If PDBCoordinates is not present, the program reads the atomic coordinates from the XYZ file specified by the variable XYZCoordinates – in case this variable is present. The XYZ format is very simple: The first line of the file has an integer indicating the number of atoms. The second can contain comments that are simply ignored by Octopus. Then there follows one line per atom, containing the chemical species and the Cartesian coordinates of the atom.
If you want to specify the unit of the XYZ file, you can use the variable UnitsXYZFiles.