oct-center-geom - Centers a molecule’s geometry
[oct-center-geom does not read the standard input: all standard input will be simply ignored. An input file named inp must be present in the running directory. Also, oct-center-geom accepts no command-line arguments, since there is not a standard way to do this with Fortran 90.]
This program is one of the Octopus utilities.
It reads the coordinates defined in the inp file, and constructs an output xyz file, that will be called adjusted.xyz file, that describes the same system but in which the atomic coordinates are centered, and (optionally) has the axes aligned.
To control the orientation of the centered molecule there are two parameters: MainAxis and AxisType.
Do not forget then to change your input file to use this file instead of your old geometry (by changing XYZCoordinates='adjusted.xyz' ).
Be careful with units, this utility honours the Units, UnitsXYZFiles and UnitsOutput variables, so the adjusted.xyz file will be in the specified output units.