! Nutrient-Phytoplankton-Zooplankton-Detritus Biological Model Parameters. !output !svn $Id: npzd_Powell.in 1396 2011-04-01 22:28:53Z kate $ !========================================================= Hernan G. Arango === ! Copyright (c) 2002-2011 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_) == 16.0d0 ! nitrate BioIni(iPhyt) == 1.0d0 ! phytoplankton BioIni(iZoop) == 1.0d0 ! zooplankton BioIni(iSDet) == 1.0d0 ! detritus ! 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 == 0.0095d0 ! k_extP ! Max nitrification rate: oxidation of NH4 to NO3 [1/day], {0.05d0}. !cf. - (Chapelle et al. (2000) Ecolog. Modell 127, 161-181 NitriR == 0.1d0 !0.1d0 ! Light limitation parameters of nitrification. ! Table 1 of Fennel et al. (2006) - Global Biogeochem. Cycles, 20, ! GB3007, doi:10.1029/2005GB002456 KI == 0.1d0 ! W m-2 Light intensity at which the !inhibition of nitrification is half-saturated I0 == 0.0095d0 ! W m-2 Light intensity threshold for !light-inhibition of nitrification ! Denitrification rate: reduction of NO3 to NH4 and N2 [1/day], !(Chapelle et al. (2000) - Ecolog. Modell 80: 131-147) kdenit == 0.0d0 !0.3d0 ! Half-saturation constant for oxygen limitation of nitrification ! [mg O2 L-1], {4.00d0}, as in EcoDynamo model, !(Chapelle et al. (1995) - Ecolog. Modell 80: 131-147) knitO2 == 2.00d0 ! Parameter of the oxygen inhibition denitrification function ![mg O2 L-1], {2.00d0}, as in EcoDynamo model, !(Chapelle et al. (1995) - Ecolog. Modell 80: 131-147) kdenitO2 == 2.00d0 ! Temperature limiting factor for mineralization, nitrification, denitrification,... ! Degrees centigrades-1 !(Chapelle et al. (1995) - Ecolog. Modell 80: 131-147) kt == 0.069d0 ! Proportion of NH4 from denitrification (remaining fraction is N2) ! Dimensionless !(Chapelle et al. (1995) - Ecolog. Modell 80: 131-147) DenitNH4 == 1.0d0 ! Fraction of dissolved organic nitrogen that is mineralized to ammonia ! Dimensionless !(Chapelle et al. (1995) - Ecolog. Modell 80: 131-147) MinToNH4 == 1.0d0 ! Mineralization rate of particulate organic matter !days-1 ! Table 1 of Fennel et al. (2006) - Global Biogeochem. Cycles, 20, ! GB3007, doi:10.1029/2005GB002456, values for remineralization rate ! of suspended detritus minRateC == 0.03d0 !0.03 minRateN == 0.03d0 !0.03 minRateP == 0.03d0 !0.03 ! Oxygen half saturation constant for mineralization !mg O2 / L !Henriksen & Kemp (1988) fide Chapelle (1995,2000) !Henriksen, K., Kemp. W.M., 1988. Nitrification in estuarine and coastal !marine sediments. In: Backburn, T.H., Sorensen, J. (Eds.), Nitrogen !cycling in coastal marine environments. John Wiley & Sons, New York, pp. 207-249. KminO2 == 0.5d0 ! CO2 partial pressure in the air (parts per million by volume), ! {377.0d0}. pCO2air == 370.0d0 !Number of phytoplankton groups/taxa/species Phyto_groups == 2 !********************************************Generic phytoplankton (I am using it for flagellates for the time being)********** ! Phytoplankton, initial slope of P-I curve [mg C mg C-1 h-1 W m2], {0.025d0}. ! The value used here is based on Table S4 of Assmy et al. (2017) Sci. Rep. 7, 40850 ! after multiplying the value of the mentioned table for P. pouchetii (0.09 mg C mg Chyl a-1 h-1 umol photons m2 s) by ! 0.014 mg Chl/mg C, which is the value given in Box 7.5 of Sakshaug et al. (2009) and then converting from micro Einsteins to W ! by dividing by 4.6 micro Einsteins W-1 PhyIS == 0.000274d0 ! 0.000654 (old value) alpha checked [mg C mg C-1 h-1 W m2]! ! Phytoplankton, negative slope of P-I curve [mg C mg C-1 h-1 W m2] ! The value used here is based on Table S4 of Assmy et al. (2017) Sci. Rep. 7, 40850 ! after multiplying the value of the mentioned table for P. pouchetii (2.6X10-3 mg C mg Chyl a-1 h-1 umol photons m2 s) by ! 0.014 mg Chl/mg C, which is the value given in Box 7.5 of Sakshaug et al. (2009) Beta == 0.00000791304d0 ! 0.0716 (old value) beta checked [mg C mg C-1 h-1 W m2]! ! Nitrate uptake rate, [1/day], {1.5d0}. Vm_NO3 == 1.5d0 ! 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 ! [millimole_N m-3)], {1.0d0}. K_NO3 == 0.2d0 ! Checked 1.0d0 ! k_N !***EcoDynamo stuff added to Powell model parameters********** ! Maximum photosynthetic rate 1/h] {0.05} ! The value used here (0.7062) is based on Table S4 of Assmy et al. (2017) Sci. Rep. 7, 40850 ! after multiplying the value of the mentioned table for P. pouchetii (13.2 mg C mg Chl a-1 h-1) by ! 0.014 mg Chl/mg C, which is the value given in Box 7.5 of Sakshaug et al. (2009) Pmax == 0.1848d0 !0.453d0 (old value) h-1 Checked ! Optimal light intensity [microEisntein/m2/s] {500} Iopt == 185d0 ! Saturation light intensity [microEisntein/m2/s] {500} ImaxE == 185.0d0 ! Parameter of the Eilers & Peeters equation [microEinstein/m2/s] AEiler == 0.0d0 ! Parameter of the Eilers & Peeters equation [microEinstein/m2/s] BEiler == 1.0d0 ! Parameter of the Eilers & Peeters equation [microEinstein/m2/s] CEiler == 1.0d0 ! MaintResp Maintenance respiration [mmol O2/mg Chl/h]{0.01} MaintResp == 0.002d0 ! Checked 0.002d0 ! RespCoeff Respiration coefficient [nondimensional] {0.3} RespCoeff == 0.184d0 ! Checked 0.3 ! Fraction of GPP lost as dissolved organics [nondimensional] {0.1} DocStressLoss == 0.1d0 ! Checked 0.33 ! Redfield "default" C in mass RedfieldC == 1273.06d0 ! Checked (old mass per mass 41) ! Redfield "default" N in mass RedfieldN == 224.16d0 ! Checked (old mass per mass 7.2) ! Redfield "default" P in mass RedfieldP == 30.97d0 ! Checked ! Exponent of the temperature limiting function [1/degrees] TemperatureAugmentationRate == 0.069d0 ! Checked 0.0663 ! Ratio between respiration in the light and respiration in the darkness [nondimensional] RatioLightDarkRespiration == 2.0d0 ! Checked ! Minimal N:P cell ratio [mgN/mgP] minNPRatio == 4.0d0 ! Checked ! Maximal N:P cell ratio [mgN/mgP] maxNPRatio == 291.0d0 ! Checked ! Maximal phosphorus uptake [1/h] PMaxUptake == 0.1848d0 ! Checked ! Maximal nitrogen uptake [1/h] NMaxUptake == 0.1848d0 ! Checked ! NMaxUptake == 0.0 ! Half-saturation constant for P uptake [microM] KP == 0.03d0 ! Checked ! Half-saturation constant for ammonia uptake [microM] KNH4 == 0.10d0 ! Checked ! Minimal P cell contents [mgP/mgC] MinPCellQuota == 0.008d0 ! Checked ! Maximal P cell contents [mgP/mgC] MaxPCellQuota == 0.1d0 ! Checked ! Minimal N cell contents [mgN/mgC] MinNCellQuota == 0.054d0 ! Checked ! Maximal N cell contents [mgN/mgC] MaxNCellQuota == 0.25d0 ! 0.53 Checked ! Half saturation constant for internal P limitation [mgP/mgC] KPInternal == 0.008d0 ! Checked ! Half saturation constant for internal N limitation [mgN/mgC] KNInternal == 0.054d0 ! Checked ! Mass ratio between carbon fixed and oxygen released during photosynthesis [mgC/mgO2] CarbonToOxygenProd == 0.3125d0 ! Checked ! Mass ratio between carbon released and oxygen consumed during respiration [mgC/mgO2] CarbonToOxygenResp == 0.3125d0 ! Checked ! Parameter of the exponent of the temperature limiting function for respiration [1/degrees] TminRespiration == 0d0 ! Checked ! Parameter of the exponent of the temperature limiting function for photosynthesis [1/degrees] TminPhotosynthesis == 0d0 ! Checked ! Option for not including (0) or including N limitation [nondimensional] NitrogenLimitation == 1 ! Option for not including (0) or including P limitation [nondimensional] PhosphorusLimitation == 0 ! Maximum chlorophyll to carbon ratio [mg Chl / mg C] {0.0535d0} as in Fennels' model !Chl2C_m = 0.0535d0 0.0635d0 Chl2C_m == 0.0535d0 ! Phytoplankton sinking rate, [m/day], {0.0d0}. wPhy == 0.0d0 ! wP ! P-I function PIFunction == 4 ! Type of nutrient limitation NutLimType == 1 !********************************************Diatom phytoplankton************************************************** ! Phytoplankton, initial slope of P-I curve [mg C mg C-1 h-1 W m2], {0.025d0}. PhyISDiatoms == 0.000104d0 ! alpha checked! ! Phytoplankton, negative slope of P-I curve [mg C mg C-1 h-1 W m2] BetaDiatoms == 0.000000835d0 ! [0.073982d0 - this value is too high] beta checked! ! Nitrate uptake rate, [1/day], {1.5d0}. Vm_NO3Diatoms == 1.5d0 ! Vm ! Phytoplankton mortality rate to Detritus pool [1/day], {0.1d0}. PhyMRDDiatoms == 0.1d0 ! sigmaD ! Phytoplankton mortality rate to Nitrogen pool [1/day], {0.0d0}. PhyMRNDiatoms == 0.0d0 ! sigmaN ! Inverse half-saturation for phytoplankton nitrate uptake ! [millimole_N m-3)], {1.0d0}. K_NO3Diatoms == 0.2d0 ! k_N !***EcoDynamo stuff added to Powell model parameters********** ! Maximum photosynthetic rate [1/h] {0.05} PmaxDiatoms == 0.048d0 !Checked! ! Optimal light intensity [microEisntein/m2/s] {500} IoptDiatoms == 185.0d0 ! Saturation light intensity [microEisntein/m2/s] {500} ImaxEDiatoms == 185.0d0 ! Parameter of the Eilers & Peeters equation [microEinstein/m2/s] AEilerDiatoms == 0.0d0 ! Parameter of the Eilers & Peeters equation [microEinstein/m2/s] BEilerDiatoms == 1.0d0 ! Parameter of the Eilers & Peeters equation [microEinstein/m2/s] CEilerDiatoms == 1.0d0 ! MaintResp Maintenance respiration [mmol O2/mg Chl/h]{0.01} MaintRespDiatoms == 0.002d0 !0.01 ! RespCoeff Respiration coefficient [nondimensional] {0.3} RespCoeffDiatoms == 0.184d0 !0.3 ! Fraction of GPP lost as dissolved organics [nondimensional] {0.1} DocStressLossDiatoms == 0.1d0 ! Redfield "default" mass of C per mass of P [gC/gP] RedfieldCDiatoms == 41.0d0 ! Redfield "default" mass of N per mass of P [gN/gP] RedfieldNDiatoms == 7.2d0 ! Redfield "default" mass of P RedfieldPDiatoms == 1.0d0 ! Redfield "default" mass of Si per mass of P [gSi/gP] RedfieldSi == 7.0d0 ! Exponent of the temperature limiting function [1/degrees] TemperatureAugmentationRateDiatoms == 0.069d0 ! Ratio between respiration in the light and respiration in the darkness [nondimensional] RatioLightDarkRespirationDiatoms == 2.0d0 ! Minimal N:P cell ratio [mgN/mgP] minNPRatioDiatoms == 4.0d0 ! Maximal N:P cell ratio [mgN/mgP] maxNPRatioDiatoms == 291.0d0 ! Maximal phosphorus uptake [1/h] PMaxUptakeDiatoms == 0.048d0 ! Maximal nitrogen uptake [1/h] NMaxUptakeDiatoms == 0.048d0 ! Maximal silica uptake [1/h] SiMaxUptake == 0.045d0 ! Half-saturation constant for P uptake [microM] KPDiatoms == 0.03d0 ! Half-saturation constant for ammonia uptake [microM] KNH4Diatoms == 0.1d0 ! Half-saturation constant for Si uptake [microM] KSi == 0.2d0 ! Minimal P cell contents [mgP/mgC] MinPCellQuotaDiatoms == 0.008d0 ! Maximal P cell contents [mgP/mgC] MaxPCellQuotaDiatoms == 0.1d0 ! Minimal N cell contents [mgN/mgC] MinNCellQuotaDiatoms == 0.054d0 ! Maximal N cell contents [mgN/mgC] MaxNCellQuotaDiatoms == 0.25d0 ! Minimal Si cell contents [mgSi/mgC] MinSiCellQuota == 0.054d0 ! Maximal Si cell contents [mgSi/mgC] MaxSiCellQuota == 0.25d0 ! Minimal N:Si cell ratio [mgN/mgSi] minNSiRatio == 0.25d0 ! ! Half saturation constant for internal P limitation [mgP/mgC] KPInternalDiatoms == 0.004d0 ! Half saturation constant for internal N limitation [mgN/mgC] KNInternalDiatoms == 0.028d0 ! Half saturation constant for internal Si limitation [mgSi/mgC] KSiInternal == 0.004d0 ! Mass ratio between carbon fixed and oxygen released during photosynthesis [mgC/mgO2] CarbonToOxygenProdDiatoms == 0.3125d0 ! Mass ratio between carbon released and oxygen consumed during respiration [mgC/mgO2] CarbonToOxygenRespDiatoms == 0.3125d0 ! Parameter of the exponent of the temperature limiting function for respiration [1/degrees] TminRespirationDiatoms == 0.0d0 ! Parameter of the exponent of the temperature limiting function for photosynthesis [1/degrees] TminPhotosynthesisDiatoms == 0.0d0 ! Option for not including (0) or including N limitation [nondimensional] NitrogenLimitationDiatoms == 1 ! Option for not including (0) or including P limitation [nondimensional] PhosphorusLimitationDiatoms == 0 ! Option for not including (0) or including Si limitation [nondimensional] SilicaLimitation == 1 ! Maximum chlorophyll to carbon ratio [mg Chl / mg C] {0.0535d0} as in Fennels' model Chl2C_mDiatoms == 0.0535d0 ! Phytoplankton sinking rate, [m/day], {0.0d0}. wPhyDiatoms == 5.0d0 ! wP ! P-I function PIFunctionDiatoms == 4 ! Type of nutrient limitation NutLimTypeDiatoms == 1 !********************************************Zooplankton*********************************************************** ! Ivlev constant for zooplankton grazing parameterization ! [Nondimensional], {112*0.06=0.84d0} Ivlev == 0.84d0 ! Zooplankton grazing rate, [1/day], {0.52}. ! ZooGR == 0.52d0 ! 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 ! Fennel zooplankton model paramaters ! 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 ! Zooplankton half-saturation constant (squared) for ingestion [millimole_N m-3]2, {1.0d0}. K_Phy == 2.0d0 !**************************************************************************************************************** ! Detritus remineralization rate, [1/day], {0.1d0}. DetRR == 1.03d0 ! delta ! Detrital sinking rate, [m/day], {8.0d0}. wDet == 8.0d0 ! wD ! CO2 partial pressure in the air [parts per million by volume],As in Fennels' model ! {377.0d0}. pCO2air == 370.0d0 ! Harmonic/biharmonic horizontal diffusion of biological tracer for ! nonlinear model and adjoint-based algorithms: [1:NBT,Ngrids]. TNU2 == 21*0.0d0 ! m2/s TNU4 == 21*0.0d0 ! m4/s ad_TNU2 == 21*0.0d0 ! m2/s ad_TNU4 == 21*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 == 21*1.0d-6 ! m2/s ad_AKT_fac == 21*1.0d0 ! nondimensional ! Nudging/relaxation time scales, inverse scales will be computed ! internally: [1:NBT,Ngrids]. TNUDG == 21*0.0d0 ! days ! KK 2017-11-24 ! Set lateral boundary conditions keyword. Notice that a value is expected ! for each boundary segment per nested grid for each state variable. ! ! The biological tracer variables require [1:4,1:NBT,Ngrids] values. The ! boundary order is: 1=west, 2=south, 3=east, and 4=north. That is, ! anticlockwise starting at the western boundary. ! ! The keyword is case insensitive and usually has three characters. However, ! it is possible to have compound keywords, if applicable. For example, the ! keyword "RadNud" implies radiation boundary condition with nudging. This ! combination is usually used in active/passive radiation conditions. ! ! NOTICE: It is possible to specify the lateral boundary conditions for ! ====== all biological tracers in a compact form with a single entry. ! If so, all the biological tracers are assumed to have the same boundary ! condition as in the single entry. ! ! Keyword Lateral Boundary Condition Type ! ! Cla Clamped _____N_____ j=Mm ! Clo Closed | 4 | ! Gra Gradient | | ! Nes Nested 1 W E 3 ! Nud Nudging | | ! Per Periodic |_____S_____| ! Rad Radiation 2 j=1 ! i=1 i=Lm ! W S E N ! e o a o ! s u s r ! t t t t ! h h ! ! 1 2 3 4 LBC(isTvar) == RadNud RadNud RadNud RadNud \ ! idbio(1), NO3 RadNud RadNud RadNud RadNud \ ! idbio(2), phytoplankton RadNud RadNud RadNud RadNud \ ! idbio(3), zooplankton RadNud RadNud RadNud RadNud \ ! idbio(4), detritus RadNud RadNud RadNud RadNud \ ! NH4 RadNud RadNud RadNud RadNud \ ! PO4 RadNud RadNud RadNud RadNud \ ! Phy_N RadNud RadNud RadNud RadNud \ ! Phy_P RadNud RadNud RadNud RadNud \ ! SdetritusN RadNud RadNud RadNud RadNud \ ! SdetritusP RadNud RadNud RadNud RadNud \ ! zooplanktonN RadNud RadNud RadNud RadNud \ ! zooplanktonP RadNud RadNud RadNud RadNud \ ! chlorophyll ! RadNud RadNud RadNud RadNud \ ! TIC RadNud RadNud RadNud RadNud \ ! alkalinity RadNud RadNud RadNud RadNud \ ! oxygen RadNud RadNud RadNud RadNud \ ! silicic acid RadNud RadNud RadNud RadNud \ ! diatom RadNud RadNud RadNud RadNud \ ! diatomN RadNud RadNud RadNud RadNud \ ! diatomP RadNud RadNud RadNud RadNud \ ! diatomSi RadNud RadNud RadNud RadNud ! diatomChl ! Adjoint-based algorithms can have different lateral boundary ! conditions keywords. ad_LBC(isTvar) == RadNud RadNud RadNud RadNud \ ! idbio(1), NO3 RadNud RadNud RadNud RadNud \ ! idbio(2), phytoplankton RadNud RadNud RadNud RadNud \ ! idbio(3), zooplankton RadNud RadNud RadNud RadNud \ ! idbio(4), detritus RadNud RadNud RadNud RadNud \ ! NH4 RadNud RadNud RadNud RadNud \ ! PO4 RadNud RadNud RadNud RadNud \ ! Phy_N RadNud RadNud RadNud RadNud \ ! Phy_P RadNud RadNud RadNud RadNud \ ! SdetritusN RadNud RadNud RadNud RadNud \ ! SdetritusP RadNud RadNud RadNud RadNud \ ! zooplanktonN RadNud RadNud RadNud RadNud \ ! zooplanktonP RadNud RadNud RadNud RadNud \ ! chlorophyll ! RadNud RadNud RadNud RadNud \ ! TIC RadNud RadNud RadNud RadNud \ ! alkalinity RadNud RadNud RadNud RadNud \ ! oxygen RadNud RadNud RadNud RadNud \ ! silicic acid RadNud RadNud RadNud RadNud \ ! diatom RadNud RadNud RadNud RadNud \ ! diatomN RadNud RadNud RadNud RadNud \ ! diatomP RadNud RadNud RadNud RadNud \ ! diatomSi RadNud RadNud RadNud RadNud ! diatomChl ! Logical switches (TRUE/FALSE) to specify which variables to process for ! tracers climatology: [NBT,Ngrids] values are expected. See glossary below ! for details. LtracerCLM == 21*F ! 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 == 21*F ! LtracerSrc(idbio(1),ng) ! LtracerSrc(idbio(5),ng) ! LtracerSrc(idbio(6),ng) LtracerSrc == F F F F F F F F F F F F F F F F F F F F F ! nitrate, ammonia, phosphate ! Logical switches (TRUE/FALSE) to activate writing of biological fields ! into HISTORY output files: [1:NBT,Ngrids]. Hout(idTvar) == 21*T ! NO3, ... biological tracer Hout(idTsur) == 21*F ! NO3_sflux, ... surface tracer flux ! Logical switches (TRUE/FALSE) to activate writing of time-averaged fields ! into AVERAGE output file: [1:NBT,Ngrids]. Aout(idTvar) == 21*T ! ..., NO3, ... biological tracer Aout(idTTav) == 21*F ! ..., NO3_2, ... quadratic tracer terms Aout(idUTav) == 21*F ! ..., u_NO3, ... quadratic tracer terms Aout(idVTav) == 21*F ! ..., v_NO3, ... quadratic tracer terms Aout(iHUTav) == 21*F ! ..., Huon_NO3, ... tracer volume flux, Aout(iHVTav) == 21*F ! ..., Hvom_NO3, ... tracer volume flux, ! Logical switches (TRUE/FALSE) to activate writing of time-averaged, ! biological tracer diagnostic terms into DIAGNOSTIC output file: ! [1:NBT,Ngrids]. Dout(iTrate) == 21*F ! NO3_rate, ... time rate of change Dout(iThadv) == 21*F ! NO3_hadv, ... horizontal total advection Dout(iTxadv) == 21*F ! NO3_xadv, ... horizontal XI-advection Dout(iTyadv) == 21*F ! NO3_yadv, ... horizontal ETA-advection Dout(iTvadv) == 21*F ! NO3_vadv, ... vertical advection Dout(iThdif) == 21*F ! NO3_hdiff, ... horizontal total diffusion Dout(iTxdif) == 21*F ! NO3_xdiff, ... horizontal XI-diffusion Dout(iTydif) == 21*F ! NO3_ydiff, ... horizontal ETA-diffusion Dout(iTsdif) == 21*F ! NO3_sdiff, ... horizontal S-diffusion Dout(iTvdif) == 21*F ! NO3_vdiff, ... vertical diffusion ! Logical switches (TRUE/FALSE) to activate writing of time-averaged, ! biological processes diagnostics terms into DIAGNOSTIC output file [Ngrids]. !Dout(iCOfx) == T ! CO2_airsea air-sea CO2 flux Dout(iDNIT) == T ! denitrification denitrification flux !Dout(ipCO2) == T ! pCO2 CO2 partial pressure !Dout(iO2fx) == T ! O2_airsea air-sea O2 flux Dout(iPPro) == T ! P_Production primary production Dout(iNO3u) == F ! NO3_uptake NO3 uptake ! ! GLOSSARY: ! ========= ! !------------------------------------------------------------------------------ ! NPZD (Powell et al, 2006) Biological Model Parameters. Currently, it is ! configured with 4 biological tracers: ! ! idbio(1) NO3 Nitrate concentration ! idbio(2) phytoplankton Phytoplankton biomass ! idbio(3) zooplankton Zooplankton biomass ! idbio(4) detritus Detritus concentration ! !------------------------------------------------------------------------------ ! ! 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 ! ! 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]. ! ! !------------------------------------------------------------------------------ ! 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 ! ! 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 HISTORY files. !------------------------------------------------------------------------------ ! ! Hout Logical switches to write out biological fields into ! output HISTORY 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 ! !------------------------------------------------------------------------------ ! Logical switches (T/F) to activate writing of fields into AVERAGE file. !------------------------------------------------------------------------------ ! ! Aout Logical switches to write out biological fields into ! output AVERAGE NetCDF file, [1:NBT,1:Ngrids] values ! are expected: ! ! Aout(idTvar) biological tracers ! ! The idTvar(idbio(:)) are the same to those in the HISTORY ! file. ! !------------------------------------------------------------------------------ ! Logical switches (T/F) to activate writing of time-averaged fields into ! DIAGNOSTIC file. !------------------------------------------------------------------------------ ! ! Time-averaged, biological tracers diagnostic terms, [1:NBT,Ngrids] values ! expected: (if DIAGNOSTICS_TS) ! ! Dout(idDtrc(idbio(1:NBT),iT....),1:Ngrids) ! ! Dout(iTrate) Write out time rate of change. ! Dout(iThadv) Write out horizontal total advection. ! Dout(iTxadv) Write out horizontal XI-advection. ! Dout(iTyadv) Write out horizontal ETA-advection. ! Dout(iTvadv) Write out vertical advection. ! Dout(iThdif) Write out horizontal total diffusion, if TS_DIF2 or TS_DIF4. ! Dout(iTxdif) Write out horizonta1 XI-diffusion, if TS_DIF2 or TS_DIF4. ! Dout(iTydif) Write out horizontal ETA-diffusion, if TS_DIF2 or TS_DIF4. ! Dout(iTsdif) Write out horizontal S-diffusion, if TS_DIF2 or TS_DIF4 and ! rotated tensor (MIX_GEO_TS or MIX_ISO_TS). ! Dout(iTvdif) Write out vertical diffusion. !