Coherens model description

The source code of the program is written in FORTRAN 77 and has four major components:

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.

The design of the program consists of a "core" part and of a series of modules. This modular design allows easy updating of any particular process, or the inclusion of an alternative solution method, or the addition of new processes. The core updates the current field by solving the Navier-Stokes equations and contains the advection-diffusion module. A series of switches is implemented permitting the user, for a particular simulation, to select whichever processes are required.

The characteristics of the program can be summarised as follows:

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.

A number of values for switches and model parameters (hydrodynamics only, default turbulence scheme, ...) are adopted by default, making it easier for a less experienced user to run the model. A set of test cases has already been developed. They are intended to check the portability of the code, to test a particular scheme or specific module, or to show some realistic responses (e.g. seasonal cycles in the North Sea, idealised river outflow).