| 1 | !!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 2 | !! SEDIMENT reference namelist |
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| 3 | !! 1 - run characteristics (nam_run) |
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| 4 | !! 2 - sediment geometry (nam_geom) |
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| 5 | !! 3 - prognostic variables (nam_trased) |
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| 6 | !! 4 - diagnostic arrays (nam_diased) |
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| 7 | !! 5 - parameters for clay/silicium (nam_reac) |
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| 8 | !! 6 - parameters for redox reactions (nam_poc) |
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| 9 | !! 7 - parameters for calcite (nam_cal) |
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| 10 | !! 8 - parameters for restarting (nam_rst) |
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| 11 | !----------------------------------------------------------------------- |
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| 12 | &nam_run ! Characteristics of the simulation |
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| 13 | !----------------------------------------------------------------------- |
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| 14 | nrseddt = 1 ! Nb of iterations for fast species |
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| 15 | ln_sed_2way = .false. ! 2 way coupling with pisces |
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| 16 | / |
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| 17 | !----------------------------------------------------------------------- |
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| 18 | &nam_geom ! Characteristics of the sediment columns |
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| 19 | !----------------------------------------------------------------------- |
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| 20 | jpksed = 11 ! Number of vertical layers |
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| 21 | sedzmin = 0.3 ! Minimum vertical spacing |
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| 22 | sedhmax = 10.0 ! Maximum depth of the sediment |
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| 23 | sedkth = 7.0 ! Default parameters |
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| 24 | sedacr = 2.0 ! Default parameters |
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| 25 | porsurf = 0.9 ! Sediment porosity at the surface |
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| 26 | porinf = 0.75 ! Sediment porosity at infinite depth |
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| 27 | rhox = 0.33 ! Length scale of porosity variation (cm) |
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| 28 | / |
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| 29 | !----------------------------------------------------------------------- |
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| 30 | &nam_trased ! Prognostic variables |
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| 31 | !----------------------------------------------------------------------- |
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| 32 | ! ! ! ! ! |
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| 33 | ! ! name ! title of the field ! units ! initial data from file or not ! |
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| 34 | ! ! ! ! ! |
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| 35 | sedsol(1) = 'SedBSi ' , 'Biogenic Silicate Concentration ', '%' |
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| 36 | sedsol(2) = 'SedClay ' , 'Clay Concentration ', '%' |
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| 37 | sedsol(3) = 'SedPOC ' , 'POC Concentration ', '%' |
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| 38 | sedsol(4) = 'SedCaCO3' , 'Calcite Concentration ', '%' |
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| 39 | sedsol(5) = 'SedPOS ' , 'Semi-ref POC Concentration ', '%' |
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| 40 | sedsol(6) = 'SedPOR ' , 'Refractory POC Concentration ', '%' |
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| 41 | sedsol(7) = 'SedFeO ' , 'Fe(OH)3 Concentration ', '%' |
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| 42 | sedsol(8) = 'SedFeS ' , 'FeS Concentration ', '%' |
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| 43 | sedwat(1) = 'SedSil ' , 'Silicate Concentration ', 'mol/L' |
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| 44 | sedwat(2) = 'SedO2 ' , 'Dissolved Oxygen Concentration ', 'mol/L' |
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| 45 | sedwat(3) = 'SedDIC ' , 'Dissolved inorganic Concentration ', 'mol/L' |
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| 46 | sedwat(4) = 'SedNO3 ' , 'Nitrates Concentration ', 'mol/L' |
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| 47 | sedwat(5) = 'SedPO4 ' , 'Phosphate Concentration ', 'mol/L' |
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| 48 | sedwat(6) = 'SedAlkalini' , 'Total Alkalinity Concentration ', 'eq/L ' |
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| 49 | sedwat(7) = 'SedNH4 ' , 'Total Ammonium Concentration ', 'mol/L ' |
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| 50 | sedwat(8) = 'SedH2S ' , 'Total H2S Concentration ', 'mol/L ' |
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| 51 | sedwat(9) = 'SedSO4 ' , 'Total SO4 Concentration ', 'mol/L ' |
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| 52 | sedwat(10) = 'SedFe2 ' , 'Total Fe2+ Concentration ', 'mol/L ' |
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| 53 | / |
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| 54 | !----------------------------------------------------------------------- |
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| 55 | &nam_diased ! Diagnostic arrays |
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| 56 | !----------------------------------------------------------------------- |
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| 57 | ! |
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| 58 | seddiag3d(1) = 'SedpH ' , 'pH ', '- ' |
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| 59 | seddiag3d(2) = 'SedCO3por ' , 'Dissolved CO3 cocnentration ', 'mol/L' |
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| 60 | seddiag2d(1) = 'FlxSi ' , 'Silicate flux ', 'mol/cm2/s' |
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| 61 | seddiag2d(2) = 'FlxO2 ' , 'Dissolved Oxygen Flux ', 'mol/L' |
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| 62 | seddiag2d(3) = 'FlxDIC ' , 'Dissolved inorganic carbon flux ', 'mol/cm2/s' |
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| 63 | seddiag2d(4) = 'FlxNO3 ' , 'Nitrates flux ', 'mol/cm2/s' |
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| 64 | seddiag2d(5) = 'FlxPO4 ' , 'Phosphate flux ', 'mol/cm2/s' |
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| 65 | seddiag2d(6) = 'FlxAlkalini' , 'Total Alkalinity flux ', 'mol/cm2/s' |
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| 66 | seddiag2d(7) = 'FlxNH4 ' , 'Total Ammonium flux ', 'mol/cm2/s' |
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| 67 | seddiag2d(8) = 'FlxH2S ' , 'Total H2S flux ', 'mol/cm2/s' |
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| 68 | seddiag2d(9) = 'FlxSO4 ' , 'Total SO4 flux ', 'mol/cm2/s' |
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| 69 | seddiag2d(10) = 'FlxFe2 ' , 'Total Fe2+ flux ', 'mol/cm2/s' |
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| 70 | seddiag2d(11) = 'Flxtot ' , 'Total net sediment burial rate ', 'cm/s' |
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| 71 | seddiag2d(12) = 'dzdep ' , 'Sedimentation rate ', 'cm/s' |
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| 72 | / |
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| 73 | !----------------------------------------------------------------------- |
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| 74 | &nam_inorg ! Inorganic chemistry in sediments (CacO3, Si) |
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| 75 | !----------------------------------------------------------------------- |
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| 76 | rcopal = 0.1 ! Reactivity for clay [l.mol-1.an-1] |
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| 77 | dcoef = 8.0E-6 ! Diffusion coefficient in sediments (in cm**2/s) |
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| 78 | rccal = 0.014 ! Dissolution rate of calcite [in yr-1] |
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| 79 | rcligc = 0.1 ! Degradation rate of ligands [in yr-1] |
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| 80 | ratligc = 1.E-4 ! L/C ratio in POC |
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| 81 | / |
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| 82 | !----------------------------------------------------------------------- |
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| 83 | &nam_poc ! parameters for the redox reactions of the sediment module |
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| 84 | !----------------------------------------------------------------------- |
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| 85 | redO2 = 140. ! Redfield coef for Oxygen |
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| 86 | redNo3 = 16. ! Redfield coef for Nitrate |
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| 87 | redPo4 = 1. ! Redfield coef for Phosphate |
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| 88 | redC = 122. ! Redfield coef for Carbon |
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| 89 | redfep = 0.05 ! Ration of Fe bound P |
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| 90 | rcorgl = 10. ! Reactivity for labile POC [an-1] |
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| 91 | rcorgs = 0.1 ! Reactivity for semi-refractory POC [an-1] |
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| 92 | rcorgr = 1.E-4 ! Reactivity for refractory POC [an-1] |
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| 93 | rcnh4 = 1E7 ! Reactivity for O2/NH4 [l.mol-1.an-1] |
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| 94 | rch2s = 1E5 ! Reactivity for O2/H2S [l.mol-1.an-1] |
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| 95 | rcfe2 = 1E8 ! Reactivity for O2/Fe2+ [l.mol-1.an-1] |
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| 96 | rcfeh2s = 1E4 ! Reactivity for FEOH/H2S [l.mol-1.an-1] |
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| 97 | rcfes = 1E5 ! Reactivity for FE2+/H2S [l.mol-1.an-1] |
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| 98 | rcfeso = 3E5 ! Reactivity for FES/O2 [l.mol-1.an-1] |
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| 99 | xksedo2 = 1.E-6 ! Half-saturation constant for oxic remin [mol/l] |
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| 100 | xksedno3 = 10.E-6 ! Half-saturation constant for denitrification [mol/l] |
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| 101 | xksedfeo = 0.6 ! Half-saturation constant for iron remin [%] |
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| 102 | xksedso4 = 2E-3 ! Half-saturation constant for SO4 remin [mol/l] |
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| 103 | / |
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| 104 | !----------------------------------------------------------------------- |
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| 105 | &nam_btb ! parameters for bioturbation and bioirrigation |
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| 106 | !----------------------------------------------------------------------- |
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| 107 | dbiot = 5. ! Bioturbation coefficient (in cm2/yr) |
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| 108 | ln_btbz = .false. ! Depth varying bioturbation |
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| 109 | dbtbzsc = 10.0 ! coefficient for btb attenuation. If no variation, depth of the mixed layer |
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| 110 | adsnh4 = 1.3 ! Adsorption coefficient of NH4 |
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| 111 | ln_irrig = .true. ! Bioirrigation in sediment |
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| 112 | xirrzsc = 1.5 ! Vertical scale of the attentuation of bioirrigation [cm] |
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| 113 | / |
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| 114 | !----------------------------------------------------------------------- |
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| 115 | &nam_rst ! parameters for restarting the sediment module |
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| 116 | !----------------------------------------------------------------------- |
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| 117 | ln_rst_sed = .false. ! restart flag |
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| 118 | cn_sedrst_in = "restart_sed" ! name of the input restart file name of the sediment module |
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| 119 | cn_sedrst_indir = "." ! directory from which to read input sediment restarts |
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| 120 | cn_sedrst_out = "restart_sed" ! suffix of pass. [sediment] restart name (output) |
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| 121 | cn_sedrst_outdir = "." ! directory to which to write output sediment restarts |
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| 122 | / |
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