Yang Shuyang, Bier Imanuel, Wen Wen, Zhan Jiawei, Moayedpour Saeed, Marom Noa
Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.
Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.
J Chem Phys. 2020 Jun 28;152(24):244122. doi: 10.1063/5.0010615.
We present Ogre, an open-source code for generating surface slab models from bulk molecular crystal structures. Ogre is written in Python and interfaces with the FHI-aims code to calculate surface energies at the level of density functional theory (DFT). The input of Ogre is the geometry of the bulk molecular crystal. The surface is cleaved from the bulk structure with the molecules on the surface kept intact. A slab model is constructed according to the user specifications for the number of molecular layers and the length of the vacuum region. Ogre automatically identifies all symmetrically unique surfaces for the user-specified Miller indices and detects all possible surface terminations. Ogre includes utilities to analyze the surface energy convergence and Wulff shape of the molecular crystal. We present the application of Ogre to three representative molecular crystals: the pharmaceutical aspirin, the organic semiconductor tetracene, and the energetic material HMX. The equilibrium crystal shapes predicted by Ogre are in agreement with experimentally grown crystals, demonstrating that DFT produces satisfactory predictions of the crystal habit for diverse classes of molecular crystals.
我们展示了Ogre，这是一个用于从块状分子晶体结构生成表面平板模型的开源代码。Ogre用Python编写，并与FHI-aims代码接口，以在密度泛函理论（DFT）水平上计算表面能。Ogre的输入是块状分子晶体的几何结构。表面从块状结构中劈开，表面上的分子保持完整。根据用户指定的分子层数和真空区域长度构建平板模型。Ogre会自动为用户指定的米勒指数识别所有对称独特的表面，并检测所有可能的表面终止情况。Ogre包括用于分析分子晶体表面能收敛和伍尔夫形状的实用工具。我们展示了Ogre在三种代表性分子晶体上的应用：药物阿司匹林、有机半导体并四苯和含能材料HMX。Ogre预测的平衡晶体形状与实验生长的晶体一致，表明DFT对不同类别的分子晶体的晶体习性产生了令人满意的预测。
