Using distorter

The concept of cation mutation (ion substitution) to tune the properties of compounds has been around at least since the 1950s and has proved a useful concept in more more recent studies.

In this notebook, we demonstrate the process of generating all possible (symmetry inequivalent) substitutions of Sr on Ba sites in the cubic perovskite BaTiO₃, considering both single and double substitutions. The distorter module leverages the ASE Python library.

import smact.builder as builder
import smact.distorter as distorter
import numpy as np

# Step 1: Build the initial cubic perovskite structure
smact_lattice, test_case = builder.cubic_perovskite(["Ba", "Ti", "O"], repetitions=[2, 2, 2])

# Step 2: Perform a single substitution
subs_site = [0.0, 0.0, 0.0]
single_substitution = distorter.make_substitution(test_case, subs_site, "Sr")

# Step 3: Build a sub-lattice for disorder
sub_lattice = distorter.build_sub_lattice(single_substitution, "Ba")

# Step 4: Extract the required data
lattice_matrix = single_substitution.get_cell()  # Get the lattice matrix
positions = single_substitution.get_scaled_positions()  # Get scaled positions (fractional coordinates)
atomic_numbers = single_substitution.get_atomic_numbers()  # Get atomic numbers

# Package the data into the expected format: (lattice, positions, atomic numbers)
lattice_data = (lattice_matrix, positions, atomic_numbers)

# Step 5: Enumerate inequivalent sites using the properly formatted data
inequivalent_sites = distorter.get_inequivalent_sites(sub_lattice, lattice_data)

# Step 6: Replace Ba at inequivalent sites with Sr and store the structures
substituted_structures = []

for i, inequivalent_site in enumerate(inequivalent_sites):
    print(f"Substitution {i + 1}: Replacing Ba with Sr at site {inequivalent_site}")
    distorted = distorter.make_substitution(single_substitution, inequivalent_site, "Sr")
    substituted_structures.append(distorted)  # Store the structure for visualization
    print("-" * 40)

print("Substitutions completed")

Substitution 1: Replacing Ba with Sr at site [0.  0.  0.5]
----------------------------------------
Substitution 2: Replacing Ba with Sr at site [0.  0.5 0.5]
----------------------------------------
Substitution 3: Replacing Ba with Sr at site [0.5 0.  0. ]
----------------------------------------
Substitution 4: Replacing Ba with Sr at site [0.5 0.  0.5]
----------------------------------------
Substitution 5: Replacing Ba with Sr at site [0.5 0.5 0.5]
----------------------------------------
Substitutions completed

# The distorted objects are of the ase atoms class,
# so can be written out to a crystal structure file like a cif
distorted.write("example_output.cif")