Metos3D - A Marine Ecosystem Toolkit for Optimization and Simulation in 3-D

The toolkit is divided into three packages, namely the Simulation Package, the Sensitivity Package and the Optimization Package. All packages are built around a general and flexible interface (Metos3D API) giving biogechemical modelers the possibility to develop and distribute their models separately (Metos3D Models). Metos3D was developed to use data provided by the Transport Matrix Method (Metos3D Data).

Metos3D Packages

Metos3D Simulation Package 

The Metos3D Simulation Package employs a PETSc implementation of a matrix-free Newton-Krylov solver to compute periodic (stationary) solutions [Piwonski,Slawig, 2010]. Moreover a fixed point iteration (spin-up), as described in [Khatiwala, 2007], is part of the implementation too. A short documentation and examples of Metos3D API conforming models are included.

Documentation

Download (github)

Metos3D Sensitivity Package

The Metos3D Sensitivity Package employs a PETSc implementation of a Krylov-subspace solver to compute fixed point (equilibium) sensitivities without the need of an adjoint model [Kaminski,Giering,Voßbeck, 2005].

This package is in preparation.

Metos3D Optimization Package

The Metos3D Optimization Package is an implementation of a One-Shot Lagrangian approach [Hamdi,Griewank, 2008] allowing the simultaneous simulation of tracers and optimization of model parameters. The adjoint model is provided with the automatic differentiation tool TAF (www.fastopt.com).

This package is in preparation.

Metos3D API

Metos3D defines a general Application Programming Interface (API) to decouple biogeochemical models (BGC) and driver routines (ocean circulation, forcing, geometry) programmatically. The interface allows for an arbitrary number of tracers, parameters, boundary and domain conditions. It was additionally designed to support optimal control and parameter identification/estimation/optimization, also via Automatic Differentiation (AD).

Metos3D Models

Metos3D can be coupled to every (biogeochemical) model that conforms to the Metos3D BGC API. Due to the interface the models are developed and distributed separately. Metos3D provides fully functional examples on how the interface can exploited.

Download (github)

Metos3D Data

Metos3D was developed to use data provided by the Transport Matrix Method in the first place. This data is maintained by Samar Khatiwala. Metos3D supplies you with a MATLAB (MATLAB is a registered trademark of The MathWorks, Inc.) script to prepare the data for usage.

Download (github)