Sarkas: A Fast Pure-Python Molecular Dynamics Suite for Non-Ideal Plasmas

Molecular Dynamics (MD) is a powerful tool for simulating complex dynamical systems. MD is used across several disciplines and their sub-fields, e.g. biology, chemistry, material science. As a matter of fact for each of these research fields we can find MD codes, open-source or proprietary, optimized for the simulation of their respective dynamical systems. No such code exists for Non-Ideal Plasmas. This generates several difficulties for researchers. On one hand researchers are forced to modify existing codes and/or write their own. This requires an extensive knowledge of computing as all of the available codes have been developed in low-level languages, e.g. C or Fortran. Furthermore, the codes have been optimized for the simulation of systems other than non-ideal plasmas and as such are often difficult to modify. On the other hand most MD codes provide only a code for the simulation phase and lack pre-processing and/or post-processing analysis tools. Several open-source packages are available for post-processing, but again they are specific to systems other than non-ideal plasmas and are often developed in interpretative languages, e.g. Python.