!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> !! PISCES : 1 - air-sea exchange (nampisext) !! namelists 2 - biological parameters (nampisbio) !! 3 - parameters for nutrient limitations (nampislim) !! 4 - parameters for phytoplankton (nampisprod,nampismort) !! 5 - parameters for zooplankton (nampismes,nampiszoo) !! 6 - parameters for remineralization (nampisrem) !! 7 - parameters for calcite chemistry (nampiscal) !! 8 - parameters for inputs deposition (nampissed) !! 9 - parameters for Kriest parameterization (nampiskrp, nampiskrs) !! 10 - additional 2D/3D diagnostics (nampisdia) !! 11 - Damping (nampisdmp) !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' &nampistrc ! tracers definition !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ! ! ! name ! title of the field ! units ! ! ! ! ! ! ! ! tracer(1) = 'DIC ' , 'Dissolved inorganic Concentration ', 'mmol/m3' tracer(2) = 'Alkalini' , 'Total Alkalinity Concentration ', 'meq/m3 ' tracer(3) = 'O2 ' , 'Dissolved Oxygen Concentration ', 'mmol/m3' tracer(4) = 'CaCO3 ' , 'Calcite Concentration ', 'mmol/m3' tracer(5) = 'PO4 ' , 'Phosphate Concentration ', 'mmol/m3' tracer(6) = 'POC ' , 'Small organic carbon Concentration ', 'mmol/m3' tracer(7) = 'Si ' , 'Silicate Concentration ', 'mmol/m3' tracer(8) = 'PHY ' , 'Nanophytoplankton Concentration ', 'mmol/m3' tracer(9) = 'ZOO ' , 'Microzooplankton Concentration ', 'mmol/m3' tracer(10) = 'DOC ' , 'Dissolved organic Concentration ', 'mmol/m3' tracer(11) = 'PHY2 ' , 'Diatoms Concentration ', 'mmol/m3' tracer(12) = 'ZOO2 ' , 'Mesozooplankton Concentration ', 'mmol/m3' tracer(13) = 'BSi ' , 'Diatoms Silicate Concentration ', 'mmol/m3' tracer(14) = 'Fer ' , 'Dissolved Iron Concentration ', 'mmol/m3' tracer(15) = 'BFe ' , 'Big iron particles Concentration ', 'mmol/m3' tracer(16) = 'GOC ' , 'Big organic carbon Concentration ', 'mmol/m3' tracer(17) = 'SFe ' , 'Small iron particles Concentration ', 'mmol/m3' tracer(18) = 'DFe ' , 'Diatoms iron Concentration ', 'mmol/m3' tracer(19) = 'DSi ' , 'Sinking biogenic Silicate Concentration', 'mmol/m3' tracer(20) = 'NFe ' , 'Nano iron Concentration ', 'mmol/m3' tracer(21) = 'NCHL ' , 'Nano chlorophyl Concentration ', 'mg/m3' tracer(22) = 'DCHL ' , 'Diatoms chlorophyl Concentration ', 'mg/m3' tracer(23) = 'NO3 ' , 'Nitrates Concentration ', 'mmol/m3' tracer(24) = 'NH4 ' , 'Ammonium Concentration ', 'mmol/m3' tracer(25) = 'LGW ' , 'Ligands Concentration ', 'mmol/m3' / !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' &nampisext ! air-sea exchange !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, atcco2 = 287. ! atmospheric pCO2 / !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' &nampisbio ! biological parameters !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, nrdttrc = 1 ! time step frequency for biology wsbio = 2. ! POC sinking speed xkmort = 2.E-7 ! half saturation constant for mortality ferat3 = 10.E-6 ! Fe/C in zooplankton wsbio2 = 50. ! Big particles sinking speed wsbio2max = 50. ! Big particles maximum sinking speed wsbio2scale = 5000. ! Big particles length scale of sinking ln_sink_new = .false. ! New sedimentation scheme niter1max = 10 ! Number of iterations for slow sinking particles niter2max = 50 ! Maximum number of iterations for fast sinking particles ! ! ln_ligand enabled ldocp = 1.E-4 ! Phyto ligand production per unit doc ldocz = 1.E-4 ! Zoo ligand production per unit doc lthet = 1.0 ! Proportional loss of ligands due to Fe uptake ! ! ln_p5z enabled no3rat3 = 0.182 ! N/C ratio in zooplankton po4rat3 = 0.0094 ! P/C ratio in zooplankton / !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' &namp4zlim ! parameters for nutrient limitations !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, concnno3 = 1.e-6 ! Nitrate half saturation of nanophytoplankton concdno3 = 3.E-6 ! Nitrate half saturation for diatoms concnnh4 = 1.E-7 ! NH4 half saturation for phyto concdnh4 = 3.E-7 ! NH4 half saturation for diatoms concnfer = 1.E-9 ! Iron half saturation for phyto concdfer = 3.E-9 ! Iron half saturation for diatoms concbfe = 1.E-11 ! Iron half-saturation for DOC remin. concbnh4 = 2.E-8 ! NH4 half saturation for DOC remin. concbno3 = 2.E-7 ! Nitrate half saturation for DOC remin. xsizedia = 1.E-6 ! Minimum size criteria for diatoms xsizephy = 1.E-6 ! Minimum size criteria for phyto xsizern = 3.0 ! Size ratio for nanophytoplankton xsizerd = 3.0 ! Size ratio for diatoms xksi1 = 2.E-6 ! half saturation constant for Si uptake xksi2 = 20E-6 ! half saturation constant for Si/C xkdoc = 417.E-6 ! half-saturation constant of DOC remineralization qnfelim = 7.E-6 ! Optimal quota of phyto qdfelim = 7.E-6 ! Optimal quota of diatoms caco3r = 0.3 ! mean rain ratio oxymin = 1.E-6 ! Half-saturation constant for anoxia / !----------------------------------------------------------------------- &namp5zlim ! parameters for nutrient limitations PISCES QUOTA - ln_p5z !----------------------------------------------------------------------- concnno3 = 3e-6 ! Nitrate half saturation of nanophytoplankton concpno3 = 1e-6 concdno3 = 4E-6 ! Phosphate half saturation for diatoms concnnh4 = 1.5E-6 ! NH4 half saturation for phyto concpnh4 = 4E-7 concdnh4 = 2E-6 ! NH4 half saturation for diatoms concnpo4 = 3E-6 ! PO4 half saturation for phyto concppo4 = 1.5E-6 concdpo4 = 4E-6 ! PO4 half saturation for diatoms concnfer = 3E-9 ! Iron half saturation for phyto concpfer = 1.5E-9 concdfer = 4E-9 ! Iron half saturation for diatoms concbfe = 1.E-11 ! Half-saturation for Fe limitation of Bacteria concbnh4 = 1.E-7 ! NH4 half saturation for phyto concbno3 = 5.E-7 ! Phosphate half saturation for diatoms concbpo4 = 1E-7 ! Phosphate half saturation for bacteria xsizedia = 1.E-6 ! Minimum size criteria for diatoms xsizephy = 1.E-6 ! Minimum size criteria for phyto xsizepic = 1.E-6 xsizern = 1.0 ! Size ratio for nanophytoplankton xsizerp = 1.0 xsizerd = 4.0 ! Size ratio for diatoms xksi1 = 2.E-6 ! half saturation constant for Si uptake xksi2 = 20E-6 ! half saturation constant for Si/C xkdoc = 417.E-6 ! half-saturation constant of DOC remineralization caco3r = 0.35 ! mean rain ratio oxymin = 1.E-6 ! Half-saturation constant for anoxia / !----------------------------------------------------------------------- &namp5zquota ! parameters for nutrient limitations PISCES quota - ln_p5z !----------------------------------------------------------------------- qfnopt = 7.E-6 ! Optimal Fe quota of nanophyto qfpopt = 7.E-6 ! Optimal Fe quota of picophyto qfdopt = 7.E-6 ! Optimal quota of diatoms qnnmin = 0.29 ! Minimal N quota for nano qnnmax = 1.39 ! Maximal N quota for nano qpnmin = 0.28 ! Minimal P quota for nano qpnmax = 1.06 ! Maximal P quota for nano qnpmin = 0.42 ! Minimal N quota for pico qnpmax = 1.39 ! Maximal N quota for pico qppmin = 0.25 ! Minimal P quota for pico qppmax = 0.7 ! Maximal P quota for pico qndmin = 0.25 ! Minimal N quota for diatoms qndmax = 1.39 ! Maximal N quota for diatoms qpdmin = 0.29 ! Minimal P quota for diatoms qpdmax = 1.32 ! Maximal P quota for diatoms qfnmax = 40E-6 ! Maximal Fe quota for nano qfpmax = 40E-6 ! Maximal Fe quota for pico qfdmax = 40E-6 ! Maximal Fe quota for diatoms / !----------------------------------------------------------------------- &nampisopt ! parameters for optics !----------------------------------------------------------------------- parlux = 0.43 ! Fraction of shortwave as PAR / !----------------------------------------------------------------------- &namp4zprod ! parameters for phytoplankton growth for PISCES std - ln_p4z !----------------------------------------------------------------------- pislopen = 2. ! P-I slope pisloped = 2. ! P-I slope for diatoms xadap = 0. ! Adaptation factor to low light excretn = 0.05 ! excretion ratio of phytoplankton excretd = 0.05 ! excretion ratio of diatoms bresp = 0.033 ! Basal respiration rate chlcnm = 0.033 ! Maximum Chl/C in nanophytoplankton chlcdm = 0.05 ! Maximum Chl/C in diatoms chlcmin = 0.004 ! Minimum Chl/c in phytoplankton fecnm = 80E-6 ! Maximum Fe/C in nanophytoplankton fecdm = 80E-6 ! Maximum Fe/C in diatoms grosip = 0.159 ! mean Si/C ratio / !----------------------------------------------------------------------- &namp5zprod ! parameters for phytoplankton growth for PISCES quota- ln_p5z !----------------------------------------------------------------------- pislopen = 3. ! P-I slope pislopep = 3. ! P-I slope for picophytoplankton pisloped = 3. ! P-I slope for diatoms excretn = 0.05 ! excretion ratio of phytoplankton excretp = 0.05 ! excretion ratio of picophytoplankton excretd = 0.05 ! excretion ratio of diatoms xadap = 0. ! Adaptation factor to low light bresp = 0.02 ! Basal respiration rate thetannm = 0.25 ! Maximum Chl/N in nanophytoplankton thetanpm = 0.25 ! Maximum Chl/N in picophytoplankton thetandm = 0.3 ! Maximum Chl/N in diatoms chlcmin = 0.004 ! Minimum Chl/c in phytoplankton grosip = 0.131 ! mean Si/C ratio / !----------------------------------------------------------------------- &namp4zmort ! parameters for phytoplankton sinks for PISCES std - ln_p4z !----------------------------------------------------------------------- wchl = 0.01 ! quadratic mortality of phytoplankton wchld = 0.01 ! maximum quadratic mortality of diatoms wchldm = 0.03 ! maximum quadratic mortality of diatoms mprat = 0.01 ! phytoplankton mortality rate mprat2 = 0.01 ! Diatoms mortality rate / !----------------------------------------------------------------------- &namp5zmort ! parameters for phytoplankton sinks for PISCES quota - ln_p5z !----------------------------------------------------------------------- wchln = 0.01 ! quadratic mortality of nanophytoplankton wchlp = 0.01 ! quadratic mortality of picophytoplankton wchld = 0.01 ! maximum quadratic mortality of diatoms wchldm = 0.02 ! maximum quadratic mortality of diatoms mpratn = 0.01 ! nanophytoplankton mortality rate mpratp = 0.01 ! picophytoplankton mortality rate mpratd = 0.01 ! Diatoms mortality rate / !----------------------------------------------------------------------- &namp4zmes ! parameters for mesozooplankton for PISCES std - ln_p4z !----------------------------------------------------------------------- part2 = 0.75 ! part of calcite not dissolved in mesozoo guts grazrat2 = 0.75 ! maximal mesozoo grazing rate resrat2 = 0.005 ! exsudation rate of mesozooplankton mzrat2 = 0.03 ! mesozooplankton mortality rate xpref2d = 1. ! mesozoo preference for diatoms xpref2n = 0.3 ! mesozoo preference for nanophyto. xpref2z = 1. ! mesozoo preference for microzoo. xpref2c = 0.3 ! mesozoo preference for poc xthresh2zoo = 1E-8 ! zoo feeding threshold for mesozooplankton xthresh2dia = 1E-8 ! diatoms feeding threshold for mesozooplankton xthresh2phy = 1E-8 ! nanophyto feeding threshold for mesozooplankton xthresh2poc = 1E-8 ! poc feeding threshold for mesozooplankton xthresh2 = 3E-7 ! Food threshold for grazing xkgraz2 = 20.E-6 ! half saturation constant for meso grazing epsher2 = 0.35 ! Efficicency of Mesozoo growth epsher2min = 0.35 ! Minimum efficiency of mesozoo growth sigma2 = 0.6 ! Fraction of mesozoo excretion as DOM unass2 = 0.3 ! non assimilated fraction of P by mesozoo grazflux = 3.e3 ! flux-feeding rate / !----------------------------------------------------------------------- &namp5zmes ! parameters for mesozooplankton !----------------------------------------------------------------------- part2 = 0.75 ! part of calcite not dissolved in mesozoo guts grazrat2 = 0.85 ! maximal mesozoo grazing rate bmetexc2 = .true. ! Metabolic use of excess carbon resrat2 = 0.005 ! exsudation rate of mesozooplankton mzrat2 = 0.02 ! mesozooplankton mortality rate xpref2d = 1. ! zoo preference for phyto xpref2n = 0.3 ! mesozoo preference for nanophyto. xpref2z = 1. ! zoo preference for zoo xpref2m = 0.2 ! meso preference for zoo xpref2c = 0.3 ! zoo preference for poc xthresh2zoo = 1E-8 ! zoo feeding threshold for mesozooplankton xthresh2dia = 1E-8 ! diatoms feeding threshold for mesozooplankton xthresh2phy = 1E-8 ! nanophyto feeding threshold for mesozooplankton xthresh2mes = 1E-8 ! meso feeding threshold for mesozooplankton xthresh2poc = 1E-8 ! poc feeding threshold for mesozooplankton xthresh2 = 3E-7 ! Food threshold for grazing xkgraz2 = 20.E-6 ! half sturation constant for meso grazing epsher2 = 0.5 ! Efficicency of Mesozoo growth epsher2min = 0.2 ! Minimum efficiency of mesozoo growth ssigma2 = 0.5 ! Fraction excreted as semi-labile DOM srespir2 = 0.2 ! Active respiration unass2c = 0.3 ! non assimilated fraction of P by mesozoo unass2n = 0.3 ! non assimilated fraction of N by mesozoo unass2p = 0.3 ! non assimilated fraction of P by mesozoo grazflux = 3.e3 ! flux-feeding rate / !----------------------------------------------------------------------- &namp4zzoo ! parameters for microzooplankton for PISCES std - ln_p4z !----------------------------------------------------------------------- part = 0.5 ! part of calcite not dissolved in microzoo guts grazrat = 3.0 ! maximal zoo grazing rate resrat = 0.03 ! exsudation rate of zooplankton mzrat = 0.004 ! zooplankton mortality rate xprefc = 0.1 ! Microzoo preference for POM xprefn = 1. ! Microzoo preference for Nanophyto xprefd = 0.6 ! Microzoo preference for Diatoms xthreshdia = 1.E-8 ! Diatoms feeding threshold for microzooplankton xthreshphy = 1.E-8 ! Nanophyto feeding threshold for microzooplankton xthreshpoc = 1.E-8 ! POC feeding threshold for microzooplankton xthresh = 3.E-7 ! Food threshold for feeding xkgraz = 20.E-6 ! half sturation constant for grazing epsher = 0.3 ! Efficiency of microzoo growth epshermin = 0.3 ! Minimum efficiency of microzoo growth sigma1 = 0.6 ! Fraction of microzoo excretion as DOM unass = 0.3 ! non assimilated fraction of phyto by zoo / !----------------------------------------------------------------------- &namp5zzoo ! parameters for microzooplankton !----------------------------------------------------------------------- part = 0.5 ! part of calcite not dissolved in microzoo gutsa grazrat = 2.75 ! maximal zoo grazing rate bmetexc = .true. ! Metabolic use of excess carbon resrat = 0.03 ! exsudation rate of zooplankton mzrat = 0.005 ! zooplankton mortality rate xprefc = 0.1 ! Microzoo preference for POM xprefn = 1. ! Microzoo preference for Nanophyto xprefp = 1.6 ! Microzoo preference for picophyto xprefd = 1.0 ! Microzoo preference for Diatoms xprefz = 0.3 ! Microzoo preference for microzooplankton xthreshdia = 1.E-8 ! Diatoms feeding threshold for microzooplankton xthreshphy = 1.E-8 ! Nanophyto feeding threshold for microzooplankton xthreshpic = 1.E-8 xthreshzoo = 1.E-8 ! Nanophyto feeding threshold for microzooplankton xthreshpoc = 1.E-8 ! POC feeding threshold for microzooplankton xthresh = 3.E-7 ! Food threshold for feeding xkgraz = 20.E-6 ! half sturation constant for grazing epsher = 0.5 ! Efficiency of microzoo growth epshermin = 0.2 ! Minimum efficiency of microzoo growth ssigma = 0.5 ! Fraction excreted as semi-labile DOM srespir = 0.2 ! Active respiration unassc = 0.3 ! non assimilated fraction of C by zoo unassn = 0.3 ! non assimilated fraction of C by zoo unassp = 0.3 ! non assimilated fraction of C by zoo / !----------------------------------------------------------------------- &nampisfer ! parameters for iron chemistry !----------------------------------------------------------------------- ln_ligvar = .false. ! variable ligand concentration xlam1 = 0.15 ! scavenging rate of Iron xlamdust = 150.0 ! Scavenging rate of dust ligand = 0.7E-9 ! Ligands concentration kfep = 0.01 ! Nanoparticle formation rate constant / !----------------------------------------------------------------------- &nampisrem ! parameters for remineralization !----------------------------------------------------------------------- xremik = 0.3 ! remineralization rate of DOC nitrif = 0.05 ! NH4 nitrification rate xsirem = 0.003 ! remineralization rate of Si xsiremlab = 0.03 ! fast remineralization rate of Si xsilab = 0.5 ! Fraction of labile biogenic silica feratb = 10.E-6 ! Fe/C quota in bacteria xkferb = 3E-10 ! Half-saturation constant for bacteria Fe/C ! ! ln_p5z xremikc = 0.25 ! remineralization rate of DOC xremikn = 0.35 ! remineralization rate of DON xremikp = 0.4 ! remineralization rate of DOP ! feratb = 20E-6 ! Bacterial Fe/C ratio ! xkferb = 3E-10 ! Half-saturation constant for bact. Fe/C / !----------------------------------------------------------------------- &nampispoc ! parameters for organic particles !----------------------------------------------------------------------- xremip = 0.035 ! remineralisation rate of PON jcpoc = 15 ! Number of lability classes rshape = 1.0 ! Shape of the gamma function ! ! ln_p5z xremipc = 0.02 ! remineralisation rate of POC xremipn = 0.025 ! remineralisation rate of PON xremipp = 0.03 ! remineralisation rate of POP / !----------------------------------------------------------------------- &nampiscal ! parameters for Calcite chemistry !----------------------------------------------------------------------- kdca = 6. ! calcite dissolution rate constant (1/time) nca = 1. ! order of dissolution reaction (dimensionless) / !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' &nampissbc ! parameters for inputs deposition !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ln_dust = .true. ! boolean for dust input from the atmosphere ln_river = .false. ! boolean for river input of nutrients ln_ndepo = .false. ! boolean for atmospheric deposition of N ln_ironsed = .true. ! boolean for Fe input from sediments sedfeinput = 2E-9 ! Coastal release of Iron dustsolub = 0.014 ! Solubility of the dust mfrac = 0.035 ! Fe mineral fraction of dust wdust = 2.0 ! Dust sinking speed diazolight = 50 ! Diazotrophs sensitivity to light (W/m2) nitrfix = 1.E-7 ! Nitrogen fixation rate concfediaz = 1.E-10 ! Diazotrophs half-saturation Cste for Iron / !----------------------------------------------------------------------- &nampislig ! Namelist parameters for ligands, nampislig !----------------------------------------------------------------------- rlgw = 100. ! Lifetime (years) of weak ligands rlig = 1.E-4 ! Remin ligand production per unit C prlgw = 1.E-4 ! Photolysis of weak ligand rlgs = 1. ! Lifetime (years) of strong ligands /