| Literature DB >> 32610993 |
Shuyang Yang1, Imanuel Bier1, Wen Wen2, Jiawei Zhan3, Saeed Moayedpour2, Noa Marom1.
Abstract
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.Entities:
Year: 2020 PMID: 32610993 DOI: 10.1063/5.0010615
Source DB: PubMed Journal: J Chem Phys ISSN: 0021-9606 Impact factor: 3.488