UMD package

We realised a python-based open-source package to analyse the results stemming from ab initio molecular-dynamics simulations of fluids. The library is a collection of python scripts that include two major libraries dealing with file formats and with crystallography. We propose a simplified format to store the extracted trajectories and relevant thermodynamic information of the simulations, which is saved in UMD (“Universal Molecular Dynamics”) files. The package allows the computation of a series of structural, transport and thermodynamic properties. Starting with the pair-distribution function it defines bond lengths, builds an interatomic connectivity matrix, and eventually determines the chemical speciation. Determining the lifetime of the chemical species allows to run a full statistical analysis. Then dedicated scripts compute the mean-square displacements for the atoms as well as for the chemical species, and determine the diffusion coefficients. The implemented self-correlation analysis of the atomic velocities yield the diffusion coefficients and the vibrational spectrum, and of the stresses the viscosity. The package is available via the github website as an open-access package and we encourage further collaborators. A compact archive can be soon downloaded here: the UMD package.

Copyright Razvan Caracas' Lab 2019
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