bio Fennel.in

Fennel Model Input Script - bio_Fennel.in

The bio_Fennel.in file sets the parameters for the bio_Fennel (formerly bio_Fasham) model. The name of this file is set by the BPARNAM keyword in the ocean.in file. A default bio_Fennel.in standard input ASCII file can be found in the User/External subdirectory of the ROMS source code. In order to include the bio_Fennel model in ROMS you must set BPARNAM correctly and activate the BIO_FENNEL CPP option.

#	index	Description	Units	NetCDF variable
1	iNO3_	Nitrate concentration	mmol/m3	NO3
2	iNH4_	Ammonium concentration	mmol/m3	NH4
3	iChlo	Chorophyll concentration	mmol/m3	chlorophyll
4	iPhyt	Phytoplankton biomass	mmol/m3	phytoplankton
5	iZoop	Zooplankton biomass	mmol/m3	zooplankton
6	iLDeN	Large detritus N-concentration	mmol/m3	LdetritusN
7	iSDeN	Small detritus N-concentration	mmol/m3	SdetritusN
8	iLDeC	Large detritus C-concentration	mmol/m3	LdetritusC
9	iSDeC	Small detritus C-concentration	mmol/m3	SdetritusC
10	iTIC_	Total inorganic carbon	mmol/m3	TIC
11	iTAlk	Alkalinity	mmol/m3	alkalinity
12	iOxyg	Oxygen concentration	mmol/m3	oxygen

The "#" column denotes the internal index number within the idbio array while the "index" column is the index within the tracer array t(:,:,:,:,index).

The Fennel model equations and representative parameters may be found in:

• Fasham et al. 1990a

Notice: Detailed information about ROMS input script file syntax can be found here.

Biological Model Parameters

Input parameter units are specified within brackets ([ ])and default values are specified within braces ({ }).

• This switch controls the computation of bioFennel within nested and/or multiple connected grids. By default this switch is set to TRUE in mod_scalars.F for all grids. Ngrids values are expected. The user has the option, for example, to compute the biology in just one of the nested grids. If so, this switch needs to be consistent with the dimension parameter NBT in mod_param.F. In order to make the model more efficient in memory usage, NBT(:) should be zero in such grids.

Lbiology == T

• Maximum number of iterations to achieve convergence of the nonlinear solution.

BioIter == 1

• Light attenuation due to seawater [1/m], {0.04d0}.

AttSW == 0.04d0

• Light attenuation by chlorophyll [1/(mg_Chl m²)], {0.02486d0}.

AttChl == 0.02486d0

• Fraction of shortwave radiation that is photosynthetically active [nondimensional], {0.43d0}.

PARfrac == 0.43d0

• Eppley temperature-limited growth parameter [nondimensional], {1.0d0}.

Vp0 == 1.0d0

• Radiation threshold for nitrification inhibition [Watts/m²], {0.0095d0}.

I_thNH4 == 0.0095d0

• Half-saturation radiation for nitrification inhibition [Watts/m²], {0.036d0}.

D_p5NH4 == 0.1d0

• Nitrification rate: oxidation of NH₄ to NO₃ [1/day], {0.05d0}.

NitriR == 0.05d0

• Inverse half-saturation for phytoplankton NO₃ uptake [1/(millimole_N m^-3)], {2.0d0}.

K_NO3 == 2.0d0

• Inverse half-saturation for phytoplankton NH₄ uptake [1/(millimole_N m^-3)], {2.0d0}.

K_NH4 == 2.0d0

• Zooplankton half-saturation constant (squared) for ingestion [millimole_N m^-3]², {1.0d0}.

K_Phy == 2.0d0

• Maximum chlorophyll to carbon ratio [mg_Chl/mg_C], {0.0535d0}.

Chl2C_m == 0.0535d0

• Chlorophyll minimum threshold value [mg_Chl/m³], {0.0d0}.

ChlMin == 0.001d0

• Phytoplankton Carbon:Nitrogen ratio [mole_C/mole_N] , {6.625d0}.

PhyCN == 6.625d0

• Phytoplankton, NH₄ inhibition parameter [1/(millimole_N)], {1.5d0}.

PhyIP == 1.5d0

• Phytoplankton, initial slope of P-I curve [mg_C/(mg_Chl Watts m^-2 day)], {0.025d0}.

PhyIS == 0.025d0

• Phytoplankton minimum threshold value [millimole_N/m³], {0.0d0}.

PhyMin == 0.001d0

• Phytoplankton mortality rate [1/day], {0.072d0}.

PhyMR == 0.15d0

• Zooplankton Nitrogen assimilation efficiency [nondimesnional], {0.75d0}.

ZooAE_N == 0.75d0

• Zooplankton Basal metabolism [1/day], {0.1d0}.

ZooBM == 0.1d0

• Zooplankton Carbon:Nitrogen ratio [mole_C/mole_N], {5.0d0}.

ZooCN == 6.625d0

• Zooplankton specific excretion rate [1/day], {0.1d0}.

ZooER == 0.1d0

• Zooplankton maximum growth rate [1/day], {0.75d0}.

ZooGR == 0.6d0

• Zooplankton minimum threshold value [millimole_N/m³], {0.0d0}.

ZooMin == 0.001d0

• Zooplankton mortality rate [1/day], {0.025d0}.

ZooMR == 0.025d0

• Large detritus remineralization rate N-fraction [1/day], {0.01d0}.

LDeRRN == 0.01d0

• Large detritus remineralization rate C-fraction [1/day].

LDeRRC == 0.01d0

• Coagulation rate: aggregation rate of SDeN + Phy ==> LDeN [1/day], {0.005d0}.

CoagR == 0.005d0

• Small detritus remineralization rate N-fraction [1/day], {0.03d0}.

SDeRRN == 0.03d0

• Small detritus remineralization rate C-fraction[1/day].

SDeRRC == 0.03d0

• Vertical sinking velocity for phytoplankton [m/day], {0.1d0}.

wPhy == 0.1d0

• Vertical sinking velocity for large detritus [m/day], {1.0d0}.

wLDet == 1.0d0

• Vertical sinking velocity for small detritus [m/day], {0.1d0}.

wSDet == 0.1d0

• CO₂ partial pressure in the air (parts per million by volume), {377.0d0}.

pCO2air == 370.0d0

• Lateral, constant, harmonic/biharmonic horizontal diffusion of biological tracer for nonlinear model and adjoint-based algorithms: [1:NBT,Ngrids] values expected. The 12 values correspond to the Variable Index Table at the top of this page.

TNU2 == 12*0.0d0  ! m²/s
TNU4 == 12*0.0d0  ! m⁴/s

ad_TNU2 == 12*0.0d0  ! m²/s
ad_TNU4 == 12*0.0d0  ! m⁴/s

• Vertical mixing coefficients for biological tracers: [1:NBT,Ngrids] values expected. The 12 values correspond to the Variable Index Table at the top of this page.

AKT_BAK == 12*1.0d-6  ! m²/s

ad_AKT_fac == 12*1.0d0  ! nondimensional

• Nudging/relaxation time scales, inverse scales will be computed internally: [1:NBT,Ngrids] values expected. The 12 values correspond to the Variable Index Table at the top of this page.

TNUDG == 12*0.0d0  ! days

• Logical switches to specify which variables to consider on tracers point Sources/Sinks (like river runoff): [1:NBT,Ngrids] values expected. The 12 switches correspond to the Variable Index Table at the top of this page.

LtracerSrc == 12*F

• Logical switches to activate writing of biological tracers into history output file: [1:NBT,Ngrids] values expected. The 12 switches correspond to the Variable Index Table at the top of this page.

Hout(idTvar) == 12*T  ! biological tracer
Hout(idTsur) == 12*F  ! surface tracer flux

• Logical switches to activate writing of diagnostics terms into diagnostic output file [1:Ngrids] values expected.

Hout(iCOfx) == T  ! air-sea CO₂ flux
Hout(iDNIT) == T  ! denitrification flux
Hout(ipCO2) == T  ! CO₂ partial pressure
Hout(iO2fx) == T  ! air-sea O₂ flux
Hout(iPPro) == T  ! primary production
Hout(iNO3u) == T  ! NO₃ uptake