Literature DB >> 32610993

Ogre: A Python package for molecular crystal surface generation with applications to surface energy and crystal habit prediction.

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


  3 in total

1.  Interfacial Charge Transfer Influences Thin-Film Polymorphism.

Authors:  Fabio Calcinelli; Andreas Jeindl; Lukas Hörmann; Simiam Ghan; Harald Oberhofer; Oliver T Hofmann
Journal:  J Phys Chem C Nanomater Interfaces       Date:  2022-02-01       Impact factor: 4.126

2.  Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis.

Authors:  Miguel Steiner; Markus Reiher
Journal:  Top Catal       Date:  2022-01-13       Impact factor: 2.910

3.  Describing chain-like assembly of ethoxygroup-functionalized organic molecules on Au(111) using high-throughput simulations.

Authors:  Jeffrey Kelling; Robin Ohmann; Peter Zahn; Jörg Meyer; Tim Kühne; Gianaurelio Cuniberti; Jannic Wolf; Guido Juckeland; Thomas Huhn; Francesca Moresco; Sibylle Gemming
Journal:  Sci Rep       Date:  2021-07-19       Impact factor: 4.379

  3 in total

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