1 | # |
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2 | # bio.param |
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3 | # |
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4 | # Parameter file for sea ice biogeochemistry BARROW, source v3.20 |
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5 | # |
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6 | # (c) Martin, Dec 2015, Paris |
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7 | # |
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8 | #================================================================================= |
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9 | # |
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10 | #--------------------------------------------------------------------------------- |
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11 | # Type of model and fluxes |
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12 | #--------------------------------------------------------------------------------- |
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13 | # |
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14 | # c_grid : type of grid: multilayer 'ML', deformed three layer 'DL', skeletal 'SL', or biologically-active 'BA' |
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15 | ML |
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16 | # h_skel : prescribed biologically active layers thickness (SL & DL) |
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17 | 0.10 |
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18 | # e_thr_bal : prescribed permeability threshold for BAL |
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19 | 0.05 |
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20 | # |
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21 | #--------------------------------------------------------------------------------- |
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22 | # Process switches |
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23 | #--------------------------------------------------------------------------------- |
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24 | # |
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25 | # ln_trbo : bottom entrapment for tracers or not |
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26 | .TRUE. |
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27 | # ln_trsi : snow-ice entrapment for tracers or not |
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28 | .TRUE. |
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29 | # ln_trdiff : diffusion of tracers or not |
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30 | .TRUE. |
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31 | # ln_trremp : remapping of tracers or not |
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32 | .TRUE. |
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33 | # ln_lim_dsi : limitation of growth by DSi or not |
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34 | .TRUE. |
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35 | # ln_lim_no3 : limitation of growth by NO3 |
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36 | .TRUE. |
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37 | # ln_lim_po4 : limitation of growth by PO3 |
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38 | .TRUE. |
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39 | # ln_lim_lig : light limitation or not |
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40 | .TRUE. |
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41 | # ln_lim_tem : temperature inhibition or not |
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42 | .TRUE. |
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43 | # ln_lim_sal : brine salinity inhibition or not |
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44 | .TRUE. |
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45 | # ln_lys : lysis or not |
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46 | .TRUE. |
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47 | # ln_rem : remineralization or not |
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48 | .TRUE. |
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49 | # ln_syn : diatom synthesis or not |
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50 | .TRUE. |
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51 | # ln_bubform : gas buble formation |
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52 | .TRUE. |
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53 | # ln_bubrise : gas buble ascent |
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54 | .TRUE. |
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55 | # ln_gasflux : gas flux to ATM |
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56 | .TRUE. |
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57 | # ln_carbon : activate carbon cycle |
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58 | .TRUE. |
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59 | # ln_ikaite : activate CaCO3 precipitation |
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60 | .TRUE. |
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61 | # |
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62 | #--------------------------------------------------------------------------------- |
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63 | # Gas exchange / carbonate system / ikaite |
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64 | #--------------------------------------------------------------------------------- |
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65 | # |
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66 | # i_gas_flux : Type of gas flux (1=Noflux, 2=ice-atm diffusive flux) |
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67 | 2 |
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68 | # brines_ar : brines aspect ratio (vertical ellipsoid: <1; spheres: 1) |
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69 | 1.00 |
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70 | # bub_form_rate : Gas Bubble formation rate (s-1) 2.5e-7 |
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71 | 2.5e-7 |
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72 | # bub_diss_rate : Gas Bubble dissolution rate (s-1) 2.5e-3 |
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73 | 2.5e-3 |
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74 | # h_bl_gas : Boundary layer thickness for diffusive gas flux (Moreau et al. 2005) |
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75 | 0.5e-6 |
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76 | # e_thr_gasflux : Brine volume fraction threshold for gas fluxes |
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77 | 0.05 |
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78 | # e_thr_bubrise : Brine volume fraction thershold for bubble rise |
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79 | 0.10 |
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80 | # sursat_gas : Sursaturation tolerated in brines (1 = 100%) |
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81 | 1.00 |
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82 | # nn_carbonate : 1=Roy; 2=Mehrbach equilibration CO2 constants; Mehrbach (2) is default |
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83 | 2 |
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84 | # caco3_time : CaCO3 precipitation/dissolution time scale rate (360000s=100h by default) |
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85 | 360000. |
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86 | # |
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87 | #--------------------------------------------------------------------------------- |
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88 | # Physiological parameters |
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89 | #--------------------------------------------------------------------------------- |
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90 | # |
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91 | # nn_bio_opt : type of biological model (0=NP; 1=NPD Redfield; 2=NPD + Si; 3=NPD non-RedF; 4=NPD n.r + iron, 5=carbon cycle & gases) |
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92 | 5 |
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93 | #--- Bio-optical parameters |
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94 | # |
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95 | # astar_alg : specific attenuation coefficient ( m-1 / ( mg chla m-3 ) ) - 0.01 Tedesco |
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96 | 0.005 |
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97 | # fdet_alg : fraction of detrital radiation absorption versus algal absorption - 0.2 (Arrigo et al 1993) |
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98 | 0.2 |
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99 | # |
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100 | #--- Growth, loss, remineralization |
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101 | # |
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102 | # pp_presc : prescribed GPP (ln_syn = false, mmol C m-3 s-1 ) DEFLT 1.0e-5 |
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103 | 0.0e-5 |
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104 | # mumax_bio : maximum specific growth rate (s-1) ( Sarthou 5e-6 -> 3.8e-5 ) |
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105 | 1.80e-5 |
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106 | # klys_bio : loss rate (s-1) ( Sarthou 5.8e-8 -> 2.75e-6 ) |
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107 | 1.80e-6 |
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108 | # krsp_bio : respiration rate (s-1) |
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109 | 1.0e-6 |
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110 | # krem_bio : remineralization rate for carbon (2.0e-7 Moreau et al Elementa Oxy 2015) |
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111 | 5.0e-6 |
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112 | # frem_bio : Fraction of nutrient loss that is remineralized in case of an N-P formulation |
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113 | 1.00 |
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114 | # |
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115 | #--- Photosynthesis / light limitation |
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116 | # |
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117 | # nn_phs : type of photosynthesis parameterization (1-4) |
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118 | 4 |
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119 | # ek_bio : Light adaptation parameter (nn_phs = 1, muE m-2 s-1) - DEFLT 2 |
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120 | 2 |
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121 | # alpha_bio : Photosynthetic efficiency (nn_phs > 1, gC/gchla/s/(muE/m2/s)) DEFLT 1.8e-4 - Fragiliariopsis 5.56e-5 (Mar FM) |
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122 | 3.6e-4 |
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123 | # chla_c : Chl/C in ice algae (g/g) - DEFLT 0.05 - Loern 95 0.003 - 0.05 |
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124 | 0.05 |
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125 | # Estar : PAR value at which Chl/C=min (nn_phs = 4) 360. |
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126 | 50. |
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127 | # nn_lys : type of lysis [ 1: klys_bio prescribed; 2: klys_bio*exp(rg_bio*T) ] |
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128 | 2 |
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129 | # nn_rem : type of remineralization [1: krem_bio prescribed; 2: krem_bio*exp(rg_bac*T) ] |
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130 | 2 |
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131 | # |
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132 | #--- Redfield ratios |
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133 | # |
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134 | # si_c : silicon to carbon molar ratio in diatoms (mol/mol) - 0.11 Sarthou 2005 |
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135 | 0.11 |
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136 | # no3_c : nitrogen to carbon molar ratio in diatoms (mol/mol) - 0.14 Sarthou 2005; Redf - 0.151 |
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137 | 0.14 |
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138 | # po4_c : phosphorus to carbon molar ratio in diatoms (mol/mol) - 0.014 Sarthou 2005; 0.0094 |
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139 | 0.014 |
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140 | # oxy_c : oxygen release to carbon uptake ratio during photosynthesis (mol/mol) - Redf = 138/106 = 1.30 / Sarmiento Gruber 2006 150/106 = 1.41, Anderson et al |
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141 | 1.30 |
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142 | # |
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143 | #--- Nutrient limitation, temperature and salinity inhibition |
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144 | # |
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145 | # khs_si_bio : halfsat cst for Si uptake (micrmol m-3) - 3.9 Sarthou et al |
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146 | 3.9 |
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147 | # khs_n_bio : halfsat cst for N uptake (micrmol m-3) - 1.6 Sarthou et al |
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148 | 1.6 |
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149 | # khs_p_bio : halfsat cst for P uptake (micrmol m-3) - 0.24 Sarthou et al. |
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150 | 0.24 |
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151 | # rg_bio : Temperature coefficient for algal physiological processes (0.0633 degC-1; Eppley, 1972) |
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152 | 0.0633 |
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153 | # rg_bac : Temperature coefficient for bacterial respiration (0.41 degC-1; Moreau et al, Elementa 2015) |
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154 | 0.41 |
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155 | # nn_lim_sal : Salinity lim. 1=Power-log gaussian, Arrigo 93 data; 2=Gaussian |
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156 | 1 |
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157 | # lim_sal_wid : Width of the limitation function (nn_lim_sal=2) |
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158 | 20.0 |
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159 | # lim_sal_smax: Salinity where limitation function equals 1 (nn_lim_sal=2) |
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160 | 34.0 |
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