Sets up the AbstractGeometry for the local geometry of site with index isite.
        :param isite: Index of the site for which the local geometry has to be set up
        :param coords: The coordinates of the (local) neighbors

def setup_local_geometry(self, isite, coords, optimization=None):
        """
        Sets up the AbstractGeometry for the local geometry of site with index isite.
        :param isite: Index of the site for which the local geometry has to be set up
        :param coords: The coordinates of the (local) neighbors
        """
        self.local_geometry = AbstractGeometry(
            central_site=self.structure.cart_coords[isite],
            bare_coords=coords,
            centering_type=self.centering_type,
            include_central_site_in_centroid=
            self.include_central_site_in_centroid,
            optimization=optimization)