A Software Framework for the Automatic Evaluation of Physical Properties from Atomistic Simulations

Molecular Dynamics is an important scientific field that involves a multidisciplinary context. Specific disciplines like Material Science, Chemistry, Mathematics and Computer Science works together to develop this extraordinary field. Researchers in Molecular Dynamics work directly with High Performance Computing systems, and need to execute simulations using popular software packages like LAMMPS, GROMACS, CHARMM, CP2K, etc. The overall process for simulation could be a little tedious for novel or experienced users, the reasons will be discussed along this work, but in general, the time consuming for preparing input files, analysis of output files and resource checking like processors and GPU availability, from HPC systems are those ones. This work presents a software solution, in concrete, a software framework for the automatic evaluation of physical properties from atomistic simulations. The solution is developed using the specific software tools and focused on package LAMMPS for simulations. For software framework, a command line interface and a colored output was considered, to make the user experience more comfortable and familiar because interfaces of molecular dynamics packages are command line generally. And finally a future work topics are presented. It is interesting to know that not all work is done in the Molecular Dynamics field, and of course developing software tools to automate the entire process and minimize the effort on running simulations and focus the energy in research.