GEMDAT

The goal of this project was to create a modern, open-access analysis tool for molecular dynamics (MD) simulations, a widely used technique in physics, chemistry, biology, and engineering to study the behavior of materials at the atomic level. While MD simulations can generate deep insights into material properties, existing analysis tools are often limited, extracting only basic parameters such as diffusivity and activation energy. Our aim was to go beyond this by developing an advanced, flexible Python-based tool—GEMDAT (Generalized Molecular Dynamics Analysis Tool)—that captures a much broader range of material characteristics and enables intuitive 3D visualization of atomic diffusion processes.

By transitioning from a rigid MATLAB implementation to an open Python framework, we have empowered researchers with a user-friendly, modular tool that supports a wide array of simulation outputs and can analyze complex diffusion behavior at interfaces, such as those found in cutting-edge solid-state batteries. This tool makes it easier for scientists to uncover limiting factors in materials and design better-performing alternatives, especially for energy storage applications.

The impact of this project is twofold: it enhances the depth of analysis in molecular dynamics and democratizes access to high-quality materials research tools. The software is already being used by research teams at TU Delft and has attracted interest from leading groups in the UK, USA, and France, laying the foundation for a wider international user base.

This work was important to us because it addresses a critical gap in how researchers explore the kinetic and thermodynamic properties of materials—a key challenge in developing safer, more efficient technologies such as next-generation batteries. Not only did we meet our initial objectives, but the development process also allowed us to expand the tool's capabilities further than anticipated, particularly in terms of visualization and compatibility with multiple MD platforms.

The primary audience for this tool includes materials scientists, computational chemists, physicists, and engineers working with molecular dynamics simulations, particularly those focused on energy materials. We also see value in engaging educators and students, thanks to the tool’s accessibility and integration into university courses.

Following the project, we plan to continue expanding the capabilities of GEMDAT, maintain community support, and embed it more deeply into collaborative and educational frameworks. We invite researchers and educators to access, use, and contribute to the tool, which is freely available on GitHub.

Call-to-action: Explore, use, or contribute to GEMDAT via our open-source repository: https://github.com/GEMDAT-repos/GEMDAT