This is a collection of FABM ports of the ICM model and the CoSINE model.
This code must be compiled together with FABM. To do this, provide the following additional arguments to cmake when you build FABM: -DFABM_INSTITUTES=vims -DFABM_VIMS_BASE=</path/to/fabm-vims>
Here, </path/to/fabm-vims> is the directory with the FABM-VIMS code (the same directory that contains this ReadMe file). Note that -DFABM_INSTITUTES=vims will make FABM compile ICM and CoSINE 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="vims;iow" (to prevent the shell from interpreting the semi-colons, you typically have to enclose this list with quotes).
For instance, to use VIMS models with the latest stable release of the Semi-implicit Cross-scale Hydroscience Integrated System Model (SCHISM), do the following:
git clone --recurse-submodules --depth 1 https://github.com/schism-dev/schism.git clone --depth 1 https://github.com/fabm-model/fabm.git
git clone --depth 1 https://github.com/schism-dev/fabm-vims.git
wget https://raw.githubusercontent.com/platipodium/fabm/patch-1/src/drivers/schism/fabm_driver.h -O fabm/src/drivers/schism/fabm_driver.h
mkdir build
cd build
cmake ../schism/src -DBLD_STANDALONE=ON -DUSE_FABM=ON -DFABM_BASE=../fabm -DFABM_INSTITUTES=vims -DFABM_VIMS_BASE=../fabm-vims
make pschism
This will create the pschism executable with support for FABM ICM and COSINE.
Two sample fabm.yaml files are provided: fabm-vims-cosine.yaml and fabm-vims-icm.yaml under </path/to/fabm-vims>/testcases. You can drop this file (and link to or rename it fabm.yaml) in the working directory of a FABM-compatible model such as SCHISM to use it during simulation.
Build test with build chain suggested above
| System | Type | Compiler | Status |
|---|---|---|---|
| quoll | arm64 | gfortran | |
| femto | x86-64 | ifort | yes |
| kuro | x86-64 | intel/openmpi | yes |
| strand | x86-64 | ifort |