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.
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
- 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].
- Phytoplankton photoinhibition coefficient, [1/(W/m2) 1/day].
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].
- Phytoplankton half saturation constant for Nitrate [millimole_N/m3].
- Phytoplankton half saturation constant for Ammonium [millimole_N/m3].
- Phytoplankton half saturation constant for Silicate [millimole_Si/m3].
- KSiL == 6.0d0 ! large biomass
- Phytoplankton Ammonium inhibition coefficient [m3/millimole_N].
- Phytoplankton temperature coefficient for photosynthetic rate [1/Celsius].
- Phytoplankton respiration rate at 0 Celsius [1/day].
- Phytoplankton temperature coefficient for respiration [1/Celsius].
- Phytoplankton ratio of extracellular excretion to photosynthesis [nondimensional].
- Phytoplankton mortality rate at 0 Celsius [m3/millimole_N 1/day].
- Phytoplankton temperature coefficient for mortality [1/Celsius].
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].
Zooplankton Ivlev constant [m3/millimole_N].
- 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].
- Zooplankton mortality rate at 0 Celsius [m3/millimole_N 1/day].
- Zooplankton temperature coefficient for mortality [1/Celsius].
- Zooplankton assimilation efficiency [nondimemsional].
- Zooplankton growth efficiency [nondimensional].
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].
- Temperature coefficients for decomposition [1/Celsius]
- Si:N ratio [millimole_Si/millimole_N].
- RSiN == 2.0d0
- Settling (sinking) velocities [m/day].
Other Parameters
Unless specified, [1:NBT,Ngrids] values expected for each parameter.
- Lateral, constant, harmonic/biharmonic mixing coefficient for biological tracer variables. If variable horizontal diffusion is activated, TNU2 and TNU4 are the mixing coefficient for the largest grid-cell in the domain.
- Background Vertical mixing coefficients for biological tracer variables..
- AKT_BAK == 11*1.0d-6 ! m2/s
- Nudging time scale. Inverse scale will be computed internally.
- TNUDG == 11*0.0d0 ! days
- Logical switches to write out biological data into output History/Average NetCDF files. Currently, NEMURO has NBT=11 ecosystem compartments.
- Hout(idTvar) == 11*T ! biological tracers
Hout(idTsur) == 11*F ! biological tracers surface flux
! idTvar( 1)=iPhyL Large Phytoplankton biomass
! idTvar( 2)=iPhyS Small Phytoplankton biomass
! idTvar( 3)=iZooL Large Zooplankton biomass
! idTvar( 4)=iZooS Small Zooplankton biomass
! idTvar( 5)=iZooP Predator Zooplankton biomass
! idTvar( 6)=iNO3_ Nitrate concentration
! idTvar( 7)=iNH4_ Ammonium concentration
! idTvar( 8)=iPON_ Particulate Organic Nitrogen
! idTvar( 9)=iDON_ Dissolved Organic Nitrogen
! idTvar(10)=iSiOH Silicate concentration
! idTvar(11)=iopal Particulate organic silica