BVlain is a python library for bond valence site energy calculations. The functionality includes calculation of the 1-3D percolation barrier and radius of a mobile ion (e.g. Li+), calculation of the bond valence sum mismatch, writing of volumetric data files (.grd or .cube) for visualization of a mobile ion diffusion map.

For more details, see documentation.

Installation

pip install bvlain

Examples

Percolation barriers

from bvlain import Lain

file = './Downloads/LiFePO4.cif'
calc = Lain(verbose = False)
atoms = calc.read_file(file)       # alternatively, you can use read_atoms() or read_structure()

params = {'mobile_ion': 'Li1+',              # mobile specie
		  'r_cut': 10.0,                     # cutoff for interaction between the mobile species and framework
		  'resolution': 0.2,	             # distance between the grid points
		  'k': 100,                          # maximum number of neighbors to be collected for each point
          'use_softbv_covalent_radii': False # default is False, use True to compare results with softBV
}
_ = calc.bvse_distribution(**params)
energies = calc.percolation_barriers(encut = 5.0)
for key in energies.keys():
    print(f'{key[-2:]} percolation barrier is {round(energies[key], 4)} eV')

1D percolation barrier is 0.4395 eV
2D percolation barrier is 3.3301 eV
3D percolation barrier is 3.3594 eV

Save volumetric data for visualization (.grd or .cube)

from bvlain import Lain

file = './Downloads/LiFePO4.cif'
calc = Lain(verbose = False)
atoms = calc.read_file(file)

params = {'mobile_ion': 'Li1+',    # mobile specie
		  'r_cut': 10.0,           # cutoff for interaction between the mobile species and framework
		  'resolution': 0.2,	   # distance between the grid points
		  'k': 100                 # maximum number of neighbors to be collected for each point
}
_ = calc.bvse_distribution(**params)

calc.write_grd(file + '_bvse', task = 'bvse')  # saves .grd file
# calc.write_cube(file + '_bvse', task = 'bvse') # alternatively, save .cube file

Percolation radii

from bvlain import Lain

file = './Downloads/LiFePO4.cif'
calc = Lain(verbose = False)
atoms = calc.read_file(file)

params = {'mobile_ion': 'Li1+',    # mobile specie
		  'r_cut': 10.0,           # cutoff for interaction between the mobile species and framework
		  'resolution': 0.2,	   # distance between the grid points
}
_ = calc.void_distribution(**params)
radii = calc.percolation_radii()
for key in radii.keys():
    print(f'{key[-2:]} percolation barrier is {round(radii[key], 4)} angstrom')

1D percolation barrier is 0.3943 angstrom
2D percolation barrier is 0.2957 angstrom
3D percolation barrier is 0.1972 angstrom

calc.write_grd(file + '_void', task = 'void') # # save void distribution

Bond valence sum mismatch

from bvlain import Lain

file = './Downloads/LiFePO4.cif'
calc = Lain(verbose = False)
atoms = calc.read_file(file)
dataframe = calc.mismatch(r_cut = 3.5)

For more examples, see documentation.

The library is under active development and it is not guaranteed that there are no bugs. If you observe not expected results, errors, please report an issue at github.