Skip to content

Biogeochemical models in FABM

Jorn Bruggeman edited this page Apr 4, 2024 · 113 revisions

FABM comes with a number of examples and third-party biogeochemical models. In addition, several people, research organizations and companies develop and maintain their own FABM-based biogeochemical models, which are often publicly available. This page provides a non-exhaustive overview of available models.

Configuration files for the built-in biogeochemical models are provided in the testcases directory; to use them, pick one of these and copy it to your model setup directory as fabm.yaml. If you would like to see how these models work: their source code is located in the src/models directory.

Externally maintained biogeochemical models can often be found in public code repositories (see table below). Typically they can be integrated in FABM at build time without making any changes to the FABM source code. Instead, you provide arguments to cmake to specify the name and source code location of externally maintained models. This is done with the arguments -DFABM_EXTRA_INSTITUTES=<INSTITUTE-NAMES> and -DFABM_<INSTITUTE>_BASE=<DIR>. Here, <INSTITUTE-NAMES> is a semicolon-separated list of the names of external biogeochemical model codebase you would like to include. For each of these, you need to point FABM to the directory with the source code by specifying -DFABM_<INSTITUTE>_BASE=<DIR>. For instance, to build FABM with the PISCES model, use -DFABM_EXTRA_INSTITUTES=pisces -DFABM_PISCES_BASE=<PISCES-DIR>.

Available models

Note: this is a non-exhaustive list, as people developing FABM models are not in any way required to advertise them. If you have developed a FABM-based biogeochemical model that you would like to see listed here, please let us know.

Name Features Availability Reference
BFM dynamics of major biogeochemical properties in lower trophic levels of marine ecosystems; used in the CMCC Earth System Model and in Copernicus Marine Service for the Mediterranean Sea code accessible after requesting access
BioPlast microplastics transformation in the aquatic environment, including biofouling of microplastics particles, ingestion and egestion by zooplankton and transport of microplastics in detritus; works with OxyDep, but can be adapted to another biogeochemical model comes with FABM: configuration, code Berezina et al. 2021
BROM model for biogeochemical processes in the water and sediments, with emphasis on how chemical elements (e.g., C, N, P, O, Si, Fe, Mn, S) alter the redox state and marine carbonate system comes with FABM: configuration, code Yakushev et al. 2017
BSEM intermediate-complexity ecosystem model developed for the Black Sea; includes gelatinous zooplankton; part of the JRC marine modelling framework comes with FABM: configuration, code Stips et al. 2018
CSIB-1D Canadian Sea Ice Biogeochemistry: a coupled ocean sea-ice model for Ice Algae, Carbon and DMS cycles. Requires ice-related variables such as those provided by GOTM UVic Ice model. public repository, for more information contact Nadja Steiner or Patrick Farnole Mortenson et al. 2017; Mortenson et al. 2018; Hayashida et al. 2017
csiro/seagrass seagrass model developed by CSIRO comes with FABM: code Baird et al. 2016
DEB a depth-integrated Dynamic Energy Budget population model for a heterotrophic species, structured along a structural volume axis public repository
ECOSMO intermediate-complexity lower trophic level pelagic model with an explicit sediment layer, developed for the high latitudes (>50°N) in the North Atlantic including the Baltic Sea; used in the Copernicus Marine Service for the Arctic Ocean. the ECOSMO version used for CMEMS comes with FABM: configuration, code. For other versions, please contact Annette Samuelsen Daewel & Schrum 2013; Yumruktepe et al. 2022
ERSEM ecosystem model for global to coastal applications; variable stoichiometry; detailed benthic system; used in the Copernicus Marine Service for the European North West Shelf; part of the JRC marine modelling framework public repository; Butenschön et al. 2016
Fasham-Ducklow-McKelvie open ocean nitrogen-based plankton ecosystem model comes with FABM: configuration, code Fasham et al. 1990; Burchard et al. 2006
Fennel 2P2Z Intermediate-complexity biogeochemical model (2P2Z); based on Fennel et al. 2006 and Laurent et al. 2021; updated to include two different sinking schemes of large POC to reproduce the slowed attenuation of vertical carbon flux with depth via simulating the protection by ballast minerals from remineralization and allowing for an increase of sinking velocity. public repository Wang & Fennel 2023; Fennel et al. 2006; Laurent et al. 2021
iHAMOCC intermediate-complexity biogeochemical model; used in the the Norwegian Earth System Model (NorESM) public repository Tjiputra et al. 2020
MedERGOM intermediate-complexity biogeochemical model; based on ERGOM, adapted for the pelagic ecosystem of the Mediterranean Sea; part of the JRC marine modelling framework comes with FABM: configuration, code Macias et al. 2018
MEDUSA intermediate-complexity biogeochemical model of the marine carbon cycle for climate change and ocean acidification studies; used in the UK Earth System Model public repository Yool et al. 2013; Lessin et al. 2020
MIZER size-structured higher trophic level model; suitable for two-way coupling to biogeochemistry public repository Scott et al. 2014; Bruggeman 2021
MOPS Model of Oceanic Pelagic Stoichiometry is a marine biogeochemical model that simulates 9 biogeochemical tracers: dissolved inorganic and organic phosphate, dissolved inorganic nitrate, dissolved oxygen, phytoplankton, zooplankton, and detritus public repository Kriest & Oschlies 2015
OxyDep Simplified version of Bottom RedOx Model (BROM) with plankton functional groups, dissolved and particulate organic matter, nutrients, dissolved oxygen; simple, generalized parameterization of principal biogeochemical processes in the water column and at the water/bottom interface, with a emphasis on oxygen-deficient conditions comes with FABM: configuration, code Berezina et al. 2021; Yakushev et al. 2011
PISCES intermediate-complexity biogeochemical model for lower trophic levels and cycles of C, P, N, Fe, Si; used in the IPSL Earth System Model and the Copernicus Marine Service for the global and Iberia-Biscay-Irish MFCs public repository Aumont et al. 2015;
Selmaprotbas NPZD model of intermediate complexity; adaptation of the SELMA/ERGOM model public repository Mesman et al. 2022
ShellSIM shellfish growth model based on energy budgets; tailored to aquaculture applications (environment impacting e.g. carrying capacity, time to market); also supporting feedback to biogeochemistry (shellfish impacting the marine ecosystem) please contact Yuri Artioli Hawkins et al. 2013
Spectral spectrally resolved direct and diffuse irradiance in atmosphere and oceans; based on OASIM; suitable for two-way coupling to biogeochemistry public repository Bruggeman et al. 2021; Skákala et al. 2022; Skákala et al. 2020
su/mixo model for mixotrophic protists; able to integrate with ERSEM comes with FABM: configuration, code Leles et al. 2021; Leles et al. 2018
WET modularized aquatic ecosystem model for cycles of N, P, DW and Si; includes modules for entire food web ranging from benthic and pelagic primary producers to predatory fish repository accessible after requesting access (GitLab account required); Schnedler-Meyer et al. 2021; Schnedler-Meyer et al. 2022