MDSuite: comprehensive post-processing tool for particle simulations

Journal of Cheminformatics

Software

Francisco Torres-Herrador¹  Samuel Tovey²  Marco Brückner²  Christoph Lohrmann²  Christian Holm²  Fabian Zills² 

[1] Aeronautics and Aerospace Department, von Karman Institute for Fluid Dynamics, Rhode-St-Genese, Belgium;Thermo and Fluid Dynamics (FLOW), Vrije Universiteit Brussel, Brussels, Belgium;Laboratory for Chemical Technology (LCT), Ghent University, Ghent, Belgium;Institute for Computational Physics, Universität Stuttgart, Stuttgart, Germany;

关键词: Molecular dynamics;    Computational physics;    Material properties;    High performance computing;    TensorFlow;    FAIR data;   

DOI  :  10.1186/s13321-023-00687-y

 received in 2022-03-10, accepted in 2023-01-22,  发布年份 2023

来源: Springer

【 摘 要 】

Particle-Based (PB) simulations, including Molecular Dynamics (MD), provide access to system observables that are not easily available experimentally. However, in most cases, PB data needs to be processed after a simulation to extract these observables. One of the main challenges in post-processing PB simulations is managing the large amounts of data typically generated without incurring memory or computational capacity limitations. In this work, we introduce the post-processing tool: MDSuite. This software, developed in Python, combines state-of-the-art computing technologies such as TensorFlow, with modern data management tools such as HDF5 and SQL for a fast, scalable, and accurate PB data processing engine. This package, built around the principles of FAIR data, provides a memory safe, parallelized, and GPU accelerated environment for the analysis of particle simulations. The software currently offers 17 calculators for the computation of properties including diffusion coefficients, thermal conductivity, viscosity, radial distribution functions, coordination numbers, and more. Further, the object-oriented framework allows for the rapid implementation of new calculators or file-readers for different simulation software. The Python front-end provides a familiar interface for many users in the scientific community and a mild learning curve for the inexperienced. Future developments will include the introduction of more analysis associated with ab-initio methods, colloidal/macroscopic particle methods, and extension to experimental data.

【 授权许可】

CC BY   
© The Author(s) 2023

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