dsenum

Derivative structure enumerator for multilattice

Github: https://github.com/lan496/dsenum
PyPI: https://pypi.org/project/dsenum/

Installation

dsenum works with Python3.8+ and can be installed via PyPI:

pip install dsenum

Or in local:

git clone git@github.com:lan496/dsenum.git
cd dsenum
pip install -e .

Usage

import numpy as np
from pymatgen.core import Lattice, Structure
from pymatgen.core.periodic_table import DummySpecie

from dsenum import StructureEnumerator

latt = Lattice(np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]]))
coords = [[0, 0, 0]]
structure = Structure(latt, [DummySpecie('X')] * len(coords), coords)

num_type = 2
index = 4

dstructs = StructureEnumerator(structure, index, num_type).generate()
print(len(dstructs))  # -> 12

See docs/examples/constraints.ipynb for more complicated use cases.

How to cite dsenum

If you use dsenum.ZddStructureEnumerator in your research, please cite the following articles.

@article{doi:10.1063/5.0021663,
    author = {Shinohara,Kohei  and Seko,Atsuto  and Horiyama,Takashi  and Ishihata,Masakazu  and Honda,Junya  and Tanaka,Isao },
    title = {Enumeration of nonequivalent substitutional structures using advanced data structure of binary decision diagram},
    journal = {J. Chem. Phys.},
    volume = {153},
    number = {10},
    pages = {104109},
    year = {2020},
    doi = {10.1063/5.0021663},
    URL = {https://doi.org/10.1063/5.0021663},
}

@inproceedings{Horiyama2018,
  memo ={Isomorphism Elimination by Zero-Suppressed Binary Decision Diagrams},
  author={Takashi Horiyama and Masahiro Miyasaka and Riku Sasaki},
  booktitle={the Canadian Conference on Computational Geometry},
  pages={360--366},
  address={Winnipeg, Manitoba, Canada}
  year={2018},
  url={http://www.cs.umanitoba.ca/~cccg2018/papers/session7B-p2.pdf}
}

Acknowledgments

I acknowledge Dr. Takashi Horiyama for sharing his implementation of the frontier method for isomorphism-elimination decision diagram. I also appreciate his kindness to allow publishing the code.