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We develop a Python-based open-source package to analyze the results stemmingfrom ab initio molecular-dynamics simulations of fluids. The package is bestsuited for applications on natural systems, like silicate and oxide melts,water-based fluids, various supercritical fluids. The package is a collectionof Python scripts that include two major libraries dealing with file formatsand with crystallography. All the scripts are run at the command line. Wepropose a simplified format to store the atomic trajectories and relevantthermodynamic information of the simulations, which is saved in UMD files,standing for Universal Molecular Dynamics. The UMD package allows thecomputation of a series of structural, transport and thermodynamic properties.Starting with the pair-distribution function it defines bond lengths, builds aninteratomic connectivity matrix, and eventually determines the chemicalspeciation. Determining the lifetime of the chemical species allows running afull statistical analysis. Then dedicated scripts compute the mean-squaredisplacements for the atoms as well as for the chemical species. Theimplemented self-correlation analysis of the atomic velocities yields thediffusion coefficients and the vibrational spectrum. The same analysis appliedon the stresses yields the viscosity. The package is available via the GitHubwebsite and via its own dedicated page of the ERC IMPACT project as open-accesspackage.

Analyzing melts and fluids from ab initio molecular dynamics simulations with the UMD package