First, doing the Bader analysis slice-by-slice is not expected to be accurate. When the normal to the Bader volumes are not contained within the slice, the algorithm will not give accurate zero-flux surfaces.

Second, it is not entirely clear to me how the normalization of your charge density is working. The definition of the CHGCAR in vasp ( http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html ) defines the values at each cell to be the total charge in the cell (rho * V_cell). In this way, addition of the values in the CHGCAR file will give a total charge. If you have multiplied by volume (and you must think about if this is V_tot or V_cell) you will have to have a different normalization for the integration. For example, if you have a true charge density, you will have to multiply by the volume element when integrating (V_tot/(Nx*Ny*Nz)), which could be the reason why you find that you have to divide by the number of cells.

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