PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids
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SOFTWARE REPORT
PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids Yunwen Tao1 · Wenli Zou2 · Sadisha Nanayakkara1 · Elfi Kraka1 Received: 30 June 2020 / Accepted: 4 August 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Visualizing vibrational motions calculated with different ab initio packages requires dedicated post-processing tools. Here, we present a PyMOL plugin called PyVibMS for visualizing the vibrational motions for both molecular and solid systems calculated by mainstream quantum chemical computer programs including Gaussian, Q–Chem, VASP, and CRYSTAL. Benefiting from the continuing development of the PyMOL platform, PyVibMS provides powerful functionalities and userfriendly interface. PyVibMS was written in Python and its open-source nature makes it flexible and sustainable. As an example, the motions of the Konkoli-Cremer local vibrational modes are shown in this work for the first time. PyVibMS is freely available at https://github.com/smutao/PyVibMS. Keywords Vibrational spectroscopy · PyMOL · Phonon · Normal mode · Harmonic approximation · Local vibrational mode theory
Introduction Vibrational spectroscopy is a fundamental analytical tool to study structural properties and dynamics of molecules and solids [1–4]. Infrared (IR) and Raman spectroscopy can be employed to determine the microscopic structure by assigning observed frequency peaks to the vibrations of specific functional groups [5, 6] or to characterize intermolecular forces, e.g., hydrogen bonding [7–9], in both molecular and solid systems [10–14]. With the rapid development in the field of computational chemistry, the theoretical prediction of vibrational spectra of molecular systems within the harmonic approximation based on analytic Hessian matrices is nowadays a routine procedure, which has been implemented in various quantum chemical packages [15, 16]. Extracting vibrational spectra for liquid and solution systems with time-correlation functions of velocities from molecular dynamics simulation Elfi Kraka
[email protected] 1
Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX, 75275-0314, USA
2
Shaanxi Key Laboratory for Theoretical Physics Frontiers, Institute of Modern Physics, Northwest University, Xi’an, Shaanxi, 710127, People’s Republic of China
trajectories is also on the rise [17–20]. Theoretical modeling of solids, e.g., crystals, although lagging behind the modeling of isolated molecules, has witnessed the development of several first-principles calculation packages (e.g., VASP, CASTEP, CP2K, Quantum ESPRESSO, WIEN2k, DMol3, and CRYSTAL) that allow the calculation of vibrational frequencies of solids [21, 22]. After the lattice vibrational modes and associated frequencies have been calculated for a crystal or other periodic system, it is necessary to visualize the atomic vibrational motions if assigning a vibrational frequency to a certain functional group is desired. When modeling the heterogeneous catalysis on metal surfaces, it woul
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