Atomistic Composite Simulations with Modular Software Tools on nanoHUB.org

Abstract

The use of polymers and composites is growing significantly and enabling emerging technologies. Molecular dynamics simulations of this class of materials plays an important role in our understanding of the fundamental physics of these systems. These techniques are also being used to guide the design of novel materials with customized properties. Simulating amorphous systems at molecular scales is often more challenging than simulating other materials due to the wide range of relaxation timescales, often exceeding those possible by direct MD simulations. The creation of well- relaxed structures is challenging and, though advanced methods have been designed to address this problem, not all are easily available or accessible. Many researchers use suboptimal approaches. In addition, the use of closed- source or proprietary software and the lack of molecular structure repositories can lead to unreproducible results. We are developing a framework for molecular simulations of polymers and amorphous systems. The tools we develop are universally accessible and useful to the community for cloud computing via nanoHUB. The framework consists of a stateof- the-art molecular builder, a parallel MD engine with stencils that enable efficient structure relaxation and property characterization, atomistic visualization, and postprocessing codes, all accessible from Jupyter notebooks running on nanoHUB. These notebooks can also access databases of force fields and molecular structures. Users do not need to download or install any software nor provide compute cycles. Expert users can extend the Python code in the notebooks or download it and run it in their own resources.