COHERENS

Model description

1. A physical part with a circulation module and a general module for solving advection-diffusion equations.
2. A microplankton module.
3. An Eulerian sediment module.
4. A component with both an Eulerian and a Lagrangian transport model for contaminant distributions.

General

• Cartesian or spherical grid
• sigma-coordinates in the vertical with the possibility to use non-uniform grid sizes
• the possibility to run the program as a one-dimensional point model in the vertical
• one time step for the update of all 3-D quantities
• different schemes for advection which can be updated in future versions (upwind, Lax-Wendroff, TVD)
• the possibility to perform a harmonic analysis on user-defined variables
• various forms of data input with the possibility to use different time intervals for different components of the program (physics, biology, suspended material)
• type of output specified by the user (format, time step, grid locations, variables; time series, harmonic or time-averaged output; particle trajectories)
• error traps which stop execution of the program after improper initialisation and in some other cases, and which provide an explanatory message
• interface module which converts model output into portable netCDF format

Physics

• The mode-splitting technique is used to solve the 2-D and 3-D momentum equations and continuity equations as in the Princeton Ocean Model.
• The possibility is foreseen to include temperature, salinity or both.
• The absorption of solar radiation in the upper part of the water column is implemented by an optical module.
• Density effects in the momentum and turbulence equations are included via an equation of state.
• The program incorporates a variety of turbulence closure schemes ranging from simple algebraic expressions to one- or two-equation turbulence energy models.
• Various types of radiation conditions can be used at the open sea and river boundaries.
• The effect of wave-current interaction on the bottom shear stress can be included.
• Different formulations for the wind stress and surface heat fluxes are available.

Biology

• Water-column biology and nutrient cycling are described by a microplankton-detritus module with associated optical equations which take account of light attenuation by all organic and inorganic particulates.
• The module describes the cycling of carbon and nitrogen through microplankton and detrital compartments, with corresponding changes in dissolved concentrations of nitrate, ammonium and oxygen.
• The microplankton compartment provides an efficient parameterisation of fast autotrophic and heterotrophic processes, effectively including most of the types of organisms that are specified separately in "microbiological loop" models.
• Microplankton dynamics are mainly those suggested by the "cell-quota, threshold-limitation" theory.
• The effects of mesozooplankton are imposed as a grazing pressure, which removes some microplankton and converts the rest to detritus, with a slower rate of decay.

Sediments

• All particulate compartments of the biological model have a sinking rate, and can deposit to the sea-bed.
• The sediment model also describes suspended inorganic particle concentrations as one or two state variables, which may carry contaminants (in future versions) and which influence light attenuation.
• Deposition and resuspension of particulates involves a "fluff" layer of finite capacity.
• Resuspension increases as a power function of bed stress, and the absence of the usual threshold for the resuspension of cohesive sediments can be seen as a simple parameterisation for a heterogeneous population of particles and bed types.

Contaminants

• Two transport models are available.
• The first one uses an Eulerian approach and solves advection-diffusion type equations for a number of user-defined dissolved substances.
• The second is a Lagrangian type model using passive tracers. Vertical and horizontal diffusion of suspended particles is determined by a random walk method.
• In both models new input of suspended material either by river discharge or at open sea boundaries can be defined by the user.