postopus is a post-processing tool for Octopus (POSTprocessing for OctoPUS). It provides a user-friendly interface to find and read data written by Octopus throughout a simulation and offers common operations to evaluate this data. A quick demonstration of Postopus can be found in the Visualization tutorial. The full documentation of Postopus can be found here.
XCrySDen
Atomic coordinates (finite or periodic), forces, and functions on a grid can be plotted with the free program XCrySDen. Its XSF format also can be read by V_sim and Vesta. Beware, these all probably assume that your output is in Angstrom units (according to the specification), so use UnitsOutput = eV_Angstrom, or your data will be misinterpreted by the visualization software.
CUBE
The Gaussian cube format (see https://gaussian.com/cubegen/, https://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html and https://h5cube-spec.readthedocs.io/en/latest/cubeformat.html for a more detailed description of the format) can be output, and can be read by VMD, XCrysDen, Avogadro, and other software. Note that CUBE files are always in atomic units, so the UnitsOutput input option will be ignored.
PDB
Everything is supposed to be in Angstroms: https://deposit.rcsb.org/adit/docs/pdb_atom_format.html
XYZ
Generally considered to be in Angstroms: https://openbabel.org/wiki/XYZ_%28format%29, https://en.wikipedia.org/wiki/XYZ_file_format, https://www.molpro.net/info/2012.1/doc/manual/node100.html, https://departments.icmab.es/leem/siesta/Documentation/Manuals/siesta-3.1-manual/node32.html