darwin_31P+16Z+3B code, run time files, and parameter values

This version of the model was used in Dutkiewicz et al (2023) "Biotic Interactions" paper.

Provided here are the code, including specific modifications for this setup. We are using the darwin3 version of the darwin model (available at https://github.com/darwinproject/darwin3).

The model resolves the cycling of carbon, phosphorus, nitrogen silica, iron, and oxygen through inorganic, living, dissolved and particulate organic phases (including CDOM). The biogeochemical and biological tracers are transported and mixed by the MIT general circulation model (MITgcm, Marshall et al., 1997) constrained to be consistent with altimetric and hydrographic observations (the ECCO-GODAE state estimates, Wunsch and Heimbach, 2007). This three dimensional configuration has coarse resolution (1o×1o horizontally) and 23 levels ranging from 10m in the surface to 500m at depth.

The setup is the same as in Follett et al (2022), though with slightly different iron dust input. We resolve 31 phytoplankton types, covering several functional groups (picophytoplankton, coccolithophores, diazotrophs, diatoms, mixotrophic dinoflagellates), and 15 size classes (from 0.6 to 104um equivalent spherical diameter). There are 16 grazer size classes from 4.5 to 1636um equivalent spherical diameter and 3 size classes of heterotrophic bacteria ranging from 0.4 to 0.9um), The phytoplankton types differ in the types of nutrients they require (e.g. diatoms require silica), maximum growth rate, nutrient half saturation constants, sinking rates, and palatability to grazers. Grazers and heterotrophic rates are also determined allometrically.

Exact version, modifications and input datafiles used in Dutkiewicz et al (2023)  are in the tarball available here. See directory dar6 in the tarball:

code modifications are in "code_31+16+3"

Model parameters for the default simulation (EXP-0) are listed in darwin_params.txt and darwin_traits.txt.

References:

Follett, C.L., S. Dutkiewicz, F, Ribalet, E. Zakem, D. Caron, V. Armbrust and M.J. Follows, 2022. Trophic Interactions with heterotrophic bacteria limit the range of Prochlorococcus. Proceedings of the National Academy of Sciences, 119, e2110993118, doing:10.1073/pnas.2110993118.