Description of a flexible and extendable physical–biogeochemical model system for the water column

Burchard, Hans; Bolding, Karsten; Kühn, Wilfried; Meister, Andreas; Neumann, Thomas; Umlauf, Lars

doi:10.1016/j.jmarsys.2005.04.011

Cited by 126 publications

(123 citation statements)

References 43 publications

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“…Details about GOTM can be found in Burchard et al (2006). For the application of GOTM to Lake Bourget, eddy di usivity was calculated using kclosure using default model parameters.…”

Section: Physical Modelmentioning

confidence: 99%

Modelling the plankton groups of the deep, peri-alpine Lake Bourget

Kerimoglu

Jacquet²,

Vinçon‐Leite

et al. 2017

Ecological Modelling

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Predicting phytoplankton succession and variability in natural systems remains to be a grand challenge in aquatic ecosystems research. In this study, we identi ed six major plankton groups in Lake Bourget (France), based on cell size, taxonomic properties, food-web interactions and occurrence patterns: cyanobacterium Planktothrix rubescens, small and large phytoplankton, mixotrophs, herbivorous and carnivorous zooplankton. We then developed a deterministic dynamic model that describes the dynamics of these groups in terms of carbon and phosphorus uxes, as well as of particulate organic phosphorus and dissolved inorganic provide evidence for the hypothesis that the abundance of this species before the onset of strati cation is critical for its success later in the growing season, pointing thereby to a priority e ect.

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“…Details about GOTM can be found in Burchard et al (2006). For the application of GOTM to Lake Bourget, eddy di usivity was calculated using kclosure using default model parameters.…”

Section: Physical Modelmentioning

confidence: 99%

Modelling the plankton groups of the deep, peri-alpine Lake Bourget

Kerimoglu

Jacquet²,

Vinçon‐Leite

et al. 2017

Ecological Modelling

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“…In a few cases, a single coupling API is used by different hydrodynamic models. For instance, the 1D General Ocean Turbulence Model and 3D General Estuarine Transport Model share a single "bio" API (Burchard et al, 2006), and the Modular Ocean Model (Griffies et al, 2005) and Generalized Ocean Layer Dynamics model share a single "generic tracer" API. However, these are the exception rather than the rule, and their individual APIs still differ greatly.…”

Section: Introductionmentioning

confidence: 99%

“…The first section describes the considerations that have guided the design and implementation of FABM; two separate boxes provide step-by-step instructions on how to couple FABM with biogeochemical and hydrodynamic models. The second section presents a worked example, in which a modular nutrient-phytoplankton-zooplankton-detritus-carbonate model is run within a 1D water column driven by the General Ocean Turbulence Model (Burchard et al, 2006), and subsequently ported unmodified to the 3D global ocean, driven by the Modular Ocean Model (Griffies et al, 2005). The third section describes the present state of the framework, along with the biogeochemical and hydrodynamic models that it connects to, and planned future developments.…”

Section: Introductionmentioning

confidence: 99%

A general framework for aquatic biogeochemical models

Bruggeman

Bolding²

2014

Environmental Modelling & Software

Self Cite

230

175

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a b s t r a c tOne of the most of challenging steps in the development of coupled hydrodynamic-biogeochemical models is the combination of multiple, often incompatible computer codes that describe individual physical, chemical, biological and geological processes. This "coupling" is time-consuming, error-prone, and demanding in terms of scientific and programming expertise. The open source, Fortran-based Framework for Aquatic Biogeochemical Models addresses these problems by providing a consistent set of programming interfaces through which hydrodynamic and biogeochemical models communicate. Models are coded once to connect to FABM, after which arbitrary combinations of hydrodynamic and biogeochemical models can be made. Thus, a biogeochemical model code works unmodified within models of a chemostat, a vertically structured water column, and a three-dimensional basin. Moreover, complex biogeochemistry can be distributed over many compact, self-contained modules, coupled at run-time. By enabling distributed development and user-controlled coupling of biogeochemical models, FABM enables optimal use of the expertise of scientists, programmers and end-users.

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“…For example (2), one can easily check that the product of (4) and (3) indeed renders the ODEs given in (1).…”

Section: Definitionmentioning

confidence: 99%

“…For instance, in fluid flow dynamics the use of Courant-type conditions to ensure positivity (as well as stability) is prevalent [17]. However, we aim to apply integration schemes to biochemical systems hosted in an existing biogeochemical modeling framework for water columns [2]. This comprehensive framework imposes a global time step; within a step, splitting schemes are applied in order to solve different parts of the problem -advection, diffusion, biochemistry -with different numerical methods.…”

Section: Introductionmentioning

confidence: 99%

A second-order, unconditionally positive, mass-conserving integration scheme for biochemical systems

Bruggeman

Burchard

Kooi

et al. 2007

Applied Numerical Mathematics

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C e n t r u m v o o r W i s k u n d e e n I n f o r m a t i c a MAS Modelling, Analysis and Simulation Modelling, Analysis and SimulationA second-order, unconditionally positive, mass-conserving integration scheme for biochemical systems J. Bruggeman, H. Burchard, B. Kooi, B.P. Sommeijer A second-order, unconditionally positive, massconserving integration scheme for biochemical systems ABSTRACT Biochemical systems are bound by two mathematically-relevant restrictions. First, state variables in such systems represent non-negative quantities, such as concentrations of chemical compounds. Second, biochemical systems conserve mass and energy. Both properties must be reflected in results of an integration scheme applied to biochemical models. This paper first presents a mathematical framework for biochemical problems, which includes an exact definition of biochemical conservation: elements and energy, rather than state variable units, are conserved. We then analyze various fixed-step integration schemes, including traditional Euler-based schemes and the recently published modified Patankar schemes, and conclude that none of these deliver unconditional positivity and biochemical conservation in combination with higher-order accuracy. Finally, we present two new fixed-step integration schemes, one first-order and one second-order accurate, which do guarantee positivity and (biochemical) conservation. REPORT MAS-R0601 JANUARY 2006 AbstractBiochemical systems are bound by two mathematically-relevant restrictions. First, state variables in such systems represent non-negative quantities, such as concentrations of chemical compounds. Second, biochemical systems conserve mass and energy. Both properties must be reflected in results of an integration scheme applied to biochemical models. This paper first presents a mathematical framework for biochemical problems, which includes an exact definition of biochemical conservation: elements and energy, rather than state variable units, are conserved. We then analyze various fixed-step integration schemes, including traditional Euler-based schemes and the recently published Modified Patankar schemes, and conclude that none of these deliver unconditional positivity and biochemical conservation in combination with higher-order accuracy. Finally, we present two new fixed-step integration schemes, one first-order and one second-order accurate, which do guarantee positivity and (biochemical) conservation.

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Description of a flexible and extendable physical–biogeochemical model system for the water column

Cited by 126 publications

References 43 publications

Modelling the plankton groups of the deep, peri-alpine Lake Bourget

Modelling the plankton groups of the deep, peri-alpine Lake Bourget

A general framework for aquatic biogeochemical models

A second-order, unconditionally positive, mass-conserving integration scheme for biochemical systems

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