FABM-hereon

This is a collection of FABM models developed at Helmholtz-Zentrum hereon GmbH by the ecosystem modeling group. It currently includes

1. A light model, based on the GOTM light implementation but with more exact layer averaging
2. The OMExDia model in several variations. OMExDia is a sediment biogeochemical model

• OMExDia with phosphorus (omexdia_p)
• OMExDia with methane (omexdia_c)

1. The NOPE model for Nitrous Oxide Production and Emission

How to build

This code must be compiled together with FABM. To do this, provide the following additional arguments to cmake when you build FABM: -DFABM_INSTITUTES=hereon -DFABM_HEREON_BASE=$FABM_HEREON_BASE

Here, $FABM_HEREON_BASE is an environment variable pointing to the directory with the FABM-hereon code (the src subdirectory as seen from the directory containing this ReadMe file). Note that -DFABM_INSTITUTES=hereon will make FABM compile NOPE, OMExDia and light as the only available biogeochemical models. If you additionally want to have access to other biogeochemical models included with FABM, you can set FABM_INSTITUTES to a semi-colon separated list, e.g., -DFABM_INSTITUTES="hereon;iow" (to prevent the shell from interpreting the semi-colons, you typically have to enclose this list with quotes).

Building with GOTM

To use hereon models with the General Ocean Turbulence Model (GOTM), do the following, after defining GOTM_BASE and FABM_HEREON_BASE

git clone --recursive https://github.com/gotm-model/code.git $GOTM_BASE
git clone https://github.com/schism-dev/fabm-hereon.git $FABM_HEREON_BASE

cd $GOTM_BASE && git submodule update --init --recursive
mkdir -p $GOTM_BASE/build
cd $GOTM_BASE/build 
cmake -B $GOTM_BASE/build -S $GOTM_BASE  -DGOTM_USE_FABM=ON -DFABM_INSTITUTES=hereon -DFABM_HEREON_BASE=$FABM_HEREON_BASE
make

This will create the gotm executable with support for FABM light and omexdia.

Building with SCHISM

To use hereon models with the latest stable release of the Semi-implicit Cross-scale Hydroscience Integrated System Model (SCHISM), do the following:

git clone --recurse-submodules -b v5.11.1 https://github.com/schism-dev/schism.git schism
git clone https://github.com/fabm-model/fabm.git
git clone https://github.com/schism-dev/fabm-hereon.git
mkdir build
cd build
cmake ../schism/src -DBLD_STANDALONE=ON -DUSE_FABM=ON -DFABM_BASE=../fabm -DFABM_INSTITUTES=hereon -DFABM_HEREON_BASE=../fabm-hereon
make pschism

This will create the pschism executable with support for FABM light and omexdia.

Building the 0D driver

To use hereon models in a 0d setup, do the following, after defining FABM_BASE, GOTM_BASE and FABM_HEREON_BASE.

mkdir $FABM_BASE/build-0d
cmake -B $FABM_BASE/build-0d -S $FABM_BASE/src/drivers/0d -DGOTM_BASE=$GOTM_BASE -DFABM_INSTITUTES=hereon -DFABM_HEREON_BASE=$FABM_HEREON_BASE
make

Building pyfabm

To use hereon models with pyfabm, do the following, after defining FABM_BASE and FABM_HEREON_BASE. See also the detailed instructions at https://github.com/fabm-model/fabm/wiki/python.

cat <<EOT > $FABM_BASE/setup.cfg
[build_ext]
cmake_opts=-DFABM_EXTRA_INSTITUTES=hereon -DFABM_HEREON_BASE="$FABM_HEREON_BASE"
force=1
debug=1
EOT

python -m pip install $FABM_BASE/setup.cfg

How to couple

FABM provides several built-in models that you can use to provide source and sink terms, as well as boundary conditions. The following models are available

• interior_constant, horizontal_constant
• surface_flux, constant_surface_flux, external_surface_flux
• external_bottom_flux
• interior_source
• bottom_source
• interior_relaxation
• column_projection
• weighted_sum
• horizontal_weighted_sum
• bottom_field

Interior sources

You can convert the flux from one model source to another model target by specifying an interior_source model:

instances:
 interior_source:
   model: interior_source
   coupling:
     source: source/flux
     target: target/c

Horizontal constant

You can specify a new horizontally constant property, that can be used in the coupling: section of onother model as horizontal_constant/data:

instances:
  horizontal_constant:
    model: horizontal_constant
    parameters:
      value: 0.0001                   # value