Coherens documentation

A full documentation with a detailed user guide is available within the COHERENS distribution file. This is composed of the following parts:

• Part I is considered as an introductory manual. "Getting started'' sections with instructions for preparing and running a pre-defined test case or a user application are given in Chapter I-2. Model setup with the aid of the generic code examples is discussed in Chapter I-3. Installation and use of the graphical interface, and instructions for displaying output from test case simulations using the FERRET graphical freeware is given in Chapter I-4.
• Ten test cases and two more realistic applications are presented in Part II which contains the following seven chapters: computing platforms and portability (II-1), test cases for advection (II-2), test cases for turbulence (II-3), plume test cases (II-4), biological test cases (II-5), the NOMADS tracer experiments (II-6) and the simulation of a yearly cycle in the North Sea using the integrated model (II-7). Each test case is provided with a number of experiments testing the role of program switches, model parameters or different types of boundary conditions. A total number of 51 experiments can be performed by the user in this way. The aim is to test the portability of the code, to illustrate how model setup is performed and to show different types of applications.
• The scientific aspects of COHERENS are fully explained in Part III (Model Description) where all model equations and numerical schemes are written out in detail and the scientific background is discussed. This part is further divided in five chapters: physics (III-1), biology and sediments (III-2), particle module and contaminants (III-3), numerical methods (III-4) and a final chapter (III-5) with suggestions for improvement and future updates of COHERENS.
• Part IV is the User Manual covering all programming aspects of COHERENS, model setup, compiling and running the program, input/output files, .... The structure of COHERENS and technical features of the code are analysed in Chapter IV-1. The remaining chapters deal with the preparation of model input (IV-2), model output (IV-3), the input/output structure including how to read model output (IV-4) and additional issues such as compilation, error messages and splitting a simulation into several runs (IV-5).
• Part~V is the Reference Manual. The purpose of each module is described in the first chapter (V-1) with the aid of a few flow charts. A listing of program variables with their FORTRAN name and purpose is presented in Chapter V-2. Bibliographic references are given at the end.