| 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 individual tracers |
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| 9 | !! - ! 2001-03 (M. Levy) LNO3 + dia2d |
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| 10 | !! 2.0 ! 2007-12 (C. Deltel, G. Madec) F90 |
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| 11 | !! - ! 2008-08 (K. Popova) adaptation for MEDUSA |
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| 12 | !! - ! 2008-11 (A. Yool) continuing adaptation for MEDUSA |
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| 13 | !! - ! 2010-03 (A. Yool) updated for branch inclusion |
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| 14 | !! - ! 2011-08 (A. Yool) updated for ROAM (see below) |
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| 15 | !! - ! 2013-03 (A. Yool) updated for iMARNET |
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| 16 | !! - ! 2013-05 (A. Yool) updated for v3.5 |
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| 17 | !! - ! 2014-08 (A. Yool, J. Palm) Add DMS module for UKESM1 model |
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| 18 | !! - ! 2015-06 (A. Yool) Update to include MOCSY |
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| 19 | !! - ! 2015-07 (A. Yool) Update for rolling averages |
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| 20 | !! - ! 2015-10 (J. Palm) Update for diag outputs through iom_use |
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| 21 | !! - ! 2016-11 (A. Yool) Updated diags for CMIP6 |
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| 22 | !!---------------------------------------------------------------------- |
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| 23 | !! |
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| 24 | #if defined key_roam |
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| 25 | !!---------------------------------------------------------------------- |
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| 26 | !! Updates for the ROAM project include: |
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| 27 | !! - addition of DIC, alkalinity, detrital carbon and oxygen tracers |
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| 28 | !! - addition of air-sea fluxes of CO2 and oxygen |
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| 29 | !! - periodic (monthly) calculation of full 3D carbonate chemistry |
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| 30 | !! - detrital C:N ratio now free to evolve dynamically |
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| 31 | !! - benthic storage pools |
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| 32 | !! |
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| 33 | !! Opportunity also taken to add functionality: |
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| 34 | !! - switch for Liebig Law (= most-limiting) nutrient uptake |
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| 35 | !! - switch for accelerated seafloor detritus remineralisation |
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| 36 | !! - switch for fast -> slow detritus transfer at seafloor |
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| 37 | !! - switch for ballast vs. Martin vs. Henson fast detritus remin. |
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| 38 | !! - per GMD referee remarks, xfdfrac3 introduced for grazed PDS |
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| 39 | !!---------------------------------------------------------------------- |
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| 40 | #endif |
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| 41 | !! |
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| 42 | #if defined key_mocsy |
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| 43 | !!---------------------------------------------------------------------- |
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| 44 | !! Updates with the addition of MOCSY include: |
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| 45 | !! - option to use PML or MOCSY carbonate chemistry (the latter is |
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| 46 | !! preferred) |
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| 47 | !! - central calculation of gas transfer velocity, f_kw660; previously |
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| 48 | !! this was done separately for CO2 and O2 with predictable results |
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| 49 | !! - distribution of f_kw660 to both PML and MOCSY CO2 air-sea flux |
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| 50 | !! calculations and to those for O2 air-sea flux |
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| 51 | !! - extra diagnostics included for MOCSY |
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| 52 | !!---------------------------------------------------------------------- |
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| 53 | #endif |
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| 54 | !! |
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| 55 | #if defined key_medusa |
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| 56 | !!---------------------------------------------------------------------- |
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| 57 | !! MEDUSA bio-model |
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| 58 | !!---------------------------------------------------------------------- |
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| 59 | !! trc_bio_medusa : |
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| 60 | !!---------------------------------------------------------------------- |
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| 61 | USE oce_trc |
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| 62 | USE trc |
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| 63 | USE sms_medusa |
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| 64 | USE lbclnk |
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| 65 | USE prtctl_trc ! Print control for debugging |
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| 66 | USE trcsed_medusa |
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| 67 | USE sbc_oce ! surface forcing |
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| 68 | USE sbcrnf ! surface boundary condition: runoff variables |
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| 69 | USE in_out_manager ! I/O manager |
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| 70 | # if defined key_iomput |
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| 71 | USE iom |
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| 72 | USE trcnam_medusa ! JPALM 13-11-2015 -- if iom_use for diag |
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| 73 | !!USE trc_nam_iom_medusa ! JPALM 13-11-2015 -- if iom_use for diag |
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| 74 | # endif |
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| 75 | # if defined key_roam |
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| 76 | USE gastransfer |
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| 77 | # if defined key_mocsy |
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| 78 | USE mocsy_wrapper |
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| 79 | # else |
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| 80 | USE trcco2_medusa |
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| 81 | # endif |
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| 82 | USE trcoxy_medusa |
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| 83 | !! Jpalm (08/08/2014) |
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| 84 | USE trcdms_medusa |
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| 85 | # endif |
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| 86 | !! AXY (18/01/12): brought in for benthic timestepping |
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| 87 | USE trcnam_trp ! AXY (24/05/2013) |
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| 88 | USE trdmxl_trc |
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| 89 | USE trdtrc_oce ! AXY (24/05/2013) |
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| 90 | |
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| 91 | !! AXY (30/01/14): necessary to find NaNs on HECTOR |
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| 92 | USE, INTRINSIC :: ieee_arithmetic |
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| 93 | |
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| 94 | !! JPALM (27-06-2016): add lk_oasis for CO2 and DMS coupling with atm |
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| 95 | USE sbc_oce, ONLY: lk_oasis |
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| 96 | USE oce, ONLY: CO2Flux_out_cpl, DMS_out_cpl, & |
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| 97 | PCO2a_in_cpl |
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| 98 | USE bio_medusa_mod |
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| 99 | USE bio_medusa_init_mod, ONLY: bio_medusa_init |
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| 100 | USE carb_chem_mod, ONLY: carb_chem |
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| 101 | USE air_sea_mod, ONLY: air_sea |
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| 102 | USE plankton_mod, ONLY: plankton |
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| 103 | USE iron_chem_scav_mod, ONLY: iron_chem_scav |
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| 104 | USE detritus_mod, ONLY: detritus |
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| 105 | USE bio_medusa_update_mod, ONLY: bio_medusa_update |
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| 106 | USE bio_medusa_diag_mod, ONLY: bio_medusa_diag |
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| 107 | USE bio_medusa_diag_slice_mod, ONLY: bio_medusa_diag_slice |
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| 108 | USE bio_medusa_fin_mod, ONLY: bio_medusa_fin |
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| 109 | |
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| 110 | IMPLICIT NONE |
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| 111 | PRIVATE |
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| 112 | |
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| 113 | PUBLIC trc_bio_medusa ! called in trcsms_medusa.F90 |
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| 114 | |
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| 115 | !!* Substitution |
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| 116 | # include "domzgr_substitute.h90" |
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| 117 | !!---------------------------------------------------------------------- |
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| 118 | !! NEMO/TOP 2.0 , LOCEAN-IPSL (2007) |
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| 119 | !! $Id$ |
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| 120 | !! Software governed by the CeCILL licence (modipsl/doc/NEMO_CeCILL.txt) |
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| 121 | !!---------------------------------------------------------------------- |
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| 122 | |
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| 123 | CONTAINS |
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| 124 | |
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| 125 | SUBROUTINE trc_bio_medusa( kt ) |
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| 126 | !!--------------------------------------------------------------------- |
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| 127 | !! *** ROUTINE trc_bio *** |
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| 128 | !! |
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| 129 | !! ** Purpose : compute the now trend due to biogeochemical processes |
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| 130 | !! and add it to the general trend of passive tracers equations |
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| 131 | !! |
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| 132 | !! ** Method : each now biological flux is calculated in function of now |
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| 133 | !! concentrations of tracers. |
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| 134 | !! depending on the tracer, these fluxes are sources or sinks. |
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| 135 | !! the total of the sources and sinks for each tracer |
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| 136 | !! is added to the general trend. |
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| 137 | !! |
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| 138 | !! tra = tra + zf...tra - zftra... |
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| 139 | !! | | |
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| 140 | !! | | |
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| 141 | !! source sink |
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| 142 | !! |
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| 143 | !! IF 'key_trc_diabio' defined , the biogeochemical trends |
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| 144 | !! for passive tracers are saved for futher diagnostics. |
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| 145 | !!--------------------------------------------------------------------- |
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| 146 | !! |
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| 147 | !! |
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| 148 | !!---------------------------------------------------------------------- |
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| 149 | !! Variable conventions |
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| 150 | !!---------------------------------------------------------------------- |
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| 151 | !! |
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| 152 | !! names: z*** - state variable |
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| 153 | !! f*** - function (or temporary variable used in part of a function) |
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| 154 | !! x*** - parameter |
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| 155 | !! b*** - right-hand part (sources and sinks) |
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| 156 | !! i*** - integer variable (usually used in yes/no flags) |
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| 157 | !! |
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| 158 | !! time (integer timestep) |
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| 159 | INTEGER, INTENT( in ) :: kt |
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| 160 | !! |
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| 161 | !! spatial array indices |
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| 162 | INTEGER :: ji,jj,jk,jn |
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| 163 | !! |
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| 164 | !! AXY (27/07/10): add in indices for depth horizons (for sinking flux |
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| 165 | !! and seafloor iron inputs) |
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| 166 | !! INTEGER :: i0100, i0200, i0500, i1000, i1100 |
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| 167 | !! |
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| 168 | !! model state variables |
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| 169 | ! REAL(wp), DIMENSION(jpi,jpj) :: zchn,zchd,zphn,zphd,zpds,zzmi |
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| 170 | ! REAL(wp), DIMENSION(jpi,jpj) :: zzme,zdet,zdtc,zdin,zsil,zfer |
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| 171 | ! zage doesn't seem to be used - marc 19/4/17 |
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| 172 | ! REAL(wp) :: zage |
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| 173 | !# if defined key_roam |
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| 174 | ! REAL(wp), DIMENSION(jpi,jpj) :: zdic, zalk, zoxy |
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| 175 | ! REAL(wp), DIMENSION(jpi,jpj) :: ztmp, zsal |
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| 176 | !# endif |
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| 177 | !# if defined key_mocsy |
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| 178 | ! REAL(wp), DIMENSION(jpi,jpj) :: zpho |
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| 179 | !# endif |
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| 180 | !! |
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| 181 | !! integrated source and sink terms |
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| 182 | ! REAL(wp) :: b0 |
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| 183 | !! AXY (23/08/13): changed from individual variables for each flux to |
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| 184 | !! an array that holds all fluxes |
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| 185 | REAL(wp), DIMENSION(jpi,jpj,jp_medusa) :: btra |
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| 186 | !! |
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| 187 | !! primary production and chl related quantities |
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| 188 | ! REAL(wp), DIMENSION(jpi,jpj) :: fthetan,faln,fchn1,fchn,fjln,fprn,frn |
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| 189 | ! REAL(wp), DIMENSION(jpi,jpj) :: fthetad,fald,fchd1,fchd,fjld,fprd,frd |
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| 190 | !! AXY (23/11/16): add in light-only limitation term (normalised 0-1 range) |
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| 191 | ! REAL(wp), DIMENSION(jpi,jpj) :: fjlim_pn, fjlim_pd |
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| 192 | !! AXY (03/02/11): add in Liebig terms |
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| 193 | ! REAL(wp), DIMENSION(jpi,jpj) :: fpnlim, fpdlim |
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| 194 | !! AXY (16/07/09): add in Eppley curve functionality |
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| 195 | ! REAL(wp), DIMENSION(jpi,jpj) :: fun_T,xvpnT,xvpdT |
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| 196 | INTEGER :: ieppley |
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| 197 | !! AXY (16/05/11): per Katya's prompting, add in new T-dependence |
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| 198 | !! for phytoplankton growth only (i.e. no change |
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| 199 | !! for remineralisation) |
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| 200 | ! REAL(wp), DIMENSION(jpi,jpj) :: fun_Q10 |
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| 201 | !! AXY (01/03/10): add in mixed layer PP diagnostics |
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| 202 | ! REAL(wp), DIMENSION(jpi,jpj) :: fprn_ml,fprd_ml |
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| 203 | !! |
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| 204 | !! nutrient limiting factors |
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| 205 | ! REAL(wp), DIMENSION(jpi,jpj) :: fnln,ffln2 !! N and Fe |
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| 206 | ! REAL(wp), DIMENSION(jpi,jpj) :: fnld,ffld,fsld,fsld2 !! N, Fe and Si |
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| 207 | !! |
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| 208 | !! silicon cycle |
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| 209 | ! REAL(wp), DIMENSION(jpi,jpj) :: fsin,fnsi,fprds,fsdiss |
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| 210 | REAL(wp) :: fsin1,fnsi1,fnsi2 |
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| 211 | !! |
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| 212 | !! iron cycle; includes parameters for Parekh et al. (2005) iron scheme |
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| 213 | ! REAL(wp), DIMENSION(jpi,jpj) :: ffetop,ffebot,ffescav |
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| 214 | REAL(wp) :: xLgF, xFeT, xFeF, xFeL !! state variables for iron-ligand system |
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| 215 | ! REAL(wp), DIMENSION(jpi,jpj) :: xFree !! state variables for iron-ligand system |
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| 216 | REAL(wp) :: xb_coef_tmp, xb2M4ac !! iron-ligand parameters |
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| 217 | REAL(wp) :: xmaxFeF,fdeltaFe !! max Fe' parameters |
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| 218 | !! |
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| 219 | !! local parameters for Moore et al. (2004) alternative scavenging scheme |
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| 220 | REAL(wp) :: fbase_scav,fscal_sink,fscal_part,fscal_scav |
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| 221 | !! |
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| 222 | !! local parameters for Moore et al. (2008) alternative scavenging scheme |
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| 223 | REAL(wp) :: fscal_csink,fscal_sisink,fscal_casink |
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| 224 | !! |
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| 225 | !! local parameters for Galbraith et al. (2010) alternative scavenging scheme |
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| 226 | REAL(wp) :: xCscav1, xCscav2, xk_org, xORGscav !! organic portion of scavenging |
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| 227 | REAL(wp) :: xk_inorg, xINORGscav !! inorganic portion of scavenging |
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| 228 | !! |
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| 229 | !! microzooplankton grazing |
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| 230 | ! REAL(wp), DIMENSION(jpi,jpj) :: fmi1,fmi,fgmipn,fgmid,fgmidc |
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| 231 | ! REAL(wp), DIMENSION(jpi,jpj) :: finmi,ficmi,fstarmi,fmith,fmigrow,fmiexcr,fmiresp |
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| 232 | !! |
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| 233 | !! mesozooplankton grazing |
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| 234 | ! REAL(wp), DIMENSION(jpi,jpj) :: fme1,fme,fgmepn,fgmepd,fgmepds,fgmezmi,fgmed,fgmedc |
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| 235 | ! REAL(wp), DIMENSION(jpi,jpj) :: finme,ficme,fstarme,fmeth,fmegrow,fmeexcr,fmeresp |
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| 236 | !! |
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| 237 | !! mortality/Remineralisation (defunct parameter "fz" removed) |
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| 238 | ! REAL(wp), DIMENSION(jpi,jpj) :: fdpn,fdpd,fdpds,fdzmi,fdzme,fdd |
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| 239 | # if defined key_roam |
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| 240 | ! REAL(wp), DIMENSION(jpi,jpj) :: fddc |
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| 241 | # endif |
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| 242 | ! REAL(wp), DIMENSION(jpi,jpj) :: fdpn2,fdpd2,fdpds2,fdzmi2,fdzme2 |
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| 243 | ! REAL(wp), DIMENSION(jpi,jpj) :: fslown, fslowc |
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| 244 | ! REAL(wp), DIMENSION(jpi,jpj) :: fslownflux, fslowcflux |
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| 245 | REAL(wp), DIMENSION(jpi,jpj) :: fregen,fregensi |
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| 246 | ! REAL(wp), DIMENSION(jpi,jpj) :: fregenfast,fregenfastsi |
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| 247 | # if defined key_roam |
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| 248 | !! Doesn't look like this is used - marc 10/4/17 |
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| 249 | !! REAL(wp), DIMENSION(jpi,jpj) :: fregenc |
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| 250 | ! REAL(wp), DIMENSION(jpi,jpj) :: fregenfastc |
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| 251 | # endif |
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| 252 | !! |
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| 253 | !! particle flux |
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| 254 | ! REAL(WP), DIMENSION(jpi,jpj) :: fdep1,fcaco3 |
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| 255 | ! REAL(WP), DIMENSION(jpi,jpj) :: ftempn,ftempsi,ftempfe,ftempc,ftempca |
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| 256 | ! REAL(wp), DIMENSION(jpi,jpj) :: freminn,freminsi,freminfe,freminc,freminca |
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| 257 | ! REAL(wp), DIMENSION(jpi,jpj) :: ffastn,ffastsi,ffastfe,ffastc,ffastca |
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| 258 | ! REAL(wp), DIMENSION(jpi,jpj) :: fprotf |
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| 259 | ! REAL(wp), DIMENSION(jpi,jpj) :: fsedn,fsedsi,fsedfe,fsedc,fsedca |
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| 260 | ! REAL(wp), DIMENSION(jpi,jpj) :: fccd |
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| 261 | ! REAL(wp), DIMENSION(jpi,jpj) :: fccd_dep |
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| 262 | !! |
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| 263 | !! AXY (06/07/11): alternative fast detritus schemes |
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| 264 | REAL(wp) :: fb_val, fl_sst |
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| 265 | !! |
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| 266 | !! AXY (08/07/11): fate of fast detritus reaching the seafloor |
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| 267 | ! I don't think ffast2slowfe is used - marc 10/4/17 |
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| 268 | ! REAL(wp), DIMENSION(jpi,jpj) :: ffast2slown,ffast2slowfe,ffast2slowc |
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| 269 | ! REAL(wp), DIMENSION(jpi,jpj) :: ffast2slown,ffast2slowc |
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| 270 | !! |
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| 271 | !! conservation law |
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| 272 | REAL(wp) :: fnit0,fsil0,ffer0 |
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| 273 | # if defined key_roam |
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| 274 | REAL(wp) :: fcar0,falk0,foxy0 |
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| 275 | # endif |
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| 276 | !! |
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| 277 | !! temporary variables |
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| 278 | REAL(wp) :: fq0,fq1,fq2,fq3,fq4,fq5,fq6,fq7,fq8,fq9 |
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| 279 | !! |
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| 280 | !! water column nutrient and flux integrals |
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| 281 | ! REAL(wp), DIMENSION(jpi,jpj) :: ftot_n,ftot_si,ftot_fe |
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| 282 | ! REAL(wp), DIMENSION(jpi,jpj) :: fflx_n,fflx_si,fflx_fe |
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| 283 | ! REAL(wp), DIMENSION(jpi,jpj) :: fifd_n,fifd_si,fifd_fe |
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| 284 | ! REAL(wp), DIMENSION(jpi,jpj) :: fofd_n,fofd_si,fofd_fe |
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| 285 | # if defined key_roam |
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| 286 | ! REAL(wp), DIMENSION(jpi,jpj) :: ftot_c,ftot_a,ftot_o2 |
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| 287 | ! REAL(wp), DIMENSION(jpi,jpj) :: fflx_c,fflx_a,fflx_o2 |
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| 288 | ! REAL(wp), DIMENSION(jpi,jpj) :: fifd_c,fifd_a,fifd_o2 |
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| 289 | ! REAL(wp), DIMENSION(jpi,jpj) :: fofd_c,fofd_a,fofd_o2 |
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| 290 | # endif |
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| 291 | !! |
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| 292 | !! zooplankton grazing integrals |
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| 293 | ! REAL(wp), DIMENSION(jpi,jpj) :: fzmi_i,fzmi_o,fzme_i,fzme_o |
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| 294 | !! |
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| 295 | !! limitation term temporary variables |
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| 296 | ! REAL(wp), DIMENSION(jpi,jpj) :: ftot_pn,ftot_pd |
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| 297 | ! REAL(wp), DIMENSION(jpi,jpj) :: ftot_zmi,ftot_zme,ftot_det,ftot_dtc |
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| 298 | !! use ballast scheme (1) or simple exponential scheme (0; a conservation test) |
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| 299 | INTEGER :: iball |
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| 300 | !! use biological fluxes (1) or not (0) |
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| 301 | ! INTEGER :: ibio_switch |
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| 302 | !! |
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| 303 | !! diagnose fluxes (should only be used in 1D runs) |
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| 304 | ! INTEGER :: idf, idfval |
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| 305 | !! |
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| 306 | !! nitrogen and silicon production and consumption |
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| 307 | REAL(wp) :: fn_prod, fn_cons, fs_prod, fs_cons |
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| 308 | ! REAL(wp), DIMENSION(jpi,jpj) :: fnit_prod, fnit_cons, fsil_prod, fsil_cons |
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| 309 | # if defined key_roam |
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| 310 | !! |
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| 311 | !! flags to help with calculating the position of the CCD |
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| 312 | ! Moved into carb_chem.F90 - marc 20/4/17 |
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| 313 | ! INTEGER, DIMENSION(jpi,jpj) :: i2_omcal,i2_omarg |
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| 314 | !! |
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| 315 | !! AXY (24/11/16): add xCO2 variable for atmosphere (what we actually have) |
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| 316 | ! REAL(wp) :: f_xco2a |
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| 317 | ! REAL(wp), DIMENSION(jpi,jpj) :: f_ph, f_pco2w, f_h2co3, f_hco3, f_co3, f_co2flux |
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| 318 | ! REAL(wp), DIMENSION(jpi,jpj) :: f_TDIC, f_TALK, f_dcf, f_henry |
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| 319 | ! REAL(wp), DIMENSION(jpi,jpj) :: f_pp0 |
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| 320 | ! REAL(wp), DIMENSION(jpi,jpj) :: f_kw660, f_o2flux, f_o2sat |
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| 321 | REAL(wp) :: f_o2sat3 |
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| 322 | ! REAL(wp), DIMENSION(jpi,jpj) :: f_omcal, f_omarg |
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| 323 | !! |
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| 324 | !! AXY (23/06/15): additional diagnostics for MOCSY and oxygen |
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| 325 | ! REAL(wp), DIMENSION(jpi,jpj) :: f_fco2w, f_BetaD, f_rhosw, f_opres, f_insitut, f_pco2atm, f_fco2atm |
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| 326 | ! REAL(wp), DIMENSION(jpi,jpj) :: f_schmidtco2, f_kwco2, f_K0, f_co2starair, f_dpco2, f_kwo2 |
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| 327 | !! jpalm 14-07-2016: convert CO2flux diag from mmol/m2/d to kg/m2/s |
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| 328 | REAL, PARAMETER :: weight_CO2_mol = 44.0095 !! g / mol |
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| 329 | REAL, PARAMETER :: secs_in_day = 86400.0 !! s / d |
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| 330 | REAL, PARAMETER :: CO2flux_conv = (1.e-6 * weight_CO2_mol) / secs_in_day |
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| 331 | |
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| 332 | !! |
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| 333 | ! INTEGER, DIMENSION(jpi,jpj) :: iters |
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| 334 | REAL(wp) :: f_year |
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| 335 | INTEGER :: i_year |
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| 336 | INTEGER :: iyr1, iyr2 |
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| 337 | !! |
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| 338 | !! carbon, alkalinity production and consumption |
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| 339 | REAL(wp) :: fc_prod, fc_cons, fa_prod, fa_cons |
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| 340 | ! REAL(wp), DIMENSION(jpi,jpj) :: fcomm_resp |
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| 341 | ! REAL(wp), DIMENSION(jpi,jpj) :: fcar_prod, fcar_cons |
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| 342 | !! |
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| 343 | !! oxygen production and consumption (and non-consumption) |
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| 344 | REAL(wp), DIMENSION(jpi,jpj) :: fo2_prod, fo2_cons, fo2_ncons, fo2_ccons |
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| 345 | ! REAL(wp), DIMENSION(jpi,jpj) :: foxy_prod, foxy_cons, foxy_anox |
|---|
| 346 | !! Jpalm (11-08-2014) |
|---|
| 347 | !! add DMS in MEDUSA for UKESM1 model |
|---|
| 348 | ! REAL(wp), DIMENSION(jpi,jpj) :: dms_surf |
|---|
| 349 | !! AXY (13/03/15): add in other DMS calculations |
|---|
| 350 | ! REAL(wp), DIMENSION(jpi,jpj) :: dms_andr, dms_simo, dms_aran, dms_hall |
|---|
| 351 | |
|---|
| 352 | # endif |
|---|
| 353 | !! |
|---|
| 354 | !! benthic fluxes |
|---|
| 355 | ! INTEGER :: ibenthic |
|---|
| 356 | ! REAL(wp), DIMENSION(jpi,jpj) :: f_sbenin_n, f_sbenin_fe, f_sbenin_c |
|---|
| 357 | ! REAL(wp), DIMENSION(jpi,jpj) :: f_fbenin_n, f_fbenin_fe, f_fbenin_si, f_fbenin_c, f_fbenin_ca |
|---|
| 358 | ! REAL(wp), DIMENSION(jpi,jpj) :: f_benout_n, f_benout_fe, f_benout_si, f_benout_c, f_benout_ca |
|---|
| 359 | REAL(wp) :: zfact |
|---|
| 360 | !! |
|---|
| 361 | !! benthic fluxes of CaCO3 that shouldn't happen because of lysocline |
|---|
| 362 | ! REAL(wp), DIMENSION(jpi,jpj) :: f_benout_lyso_ca |
|---|
| 363 | !! |
|---|
| 364 | !! riverine fluxes |
|---|
| 365 | ! REAL(wp), DIMENSION(jpi,jpj) :: f_runoff, f_riv_n, f_riv_si, f_riv_c, f_riv_alk |
|---|
| 366 | !! AXY (19/07/12): variables for local riverine fluxes to handle inputs below surface |
|---|
| 367 | ! REAL(wp), DIMENSION(jpi,jpj) :: f_riv_loc_n, f_riv_loc_si, f_riv_loc_c, f_riv_loc_alk |
|---|
| 368 | !!--------------------------------------------------------------------- |
|---|
| 369 | |
|---|
| 370 | # if defined key_debug_medusa |
|---|
| 371 | IF (lwp) write (numout,*) 'trc_bio_medusa: variables defined' |
|---|
| 372 | CALL flush(numout) |
|---|
| 373 | # endif |
|---|
| 374 | |
|---|
| 375 | !! AXY (20/11/14): alter this to report on first MEDUSA call |
|---|
| 376 | !! IF( kt == nit000 ) THEN |
|---|
| 377 | IF( kt == nittrc000 ) THEN |
|---|
| 378 | IF(lwp) WRITE(numout,*) |
|---|
| 379 | IF(lwp) WRITE(numout,*) ' trc_bio: MEDUSA bio-model' |
|---|
| 380 | IF(lwp) WRITE(numout,*) ' ~~~~~~~' |
|---|
| 381 | IF(lwp) WRITE(numout,*) ' kt =',kt |
|---|
| 382 | ENDIF |
|---|
| 383 | |
|---|
| 384 | !! AXY (13/01/12): is benthic model properly interactive? 0 = no, 1 = yes |
|---|
| 385 | ibenthic = 1 |
|---|
| 386 | |
|---|
| 387 | !! not sure what this is for; it's not used anywhere; commenting out |
|---|
| 388 | !! fbodn(:,:) = 0.e0 |
|---|
| 389 | |
|---|
| 390 | !! |
|---|
| 391 | IF( ln_diatrc ) THEN |
|---|
| 392 | !! blank 2D diagnostic array |
|---|
| 393 | trc2d(:,:,:) = 0.e0 |
|---|
| 394 | !! |
|---|
| 395 | !! blank 3D diagnostic array |
|---|
| 396 | trc3d(:,:,:,:) = 0.e0 |
|---|
| 397 | ENDIF |
|---|
| 398 | |
|---|
| 399 | !!---------------------------------------------------------------------- |
|---|
| 400 | !! b0 is present for debugging purposes; using b0 = 0 sets the tendency |
|---|
| 401 | !! terms of all biological equations to 0. |
|---|
| 402 | !!---------------------------------------------------------------------- |
|---|
| 403 | !! |
|---|
| 404 | !! AXY (03/09/14): probably not the smartest move ever, but it'll fit |
|---|
| 405 | !! the bill for now; another item on the things-to-sort- |
|---|
| 406 | !! out-in-the-future list ... |
|---|
| 407 | # if defined key_kill_medusa |
|---|
| 408 | b0 = 0. |
|---|
| 409 | # else |
|---|
| 410 | b0 = 1. |
|---|
| 411 | # endif |
|---|
| 412 | !!---------------------------------------------------------------------- |
|---|
| 413 | !! fast detritus ballast scheme (0 = no; 1 = yes) |
|---|
| 414 | !! alternative to ballast scheme is same scheme but with no ballast |
|---|
| 415 | !! protection (not dissimilar to Martin et al., 1987) |
|---|
| 416 | !!---------------------------------------------------------------------- |
|---|
| 417 | !! |
|---|
| 418 | iball = 1 |
|---|
| 419 | |
|---|
| 420 | !!---------------------------------------------------------------------- |
|---|
| 421 | !! full flux diagnostics (0 = no; 1 = yes); appear in ocean.output |
|---|
| 422 | !! these should *only* be used in 1D since they give comprehensive |
|---|
| 423 | !! output for ecological functions in the model; primarily used in |
|---|
| 424 | !! debugging |
|---|
| 425 | !!---------------------------------------------------------------------- |
|---|
| 426 | !! |
|---|
| 427 | idf = 0 |
|---|
| 428 | !! |
|---|
| 429 | !! timer mechanism |
|---|
| 430 | if (kt/120*120.eq.kt) then |
|---|
| 431 | idfval = 1 |
|---|
| 432 | else |
|---|
| 433 | idfval = 0 |
|---|
| 434 | endif |
|---|
| 435 | |
|---|
| 436 | !!---------------------------------------------------------------------- |
|---|
| 437 | !! Initialise arrays to zero and set up arrays for diagnostics |
|---|
| 438 | !!---------------------------------------------------------------------- |
|---|
| 439 | ! tmp - marc |
|---|
| 440 | write(numout,*) 'bbb13. before call to bio_medusa_init,kt=',kt |
|---|
| 441 | flush(numout) |
|---|
| 442 | ! |
|---|
| 443 | CALL bio_medusa_init( kt ) |
|---|
| 444 | ! tmp - marc |
|---|
| 445 | write(numout,*) 'bbb14. after call to bio_medusa_init,kt=',kt |
|---|
| 446 | flush(numout) |
|---|
| 447 | ! |
|---|
| 448 | !! |
|---|
| 449 | # if defined key_axy_nancheck |
|---|
| 450 | DO jn = 1,jptra |
|---|
| 451 | !! fq0 = MINVAL(trn(:,:,:,jn)) |
|---|
| 452 | !! fq1 = MAXVAL(trn(:,:,:,jn)) |
|---|
| 453 | fq2 = SUM(trn(:,:,:,jn)) |
|---|
| 454 | !! if (lwp) write (numout,'(a,2i6,3(1x,1pe15.5))') 'NAN-CHECK', & |
|---|
| 455 | !! & kt, jn, fq0, fq1, fq2 |
|---|
| 456 | !! AXY (30/01/14): much to our surprise, the next line doesn't work on HECTOR |
|---|
| 457 | !! and has been replaced here with a specialist routine |
|---|
| 458 | !! if (fq2 /= fq2 ) then |
|---|
| 459 | if ( ieee_is_nan( fq2 ) ) then |
|---|
| 460 | !! there's a NaN here |
|---|
| 461 | if (lwp) write(numout,*) 'NAN detected in field', jn, 'at time', kt, 'at position:' |
|---|
| 462 | DO jk = 1,jpk |
|---|
| 463 | DO jj = 1,jpj |
|---|
| 464 | DO ji = 1,jpi |
|---|
| 465 | !! AXY (30/01/14): "isnan" problem on HECTOR |
|---|
| 466 | !! if (trn(ji,jj,jk,jn) /= trn(ji,jj,jk,jn)) then |
|---|
| 467 | if ( ieee_is_nan( trn(ji,jj,jk,jn) ) ) then |
|---|
| 468 | if (lwp) write (numout,'(a,1pe12.2,4i6)') 'NAN-CHECK', & |
|---|
| 469 | & tmask(ji,jj,jk), ji, jj, jk, jn |
|---|
| 470 | endif |
|---|
| 471 | enddo |
|---|
| 472 | enddo |
|---|
| 473 | enddo |
|---|
| 474 | CALL ctl_stop( 'trcbio_medusa, NAN in incoming tracer field' ) |
|---|
| 475 | endif |
|---|
| 476 | ENDDO |
|---|
| 477 | CALL flush(numout) |
|---|
| 478 | # endif |
|---|
| 479 | |
|---|
| 480 | # if defined key_debug_medusa |
|---|
| 481 | IF (lwp) write (numout,*) 'trc_bio_medusa: variables initialised and checked' |
|---|
| 482 | CALL flush(numout) |
|---|
| 483 | # endif |
|---|
| 484 | |
|---|
| 485 | # if defined key_roam |
|---|
| 486 | !!---------------------------------------------------------------------- |
|---|
| 487 | !! calculate atmospheric pCO2 |
|---|
| 488 | !!---------------------------------------------------------------------- |
|---|
| 489 | !! |
|---|
| 490 | !! what's atmospheric pCO2 doing? (data start in 1859) |
|---|
| 491 | iyr1 = nyear - 1859 + 1 |
|---|
| 492 | iyr2 = iyr1 + 1 |
|---|
| 493 | if (iyr1 .le. 1) then |
|---|
| 494 | !! before 1860 |
|---|
| 495 | f_xco2a(:,:) = hist_pco2(1) |
|---|
| 496 | elseif (iyr2 .ge. 242) then |
|---|
| 497 | !! after 2099 |
|---|
| 498 | f_xco2a(:,:) = hist_pco2(242) |
|---|
| 499 | else |
|---|
| 500 | !! just right |
|---|
| 501 | fq0 = hist_pco2(iyr1) |
|---|
| 502 | fq1 = hist_pco2(iyr2) |
|---|
| 503 | fq2 = real(nsec_day) / (60.0 * 60.0 * 24.0) |
|---|
| 504 | !! AXY (14/06/12): tweaked to make more sense (and be correct) |
|---|
| 505 | # if defined key_bs_axy_yrlen |
|---|
| 506 | fq3 = (real(nday_year) - 1.0 + fq2) / 360.0 !! bugfix: for 360d year with HadGEM2-ES forcing |
|---|
| 507 | # else |
|---|
| 508 | fq3 = (real(nday_year) - 1.0 + fq2) / 365.0 !! original use of 365 days (not accounting for leap year or 360d year) |
|---|
| 509 | # endif |
|---|
| 510 | fq4 = (fq0 * (1.0 - fq3)) + (fq1 * fq3) |
|---|
| 511 | f_xco2a(:,:) = fq4 |
|---|
| 512 | endif |
|---|
| 513 | # if defined key_axy_pi_co2 |
|---|
| 514 | f_xco2a(:,:) = 284.725 !! OCMIP pre-industrial pCO2 |
|---|
| 515 | # endif |
|---|
| 516 | !! IF(lwp) WRITE(numout,*) ' MEDUSA nyear =', nyear |
|---|
| 517 | !! IF(lwp) WRITE(numout,*) ' MEDUSA nsec_day =', real(nsec_day) |
|---|
| 518 | !! IF(lwp) WRITE(numout,*) ' MEDUSA nday_year =', real(nday_year) |
|---|
| 519 | !! AXY (29/01/14): remove surplus diagnostics |
|---|
| 520 | !! IF(lwp) WRITE(numout,*) ' MEDUSA fq0 =', fq0 |
|---|
| 521 | !! IF(lwp) WRITE(numout,*) ' MEDUSA fq1 =', fq1 |
|---|
| 522 | !! IF(lwp) WRITE(numout,*) ' MEDUSA fq2 =', fq2 |
|---|
| 523 | !! IF(lwp) WRITE(numout,*) ' MEDUSA fq3 =', fq3 |
|---|
| 524 | IF(lwp) WRITE(numout,*) ' MEDUSA atm pCO2 =', f_xco2a(1,1) |
|---|
| 525 | # endif |
|---|
| 526 | |
|---|
| 527 | # if defined key_debug_medusa |
|---|
| 528 | IF (lwp) write (numout,*) 'trc_bio_medusa: ready for carbonate chemistry' |
|---|
| 529 | IF (lwp) write (numout,*) 'trc_bio_medusa: kt = ', kt |
|---|
| 530 | IF (lwp) write (numout,*) 'trc_bio_medusa: nittrc000 = ', nittrc000 |
|---|
| 531 | CALL flush(numout) |
|---|
| 532 | # endif |
|---|
| 533 | |
|---|
| 534 | # if defined key_roam |
|---|
| 535 | !! AXY (20/11/14): alter to call on first MEDUSA timestep and then every |
|---|
| 536 | !! month (this is hardwired as 960 timesteps but should |
|---|
| 537 | !! be calculated and done properly |
|---|
| 538 | !! IF( kt == nit000 .or. mod(kt,1920) == 0 ) THEN |
|---|
| 539 | !! IF( kt == nittrc000 .or. mod(kt,960) == 0 ) THEN |
|---|
| 540 | !!============================= |
|---|
| 541 | !! Jpalm -- 07-10-2016 -- need to change carb-chem frequency call : |
|---|
| 542 | !! we don't want to call on the first time-step of all run submission, |
|---|
| 543 | !! but only on the very first time-step, and then every month |
|---|
| 544 | !! So we call on nittrc000 if not restarted run, |
|---|
| 545 | !! else if one month after last call. |
|---|
| 546 | !! assume one month is 30d --> 3600*24*30 : 2592000s |
|---|
| 547 | !! try to call carb-chem at 1st month's tm-stp : x * 30d + 1*rdt(i.e: mod = rdt) |
|---|
| 548 | !! ++ need to pass carb-chem output var through restarts |
|---|
| 549 | If ( ( kt == nittrc000 .AND. .NOT.ln_rsttr ) .OR. mod(kt*rdt,2592000.) == rdt ) THEN |
|---|
| 550 | !!---------------------------------------------------------------------- |
|---|
| 551 | !! Calculate the carbonate chemistry for the whole ocean on the first |
|---|
| 552 | !! simulation timestep and every month subsequently; the resulting 3D |
|---|
| 553 | !! field of omega calcite is used to determine the depth of the CCD |
|---|
| 554 | !!---------------------------------------------------------------------- |
|---|
| 555 | CALL carb_chem( kt ) |
|---|
| 556 | |
|---|
| 557 | ENDIF |
|---|
| 558 | # endif |
|---|
| 559 | |
|---|
| 560 | # if defined key_debug_medusa |
|---|
| 561 | IF (lwp) write (numout,*) 'trc_bio_medusa: ready for full domain calculations' |
|---|
| 562 | CALL flush(numout) |
|---|
| 563 | # endif |
|---|
| 564 | |
|---|
| 565 | !!---------------------------------------------------------------------- |
|---|
| 566 | !! MEDUSA has unified equation through the water column |
|---|
| 567 | !! (Diff. from LOBSTER which has two sets: bio- and non-bio layers) |
|---|
| 568 | !! Statement below in LOBSTER is different: DO jk = 1, jpkbm1 |
|---|
| 569 | !!---------------------------------------------------------------------- |
|---|
| 570 | !! |
|---|
| 571 | !! NOTE: the ordering of the loops below differs from that of some other |
|---|
| 572 | !! models; looping over the vertical dimension is the outermost loop and |
|---|
| 573 | !! this complicates some calculations (e.g. storage of vertical fluxes |
|---|
| 574 | !! that can otherwise be done via a singular variable require 2D fields |
|---|
| 575 | !! here); however, these issues are relatively easily resolved, but the |
|---|
| 576 | !! loops CANNOT be reordered without potentially causing code efficiency |
|---|
| 577 | !! problems (e.g. array indexing means that reordering the loops would |
|---|
| 578 | !! require skipping between widely-spaced memory location; potentially |
|---|
| 579 | !! outside those immediately cached) |
|---|
| 580 | !! |
|---|
| 581 | !! OPEN vertical loop |
|---|
| 582 | DO jk = 1,jpk |
|---|
| 583 | !! OPEN horizontal loops |
|---|
| 584 | DO jj = 2,jpjm1 |
|---|
| 585 | DO ji = 2,jpim1 |
|---|
| 586 | !! OPEN wet point IF..THEN loop |
|---|
| 587 | if (tmask(ji,jj,jk) == 1) then |
|---|
| 588 | !!=========================================================== |
|---|
| 589 | !! SETUP LOCAL GRID CELL |
|---|
| 590 | !!=========================================================== |
|---|
| 591 | !! |
|---|
| 592 | !!----------------------------------------------------------- |
|---|
| 593 | !! Some notes on grid vertical structure |
|---|
| 594 | !! - fsdepw(ji,jj,jk) is the depth of the upper surface of |
|---|
| 595 | !! level jk |
|---|
| 596 | !! - fsde3w(ji,jj,jk) is *approximately* the midpoint of |
|---|
| 597 | !! level jk |
|---|
| 598 | !! - fse3t(ji,jj,jk) is the thickness of level jk |
|---|
| 599 | !!----------------------------------------------------------- |
|---|
| 600 | !! |
|---|
| 601 | !! AXY (01/03/10): set up level depth (bottom of level) |
|---|
| 602 | fdep1(ji,jj) = fsdepw(ji,jj,jk) + fse3t(ji,jj,jk) |
|---|
| 603 | !! AXY (28/11/16): local seafloor depth |
|---|
| 604 | !! previously mbathy(ji,jj) - 1, now |
|---|
| 605 | !! mbathy(ji,jj) |
|---|
| 606 | ! I should be able to remove this - marc 5/5/17 |
|---|
| 607 | ! mbathy(ji,jj) = mbathy(ji,jj) |
|---|
| 608 | !! |
|---|
| 609 | !! set up model tracers |
|---|
| 610 | !! negative values of state variables are not allowed to |
|---|
| 611 | !! contribute to the calculated fluxes |
|---|
| 612 | !! non-diatom chlorophyll |
|---|
| 613 | zchn(ji,jj) = max(0.,trn(ji,jj,jk,jpchn)) |
|---|
| 614 | !! diatom chlorophyll |
|---|
| 615 | zchd(ji,jj) = max(0.,trn(ji,jj,jk,jpchd)) |
|---|
| 616 | !! non-diatoms |
|---|
| 617 | zphn(ji,jj) = max(0.,trn(ji,jj,jk,jpphn)) |
|---|
| 618 | !! diatoms |
|---|
| 619 | zphd(ji,jj) = max(0.,trn(ji,jj,jk,jpphd)) |
|---|
| 620 | !! diatom silicon |
|---|
| 621 | zpds(ji,jj) = max(0.,trn(ji,jj,jk,jppds)) |
|---|
| 622 | !! AXY (28/01/10): probably need to take account of |
|---|
| 623 | !! chl/biomass connection |
|---|
| 624 | if (zchn(ji,jj).eq.0.) zphn(ji,jj) = 0. |
|---|
| 625 | if (zchd(ji,jj).eq.0.) zphd(ji,jj) = 0. |
|---|
| 626 | if (zphn(ji,jj).eq.0.) zchn(ji,jj) = 0. |
|---|
| 627 | if (zphd(ji,jj).eq.0.) zchd(ji,jj) = 0. |
|---|
| 628 | !! AXY (23/01/14): duh - why did I forget diatom silicon? |
|---|
| 629 | if (zpds(ji,jj).eq.0.) zphd(ji,jj) = 0. |
|---|
| 630 | if (zphd(ji,jj).eq.0.) zpds(ji,jj) = 0. |
|---|
| 631 | !! microzooplankton |
|---|
| 632 | zzmi(ji,jj) = max(0.,trn(ji,jj,jk,jpzmi)) |
|---|
| 633 | !! mesozooplankton |
|---|
| 634 | zzme(ji,jj) = max(0.,trn(ji,jj,jk,jpzme)) |
|---|
| 635 | !! detrital nitrogen |
|---|
| 636 | zdet(ji,jj) = max(0.,trn(ji,jj,jk,jpdet)) |
|---|
| 637 | !! dissolved inorganic nitrogen |
|---|
| 638 | zdin(ji,jj) = max(0.,trn(ji,jj,jk,jpdin)) |
|---|
| 639 | !! dissolved silicic acid |
|---|
| 640 | zsil(ji,jj) = max(0.,trn(ji,jj,jk,jpsil)) |
|---|
| 641 | !! dissolved "iron" |
|---|
| 642 | zfer(ji,jj) = max(0.,trn(ji,jj,jk,jpfer)) |
|---|
| 643 | # if defined key_roam |
|---|
| 644 | !! detrital carbon |
|---|
| 645 | zdtc(ji,jj) = max(0.,trn(ji,jj,jk,jpdtc)) |
|---|
| 646 | !! dissolved inorganic carbon |
|---|
| 647 | zdic(ji,jj) = max(0.,trn(ji,jj,jk,jpdic)) |
|---|
| 648 | !! alkalinity |
|---|
| 649 | zalk(ji,jj) = max(0.,trn(ji,jj,jk,jpalk)) |
|---|
| 650 | !! oxygen |
|---|
| 651 | zoxy(ji,jj) = max(0.,trn(ji,jj,jk,jpoxy)) |
|---|
| 652 | # if defined key_axy_carbchem && defined key_mocsy |
|---|
| 653 | !! phosphate via DIN and Redfield |
|---|
| 654 | zpho(ji,jj) = max(0.,trn(ji,jj,jk,jpdin)) / 16.0 |
|---|
| 655 | # endif |
|---|
| 656 | !! |
|---|
| 657 | !! also need physical parameters for gas exchange calculations |
|---|
| 658 | ztmp(ji,jj) = tsn(ji,jj,jk,jp_tem) |
|---|
| 659 | zsal(ji,jj) = tsn(ji,jj,jk,jp_sal) |
|---|
| 660 | !! |
|---|
| 661 | !! AXY (28/02/14): check input fields |
|---|
| 662 | if (ztmp(ji,jj) .lt. -3.0 .or. ztmp(ji,jj) .gt. 40.0 ) then |
|---|
| 663 | IF(lwp) WRITE(numout,*) ' trc_bio_medusa: T WARNING 2D, ', & |
|---|
| 664 | tsb(ji,jj,jk,jp_tem), tsn(ji,jj,jk,jp_tem), ' at (', & |
|---|
| 665 | ji, ',', jj, ',', jk, ') at time', kt |
|---|
| 666 | IF(lwp) WRITE(numout,*) ' trc_bio_medusa: T SWITCHING 2D, ',& |
|---|
| 667 | tsn(ji,jj,jk,jp_tem), ' -> ', tsb(ji,jj,jk,jp_tem) |
|---|
| 668 | !! temperatur |
|---|
| 669 | ztmp(ji,jj) = tsb(ji,jj,jk,jp_tem) |
|---|
| 670 | endif |
|---|
| 671 | if (zsal(ji,jj) .lt. 0.0 .or. zsal(ji,jj) .gt. 45.0 ) then |
|---|
| 672 | IF(lwp) WRITE(numout,*) ' trc_bio_medusa: S WARNING 2D, ', & |
|---|
| 673 | tsb(ji,jj,jk,jp_sal), tsn(ji,jj,jk,jp_sal), ' at (', & |
|---|
| 674 | ji, ',', jj, ',', jk, ') at time', kt |
|---|
| 675 | endif |
|---|
| 676 | # else |
|---|
| 677 | !! implicit detrital carbon |
|---|
| 678 | zdtc(ji,jj) = zdet(ji,jj) * xthetad |
|---|
| 679 | # endif |
|---|
| 680 | # if defined key_debug_medusa |
|---|
| 681 | if (idf.eq.1) then |
|---|
| 682 | !! AXY (15/01/10) |
|---|
| 683 | if (trn(ji,jj,jk,jpdin).lt.0.) then |
|---|
| 684 | IF (lwp) write (numout,*) '------------------------------' |
|---|
| 685 | IF (lwp) write (numout,*) 'NEGATIVE DIN ERROR =', & |
|---|
| 686 | trn(ji,jj,jk,jpdin) |
|---|
| 687 | IF (lwp) write (numout,*) 'NEGATIVE DIN ERROR @', & |
|---|
| 688 | ji, jj, jk, kt |
|---|
| 689 | endif |
|---|
| 690 | if (trn(ji,jj,jk,jpsil).lt.0.) then |
|---|
| 691 | IF (lwp) write (numout,*) '------------------------------' |
|---|
| 692 | IF (lwp) write (numout,*) 'NEGATIVE SIL ERROR =', & |
|---|
| 693 | trn(ji,jj,jk,jpsil) |
|---|
| 694 | IF (lwp) write (numout,*) 'NEGATIVE SIL ERROR @', & |
|---|
| 695 | ji, jj, jk, kt |
|---|
| 696 | endif |
|---|
| 697 | # if defined key_roam |
|---|
| 698 | if (trn(ji,jj,jk,jpdic).lt.0.) then |
|---|
| 699 | IF (lwp) write (numout,*) '------------------------------' |
|---|
| 700 | IF (lwp) write (numout,*) 'NEGATIVE DIC ERROR =', & |
|---|
| 701 | trn(ji,jj,jk,jpdic) |
|---|
| 702 | IF (lwp) write (numout,*) 'NEGATIVE DIC ERROR @', & |
|---|
| 703 | ji, jj, jk, kt |
|---|
| 704 | endif |
|---|
| 705 | if (trn(ji,jj,jk,jpalk).lt.0.) then |
|---|
| 706 | IF (lwp) write (numout,*) '------------------------------' |
|---|
| 707 | IF (lwp) write (numout,*) 'NEGATIVE ALK ERROR =', & |
|---|
| 708 | trn(ji,jj,jk,jpalk) |
|---|
| 709 | IF (lwp) write (numout,*) 'NEGATIVE ALK ERROR @', & |
|---|
| 710 | ji, jj, jk, kt |
|---|
| 711 | endif |
|---|
| 712 | if (trn(ji,jj,jk,jpoxy).lt.0.) then |
|---|
| 713 | IF (lwp) write (numout,*) '------------------------------' |
|---|
| 714 | IF (lwp) write (numout,*) 'NEGATIVE OXY ERROR =', & |
|---|
| 715 | trn(ji,jj,jk,jpoxy) |
|---|
| 716 | IF (lwp) write (numout,*) 'NEGATIVE OXY ERROR @', & |
|---|
| 717 | ji, jj, jk, kt |
|---|
| 718 | endif |
|---|
| 719 | # endif |
|---|
| 720 | endif |
|---|
| 721 | # endif |
|---|
| 722 | # if defined key_debug_medusa |
|---|
| 723 | !! report state variable values |
|---|
| 724 | if (idf.eq.1.AND.idfval.eq.1) then |
|---|
| 725 | IF (lwp) write (numout,*) '------------------------------' |
|---|
| 726 | IF (lwp) write (numout,*) 'fthk(',jk,') = ', fse3t(ji,jj,jk) |
|---|
| 727 | IF (lwp) write (numout,*) 'zphn(',jk,') = ', zphn(ji,jj) |
|---|
| 728 | IF (lwp) write (numout,*) 'zphd(',jk,') = ', zphd(ji,jj) |
|---|
| 729 | IF (lwp) write (numout,*) 'zpds(',jk,') = ', zpds(ji,jj) |
|---|
| 730 | IF (lwp) write (numout,*) 'zzmi(',jk,') = ', zzmi(ji,jj) |
|---|
| 731 | IF (lwp) write (numout,*) 'zzme(',jk,') = ', zzme(ji,jj) |
|---|
| 732 | IF (lwp) write (numout,*) 'zdet(',jk,') = ', zdet(ji,jj) |
|---|
| 733 | IF (lwp) write (numout,*) 'zdin(',jk,') = ', zdin(ji,jj) |
|---|
| 734 | IF (lwp) write (numout,*) 'zsil(',jk,') = ', zsil(ji,jj) |
|---|
| 735 | IF (lwp) write (numout,*) 'zfer(',jk,') = ', zfer(ji,jj) |
|---|
| 736 | # if defined key_roam |
|---|
| 737 | IF (lwp) write (numout,*) 'zdtc(',jk,') = ', zdtc(ji,jj) |
|---|
| 738 | IF (lwp) write (numout,*) 'zdic(',jk,') = ', zdic(ji,jj) |
|---|
| 739 | IF (lwp) write (numout,*) 'zalk(',jk,') = ', zalk(ji,jj) |
|---|
| 740 | IF (lwp) write (numout,*) 'zoxy(',jk,') = ', zoxy(ji,jj) |
|---|
| 741 | # endif |
|---|
| 742 | endif |
|---|
| 743 | # endif |
|---|
| 744 | |
|---|
| 745 | # if defined key_debug_medusa |
|---|
| 746 | if (idf.eq.1.AND.idfval.eq.1.AND.jk.eq.1) then |
|---|
| 747 | IF (lwp) write (numout,*) '------------------------------' |
|---|
| 748 | IF (lwp) write (numout,*) 'dust = ', dust(ji,jj) |
|---|
| 749 | endif |
|---|
| 750 | # endif |
|---|
| 751 | |
|---|
| 752 | !! sum tracers for inventory checks |
|---|
| 753 | IF( lk_iomput ) THEN |
|---|
| 754 | IF ( med_diag%INVTN%dgsave ) THEN |
|---|
| 755 | ftot_n(ji,jj) = ftot_n(ji,jj) + & |
|---|
| 756 | (fse3t(ji,jj,jk) * ( zphn(ji,jj) + zphd(ji,jj) + & |
|---|
| 757 | zzmi(ji,jj) + zzme(ji,jj) + & |
|---|
| 758 | zdet(ji,jj) + zdin(ji,jj) ) ) |
|---|
| 759 | ENDIF |
|---|
| 760 | IF ( med_diag%INVTSI%dgsave ) THEN |
|---|
| 761 | ftot_si(ji,jj) = ftot_si(ji,jj) + & |
|---|
| 762 | (fse3t(ji,jj,jk) * ( zpds(ji,jj) + zsil(ji,jj) ) ) |
|---|
| 763 | ENDIF |
|---|
| 764 | IF ( med_diag%INVTFE%dgsave ) THEN |
|---|
| 765 | ftot_fe(ji,jj) = ftot_fe(ji,jj) + & |
|---|
| 766 | (fse3t(ji,jj,jk) * ( xrfn * & |
|---|
| 767 | ( zphn(ji,jj) + zphd(ji,jj) + & |
|---|
| 768 | zzmi(ji,jj) + zzme(ji,jj) + & |
|---|
| 769 | zdet(ji,jj) ) + zfer(ji,jj) ) ) |
|---|
| 770 | ENDIF |
|---|
| 771 | # if defined key_roam |
|---|
| 772 | IF ( med_diag%INVTC%dgsave ) THEN |
|---|
| 773 | ftot_c(ji,jj) = ftot_c(ji,jj) + & |
|---|
| 774 | (fse3t(ji,jj,jk) * ( (xthetapn * zphn(ji,jj)) + & |
|---|
| 775 | (xthetapd * zphd(ji,jj)) + & |
|---|
| 776 | (xthetazmi * zzmi(ji,jj)) + & |
|---|
| 777 | (xthetazme * zzme(ji,jj)) + & |
|---|
| 778 | zdtc(ji,jj) + zdic(ji,jj) ) ) |
|---|
| 779 | ENDIF |
|---|
| 780 | IF ( med_diag%INVTALK%dgsave ) THEN |
|---|
| 781 | ftot_a(ji,jj) = ftot_a(ji,jj) + (fse3t(ji,jj,jk) * & |
|---|
| 782 | zalk(ji,jj)) |
|---|
| 783 | ENDIF |
|---|
| 784 | IF ( med_diag%INVTO2%dgsave ) THEN |
|---|
| 785 | ftot_o2(ji,jj) = ftot_o2(ji,jj) + (fse3t(ji,jj,jk) * & |
|---|
| 786 | zoxy(ji,jj)) |
|---|
| 787 | ENDIF |
|---|
| 788 | !! |
|---|
| 789 | !! AXY (10/11/16): CMIP6 diagnostics |
|---|
| 790 | IF ( med_diag%INTDISSIC%dgsave ) THEN |
|---|
| 791 | intdissic(ji,jj) = intdissic(ji,jj) + & |
|---|
| 792 | (fse3t(ji,jj,jk) * zdic(ji,jj)) |
|---|
| 793 | ENDIF |
|---|
| 794 | IF ( med_diag%INTDISSIN%dgsave ) THEN |
|---|
| 795 | intdissin(ji,jj) = intdissin(ji,jj) + & |
|---|
| 796 | (fse3t(ji,jj,jk) * zdin(ji,jj)) |
|---|
| 797 | ENDIF |
|---|
| 798 | IF ( med_diag%INTDISSISI%dgsave ) THEN |
|---|
| 799 | intdissisi(ji,jj) = intdissisi(ji,jj) + & |
|---|
| 800 | (fse3t(ji,jj,jk) * zsil(ji,jj)) |
|---|
| 801 | ENDIF |
|---|
| 802 | IF ( med_diag%INTTALK%dgsave ) THEN |
|---|
| 803 | inttalk(ji,jj) = inttalk(ji,jj) + & |
|---|
| 804 | (fse3t(ji,jj,jk) * zalk(ji,jj)) |
|---|
| 805 | ENDIF |
|---|
| 806 | IF ( med_diag%O2min%dgsave ) THEN |
|---|
| 807 | if ( zoxy(ji,jj) < o2min(ji,jj) ) then |
|---|
| 808 | o2min(ji,jj) = zoxy(ji,jj) |
|---|
| 809 | IF ( med_diag%ZO2min%dgsave ) THEN |
|---|
| 810 | !! layer midpoint |
|---|
| 811 | zo2min(ji,jj) = (fsdepw(ji,jj,jk) + & |
|---|
| 812 | fdep1(ji,jj)) / 2.0 |
|---|
| 813 | ENDIF |
|---|
| 814 | endif |
|---|
| 815 | ENDIF |
|---|
| 816 | # endif |
|---|
| 817 | ENDIF |
|---|
| 818 | |
|---|
| 819 | CALL flush(numout) |
|---|
| 820 | |
|---|
| 821 | ENDIF |
|---|
| 822 | ENDDO |
|---|
| 823 | ENDDO |
|---|
| 824 | |
|---|
| 825 | !!---------------------------------------------------------------- |
|---|
| 826 | !! Calculate air-sea gas exchange and river inputs |
|---|
| 827 | !!---------------------------------------------------------------- |
|---|
| 828 | IF ( jk == 1 ) THEN |
|---|
| 829 | call air_sea( kt ) |
|---|
| 830 | END IF |
|---|
| 831 | |
|---|
| 832 | # if defined key_roam |
|---|
| 833 | |
|---|
| 834 | ! Moved from above - marc 21/4/17 |
|---|
| 835 | ! I think this should be moved into diagnostics at bottom - it |
|---|
| 836 | ! doesn't like it is used anyway else - marc 21/4/17 |
|---|
| 837 | DO jj = 2,jpjm1 |
|---|
| 838 | DO ji = 2,jpim1 |
|---|
| 839 | !! OPEN wet point IF..THEN loop |
|---|
| 840 | if (tmask(ji,jj,jk) == 1) then |
|---|
| 841 | |
|---|
| 842 | !! AXY (11/11/16): CMIP6 oxygen saturation 3D diagnostic |
|---|
| 843 | IF ( med_diag%O2SAT3%dgsave ) THEN |
|---|
| 844 | call oxy_sato( ztmp(ji,jj), zsal(ji,jj), f_o2sat3 ) |
|---|
| 845 | o2sat3(ji, jj, jk) = f_o2sat3 |
|---|
| 846 | ENDIF |
|---|
| 847 | ENDIF |
|---|
| 848 | ENDDO |
|---|
| 849 | ENDDO |
|---|
| 850 | # endif |
|---|
| 851 | |
|---|
| 852 | !!------------------------------------------------------------------ |
|---|
| 853 | !! Phytoplankton growth, zooplankton grazing and miscellaneous |
|---|
| 854 | !! plankton losses. |
|---|
| 855 | !!------------------------------------------------------------------ |
|---|
| 856 | CALL plankton( jk ) |
|---|
| 857 | |
|---|
| 858 | !!---------------------------------------------------------------- |
|---|
| 859 | !! Iron chemistry and scavenging |
|---|
| 860 | !!---------------------------------------------------------------- |
|---|
| 861 | CALL iron_chem_scav( jk ) |
|---|
| 862 | |
|---|
| 863 | ! Miscellaneous processes - marc |
|---|
| 864 | |
|---|
| 865 | DO jj = 2,jpjm1 |
|---|
| 866 | DO ji = 2,jpim1 |
|---|
| 867 | !! OPEN wet point IF..THEN loop |
|---|
| 868 | if (tmask(ji,jj,jk) == 1) then |
|---|
| 869 | |
|---|
| 870 | !!---------------------------------------------------------------------- |
|---|
| 871 | !! Miscellaneous |
|---|
| 872 | !!---------------------------------------------------------------------- |
|---|
| 873 | !! |
|---|
| 874 | !! diatom frustule dissolution |
|---|
| 875 | fsdiss(ji,jj) = xsdiss * zpds(ji,jj) |
|---|
| 876 | |
|---|
| 877 | # if defined key_debug_medusa |
|---|
| 878 | !! report miscellaneous calculations |
|---|
| 879 | if (idf.eq.1.AND.idfval.eq.1) then |
|---|
| 880 | IF (lwp) write (numout,*) '------------------------------' |
|---|
| 881 | IF (lwp) write (numout,*) 'fsdiss(',jk,') = ', fsdiss(ji,jj) |
|---|
| 882 | endif |
|---|
| 883 | # endif |
|---|
| 884 | |
|---|
| 885 | !!---------------------------------------------------------------------- |
|---|
| 886 | !! Slow detritus creation |
|---|
| 887 | !!---------------------------------------------------------------------- |
|---|
| 888 | !! this variable integrates the creation of slow sinking detritus |
|---|
| 889 | !! to allow the split between fast and slow detritus to be |
|---|
| 890 | !! diagnosed |
|---|
| 891 | fslown(ji,jj) = fdpn(ji,jj) + fdzmi(ji,jj) + ((1.0 - xfdfrac1) * fdpd(ji,jj)) + & |
|---|
| 892 | ((1.0 - xfdfrac2) * fdzme(ji,jj)) + ((1.0 - xbetan) * (finmi(ji,jj) + finme(ji,jj))) |
|---|
| 893 | !! |
|---|
| 894 | !! this variable records the slow detrital sinking flux at this |
|---|
| 895 | !! particular depth; it is used in the output of this flux at |
|---|
| 896 | !! standard depths in the diagnostic outputs; needs to be |
|---|
| 897 | !! adjusted from per second to per day because of parameter vsed |
|---|
| 898 | fslownflux(ji,jj) = zdet(ji,jj) * vsed * 86400. |
|---|
| 899 | # if defined key_roam |
|---|
| 900 | !! |
|---|
| 901 | !! and the same for detrital carbon |
|---|
| 902 | fslowc(ji,jj) = (xthetapn * fdpn(ji,jj)) + (xthetazmi * fdzmi(ji,jj)) + & |
|---|
| 903 | (xthetapd * (1.0 - xfdfrac1) * fdpd(ji,jj)) + & |
|---|
| 904 | (xthetazme * (1.0 - xfdfrac2) * fdzme(ji,jj)) + & |
|---|
| 905 | ((1.0 - xbetac) * (ficmi(ji,jj) + ficme(ji,jj))) |
|---|
| 906 | !! |
|---|
| 907 | !! this variable records the slow detrital sinking flux at this |
|---|
| 908 | !! particular depth; it is used in the output of this flux at |
|---|
| 909 | !! standard depths in the diagnostic outputs; needs to be |
|---|
| 910 | !! adjusted from per second to per day because of parameter vsed |
|---|
| 911 | fslowcflux(ji,jj) = zdtc(ji,jj) * vsed * 86400. |
|---|
| 912 | # endif |
|---|
| 913 | |
|---|
| 914 | !!---------------------------------------------------------------------- |
|---|
| 915 | !! Nutrient regeneration |
|---|
| 916 | !! this variable integrates total nitrogen regeneration down the |
|---|
| 917 | !! watercolumn; its value is stored and output as a 2D diagnostic; |
|---|
| 918 | !! the corresponding dissolution flux of silicon (from sources |
|---|
| 919 | !! other than fast detritus) is also integrated; note that, |
|---|
| 920 | !! confusingly, the linear loss terms from plankton compartments |
|---|
| 921 | !! are labelled as fdX2 when one might have expected fdX or fdX1 |
|---|
| 922 | !!---------------------------------------------------------------------- |
|---|
| 923 | !! |
|---|
| 924 | !! nitrogen |
|---|
| 925 | fregen(ji,jj) = (( (xphi * (fgmipn(ji,jj) + fgmid(ji,jj))) + & ! messy feeding |
|---|
| 926 | (xphi * (fgmepn(ji,jj) + fgmepd(ji,jj) + fgmezmi(ji,jj) + fgmed(ji,jj))) + & ! messy feeding |
|---|
| 927 | fmiexcr(ji,jj) + fmeexcr(ji,jj) + fdd(ji,jj) + & ! excretion + D remin. |
|---|
| 928 | fdpn2(ji,jj) + fdpd2(ji,jj) + fdzmi2(ji,jj) + fdzme2(ji,jj)) * fse3t(ji,jj,jk)) ! linear mortality |
|---|
| 929 | !! |
|---|
| 930 | !! silicon |
|---|
| 931 | fregensi(ji,jj) = (( fsdiss(ji,jj) + ((1.0 - xfdfrac1) * fdpds(ji,jj)) + & ! dissolution + non-lin. mortality |
|---|
| 932 | ((1.0 - xfdfrac3) * fgmepds(ji,jj)) + & ! egestion by zooplankton |
|---|
| 933 | fdpds2(ji,jj)) * fse3t(ji,jj,jk)) ! linear mortality |
|---|
| 934 | # if defined key_roam |
|---|
| 935 | !! |
|---|
| 936 | !! carbon |
|---|
| 937 | ! Doesn't look this is used - marc 10/4/17 |
|---|
| 938 | ! fregenc(ji,jj) = (( (xphi * ((xthetapn * fgmipn(ji,jj)) + fgmidc(ji,jj))) + & ! messy feeding |
|---|
| 939 | ! (xphi * ((xthetapn * fgmepn(ji,jj)) + (xthetapd * fgmepd(ji,jj)) + & ! messy feeding |
|---|
| 940 | ! (xthetazmi * fgmezmi(ji,jj)) + fgmedc(ji,jj))) + & ! messy feeding |
|---|
| 941 | ! fmiresp(ji,jj) + fmeresp(ji,jj) + fddc(ji,jj) + & ! respiration + D remin. |
|---|
| 942 | ! (xthetapn * fdpn2(ji,jj)) + (xthetapd * fdpd2(ji,jj)) + & ! linear mortality |
|---|
| 943 | ! (xthetazmi * fdzmi2(ji,jj)) + (xthetazme * fdzme2(ji,jj))) * fse3t(ji,jj,jk)) ! linear mortality |
|---|
| 944 | # endif |
|---|
| 945 | |
|---|
| 946 | ENDIF |
|---|
| 947 | ENDDO |
|---|
| 948 | ENDDO |
|---|
| 949 | |
|---|
| 950 | !!------------------------------------------------------------------ |
|---|
| 951 | !! Detritus process |
|---|
| 952 | !!------------------------------------------------------------------ |
|---|
| 953 | CALL detritus( jk, iball ) |
|---|
| 954 | |
|---|
| 955 | !!------------------------------------------------------------------ |
|---|
| 956 | !! Updating tracers |
|---|
| 957 | !!------------------------------------------------------------------ |
|---|
| 958 | CALL bio_medusa_update( kt, jk ) |
|---|
| 959 | |
|---|
| 960 | !!------------------------------------------------------------------ |
|---|
| 961 | !! Diagnostics |
|---|
| 962 | !!------------------------------------------------------------------ |
|---|
| 963 | CALL bio_medusa_diag( kt, jk ) |
|---|
| 964 | |
|---|
| 965 | IF( lk_iomput .AND. .NOT. ln_diatrc ) THEN |
|---|
| 966 | |
|---|
| 967 | !!------------------------------------------------------- |
|---|
| 968 | !! 2d specific k level diags |
|---|
| 969 | !!------------------------------------------------------- |
|---|
| 970 | CALL bio_medusa_diag_slice( jk ) |
|---|
| 971 | |
|---|
| 972 | ENDIF |
|---|
| 973 | |
|---|
| 974 | !! CLOSE vertical loop |
|---|
| 975 | ENDDO |
|---|
| 976 | |
|---|
| 977 | !!---------------------------------------------------------------------- |
|---|
| 978 | !! Final calculations for diagnostics |
|---|
| 979 | !!---------------------------------------------------------------------- |
|---|
| 980 | CALL bio_medusa_fin( kt ) |
|---|
| 981 | |
|---|
| 982 | # if defined key_trc_diabio |
|---|
| 983 | !! Lateral boundary conditions on trcbio |
|---|
| 984 | DO jn=1,jp_medusa_trd |
|---|
| 985 | CALL lbc_lnk(trbio(:,:,1,jn),'T',1. ) |
|---|
| 986 | ENDDO |
|---|
| 987 | # endif |
|---|
| 988 | |
|---|
| 989 | # if defined key_debug_medusa |
|---|
| 990 | IF(lwp) WRITE(numout,*) ' MEDUSA exiting trc_bio_medusa at kt =', kt |
|---|
| 991 | CALL flush(numout) |
|---|
| 992 | # endif |
|---|
| 993 | |
|---|
| 994 | END SUBROUTINE trc_bio_medusa |
|---|
| 995 | |
|---|
| 996 | #else |
|---|
| 997 | !!====================================================================== |
|---|
| 998 | !! Dummy module : No MEDUSA bio-model |
|---|
| 999 | !!====================================================================== |
|---|
| 1000 | CONTAINS |
|---|
| 1001 | SUBROUTINE trc_bio_medusa( kt ) ! Empty routine |
|---|
| 1002 | INTEGER, INTENT( in ) :: kt |
|---|
| 1003 | WRITE(*,*) 'trc_bio_medusa: You should not have seen this print! error?', kt |
|---|
| 1004 | END SUBROUTINE trc_bio_medusa |
|---|
| 1005 | #endif |
|---|
| 1006 | |
|---|
| 1007 | !!====================================================================== |
|---|
| 1008 | END MODULE trcbio_medusa |
|---|
