npzd iron.in

NPZD-Iron Biological Model Input Script - npzd_iron.in

The npzd_iron.in file sets the parameters for the Fiechter et al. NPZD model. The name of this file is set by the BPARNAM keyword in the ocean.in file. A default npzd_iron.in standard input ASCII file can be found in the User/External subdirectory of the ROMS source code. In order to include the Fiechter et al. NPZD model in ROMS you must set BPARNAM correctly and activate the NPZD_IRON CPP option.

#	index	Description	Units	NetCDF variable
1	iNO3_	Nitrate concentration	mmol/m3	NO3
2	iPhyt	Phytoplankton biomass	mmol/m3	phytoplankton
3	iZoop	Zooplankton biomass	mmol/m3	zooplankton
4	iSDet	Detritus concentration	mmol/m3	detritus
5	iFdis	Dissolved iron concentration	mmol/m3	iron
4	iFphy	Phytoplankton Iron concentration	mmol/m3	phytoplanktonFe

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 NPZD-Iron model equations and representative parameters may be found in:

• Fiechter et al. 2009a

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 to control the computation of npzd_Franks 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

• Initial concentration for analytical uniform initial conditions, [millimole/m³]. It is only used when ANA_BIOLOGY is activated.

BioIni(iNO3_) == 17.0d0  ! nitrate
BioIni(iPhyt) == 1.0d0  ! phytoplankton
BioIni(iZoop) == 1.0d0  ! zooplankton
BioIni(iSDet) == 1.0d0  ! detritus
BioIni(iFdis) == 0.0d0  ! dissolved iron
BioIni(iFphy) == 0.0d0  ! iron in phytoplankton

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

PARfrac == 0.43d0

• Light attenuation due to seawater, [1/m], {0.067d0}.

AttSW == 0.067d0  ! k_ext

• Light attenuation due to phytoplankton, self-shading coefficient, [m²/millimole_N], {0.0095d0}.

AttPhy == 0.04d0  ! k_extP

• Phytoplankton, initial slope of P-I curve [m²/W], {0.025d0}.

PhyIS == 0.02d0  ! alpha

• Nitrate uptake rate, [1/day], {1.0d0}.

Vm_NO3 == 1.0d0 !Vm

• Phytoplankton mortality rate to Detritus pool, [1/day], {0.1d0}.

PhyMRD == 0.1d0  ! sigmaD

• Phytoplankton mortality rate to Nitrogen pool, [1/day], {0.0d0}.

PhyMRN == 0.0d0  ! sigmaN

• Half-saturation for phytoplankton nitrate uptake [1/millimole_N m^-3], {1.0d0}.

K_NO3 == 1.0d0  ! k_N

• Ivlev constant for zooplankton grazing parameterization [Nondimensional], {14*0.06=0.84d0}

Ivlev == 0.84d0

• Zooplankton grazing rate, [1/day], {0.52d0}.

ZooGR == 0.65d0  ! R_m

• Zooplankton excretion efficiency to Detritus pool [nondimensional], {0.3d0}

ZooEED == 0.0d0  ! gammaD

• Zooplankton excretion efficiency to Nitrogen pool [nondimensional], {0.3d0}

ZooEEN == 0.3d0  ! gammaN

• Zooplankton mortality rate to Detritus pool, [1/day], {0.0d0}.

ZooMRD == 0.145d0  ! zetaD

• Zooplankton mortality rate to Nitrogen pool, [1/day], {0.145d0}.

ZooMRN == 0.0d0  ! zetaN

• Detritus remineralization rate, [1/day], {0.1d0}.

DetRR == 0.1d0  ! delta

• Vertical sinking velocity for phytoplankton, [m/day], {0.0d0}.

wPhy == 0.0d0  ! wP

• Detrital sinking rate, [m/day], {8.0d0}.

wDet == 5.0d0  ! wD

• Iron uptake timescale, [day], {1.0d0}.

T_Fe == 1.0d0  ! T_Fe

• Empirical Fe:C power, [nondimensional], {0.6d0}.

A_Fe == 0.6d0  ! A_Fe

• Empirical Fe:C coefficient, [1/M-C], {64.0d0}.

B_Fe == 64.0d0  ! B_Fe

• Fe:C at F=0.5, [muM-Fe/M-C], {16.9d0}.

K_FeC == 16.9d0  ! K_FeC

• Fe remineralization rate, [1/day], {1.0d0}.

FeRR == 0.5d0  ! FeRR

• If applicable, dissolved Fe relaxation (nudging) parameters to simulate Fe source over the shelf (h <= FeHmin).

FeHmin == 200.0d0  ! minimum depth(m)
FeNudgTime == 5.0d  ! nudging time (days)
FeMax == 2.0d0  ! Fe value (mmole/m3) to nudge

• Lateral, constant, harmonic/biharmonic horizontal diffusion of biological tracer for nonlinear model and adjoint-based algorithms: [1:NBT,Ngrids] values expected.

TNU2 == 6*5.0d0  ! m²/s
TNU4 == 6*0.0d0  ! m⁴/s

ad_TNU2 == 6*0.0d0  ! m²/s
ad_TNU4 == 6*0.0d0  ! m⁴/s

• Vertical mixing coefficients for biological tracers: [1:NBT,Ngrids] values expected.

AKT_BAK == 6*1.0d-6  ! m²/s

ad_AKT_fac == 6*1.0d0  ! nondimensional

• Nudging/relaxation time scales, inverse scales will be computed internally: [1:NBT,Ngrids] values expected.

TNUDG == 6*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 switches correspond to the Variable Index Table at the top of this page.

LtracerSrc == 6*F

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

Hout(idTvar) == 6*T  ! biological tracer
Hout(idTsur) == 6*F  ! surface tracer flux

• Logical switches to activate writing of time-averaged fields into averages file. [1:NBT,Ngrids] values expected.

Aout(idTvar) == 6*T  ! biological tracer

• Logical switches to activate writing of time-averaged, biological tracer diagnostic terms into the diagnostic output file. [1:NBT,Ngrids] values expected.

Dout(iTrate) == 6*T  ! time rate of change
Dout(iThadv) == 6*T  ! horizontal total advection
Dout(iTxadv) == 6*T  ! horizontal XI-advection
Dout(iTyadv) == 6*T  ! horizontal ETA-advection
Dout(iTvadv) == 6*T  ! vertical advection
Dout(iThdif) == 6*T  ! horizontal total diffusion
Dout(iTxdif) == 6*T  ! horizontal XI-diffusion
Dout(iTydif) == 6*T  ! horizontal ETA-diffusion
Dout(iTsdif) == 6*T  ! horizontal S-diffusion
Dout(iTvdif) == 6*T  ! vertical diffusion