1.Do the single calculation for the material you want to do bader analysis on. 2. Perform the charge calculation on the valence electrons and for all the electrons of your system, using pp.x. 3. Perform bader calculation using: ./bader valence.xsf -ref all_electron.xsf. And note that the bader should be executable, you can make it executable using chmod + x bader. All the calculations should be done in the same directory. The key is to obtain the ACF.dat file.
Why the coordinates in your ACF.dat file are different with respect to the ones appearing in the CONTCAR file? I'm asking because I encounter the same "problem": I use Quantum Espresso, and the coordinates in my SCF file (already in cartesian coordinates) aren't the same of my ACF.dat file Thank you in advanced and thanks a lot for your video, it is extremely useful!