eval_bader

This program evaulates Bader charge calculations and directly gives the partial charge per atom in e and files charges.pdb (to visualize the charges in vmd or similar programs) and POSCAR_charge better comparison of structure and partial charges.

Before applying this program, perform a Bader charge calculation as described in the Bader charge wiki page.

If everything is completed (including application of the chgsum.pl script and the bader program!), the file ACF.dat should have been generated in the calculation folder. This file, however, only shows the total number of valence electrons assigned to each atom and not the actual partial charge!

Now, simply apply the program by typing (ACF.dat and POSCAR need to be present in the folder):

eval_bader

and the analysis is done in usually less than a second. In the command line output, there is first given an information about the number of valence electrons per element, e.g.:

 Number of elements in POSCAR:      2
  Used number of valence electrons for the included elements:
   -Ni:   10.000000
   -H :    1.000000

Here, for each element included into the POSCAR, the number of valence electrons of the default POTCAR file as recommended by the VASP developers on their VASP-Wiki page is assumed and based on this the partial charge is calculated by the difference to the actual electron number in the ACF.dat file (if more electrons, the charge is negative, if less electrons, the charge is positive). If you chose another POTCAR file, for example Ni_pv with 16 valence electrons, simply add the valence keyword to the program, e.g.:

eval_bader -valence:Ni=16

This can be done for an arbitrary number of elements at once.

After evaluation, the average charges of all elements in the system are also printed out, giving hints to some general trends, e.g.:

 The resulting average charges are:
   -Ni:      0.002242
   -H :     -0.224199

Further, a number of output files is generated:

• bader_charges.dat contains the charges of all atoms in a simple data file, with one line per charge; the atom index in the first column and the respective charge in the second column.
• charges.pdb contains a pdb file of the current structure as well as the partial charges written in the column after the three coordinate columns. This file can be used to visualize the charges, e.g., with vmd. Open the pdb file and go to Graphics -> Representations -> Coloring Method -> Occupancy. Then, the atoms should be colored such that negatively charged atoms are red and positively are blue (almost neutral ones are white). The range of the colors can be adapted as well: Go to Trajectory in the Representations window and change there the values in the Color Scale Data Range.
• POSCAR_charge contains the POSCAR file of the system, with the charges as fourth column after the coordinates.