Treffer: Zelll : a fast, framework-free, and flexible implementation of the cell lists algorithm for the Rust programming language

Summary The cell lists algorithm is widely used to compute pairwise particle interactions below a fixed cutoff distance in approximately linear time. Prominent molecular dynamics frameworks implementing cell lists variants assume pre-determined and densely populated simulation boxes suitable for e.g. all-atom simulations with explicit solvents. zelll implements a simple yet efficient variant of the cell lists algorithm that uses sparse storage for the underlying partitioning grid. This allows for applications with dynamic simulation boundaries and sparsely populated simulation space not strictly fitting into the scope of common molecular dynamics frameworks, such as many coarse-grained simulations. For this reason, zelll does not target specific frameworks. Availability and implementation zelll is an open-source Rust library available under the MIT license at https://github.com/microscopic-image-analysis/zelll and https://crates.io/crates/zelll. Python bindings are available at https://pypi.org/project/zelll. Supplementary information Supplementary information is available at Bioinformatics Advances online.