Biogeochemical models in FABM

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; included in FABM-plus	http://www.bfm-community.eu
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; included in FABM-plus	https://ersem.com; 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; included in FABM-plus	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; included in FABM-plus	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; included in FABM-plus	Aumont et al. 2015; https://www.pisces-community.org
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)	https://www.wet.au.dk; Schnedler-Meyer et al. 2021; Schnedler-Meyer et al. 2022