Ionic radius, bond valence, bond valence force field parameters
Project description
About
ions is a small python library made for
-
handling data associated with ionic crystals
-
decoration of ase's Atoms objects with oxidation states
Note: The decoration method is based on the pymatgen's implementaion for Structure object
Installation
pip install ions
Available data
-
bv_data - bond valence parameters [1]
-
bvse_data - bond valence site energy parameters[2]
-
ionic_radii - Shannon ionic radii [3, 4]
-
crystal_radii - Shannon crystal radii [3, 4]
-
elneg_pauling - Pauling's elenctronegativities [5]
References
[1]. https://www.iucr.org/resources/data/datasets/bond-valence-parameters (bvparam2020.cif)
[2]. He, B., Chi, S., Ye, A. et al. High-throughput screening platform for solid electrolytes combining hierarchical ion-transport prediction algorithms. Sci Data 7, 151 (2020). https://doi.org/10.1038/s41597-020-0474-y
[3] http://abulafia.mt.ic.ac.uk/shannon/ptable.php
[4] https://github.com/prtkm/ionic-radii
[5] https://mendeleev.readthedocs.io/en/stable/
How to handle data
from ions.data import ionic_radii, crystal_radii, bv_data, bvse_data
#ionic radius
symbol, valence = 'V', 4
r_ionic = ionic_radii[symbol][valence]
#crystal radius
symbol, valence = 'F', -1
r_crystal = crystal_radii[symbol][valence]
# bond valence parameters
source, source_valence = 'Li', 1
target, target_valence = 'O', -2
params = bv_data[source][source_valence][target][target_valence]
r0, b = params['r0'], params['b']
# bond valence site energy parameters
source, source_valence = 'Li', 1
target, target_valence = 'O', -2
params = bvse_data[source][source_valence][target][target_valence]
r0, r_min, alpha, d0 = params['r0'], params['r_min'], params['alpha'], params['d0']
How to decorate ase's Atoms
from ase.io import read
from ions import Decorator
file = '/Users/artemdembitskiy/Desktop/crystaldata/src/ions/data/Li2O_mp-1960.cif'
atoms = read(file)
calc = Decorator()
atoms = calc.decorate(atoms)
oxi_states = atoms.get_array('oxi_states')
list(zip(atoms.symbols, oxi_states))
[('Li', 1),
('Li', 1),
('Li', 1),
('Li', 1),
('Li', 1),
('Li', 1),
('Li', 1),
('Li', 1),
('O', -2),
('O', -2),
('O', -2),
('O', -2)]
Aplication example
import numpy as np
from ions import Decorator
from ase.io import read
from ase.neighborlist import neighbor_list
from ions.data import bv_data
file = '/Users/artemdembitskiy/Desktop/crystaldata/src/ions/data/Li2O_mp-1960.cif'
atoms = read(file)
calc = Decorator()
atoms = calc.decorate(atoms)
ii, jj, dd = neighbor_list('ijd', atoms, 5.0)
symbols = atoms.symbols
valences = atoms.get_array('oxi_states')
for i in np.unique(ii):
source = symbols[i]
source_valence = valences[i]
neighbors = jj[ii == i]
distances = dd[ii == i]
if source_valence > 0:
bvs = 0
for n, d in zip(neighbors, distances):
target = symbols[n]
target_valence = valences[n]
if source_valence * target_valence < 0:
params = bv_data[source][source_valence][target][target_valence]
r0, b = params['r0'], params['b']
bvs += np.exp((r0 - d) / b)
print(f'Bond valence sum for {source} is {round(bvs, 4)}')
Bond valence sum for Li is 0.9605
Bond valence sum for Li is 0.9605
Bond valence sum for Li is 0.9605
Bond valence sum for Li is 0.9605
Bond valence sum for Li is 0.9605
Bond valence sum for Li is 0.9605
Bond valence sum for Li is 0.9605
Bond valence sum for Li is 0.9605
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