Computational aspects

The computational structure of the coupled physical-biogeochemical model system implemented here has been designed under consideration of various objectives. In this section a description of the various design related decisions is given. The major objectives are:

For the biogeochemical model, we have adopted the same design strategy as has been used for the turbulence module of GOTM. The interface between an application using the turbulence module consists of two subroutine calls only: init_turbulence() and do_turbulence(). The subroutine init_turbulence() is responsible for initialising the parameters of the turbulence module and called as part of the initialisation of the entire model. For the turbulence module the initialisation includes reading namelists with the model configuration, allocating memory for all necessary variables and initialising these variables with sensible values. init_turbulence() should only be called once during program execution and after this call all public and private variables of the turbulence module should be in a consistently initialised state. During the time integration of the model, do_turbulence() has to be called at each time step. It is called with a number of parameters to transfer information e.g. from the mean-flow module to the turbulence module but also to receive the variables updated by the turbulence module.

Using the same strategy for the biogeochemical module has some problematic implications which are described here. In analogy to the turbulence module, the interface is given via the two subroutines init_bio() and do_bio(). The major difference between the turbulence module and the biogeochemical module in terms of implementation is that in the former the number of variables are known at compilation time and the dimensions are specified at run time where as in the latter both the number of state variables and their dimension are known only at run time. The general interface has to be able to handle not only the different biogeochemical models implemented at present but also to provide a framework for developing future models. There are two major items to address: 1. how to initialise the biogeochemical model and 2. how to select the right biogeochemical model during the time integration and use the selected ordinary differential equation (ODE) solver.

To solve the initialisation problem we have chosen a two-level initialisation approach. At the first level variables not specific to any of the biogeochemical models are initialised. The single most important variable during this phase is bio_model, which contains the identification number for all implemented biogeochemical models. Depending on the value of bio_model, the second level of initialisation is started. At this level all model specific variables (such as process rates) are initialised. The most important variable at the second level is $ I$ (number of state variables). After this step, the system returns to the first level, and now all information is available for allocating memory and initialising all variables. The most important data structure provided to the individual biogeochemical models will briefly be mentioned here. $ c_{i,k}$ with $ 1\leq i\leq I$ and $ 1\leq k\leq N$ (number of vertical layers) is a two-dimensional array containing the concentrations of each variable at each depth. $ I$ is supplied by the individual biogeochemical model and $ N$ is transferred in the call to init_bio() from the physical model.

After the initialisation, all variables are initialised in a common data structure where the only link to the specific model is via bio_model and $ I$. The next step is to design the actual time integration in such a way that selected biogeochemical model operates on the common data structure using the selected ODE solver in a transparent way.

Figure 3: The structure of the do_bio() subroutine. This subroutine is responsible for updating all variables in the biogeochemical model in question at each time-step. do_bio() essentially works as a wrapper around all biogeochemical models implemented. The hatched arrows from process model to ODE solvers indicate that between one and four calls of process model per time step are performed, depending on the order of the chosen ODE solver.
\scalebox{0.5}{\includegraphics{figures/structure_gotmbio.eps}}

Figure 3 shows a sketch of how this is organised in the model source code. The sketch should be be read from left to right. At the left side we have the interface do_bio(), which is the only connection to the calling program. The next level shows a sequence of steps necessary to do the time integration. It should be noted that not all biogeochemical models necessarily have to execute all the steps, some models do e.g. not need any surface fluxes or short-wave radiation. For the diffusion/advection part a general subroutine is called which is also used by the physical model. After having calculated $ I_{PAR}$ and $ B$ (see eqs. (29) and ([*]), the next step is the step at which the production and destruction terms ($ p_{i,j,k}$ and $ d_{i,j,k}$) of the biogeochemical models are calculated. This is done via a call to ode_solver(). After the call to ode_solver(), $ c_{i,k}$ has been updated with the new values of all variables in the biogeochemical model. Which ODE solver to use is determined during the initialisation phase (ode_method). It should be noted that for some of the solution methods the biogeochemical processes have to be evaluated more than once. Instead of having ode_solver() being responsible for calling the chosen biogeochemical model, an additional subroutine has been introduced: process_model, is a simple wrapper routine calling the selected biogeochemical model.

The implementation of this biogeochemical module into three-dimensional models is straight-forward. The 3D model has to take care of storing all three-dimensional state variables and calculate their advection with the mean flow and the horizontal diffusion. Settling, migration, vertical diffusion and the production/destruction processes are calculated by the biogeochemical module which has to be called by means of a loop over all horizontal grid boxes of the 3D model.

This text has been adapted from Burchard et al. (2006).

Karsten Bolding 2012-12-28