Atom2Vec
A python implement of Atom2Vec: a simple way to describe atoms for machine learning
(Updated 06/21/2021: We refactored the code with pymatgen, you can find old version in branch old_version. Now the code is fully typed and tested.)
Background
Atom2Vec is first proposed on Zhou Q, Tang P, Liu S, et al. Learning atoms for materials discovery[J]. Proceedings of the National Academy of Sciences, 2018, 115(28): E6411-E6417.
Demo
Installation
pip install atom2vecUsage
Generating atom vectors and atom similarity matrix
We use pymatgen.core.Structure to store all the structures.
from atom2vec import AtomSimilarity
from pymatgen.core import Structure
from typing import List
structures: List[Structure]
atom_similarity = AtomSimilarity.from_structures(structures,
k_dim=100, max_elements=3)Query atom vectors
from atom2vec import AtomSimilarity
from pymatgen.core import Element
from typing import List
atom_similarity: AtomSimilarity
atom_vector: List[float]
atom_vector = atom_similarity.get_atom_vector(1) # atomic index
atom_vector = atom_similarity.get_atom_vector("H") # atom's name
atom_vector = atom_similarity.get_atom_vector(Element("H")) # pymatgen Element EnumQuery atom similarity
from atom2vec import AtomSimilarity
from pymatgen.core import Element
atom_similarity: AtomSimilarity
similarity: float
similarity = atom_similarity["Ca", "Sr"]
