Ogre: A Python package for molecular crystal surface generation with applications to surface energy and crystal habit prediction
| Autor: | Noa Marom, Shuyang Yang, Jiawei Zhan, Saeed Moayedpour, Imanuel Bier, Wen Wen |
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| Rok vydání: | 2020 |
| Předmět: |
Materials science
010304 chemical physics General Physics and Astronomy Crystal structure 010402 general chemistry 01 natural sciences Molecular physics Surface energy 0104 chemical sciences ComputingMilieux_GENERAL Crystal Organic semiconductor chemistry.chemical_compound Tetracene chemistry 0103 physical sciences Molecule Density functional theory Physical and Theoretical Chemistry Crystal habit |
| Zdroj: | The Journal of chemical physics. 152(24) |
| ISSN: | 1089-7690 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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