The charge density (electron distribution) is calculated self-consistently by employing DFT, so a question arises here: where are the atoms located, or are their positions fixed?
The atom is divided in three parts: the nuclei, the core electrons and the valence electrons. Each one is treated in a different way.
You can do two type of calculation when talking about the system geometry: single-point calculation and geometry optimization.
In the case of single-point, the nuclei positions are keep fixed and only the electrons are allowed to move.
In the case of geometry optimization, the nuclei positions and the electrons are all allowed to move. A description about how the geometry of the system is optimized is described here.
where are the atoms located, or are their positions fixed?
As mentioned above, the atoms are divided (nuclei+electrons): the nuclei are keep fixed (single-point) or allowed to move (geometry optimization), depending of your needs. The electrons are always moving, delocalized.