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


Journal

The Journal of chemical physics
ISSN: 1089-7690
Titre abrégé: J Chem Phys
Pays: United States
ID NLM: 0375360

Informations de publication

Date de publication:
28 Jun 2020
Historique:
entrez: 3 7 2020
pubmed: 3 7 2020
medline: 3 7 2020
Statut: ppublish

Résumé

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.

Identifiants

pubmed: 32610993
doi: 10.1063/5.0010615
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

244122

Auteurs

Shuyang Yang (S)

Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.

Imanuel Bier (I)

Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.

Wen Wen (W)

Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.

Jiawei Zhan (J)

School of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China.

Saeed Moayedpour (S)

Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.

Noa Marom (N)

Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.

Classifications MeSH