pyMolDyn: Identification, Structure, and Properties of Cavities/Vacancies in Condensed Matter and Molecules
pyMolDyn: Identification, Structure, and Properties of Cavities/Vacancies in Condensed Matter and Molecules
复制标题
DOI：
10.1002/jcc.24697
复制
发表时间：
2017-03-01
影响因子：
3
通讯作者：
Jones, Robert O.
中科院分区：
文献类型：
--
作者：
Heimbach, Ingo;Rhiem, Florian;Jones, Robert O.
pyMolDyn是一个在单元胞中定义的原子系统的交互式查看器，对晶体和非晶材料特别有用。它识别和可视化模拟单元中对应于所有七个三维Bravais晶格的空腔（空位，空隙），不假设空腔形状，允许不同大小的原子，并定位空腔中心（不包括原子中心的最大球体的中心）。我们定义了三种类型的空腔，并开发了一种基于分割和合并算法的方法来计算这三种类型的空腔。空腔的可视化使用了移动立方体算法。该程序允许计算和导出对分布函数（原子和/或空腔之间），以及键合和二面角，空腔体积和表面积，以及空腔形状的测量，包括非球面，非圆柱体和相对形状各向异性。开源Python程序基于GR框架和GR3例程，可用于生成高分辨率图形和视频。(C) 2016 Wiley期刊公司
pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center). We define three types of cavity and develop a method based on the split and merge algorithm to calculate all three. The visualization of the cavities uses the marching cubes algorithm. The program allows one to calculate and export pair distribution functions (between atoms and/ or cavities), as well as bonding and dihedral angles, cavity volumes and surface areas, and measures of cavity shapes, including asphericity, acylindricity, and relative shape anisotropy. The open source Python program is based on GR framework and GR3 routines and can be used to generate high resolution graphics and videos. (C) 2016 Wiley Periodicals, Inc.