Data for "Alignment-induced self-organization of autonomously steering microswimmers: Turbulence, clusters, vortices, and jets"
DOI10.5281/zenodo.14649945Zenodo14649945MaRDI QIDQ6696369FDOQ6696369
Dataset published at Zenodo repository.
Elmar Westphal, Roland G. Winkler, Segun Goh, Gerhard Gompper
Publication date: 15 January 2025
Copyright license: Creative Commons Attribution 4.0 International
Introduction This repository contains representative data and exemplary data-analysis codes supplementing the manuscript Goh et al., Alignment-induced self-organization of autonomously steering microswimmers: Turbulence, clusters, vortices, and jets, Phys. Rev. Research7, 013142 (2025), which investigates the collective motion of autonomously aligning microswimmers by large-scale multiparticle collision dynamics (MPC) simulations. Data 1. Pusher Parameters Pclet number ${\rm Pe} = 128$, maneuverability $\Omega=512$, system size $(L/a)^3=512^3$ collision cells, and number of squirmers $N_{\rm sq}=110,592$ Squirmer data File name: pusher.squirmer.dat 301 snapshots with a print interval of 2500 MPC steps Data structure Each row: a snapshot of the squirmers at a given MPC step Column: $N_{\rm sq}$ state vectors (space-separated) State vectors (12 components, space-separated): position (3D), velocity (3D), orientation (3D), angular velocity (3D) Fluid data File name: pusher.fluid.dat A snapshot of fluid data at $300 \times 2500$ MPC step, $512 \times 512 \times 512$ cells The velocity of each cell is averaged over 2500 MPC steps Data structure Column: cell position (3D), velocity (3D) Data 2. Puller Parameters Pclet number ${\rm Pe} = 128$, maneuverability $\Omega=2048$, system size $(L/a)^3 = 768^3$ collision cells, and number of squirmers $N_{\rm sq}=373,248$ Squirmer data File name: puller.squirmer.dat 301 snapshots with a print interval of 2500 MPC steps Data structure Each row: a snapshot of the squirmers at a given MPC step Column: $N_{\rm sq}$ state vectors (space-separated) State vectors (12 components, space-separated): position (3D), velocity (3D), orientation (3D), angular velocity (3D) Fluid data File name: puller.fluid.dat A snapshot of fluid data at $300 \times 2500$ MPC step, rescaled to $512 \times 512 \times 512$ cells The velocity of each cell is averaged over 2500 MPC steps Data structure Column: cell position (3D), velocity (3D) Exemplary script Squirmer MSD C code computing $(\Delta r)^2$ with an initial time of $200 \times 2500$ MPC step from the squirmer data files File name: squirmer_MSD.c Compile gcc -o squirmer_MSD squirmer_MSD.c Usage ./squirmer_MSD pusher.squirmer.dat 512 110592 Output pusher.squirmer.dat.MSD Fluid energy spectrum Python script computing $E(k)$ from the fluid data files File name: fluid_energy_spectrum.py Usage (prerequisite: NumPy) python fluid_energy_spectrum.py pusher.fluid.dat pusher.fluid.espec Appendix. Meta-data Units Time: in units of $a\sqrt{m/(k_{\rm B}T)}$ Length: in units of the side length of a collision cell $a$ Energy: in units of $k_BT$ MPC fluid Viscosity $\eta = 42.6\sqrt{mk_BT}/a^2$ Parameter Description Value $\alpha$ collision angle $130^\circ$ $h$ collision time $0.02$ $\langle N_c \rangle$ MPC density (MPC particles per cell) $20$ Squirmer Rotational diffusion coefficient $D_R = 0.000041\sqrt{k_BT/m}/a$ Parameter Description Value $R_{\rm sq}$ squirmer radius $3$ $\epsilon_0$ LJ potential strength $5$ $v_0$ self-propulsion speed $0.031488$ (${\rm Pe}=128$) $\beta$ active stress $-3$ (pusher) $3$ (puller) $R_a$ sensing range $12$ $C_0$ self-steering angular speed $0.083968$ ($\Omega=2048$) $0.335872$ ($\Omega=8192$)
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