dsenum

多晶格派生结构枚举器

• Github: https://github.com/lan496/dsenum
• PyPI: https://pypi.ac.cn/project/dsenum/

安装

dsenum与Python3.8+兼容，可以通过PyPI安装

pip install dsenum

或本地

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

使用方法

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

有关更复杂的用例，请参阅docs/examples/constraints.ipynb。

如何引用dsenum

如果您在研究中使用了dsenum.ZddStructureEnumerator，请引用以下文章。

@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}
}

致谢

我要感谢Horiyama博士分享了他的同构消除决策图前缀方法的实现。我还要感谢他允许发布代码的善意。