Opened 4 months ago

Closed 4 months ago

#868 closed upgrade (Done)

IMPORTANT: BIO_FENNEL Ecosystem Model Updated

Reported by: arango Owned by:
Priority: major Milestone: Release ROMS/TOMS 3.9
Component: Nonlinear Version: 3.9
Keywords: Cc:

Description (last modified by arango)

This update includes several enhancements to the BIO_FENNEL ecosystem module. Many thanks to Katja Fennel and Arnaud Laurent for providing the updated fennel.h, fennel_def.h, fennel_inp.h, fennel_mod.h, fennel_var.h, and fennel_wrt.h files.

  • The ecosystem model can be configurated up to 15 biological tracers:
        NO3               Nitrate concentration
        NH4               Ammonium concentration
        chlorophyll       Chorophyll concentration
        phytoplankton     Phytoplankton biomass
        zooplankton       Zooplankton biomass
        LdetritusN        Large detritus N-concentration
        SdetritusN        Small detritus N-concentration
        LdetritusC        Large detritus C-concentration     if CARBON
        SdetritusC        Small detritus C-concentration     if CARBON
        TIC               Total inorganic carbon             if CARBON
        alkalinity        Alkalinity                         if CARBON
        oxygen            Oxygen concentration               if OXYGEN
        PO4               Phosphate concentration            if PO4
        RdetritusN        River detritus N-concentration     if RIVER_DON
        RdetritusC        River detritus C-concentration     if RIVER_DON
  • If P04 is activated, an additional component is added representing phosphate concentration. With this option, the phytoplankton growth can be limited by either nitrogen or phosphorous (see Laurent et al., 2012).
  • RIVER_DON is activated, an additional biological tracer (or two if CARBON is defined) is added, representing the non-sinking dissolved organic matter from rivers described in Yu et al. (2015).
  • If the RW14_OXYGEN_SC and or RW14_CO2_SC options are used, the model will use Wanninkhof (2014) air-sea flux parameterization of the Schmidt transfer coefficients. With the TALK_NONCONSERV option, alkalinity is affected by biological fluxes, as described in Laurent et al. (2017).
  • With the PCO2AIR_DATA option, atmospheric pCO2 uses Laurent et al. (2017) annual climatory curve. The PCO2AIR_SECULARoption provides an alternative time-dependent atmospheric pCO2 evolution. If none of the two options are defined, atmospheric pCO2 is constant.
  • WARNING: The input script was modified to include new parameters. Also, several new variables were added to the varinfo.dat metadata file.


Laurent, A., Fennel, K., Hu, J., Hetland, R. 2012: Simulating the Effects of Phosphorus Limitation in the Mississippi and Atchafalaya River Plumes, Biogeosciences, 9 (11), 4707-4723, doi:10.5194/bg-9-4707-2012.

Yu, L., Fennel, K., Laurent, A., Murrell, M. C., Lehrter, J. C. 2015: Numerical Analysis of the Primary Processes Controlling Oxygen Dynamics on the Louisiana Shelf, Biogeosciences, 12 (7), 2063-2076, doi:10.5194/bg-12-2063-2015.

Wanninkhof, R. 2014: Relationship between Wind Speed and Gas Exchange over the Ocean Revisited, Limnol. Oceanogr. Methods, 12 (6), 351-362, doi:10.4319/lom.2014.12.351.

Also, included minor updates to few files:

  • mp_routines.F: Added Fortran 2003 FLUSH (unit) intrinsic to my_flush subroutine to flush the contents of a unit buffer.
  • comp_Jb0.F: Removed CPP conditional around USE mod_scalars to avoid compilation errors.
  • Change information format in get_2dfld.F, get_2dfldr.F, get_3dfld.F, and get_3dfldr.F.

Change History (1)

comment:1 Changed 4 months ago by arango

  • Description modified (diff)
  • Resolution set to Done
  • Status changed from new to closed
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