nemuro.in

NEMURO Model Input Script - nemuro.in

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

#	index	Description	Units	NetCDF variable
1	iSphy	Small Phytoplankton biomass	mmol/m3	nanophytoplankton
2	iLphy	Large Phytoplankton biomass	mmol/m3	diatom
3	iSzoo	Small Zooplankton biomass	mmol/m3	microzooplankton
4	iLzoo	Large Zooplankton biomass	mmol/m3	mesozooplankton
5	iPzoo	Predator Zooplankton biomass	mmol/m3	Pzooplankton
6	iNO3_	Nitrate concentration	mmol/m3	NO3
7	iNH4_	Ammonium concentration	mmol/m3	NH4
8	iPON_	Particulate Organic Nitrogen	mmol/m3	PON
9	iDON_	Dissolved Organic Nitrogen	mmol/m3	DON
10	iSiOH	Silicate concentration	mmol/m3	SiOH4
11	iopal	Particulate organic silica	mmol/m3	opal

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

NEMURO equations and representative parameters may be found in:

• Kishi et al. 2007a

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

Biological Model Parameters

• This switch to control the computation of NEMURO 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 Parameters

Input parameter units are specified within brackets ([ ]). Unless specified, [1:Ngrids] values expected for each parameter.

• Light attenuation due to seawater [1/m].

AttSW == 0.04d0

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

AttPS == 0.04d0  ! small biomass
AttPL == 0.04d0  ! large biomass

• Fraction of shortwave radiation that is photosynthetically active, [nondimensional].

PARfrac == 0.43d0

• Phytoplankton photochemical reaction coefficient, initial slope of the P-I curve [1/(W/m²) 1/day].

AlphaPS == 0.01d0  ! small biomass
AlphaPL == 0.01d0  ! large biomass

• Phytoplankton photoinhibition coefficient, [1/(W/m²) 1/day].

BetaPS == 4.5d-4  ! small biomass
BetaPL == 4.5d-4  ! large biomass

Phytoplankton Parameters

Input parameter units are specified within brackets ([ ]). Unless specified, [1:Ngrids] values expected for each parameter.

• Phytoplankton maximum photosynthetic rate at 0 Celsius [1/day].

VmaxS == 0.4d0  ! small biomass
VmaxL == 0.8d0  ! large biomass

• Phytoplankton half saturation constant for Nitrate [millimole_N/m³].

KNO3S == 1.0d0  ! small biomass
KNO3L == 3.0d0  ! large biomass

• Phytoplankton half saturation constant for Ammonium [millimole_N/m³].

KNH4S == 0.1d0  ! small biomass
KNH4L == 0.3d0  ! large biomass

• Phytoplankton half saturation constant for Silicate [millimole_Si/m³].

KSiL == 6.0d0  ! large biomass

• Phytoplankton Ammonium inhibition coefficient [m³/millimole_N].

PusaiS == 1.5d0  ! small biomass
PusaiL == 1.5d0  ! large biomass

• Phytoplankton temperature coefficient for photosynthetic rate [1/Celsius].

KGppS == 6.93d-2  ! small biomass
KGppL == 6.93d-2  ! large biomass

• Phytoplankton respiration rate at 0 Celsius [1/day].

ResPS0 == 0.03d0  ! small biomass
ResPL0 == 0.03d0  ! large biomass

• Phytoplankton temperature coefficient for respiration [1/Celsius].

KResPS == 0.0519d0  ! small biomass
KResPL == 0.0519d0  ! large biomass

• Phytoplankton ratio of extracellular excretion to photosynthesis [nondimensional].

GammaS == 0.135d0  ! small biomass
GammaL == 0.135d0  ! large biomass

• Phytoplankton mortality rate at 0 Celsius [m³/millimole_N 1/day].

MorPS0 == 58.5d-3  ! small biomass
MorPL0 == 29.0d-3  ! large biomass

• Phytoplankton temperature coefficient for mortality [1/Celsius].

KMorPS == 6.93d-2  ! small biomass
KMorPL == 6.93d-2  ! large biomass

Zooplankton Parameters

Input parameter units are specified within brackets ([ ]). Unless specified, [1:Ngrids] values expected for each parameter.

• Zooplankton maximum grazing rate at 0 Celsius [1/day].

GRmaxSps == 0.40d0  ! small Zoo on small phy
GRmaxLps == 0.10d0  ! large Zoo on small Phy
GRmaxLpl == 0.40d0  ! large Zoo on large Phy
GRmaxLzs == 0.40d0  ! large Zoo on small Zoo
GRmaxPpl == 0.20d0  ! predator Zoo on large Phy
GRmaxPzs == 0.20d0  ! predator Zoo on small Zoo
GRmaxPzl == 0.20d0  ! predator Zoo on large Zoo

• Zooplankton temperature coefficient for grazing [1/Celsius].

KGraS == 6.93d-2  ! small biomass
KGraL == 6.93d-2  ! large biomass
KGraP == 6.93d-2  ! predator biomass

Zooplankton Ivlev constant [m³/millimole_N].

LamS == 1.4d0  ! small biomass
LamL == 1.4d0  ! large biomass
LamP == 1.4d0  ! predator biomass

• Zooplankton half-saturation coefficient (squared) for ingestion used only when the Holling-type grazing formulation is activated [millimole_N/m³]².

KPS2ZS == 0.16d0  ! small Zoo on small Phy
KPS2ZL == 0.16d0  ! large Zoo on small Phy
KPL2ZL == 0.16d0  ! large Zoo on large Phy
KZS2ZL == 0.16d0  ! large Zoo on small Zoo
KPL2ZP == 0.16d0  ! predator Zoo on large Phy
KZS2ZP == 0.16d0  ! predator Zoo on small Zoo
KZL2ZP == 0.16d0  ! predator Zoo on large Zoo

• Zooplankton threshold value for grazing [millimole_N/m³].

PS2ZSstar == 4.3d-2  ! small Zoo on small Phy
PS2ZLstar == 4.0d-2  ! large Zoo on small Phy
PL2ZLstar == 4.0d-2  ! large Zoo on large Phy
ZS2ZLstar == 4.0d-2  ! large Zoo on small Zoo
PL2ZPstar == 4.0d-2  ! predator Zoo on large Phy
ZS2ZPstar == 4.0d-2  ! predator Zoo on small Zoo
ZL2ZPstar == 4.0d-2  ! predator Zoo on large Zoo

• Zooplankton grazing inhibition coefficient [m³/millimole_N].

PusaiPL == 4.605d0  ! predator Zoo on large Phy
PusaiZS == 3.010d0  ! predator Zoo on small Zoo

• Zooplankton mortality rate at 0 Celsius [m³/millimole_N 1/day].

MorZS0 == 58.5d-3  ! small biomass
MorZL0 == 58.5d-3  ! large biomass
MorZP0 == 58.5d-3  ! predator biomass

• Zooplankton temperature coefficient for mortality [1/Celsius].

KMorZS == 0.0693d0  ! small biomass
KMorZL == 0.0693d0  ! large biomass
KMorZP == 0.0693d0  ! predator biomass

• Zooplankton assimilation efficiency [nondimemsional].

AlphaZS == 0.70d0  ! small biomass
AlphaZL == 0.70d0  ! large biomass
AlphaZP == 0.70d0  ! predator biomass

• Zooplankton growth efficiency [nondimensional].

BetaZS == 0.30d0  ! small biomass
BetaZL == 0.30d0  ! large biomass
BetaZP == 0.30d0  ! predator biomass

Nutrient Parameters

Input parameter units are specified within brackets ([ ]). Unless specified, [1:Ngrids] values expected for each parameter.

• Decomposition rates at 0 Celsius [1/day].

Nit0 == 0.03d0  ! NH₄ nitrification
VP2N0 == 0.10d0  ! PON to NH₄
VP2D0 == 0.10d0  ! PON to DON
VD2N0 == 0.20d0  ! DON to NH₄
VO2S0 == 0.10d0  ! Opal to Silicate

• Temperature coefficients for decomposition [1/Celsius]

KNit == 6.93d-2  ! NH₄ nitrification
KP2D == 6.93d-2  ! PON to DON
KP2N == 6.93d-2  ! PON to NH₄
KD2N == 6.93d-2  ! DON to NH₄
KO2S == 6.93d-2  ! Opal to Silicate

• Si:N ratio [millimole_Si/millimole_N].

RSiN == 2.0d0

• Settling (sinking) velocities [m/day].

setVPON == 40.0d0  ! PON
setVOpal == 40.0d0  ! Opal

Other Parameters

Unless specified, [1:NBT,Ngrids] values expected for each parameter.

• Lateral, constant, harmonic/biharmonic horizontal diffusion of biological tracer for nonlinear model and adjoint-based algorithms: [1:NBT,Ngrids] values expected. The 11 values correspond to the Variable Index Table at the top of this page.

TNU2 == 11*0.0d0  ! m²/s
TNU4 == 11*0.0d0  ! m⁴/s

ad_TNU2 == 11*0.0d0  ! m²/s
ad_TNU4 == 11*0.0d0  ! m⁴/s

• Vertical mixing coefficients for biological tracers: [1:NBT,Ngrids] values expected. The 11 values correspond to the Variable Index Table at the top of this page.

AKT_BAK == 11*1.0d-6  ! m²/s

ad_AKT_fac == 11*1.0d0  ! nondimensional

• Nudging/relaxation time scale. Inverse scale will be computed internally: [1:NBT,Ngrids] values expected. The 11 values correspond to the Variable Index Table at the top of this page.

TNUDG == 11*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 11 switches correspond to the Variable Index Table at the top of this page.

LtracerSrc == 11*F

• Logical switches to activate writing of biological tracers into history output file: [1:NBT,Ngrids] values expected. Currently, NEMURO has NBT=11 ecosystem compartments. The 11 switches correspond to the Variable Index Table at the top of this page.

Hout(idTvar) == 11*T  ! ..., NO3, ... biological tracers
Hout(idTsur) == 11*F  ! ..., NO3_sflux, ... surface tracer flux

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

Aout(idTvar) == 11*T  ! ..., NO3, ... 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) == 11*T  ! ..., NO3_rate, ... time rate of change
Dout(iThadv) == 11*T  ! ..., NO3_hadv, ... horizontal total advection
Dout(iTxadv) == 11*T  ! ..., NO3_xadv, ... horizontal XI-advection
Dout(iTyadv) == 11*T  ! ..., NO3_yadv, ... horizontal ETA-advection
Dout(iTvadv) == 11*T  ! ..., NO3_vadv, ... vertical advection
Dout(iThdif) == 11*T  ! ..., NO3_hdiff, ... horizontal total diffusion
Dout(iTxdif) == 11*T  ! ..., NO3_xdiff, ... horizontal XI-diffusion
Dout(iTydif) == 11*T  ! ..., NO3_ydiff, ... horizontal ETA-diffusion
Dout(iTsdif) == 11*T  ! ..., NO3_sdiff, ... horizontal S-diffusion
Dout(iTvdif) == 11*T  ! ..., NO3_vdiff, ... vertical diffusion