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atommovr: An open-source simulation framework for rearrangement in atomic arrays

Nikhil K Harle, Bo-Yu Chen, Bob Bao, and Hannes Bernien

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AbstractThe task of atom rearrangement has emerged in the last decade as a fundamental building block in the development of neutral atom-based quantum processors. As such processors grow to thousands of atoms, it becomes increasingly important to design algorithms robust to experimental sources of error. While recent progress has been made towards developing algorithms with favorable time scaling, such work has been limited to noiseless settings. Moreover, there is a lack of open-source code for reproducing and benchmarking existing algorithms. To address these deficiencies, we develop an open-source simulation framework, atommovr, and leverage it to study three distinct settings: 1) time-optimal, noiseless rearrangement, 2) noisy rearrangement under realistic error models, and 3) noiseless dual-species rearrangement. We extract lower bounds for time-optimal rearrangement, study advantageous strategies across different error regimes, and develop a novel dual-species algorithm, InsideOut, capable of avoiding 'blocked' configurations with a near-unity success rate. We hope that atommovr can serve as a common tool for the community to study rearrangement, lower the barrier to entry for new experimental groups, and stimulate progress in developing algorithms tailored to minimize atom loss in experiment.Featured image: $\href{https://github.com/bernienlab/atommovr}{\text{atommovr}}$Popular summaryNeutral atoms confined by tightly focused beams of light called 'optical tweezers' are a promising prototype for a quantum computer. Hundreds or thousands of atoms can be trapped this way, and arranged into a grid to form a register of quantum bits. However, there is a catch in how this register is formed. Tweezers are loaded by being overlapped with a cold cloud of atoms, and the loading is probabilistic: what comes out is a grid with random gaps in it. Before a computation can begin, the trapped atoms must be shuffled around to form a regular configuration. But this shuffling is a race: each move operation takes time and risks spilling the atom, and the atoms typically survive only for seconds to tens of minutes before being hit by background gas particles. The problem of how to efficiently sort atoms is called 'rearrangement'. Here, we develop $\text{atommovr}$, an open-source Monte Carlo simulation framework for evaluating rearrangement algorithms and measuring how they hold up against the atom losses and timing constraints of a real experiment. $\text{atommovr}$ is designed to be built upon by the community. Up-to-date information concerning new features and opportunities for contribution can be found on the project's $\href{https://github.com/bernienlab/atommovr}{\text{GitHub}}$ page.► BibTeX data@article{Harle2026atommovropensource, doi = {10.22331/q-2026-07-29-2177}, url = {https://doi.org/10.22331/q-2026-07-29-2177}, title = {atommovr: {A}n open-source simulation framework for rearrangement in atomic arrays}, author = {Harle, Nikhil K and Chen, Bo-Yu and Bao, Bob and Bernien, Hannes}, journal = {{Quantum}}, issn = {2521-327X}, publisher = {{Verein zur F{\"{o}}rderung des Open Access Publizierens in den Quantenwissenschaften}}, volume = {10}, pages = {2177}, month = jul, year = {2026} }► References [1] W. Lee, H. Kim, and J. Ahn. ``Three-dimensional rearrangement of single atoms using actively controlled optical microtraps''. Opt. Express 24, 9816–9825 (2016). https://doi.org/10.1364/OE.24.009816 [2] D. Barredo, S. de Léséleuc, V. Lienhard, T. Lahaye, and A. Browaeys. ``An atom-by-atom assembler of defect-free arbitrary two-dimensional atomic arrays''. Science 354, 1021–1023 (2016). https://doi.org/10.1126/science.aah3778 [3] M. Endres, H. Bernien, A. Keesling, H. Levine, E. R. Anschuetz, A. Krajenbrink, C. Senko, V. Vuletić, M. Greiner, and M. D. Lukin. ``Atom-by-atom assembly of defect-free one-dimensional cold atom arrays''. Science 354, 1024–1027 (2016). https://doi.org/10.1126/science.aah3752 [4] H. Kim, W. Lee, H. Lee, H. Jo, Y. Song, and J. Ahn. ``In situ single-atom array synthesis using dynamic holographic optical tweezers''. Nature Communications 7, 13317 (2016). https://doi.org/10.1038/ncomms13317 [5] T. M. Graham, Y. Song, J. Scott, C. Poole, L. Phuttitarn, K. Jooya, P. Eichler, X. Jiang, A. Marra, B. Grinkemeyer, M. Kwon, M. Ebert, J. Cherek, M. T. Lichtman, M. Gillette, J. Gilbert, D. Bowman, T. Ballance, C. Campbell, E. D. Dahl, O. Crawford, N. S. Blunt, B. Rogers, T. Noel, and M. 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Nature 529, 484–489 (2016). https://doi.org/10.1038/nature16961 [51] D. Silver et al. ``Mastering the game of Go without human knowledge''. Nature 550, 354–359 (2017). https://doi.org/10.1038/nature24270 [52] D. Silver et al. ``A general reinforcement learning algorithm that masters chess, shogi, and Go through self-play''. Science 362, 1140–1144 (2018). https://doi.org/10.1126/science.aar6404 [53] T. Moerland. ``Single player Alpha Zero implementation''. https://github.com/tmoer/alphazero_singleplayer (2022). Accessed: 2025-07-11. https://github.com/tmoer/alphazero_singleplayerCited byCould not fetch Crossref cited-by data during last attempt 2026-07-29 09:51:31: Could not fetch cited-by data for 10.22331/q-2026-07-29-2177 from Crossref. This is normal if the DOI was registered recently. Could not fetch ADS cited-by data during last attempt 2026-07-29 09:51:31: Cannot retrieve data from ADS due to rate limitations.This Paper is published in Quantum under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. Copyright remains with the original copyright holders such as the authors or their institutions. AbstractThe task of atom rearrangement has emerged in the last decade as a fundamental building block in the development of neutral atom-based quantum processors. As such processors grow to thousands of atoms, it becomes increasingly important to design algorithms robust to experimental sources of error. While recent progress has been made towards developing algorithms with favorable time scaling, such work has been limited to noiseless settings. Moreover, there is a lack of open-source code for reproducing and benchmarking existing algorithms. To address these deficiencies, we develop an open-source simulation framework, atommovr, and leverage it to study three distinct settings: 1) time-optimal, noiseless rearrangement, 2) noisy rearrangement under realistic error models, and 3) noiseless dual-species rearrangement. We extract lower bounds for time-optimal rearrangement, study advantageous strategies across different error regimes, and develop a novel dual-species algorithm, InsideOut, capable of avoiding 'blocked' configurations with a near-unity success rate. We hope that atommovr can serve as a common tool for the community to study rearrangement, lower the barrier to entry for new experimental groups, and stimulate progress in developing algorithms tailored to minimize atom loss in experiment.Featured image: $\href{https://github.com/bernienlab/atommovr}{\text{atommovr}}$Popular summaryNeutral atoms confined by tightly focused beams of light called 'optical tweezers' are a promising prototype for a quantum computer. Hundreds or thousands of atoms can be trapped this way, and arranged into a grid to form a register of quantum bits. However, there is a catch in how this register is formed. Tweezers are loaded by being overlapped with a cold cloud of atoms, and the loading is probabilistic: what comes out is a grid with random gaps in it. Before a computation can begin, the trapped atoms must be shuffled around to form a regular configuration. But this shuffling is a race: each move operation takes time and risks spilling the atom, and the atoms typically survive only for seconds to tens of minutes before being hit by background gas particles. The problem of how to efficiently sort atoms is called 'rearrangement'. Here, we develop $\text{atommovr}$, an open-source Monte Carlo simulation framework for evaluating rearrangement algorithms and measuring how they hold up against the atom losses and timing constraints of a real experiment. $\text{atommovr}$ is designed to be built upon by the community. Up-to-date information concerning new features and opportunities for contribution can be found on the project's $\href{https://github.com/bernienlab/atommovr}{\text{GitHub}}$ page.► BibTeX data@article{Harle2026atommovropensource, doi = {10.22331/q-2026-07-29-2177}, url = {https://doi.org/10.22331/q-2026-07-29-2177}, title = {atommovr: {A}n open-source simulation framework for rearrangement in atomic arrays}, author = {Harle, Nikhil K and Chen, Bo-Yu and Bao, Bob and Bernien, Hannes}, journal = {{Quantum}}, issn = {2521-327X}, publisher = {{Verein zur F{\"{o}}rderung des Open Access Publizierens in den Quantenwissenschaften}}, volume = {10}, pages = {2177}, month = jul, year = {2026} }► References [1] W. Lee, H. Kim, and J. Ahn. ``Three-dimensional rearrangement of single atoms using actively controlled optical microtraps''. Opt. Express 24, 9816–9825 (2016). https://doi.org/10.1364/OE.24.009816 [2] D. Barredo, S. de Léséleuc, V. Lienhard, T. Lahaye, and A. Browaeys. ``An atom-by-atom assembler of defect-free arbitrary two-dimensional atomic arrays''. Science 354, 1021–1023 (2016). https://doi.org/10.1126/science.aah3778 [3] M. Endres, H. Bernien, A. Keesling, H. Levine, E. R. Anschuetz, A. Krajenbrink, C. Senko, V. Vuletić, M. Greiner, and M. D. Lukin. ``Atom-by-atom assembly of defect-free one-dimensional cold atom arrays''. Science 354, 1024–1027 (2016). https://doi.org/10.1126/science.aah3752 [4] H. Kim, W. Lee, H. Lee, H. Jo, Y. Song, and J. Ahn. ``In situ single-atom array synthesis using dynamic holographic optical tweezers''. Nature Communications 7, 13317 (2016). https://doi.org/10.1038/ncomms13317 [5] T. M. Graham, Y. Song, J. Scott, C. Poole, L. Phuttitarn, K. Jooya, P. Eichler, X. Jiang, A. Marra, B. Grinkemeyer, M. Kwon, M. Ebert, J. Cherek, M. T. Lichtman, M. Gillette, J. Gilbert, D. Bowman, T. Ballance, C. Campbell, E. D. Dahl, O. Crawford, N. S. Blunt, B. Rogers, T. Noel, and M. Saffman. ``Multi-qubit entanglement and algorithms on a neutral-atom quantum computer''. Nature 604, 457–462 (2022). https://doi.org/10.1038/s41586-022-04603-6 [6] D. Bluvstein, H. Levine, G. Semeghini, T. T. Wang, S. Ebadi, M. Kalinowski, A. Keesling, N. Maskara, H. Pichler, M. Greiner, V. Vuletić, and M. D. Lukin. ``A quantum processor based on coherent transport of entangled atom arrays''. Nature 604, 451–456 (2022). https://doi.org/10.1038/s41586-022-04592-6 [7] B. W. Reichardt et al. ``Logical computation demonstrated with a neutral atom quantum processor''. arXiv:2411.11822 (2024). https://doi.org/10.48550/arXiv.2411.11822 arXiv:2411.11822 [8] D. Bluvstein et al. ``Logical quantum processor based on reconfigurable atom arrays''. Nature 626, 58–65 (2024). https://doi.org/10.1038/s41586-023-06927-3 [9] B. Zhang, G. Liu, G. Bornet, S. P. Horvath, P. Peng, S. Ma, S. Huang, S. Puri, and J. D. Thompson. ``Logical qubits with erasure conversion using metastable neutral atoms''. 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atommovr: An open-source simulation framework for rearrangement in atomic arrays

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