Linked Cell Traversal Algorithms for Three-Body Interactions in Molecular Dynamics
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arXiv
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| Main Authors: | , , , |
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| Format: | Preprint |
| Published: |
2025
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| _version_ | 1866908609718255616 |
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| author | Escobar, Jose Alfonso Pinzon Mühlhäußer, Markus Bungartz, Hans-Joachim Neumann, Philipp |
| author_facet | Escobar, Jose Alfonso Pinzon Mühlhäußer, Markus Bungartz, Hans-Joachim Neumann, Philipp |
| contents | In this work, algorithms for the parallel computation of three-body interactions in molecular dynamics are developed. While traversals for the computation of pair interactions are readily available in the literature, here, such traversals are extended to allow for the computation between molecules stored across three cells. A general framework for the computation of three-body interactions in linked cells is described, and then used to implement the corresponding traversals. In addition, our analysis is combined with the commonly used cutoff conditions, because they influence the total workload of the computation of interactions. The combinations between traversals and truncation conditions are validated using the well-known Lennard-Jones fluid. Validation case studies are taken from the literature and configured into homogeneous and inhomogeneous scenarios. Finally, strong scalability and performance in terms of molecule updates are measured at node-level. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2510_21230 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Linked Cell Traversal Algorithms for Three-Body Interactions in Molecular Dynamics Escobar, Jose Alfonso Pinzon Mühlhäußer, Markus Bungartz, Hans-Joachim Neumann, Philipp Computational Engineering, Finance, and Science Computational Physics 65Y05 In this work, algorithms for the parallel computation of three-body interactions in molecular dynamics are developed. While traversals for the computation of pair interactions are readily available in the literature, here, such traversals are extended to allow for the computation between molecules stored across three cells. A general framework for the computation of three-body interactions in linked cells is described, and then used to implement the corresponding traversals. In addition, our analysis is combined with the commonly used cutoff conditions, because they influence the total workload of the computation of interactions. The combinations between traversals and truncation conditions are validated using the well-known Lennard-Jones fluid. Validation case studies are taken from the literature and configured into homogeneous and inhomogeneous scenarios. Finally, strong scalability and performance in terms of molecule updates are measured at node-level. |
| title | Linked Cell Traversal Algorithms for Three-Body Interactions in Molecular Dynamics |
| topic | Computational Engineering, Finance, and Science Computational Physics 65Y05 |
| url | https://arxiv.org/abs/2510.21230 |