(736d) Interactive Extensible Molecular Simulations with Etomica

Authors: 
Schultz, A. J., University at Buffalo, The State University of New York
Kofke, A. D., University at Buffalo
Kofke, D. A., University at Buffalo, The State University of New York
Etomica is an object-oriented molecular simulation programming framework [1]. It is written in Java, and was developed with a strong emphasis on modularity and extensibility. Etomica can accommodate almost any type of particle-based interaction model and any type of law governing the particles’ behavior. It can allow both hard and soft potentials, any spatial dimension, on- or off-lattice, pairwise-additive or multibody potentials, Monte Carlo or molecular dynamics (or other) simulations, and so on. It also is suitable for both batch and interactive use, allowing simulation parameters, integration method, measured quantities, and other features to be modified while the simulation proceeds. This capability has led us to use Etomica to develop a suite of interactive molecular simulation modules targeted for instructional purposes [2]. However, it is also the code base we use for many of our research applications. In addition to standard molecular simulation capabilities, Etomica has a variety of tools for calculation of virial coefficients and other cluster integrals using Mayer sampling Monte Carlo.

Recently we have performed development to expand the usefulness of the Etomica framework. In particular, we have introduced capabilities for simulations to be specified using input files defined by standard packages (e.g., LAMMPS, GROMACS). We are also developing features to enhance the interactive capabilities, such that Etomica may be configured and operated interactively in a client-server configuration. In this manner we aim to offset the increasing problems associated with interactive use when based on Java running in the browser. We describe and demonstrate these developments, and discuss our plans for further expansion of Etomica’s features and capabilities.

[1] A. J. Schultz and D. A. Kofke, “Etomica: An object-oriented framework for molecular simulation” J Comput. Chem. 36, 573 (2015).

[2] http://modules.etomica.org

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