MDSuite: comprehensive post-processing tool for particle simulations

Abstract

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.

Collaboration on Machine-Learned Potentials with IPSuite: A Modular Framework for Learning-on-the-Fly

“…For all simulations, a time step of d t = 0.5 fs was used to properly resolve the movement of the hydrogen atoms. The production simulation used a Nosé–Hoover chain thermostat at 360 K. Analysis of the trajectory was performed using MDSuite . The radial distribution functions (RDFs) for the homologous heavy atom pairs and the intramolecular and first intermolecular peaks from the O–H RDF together with their fits are displayed in Figure .…”

“…(a) RDFs of the heavy atom pairs r C,C , r O,O , and r S,S using MDSuite . RDFs are shifted vertically for better visualization.…”

“…The production simulation used a Nose− Hoover chain thermostat at 360 K. Analysis of the trajectory was performed using MDSuite. 109 The radial distribution functions (RDFs) for the homologous heavy atom pairs and the intramolecular and first intermolecular peaks from the O− H RDF together with their fits are displayed in Figure 13. Each was computed with a bin width of 0.01 Å over 5000 equally spaced configurations from the simulation.…”