Bader: Oxidation States

This tutorial provides a basic example of calculating oxidation states using VASP and BaderKit.

VASP¶

Create your POSCAR file. As an example, we used the following NaCl structure.

Na1 Cl1
1.0
3.4220145991671784    0.0000000000000000    1.9757010500000005
1.1486715330557264    3.2263063045206364    1.9757010500000005
0.0000000000000000    0.0000000000000000    3.9514821000000001
Na Cl
1 1
direct
0.0000000000000000    0.0000000000000000    0.0000000000000000 Na+
0.5000000000000000    0.5000000000000000    0.5000000000000000 Cl-

2. Create your INCAR file. Below is a minimal example that writes a reasonable charge density for the above NaCl structure. In general, the grid density should be at least 10 pts/Å along each lattice vector for well converged Bader analysis.

Global Parameters
ISTART =  1            (Read existing wavefunction, if there)
ISPIN  =  1            (Non-Spin polarised DFT)
LREAL  = AUTO          (Projection operators: automatic)
LWAVE  = .TRUE.        (Write WAVECAR or not)
LCHARG = .TRUE.        (Write CHGCAR or not)

Static Calculation
ISMEAR =  0            (gaussian smearing method)
SIGMA  =  0.05         (please check the width of the smearing)
NELM   =  60           (Max electronic SCF steps)
EDIFF  =  1E-06        (SCF energy convergence, in eV)

LAECHG = .TRUE.        (Activate AECCAR files)
LELF   = .TRUE.        (Activate ELF)

Grid Size              (Must set fine grid to be the same)
NGX    = 48
NGY    = 48
NGZ    = 48
NGXF    = 48
NGYF    = 48
NGZF    = 48

Create your POTCAR. We cannot provide an example for this as the files are proprietary.
Run VASP. Depending on your system how you do this may vary. On our system we use the following command.
```
mpirun -np 12 vasp_std
```

BaderKit¶

PythonCommand Line

If you would like to follow along, open your preferred IDE in an environment with BaderKit installed. Alternatively, the complete python script from this tutorial is available at the end of this page.
Import the Grid utility class and main Bader class.
```
from baderkit import Grid, Bader
```
We recommend using the reconstructed total charge density as a reference for Bader partitioning when possible. In VASP we can construct this from the AECCAR files.
```
core_grid = Grid.from_vasp("AECCAR0")
val_grid = Grid.from_vasp("AECCAR2")
total = core_grid.linear_add(val_grid)
total.write_vasp("CHGCAR_sum")
```

Now create the Bader class instance.

charge = Grid.from_vasp("CHGCAR")

bader = Bader(
    charge_filename="CHGCAR", 
    total_charge_filename="CHGCAR_sum",
    pseudopotential_filename="POTCAR"
)

Finally, we can print the oxidation states to console.
```
print(bader.oxidation_states)
```
You should see logging information as BaderKit runs, then the oxidation states of each atom in the structure: array([ 0.86221034 -0.86220696])

If you are using an environment manager, load your baderkit environment. For conda:
```
conda activate baderkit
```
We recommend using the reconstructed total charge density as a reference for Bader partitioning when possible. In VASP we can construct this from the AECCAR files.
```
baderkit sum AECCAR0 AECCAR2
```
Run the Bader analysis.
```
baderkit bader CHGCAR -tot CHGCAR_sum
```
You should see logging information printed to the console and once complete a bader.json file will be written which summarizes the results of the calculation.

And that's it! Try playing around with what else the Bader class offers.

Download Resources¶

Tutorial Script: oxidation_states.py

VASP Inputs/Outputs: NaCl.zip