How to add Li atoms appropriately in vacancies?

Zhu_Haotian · August 31, 2023, 7:27am

How can I appropriately add Li atoms (6 Li) to the vacancies in V2O5 (which actually has 4 V and 10 O) to make it Li3V2O5. I have tried randomly generating the coordinates for the addition of the Li atoms, but the initial structure generated is quite irrational. I’d like to ask if pymatgen has any automatic method to detect the coordinates of the vacancies?

mattmcdermott · August 31, 2023, 8:55pm

Hi @Zhu_Haotian,

Please check out the pymatgen-analysis-defects package:

https://materialsproject.github.io/pymatgen-analysis-defects/intro.html

In particular, check out the defect generators here:

github.com

materialsproject/pymatgen-analysis-defects/blob/74b123bed4b38c9185572de5c918f0ce9113fa53/pymatgen/analysis/defects/generators.py

"""Defect generators."""

from __future__ import annotations

import collections
import itertools
import logging
from abc import ABCMeta
from itertools import combinations
from typing import Generator

from monty.json import MSONable
from pymatgen.core import Element, PeriodicSite, Species, Structure
from pymatgen.io.vasp import Chgcar
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer

from pymatgen.analysis.defects.core import Defect, Interstitial, Substitution, Vacancy
from pymatgen.analysis.defects.utils import (
    ChargeInsertionAnalyzer,
    TopographyAnalyzer,

This file has been truncated. show original