! Fennel et al (2006) Nitrogen-based Biological Model Parameters. ! !svn $Id: bio_Fennel.in 323 2009-03-06 23:58:50Z 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 ! 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: [1:NBT,Ngrids]. TNU2 == 12*0.0d0 ! m2/s TNU4 == 12*0.0d0 ! m4/s ! Vertical mixing coefficients for biological tracers: [1:NBT,Ngrids]. AKT_BAK == 12*1.0d-6 ! m2/s ! Nudging/relaxation time scales, inverse scales will be computed ! internally: [1:NBT,Ngrids]. TNUDG == 12*0.0d0 ! days ! Logical switches (TRUE/FALSE) to activate writing of biological tracers ! into HISTORY output file: [1:NBT,Ngrids]. Hout(idTvar) == 12*T ! biological tracer Hout(idTsur) == 12*F ! surface tracer flux ! Logical switches (TRUE/FALSE) to activate writing of diagnostics terms ! into diagnostic output file [Ngrids]. 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 ! ! GLOSSARY: ! ========= ! !------------------------------------------------------------------------------ ! Fennel et al (2006), Nitrogen-based Biological Model Parameters. !------------------------------------------------------------------------------ ! ! 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 solution. ! ! AttSW Light attenuation due to seawater [1/m]. ! ! AttChl Light attenuation by chlorophyll [1/(mg_Chl m2)]. ! ! PARfrac Fraction of shortwave radiation that is photosynthetically ! active (nondimensional). ! ! Vp0 Eppley temperature-limited and light-limited growth tuning ! parameter [nondimensional]. ! ! I_thNH4 Radiation threshold for nitrification inhibition [Watts/m2]. ! ! D_p5HN4 Half-saturation radiation for nitrification inhibition ! [Watts/m2]. ! ! NitriR Nitrification rate: oxidation of NH4 to NO3 [day-1]. ! ! K_NO3 Inverse half-saturation for phytoplankton NO3 uptake ! [1/(millimole_N m-3)]. ! ! K_NH4 Inverse half-saturation for phytoplankton NH4 uptake ! [1/(millimole_N m-3)]. ! ! K_Phy Zooplankton half-saturation, squared constant for ingestion ! [millimole_N m-3]^2. ! ! Chl2C_m Maximum chlorophyll to carbon ratio [mg_Chl/mg_C]. ! ! ChlMin Chlorophyll minimum threshold value [mg_Chl/m3]. Set to ! zero to avoid limiting. ! ! PhyCN Phytoplankton Carbon:Nitrogen ratio [mole_C/mole_N]. ! ! PhyIP Phytoplankton, NH4 inhibition parameter [1/(millimole_N)]. ! ! PhyIS Phytoplankton, initial slope of P-I curve ! [(mg_C)/(mg_Chl Watts m-2 day)]. ! ! PhyMin Phytoplankton minimum threshold value [millimole_N/m3]. ! Set to zero to avoid limiting. ! ! PhyMR Phytoplankton mortality rate [1/day]. ! ! ZooAE_N Zooplankton Nitrogen assimilation efficiency [nondimensional]. ! ! ZooBM Basal metabolism of zooplankton [1/day]. ! ! ZooCN Zooplankton Carbon:Nitrogen ratio [mole_C/mole_N]. ! ! ZooER Zooplankton specific excretion rate [1/day]. ! ! ZooGR Zooplankton maximum growth rate [1/day]. ! ! ZooMin Zooplankton minimum threshold value [millimole_N/m3]. ! Set to zero to avoid limiting. ! ! ZooMR Zooplankton mortality rate [1/day]. ! ! LDeRRN Large nitrogen detritus remineralization rate [day-1]. ! ! LDeRRC Large carbon detritus remineralization rate [day-1]. ! ! CoagR Coagulation rate: aggregation rate of SDeN + Phyt ==> LDeN ! [day-1]. ! ! SDeRRN Small nitrogen detritus remineralization rate [day-1]. ! ! SDeRRC Small carbon detritus remineralization rate [day-1]. ! ! wPhy Vertical sinking velocity for phytoplankton [m/day]. ! ! wLDet Vertical sinking velocity for large detritus ! [m/day]. ! ! wLDet Vertical sinking velocity for large detritus ! [m/day]. ! ! pCO2air CO2 partial pressure in the air (parts per million by volume) ! ! TNU2 Lateral, Laplacian, 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 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. ! ! AKT_BAK Background vertical mixing coefficient (m2/s) for biological ! tracer variables, [1:NBT,1:Ngrids] values are expected. ! ! TNUDG Nudging time scale (days), [1:NBT,1:Ngrids]. Inverse scale will ! be computed internally. ! ! Hout Logical switches (T/F) to write out biological data into output ! NetCDF files: ! ! History/Average file, [1:NBT,1:Ngrids] values are expected: ! ! Hout(idTvar) biological tracers ! Hout(idTsur) biological tracers surface flux ! ! Diagnostics file, [Ngrids] values are expected: ! ! Hout(iCOfx) air-sea CO2 flux ! Hout(iDNIT) denitrification flux ! Hout(ipCO2) CO2 partial pressure ! Hout(iO2fx) air-sea O2 flux ! Hout(iPPro) primary production ! Hout(iNO3u) NO3 uptake