Models and utilities

Numerical models
FABM

The Framework for Aquatic Biogeochemical Models (FABM) provides a generic, easy to use, high performance coupling layer that connects a hydrodynamic model (e.g., 1D water column, 3D world ocean) with multiple biogeochemical submodels.

Development of FABM was initiated in the EU FP7 project MEECE. Since then, BB has continued to maintain and further develop FABM, with all changes made publicly available under the GPL.

fabm_1
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GOTM

General Ocean Turbulence Model (GOTM) was initiated by Hans Burchard and Karsten Bolding in 1998 and the first public release was in 1999. BB has always been responsible for maintaining the code – first using CVS and later using git. BB has provided numerous code contributions and has participated very active on the developers and users mailing lists.

GOTM is used as the primary test bed for Framework for Biogeochemical Models (FABM).

 

GETM

General Estuarine Transport Model (GETM) was initiated by Hans Burchard and Karsten Bolding in 1999. GETM is a 3D primitive equation numerical ocean model using the turbulence library from GOTM. BB has – as with GOTM – always been responsible for maintaining the code – first using CVS and later using git. BB has provided numerous code contributions and has participated very active on the developers and users mailing lists.

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Utilities

BB has also added to the project by developing utilities making operation of GOTM easier – specifically editscenario.py and pyncview.py.

Editscenario

editscenario.py is a python script used to generate Fortran namelist files through XML configuration files. editscenario.py can be operated in both a scriptable and GUI based way.

editscenario.py requires a schema definition for the Fortran namelists to generate as well as a file with actual settings for a specific configuration. The use of XML as configuration language allows for a much richer experince compared to Fortran namelists including – in addition to variable values – human readable descriptions and variable units.

An example of editscenario.py executed in GUI mode for the GOTM nns_annual test case.

 

pyncview
PyNcView

PyNcView is a stand-alone application for viewing NetCDF files on Windows, Linux and Mac OS. It is written in Python and builds upon MatPlotLib and Qt.

PyNcView can visualize arbitrary CF compliant NetCDF files. It is also aware of the coordinate systems of GOTM and GETM, and provides additional functionality for files created by these models.

 

Auto Calibration in Python – ACPy

ACPy is a set of python scripts used to make an auto-calibration for – presently only GOTM – simulations.

ACPy is configured via an xml formatted file. The example below is from the PROGNOS project, Lake Erken GOTM set-up. The configuration file consists of 5 sections transports, executable, setup, parameters and observations.