Computational models of the ocean plankton ecosystem are traditionally based on simulating entire populations of microbes using sets of coupled differential equations. However, due to recent advances in high-performance computing, a new class of individual-based models (IBM) has come to the fore, which uses computational agents to model individual sub-populations of marine plankton. Although computationally more expensive, these agent-based models offer features that cannot be re-created using population-level dynamics, such as individual life cycles, intra-population variability and an increased stability over parameter ranges. The main focus of this thesis is the implementation and verification of an embedded modelling framework for creating agent-based plankton ecology models in Fluidity-ICOM, a state-of-the-art ocean model that solves the Navier-Stokes equations on adaptive unstructured finite element meshes. Since Fluidity-ICOM provides an interface for creating population-based ecology models, a generic agent-based framework not only enables the integration of existing plankton IBMs with adaptive remeshing technology, but also allows individual and population-based components to be used within a single hybrid ecosystem. This thesis gives a full account of the implementation of such a framework, focusing in particular on the movement and tracking of agents in an unstructured finite element mesh and the coupling mechanism used to facilitate agent-mesh and agent-agent interactions. The correctness of the framework is verified using an existing agent-based ecosystem model with four trophic levels, which is shown to settle on a stationary annual attractor given a stable cycle of annual forcing. A regular cycle of phytoplankton primary production and zooplankton reproduction is achieved using a purely agent-based implementation and a hybrid food chain version of the model, where the two top-level components of the ecosystem are modelled using Eulerian field equations. Finally, a standalone phytoplankton model is used to investigate the effects of vertical mesh adaptivity on the ecosystem in a three-dimensional mesh.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:631216 |
| Date | January 2014 |
| Creators | Lange, Michael |
| Contributors | Field, Anthony ; Gorman, Gerard |
| Publisher | Imperial College London |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | http://hdl.handle.net/10044/1/18051 |
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