PlanktonIndividuals.jl: A GPU supported individual-based phytoplankton life cycle model

Abstract

Marine phytoplankton contributes ~50% of the total primary production on Earth forming the basis of the food web in the oceans. Understanding the spatial distribution and temporal variations of the phytoplankton community is essential to the global carbon and nutrient cycles. PlanktonIndividuals.jl is a fast individual-based model that represents the phytoplankton life cycle in detail, is written in Julia, and runs on both CPU and GPU. The model is used to elucidate temporal and spatial variations in phytoplankton cell density and stoichiometry, as well as growth and division behaviors induced by diel cycle and physical motions ranging from sub-mesoscale to large scale processes. PlanktonIndividuals.jl can simulate multiple functional groups of phytoplankton with different growth and division strategies. It can thus effectively represent the interactions within and between functional groups. It simulates phytoplankton cells as Lagrangian particles (moving frame) while nutrients are represented as Eulerian tracers (fixed frame). The model thus takes advantage of both frameworks-Eulerian simulations employ a fixed mesh to represent flow fields on a grid, while plankton individuals move following the velocity field interpolated to their locations. Figure 1: Schematic diagram of phytoplankton physiology described in PlanktonIndividuals.jl. The equations included in PlanktonIndividuals.jl to describe phytoplankton physiology are Wu, & Forget. (2022). PlanktonIndividuals.jl: A GPU supported individual-based phytoplankton life cycle model. Journal of Open Source Software, 7 (73), 4207. https://doi.org/10.21105/joss.04207.