Hypoxia Simple Respiration Model

[arango]

Added the Hypoxia Simple Respiration Model. It can be activated with CPP option HYPOXIA_SRM. It needs total respiration rate as input that can be read from a forcing NetCDF file or can be set with analytical functions (ANA_RESPIRATION) in ana_respiration.h.

The Metadata for respiration rate is as follows:

        double respiration_time(respiration_time) ;
                respiration_time:long_name = "respiration date time" ;
                respiration_time:units = "days since 1992-01-01 00:00:00" ;
        double respiration(respiration_time, s_rho, eta_rho, xi_rho) ;
                respiration:long_name = "respiration rate" ;
                respiration:units = "day-1" ;
                respiration:time = "respiration_time" ;

You can set respiration to zero in places with no respiration like very deep water. Recall that hypoxia occurs in coastal and shallow waters, like estuaries. Use frc_respiration.cdl as a guideline to create input NetCDF file for respiration. It can have time records. If this is the case, ROMS will interpolate in time between snapshots.

The model code follows ROMS design and is added as include files:

ROMS/Nonlinear/Biology/hypoxia_srm_def.h
ROMS/Nonlinear/Biology/hypoxia_srm_inp.h
ROMS/Nonlinear/Biology/hypoxia_srm_mod.h
ROMS/Nonlinear/Biology/hypoxia_srm_var.h
ROMS/Nonlinear/Biology/hypoxia_srm_wrt.h

The input parameters are specified in hypoxia_srm.in.

CPP Options:

• ANA_RESPIRATION: use analytical respiration rate. If not activated, it will read from input forcing NetCDF file (see Data/ROMS/CDL/frc_respiration.cdl for metadata).

• HYPOXIA_SRM: use to activate this Hypoxia Simple Respiration Model.

• OCMIP_OXYGEN_SC: use Schmidt number from Keeling et al. (1998) to compute surface dissolved oxygen. Otherwise, use Schmidt number from Wanninkhof (1992). This option needs to be used in conjunction with SURFACE_DO_SATURATION.

• SURFACE_DO_SATURATION: use surface dissolved oxygen saturation at the model surface level instead of a surface dissolved oxygen flux.

References:

Scully, M.E., 2010: Wind Modulation of Dissolved Oxygen in the Chesapeake Bay, Estuaries and Coasts, 33, 1164-1175.

Scully, M.E., 2013: Physical control on hypoxia in the Chesapeake Bay: A numerical modeling study, J. Geophys. Res., 118, 1239-1256.

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The original model was written by Malcolm Scully. It was adapted to follow ROMS design and ecological models numerical algorithms. Many thanks to Marjy Friedrichs, Aaron Bever, and others for helping debug and test this model.