PyXtal: A Python library for crystal structure generation and symmetry analysis
PyXtal: A Python library for crystal structure generation and symmetry analysis
复制标题
DOI：
10.1016/j.cpc.2020.107810
复制
发表时间：
2021-01-11
影响因子：
6.3
通讯作者：
Zhu, Qiang
中科院分区：
文献类型：
--
作者：
Fredericks, Scott;Parrish, Kevin;Zhu, Qiang
我们推出了 PyXtal，一个基于 Python 编程语言的新软件包，用于为原子和分子系统生成具有特定对称性和化学成分的结构。该软件为通过点、杆、层和空间群对称性描述的各种系统提供支持。只需输入化学成分和对称群信息，PyXtal 就可以通过逐步合并方案自动找到合适的 Wyckoff 位置组合。此外，当给定分子几何形状时，PyXtal 可以生成不同维度的有机晶体，其中分子占据一般和特殊威科夫位置。 PyXtal 还可以选择接受用户定义的参数（例如，单元参数、最小距离和威科夫位置）。一般来说，PyXtal 有三个目的：(1) 生成自定义结构，(2) 通过对称关系调制结构，(3) 连接需要生成随机对称结构的现有结构预测代码。此外，我们还提供多种有助于结构分析的实用程序，包括对称分析、几何优化和粉末 X 射线衍射 (XRD) 模拟。 PyXtal 的完整文档可在 https://pyxtal.readthedocs.io 上找到。 (c) 2021 Elsevier B.V. 保留所有权利。
We present PyXtal, a new package based on the Python programming language, used to generate structures with specific symmetry and chemical compositions for both atomic and molecular systems. This software provides support for various systems described by point, rod, layer, and space group symmetries. With only the inputs of chemical composition and symmetry group information, PyXtal can automatically find a suitable combination of Wyckoff positions with a step-wise merging scheme. Further, when the molecular geometry is given, PyXtal can generate different dimensional organic crystals with molecules occupying both general and special Wyckoff positions. Optionally, PyXtal also accepts user-defined parameters (e.g., cell parameters, minimum distances and Wyckoff positions). In general, PyXtal serves three purposes: (1) to generate custom structures, (2) to modulate the structure by symmetry relations, (3) to interface the existing structure prediction codes that require the generation of random symmetric structures. In addition, we provide several utilities that facilitate the analysis of structures, including symmetry analysis, geometry optimization, and simulations of powder X-ray diffraction (XRD). Full documentation of PyXtal is available at https://pyxtal.readthedocs.io. (c) 2021 Elsevier B.V. All rights reserved.