1 | !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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2 | ! |
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3 | ! BIO namelist : MEDUSA biological model option and parameter input |
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4 | ! ------------- |
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5 | ! |
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6 | !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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7 | !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' |
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8 | ! natbio Shared parameters for dynamics/advection/thermo |
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9 | !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, |
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10 | ! |
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11 | !! Primary production and chl related quantities |
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12 | !! xxi : conversion factor from gC to mmolN |
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13 | !! xaln : Chl-a specific initial slope of P-I curve for non-diatoms |
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14 | !! xald : Chl-a specific initial slope of P-I curve for diatoms |
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15 | !! jphy : phytoplankton T-dependent growth switch |
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16 | !! xvpn : maximum growth rate for non-diatoms |
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17 | !! xvpd : maximum growth rate for diatoms |
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18 | !! xthetam : maximum Chl to C ratio for non-diatoms |
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19 | !! xthetamd : maximum Chl to C ratio for diatoms |
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20 | !! |
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21 | !! Diatom silicon parameters |
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22 | !! xsin0 : minimum diatom Si:N ratio |
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23 | !! xnsi0 : minimum diatom N:Si ratio |
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24 | !! xuif : hypothetical growth ratio at infinite Si:N ratio |
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25 | !! |
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26 | !! Nutrient limitation |
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27 | !! jliebig : Liebig nutrient uptake switch |
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28 | !! xnln : half-sat constant for DIN uptake by non-diatoms |
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29 | !! xnld : half-sat constant for DIN uptake by diatoms |
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30 | !! xsl : half-sat constant for Si uptake by diatoms |
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31 | !! xfld : half-sat constant for Fe uptake by diatoms |
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32 | !! xfln : half-sat constant for Fe uptake by non-datoms |
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33 | !! |
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34 | !! Grazing |
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35 | !! xgmi : microzoo maximum growth rate |
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36 | !! xgme : mesozoo maximum growth rate |
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37 | !! xkmi : microzoo grazing half-sat parameter |
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38 | !! xkme : mesozoo grazing half-sat parameter |
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39 | !! xphi : micro/mesozoo grazing inefficiency |
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40 | !! xbetan : micro/mesozoo N assimilation efficiency |
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41 | !! xbetac : micro/mesozoo C assimilation efficiency |
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42 | !! xkc : micro/mesozoo net C growth efficiency |
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43 | !! xpmipn : grazing preference of microzoo for non-diatoms |
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44 | !! xpmid : grazing preference of microzoo for diatoms |
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45 | !! xpmepn : grazing preference of mesozoo for non-diatoms |
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46 | !! xpmepd : grazing preference of mesozoo for diatoms |
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47 | !! xpmezmi : grazing preference of mesozoo for microzoo |
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48 | !! xpmed : grazing preference of mesozoo for detritus |
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49 | !! |
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50 | !! Metabolic losses |
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51 | !! xmetapn : non-diatom metabolic loss rate |
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52 | !! xmetapd : diatom metabolic loss rate |
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53 | !! xmetazmi : microzoo metabolic loss rate |
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54 | !! xmetazme : mesozoo metabolic loss rate |
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55 | !! |
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56 | !! Mortality losses |
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57 | !! jmpn : non-diatom mortality functional form |
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58 | !! xmpn : non-diatom mortality rate |
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59 | !! xkphn : non-diatom mortality half-sat constant |
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60 | !! jmpd : diatom mortality functional form |
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61 | !! xmpd : diatom mortality rate |
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62 | !! xkphd : diatom mortality half-sat constant |
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63 | !! jmzmi : microzoo mortality functional form |
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64 | !! xmzmi : microzoo mortality rate |
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65 | !! xkzmi : microzoo mortality half-sat constant |
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66 | !! jmzme : mesozoo mortality functional form |
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67 | !! xmzme : mesozoo mortality rate |
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68 | !! xkzme : mesozoo mortality half-sat constant |
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69 | !! |
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70 | !! Remineralisation |
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71 | !! jmd : detritus T-dependent remineralisation switch |
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72 | !! jsfd : accelerate seafloor detritus remin. switch |
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73 | !! xmd : detrital nitrogen remineralisation rate |
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74 | !! xmdc : detrital carbon remineralisation rate |
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75 | !! |
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76 | !! Stochiometric ratios |
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77 | !! xthetapn : non-diatom C:N ratio |
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78 | !! xthetapd : diatom C:N ratio |
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79 | !! xthetazmi : microzoo C:N ratio |
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80 | !! xthetazme : mesozoo C:N ratio |
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81 | !! xthetad : detritus C:N ratio (FOR IMPLICIT DTC ONLY) |
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82 | !! xrfn : phytoplankton Fe:N ratio |
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83 | !! xrsn : phytoplankton Si:N ratio (LEGACY; NOT USED) |
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84 | !! |
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85 | !! Iron parameters |
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86 | !! jiron : iron scavenging submodel switch |
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87 | !! xfe_mass : iron atomic mass |
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88 | !! xfe_sol : aeolian iron solubility |
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89 | !! xfe_sed : sediment iron input |
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90 | !! xLgT : total ligand concentration (umol/m3) |
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91 | !! xk_FeL : dissociation constant for (Fe + L) |
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92 | !! xk_sc_Fe : scavenging rate of "free" iron |
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93 | !! |
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94 | !! Fast-sinking detritus parameters |
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95 | !! jmartin : fast detritus remineralisation switch |
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96 | !! jfdfate : fate of fast detritus at seafloor switch |
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97 | !! jrratio : rain ratio switch |
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98 | !! jocalccd : CCD switch |
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99 | !! xridg_r0 : Ridgwell rain ratio coefficient |
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100 | !! xfdfrac1 : fast-sinking fraction of diatom nat. mort. losses |
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101 | !! xfdfrac2 : fast-sinking fraction of mesozooplankton mort. losses |
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102 | !! xfdfrac3 : fast-sinking fraction of diatom silicon grazing losses |
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103 | !! xcaco3a : polar (high latitude) CaCO3 fraction |
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104 | !! xcaco3b : equatorial (low latitude) CaCO3 fraction |
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105 | !! xmassc : organic C mass:mole ratio, C106 H175 O40 N16 P1 |
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106 | !! xmassca : calcium carbonate mass:mole ratio, CaCO3 |
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107 | !! xmasssi : biogenic silicon mass:mole ratio, (H2SiO3)n |
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108 | !! xprotca : calcium carbonate protection ratio |
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109 | !! xprotsi : biogenic silicon protection ratio |
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110 | !! xfastc : organic C remineralisation length scale |
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111 | !! xfastca : calcium carbonate dissolution length scale |
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112 | !! xfastsi : biogenic silicon dissolution length scale |
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113 | !! |
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114 | !! Benthos parameters |
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115 | !! jorgben : does organic detritus go to the benthos? |
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116 | !! jinorgben : does inorganic detritus go to the benthos? |
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117 | !! xsedn : organic nitrogen sediment remineralisation rate |
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118 | !! xsedfe : organic iron sediment remineralisation rate |
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119 | !! xsedsi : inorganic silicon sediment dissolution rate |
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120 | !! xsedc : organic carbon sediment remineralisation rate |
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121 | !! xsedca : inorganic carbon sediment dissolution rate |
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122 | !! xburial : burial fraction of sediment material |
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123 | !! |
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124 | !! River parameters |
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125 | !! jriver_n : riverine N input? |
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126 | !! jriver_si : riverine Si input? |
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127 | !! jriver_c : riverine C input? |
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128 | !! jriver_alk : riverine alkalinity input? |
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129 | !! jriver_dep : depth of riverine input? |
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130 | !! |
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131 | !! Miscellaneous |
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132 | !! xsdiss : diatom frustule dissolution rate |
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133 | !! |
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134 | !! Gravitational sinking |
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135 | !! vsed : detritus gravitational sinking rate |
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136 | !! xhr : coeff for Martin's remineralisation profile |
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137 | !! |
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138 | !! Additional parameters |
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139 | !! jpkb : vertical layer for diagnostic of the vertical flux |
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140 | !! |
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141 | !! UKESM1 - new diagnostics !! Jpalm |
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142 | !! jdms : include dms diagnostics |
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143 | !! jdms_input : use instant (0) or diel-avg (1) inputs |
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144 | !! jdms_model : which DMS model is passed to atmosphere |
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145 | !! |
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146 | !! |
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147 | &natbio |
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148 | ! |
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149 | !! Primary production and chl related quantities |
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150 | xxi = 0.01257 !! |
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151 | xaln = 15.0 !! EKP (05/03/09) |
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152 | xald = 11.25 !! EKP (05/03/09) |
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153 | jphy = 1 !! 0 = T-independent; 1 = T-dependent; 2 = T-dependent-Q10 |
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154 | xvpn = 0.640 !! EKP (05/03/09) -- daily avg = 0.530; daily cycle = 1.060; Q10 = 0.64 |
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155 | xvpd = 0.600 !! EKP (05/03/09) -- daily avg = 0.500; daily cycle = 1.000; Q10 = 0.6 |
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156 | xthetam = 0.05 !! EKP (05/03/09) |
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157 | xthetamd = 0.05 !! EKP (05/03/09) |
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158 | jq10 = 1.50 !! Jpalm (17-06-2016) |
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159 | !! |
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160 | !! Diatom silicon parameters |
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161 | xsin0 = 0.2 !! Mongin et al. (2003) |
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162 | xnsi0 = 0.2 !! Mongin et al. (2003) |
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163 | xuif = 1.5 !! Mongin et al. (2003) |
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164 | !! |
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165 | !! Nutrient limitation |
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166 | jliebig = 0 !! 0 = multiplicative, 1 = Liebig |
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167 | xnln = 0.5 !! Fasham (1993) |
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168 | xnld = 0.75 !! EKP (05/03/09) |
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169 | xsld = 3.00 !! Fasham et al. (2006)-ish |
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170 | xfln = 0.00033 !! EKP (29/10/09); Parekh et al. (2005) |
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171 | xfld = 0.00067 !! EKP (29/10/09); Parekh et al. (2005); filtered through Moore et al. (2004) |
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172 | !! |
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173 | !! Grazing |
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174 | xgmi = 2.0 !! EKP (05/03/09) |
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175 | xgme = 0.5 !! AXY (21/12/09) |
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176 | xkmi = 0.8 !! EKP (26/02/09) |
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177 | xkme = 0.3 !! EKP (26/02/09) |
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178 | xphi = 0.20 !! Anderson & Pondaven (2003; 0.23); EKP (05/03/09; 0.20) |
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179 | xbetan = 0.77 !! Anderson & Pondaven (2003) |
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180 | xbetac = 0.64 !! Anderson & Pondaven (2003) |
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181 | !! xbetan = 0.69 !! compromise values inbetween those from ... |
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182 | !! xbetac = 0.69 !! Anderson & Pondaven (2003)for detrital carbon model |
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183 | xkc = 0.80 !! Anderson & Pondaven (2003) |
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184 | xpmipn = 0.75 !! |
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185 | xpmid = 0.25 !! |
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186 | xpmepn = 0.15 !! EKP (26/02/09) |
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187 | xpmepd = 0.35 !! EKP (26/02/09) |
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188 | xpmezmi = 0.35 !! EKP (26/02/09) |
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189 | xpmed = 0.15 !! EKP (26/02/09) |
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190 | !! |
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191 | !! Metabolic losses |
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192 | xmetapn = 0.02 !! |
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193 | xmetapd = 0.02 !! |
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194 | xmetazmi = 0.02 !! |
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195 | xmetazme = 0.02 !! |
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196 | !! |
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197 | !! Mortality losses |
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198 | jmpn = 3 !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid |
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199 | xmpn = 0.1 !! |
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200 | xkphn = 0.5 !! EKP (26/02/09): new parameter |
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201 | jmpd = 3 !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid |
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202 | xmpd = 0.1 !! |
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203 | xkphd = 0.5 !! EKP (26/02/09): new parameter |
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204 | jmzmi = 3 !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid |
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205 | xmzmi = 0.1 !! |
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206 | xkzmi = 0.5 !! |
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207 | jmzme = 3 !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid |
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208 | xmzme = 0.2 !! EKP (26/02/09) |
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209 | xkzme = 0.75 !! EKP (26/02/09) |
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210 | !! |
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211 | !! Remineralisation |
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212 | jmd = 2 !! 0 = T-independent; 1 = T-dependent; 2 = T-dependent-Q10 |
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213 | jsfd = 0 !! 0 = unchanged seafloor remin.; 1 = accelerated seafloor remin. |
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214 | xmd = 0.0190 !! T-dependent; 0.05 at 18C (Yool et al., 2010) - Q10 = 0.0190 |
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215 | xmdc = 0.0152 !! T-dependent; 0.04 at 18C (Yool et al., 2010) - Q10 = 0.0152 |
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216 | !! |
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217 | !! Stochiometric ratios |
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218 | xthetapn = 6.625 !! Redfield |
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219 | xthetapd = 6.625 !! Redfield |
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220 | xthetazmi = 5.625 !! Redfield |
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221 | xthetazme = 5.625 !! Redfield |
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222 | !! AXY (26/11/08): implicit detrital carbon change |
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223 | xthetad = 6.625 !! Redfield |
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224 | xrfn = 30.0e-6 !! Parekh et al. (2005) |
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225 | xrsn = 1.0 !! not used here; retained for Lobster |
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226 | !! |
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227 | !! Iron parameters |
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228 | jiron = 1 !! iron scavenging submodel switch |
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229 | xfe_mass = 55.485 !! Fe atomic mass |
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230 | xfe_sol = 0.00532 !! scaled to get same input as Parekh et al. (2005) |
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231 | xfe_sed = 0.000228 !! AXY (10/07/12): Moore-ish |
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232 | xLgT = 1.0 !! from Diat-HadOCC; from Parekh et al. (2005) |
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233 | xk_FeL = 100.0 !! from Diat-HadOCC |
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234 | xk_sc_Fe = 1.e-3 !! from Dutkiewicz et al. (2005) |
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235 | !! |
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236 | !! Fast-sinking detritus parameters |
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237 | jexport = 1 !! 1 = ballast; 2 = Martin (1987); 3 = Henson (2011) |
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238 | jfdfate = 0 !! 0 = instant remin.; 1 = transmogrify into slow detritus |
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239 | jrratio = 2 !! 0 = Dunne (2005); 1 = Ridgwell (2007) surface; 2 = Ridgwell (2007) 3D |
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240 | jocalccd = 1 !! 0 = default, fixed; 1 = calculated, dynamic |
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241 | xridg_r0 = 0.026 !! = 0.044, Ridgwell et al. (2007); scaled to 60% from preliminary sims |
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242 | xfdfrac1 = 0.333 !! control parameter; no "real" value (AXY; 12/03/09) |
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243 | xfdfrac2 = 1.00 !! control parameter; no "real" value (AXY; 12/03/09) |
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244 | xfdfrac3 = 0.80 !! control parameter; no "real" value (AXY; 12/03/09) |
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245 | xcaco3a = 0.02 !! Dunne et al. (2005); not an exact value |
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246 | xcaco3b = 0.10 !! Dunne et al. (2005); not an exact value |
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247 | !! AXY (06/01/09): after contacting Dunne, new values are used for masses ... |
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248 | !! xmassc = 22.1188 !! |
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249 | !! xmassca = 100.086 !! original values; replaced by Dunne suggestion |
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250 | !! xmasssi = 78.0988 !! |
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251 | xmassc = 12.011 !! C atomic mass |
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252 | xmassca = 100.086 !! CaCO3; based on atomic masses |
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253 | xmasssi = 60.084 !! SiO2; based on atomic masses |
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254 | xprotca = 0.070 !! Dunne et al. (2005) |
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255 | xprotsi = 0.026 !! Dunne et al. (2005) |
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256 | xfastc = 188.0 !! Dunne et al. (2005) |
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257 | xfastca = 3500.0 !! Dunne et al. (2005) |
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258 | xfastsi = 2000.0 !! Dunne et al. (2005) |
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259 | !! |
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260 | !! Benthos parameters |
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261 | jorgben = 1 !! 0 = no; 1 = yes |
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262 | jinorgben = 1 !! 0 = no; 1 = yes |
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263 | xsedn = 0.05 !! default ERSEM-ish value |
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264 | xsedfe = 0.05 !! default ERSEM-ish value |
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265 | xsedsi = 0.01 !! default ERSEM-ish value |
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266 | xsedc = 0.05 !! default ERSEM-ish value |
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267 | xsedca = 0.01 !! default ERSEM-ish value |
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268 | xburial = 0.0 !! set to zero |
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269 | !! |
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270 | !! River parameters |
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271 | jriver_n = 0 !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes |
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272 | jriver_si = 0 !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes |
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273 | jriver_c = 0 !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes |
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274 | jriver_alk= 0 !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes |
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275 | jriver_dep= 5 !! depth to which river nutrients are added |
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276 | !! |
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277 | !! Miscellaneous |
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278 | xsdiss = 0.006 !! Mongin et al. (2003); 0.006 is an alternative |
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279 | !! |
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280 | !! Gravitational sinking |
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281 | vsed = 3.472e-5 !! EKP (05/03/09) |
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282 | !! |
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283 | !! Additional parameters |
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284 | jpkb = 16 !! |
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285 | !! |
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286 | !! UKESM1 - new diagnostics !! Jpalm |
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287 | jdms = 1 !! include dms diagnostics |
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288 | jdms_input = 1 !! use instant (0) or diel-avg (1) inputs |
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289 | jdms_model = 3 !! choice of DMS model passed to atmosphere |
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290 | !! 1 = ANDR, 2 = SIMO, 3 = ARAN, 4 = HALL |
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291 | !! |
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292 | / |
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293 | !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' |
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294 | ! natroam |
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295 | !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, |
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296 | ! |
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297 | !! xthetaphy : oxygen evolution/consumption by phytoplankton |
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298 | !! = (32 / 16) + (6.625 * (119 / 106)) = (2 + 7.4375) mol O2 / mol N |
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299 | !! xthetazoo : oxygen consumption by zooplankton |
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300 | !! = (32 / 16) + (5.625 * (119 / 106)) = (2 + 6.3149) mol O2 / mol N |
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301 | !! xthetanit : oxygen consumption by nitrogen remineralisation |
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302 | !! = (32 / 16) = 2 mol O2 / mol N |
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303 | !! xthetarem : oxygen consumption by carbon remineralisation |
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304 | !! = (119 / 106) = 1.1226 mol O2 / mol C |
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305 | !! xo2min : oxygen minimum concentration |
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306 | ! |
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307 | &natroam |
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308 | xthetaphy = 9.4375 |
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309 | xthetazoo = 8.3149 |
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310 | xthetanit = 2.0 |
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311 | xthetarem = 1.1226 |
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312 | xo2min = 4.0 |
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313 | / |
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314 | !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' |
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315 | ! natopt |
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316 | !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, |
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317 | ! |
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318 | ! xkg0 : green water absorption coefficient [m-1] |
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319 | ! xkr0 : red water absorption coefficient [m-1] |
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320 | ! xkgp : pigment green absorption coefficient [m-1] |
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321 | ! xkrp : pigment red absorption coefficient [m-1] |
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322 | ! xlg : green chl exposant |
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323 | ! xlr : red chl exposant |
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324 | ! rpig : chla / (chla+phea) ratio |
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325 | ! |
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326 | &natopt |
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327 | xkg0 = 0.0232 |
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328 | xkr0 = 0.225 |
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329 | xkgp = 0.074 |
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330 | xkrp = 0.037 |
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331 | xlg = 0.629 |
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332 | xlr = 0.674 |
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333 | rpig = 0.7 |
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334 | / |
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335 | !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' |
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336 | ! natdbi used if key_trc_diabio is set |
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337 | !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, |
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338 | ! |
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339 | ! ctrbio : array of biological trend numbers |
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340 | ! ctrbil : character string describing each biological trend |
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341 | ! ctrbiu : array of unit numbers used for trend output |
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342 | ! nwritebio : frequency of biological model output [timesteps] |
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343 | ! |
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344 | &natdbi |
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345 | ctrbio = "BIO_01", "BIO_02", "BIO_03", "BIO_04", "BIO_05", "BIO_06", "BIO_07", "BIO_08", "BIO_09", "BIO_10", "BIO_11", "BIO_12", "BIO_13", "BIO_14", "BIO_15", "BIO_16", "BIO_17", "BIO_18", "BIO_19", "BIO_20", "BIO_21", "BIO_22", "BIO_23", "BIO_24", "BIO_25", "BIO_26", "BIO_27", "BIO_28", "BIO_29", "BIO_30", "BIO_31", "BIO_32", "BIO_33", "BIO_34" |
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346 | ctrbil = "BIO_01", "BIO_02", "BIO_03", "BIO_04", "BIO_05", "BIO_06", "BIO_07", "BIO_08", "BIO_09", "BIO_10", "BIO_11", "BIO_12", "BIO_13", "BIO_14", "BIO_15", "BIO_16", "BIO_17", "BIO_18", "BIO_19", "BIO_20", "BIO_21", "BIO_22", "BIO_23", "BIO_24", "BIO_25", "BIO_26", "BIO_27", "BIO_28", "BIO_29", "BIO_30", "BIO_31", "BIO_32", "BIO_33", "BIO_34" |
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347 | ctrbiu = "m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m" |
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348 | nwritebio = 10 |
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349 | !/ |
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350 | !&natopt |
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351 | / |
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352 | !================================================= |
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353 | ! nammeddia Passive tracers additional diagnostics |
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354 | !================================================= |
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355 | ! |
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356 | ! ctrc2d : 2d output field name |
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357 | ! ctrc2u : 2d output field unit |
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358 | ! ctrc2l : 2d output field long name |
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359 | ! |
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360 | ! nwriteadd: frequency of additional arrays outputs(namelist) |
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361 | &nammeddia |
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362 | / |
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363 | !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' |
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364 | &nammedsbc ! parameters for inputs deposition |
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365 | !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, |
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366 | ! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! |
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367 | ! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! |
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368 | sn_dust = 'dust.orca' , -1 , 'dust' , .true. , .true. , 'yearly' , '' , '' , '' |
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369 | ! |
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370 | cn_dir = './' ! root directory for the location of the dynamical files |
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371 | bdustfer = .true. ! boolean for dust input from the atmosphere |
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372 | / |
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