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Scaling in the context of molecular dynamics simulations with ms2 and ls1 mardyn

In: High Performance Computing in Science and Engineering '21

Author

Listed:
  • Simon Homes

    (Lehrstuhl für Thermodynamik und Thermische Verfahrenstechnik, Technische Universität Berlin)

  • Robin Fingerhut

    (Lehrstuhl für Thermodynamik und Thermische Verfahrenstechnik, Technische Universität Berlin)

  • Gabriela Guevara-Carrion

    (Lehrstuhl für Thermodynamik und Thermische Verfahrenstechnik, Technische Universität Berlin)

  • Matthias Heinen

    (Lehrstuhl für Thermodynamik und Thermische Verfahrenstechnik, Technische Universität Berlin)

  • Jadran Vrabec

    (Lehrstuhl für Thermodynamik und Thermische Verfahrenstechnik, Technische Universität Berlin)

Abstract

This chapter covers scaling issues related to our recent work in the field of molecular dynamics simulations with a focus on computational details. The first section deals with finite size effects in the context of multicomponent diffusion. Different methods to correct the influence of the finite simulation domain are compared. In the second section, the structure of a fluid near its critical point is discussed in the context of the strong scaling behavior of the code ms2. The third section discusses droplet coalescence dynamics investigated by large molecular dynamics simulations and a macroscopic phase field model, respectively. The performance of the new supercomputer Hawk is compared to that of Hazel Hen. The last section describes the influence of the direct sampling of the energy flux on the performance of the code ls1 mardyn. Various speed tests are carried out and analyzed in detail.

Suggested Citation

  • Simon Homes & Robin Fingerhut & Gabriela Guevara-Carrion & Matthias Heinen & Jadran Vrabec, 2023. "Scaling in the context of molecular dynamics simulations with ms2 and ls1 mardyn," Springer Books, in: Wolfgang E. Nagel & Dietmar H. Kröner & Michael M. Resch (ed.), High Performance Computing in Science and Engineering '21, pages 467-479, Springer.
    • Handle: RePEc:spr:sprchp:978-3-031-17937-2_29
    DOI: 10.1007/978-3-031-17937-2_29
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