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Just letting you know, the current pdf build has a number of floating images (~ 16), due to a missing placement header.

Equations in section 2.1 seem to lack formatting to be correctly displayed

You probably already knew this, but a quick comment about the example on bader analysis here:

https://github.com/jkitchin/dft-book/blob/master/dft.org#bader-analysis

If you reference the charge to to core charge it seems to give a reasonable answer. You have to run vasp with laechg=True. Then chgsum the AECCAR0 and AECCAR2 files and use it as reference to Bader. Then it seems to give values comparable to https://wiki.fysik.dtu.dk/gpaw/tutorials/bader/bader.html

Also, the attach_charges function from ase.io.bader references the charge to the atomic number, which might lead to misleading results for VASP due to only using the valence charge density.

See below. http://theory.cm.utexas.edu/henkelman/code/bader/

Note for VASP users
One major issue with the charge density (CHGCAR) files from the VASP code is that they only contain the valance charge density. The Bader analysis assumes that charge density maxima are located at atomic centers (or at pseudoatoms). Aggressive pseudopotentials remove charge from atomic centers where it is both expensive to calculate and irrelevant for the important bonding properties of atoms.

Recently, the VASP developers have added a module (aedens) which allows for the core charge to be written out from PAW calculations. This module is included in vasp version 4.6.31 08Feb07 and later. By adding the LAECHG=.TRUE. to the INCAR file, the core charge is written to AECCAR0 and the valance charge to AECCAR2. These two charge density files can be summed using the chgsum.pl script:

chgsum.pl AECCAR0 AECCAR2
The total charge will be written to CHGCAR_sum.
The bader analysis can then be done on this total charge density file:

bader CHGCAR -ref CHGCAR_sum
One finally note is that you need a fine fft grid to accurately reproduce the correct total core charge. It is essential to do a few calculations, increasing NG(X,Y,Z)F until the total charge is correct.

In section 2.3

'Nørskov' appears as 'N{ø}rskov'' in the paragraph before the last.