LModeA-nano: A PyMOL Plugin for Calculating Bond Strength in Solids, Surfaces, and Molecules via Local Vibrational
Yunwen Tao1, Wenli Zou2, Sadisha Nanayakkara1
1Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States.
Abstract:
The analysis of chemical bonding in crystal structures and surfaces is an important research topic in theoretical chemistry. In this work, we present a PyMOL plugin, named LModeA-nano, as implementation of the local vibrational mode theory for periodic systems (Tao et al. J. Chem. Theory Comput. 2019, 15, 1761) assessing bond strength in terms of local stretching force constants in extended systems of one, two, and three dimensions. LModeA-nano can also analyze chemical bonds in isolated molecular systems thus enabling a head-to-head comparison of bond strength across systems with different dimensions in periodicity (0-3D). The new code is interfaced to the output generated by various solid-state modeling packages including VASP, CP2K, Quantum ESPRESSO, CASTEP, and CRYSTAL. LModeA-nano is cross-platform, open-source and freely available on GitHub: https://github.com/smutao/LModeA-nano.
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