Baird ME, Wild-Allen KA, Parslow J, Mongin M, Robson B, Skerratt J, Rizwi F, Soja-Wozniak M, Jones E, Herzfeld M, Margvelashvili N, Andrewartha J, Langlais C, Adams MP, Cherukuru N, Gustafsson M, Hadley S, Ralph PJ, Rosebrock U, Schroeder T, Laiolo L, Harrison D, Steven ADL, Baird ME, Wild-Allen KA, Parslow J, Mongin M, Robson B, Skerratt J, Rizwi F, Soja-Wozniak M, Jones E, Herzfeld M, Margvelashvili N, Andrewartha J, Langlais C, Adams MP, Cherukuru N, Gustafsson M, Hadley S, Ralph PJ, Rosebrock U, Schroeder T, Laiolo L, Harrison D, and Steven ADL
Abstract. Since the mid-1990s, Australia's Commonwealth Science Industry and Research Organisation (CSIRO) has been developing a biogeochemical (BGC) model for coupling with a hydrodynamic and sediment model for application in estuaries, coastal waters and shelf seas. The suite of coupled models is referred to as the CSIRO Environmental Modelling Suite (EMS) and has been applied at tens of locations around the Australian continent. At a mature point in the BGC model's development, this paper presents a full mathematical description, as well as links to the freely available code and user guide. The mathematical description is structured into processes so that the details of new parameterisations can be easily identified, along with their derivation. In EMS, the underwater light field is simulated by a spectrally resolved optical model that calculates vertical light attenuation from the scattering and absorption of 20+ optically active constituents. The BGC model itself cycles carbon, nitrogen, phosphorous and oxygen through multiple phytoplankton, zooplankton, detritus and dissolved organic and inorganic forms in multiple water column and sediment layers. The water column is dynamically coupled to the sediment to resolve deposition, resuspension and benthic–pelagic biogeochemical fluxes. With a focus on shallow waters, the model also includes detailed representations of benthic plants such as seagrass, macroalgae and coral polyps. A second focus has been on, where possible, the use of geometric derivations of physical limits to constrain ecological rates. This geometric approach generally requires population-based rates to be derived from initially considering the size and shape of individuals. For example, zooplankton grazing considers encounter rates of one predator on a prey field based on summing relative motion of the predator with the prey individuals and the search area; chlorophyll synthesis includes a geometrically derived self-shading term; and the