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title: ' zelll: a fast, framework-free, and flexible implementation of the cell lists algorithm for the Rust programming language'
message: >-
If you use this software, please cite the research article
and a versioned Zenodo DOI where appropriate.
type: software
authors:
- given-names: Vincent
family-names: Messow
orcid: 'https://orcid.org/0000-0002-4467-8804'
- given-names: Christian
family-names: Höner zu Siederdissen
orcid: 'https://orcid.org/0000-0001-9517-5839'
- given-names: Michael
family-names: Habeck
orcid: 'https://orcid.org/0000-0002-2188-5667'
identifiers:
- type: doi
value: 10.1093/bioadv/vbaf330
description: Open Access Article
- type: doi
value: 10.5281/zenodo.18183795
description: >-
The unversioned DOI of the Zenodo Archive for this
work
repository-code: 'https://github.com/microscopic-image-analysis/zelll'
url: 'https://microscopic-image-analysis.github.io/zelll'
repository: 'https://crates.io/crates/zelll'
repository-artifact: 'https://pypi.python.org/pypi/zelll'
abstract: >-
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.
license: MIT