Custom Data Formats

BaderKit only provides convenience functions for loading VASP CHGCAR-like files or Gaussian cube-like files. However, as long as you can read in your charge density into a NumPy array, you can still use BaderKit by constructing the Structure, Grid, and Bader classes manually.

---

# import 
from baderkit.core import Bader, Grid, Structure
import numpy as np

# Create a PyMatGen Structure object. This is usually easiest to do from a
# file, but can also be made manually.
structure = Structure.from_file(filename = "mystructure.cif", fmt = "cif")

# Load your data, however you can, into a numpy array.
charge_data = np.array([
[[1,2,3],[3,4,5],[6,7,8]],
[[1,2,3],[3,4,5],[6,7,8]],
[[1,2,3],[3,4,5],[6,7,8]],
])

# Create a data dictionary
data = {"total": charge_data}

# create Grid objects for the charge-density (and reference file if needed)
charge_grid = Grid(structure=structure, data=data)

# Create the Bader object
bader = Bader(charge_grid = charge_grid)

Warning

The charge density data must follow VASP's conventions, i.e. it should be stored as

data(r) = n(r) x V_grid x V_cell

where

• n(r) = charge density in 1/Ang at point r
• V_grid = the total number of grid points
• V_cell = the volume of the simulation cell

See VASP's wiki for more details.