Stiff ode slovers: a review of current and coming attractions
Journal of Computational Physics
VODE: a variable-coefficient ODE solver
SIAM Journal on Scientific and Statistical Computing
Object-oriented analysis and design with applications (2nd ed.)
Object-oriented analysis and design with applications (2nd ed.)
Computer as Thinker/Doer: Problem-Solving Environments for Computational Science
IEEE Computational Science & Engineering
A method-of-lines code for carbon and nutrient diagenesis in aquatic sediments
Computers & Geosciences
Fundamentals of object-oriented design in UML
Fundamentals of object-oriented design in UML
Problem Solving Environments for Scientific Computing: Proceedings of the IFIP TC2 Wg2.5 Working Conf. on Problem Solving Environments for Scientific Computing, Sophia, Antipolis, France, 17-21 June, 1985
Reactive transport in surface sediments I. Mexity and software quality
Computers & Geosciences - Special issue: Reactive transport modeling in the geosciences
Reactive transport in surface sediments I. Mexity and software quality
Computers & Geosciences - Special issue: Reactive transport modeling in the geosciences
CHEPROO: A Fortran 90 object-oriented module to solve chemical processes in Earth Science models
Computers & Geosciences
dSED: a database tool for modeling sediment early diagenesis
Computers & Geosciences
Reactive transport in aquatic ecosystems: Rapid model prototyping in the open source software R
Environmental Modelling & Software
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The MEDIA (Modelling Early DIAgenesis) software package comprises a flexible and extensible software system that provides problem-solving assistance for simulating 1D reactive transport in surface sediments. MEDIA allows multiple diagenetic models to be built by extending a model template with new model components from a toolbox of available objects (elements, species, parameters, reactions). A detailed review is given of the transport and reaction components available for model construction. Upon assemblage, the model is channelled to the numerical subunit of the MEDIA package. Via a canonical transformation, the user-defined mixed kinetic-equilibrium model is rearranged into a proper set of differential algebraic equations (DAE), for which both steady state and transient solutions can be calculated. Steady-state profiles are obtained either directly using a Newton-Raphson method, or alternatively, as the asymptotic result of a dynamic simulation. Dynamic simulations involve a global implicit procedure based on the stiff-ODE solver package VODE, employing a direct substitution approach to reduce the number of equations in the DAE system. Verification of the MEDIA code was accomplished (1) by comparison with analytic models and (2) by emulating the model formulation and output of the existing diagenetic model code STEADYSED. As an example application, a diagenetic model was constructed to analyse an extensive dataset collected from a marine sediment in the Santa Barbara Basin (California). The different pathways of organic matter mineralization were modelled, and the coupling among the biogeochemical cycles of C, O, N, S, Mn and Fe was investigated. Depth profiles of both porewater and solid-phase constituents could be reproduced with great accuracy.