!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> !! SEDIMENT reference namelist !! 1 - run characteristics (nam_run) !! 2 - sediment geometry (nam_geom) !! 3 - prognostic variables (nam_trased) !! 4 - diagnostic arrays (nam_diased) !! 5 - parameters for clay/silicium (nam_reac) !! 6 - parameters for redox reactions (nam_poc) !! 7 - parameters for calcite (nam_cal) !! 8 - parameters for restarting (nam_rst) !----------------------------------------------------------------------- &nam_run ! Characteristics of the simulation !----------------------------------------------------------------------- ln_sed_2way = .false. ! 2 way coupling with pisces nrosorder = 3 ! Order of the rosenbrock methode (3,4) rosatol = 1.E-4 ! Tolerance for the absolute error rosrtol = 1.E-4 ! Tolerance for the relative error / !----------------------------------------------------------------------- &nam_geom ! Characteristics of the sediment columns !----------------------------------------------------------------------- jpksed = 18 ! Number of vertical layers sedzmin = 0.1 ! Minimum vertical spacing sedhmax = 15.0 ! Maximum depth of the sediment sedkth = 9.0 ! Default parameters sedacr = 2.0 ! Default parameters porsurf = 0.9 ! Sediment porosity at the surface porinf = 0.75 ! Sediment porosity at infinite depth rhox = 0.25 ! Length scale of porosity variation (cm) / !----------------------------------------------------------------------- &nam_trased ! Prognostic variables !----------------------------------------------------------------------- ! ! ! ! ! ! ! name ! title of the field ! units ! initial data from file or not ! ! ! ! ! ! sedsol(1) = 'SedFeO ' , 'Fe(OH)3 Concentration ', '%' sedsol(2) = 'SedFeS ' , 'FeS Concentration ', '%' sedsol(3) = 'SedPOC ' , 'POC Concentration ', '%' sedsol(4) = 'SedPOS ' , 'Semi-ref POC Concentration ', '%' sedsol(5) = 'SedPOR ' , 'Refractory POC Concentration ', '%' sedsol(6) = 'SedCaCO3' , 'Calcite Concentration ', '%' sedsol(7) = 'SedBSi ' , 'Biogenic Silicate Concentration ', '%' sedsol(8) = 'SedClay ' , 'Clay Concentration ', '%' sedwat(1) = 'SedO2 ' , 'Dissolved Oxygen Concentration ', 'mol/L' sedwat(2) = 'SedNO3 ' , 'Nitrates Concentration ', 'mol/L' sedwat(3) = 'SedPO4 ' , 'Phosphate Concentration ', 'mol/L' sedwat(4) = 'SedNH4 ' , 'Total Ammonium Concentration ', 'mol/L ' sedwat(5) = 'SedH2S ' , 'Total H2S Concentration ', 'mol/L ' sedwat(6) = 'SedSO4 ' , 'Total SO4 Concentration ', 'mol/L ' sedwat(7) = 'SedFe2 ' , 'Total Fe2+ Concentration ', 'mol/L ' sedwat(8) = 'SedAlkalini' , 'Total Alkalinity Concentration ', 'eq/L ' sedwat(9) = 'Sedligand ' , 'Total ligand Concentration ', 'mol/L ' sedwat(10) = 'SedDIC ' , 'Dissolved inorganic Concentration ', 'mol/L' sedwat(11) = 'SedSil ' , 'Silicate Concentration ', 'mol/L' / !----------------------------------------------------------------------- &nam_diased ! Diagnostic arrays !----------------------------------------------------------------------- ! seddiag3d(1) = 'SedpH ' , 'pH ', '- ' seddiag3d(2) = 'SedCO3por ' , 'Dissolved CO3 concentration ', 'mol/L' seddiag3d(3) = 'SaturCO3 ' , 'CO3 saturation ', '-' seddiag2d(1) = 'FlxO2 ' , 'Dissolved Oxygen Flux ', 'mol/L' seddiag2d(2) = 'FlxNO3 ' , 'Nitrates flux ', 'mol/cm2/s' seddiag2d(3) = 'FlxPO4 ' , 'Phosphate flux ', 'mol/cm2/s' seddiag2d(4) = 'FlxNH4 ' , 'Total Ammonium flux ', 'mol/cm2/s' seddiag2d(5) = 'FlxH2S ' , 'Total H2S flux ', 'mol/cm2/s' seddiag2d(6) = 'FlxSO4 ' , 'Total SO4 flux ', 'mol/cm2/s' seddiag2d(7) = 'FlxFe2 ' , 'Total Fe2+ flux ', 'mol/cm2/s' seddiag2d(8) = 'FlxAlkalini' , 'Total Alkalinity flux ', 'mol/cm2/s' seddiag2d(9) = 'FlxLig ' , 'Total Ligand flux ', 'mol/cm2/s' seddiag2d(10) = 'FlxDIC ' , 'Dissolved inorganic carbon flux ', 'mol/cm2/s' seddiag2d(11) = 'FlxSi ' , 'Silicate flux ', 'mol/cm2/s' seddiag2d(12) = 'FlxFeO ' , 'FeO burial flux ', 'mol/cm2/s' seddiag2d(13) = 'FlxFeS ' , 'FeS burial flux ', 'mol/cm2/s' seddiag2d(14) = 'FlxPOC ' , 'POC burial flux ', 'mol/cm2/s' seddiag2d(15) = 'FlxPOS ' , 'POS burial flux ', 'mol/cm2/s' seddiag2d(16) = 'FlxPOR ' , 'POR burial flux ', 'mol/cm2/s' seddiag2d(17) = 'FlxCaCO3 ' , 'Calcite burial flux ', 'mol/cm2/s' seddiag2d(18) = 'FlxBSi ' , 'BSi burial flux ', 'mol/cm2/s' seddiag2d(19) = 'FlxClay ' , 'Clay burial flux ', 'mol/cm2/s' seddiag2d(20) = 'Flxtot ' , 'Total burial flux ', 'mol/cm2/s' seddiag2d(21) = 'dzdep ' , 'Sedimentation rate ', 'cm/s' seddiag2d(22) = 'Rstepros ' , 'Number of iterations ', '-' / !----------------------------------------------------------------------- &nam_inorg ! Inorganic chemistry in sediments (CacO3, Si) !----------------------------------------------------------------------- rcopal = 1.25 ! Reactivity for clay [l.mol-1.an-1] rccal = 0.1 ! Dissolution rate of calcite [in yr-1] rcligc = 0.1 ! Degradation rate of ligands [in yr-1] ratligc = 1.E-4 ! L/C ratio in POC / !----------------------------------------------------------------------- &nam_poc ! parameters for the redox reactions of the sediment module !----------------------------------------------------------------------- redO2 = 138. ! Redfield coef for Oxygen redNo3 = 16. ! Redfield coef for Nitrate redPo4 = 1. ! Redfield coef for Phosphate redC = 117. ! Redfield coef for Carbon redfep = 0.05 ! Ration of Fe bound P rcorgl = 10. ! Reactivity for labile POC [an-1] rcorgs = 0.1 ! Reactivity for semi-refractory POC [an-1] rcorgr = 1.E-4 ! Reactivity for refractory POC [an-1] rcnh4 = 1E7 ! Reactivity for O2/NH4 [l.mol-1.an-1] rch2s = 1E8 ! Reactivity for O2/H2S [l.mol-1.an-1] rcfe2 = 5E8 ! Reactivity for O2/Fe2+ [l.mol-1.an-1] rcfeh2s = 1E4 ! Reactivity for FEOH/H2S [l.mol-1.an-1] rcfeso = 2E6 ! Reactivity for FES/O2 [l.mol-1.an-1] rcfesp = 1E-4 ! Precipitation of FeS [mol.l-1.an-1] rcfesd = 1.E-3 ! Dissolution of FeS [an-1] xksedo2 = 1.E-6 ! Half-saturation constant for oxic remin [mol/l] xksedno3 = 5.E-6 ! Half-saturation constant for denitrification [mol/l] xksedfeo = 0.006 ! Half-saturation constant for iron remin [%] xksedso4 = 5E-4 ! Half-saturation constant for SO4 remin [mol/l] / !----------------------------------------------------------------------- &nam_btb ! parameters for bioturbation and bioirrigation !----------------------------------------------------------------------- dbiot = 8. ! Bioturbation coefficient (in cm2/yr) ln_btbz = .true. ! Depth varying bioturbation dbtbzsc = 5.0 ! coefficient for btb attenuation. If no variation, depth of the mixed layer adsnh4 = 4.16 ! Adsorption coefficient of NH4 adsfe2 = 697.0 ! Adsorption coefficient of Fe2 ln_irrig = .true. ! Bioirrigation in sediment xirrzsc = 2.0 ! Vertical scale of the attentuation of bioirrigation [cm] / !----------------------------------------------------------------------- &nam_rst ! parameters for restarting the sediment module !----------------------------------------------------------------------- ln_rst_sed = .false. ! restart flag cn_sedrst_in = "restart_sed" ! name of the input restart file name of the sediment module cn_sedrst_indir = "." ! directory from which to read input sediment restarts cn_sedrst_out = "restart_sed" ! suffix of pass. [sediment] restart name (output) cn_sedrst_outdir = "." ! directory to which to write output sediment restarts /