! Nutrient-Phytoplankton-Zooplankton-Detritus Biological Model Parameters. ! !svn $Id: npzd_iron.in 412 2009-12-03 20:46:03Z arango $ !========================================================= Hernan G. Arango === ! Copyright (c) 2002-2009 The ROMS/TOMS Group ! ! Licensed under a MIT/X style license ! ! See License_ROMS.txt ! !============================================================================== ! ! ! Input parameters can be entered in ANY order, provided that the parameter ! ! KEYWORD (usually, upper case) is typed correctly followed by "=" or "==" ! ! symbols. Any comment lines are allowed and must begin with an exclamation ! ! mark (!) in column one. Comments may appear to the right of a parameter ! ! specification to improve documentation. Comments will be ignored during ! ! reading. Blank lines are also allowed and ignored. Continuation lines in ! ! a parameter specification are allowed and must be preceded by a backslash ! ! (\). In some instances, more than one value is required for a parameter. ! ! If fewer values are provided, the last value is assigned for the entire ! ! parameter array. The multiplication symbol (*), without blank spaces in ! ! between, is allowed for a parameter specification. For example, in a two ! ! grids nested application: ! ! ! ! AKT_BAK == 2*1.0d-6 2*5.0d-6 ! m2/s ! ! ! ! indicates that the first two entries of array AKT_BAK, in fortran column- ! ! major order, will have the same value of "1.0d-6" for grid 1, whereas the ! ! next two entries will have the same value of "5.0d-6" for grid 2. ! ! ! ! In multiple levels of nesting and/or multiple connected domains step-ups, ! ! "Ngrids" entries are expected for some of these parameters. In such case, ! ! the order of the entries for a parameter is extremely important. It must ! ! follow the same order (1:Ngrids) as in the state variable declaration. The ! ! USER may follow the above guidelines for specifying his/her values. These ! ! parameters are marked by "==" plural symbol after the KEYWORD. ! ! ! !============================================================================== ! ! NOTICE: Input parameter units are specified within brackets and default ! ****** values are specified within braces. ! ! Switch to control the computation of biology within nested and/or multiple ! connected grids. Lbiology == T ! Maximum number of iterations to achieve convergence of the nonlinear ! solution. BioIter == 1 ! Initial concentration for analytical uniform initial conditions. ! [millimole/meter3]. 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], {1.5d0}. 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 ! Inverse 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], {0.52}. 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 == 1.0d0 ! delta ! Phytoplankton sinking rate, [m/day], {0.0d0}. wPhy == 0.0d0 ! wP ! Detrital sinking rate, [m/day], {8.0d0}. wDet == 8.0d0 ! 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 == 5.0d0 ! nudging time (days) FeMax == 2.0d0 ! Fe value (mmole/m3) to nudge ! Harmonic/biharmonic horizontal diffusion of biological tracer for ! nonlinear model and adjoint-based algorithms: [1:NBT,Ngrids]. 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 for nonlinear ! model and basic state scale factor in adjoint-based algorithms: ! [1:NBT,Ngrids]. 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]. TNUDG == 6*0.0d0 ! days ! Logical switches (TRUE/FALSE) to specify which variables to consider on ! tracers point Sources/Sinks (like river runoff): [NBT,Ngrids] values are ! expected. See glossary below for details. LtracerSrc == 6*F ! Logical switches (TRUE/FALSE) to activate writing of biological tracers ! into HISTORY/AVERAGE output files: [1:NBT,Ngrids]. Hout(idTvar) == 6*T ! biological tracer Hout(idTsur) == 6*F ! surface tracer flux ! ! GLOSSARY: ! ========= ! !------------------------------------------------------------------------------ ! NPZD-Iron (Fiechter et al, 2009) Biological Model Parameters. Currently, it ! is configured with 6 biological tracers: ! ! idbio(1) Nitrate concentration ! idbio(2) Phytoplankton biomass ! idbio(3) Zooplankton biomass ! idbio(4) Detritus concentration ! idbio(5) Dissolved iron concentration if IRON ! idbio(6) Iron concentration in phytoplankton if IRON ! !------------------------------------------------------------------------------ ! ! Lbiology Switch to control the computation of a particular module ! within nested and/or multiple connected grids. By default ! this switch is set to TRUE in "mod_scalars" 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". In order to make ! the model more efficient in memory usage, NBT(:) should ! be zero in such grids. ! ! BioIter Maximum number of iterations to achieve convergence of ! the nonlinear implicit solution. ! ! BioIni Initial concentration for analytical uniform initial ! conditions, [millimole/meter3]. It is only used when ! ANA_BIOLOGY is activated. ! ! BioIni(iNO3_) Nitrate concentration ! BioIni(iPhyt) Phytoplankton biomass ! BioIni(iZoop) Zooplankton biomass ! BioIni(iSDet) Detritus concentration ! BioIni(iFdis) Dissolved iron concentration ! BioIni(iFphy) Phytoplankton Iron concentration ! ! PARfrac Fraction of shortwave radiation that is photosynthetically ! active (nondimensional). ! ! AttSW Light attenuation due to seawater [1/m]. ! ! AttPhy Light attenuation by phytoplankton, self-shading ! coefficient, [m2/millimole_N]. ! ! PhyIS Phytoplankton, initial slope of P-I curve [m2/W]. ! ! Vm_NO3 Nitrate uptake rate, [1/day]. ! ! PhyMRD Phytoplankton mortality rate to Detritus, [1/day]. ! ! PhyMRN Phytoplankton mortality rate to Nitrogen, [1/day]. ! ! K_NO3 Inverse half-saturation for phytoplankton nitrate uptake ! [1/(millimole_N m-3)]. ! ! Ivlev Ivlev constant for zooplankton grazing parameterization, ! [nondimensional]. ! ! ZooGR Zooplankton grazing rate, [1/day]. ! ! ZooEED Zooplankton excretion efficiency to Detritus pool, ! [nondimensional]. ! ! ZooEEN Zooplankton excretion efficiency to Nitrogen pool, ! [nondimensional]. ! ! ZooMRD Zooplankton mortality rate to Detritus pool, [1/day]. ! ! ZooMRN Zooplankton mortality rate to Nitrogen pool, [1/day]. ! ! DetRR Detritus remineralization rate, [1/day]. ! ! wPhy Phytoplankton sinking rate, [m/day]. ! ! wDet Detrital sinking rate, [m/day]. ! ! T_Fe Iron uptake timescale, [day]. ! ! A_Fe Empirical Fe:C power, [nondimensional] ! ! B_Fe Empirical Fe:C coefficient, [1/M-C]. ! ! K_FeC Fe:C at F=0.5, [muM-Fe/M-C]. ! ! FeRR Fe remineralization rate, [1/day]. ! ! FeHmin Minimum bathymetry value (meter; positive) considered to ! nudge dissolved iron over the shelf (h <= FeHmin). ! ! FeNudgTime Dissolved iron nudging time scale (days) over the shelf. ! Inverse scale will be computed internally. ! ! FeMax Dissolved iron value (mmole/m3) to nudge over the shelf to ! simulate Fe coastal source. It is only considered when ! the IRON_RELAX c-preprocessing option is activated. ! !------------------------------------------------------------------------------ ! Physical Parameters, [1:NBT,1:Ngrids] values are expected. !------------------------------------------------------------------------------ ! ! TNU2 Nonlinear model lateral, harmonic, constant, mixing ! coefficient (m2/s) for biological tracer variables; ! [1:NBT,1:Ngrids] values are expected. If variable ! horizontal diffusion is activated, TNU2 is the mixing ! coefficient for the largest grid-cell in the domain. ! ! TNU4 Nonlinear model lateral, biharmonic, constant, mixing ! coefficient (m4/s) for biological tracer variables; ! [1:NBT,1:Ngrids] values are expected. If variable ! horizontal diffusion is activated, TNU4 is the mixing ! coefficient for the largest grid-cell in the domain. ! ! ad_TNU2 Adjoint-based algorithms lateral, harmonic, constant, ! mixing coefficient (m2/s) for biological tracer variables; ! [1:NBT,1:Ngrids] values are expected. If variable ! horizontal diffusion is activated, ad_TNU2 is the mixing ! coefficient for the largest grid-cell in the domain. ! ! ad_TNU4 Adjoint-based algorithms lateral, biharmonic, constant, ! mixing coefficient (m4/s) for biological tracer variables; ! [1:NBT,1:Ngrids] values are expected. If variable ! horizontal diffusion is activated, ad_TNU4 is the mixing ! coefficient for the largest grid-cell in the domain. ! ! AKT_BAK Background vertical mixing coefficient (m2/s) for biological ! tracer variables, [1:NBT,1:Ngrids] values are expected. ! ! ! ad_AKT_fac Adjoint-based algorithms vertical mixing, basic state, ! scale factor (nondimensional) for biological tracer ! variables; [1:NBT,1:Ngrids] values are expected. In ! some applications, a smaller/larger values of vertical ! mixing are necessary for stability. It is only used ! when FORWARD_MIXING is activated. ! ! TNUDG Nudging time scale (days), [1:NBT,1:Ngrids]. Inverse scale ! will be computed internally. ! ! !------------------------------------------------------------------------------ ! Tracer point Sources/Sink sources switches. !------------------------------------------------------------------------------ ! ! LtracerSrc Logical switches (T/F) to specify which tracer variables ! to consider when the option TS_PSOURCE is activated; ! [1:NBT,1:Ngrids] values are expected. ! ! LtracerSrc(idbio(1),ng) Nitrate concetration ! LtracerSrc(idbio(2),ng) Phytoplankton biomass ! LtracerSrc(idbio(3),ng) Zooplankton biomass ! LtracerSrc(idbio(4),ng) Detritus concentration ! LtracerSrc(idbio(5),ng) Dissolved iron concentration ! LtracerSrc(idbio(6),ng) Iron concentration ! ! Recall that TS_PSOURCE is usually activated to add river ! runoff as a point source. At minimum, it is necessary to ! specify both temperature and salinity for all rivers. The ! other tracers are optional. The user needs to know the ! correspondence between biological variables and indices ! idbio(1:NBT) when activating one or more of these switches. ! ! This logical switch REPLACES and ELIMINATES the need to ! have or read the variable "river_flag(river)" in the input ! rivers forcing NetCDF file: ! ! double river_flag(river) ! river_flag:long_name = "river runoff tracer flag" ! river_flag:option_0 = "all tracers are off" ! river_flag:option_1 = "only temperature" ! river_flag:option_2 = "only salinity" ! river_flag:option_3 = "both temperature and salinity" ! river_flag:units = "nondimensional" ! ! This logic was too cumbersome and complicated when ! additional tracers are considered. However, this change ! is backward compatible. ! ! The LtracerSrc switch will be used to activate the reading ! of respective tracer variable from input river forcing ! NetCDF file. If you want to add other tracer variables ! (other than temperature and salinity) as a source for a ! particular river(s), you just need to specify such values ! on those river(s). Then, set the values to ZERO on the ! other river(s) that do NOT require such river forcing for ! that tracer. Recall that you need to specify the tracer ! values for all rivers, even if their values are zero. ! !------------------------------------------------------------------------------ ! Logical switches (T/F) to activate writing of fields into output files. !------------------------------------------------------------------------------ ! ! Hout Logical switches (T/F) to write out biological data into ! output History/Average NetCDF file, [1:NBT,1:Ngrids] ! values are expected. ! ! Hout(idTvar) biological tracers ! Hout(idTsur) biological tracers surface flux ! ! idTvar(idbio(1))=iNO3_ Nitrate concentration ! idTvar(idbio(2))=iPhyt Phytoplankton biomass ! idTvar(idbio(3))=iZoop Zooplankton biomass ! idTvar(idbio(4))=iSdet Detritus concentration ! idTvar(idbio(5))=iFdis Dissolved iron concentration ! idTvar(idbio(6))=iFphy Phytoplankton Iron concentration !