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Description of compilation keys for the bamhbi.h90 file (MY_SRC/BAMHBI/bamhbi.h90). After each change, the model has to be recompiled.
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Options involving additional statevariables require namelist_top_cfg to be modified accordingly.
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Options involving additional diagnostic output require the modification of the filedeftop xml-file if the user desires to have this output written.
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| Compilation Key | Description | Additional Notes |
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|---------------------------|-----------------------------------------------------------------------------|--------------------------------------------------|
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| **PHYSICS** | | |
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| `forcingmodel_nemo` | Use NEMO as a forcing model | standard in our group |
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| `forcingmodel_deSolve` | Uses deSolve forcing model | |
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| `nanquest` | | |
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| **BIOLOGY** | | |
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| `aggregation` | Use aggregation model for computing sinking speeds dynamically, add state variable AGG | Not working properly (M.C.) |
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| `gelatinous` | Enable Gelatinous Zooplankton Variables (GEL and NOC) | standard in our group |
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| `smineral` | enable Mineral SPM state variable (SMI) | No foundation for the intialisation and river values |
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| `agginit` | Initializes aggregation variable from PON | |
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| `chlorophyll_geider` | | Currently commented out |
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| `clipping` | Set negative tracer values to e-12 and compute how much is "clipped away" | not compatible with NEMO trcrad negative correction option, you shouldn't use both, else the clipping output is not correct |
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| `temp_clip` | | |
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| **OPTICS** | | |
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| `simpleoptics` | Uses simplified optics model (Gregoire 2008) | not used by anyone currently |
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| `fulloptics` | Three-band light model with inherent optical properties as described in Arthur Capets phd thesis | Some parameters |
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| `radtrans` | Radtrans spectral light model in BAMHBI | |
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| `radtrans_diag` | | |
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| **BENTHIC** | | |
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| `benthic` | Use Benthic model with parameterized benthic-pelagic fluxes (Capet 2016) | standard in our group |
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| `metamodel_ORIG` | Use benthic metamodel parameter as established by Arthur | We currently don't have a (documented) alternative, could also remove this optionality |
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| `bflbounds` | | |
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| **ALKALINITY** | | |
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| `alkalinity_system` | Add negative excess charge as a state variable (CHA) for computing alkalinity | |
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| `co2syscheck` | Enable output possibility of Total Alkalinity, CO2,CO3, HCO3 | |
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| `csystemcheck` | Additional ouput regarding carbonate chemistry | |
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| `airpco2` | | |
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| **DIAGNOSTICS** | | |
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| `biodiagrates` | additional biogeochemical rates as output | |
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| `biodiagtrophic` | additional biogeochemical rates as output | |
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| `primaryprod` | Compute (and output) net and gross primary production | |
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| `botfluxdiag` | possibility of bottomflux diagnostics | |
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| `botstressdiag` | possibility of bottomstress diagnostics | |
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| `agg_diag` | possibility of aggregation diagnostics | |
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| `sedparamdiag` | Enable possibility of sediment diagnostics | |
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| **CONSERVATION & REDISTRIBUTION** | | |
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| `testcons` | | |
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| `testcons2` | | |
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| `redistributeSinking` | | |
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| `redistributeLoss` | | |
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| **R-DESOLVE SPECIFIC** | | |
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| `diffusion` | | |
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| `benthic_system` | | | |
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\ No newline at end of file |
