1 | MODULE p4zrem |
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2 | !!====================================================================== |
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3 | !! *** MODULE p4zrem *** |
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4 | !! TOP : PISCES Compute remineralization/dissolution of organic compounds |
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5 | !!========================================================================= |
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6 | !! History : 1.0 ! 2004 (O. Aumont) Original code |
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7 | !! 2.0 ! 2007-12 (C. Ethe, G. Madec) F90 |
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8 | !! 3.4 ! 2011-06 (O. Aumont, C. Ethe) Quota model for iron |
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9 | !!---------------------------------------------------------------------- |
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10 | #if defined key_pisces |
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11 | !!---------------------------------------------------------------------- |
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12 | !! 'key_top' and TOP models |
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13 | !! 'key_pisces' PISCES bio-model |
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14 | !!---------------------------------------------------------------------- |
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15 | !! p4z_rem : Compute remineralization/dissolution of organic compounds |
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16 | !! p4z_rem_init : Initialisation of parameters for remineralisation |
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17 | !! p4z_rem_alloc : Allocate remineralisation variables |
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18 | !!---------------------------------------------------------------------- |
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19 | USE oce_trc ! shared variables between ocean and passive tracers |
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20 | USE trc ! passive tracers common variables |
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21 | USE sms_pisces ! PISCES Source Minus Sink variables |
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22 | USE p4zopt ! optical model |
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23 | USE p4zche ! chemical model |
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24 | USE p4zprod ! Growth rate of the 2 phyto groups |
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25 | USE p4zmeso ! Sources and sinks of mesozooplankton |
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26 | USE p4zint ! interpolation and computation of various fields |
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27 | USE p4zlim |
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28 | USE prtctl_trc ! print control for debugging |
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29 | USE iom ! I/O manager |
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30 | |
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31 | |
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32 | IMPLICIT NONE |
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33 | PRIVATE |
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34 | |
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35 | PUBLIC p4z_rem ! called in p4zbio.F90 |
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36 | PUBLIC p4z_rem_init ! called in trcsms_pisces.F90 |
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37 | PUBLIC p4z_rem_alloc |
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38 | |
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39 | !! * Shared module variables |
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40 | REAL(wp), PUBLIC :: xremik !: remineralisation rate of POC |
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41 | REAL(wp), PUBLIC :: xremip !: remineralisation rate of DOC |
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42 | REAL(wp), PUBLIC :: nitrif !: NH4 nitrification rate |
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43 | REAL(wp), PUBLIC :: xsirem !: remineralisation rate of POC |
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44 | REAL(wp), PUBLIC :: xsiremlab !: fast remineralisation rate of POC |
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45 | REAL(wp), PUBLIC :: xsilab !: fraction of labile biogenic silica |
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46 | |
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47 | |
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48 | REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: denitr !: denitrification array |
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49 | REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: denitnh4 !: - - - - - |
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50 | |
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51 | !!---------------------------------------------------------------------- |
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52 | !! NEMO/TOP 3.3 , NEMO Consortium (2010) |
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53 | !! $Id: p4zrem.F90 3160 2011-11-20 14:27:18Z cetlod $ |
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54 | !! Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt) |
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55 | !!---------------------------------------------------------------------- |
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56 | CONTAINS |
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57 | |
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58 | SUBROUTINE p4z_rem( kt, knt ) |
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59 | !!--------------------------------------------------------------------- |
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60 | !! *** ROUTINE p4z_rem *** |
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61 | !! |
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62 | !! ** Purpose : Compute remineralization/scavenging of organic compounds |
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63 | !! |
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64 | !! ** Method : - ??? |
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65 | !!--------------------------------------------------------------------- |
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66 | ! |
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67 | INTEGER, INTENT(in) :: kt, knt ! ocean time step |
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68 | ! |
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69 | INTEGER :: ji, jj, jk |
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70 | REAL(wp) :: zremip, zremik, zsiremin |
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71 | REAL(wp) :: zsatur, zsatur2, znusil, znusil2, zdep, zdepmin, zfactdep |
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72 | REAL(wp) :: zbactfer, zorem, zorem2, zofer, zolimit |
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73 | REAL(wp) :: zosil, ztem |
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74 | #if ! defined key_kriest |
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75 | REAL(wp) :: zofer2 |
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76 | #endif |
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77 | REAL(wp) :: zonitr, zstep, zfact |
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78 | CHARACTER (len=25) :: charout |
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79 | REAL(wp), POINTER, DIMENSION(:,: ) :: ztempbac |
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80 | REAL(wp), POINTER, DIMENSION(:,:,:) :: zdepbac, zolimi, zdepprod, zw3d |
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81 | !!--------------------------------------------------------------------- |
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82 | ! |
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83 | IF( nn_timing == 1 ) CALL timing_start('p4z_rem') |
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84 | ! |
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85 | ! Allocate temporary workspace |
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86 | CALL wrk_alloc( jpi, jpj, ztempbac ) |
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87 | CALL wrk_alloc( jpi, jpj, jpk, zdepbac, zdepprod, zolimi ) |
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88 | |
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89 | ! Initialisation of temprary arrys |
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90 | zdepprod(:,:,:) = 1._wp |
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91 | ztempbac(:,:) = 0._wp |
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92 | |
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93 | ! Computation of the mean phytoplankton concentration as |
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94 | ! a crude estimate of the bacterial biomass |
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95 | ! this parameterization has been deduced from a model version |
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96 | ! that was modeling explicitely bacteria |
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97 | ! ------------------------------------------------------- |
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98 | DO jk = 1, jpkm1 |
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99 | DO jj = 1, jpj |
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100 | DO ji = 1, jpi |
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101 | zdep = MAX( hmld(ji,jj), heup(ji,jj) ) |
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102 | IF( gdept_n(ji,jj,jk) < zdep ) THEN |
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103 | zdepbac(ji,jj,jk) = MIN( 0.7 * ( trb(ji,jj,jk,jpzoo) + 2.* trb(ji,jj,jk,jpmes) ), 4.e-6 ) |
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104 | ztempbac(ji,jj) = zdepbac(ji,jj,jk) |
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105 | ELSE |
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106 | zdepmin = MIN( 1., zdep / gdept_n(ji,jj,jk) ) |
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107 | zdepbac (ji,jj,jk) = zdepmin**0.683 * ztempbac(ji,jj) |
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108 | zdepprod(ji,jj,jk) = zdepmin**0.273 |
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109 | ENDIF |
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110 | END DO |
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111 | END DO |
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112 | END DO |
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113 | |
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114 | DO jk = 1, jpkm1 |
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115 | DO jj = 1, jpj |
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116 | DO ji = 1, jpi |
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117 | zstep = xstep |
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118 | # if defined key_degrad |
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119 | zstep = zstep * facvol(ji,jj,jk) |
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120 | # endif |
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121 | ! DOC ammonification. Depends on depth, phytoplankton biomass |
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122 | ! and a limitation term which is supposed to be a parameterization |
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123 | ! of the bacterial activity. |
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124 | zremik = xremik * zstep / 1.e-6 * xlimbac(ji,jj,jk) * zdepbac(ji,jj,jk) |
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125 | zremik = MAX( zremik, 2.74e-4 * xstep ) |
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126 | ! Ammonification in oxic waters with oxygen consumption |
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127 | ! ----------------------------------------------------- |
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128 | zolimit = zremik * ( 1.- nitrfac(ji,jj,jk) ) * trb(ji,jj,jk,jpdoc) |
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129 | zolimi(ji,jj,jk) = MIN( ( trb(ji,jj,jk,jpoxy) - rtrn ) / o2ut, zolimit ) |
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130 | ! Ammonification in suboxic waters with denitrification |
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131 | ! ------------------------------------------------------- |
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132 | denitr(ji,jj,jk) = MIN( ( trb(ji,jj,jk,jpno3) - rtrn ) / rdenit, & |
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133 | & zremik * nitrfac(ji,jj,jk) * trb(ji,jj,jk,jpdoc) ) |
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134 | ! |
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135 | zolimi (ji,jj,jk) = MAX( 0.e0, zolimi (ji,jj,jk) ) |
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136 | denitr (ji,jj,jk) = MAX( 0.e0, denitr (ji,jj,jk) ) |
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137 | ! |
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138 | END DO |
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139 | END DO |
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140 | END DO |
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141 | |
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142 | |
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143 | DO jk = 1, jpkm1 |
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144 | DO jj = 1, jpj |
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145 | DO ji = 1, jpi |
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146 | zstep = xstep |
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147 | # if defined key_degrad |
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148 | zstep = zstep * facvol(ji,jj,jk) |
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149 | # endif |
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150 | ! NH4 nitrification to NO3. Ceased for oxygen concentrations |
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151 | ! below 2 umol/L. Inhibited at strong light |
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152 | ! ---------------------------------------------------------- |
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153 | zonitr =nitrif * zstep * trb(ji,jj,jk,jpnh4) / ( 1.+ emoy(ji,jj,jk) ) * ( 1.- nitrfac(ji,jj,jk) ) |
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154 | denitnh4(ji,jj,jk) = nitrif * zstep * trb(ji,jj,jk,jpnh4) * nitrfac(ji,jj,jk) |
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155 | ! Update of the tracers trends |
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156 | ! ---------------------------- |
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157 | tra(ji,jj,jk,jpnh4) = tra(ji,jj,jk,jpnh4) - zonitr - denitnh4(ji,jj,jk) |
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158 | tra(ji,jj,jk,jpno3) = tra(ji,jj,jk,jpno3) + zonitr - rdenita * denitnh4(ji,jj,jk) |
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159 | tra(ji,jj,jk,jpoxy) = tra(ji,jj,jk,jpoxy) - o2nit * zonitr |
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160 | tra(ji,jj,jk,jptal) = tra(ji,jj,jk,jptal) - 2 * rno3 * zonitr + rno3 * ( rdenita - 1. ) * denitnh4(ji,jj,jk) |
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161 | END DO |
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162 | END DO |
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163 | END DO |
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164 | |
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165 | IF(ln_ctl) THEN ! print mean trends (used for debugging) |
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166 | WRITE(charout, FMT="('rem1')") |
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167 | CALL prt_ctl_trc_info(charout) |
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168 | CALL prt_ctl_trc(tab4d=tra, mask=tmask, clinfo=ctrcnm) |
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169 | ENDIF |
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170 | |
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171 | DO jk = 1, jpkm1 |
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172 | DO jj = 1, jpj |
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173 | DO ji = 1, jpi |
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174 | |
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175 | ! Bacterial uptake of iron. No iron is available in DOC. So |
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176 | ! Bacteries are obliged to take up iron from the water. Some |
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177 | ! studies (especially at Papa) have shown this uptake to be significant |
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178 | ! ---------------------------------------------------------- |
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179 | zbactfer = 10.e-6 * rfact2 * prmax(ji,jj,jk) * xlimbacl(ji,jj,jk) & |
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180 | & * trb(ji,jj,jk,jpfer) / ( 2.5E-10 + trb(ji,jj,jk,jpfer) ) & |
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181 | & * zdepprod(ji,jj,jk) * zdepbac(ji,jj,jk) |
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182 | #if defined key_kriest |
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183 | tra(ji,jj,jk,jpfer) = tra(ji,jj,jk,jpfer) - zbactfer*0.05 |
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184 | tra(ji,jj,jk,jpsfe) = tra(ji,jj,jk,jpsfe) + zbactfer*0.05 |
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185 | #else |
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186 | tra(ji,jj,jk,jpfer) = tra(ji,jj,jk,jpfer) - zbactfer*0.16 |
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187 | tra(ji,jj,jk,jpsfe) = tra(ji,jj,jk,jpsfe) + zbactfer*0.12 |
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188 | tra(ji,jj,jk,jpbfe) = tra(ji,jj,jk,jpbfe) + zbactfer*0.04 |
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189 | #endif |
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190 | END DO |
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191 | END DO |
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192 | END DO |
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193 | |
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194 | IF(ln_ctl) THEN ! print mean trends (used for debugging) |
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195 | WRITE(charout, FMT="('rem2')") |
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196 | CALL prt_ctl_trc_info(charout) |
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197 | CALL prt_ctl_trc(tab4d=tra, mask=tmask, clinfo=ctrcnm) |
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198 | ENDIF |
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199 | |
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200 | DO jk = 1, jpkm1 |
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201 | DO jj = 1, jpj |
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202 | DO ji = 1, jpi |
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203 | zstep = xstep |
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204 | # if defined key_degrad |
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205 | zstep = zstep * facvol(ji,jj,jk) |
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206 | # endif |
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207 | ! POC disaggregation by turbulence and bacterial activity. |
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208 | ! -------------------------------------------------------- |
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209 | zremip = xremip * zstep * tgfunc(ji,jj,jk) * ( 1.- 0.55 * nitrfac(ji,jj,jk) ) |
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210 | |
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211 | ! POC disaggregation rate is reduced in anoxic zone as shown by |
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212 | ! sediment traps data. In oxic area, the exponent of the martin s |
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213 | ! law is around -0.87. In anoxic zone, it is around -0.35. This |
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214 | ! means a disaggregation constant about 0.5 the value in oxic zones |
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215 | ! ----------------------------------------------------------------- |
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216 | zorem = zremip * trb(ji,jj,jk,jppoc) |
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217 | zofer = zremip * trb(ji,jj,jk,jpsfe) |
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218 | #if ! defined key_kriest |
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219 | zorem2 = zremip * trb(ji,jj,jk,jpgoc) |
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220 | zofer2 = zremip * trb(ji,jj,jk,jpbfe) |
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221 | #else |
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222 | zorem2 = zremip * trb(ji,jj,jk,jpnum) |
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223 | #endif |
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224 | |
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225 | ! Update the appropriate tracers trends |
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226 | ! ------------------------------------- |
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227 | |
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228 | tra(ji,jj,jk,jpdoc) = tra(ji,jj,jk,jpdoc) + zorem |
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229 | tra(ji,jj,jk,jpfer) = tra(ji,jj,jk,jpfer) + zofer |
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230 | #if defined key_kriest |
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231 | tra(ji,jj,jk,jppoc) = tra(ji,jj,jk,jppoc) - zorem |
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232 | tra(ji,jj,jk,jpnum) = tra(ji,jj,jk,jpnum) - zorem2 |
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233 | tra(ji,jj,jk,jpsfe) = tra(ji,jj,jk,jpsfe) - zofer |
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234 | #else |
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235 | tra(ji,jj,jk,jppoc) = tra(ji,jj,jk,jppoc) + zorem2 - zorem |
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236 | tra(ji,jj,jk,jpgoc) = tra(ji,jj,jk,jpgoc) - zorem2 |
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237 | tra(ji,jj,jk,jpsfe) = tra(ji,jj,jk,jpsfe) + zofer2 - zofer |
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238 | tra(ji,jj,jk,jpbfe) = tra(ji,jj,jk,jpbfe) - zofer2 |
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239 | #endif |
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240 | |
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241 | END DO |
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242 | END DO |
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243 | END DO |
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244 | |
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245 | IF(ln_ctl) THEN ! print mean trends (used for debugging) |
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246 | WRITE(charout, FMT="('rem3')") |
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247 | CALL prt_ctl_trc_info(charout) |
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248 | CALL prt_ctl_trc(tab4d=tra, mask=tmask, clinfo=ctrcnm) |
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249 | ENDIF |
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250 | |
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251 | DO jk = 1, jpkm1 |
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252 | DO jj = 1, jpj |
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253 | DO ji = 1, jpi |
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254 | zstep = xstep |
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255 | # if defined key_degrad |
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256 | zstep = zstep * facvol(ji,jj,jk) |
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257 | # endif |
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258 | ! Remineralization rate of BSi depedant on T and saturation |
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259 | ! --------------------------------------------------------- |
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260 | zsatur = ( sio3eq(ji,jj,jk) - trb(ji,jj,jk,jpsil) ) / ( sio3eq(ji,jj,jk) + rtrn ) |
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261 | zsatur = MAX( rtrn, zsatur ) |
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262 | zsatur2 = ( 1. + tsn(ji,jj,jk,jp_tem) / 400.)**37 |
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263 | znusil = 0.225 * ( 1. + tsn(ji,jj,jk,jp_tem) / 15.) * zsatur + 0.775 * zsatur2 * zsatur**9.25 |
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264 | znusil2 = 0.225 * ( 1. + tsn(ji,jj,1,jp_tem) / 15.) + 0.775 * zsatur2 |
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265 | |
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266 | ! Two classes of BSi are considered : a labile fraction and |
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267 | ! a more refractory one. The ratio between both fractions is |
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268 | ! constant and specified in the namelist. |
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269 | ! ---------------------------------------------------------- |
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270 | zdep = MAX( hmld(ji,jj), heup(ji,jj) ) |
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271 | zdep = MAX( 0., gdept_n(ji,jj,jk) - zdep ) |
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272 | ztem = MAX( tsn(ji,jj,1,jp_tem), 0. ) |
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273 | zfactdep = xsilab * EXP(-( xsiremlab - xsirem ) * znusil2 * zdep / wsbio2 ) * ztem / ( ztem + 10. ) |
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274 | zsiremin = ( xsiremlab * zfactdep + xsirem * ( 1. - zfactdep ) ) * zstep * znusil |
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275 | zosil = zsiremin * trb(ji,jj,jk,jpgsi) |
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276 | ! |
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277 | tra(ji,jj,jk,jpgsi) = tra(ji,jj,jk,jpgsi) - zosil |
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278 | tra(ji,jj,jk,jpsil) = tra(ji,jj,jk,jpsil) + zosil |
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279 | ! |
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280 | END DO |
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281 | END DO |
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282 | END DO |
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283 | |
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284 | IF(ln_ctl) THEN ! print mean trends (used for debugging) |
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285 | WRITE(charout, FMT="('rem4')") |
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286 | CALL prt_ctl_trc_info(charout) |
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287 | CALL prt_ctl_trc(tab4d=tra, mask=tmask, clinfo=ctrcnm) |
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288 | ENDIF |
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289 | |
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290 | ! Update the arrays TRA which contain the biological sources and sinks |
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291 | ! -------------------------------------------------------------------- |
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292 | |
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293 | DO jk = 1, jpkm1 |
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294 | tra(:,:,jk,jppo4) = tra(:,:,jk,jppo4) + zolimi (:,:,jk) + denitr(:,:,jk) |
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295 | tra(:,:,jk,jpnh4) = tra(:,:,jk,jpnh4) + zolimi (:,:,jk) + denitr(:,:,jk) |
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296 | tra(:,:,jk,jpno3) = tra(:,:,jk,jpno3) - denitr (:,:,jk) * rdenit |
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297 | tra(:,:,jk,jpdoc) = tra(:,:,jk,jpdoc) - zolimi (:,:,jk) - denitr(:,:,jk) |
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298 | tra(:,:,jk,jpoxy) = tra(:,:,jk,jpoxy) - zolimi (:,:,jk) * o2ut |
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299 | tra(:,:,jk,jpdic) = tra(:,:,jk,jpdic) + zolimi (:,:,jk) + denitr(:,:,jk) |
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300 | tra(:,:,jk,jptal) = tra(:,:,jk,jptal) + rno3 * ( zolimi(:,:,jk) + ( rdenit + 1.) * denitr(:,:,jk) ) |
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301 | END DO |
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302 | |
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303 | IF( knt == nrdttrc ) THEN |
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304 | CALL wrk_alloc( jpi, jpj, jpk, zw3d ) |
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305 | zfact = 1.e+3 * rfact2r ! conversion from mol/l/kt to mol/m3/s |
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306 | ! |
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307 | IF( iom_use( "REMIN" ) ) THEN |
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308 | zw3d(:,:,:) = zolimi(:,:,:) * tmask(:,:,:) * zfact ! Remineralisation rate |
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309 | CALL iom_put( "REMIN" , zw3d ) |
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310 | ENDIF |
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311 | IF( iom_use( "DENIT" ) ) THEN |
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312 | zw3d(:,:,:) = denitr(:,:,:) * rdenit * rno3 * tmask(:,:,:) * zfact ! Denitrification |
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313 | CALL iom_put( "DENIT" , zw3d ) |
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314 | ENDIF |
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315 | ! |
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316 | CALL wrk_dealloc( jpi, jpj, jpk, zw3d ) |
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317 | ENDIF |
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318 | |
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319 | IF(ln_ctl) THEN ! print mean trends (used for debugging) |
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320 | WRITE(charout, FMT="('rem6')") |
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321 | CALL prt_ctl_trc_info(charout) |
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322 | CALL prt_ctl_trc(tab4d=tra, mask=tmask, clinfo=ctrcnm) |
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323 | ENDIF |
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324 | ! |
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325 | CALL wrk_dealloc( jpi, jpj, ztempbac ) |
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326 | CALL wrk_dealloc( jpi, jpj, jpk, zdepbac, zdepprod, zolimi ) |
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327 | ! |
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328 | IF( nn_timing == 1 ) CALL timing_stop('p4z_rem') |
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329 | ! |
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330 | END SUBROUTINE p4z_rem |
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331 | |
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332 | |
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333 | SUBROUTINE p4z_rem_init |
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334 | !!---------------------------------------------------------------------- |
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335 | !! *** ROUTINE p4z_rem_init *** |
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336 | !! |
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337 | !! ** Purpose : Initialization of remineralization parameters |
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338 | !! |
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339 | !! ** Method : Read the nampisrem namelist and check the parameters |
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340 | !! called at the first timestep |
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341 | !! |
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342 | !! ** input : Namelist nampisrem |
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343 | !! |
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344 | !!---------------------------------------------------------------------- |
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345 | NAMELIST/nampisrem/ xremik, xremip, nitrif, xsirem, xsiremlab, xsilab |
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346 | INTEGER :: ios ! Local integer output status for namelist read |
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347 | |
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348 | REWIND( numnatp_ref ) ! Namelist nampisrem in reference namelist : Pisces remineralization |
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349 | READ ( numnatp_ref, nampisrem, IOSTAT = ios, ERR = 901) |
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350 | 901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'nampisrem in reference namelist', lwp ) |
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351 | |
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352 | REWIND( numnatp_cfg ) ! Namelist nampisrem in configuration namelist : Pisces remineralization |
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353 | READ ( numnatp_cfg, nampisrem, IOSTAT = ios, ERR = 902 ) |
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354 | 902 IF( ios /= 0 ) CALL ctl_nam ( ios , 'nampisrem in configuration namelist', lwp ) |
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355 | IF(lwm) WRITE ( numonp, nampisrem ) |
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356 | |
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357 | IF(lwp) THEN ! control print |
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358 | WRITE(numout,*) ' ' |
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359 | WRITE(numout,*) ' Namelist parameters for remineralization, nampisrem' |
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360 | WRITE(numout,*) ' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~' |
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361 | WRITE(numout,*) ' remineralisation rate of POC xremip =', xremip |
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362 | WRITE(numout,*) ' remineralization rate of DOC xremik =', xremik |
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363 | WRITE(numout,*) ' remineralization rate of Si xsirem =', xsirem |
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364 | WRITE(numout,*) ' fast remineralization rate of Si xsiremlab =', xsiremlab |
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365 | WRITE(numout,*) ' fraction of labile biogenic silica xsilab =', xsilab |
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366 | WRITE(numout,*) ' NH4 nitrification rate nitrif =', nitrif |
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367 | ENDIF |
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368 | ! |
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369 | denitr (:,:,:) = 0._wp |
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370 | denitnh4(:,:,:) = 0._wp |
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371 | ! |
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372 | END SUBROUTINE p4z_rem_init |
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373 | |
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374 | |
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375 | INTEGER FUNCTION p4z_rem_alloc() |
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376 | !!---------------------------------------------------------------------- |
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377 | !! *** ROUTINE p4z_rem_alloc *** |
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378 | !!---------------------------------------------------------------------- |
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379 | ALLOCATE( denitr(jpi,jpj,jpk), denitnh4(jpi,jpj,jpk), STAT=p4z_rem_alloc ) |
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380 | ! |
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381 | IF( p4z_rem_alloc /= 0 ) CALL ctl_warn('p4z_rem_alloc: failed to allocate arrays') |
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382 | ! |
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383 | END FUNCTION p4z_rem_alloc |
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384 | |
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385 | #else |
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386 | !!====================================================================== |
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387 | !! Dummy module : No PISCES bio-model |
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388 | !!====================================================================== |
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389 | CONTAINS |
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390 | SUBROUTINE p4z_rem ! Empty routine |
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391 | END SUBROUTINE p4z_rem |
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392 | #endif |
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393 | |
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394 | !!====================================================================== |
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395 | END MODULE p4zrem |
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