| 1 | MODULE trcbio_medusa |
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| 2 | !!====================================================================== |
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| 3 | !! *** MODULE trcbio *** |
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| 4 | !! TOP : MEDUSA |
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| 5 | !!====================================================================== |
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| 6 | !! History : |
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| 7 | !! - ! 1999-07 (M. Levy) original code |
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| 8 | !! - ! 2000-12 (E. Kestenare) assign parameters to name |
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| 9 | !! individual tracers |
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| 10 | !! - ! 2001-03 (M. Levy) LNO3 + dia2d |
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| 11 | !! 2.0 ! 2007-12 (C. Deltel, G. Madec) F90 |
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| 12 | !! - ! 2008-08 (K. Popova) adaptation for MEDUSA |
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| 13 | !! - ! 2008-11 (A. Yool) continuing adaptation for MEDUSA |
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| 14 | !! - ! 2010-03 (A. Yool) updated for branch inclusion |
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| 15 | !! - ! 2011-08 (A. Yool) updated for ROAM (see below) |
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| 16 | !! - ! 2013-03 (A. Yool) updated for iMARNET |
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| 17 | !! - ! 2013-05 (A. Yool) updated for v3.5 |
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| 18 | !! - ! 2014-08 (A. Yool, J. Palm) Add DMS module for UKESM1 model |
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| 19 | !! - ! 2015-06 (A. Yool) Update to include MOCSY |
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| 20 | !! - ! 2015-07 (A. Yool) Update for rolling averages |
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| 21 | !! - ! 2015-10 (J. Palm) Update for diag outputs through |
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| 22 | !! iom_use |
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| 23 | !! - ! 2016-11 (A. Yool) Updated diags for CMIP6 |
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| 24 | !! - ! 2017-05 (A. Yool) Added extra DMS calculation |
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| 25 | !!---------------------------------------------------------------------- |
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| 26 | !! |
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| 27 | #if defined key_roam |
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| 28 | !!---------------------------------------------------------------------- |
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| 29 | !! Updates for the ROAM project include: |
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| 30 | !! - addition of DIC, alkalinity, detrital carbon and oxygen tracers |
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| 31 | !! - addition of air-sea fluxes of CO2 and oxygen |
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| 32 | !! - periodic (monthly) calculation of full 3D carbonate chemistry |
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| 33 | !! - detrital C:N ratio now free to evolve dynamically |
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| 34 | !! - benthic storage pools |
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| 35 | !! |
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| 36 | !! Opportunity also taken to add functionality: |
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| 37 | !! - switch for Liebig Law (= most-limiting) nutrient uptake |
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| 38 | !! - switch for accelerated seafloor detritus remineralisation |
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| 39 | !! - switch for fast -> slow detritus transfer at seafloor |
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| 40 | !! - switch for ballast vs. Martin vs. Henson fast detritus remin. |
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| 41 | !! - per GMD referee remarks, xfdfrac3 introduced for grazed PDS |
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| 42 | !!---------------------------------------------------------------------- |
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| 43 | #endif |
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| 44 | !! |
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| 45 | #if defined key_mocsy |
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| 46 | !!---------------------------------------------------------------------- |
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| 47 | !! Updates with the addition of MOCSY include: |
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| 48 | !! - option to use PML or MOCSY carbonate chemistry (the latter is |
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| 49 | !! preferred) |
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| 50 | !! - central calculation of gas transfer velocity, f_kw660; previously |
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| 51 | !! this was done separately for CO2 and O2 with predictable results |
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| 52 | !! - distribution of f_kw660 to both PML and MOCSY CO2 air-sea flux |
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| 53 | !! calculations and to those for O2 air-sea flux |
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| 54 | !! - extra diagnostics included for MOCSY |
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| 55 | !!---------------------------------------------------------------------- |
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| 56 | #endif |
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| 57 | !! |
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| 58 | #if defined key_medusa |
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| 59 | !!---------------------------------------------------------------------- |
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| 60 | !! MEDUSA bio-model |
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| 61 | !!---------------------------------------------------------------------- |
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| 62 | !! trc_bio_medusa : |
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| 63 | !!---------------------------------------------------------------------- |
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| 64 | !! AXY (30/01/14): necessary to find NaNs on HECTOR |
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| 65 | USE, INTRINSIC :: ieee_arithmetic |
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| 66 | |
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| 67 | USE bio_medusa_mod, ONLY: b0, fdep1, & |
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| 68 | ibenthic, idf, idfval, & |
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| 69 | # if defined key_roam |
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| 70 | f_xco2a, & |
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| 71 | zalk, zdic, zoxy, zsal, ztmp, & |
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| 72 | # endif |
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| 73 | # if defined key_mocsy |
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| 74 | zpho, & |
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| 75 | # endif |
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| 76 | zchd, zchn, zdet, zdin, zdtc, & |
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| 77 | zfer, zpds, zphd, zphn, zsil, & |
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| 78 | zzme, zzmi |
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| 79 | USE dom_oce, ONLY: e3t_0, e3t_n, & |
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| 80 | gdept_0, gdept_n, & |
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| 81 | gdepw_0, gdepw_n, & |
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| 82 | nday_year, nsec_day, nyear, & |
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| 83 | rdt, tmask |
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| 84 | USE in_out_manager, ONLY: lwp, numout, nn_date0 |
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| 85 | # if defined key_iomput |
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| 86 | USE iom, ONLY: lk_iomput |
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| 87 | # endif |
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| 88 | USE lbclnk, ONLY: lbc_lnk |
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| 89 | USE lib_mpp, ONLY: ctl_stop |
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| 90 | USE oce, ONLY: tsb, tsn |
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| 91 | USE par_kind, ONLY: wp |
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| 92 | USE par_medusa, ONLY: jpalk, jpchd, jpchn, jpdet, & |
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| 93 | jpdic, jpdin, jpdtc, jpfer, & |
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| 94 | jpoxy, jppds, jpphd, jpphn, & |
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| 95 | jpsil, jpzme, jpzmi |
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| 96 | USE par_oce, ONLY: jp_sal, jp_tem, jpi, jpim1, & |
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| 97 | jpj, jpjm1, jpk |
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| 98 | !! JPALM (27-06-2016): add lk_oasis for CO2 and DMS coupling with atm |
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| 99 | USE sbc_oce, ONLY: lk_oasis |
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| 100 | USE sms_medusa, ONLY: hist_pco2 |
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| 101 | USE trc, ONLY: ln_rsttr, nittrc000, trn |
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| 102 | USE bio_medusa_init_mod, ONLY: bio_medusa_init |
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| 103 | USE carb_chem_mod, ONLY: carb_chem |
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| 104 | USE air_sea_mod, ONLY: air_sea |
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| 105 | USE plankton_mod, ONLY: plankton |
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| 106 | USE iron_chem_scav_mod, ONLY: iron_chem_scav |
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| 107 | USE detritus_mod, ONLY: detritus |
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| 108 | USE bio_medusa_update_mod, ONLY: bio_medusa_update |
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| 109 | USE bio_medusa_diag_mod, ONLY: bio_medusa_diag |
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| 110 | USE bio_medusa_diag_slice_mod, ONLY: bio_medusa_diag_slice |
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| 111 | USE bio_medusa_fin_mod, ONLY: bio_medusa_fin |
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| 112 | |
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| 113 | IMPLICIT NONE |
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| 114 | PRIVATE |
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| 115 | |
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| 116 | PUBLIC trc_bio_medusa ! called in trcsms_medusa.F90 |
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| 117 | |
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| 118 | !!* Substitution |
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| 119 | # include "domzgr_substitute.h90" |
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| 120 | !!---------------------------------------------------------------------- |
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| 121 | !! NEMO/TOP 2.0 , LOCEAN-IPSL (2007) |
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| 122 | !! $Id$ |
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| 123 | !! Software governed by the CeCILL licence (modipsl/doc/NEMO_CeCILL.txt) |
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| 124 | !!---------------------------------------------------------------------- |
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| 125 | |
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| 126 | CONTAINS |
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| 127 | |
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| 128 | SUBROUTINE trc_bio_medusa( kt ) |
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| 129 | !!------------------------------------------------------------------ |
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| 130 | !! *** ROUTINE trc_bio *** |
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| 131 | !! |
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| 132 | !! ** Purpose : compute the now trend due to biogeochemical processes |
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| 133 | !! and add it to the general trend of passive tracers |
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| 134 | !! equations |
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| 135 | !! |
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| 136 | !! ** Method : each now biological flux is calculated in function of |
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| 137 | !! now concentrations of tracers. |
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| 138 | !! depending on the tracer, these fluxes are sources or |
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| 139 | !! sinks. |
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| 140 | !! The total of the sources and sinks for each tracer |
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| 141 | !! is added to the general trend. |
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| 142 | !! |
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| 143 | !! tra = tra + zf...tra - zftra... |
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| 144 | !! | | |
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| 145 | !! | | |
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| 146 | !! source sink |
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| 147 | !! |
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| 148 | !! IF 'key_trc_diabio' defined , the biogeochemical trends |
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| 149 | !! for passive tracers are saved for futher diagnostics. |
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| 150 | !!------------------------------------------------------------------ |
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| 151 | !! |
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| 152 | !! |
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| 153 | !!------------------------------------------------------------------ |
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| 154 | !! Variable conventions |
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| 155 | !!------------------------------------------------------------------ |
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| 156 | !! |
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| 157 | !! names: z*** - state variable |
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| 158 | !! f*** - function (or temporary variable used in part of |
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| 159 | !! a function) |
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| 160 | !! x*** - parameter |
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| 161 | !! b*** - right-hand part (sources and sinks) |
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| 162 | !! i*** - integer variable (usually used in yes/no flags) |
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| 163 | !! |
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| 164 | !! time (integer timestep) |
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| 165 | INTEGER, INTENT( in ) :: kt |
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| 166 | !! |
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| 167 | !! spatial array indices |
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| 168 | INTEGER :: ji,jj,jk,jn |
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| 169 | !! |
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| 170 | INTEGER :: iball |
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| 171 | # if defined key_roam |
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| 172 | !! |
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| 173 | INTEGER :: iyr1, iyr2 |
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| 174 | !! |
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| 175 | # endif |
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| 176 | !! |
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| 177 | !! temporary variables |
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| 178 | REAL(wp) :: fq0,fq1,fq2,fq3,fq4 |
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| 179 | !! |
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| 180 | !! T and S check temporary variable |
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| 181 | REAL(wp) :: sumtsn, tsnavg |
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| 182 | INTEGER :: summask |
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| 183 | !! |
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| 184 | !!------------------------------------------------------------------ |
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| 185 | |
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| 186 | # if defined key_debug_medusa |
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| 187 | IF (lwp) write (numout,*) 'trc_bio_medusa: variables defined' |
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| 188 | CALL flush(numout) |
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| 189 | # endif |
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| 190 | |
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| 191 | !! AXY (20/11/14): alter this to report on first MEDUSA call |
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| 192 | !! IF( kt == nit000 ) THEN |
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| 193 | IF( kt == nittrc000 ) THEN |
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| 194 | IF(lwp) WRITE(numout,*) |
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| 195 | IF(lwp) WRITE(numout,*) ' trc_bio: MEDUSA bio-model' |
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| 196 | IF(lwp) WRITE(numout,*) ' ~~~~~~~' |
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| 197 | IF(lwp) WRITE(numout,*) ' kt =',kt |
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| 198 | ENDIF |
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| 199 | |
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| 200 | !! AXY (13/01/12): is benthic model properly interactive? 0 = no, 1 = yes |
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| 201 | ibenthic = 1 |
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| 202 | |
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| 203 | !!------------------------------------------------------------------ |
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| 204 | !! b0 is present for debugging purposes; using b0 = 0 sets the tendency |
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| 205 | !! terms of all biological equations to 0. |
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| 206 | !!------------------------------------------------------------------ |
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| 207 | !! |
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| 208 | !! AXY (03/09/14): probably not the smartest move ever, but it'll fit |
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| 209 | !! the bill for now; another item on the things-to-sort- |
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| 210 | !! out-in-the-future list ... |
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| 211 | # if defined key_kill_medusa |
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| 212 | b0 = 0. |
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| 213 | # else |
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| 214 | b0 = 1. |
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| 215 | # endif |
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| 216 | !!------------------------------------------------------------------ |
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| 217 | !! fast detritus ballast scheme (0 = no; 1 = yes) |
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| 218 | !! alternative to ballast scheme is same scheme but with no ballast |
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| 219 | !! protection (not dissimilar to Martin et al., 1987) |
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| 220 | !!------------------------------------------------------------------ |
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| 221 | !! |
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| 222 | iball = 1 |
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| 223 | |
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| 224 | !!------------------------------------------------------------------ |
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| 225 | !! full flux diagnostics (0 = no; 1 = yes); appear in ocean.output |
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| 226 | !! these should *only* be used in 1D since they give comprehensive |
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| 227 | !! output for ecological functions in the model; primarily used in |
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| 228 | !! debugging |
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| 229 | !!------------------------------------------------------------------ |
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| 230 | !! |
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| 231 | idf = 0 |
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| 232 | !! |
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| 233 | !! timer mechanism |
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| 234 | if (kt/120*120.eq.kt) then |
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| 235 | idfval = 1 |
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| 236 | else |
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| 237 | idfval = 0 |
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| 238 | endif |
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| 239 | |
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| 240 | !!------------------------------------------------------------------ |
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| 241 | !! Initialise arrays to zero and set up arrays for diagnostics |
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| 242 | !!------------------------------------------------------------------ |
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| 243 | CALL bio_medusa_init( kt ) |
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| 244 | |
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| 245 | # if defined key_axy_nancheck |
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| 246 | DO jn = jp_msa0,jp_msa1 |
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| 247 | !! fq0 = MINVAL(trn(:,:,:,jn)) |
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| 248 | !! fq1 = MAXVAL(trn(:,:,:,jn)) |
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| 249 | fq2 = SUM(trn(:,:,:,jn)) |
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| 250 | !! if (lwp) write (numout,'(a,2i6,3(1x,1pe15.5))') 'NAN-CHECK', & |
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| 251 | !! kt, jn, fq0, fq1, fq2 |
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| 252 | !! AXY (30/01/14): much to our surprise, the next line doesn't |
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| 253 | !! work on HECTOR and has been replaced here with |
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| 254 | !! a specialist routine |
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| 255 | !! if (fq2 /= fq2 ) then |
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| 256 | if ( ieee_is_nan( fq2 ) ) then |
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| 257 | !! there's a NaN here |
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| 258 | if (lwp) write(numout,*) 'NAN detected in field', jn, & |
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| 259 | 'at time', kt, 'at position:' |
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| 260 | DO jk = 1,jpk |
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| 261 | DO jj = 1,jpj |
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| 262 | DO ji = 1,jpi |
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| 263 | !! AXY (30/01/14): "isnan" problem on HECTOR |
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| 264 | !! if (trn(ji,jj,jk,jn) /= trn(ji,jj,jk,jn)) then |
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| 265 | if ( ieee_is_nan( trn(ji,jj,jk,jn) ) ) then |
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| 266 | if (lwp) write (numout,'(a,1pe12.2,4i6)') & |
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| 267 | 'NAN-CHECK', tmask(ji,jj,jk), ji, jj, jk, jn |
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| 268 | endif |
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| 269 | enddo |
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| 270 | enddo |
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| 271 | enddo |
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| 272 | CALL ctl_stop( 'trcbio_medusa, NAN in incoming tracer field' ) |
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| 273 | endif |
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| 274 | ENDDO |
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| 275 | CALL flush(numout) |
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| 276 | # endif |
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| 277 | |
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| 278 | # if defined key_debug_medusa |
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| 279 | IF (lwp) write (numout,*) & |
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| 280 | 'trc_bio_medusa: variables initialised and checked' |
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| 281 | CALL flush(numout) |
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| 282 | # endif |
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| 283 | |
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| 284 | # if defined key_roam |
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| 285 | !!------------------------------------------------------------------ |
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| 286 | !! calculate atmospheric pCO2 |
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| 287 | !!------------------------------------------------------------------ |
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| 288 | !! |
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| 289 | !! what's atmospheric pCO2 doing? (data start in 1859) |
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| 290 | iyr1 = nyear - 1859 + 1 |
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| 291 | iyr2 = iyr1 + 1 |
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| 292 | if (iyr1 .le. 1) then |
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| 293 | !! before 1860 |
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| 294 | f_xco2a(:,:) = hist_pco2(1) |
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| 295 | elseif (iyr2 .ge. 242) then |
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| 296 | !! after 2099 |
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| 297 | f_xco2a(:,:) = hist_pco2(242) |
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| 298 | else |
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| 299 | !! just right |
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| 300 | fq0 = hist_pco2(iyr1) |
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| 301 | fq1 = hist_pco2(iyr2) |
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| 302 | fq2 = real(nsec_day) / (60.0 * 60.0 * 24.0) |
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| 303 | !! AXY (14/06/12): tweaked to make more sense (and be correct) |
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| 304 | # if defined key_bs_axy_yrlen |
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| 305 | !! bugfix: for 360d year with HadGEM2-ES forcing |
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| 306 | fq3 = (real(nday_year) - 1.0 + fq2) / 360.0 |
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| 307 | # else |
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| 308 | !! original use of 365 days (not accounting for leap year or |
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| 309 | !! 360d year) |
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| 310 | fq3 = (real(nday_year) - 1.0 + fq2) / 365.0 |
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| 311 | # endif |
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| 312 | fq4 = (fq0 * (1.0 - fq3)) + (fq1 * fq3) |
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| 313 | f_xco2a(:,:) = fq4 |
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| 314 | endif |
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| 315 | # if defined key_axy_pi_co2 |
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| 316 | !! OCMIP pre-industrial pCO2 |
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| 317 | !! f_xco2a(:,:) = 284.725 !! CMIP5 pre-industrial pCO2 |
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| 318 | f_xco2a = 284.317 !! CMIP6 pre-industrial pCO2 |
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| 319 | # endif |
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| 320 | !! IF(lwp) WRITE(numout,*) ' MEDUSA nyear =', nyear |
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| 321 | !! IF(lwp) WRITE(numout,*) ' MEDUSA nsec_day =', real(nsec_day) |
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| 322 | !! IF(lwp) WRITE(numout,*) ' MEDUSA nday_year =', real(nday_year) |
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| 323 | !! AXY (29/01/14): remove surplus diagnostics |
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| 324 | !! IF(lwp) WRITE(numout,*) ' MEDUSA fq0 =', fq0 |
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| 325 | !! IF(lwp) WRITE(numout,*) ' MEDUSA fq1 =', fq1 |
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| 326 | !! IF(lwp) WRITE(numout,*) ' MEDUSA fq2 =', fq2 |
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| 327 | !! IF(lwp) WRITE(numout,*) ' MEDUSA fq3 =', fq3 |
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| 328 | IF(lwp) WRITE(numout,*) ' MEDUSA atm pCO2 =', f_xco2a(1,1) |
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| 329 | # endif |
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| 330 | |
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| 331 | # if defined key_debug_medusa |
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| 332 | IF (lwp) write (numout,*) 'trc_bio_medusa: ready for carbonate chemistry' |
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| 333 | IF (lwp) write (numout,*) 'trc_bio_medusa: kt = ', kt |
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| 334 | IF (lwp) write (numout,*) 'trc_bio_medusa: nittrc000 = ', nittrc000 |
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| 335 | CALL flush(numout) |
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| 336 | # endif |
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| 337 | |
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| 338 | # if defined key_roam |
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| 339 | !! AXY (20/11/14): alter to call on first MEDUSA timestep and then every |
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| 340 | !! month (this is hardwired as 960 timesteps but should |
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| 341 | !! be calculated and done properly |
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| 342 | !! IF( kt == nit000 .or. mod(kt,1920) == 0 ) THEN |
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| 343 | !! IF( kt == nittrc000 .or. mod(kt,960) == 0 ) THEN |
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| 344 | !!============================= |
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| 345 | !! Jpalm -- 07-10-2016 -- need to change carb-chem frequency call : |
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| 346 | !! we don't want to call on the first time-step of all run |
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| 347 | !! submission, but only on the very first time-step, and |
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| 348 | !! then every month. So we call on nittrc000 if not |
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| 349 | !! restarted run, else if one month after last call. |
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| 350 | !! Assume one month is 30d --> 3600*24*30 : 2592000s |
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| 351 | !! try to call carb-chem at 1st month's tm-stp : |
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| 352 | !! x * 30d + 1*rdt(i.e: mod = rdt) |
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| 353 | !! ++ need to pass carb-chem output var through restarts |
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| 354 | If ( (kt == nittrc000 .AND. .NOT.ln_rsttr) .OR. & |
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| 355 | ((86400*mod(nn_date0,100) + mod(kt*rdt,2592000.)) == rdt) ) THEN |
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| 356 | !!--------------------------------------------------------------- |
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| 357 | !! Calculate the carbonate chemistry for the whole ocean on the first |
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| 358 | !! simulation timestep and every month subsequently; the resulting 3D |
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| 359 | !! field of omega calcite is used to determine the depth of the CCD |
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| 360 | !!--------------------------------------------------------------- |
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| 361 | CALL carb_chem( kt ) |
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| 362 | |
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| 363 | ENDIF |
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| 364 | # endif |
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| 365 | |
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| 366 | # if defined key_debug_medusa |
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| 367 | IF (lwp) write (numout,*) 'trc_bio_medusa: ready for full domain calculations' |
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| 368 | CALL flush(numout) |
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| 369 | # endif |
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| 370 | |
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| 371 | !!------------------------------------------------------------------ |
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| 372 | !! MEDUSA has unified equation through the water column |
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| 373 | !! (Diff. from LOBSTER which has two sets: bio- and non-bio layers) |
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| 374 | !! Statement below in LOBSTER is different: DO jk = 1, jpkbm1 |
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| 375 | !!------------------------------------------------------------------ |
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| 376 | !! |
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| 377 | !! NOTE: the ordering of the loops below differs from that of some other |
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| 378 | !! models; looping over the vertical dimension is the outermost loop and |
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| 379 | !! this complicates some calculations (e.g. storage of vertical fluxes |
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| 380 | !! that can otherwise be done via a singular variable require 2D fields |
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| 381 | !! here); however, these issues are relatively easily resolved, but the |
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| 382 | !! loops CANNOT be reordered without potentially causing code efficiency |
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| 383 | !! problems (e.g. array indexing means that reordering the loops would |
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| 384 | !! require skipping between widely-spaced memory location; potentially |
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| 385 | !! outside those immediately cached) |
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| 386 | !! |
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| 387 | !! OPEN vertical loop |
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| 388 | DO jk = 1,jpk |
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| 389 | !! OPEN horizontal loops |
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| 390 | DO jj = 2,jpjm1 |
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| 391 | DO ji = 2,jpim1 |
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| 392 | !! OPEN wet point IF..THEN loop |
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| 393 | if (tmask(ji,jj,jk) == 1) then |
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| 394 | !!====================================================== |
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| 395 | !! SETUP LOCAL GRID CELL |
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| 396 | !!====================================================== |
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| 397 | !! |
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| 398 | !!------------------------------------------------------ |
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| 399 | !! Some notes on grid vertical structure |
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| 400 | !! - fsdepw(ji,jj,jk) is the depth of the upper surface of |
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| 401 | !! level jk |
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| 402 | !! - fsde3w(ji,jj,jk) is *approximately* the midpoint of |
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| 403 | !! level jk |
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| 404 | !! - fse3t(ji,jj,jk) is the thickness of level jk |
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| 405 | !!------------------------------------------------------ |
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| 406 | !! |
|---|
| 407 | !! AXY (01/03/10): set up level depth (bottom of level) |
|---|
| 408 | fdep1(ji,jj) = fsdepw(ji,jj,jk) + fse3t(ji,jj,jk) |
|---|
| 409 | !! |
|---|
| 410 | !! set up model tracers |
|---|
| 411 | !! negative values of state variables are not allowed to |
|---|
| 412 | !! contribute to the calculated fluxes |
|---|
| 413 | !! non-diatom chlorophyll |
|---|
| 414 | zchn(ji,jj) = max(0.,trn(ji,jj,jk,jpchn)) |
|---|
| 415 | !! diatom chlorophyll |
|---|
| 416 | zchd(ji,jj) = max(0.,trn(ji,jj,jk,jpchd)) |
|---|
| 417 | !! non-diatoms |
|---|
| 418 | zphn(ji,jj) = max(0.,trn(ji,jj,jk,jpphn)) |
|---|
| 419 | !! diatoms |
|---|
| 420 | zphd(ji,jj) = max(0.,trn(ji,jj,jk,jpphd)) |
|---|
| 421 | !! diatom silicon |
|---|
| 422 | zpds(ji,jj) = max(0.,trn(ji,jj,jk,jppds)) |
|---|
| 423 | !! AXY (28/01/10): probably need to take account of |
|---|
| 424 | !! chl/biomass connection |
|---|
| 425 | if (zchn(ji,jj).eq.0.) zphn(ji,jj) = 0. |
|---|
| 426 | if (zchd(ji,jj).eq.0.) zphd(ji,jj) = 0. |
|---|
| 427 | if (zphn(ji,jj).eq.0.) zchn(ji,jj) = 0. |
|---|
| 428 | if (zphd(ji,jj).eq.0.) zchd(ji,jj) = 0. |
|---|
| 429 | !! AXY (23/01/14): duh - why did I forget diatom silicon? |
|---|
| 430 | if (zpds(ji,jj).eq.0.) zphd(ji,jj) = 0. |
|---|
| 431 | if (zphd(ji,jj).eq.0.) zpds(ji,jj) = 0. |
|---|
| 432 | ENDIF |
|---|
| 433 | ENDDO |
|---|
| 434 | ENDDO |
|---|
| 435 | |
|---|
| 436 | DO jj = 2,jpjm1 |
|---|
| 437 | DO ji = 2,jpim1 |
|---|
| 438 | if (tmask(ji,jj,jk) == 1) then |
|---|
| 439 | !! microzooplankton |
|---|
| 440 | zzmi(ji,jj) = max(0.,trn(ji,jj,jk,jpzmi)) |
|---|
| 441 | !! mesozooplankton |
|---|
| 442 | zzme(ji,jj) = max(0.,trn(ji,jj,jk,jpzme)) |
|---|
| 443 | !! detrital nitrogen |
|---|
| 444 | zdet(ji,jj) = max(0.,trn(ji,jj,jk,jpdet)) |
|---|
| 445 | !! dissolved inorganic nitrogen |
|---|
| 446 | zdin(ji,jj) = max(0.,trn(ji,jj,jk,jpdin)) |
|---|
| 447 | !! dissolved silicic acid |
|---|
| 448 | zsil(ji,jj) = max(0.,trn(ji,jj,jk,jpsil)) |
|---|
| 449 | !! dissolved "iron" |
|---|
| 450 | zfer(ji,jj) = max(0.,trn(ji,jj,jk,jpfer)) |
|---|
| 451 | ENDIF |
|---|
| 452 | ENDDO |
|---|
| 453 | ENDDO |
|---|
| 454 | |
|---|
| 455 | # if defined key_roam |
|---|
| 456 | DO jj = 2,jpjm1 |
|---|
| 457 | DO ji = 2,jpim1 |
|---|
| 458 | if (tmask(ji,jj,jk) == 1) then |
|---|
| 459 | !! detrital carbon |
|---|
| 460 | zdtc(ji,jj) = max(0.,trn(ji,jj,jk,jpdtc)) |
|---|
| 461 | !! dissolved inorganic carbon |
|---|
| 462 | zdic(ji,jj) = max(0.,trn(ji,jj,jk,jpdic)) |
|---|
| 463 | !! alkalinity |
|---|
| 464 | zalk(ji,jj) = max(0.,trn(ji,jj,jk,jpalk)) |
|---|
| 465 | !! oxygen |
|---|
| 466 | zoxy(ji,jj) = max(0.,trn(ji,jj,jk,jpoxy)) |
|---|
| 467 | # if defined key_axy_carbchem && defined key_mocsy |
|---|
| 468 | !! phosphate via DIN and Redfield |
|---|
| 469 | zpho(ji,jj) = max(0.,trn(ji,jj,jk,jpdin)) / 16.0 |
|---|
| 470 | # endif |
|---|
| 471 | !! |
|---|
| 472 | !! also need physical parameters for gas exchange |
|---|
| 473 | !! calculations |
|---|
| 474 | ztmp(ji,jj) = tsn(ji,jj,jk,jp_tem) |
|---|
| 475 | zsal(ji,jj) = tsn(ji,jj,jk,jp_sal) |
|---|
| 476 | !! |
|---|
| 477 | !! AXY (28/02/14): check input fields |
|---|
| 478 | if (ztmp(ji,jj) .lt. -3.0 .or. ztmp(ji,jj) .gt. 40.0 ) then |
|---|
| 479 | IF(lwp) WRITE(numout,*) & |
|---|
| 480 | ' trc_bio_medusa: T WARNING 3D, ', & |
|---|
| 481 | tsb(ji,jj,jk,jp_tem), tsn(ji,jj,jk,jp_tem), & |
|---|
| 482 | ' at (', ji, ',', jj, ',', jk, ') at time', kt |
|---|
| 483 | !! temperature |
|---|
| 484 | ztmp(ji,jj) = tsb(ji,jj,jk,jp_tem) |
|---|
| 485 | IF(lwp) WRITE(numout,*) & |
|---|
| 486 | ' trc_bio_medusa: Abnormal T suroundings Temp' |
|---|
| 487 | IF(lwp) WRITE(numout,*) & |
|---|
| 488 | tsn(ji-1,jj+1,jk,jp_tem), tsn(ji,jj+1,jk,jp_tem), tsn(ji+1,jj+1,jk,jp_tem) |
|---|
| 489 | IF(lwp) WRITE(numout,*) & |
|---|
| 490 | tsn(ji-1,jj,jk,jp_tem), tsn(ji,jj,jk,jp_tem), tsn(ji+1,jj,jk,jp_tem) |
|---|
| 491 | IF(lwp) WRITE(numout,*) & |
|---|
| 492 | tsn(ji-1,jj-1,jk,jp_tem), tsn(ji,jj-1,jk,jp_tem), tsn(ji+1,jj-1,jk,jp_tem) |
|---|
| 493 | sumtsn = ( tmask(ji-1,jj+1,jk) * tsn(ji-1,jj+1,jk,jp_tem) ) + & |
|---|
| 494 | ( tmask(ji ,jj+1,jk) * tsn(ji ,jj+1,jk,jp_tem) ) + & |
|---|
| 495 | ( tmask(ji+1,jj+1,jk) * tsn(ji+1,jj+1,jk,jp_tem) ) + & |
|---|
| 496 | ( tmask(ji-1,jj ,jk) * tsn(ji-1,jj ,jk,jp_tem) ) + & |
|---|
| 497 | ( tmask(ji+1,jj ,jk) * tsn(ji+1,jj ,jk,jp_tem) ) + & |
|---|
| 498 | ( tmask(ji-1,jj-1,jk) * tsn(ji-1,jj-1,jk,jp_tem) ) + & |
|---|
| 499 | ( tmask(ji ,jj-1,jk) * tsn(ji ,jj-1,jk,jp_tem) ) + & |
|---|
| 500 | ( tmask(ji+1,jj-1,jk) * tsn(ji+1,jj-1,jk,jp_tem) ) |
|---|
| 501 | IF(lwp) WRITE(numout,*) & |
|---|
| 502 | ' trc_bio_medusa: Abnormal T suroundings Sal' |
|---|
| 503 | IF(lwp) WRITE(numout,*) & |
|---|
| 504 | tsn(ji-1,jj+1,jk,jp_sal), tsn(ji,jj+1,jk,jp_sal), tsn(ji+1,jj+1,jk,jp_sal) |
|---|
| 505 | IF(lwp) WRITE(numout,*) & |
|---|
| 506 | tsn(ji-1,jj,jk,jp_sal), tsn(ji,jj,jk,jp_sal), tsn(ji+1,jj,jk,jp_sal) |
|---|
| 507 | IF(lwp) WRITE(numout,*) & |
|---|
| 508 | tsn(ji-1,jj-1,jk,jp_sal), tsn(ji,jj-1,jk,jp_sal), tsn(ji+1,jj-1,jk,jp_sal) |
|---|
| 509 | !! |
|---|
| 510 | IF(lwp) WRITE(numout,*) & |
|---|
| 511 | ' trc_bio_medusa: Abnormal T suroundings DIC' |
|---|
| 512 | IF(lwp) WRITE(numout,*) & |
|---|
| 513 | trn(ji-1,jj+1,jk,jpdic), trn(ji,jj+1,jk,jpdic), trn(ji+1,jj+1,jk,jpdic) |
|---|
| 514 | IF(lwp) WRITE(numout,*) & |
|---|
| 515 | trn(ji-1,jj,jk,jpdic), trn(ji,jj,jk,jpdic), trn(ji+1,jj,jk,jpdic) |
|---|
| 516 | IF(lwp) WRITE(numout,*) & |
|---|
| 517 | trn(ji-1,jj-1,jk,jpdic), trn(ji,jj-1,jk,jpdic), trn(ji+1,jj-1,jk,jpdic) |
|---|
| 518 | IF(lwp) WRITE(numout,*) & |
|---|
| 519 | ' trc_bio_medusa: Abnormal T suroundings Alk' |
|---|
| 520 | IF(lwp) WRITE(numout,*) & |
|---|
| 521 | trn(ji-1,jj+1,jk,jpalk), trn(ji,jj+1,jk,jpalk), trn(ji+1,jj+1,jk,jpalk) |
|---|
| 522 | IF(lwp) WRITE(numout,*) & |
|---|
| 523 | trn(ji-1,jj,jk,jpalk), trn(ji,jj,jk,jpalk), trn(ji+1,jj,jk,jpalk) |
|---|
| 524 | IF(lwp) WRITE(numout,*) & |
|---|
| 525 | trn(ji-1,jj-1,jk,jpalk), trn(ji,jj-1,jk,jpalk), trn(ji+1,jj-1,jk,jpalk) |
|---|
| 526 | IF(lwp) WRITE(numout,*) & |
|---|
| 527 | ' trc_bio_medusa: Abnormal T suroundings tmask' |
|---|
| 528 | IF(lwp) WRITE(numout,*) & |
|---|
| 529 | tmask(ji-1,jj+1,jk), tmask(ji,jj+1,jk), tmask(ji+1,jj+1,jk) |
|---|
| 530 | IF(lwp) WRITE(numout,*) & |
|---|
| 531 | tmask(ji-1,jj,jk), tmask(ji,jj,jk), tmask(ji+1,jj,jk) |
|---|
| 532 | IF(lwp) WRITE(numout,*) & |
|---|
| 533 | tmask(ji-1,jj-1,jk), tmask(ji,jj-1,jk), tmask(ji+1,jj-1,jk) |
|---|
| 534 | summask = tmask(ji-1,jj+1,jk) + tmask(ji ,jj+1,jk) + & |
|---|
| 535 | tmask(ji+1,jj+1,jk) + tmask(ji-1,jj ,jk) + & |
|---|
| 536 | tmask(ji+1,jj ,jk) + tmask(ji-1,jj-1,jk) + & |
|---|
| 537 | tmask(ji ,jj-1,jk) + tmask(ji+1,jj-1,jk) |
|---|
| 538 | tsnavg = ( sumtsn / summask ) |
|---|
| 539 | !! Correct out of range values |
|---|
| 540 | IF ( ( summask .EQ. 0.0 ) .OR. (tsnavg .LT. -3.0 ) .OR. & |
|---|
| 541 | ( tsnavg .GT. 40.0 ) ) THEN |
|---|
| 542 | IF (ztmp(ji,jj) .LT. -3.0 ) THEN |
|---|
| 543 | IF(lwp) WRITE(numout,*) & |
|---|
| 544 | ' trc_bio_medusa: T SWITCHING 3D, ', & |
|---|
| 545 | tsn(ji,jj,jk,jp_tem), ' -> -3.0 ' |
|---|
| 546 | ztmp(ji,jj) = -3.0 |
|---|
| 547 | ENDIF |
|---|
| 548 | IF (ztmp(ji,jj) .GT. 40.0 ) THEN |
|---|
| 549 | IF(lwp) WRITE(numout,*) & |
|---|
| 550 | ' trc_bio_medusa: T SWITCHING 3D, ', & |
|---|
| 551 | tsn(ji,jj,jk,jp_tem), ' -> 40.0 ' |
|---|
| 552 | ztmp(ji,jj) = 40.0 |
|---|
| 553 | ENDIF |
|---|
| 554 | ELSE |
|---|
| 555 | IF(lwp) WRITE(numout,*) & |
|---|
| 556 | ' trc_bio_medusa: T SWITCHING 3D, ', & |
|---|
| 557 | tsn(ji,jj,jk,jp_tem), ' -> surounding avg : ', tsnavg |
|---|
| 558 | ztmp(ji,jj) = tsnavg |
|---|
| 559 | ENDIF |
|---|
| 560 | endif |
|---|
| 561 | !! end T chack |
|---|
| 562 | if (zsal(ji,jj) .lt. 1.0 .or. zsal(ji,jj) .gt. 47.0 ) then |
|---|
| 563 | IF(lwp) WRITE(numout,*) & |
|---|
| 564 | ' trc_bio_medusa: S WARNING 2D, ', & |
|---|
| 565 | tsb(ji,jj,jk,jp_sal), tsn(ji,jj,jk,jp_sal), & |
|---|
| 566 | ' at (', ji, ',', jj, ',', jk, ') at time', kt |
|---|
| 567 | !! Correct out of range values |
|---|
| 568 | IF (zsal(ji,jj) .LT. 1.0 ) THEN |
|---|
| 569 | IF(lwp) WRITE(numout,*) & |
|---|
| 570 | ' trc_bio_medusa: S SWITCHING 3D, ', & |
|---|
| 571 | tsn(ji,jj,jk,jp_sal), ' -> 1.0 ' |
|---|
| 572 | zsal(ji,jj) = 1.0 |
|---|
| 573 | ENDIF |
|---|
| 574 | IF (zsal(ji,jj) .GT. 47.0 ) THEN |
|---|
| 575 | IF(lwp) WRITE(numout,*) & |
|---|
| 576 | ' trc_bio_medusa: T SWITCHING 3D, ', & |
|---|
| 577 | tsn(ji,jj,jk,jp_sal), ' -> 47.0 ' |
|---|
| 578 | zsal(ji,jj) = 47.0 |
|---|
| 579 | ENDIF |
|---|
| 580 | endif |
|---|
| 581 | !! end S check |
|---|
| 582 | ENDIF |
|---|
| 583 | ENDDO |
|---|
| 584 | ENDDO |
|---|
| 585 | # else |
|---|
| 586 | DO jj = 2,jpjm1 |
|---|
| 587 | DO ji = 2,jpim1 |
|---|
| 588 | if (tmask(ji,jj,jk) == 1) then |
|---|
| 589 | !! implicit detrital carbon |
|---|
| 590 | zdtc(ji,jj) = zdet(ji,jj) * xthetad |
|---|
| 591 | ENDIF |
|---|
| 592 | ENDDO |
|---|
| 593 | ENDDO |
|---|
| 594 | # endif |
|---|
| 595 | # if defined key_debug_medusa |
|---|
| 596 | DO jj = 2,jpjm1 |
|---|
| 597 | DO ji = 2,jpim1 |
|---|
| 598 | if (tmask(ji,jj,jk) == 1) then |
|---|
| 599 | if (idf.eq.1) then |
|---|
| 600 | !! AXY (15/01/10) |
|---|
| 601 | if (trn(ji,jj,jk,jpdin).lt.0.) then |
|---|
| 602 | IF (lwp) write (numout,*) & |
|---|
| 603 | '------------------------------' |
|---|
| 604 | IF (lwp) write (numout,*) 'NEGATIVE DIN ERROR =', & |
|---|
| 605 | trn(ji,jj,jk,jpdin) |
|---|
| 606 | IF (lwp) write (numout,*) 'NEGATIVE DIN ERROR @', & |
|---|
| 607 | ji, jj, jk, kt |
|---|
| 608 | endif |
|---|
| 609 | if (trn(ji,jj,jk,jpsil).lt.0.) then |
|---|
| 610 | IF (lwp) write (numout,*) & |
|---|
| 611 | '------------------------------' |
|---|
| 612 | IF (lwp) write (numout,*) 'NEGATIVE SIL ERROR =', & |
|---|
| 613 | trn(ji,jj,jk,jpsil) |
|---|
| 614 | IF (lwp) write (numout,*) 'NEGATIVE SIL ERROR @', & |
|---|
| 615 | ji, jj, jk, kt |
|---|
| 616 | endif |
|---|
| 617 | # if defined key_roam |
|---|
| 618 | if (trn(ji,jj,jk,jpdic).lt.0.) then |
|---|
| 619 | IF (lwp) write (numout,*) & |
|---|
| 620 | '------------------------------' |
|---|
| 621 | IF (lwp) write (numout,*) 'NEGATIVE DIC ERROR =', & |
|---|
| 622 | trn(ji,jj,jk,jpdic) |
|---|
| 623 | IF (lwp) write (numout,*) 'NEGATIVE DIC ERROR @', & |
|---|
| 624 | ji, jj, jk, kt |
|---|
| 625 | endif |
|---|
| 626 | if (trn(ji,jj,jk,jpalk).lt.0.) then |
|---|
| 627 | IF (lwp) write (numout,*) & |
|---|
| 628 | '------------------------------' |
|---|
| 629 | IF (lwp) write (numout,*) 'NEGATIVE ALK ERROR =', & |
|---|
| 630 | trn(ji,jj,jk,jpalk) |
|---|
| 631 | IF (lwp) write (numout,*) 'NEGATIVE ALK ERROR @', & |
|---|
| 632 | ji, jj, jk, kt |
|---|
| 633 | endif |
|---|
| 634 | if (trn(ji,jj,jk,jpoxy).lt.0.) then |
|---|
| 635 | IF (lwp) write (numout,*) & |
|---|
| 636 | '------------------------------' |
|---|
| 637 | IF (lwp) write (numout,*) 'NEGATIVE OXY ERROR =', & |
|---|
| 638 | trn(ji,jj,jk,jpoxy) |
|---|
| 639 | IF (lwp) write (numout,*) 'NEGATIVE OXY ERROR @', & |
|---|
| 640 | ji, jj, jk, kt |
|---|
| 641 | endif |
|---|
| 642 | # endif |
|---|
| 643 | endif |
|---|
| 644 | ENDIF |
|---|
| 645 | ENDDO |
|---|
| 646 | ENDDO |
|---|
| 647 | # endif |
|---|
| 648 | # if defined key_debug_medusa |
|---|
| 649 | ! I'M NOT SURE THIS IS USEFUL NOW THAT I'VE SPLIT THE DO LOOP - marc 8/5/17 |
|---|
| 650 | ! if (idf.eq.1.AND.idfval.eq.1) then |
|---|
| 651 | ! DO jj = 2,jpjm1 |
|---|
| 652 | ! DO ji = 2,jpim1 |
|---|
| 653 | ! if (tmask(ji,jj,jk) == 1) then |
|---|
| 654 | ! !! report state variable values |
|---|
| 655 | ! IF (lwp) write (numout,*) & |
|---|
| 656 | ! '------------------------------' |
|---|
| 657 | ! IF (lwp) write (numout,*) 'fthk(',jk,') = ', & |
|---|
| 658 | ! fse3t(ji,jj,jk) |
|---|
| 659 | ! IF (lwp) write (numout,*) 'zphn(',jk,') = ', zphn(ji,jj) |
|---|
| 660 | ! IF (lwp) write (numout,*) 'zphd(',jk,') = ', zphd(ji,jj) |
|---|
| 661 | ! IF (lwp) write (numout,*) 'zpds(',jk,') = ', zpds(ji,jj) |
|---|
| 662 | ! IF (lwp) write (numout,*) 'zzmi(',jk,') = ', zzmi(ji,jj) |
|---|
| 663 | ! IF (lwp) write (numout,*) 'zzme(',jk,') = ', zzme(ji,jj) |
|---|
| 664 | ! IF (lwp) write (numout,*) 'zdet(',jk,') = ', zdet(ji,jj) |
|---|
| 665 | ! IF (lwp) write (numout,*) 'zdin(',jk,') = ', zdin(ji,jj) |
|---|
| 666 | ! IF (lwp) write (numout,*) 'zsil(',jk,') = ', zsil(ji,jj) |
|---|
| 667 | ! IF (lwp) write (numout,*) 'zfer(',jk,') = ', zfer(ji,jj) |
|---|
| 668 | # if defined key_roam |
|---|
| 669 | ! IF (lwp) write (numout,*) 'zdtc(',jk,') = ', zdtc(ji,jj) |
|---|
| 670 | ! IF (lwp) write (numout,*) 'zdic(',jk,') = ', zdic(ji,jj) |
|---|
| 671 | ! IF (lwp) write (numout,*) 'zalk(',jk,') = ', zalk(ji,jj) |
|---|
| 672 | ! IF (lwp) write (numout,*) 'zoxy(',jk,') = ', zoxy(ji,jj) |
|---|
| 673 | # endif |
|---|
| 674 | ! ENDIF |
|---|
| 675 | ! ENDDO |
|---|
| 676 | ! ENDDO |
|---|
| 677 | ! endif |
|---|
| 678 | # endif |
|---|
| 679 | |
|---|
| 680 | # if defined key_debug_medusa |
|---|
| 681 | ! I'M NOT SURE THIS IS USEFUL NOW THAT I'VE SPLIT THE DO LOOP - marc 8/5/17 |
|---|
| 682 | ! if (idf.eq.1.AND.idfval.eq.1.AND.jk.eq.1) then |
|---|
| 683 | ! DO jj = 2,jpjm1 |
|---|
| 684 | ! DO ji = 2,jpim1 |
|---|
| 685 | ! if (tmask(ji,jj,jk) == 1) then |
|---|
| 686 | ! IF (lwp) write (numout,*) & |
|---|
| 687 | ! '------------------------------' |
|---|
| 688 | ! IF (lwp) write (numout,*) 'dust = ', dust(ji,jj) |
|---|
| 689 | ! ENDIF |
|---|
| 690 | ! ENDDO |
|---|
| 691 | ! ENDDO |
|---|
| 692 | ! endif |
|---|
| 693 | # endif |
|---|
| 694 | |
|---|
| 695 | !!--------------------------------------------------------------- |
|---|
| 696 | !! Calculate air-sea gas exchange and river inputs |
|---|
| 697 | !!--------------------------------------------------------------- |
|---|
| 698 | IF ( jk == 1 ) THEN |
|---|
| 699 | CALL air_sea( kt ) |
|---|
| 700 | ENDIF |
|---|
| 701 | |
|---|
| 702 | !!--------------------------------------------------------------- |
|---|
| 703 | !! Phytoplankton growth, zooplankton grazing and miscellaneous |
|---|
| 704 | !! plankton losses. |
|---|
| 705 | !!--------------------------------------------------------------- |
|---|
| 706 | CALL plankton( jk ) |
|---|
| 707 | |
|---|
| 708 | !!--------------------------------------------------------------- |
|---|
| 709 | !! Iron chemistry and scavenging |
|---|
| 710 | !!--------------------------------------------------------------- |
|---|
| 711 | CALL iron_chem_scav( jk ) |
|---|
| 712 | |
|---|
| 713 | !!--------------------------------------------------------------- |
|---|
| 714 | !! Detritus processes |
|---|
| 715 | !!--------------------------------------------------------------- |
|---|
| 716 | CALL detritus( jk, iball ) |
|---|
| 717 | |
|---|
| 718 | !!--------------------------------------------------------------- |
|---|
| 719 | !! Updating tracers |
|---|
| 720 | !!--------------------------------------------------------------- |
|---|
| 721 | CALL bio_medusa_update( kt, jk ) |
|---|
| 722 | |
|---|
| 723 | !!--------------------------------------------------------------- |
|---|
| 724 | !! Diagnostics |
|---|
| 725 | !!--------------------------------------------------------------- |
|---|
| 726 | CALL bio_medusa_diag( jk ) |
|---|
| 727 | |
|---|
| 728 | !!------------------------------------------------------- |
|---|
| 729 | !! 2d specific k level diags |
|---|
| 730 | !!------------------------------------------------------- |
|---|
| 731 | IF( lk_iomput ) THEN |
|---|
| 732 | CALL bio_medusa_diag_slice( jk ) |
|---|
| 733 | ENDIF |
|---|
| 734 | |
|---|
| 735 | !! CLOSE vertical loop |
|---|
| 736 | ENDDO |
|---|
| 737 | |
|---|
| 738 | !!------------------------------------------------------------------ |
|---|
| 739 | !! Final calculations for diagnostics |
|---|
| 740 | !!------------------------------------------------------------------ |
|---|
| 741 | CALL bio_medusa_fin( kt ) |
|---|
| 742 | |
|---|
| 743 | # if defined key_debug_medusa |
|---|
| 744 | IF(lwp) WRITE(numout,*) ' MEDUSA exiting trc_bio_medusa at kt =', kt |
|---|
| 745 | CALL flush(numout) |
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| 746 | # endif |
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| 747 | |
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| 748 | END SUBROUTINE trc_bio_medusa |
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| 749 | |
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| 750 | #else |
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| 751 | !!===================================================================== |
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| 752 | !! Dummy module : No MEDUSA bio-model |
|---|
| 753 | !!===================================================================== |
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| 754 | CONTAINS |
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| 755 | SUBROUTINE trc_bio_medusa( kt ) ! Empty routine |
|---|
| 756 | INTEGER, INTENT( in ) :: kt |
|---|
| 757 | WRITE(*,*) 'trc_bio_medusa: You should not have seen this print! error?', kt |
|---|
| 758 | END SUBROUTINE trc_bio_medusa |
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| 759 | #endif |
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| 760 | |
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| 761 | !!===================================================================== |
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| 762 | END MODULE trcbio_medusa |
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