Changeset 7766


Ignore:
Timestamp:
2017-03-07T19:30:03+01:00 (4 years ago)
Author:
jpalmier
Message:

JPALM — adapted MEDUSA_SBC to coupled mode, and merged this branch with RICHARD s fixes_part2 branch

Location:
branches/NERC/dev_r5518_NOC_MEDUSA_Stable/NEMOGCM
Files:
2 deleted
10 edited

Legend:

Unmodified
Added
Removed
  • branches/NERC/dev_r5518_NOC_MEDUSA_Stable/NEMOGCM/CONFIG/SHARED/iodef_medusa_et_al.xml

    r7516 r7766  
    11<!-- GO6.0 version of the XIOS namelist --> 
    2 <!-- XIOS2 version namelist --> 
    3  
     2<!-- XIOS version 2 --> 
    43<?xml version="1.0"?> 
     4 
    55<simulation>  
    66 
    7  <context id="nemo" time_origin="1950-01-01 00:00:00" > 
     7 <context id="nemo"> 
    88     
    99    <!-- $id$ --> 
     
    1515============================================================================================================ 
    1616    --> 
     17    <field_definition src="./field_def_bgc.xml"/> 
    1718    <field_definition src="./field_def.xml"/> 
    18     <field_definition src="./field_def_bgc.xml"/> 
    1919    <!--  
    2020============================================================================================================ 
     
    2424============================================================================================================ 
    2525    --> 
    26      
    27     <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="10d" min_digits="4"> 
     26 
     27    <file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1mo" min_digits="4"> 
    2828     
    2929      <file_group id="1ts" output_freq="1ts"  output_level="10" enabled=".TRUE."/> <!-- 1 time step files --> 
     
    3333      <file_group id="3h" output_freq="3h"  output_level="10" enabled=".TRUE."/> <!-- 3h files -->      
    3434      <file_group id="4h" output_freq="4h"  output_level="10" enabled=".TRUE."/> <!-- 4h files --> 
    35       <file_group id="6h" output_freq="6h"  output_level="10" enabled=".FALSE."> <!-- 6h files --> 
    36         <file id="file8" name_suffix="_UK_shelf" description="Forcings for the UK shelf seas model" > 
    37           <field field_ref="toce"         name="votemper"     grid_ref="grid_T_3D_zoom"    operation="instant" standard_name="sea_water_potential_temperature"/>  
    38           <field field_ref="soce"         name="vosaline"     grid_ref="grid_T_3D_zoom"    operation="instant" standard_name="sea_water_salinity"/>    
    39           <field field_ref="ssh"          name="sossheig"     grid_ref="grid_T_2D_zoom"    operation="instant" standard_name="sea_surface_height_above_geoid"/> 
    40           <field field_ref="uoce"         name="vozocrtx"     grid_ref="grid_U_3D_zoom"    operation="instant" standard_name="sea_water_x_velocity"/> 
    41           <field field_ref="voce"         name="vomecrty"     grid_ref="grid_V_3D_zoom"    operation="instant" standard_name="sea_water_y_velocity"/> 
    42           <field field_ref="ubar"         name="ubar"         grid_ref="grid_U_3D_zoom"    operation="instant" standard_name="ocean_barotropic_current_along_i-axis"/> 
    43           <field field_ref="vbar"         name="vbar"         grid_ref="grid_V_3D_zoom"    operation="instant" standard_name="ocean_barotropic_current_along_j-axis"/> 
    44         </file> 
    45       </file_group> 
     35      <file_group id="6h" output_freq="6h"  output_level="10" enabled=".TRUE."/> <!-- 6h files --> 
    4636      
    4737      <file_group id="1d" output_freq="1d"  output_level="10" enabled=".TRUE."/> <!-- 1d files --> 
    4838      <file_group id="3d" output_freq="3d"  output_level="10" enabled=".TRUE."/> <!-- 3d files -->     
    4939 
    50       <file_group id="10d" output_freq="10d"  output_level="10" enabled=".TRUE.">  <!-- 10d files -->    
    51      
     40      <file_group id="10d" output_freq="10d" output_level="10" enabled=".TRUE."> <!-- 10d files --> 
     41 
    5242   <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" > 
    53           <field_group group_ref="SPIN-UP_T" /> 
     43          <field field_ref="e3t"          name="e3t"        standard_name="cell_thickness" /> 
     44          <field field_ref="toce"         name="votemper"        operation="average" freq_op="1mo" > @toce_e3t / @e3t </field> 
     45          <field field_ref="toce"         name="votemper2"       operation="average" freq_op="1mo" > @toce2_e3t / @e3t </field> 
     46          <field field_ref="soce"         name="vosaline"        operation="average" freq_op="1mo" > @soce_e3t / @e3t </field> 
     47          <field field_ref="soce"         name="vosaline2"       operation="average" freq_op="1mo" > @soce2_e3t / @e3t </field> 
     48          <field field_ref="ttrd_totad"   name="opottempadvect"  operation="average" freq_op="1mo" > @ttrd_totad_e3t * 1026.0 * 3991.86795711963 </field> 
     49          <field field_ref="ttrd_iso"     name="opottemppmdiff"  operation="average" freq_op="1mo" > @ttrd_iso_e3t * 1026.0 * 3991.86795711963 </field> 
     50          <field field_ref="ttrd_zdfp"    name="opottempdiff"    operation="average" freq_op="1mo" > @ttrd_zdfp_e3t * 1026.0 * 3991.86795711963 </field> 
     51          <field field_ref="ttrd_evd"     name="ttrd_evd"        operation="average" freq_op="1mo" > @ttrd_evd_e3t / @e3t </field> 
     52          <field field_ref="ttrd_qns"     name="ttrd_qns"        operation="average" freq_op="1mo" > @ttrd_qns_e3t / @e3t_surf </field> 
     53          <field field_ref="ttrd_qsr"     name="rsdoabsorb"      operation="average" freq_op="1mo" > @ttrd_qsr_e3t * 1026.0 * 3991.86795711963 </field> 
     54          <field field_ref="ttrd_bbl"     name="ttrd_bbl"        operation="average" freq_op="1mo" > @ttrd_bbl_e3t / @e3t </field> 
     55          <field field_ref="ttrd_tot"     name="opottemptend"    operation="average" freq_op="1mo" > @ttrd_tot_e3t * 1026.0 * 3991.86795711963 </field> 
     56          <field field_ref="strd_totad"   name="osaltadvect"     operation="average" freq_op="1mo" > @strd_totad_e3t * 1026.0 * 0.001 </field> 
     57          <field field_ref="strd_iso"     name="osaltpmdiff"     operation="average" freq_op="1mo" > @strd_iso_e3t * 1026.0 * 0.001  </field> 
     58          <field field_ref="strd_zdfp"    name="osaltdiff"       operation="average" freq_op="1mo" > @strd_zdfp_e3t * 1026.0 * 0.001  </field> 
     59          <field field_ref="strd_evd"     name="strd_evd"        operation="average" freq_op="1mo" > @strd_evd_e3t / @e3t </field> 
     60          <field field_ref="strd_tot"     name="osalttend"       operation="average" freq_op="1mo" > @strd_tot_e3t * 1026.0 * 0.001 </field> 
     61          <field field_ref="strd_bbl"     name="strd_bbl"        operation="average" freq_op="1mo" > @strd_bbl_e3t / @e3t </field> 
     62     <field field_ref="ssh"          name="sossheig"   standard_name="sea_surface_height_above_geoid"                          /> 
     63          <field field_ref="ssh2"         name="zossq"      standard_name="square_of_sea_surface_height_above_geoid"                /> 
     64     <field field_ref="empmr"        name="sowaflup"   standard_name="water_flux_out_of_sea_ice_and_sea_water"                 /> 
     65     <field field_ref="saltflx"      name="sosafldo"   standard_name="salt_flux_into_sea_water"                                /> 
     66     <field field_ref="qt"           name="sohefldo"   standard_name="surface_downward_heat_flux_in_sea_water"                 /> 
     67     <field field_ref="qsr"          name="soshfldo"   standard_name="downwelling_photosynthetic_radiative_flux_in_sea_water"               /> 
     68          <field field_ref="mldkz5"       name="somixhgt"   standard_name="ocean_mixed_layer_thickness_defined_by_vertical_tracer_diffusivity"   /> 
     69          <field field_ref="mldr10_1"     name="somxl010"   standard_name="ocean_mixed_layer_thickness_defined_by_sigma_theta"      /> 
     70          <field field_ref="mldzint_1"    name="sokaraml"   standard_name="ocean_mixed_layer_thickness"                             /> 
     71          <field field_ref="mldzint_2"    name="somlddbm"   standard_name="ocean_mixed_layer_thickness"                             /> 
     72          <field field_ref="ice_cover"    name="soicecov"   standard_name="sea_ice_area_fraction"                                   /> 
     73          <field field_ref="wspd"         name="sowindsp"   standard_name="wind_speed"                                              />           
     74          <field field_ref="qhcisf"       name="sohflisf"   standard_name="ice_shelf_heat_flux"                                                        /> 
     75          <field field_ref="qlatisf"      name="soqlatisf"  standard_name="ice_shelf_latent_heat_flux"                                                        /> 
     76          <field field_ref="fwfisf"       name="sowflisf"   standard_name="ice_shelf_melting"                                                        /> 
     77          <field field_ref="berg_total_melt"       name="berg_total_melt"          standard_name=""                                 /> 
     78          <field field_ref="berg_total_heat_flux"  name="berg_total_heat_flux"     standard_name=""                                 /> 
     79          <field field_ref="runoffs"       name="sorunoff"    standard_name="water_flux_into_sea_water_from_rivers"                 /> 
     80          <field field_ref="hflx_rain_cea" name="hfrainds"    standard_name="temperature_flux_due_to_rainfall_expressed_as_heat_flux_into_sea_water"/> 
     81          <field field_ref="hflx_evap_cea" name="hfevapds"    standard_name="temperature_flux_due_to_evaporation_expressed_as_heat_flux_out_of_sea_water"/> 
     82          <field field_ref="evap_ao_cea"   name="evap_ao_cea" standard_name="water_evaporation_flux"                                /> 
     83          <field field_ref="rain"          name="pr"          standard_name="rainfall_flux"                                         /> 
     84          <field field_ref="snowpre"       name="snowpre"     standard_name="snowfall_flux"                                         /> 
     85          <field field_ref="snow_ao_cea"   name="snow_ao_cea" standard_name="snowfall_flux_over_ocean"                              /> 
     86          <field field_ref="snow_ai_cea"   name="snow_ai_cea" standard_name="snowfall_flux_over_sea_ice"                            /> 
    5487   </file> 
    5588    
    5689   <file id="file2" name_suffix="_grid_U" description="ocean U grid variables" > 
    57           <field_group group_ref="SPIN-UP_U" />  
     90          <field field_ref="e3u"          name="e3u"        standard_name="cell_thickness" /> 
     91          <field field_ref="uoce"         name="vozocrtx"     operation="average" freq_op="1mo" > @uoce_e3u / @e3u </field> 
     92          <field field_ref="uoce"         name="vozocrtx2"    operation="average" freq_op="1mo" > @uoce2_e3u / @e3u </field> 
     93          <field field_ref="ut"           name="ut"           operation="average" freq_op="1mo" > @ut_e3u / @e3u </field> 
     94          <field field_ref="us"           name="us"           operation="average" freq_op="1mo" > @us_e3u / @e3u </field> 
     95     <field field_ref="utau"         name="sozotaux"   standard_name="surface_downward_x_stress" /> 
    5896   </file> 
    5997    
    6098   <file id="file3" name_suffix="_grid_V" description="ocean V grid variables" > 
    61           <field_group group_ref="SPIN-UP_V" /> 
    62    </file> 
    63  
    64    <file id="file4" name_suffix="_grid_W" description="ocean W grid variables" > 
    65           <field_group group_ref="SPIN-UP_W" /> 
     99          <field field_ref="e3v"          name="e3v"        standard_name="cell_thickness" /> 
     100          <field field_ref="voce"         name="vomecrty"     operation="average" freq_op="1mo" > @voce_e3v / @e3v </field> 
     101          <field field_ref="voce"         name="vomecrty2"    operation="average" freq_op="1mo" > @voce2_e3v / @e3v </field> 
     102          <field field_ref="vt"           name="vt"           operation="average" freq_op="1mo" > @vt_e3v / @e3v </field> 
     103          <field field_ref="vs"           name="vs"           operation="average" freq_op="1mo" > @vs_e3v / @e3v </field> 
     104     <field field_ref="vtau"         name="sometauy"   standard_name="surface_downward_y_stress" /> 
    66105   </file> 
    67106    
    68    <file id="file5" name_suffix="_diaptr" description="process diagnostics" > 
    69           <field_group group_ref="SPIN-UP_diaptr" /> 
    70    </file>   
    71     
     107   <file id="file4" name_suffix="_grid_W" description="ocean W grid variables" > 
     108     <field field_ref="woce"         name="vovecrtz"   standard_name="upward_sea_water_velocity"                         /> 
     109          <field field_ref="wt"           name="wt"         standard_name=""                                                  /> 
     110          <field field_ref="ws"           name="ws"         standard_name=""                                                  /> 
     111     <field field_ref="avt"          name="votkeavt"   standard_name="ocean_vertical_heat_diffusivity"                   /> 
     112          <field field_ref="avm"          name="votkeavm"   standard_name="ocean_vertical_momentum_diffusivity"               /> 
     113          <field field_ref="aht2d"        name="soleahtw"   standard_name="vertical_component_of_ocean_xy_tracer_diffusivity" /> 
     114   </file> 
     115         
     116        <file id="file5" name_suffix="_diaptr" description="processed diagnostics" > 
     117     <field field_ref="zomsfglo"     name="zomsfglo"   standard_name="meridional_streamfunction_global"           grid_ref="gznl_W_3D"       /> 
     118          <field field_ref="zotemglo"     name="zotemglo"   standard_name="zonal_mean_temperature_global"              grid_ref="gznl_T_3D"       /> 
     119          <field field_ref="zosrfglo"     name="zosrfglo"   standard_name="zonal_mean_surface_global"                  grid_ref="gznl_T_3D"       /> 
     120     <field field_ref="zosalglo"     name="zosalglo"   standard_name="zonal_mean_salinity_global"                 grid_ref="gznl_T_3D"       />           
     121          <field field_ref="zomsfatl"     name="zomsfatl"   standard_name="meridional_streamfunction_atlantic"         grid_ref="gznl_W_3D"       /> 
     122          <field field_ref="zotematl"     name="zotematl"   standard_name="zonal_mean_temperature_atlantic"            grid_ref="gznl_T_3D"       /> 
     123          <field field_ref="zosrfatl"     name="zosrfatl"   standard_name="zonal_mean_surface_atlantic"                grid_ref="gznl_T_3D"       /> 
     124     <field field_ref="zosalatl"     name="zosalatl"   standard_name="zonal_mean_salinity_atlantic"               grid_ref="gznl_T_3D"       />           
     125          <field field_ref="zomsfpac"     name="zomsfpac"   standard_name="meridional_streamfunction_pacific"          grid_ref="gznl_W_3D"       /> 
     126          <field field_ref="zotempac"     name="zotempac"   standard_name="zonal_mean_temperature_pacific"             grid_ref="gznl_T_3D"       /> 
     127          <field field_ref="zosrfpac"     name="zosrfpac"   standard_name="zonal_mean_surface_pacific"                 grid_ref="gznl_T_3D"       /> 
     128     <field field_ref="zosalpac"     name="zosalpac"   standard_name="zonal_mean_salinity_pacific"                grid_ref="gznl_T_3D"       /> 
     129          <field field_ref="zomsfind"     name="zomsfind"   standard_name="meridional_streamfunction_indian"           grid_ref="gznl_W_3D"       /> 
     130          <field field_ref="zotemind"     name="zotemind"   standard_name="zonal_mean_temperature_indian"              grid_ref="gznl_T_3D"       /> 
     131          <field field_ref="zosrfind"     name="zosrfind"   standard_name="zonal_mean_surface_indian"                  grid_ref="gznl_T_3D"       /> 
     132     <field field_ref="zosalind"     name="zosalind"   standard_name="zonal_mean_salinity_indian"                 grid_ref="gznl_T_3D"       />           
     133          <field field_ref="zomsfipc"     name="zomsfipc"   standard_name="meridional_streamfunction_indian_pacific"   grid_ref="gznl_W_3D"       /> 
     134          <field field_ref="zotemipc"     name="zotemipc"   standard_name="zonal_mean_temperature_indian_pacific"      grid_ref="gznl_T_3D"       /> 
     135          <field field_ref="zosrfipc"     name="zosrfipc"   standard_name="zonal_mean_surface_indian_pacific"          grid_ref="gznl_T_3D"       /> 
     136     <field field_ref="zosalipc"     name="zosalipc"   standard_name="zonal_mean_salinity_indian_pacific"         grid_ref="gznl_T_3D"       />           
     137          <field field_ref="sophtadv"     name="sophtadv"   standard_name="advective_heat_transport"                   grid_ref="gznl_T_2D"       /> 
     138          <field field_ref="sopstadv"     name="sopstadv"   standard_name="advective_salt_transport"                   grid_ref="gznl_T_2D"       /> 
     139          <field field_ref="sophtldf"     name="sophtldf"   standard_name="diffusive_heat_transport"                   grid_ref="gznl_T_2D"       /> 
     140          <field field_ref="sopstldf"     name="sopstldf"   standard_name="diffusive_salt_transport"                   grid_ref="gznl_T_2D"       /> 
     141          <field field_ref="sophtadv_atl" name="sophtadv_atl"   standard_name="advective_heat_transport_atlantic"      grid_ref="gznl_T_2D"       /> 
     142          <field field_ref="sopstadv_atl" name="sopstadv_atl"   standard_name="advective_salt_transport_atlantic"      grid_ref="gznl_T_2D"       /> 
     143          <field field_ref="sophtldf_atl" name="sophtldf_atl"   standard_name="diffusive_heat_transport_atlantic"      grid_ref="gznl_T_2D"       /> 
     144          <field field_ref="sopstldf_atl" name="sopstldf_atl"   standard_name="diffusive_salt_transport_atlantic"      grid_ref="gznl_T_2D"       /> 
     145          <field field_ref="sophtadv_pac" name="sophtadv_pac"   standard_name="advective_heat_transport_pacific"       grid_ref="gznl_T_2D"       /> 
     146          <field field_ref="sopstadv_pac" name="sopstadv_pac"   standard_name="advective_salt_transport_pacific"       grid_ref="gznl_T_2D"       /> 
     147          <field field_ref="sophtldf_pac" name="sophtldf_pac"   standard_name="diffusive_heat_transport_pacific"       grid_ref="gznl_T_2D"       /> 
     148          <field field_ref="sopstldf_pac" name="sopstldf_pac"   standard_name="diffusive_salt_transport_pacific"       grid_ref="gznl_T_2D"       /> 
     149          <field field_ref="sophtadv_ind" name="sophtadv_ind"   standard_name="advective_heat_transport_indian"        grid_ref="gznl_T_2D"       /> 
     150          <field field_ref="sopstadv_ind" name="sopstadv_ind"   standard_name="advective_salt_transport_indian"        grid_ref="gznl_T_2D"       /> 
     151          <field field_ref="sophtldf_ind" name="sophtldf_ind"   standard_name="diffusive_heat_transport_indian"        grid_ref="gznl_T_2D"       /> 
     152          <field field_ref="sopstldf_ind" name="sopstldf_ind"   standard_name="diffusive_salt_transport_indian"        grid_ref="gznl_T_2D"       /> 
     153          <field field_ref="sophtadv_ipc" name="sophtadv_ipc"   standard_name="advective_heat_transport_indopacific"   grid_ref="gznl_T_2D"       /> 
     154          <field field_ref="sopstadv_ipc" name="sopstadv_ipc"   standard_name="advective_salt_transport_indopacific"   grid_ref="gznl_T_2D"       /> 
     155          <field field_ref="sophtldf_ipc" name="sophtldf_ipc"   standard_name="diffusive_heat_transport_indopacific"   grid_ref="gznl_T_2D"       /> 
     156          <field field_ref="sopstldf_ipc" name="sopstldf_ipc"   standard_name="diffusive_salt_transport_indopacific"   grid_ref="gznl_T_2D"       /> 
     157   </file> 
     158 
    72159        <file id="file6" name_suffix="_ptrc_T" description="Medusa sms variables" > 
    73160          <field_group group_ref="groupMEDUSA" /> 
     
    89176       
    90177   
    91       <!-- file_group id="1m" output_freq="1mo" split_freq="1mo" output_level="10" enabled=".TRUE." --> <!-- 1mo files -->    
    92       <file_group id="1m" output_freq="1mo" output_level="10" enabled=".FALSE.">  <!-- 1mo files -->    
     178      <file_group id="1m" output_freq="1mo" split_freq="1mo" output_level="10" enabled=".FALSE."> <!-- 1mo files -->    
     179      <!-- <file_group id="1m" output_freq="1mo" output_level="10" enabled=".TRUE.">  - 1mo files -->    
    93180 
    94181        <file id="file9" name_suffix="_grid_T" description="ocean T grid variables" > 
    95           <field_group group_ref="SPIN-UP_T" /> 
    96    </file> 
    97     
     182          <field field_ref="e3t"          name="e3t"        standard_name="cell_thickness" /> 
     183          <field field_ref="toce"         name="votemper"        operation="average" freq_op="1mo" > @toce_e3t / @e3t </field> 
     184          <field field_ref="toce"         name="votemper2"       operation="average" freq_op="1mo" > @toce2_e3t / @e3t </field> 
     185          <field field_ref="soce"         name="vosaline"        operation="average" freq_op="1mo" > @soce_e3t / @e3t </field> 
     186          <field field_ref="soce"         name="vosaline2"       operation="average" freq_op="1mo" > @soce2_e3t / @e3t </field> 
     187          <field field_ref="ttrd_totad"   name="opottempadvect"  operation="average" freq_op="1mo" > @ttrd_totad_e3t * 1026.0 * 3991.86795711963 </field> 
     188          <field field_ref="ttrd_iso"     name="opottemppmdiff"  operation="average" freq_op="1mo" > @ttrd_iso_e3t * 1026.0 * 3991.86795711963 </field> 
     189          <field field_ref="ttrd_zdfp"    name="opottempdiff"    operation="average" freq_op="1mo" > @ttrd_zdfp_e3t * 1026.0 * 3991.86795711963 </field> 
     190          <field field_ref="ttrd_evd"     name="ttrd_evd"        operation="average" freq_op="1mo" > @ttrd_evd_e3t / @e3t </field> 
     191          <field field_ref="ttrd_qns"     name="ttrd_qns"        operation="average" freq_op="1mo" > @ttrd_qns_e3t / @e3t_surf </field> 
     192          <field field_ref="ttrd_qsr"     name="rsdoabsorb"      operation="average" freq_op="1mo" > @ttrd_qsr_e3t * 1026.0 * 3991.86795711963 </field> 
     193          <field field_ref="ttrd_bbl"     name="ttrd_bbl"        operation="average" freq_op="1mo" > @ttrd_bbl_e3t / @e3t </field> 
     194          <field field_ref="ttrd_tot"     name="opottemptend"    operation="average" freq_op="1mo" > @ttrd_tot_e3t * 1026.0 * 3991.86795711963 </field> 
     195          <field field_ref="strd_totad"   name="osaltadvect"     operation="average" freq_op="1mo" > @strd_totad_e3t * 1026.0 * 0.001 </field> 
     196          <field field_ref="strd_iso"     name="osaltpmdiff"     operation="average" freq_op="1mo" > @strd_iso_e3t * 1026.0 * 0.001  </field> 
     197          <field field_ref="strd_zdfp"    name="osaltdiff"       operation="average" freq_op="1mo" > @strd_zdfp_e3t * 1026.0 * 0.001  </field> 
     198          <field field_ref="strd_evd"     name="strd_evd"        operation="average" freq_op="1mo" > @strd_evd_e3t / @e3t </field> 
     199          <field field_ref="strd_tot"     name="osalttend"       operation="average" freq_op="1mo" > @strd_tot_e3t * 1026.0 * 0.001 </field> 
     200          <field field_ref="strd_bbl"     name="strd_bbl"        operation="average" freq_op="1mo" > @strd_bbl_e3t / @e3t </field> 
     201          <field field_ref="ssh"          name="sossheig"   standard_name="sea_surface_height_above_geoid"                          /> 
     202          <field field_ref="ssh2"         name="zossq"      standard_name="square_of_sea_surface_height_above_geoid"                /> 
     203          <field field_ref="empmr"        name="sowaflup"   standard_name="water_flux_out_of_sea_ice_and_sea_water"                 /> 
     204          <field field_ref="saltflx"      name="sosafldo"   standard_name="salt_flux_into_sea_water"                                /> 
     205          <field field_ref="qt"           name="sohefldo"   standard_name="surface_downward_heat_flux_in_sea_water"                 /> 
     206          <field field_ref="qsr"          name="soshfldo"   standard_name="downwelling_photosynthetic_radiative_flux_in_sea_water"               /> 
     207          <field field_ref="mldkz5"       name="somixhgt"   standard_name="ocean_mixed_layer_thickness_defined_by_vertical_tracer_diffusivity"   /> 
     208          <field field_ref="mldr10_1"     name="somxl010"   standard_name="ocean_mixed_layer_thickness_defined_by_sigma_theta"      /> 
     209          <field field_ref="mldzint_1"    name="sokaraml"   standard_name="ocean_mixed_layer_thickness"                             /> 
     210          <field field_ref="mldzint_2"    name="somlddbm"   standard_name="ocean_mixed_layer_thickness"                             /> 
     211          <field field_ref="ice_cover"    name="soicecov"   standard_name="sea_ice_area_fraction"                                   /> 
     212          <field field_ref="wspd"         name="sowindsp"   standard_name="wind_speed"                                              /> 
     213          <field field_ref="qhcisf"       name="sohflisf"   standard_name="ice_shelf_heat_flux"                                                        /> 
     214          <field field_ref="qlatisf"      name="soqlatisf"  standard_name="ice_shelf_latent_heat_flux"                                                        /> 
     215          <field field_ref="fwfisf"       name="sowflisf"   standard_name="ice_shelf_melting"                                                        /> 
     216          <field field_ref="berg_total_melt"       name="berg_total_melt"          standard_name=""                                 /> 
     217          <field field_ref="berg_total_heat_flux"  name="berg_total_heat_flux"     standard_name=""                                 /> 
     218          <field field_ref="runoffs"       name="sorunoff"    standard_name="water_flux_into_sea_water_from_rivers"                 /> 
     219          <field field_ref="hflx_rain_cea" name="hfrainds"    standard_name="temperature_flux_due_to_rainfall_expressed_as_heat_flux_into_sea_water"/> 
     220          <field field_ref="hflx_evap_cea" name="hfevapds"    standard_name="temperature_flux_due_to_evaporation_expressed_as_heat_flux_out_of_sea_water"/> 
     221          <field field_ref="evap_ao_cea"   name="evap_ao_cea" standard_name="water_evaporation_flux"                                /> 
     222          <field field_ref="rain"          name="pr"          standard_name="rainfall_flux"                                         /> 
     223          <field field_ref="snowpre"       name="snowpre"     standard_name="snowfall_flux"                                         /> 
     224          <field field_ref="snow_ao_cea"   name="snow_ao_cea" standard_name="snowfall_flux_over_ocean"                              /> 
     225          <field field_ref="snow_ai_cea"   name="snow_ai_cea" standard_name="snowfall_flux_over_sea_ice"                            /> 
     226        </file> 
     227 
    98228   <file id="file10" name_suffix="_grid_U" description="ocean U grid variables" > 
    99           <field_group group_ref="SPIN-UP_U" /> 
    100    </file> 
    101     
     229          <field field_ref="e3u"          name="e3u"        standard_name="cell_thickness" /> 
     230          <field field_ref="uoce"         name="vozocrtx"     operation="average" freq_op="1mo" > @uoce_e3u / @e3u </field> 
     231          <field field_ref="uoce"         name="vozocrtx2"    operation="average" freq_op="1mo" > @uoce2_e3u / @e3u </field> 
     232          <field field_ref="ut"           name="ut"           operation="average" freq_op="1mo" > @ut_e3u / @e3u </field> 
     233          <field field_ref="us"           name="us"           operation="average" freq_op="1mo" > @us_e3u / @e3u </field> 
     234          <field field_ref="utau"         name="sozotaux"   standard_name="surface_downward_x_stress" /> 
     235        </file> 
     236 
    102237   <file id="file11" name_suffix="_grid_V" description="ocean V grid variables" > 
    103           <field_group group_ref="SPIN-UP_V" /> 
    104    </file> 
    105     
     238          <field field_ref="e3v"          name="e3v"        standard_name="cell_thickness" /> 
     239          <field field_ref="voce"         name="vomecrty"     operation="average" freq_op="1mo" > @voce_e3v / @e3v </field> 
     240          <field field_ref="voce"         name="vomecrty2"    operation="average" freq_op="1mo" > @voce2_e3v / @e3v </field> 
     241          <field field_ref="vt"           name="vt"           operation="average" freq_op="1mo" > @vt_e3v / @e3v </field> 
     242          <field field_ref="vs"           name="vs"           operation="average" freq_op="1mo" > @vs_e3v / @e3v </field> 
     243          <field field_ref="vtau"         name="sometauy"   standard_name="surface_downward_y_stress" /> 
     244        </file> 
     245 
    106246   <file id="file12" name_suffix="_grid_W" description="ocean W grid variables" > 
    107           <field_group group_ref="SPIN-UP_W" /> 
    108    </file> 
    109     
     247          <field field_ref="woce"         name="vovecrtz"   standard_name="upward_sea_water_velocity"                         /> 
     248          <field field_ref="wt"           name="wt"         standard_name=""                                                  /> 
     249          <field field_ref="ws"           name="ws"         standard_name=""                                                  /> 
     250          <field field_ref="avt"          name="votkeavt"   standard_name="ocean_vertical_heat_diffusivity"                   /> 
     251          <field field_ref="avm"          name="votkeavm"   standard_name="ocean_vertical_momentum_diffusivity"               /> 
     252          <field field_ref="aht2d"        name="soleahtw"   standard_name="vertical_component_of_ocean_xy_tracer_diffusivity" /> 
     253        </file> 
     254 
    110255   <file id="file13" name_suffix="_grid_W" description="ocean W grid variables" > 
    111           <field_group group_ref="SPIN-UP_diaptr" /> 
    112    </file> 
    113     
     256          <field field_ref="zomsfglo"     name="zomsfglo"   standard_name="meridional_streamfunction_global"           grid_ref="gznl_W_3D"       /> 
     257          <field field_ref="zotemglo"     name="zotemglo"   standard_name="zonal_mean_temperature_global"              grid_ref="gznl_T_3D"       /> 
     258          <field field_ref="zosrfglo"     name="zosrfglo"   standard_name="zonal_mean_surface_global"                  grid_ref="gznl_T_3D"       /> 
     259          <field field_ref="zosalglo"     name="zosalglo"   standard_name="zonal_mean_salinity_global"                 grid_ref="gznl_T_3D"       /> 
     260          <field field_ref="zomsfatl"     name="zomsfatl"   standard_name="meridional_streamfunction_atlantic"         grid_ref="gznl_W_3D"       /> 
     261          <field field_ref="zotematl"     name="zotematl"   standard_name="zonal_mean_temperature_atlantic"            grid_ref="gznl_T_3D"       /> 
     262          <field field_ref="zosrfatl"     name="zosrfatl"   standard_name="zonal_mean_surface_atlantic"                grid_ref="gznl_T_3D"       /> 
     263          <field field_ref="zosalatl"     name="zosalatl"   standard_name="zonal_mean_salinity_atlantic"               grid_ref="gznl_T_3D"       /> 
     264          <field field_ref="zomsfpac"     name="zomsfpac"   standard_name="meridional_streamfunction_pacific"          grid_ref="gznl_W_3D"       /> 
     265          <field field_ref="zotempac"     name="zotempac"   standard_name="zonal_mean_temperature_pacific"             grid_ref="gznl_T_3D"       /> 
     266          <field field_ref="zosrfpac"     name="zosrfpac"   standard_name="zonal_mean_surface_pacific"                 grid_ref="gznl_T_3D"       /> 
     267          <field field_ref="zosalpac"     name="zosalpac"   standard_name="zonal_mean_salinity_pacific"                grid_ref="gznl_T_3D"       /> 
     268          <field field_ref="zomsfind"     name="zomsfind"   standard_name="meridional_streamfunction_indian"           grid_ref="gznl_W_3D"       /> 
     269          <field field_ref="zotemind"     name="zotemind"   standard_name="zonal_mean_temperature_indian"              grid_ref="gznl_T_3D"       /> 
     270          <field field_ref="zosrfind"     name="zosrfind"   standard_name="zonal_mean_surface_indian"                  grid_ref="gznl_T_3D"       /> 
     271          <field field_ref="zosalind"     name="zosalind"   standard_name="zonal_mean_salinity_indian"                 grid_ref="gznl_T_3D"       /> 
     272          <field field_ref="zomsfipc"     name="zomsfipc"   standard_name="meridional_streamfunction_indian_pacific"   grid_ref="gznl_W_3D"       /> 
     273          <field field_ref="zotemipc"     name="zotemipc"   standard_name="zonal_mean_temperature_indian_pacific"      grid_ref="gznl_T_3D"       /> 
     274          <field field_ref="zosrfipc"     name="zosrfipc"   standard_name="zonal_mean_surface_indian_pacific"          grid_ref="gznl_T_3D"       /> 
     275          <field field_ref="zosalipc"     name="zosalipc"   standard_name="zonal_mean_salinity_indian_pacific"         grid_ref="gznl_T_3D"       /> 
     276          <field field_ref="sophtadv"     name="sophtadv"   standard_name="advective_heat_transport"                   grid_ref="gznl_T_2D"       /> 
     277          <field field_ref="sopstadv"     name="sopstadv"   standard_name="advective_salt_transport"                   grid_ref="gznl_T_2D"       /> 
     278          <field field_ref="sophtldf"     name="sophtldf"   standard_name="diffusive_heat_transport"                   grid_ref="gznl_T_2D"       /> 
     279          <field field_ref="sopstldf"     name="sopstldf"   standard_name="diffusive_salt_transport"                   grid_ref="gznl_T_2D"       /> 
     280          <field field_ref="sophtadv_atl" name="sophtadv_atl"   standard_name="advective_heat_transport_atlantic"      grid_ref="gznl_T_2D"       /> 
     281          <field field_ref="sopstadv_atl" name="sopstadv_atl"   standard_name="advective_salt_transport_atlantic"      grid_ref="gznl_T_2D"       /> 
     282          <field field_ref="sophtldf_atl" name="sophtldf_atl"   standard_name="diffusive_heat_transport_atlantic"      grid_ref="gznl_T_2D"       /> 
     283          <field field_ref="sopstldf_atl" name="sopstldf_atl"   standard_name="diffusive_salt_transport_atlantic"      grid_ref="gznl_T_2D"       /> 
     284          <field field_ref="sophtadv_pac" name="sophtadv_pac"   standard_name="advective_heat_transport_pacific"       grid_ref="gznl_T_2D"       /> 
     285          <field field_ref="sopstadv_pac" name="sopstadv_pac"   standard_name="advective_salt_transport_pacific"       grid_ref="gznl_T_2D"       /> 
     286          <field field_ref="sophtldf_pac" name="sophtldf_pac"   standard_name="diffusive_heat_transport_pacific"       grid_ref="gznl_T_2D"       /> 
     287          <field field_ref="sopstldf_pac" name="sopstldf_pac"   standard_name="diffusive_salt_transport_pacific"       grid_ref="gznl_T_2D"       /> 
     288          <field field_ref="sophtadv_ind" name="sophtadv_ind"   standard_name="advective_heat_transport_indian"        grid_ref="gznl_T_2D"       /> 
     289          <field field_ref="sopstadv_ind" name="sopstadv_ind"   standard_name="advective_salt_transport_indian"        grid_ref="gznl_T_2D"       /> 
     290          <field field_ref="sophtldf_ind" name="sophtldf_ind"   standard_name="diffusive_heat_transport_indian"        grid_ref="gznl_T_2D"       /> 
     291          <field field_ref="sopstldf_ind" name="sopstldf_ind"   standard_name="diffusive_salt_transport_indian"        grid_ref="gznl_T_2D"       /> 
     292          <field field_ref="sophtadv_ipc" name="sophtadv_ipc"   standard_name="advective_heat_transport_indopacific"   grid_ref="gznl_T_2D"       /> 
     293          <field field_ref="sopstadv_ipc" name="sopstadv_ipc"   standard_name="advective_salt_transport_indopacific"   grid_ref="gznl_T_2D"       /> 
     294          <field field_ref="sophtldf_ipc" name="sophtldf_ipc"   standard_name="diffusive_heat_transport_indopacific"   grid_ref="gznl_T_2D"       /> 
     295          <field field_ref="sopstldf_ipc" name="sopstldf_ipc"   standard_name="diffusive_salt_transport_indopacific"   grid_ref="gznl_T_2D"       /> 
     296        </file> 
     297 
    114298        <file id="file14" name_suffix="_ptrc_T" description="Medusa sms variables" > 
    115299          <field_group group_ref="groupMEDUSA" /> 
     
    147331============================================================================================================ 
    148332    --> 
    149  
     333     
    150334   <axis_definition> 
    151335      <axis id="deptht" standard_name="depth" long_name="Vertical T levels" unit="m" positive="down" /> 
     
    155339      <axis id="nfloat" long_name="Float number"      unit="-"  /> 
    156340      <axis id="icbcla" long_name="Iceberg class"     unit="-"  /> 
     341      <axis id="ncatice" long_name="Ice category"       unit="1"               /> 
     342      <axis id="iax_20C" long_name="20 degC isotherm"   unit="degC"            /> 
     343      <axis id="iax_28C" long_name="28 degC isotherm"   unit="degC"            /> 
     344      <axis id="deptht_surface" axis_ref="deptht" > 
     345         <zoom_axis begin=" 1 " n=" 1 " /> 
     346      </axis> 
     347 
    157348   </axis_definition> 
    158349     
    159350   <domain_definition src="./domain_def.xml"/> 
    160351    
    161    <grid_definition>     
    162      <grid id="grid_T_2D" domain_ref="grid_T"/> 
    163      <grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/> 
    164      <grid id="grid_U_2D" domain_ref="grid_U"/> 
    165      <grid id="grid_U_3D" domain_ref="grid_U" axis_ref="depthu"/> 
    166      <grid id="grid_V_2D" domain_ref="grid_V"/> 
    167      <grid id="grid_V_3D" domain_ref="grid_V" axis_ref="depthv"/> 
    168      <grid id="grid_W_2D" domain_ref="grid_W"/> 
    169      <grid id="grid_W_3D" domain_ref="grid_W" axis_ref="depthw"/> 
    170      <grid id="grid_T_2D_zoom" domain_ref="zoomT"/> 
    171      <grid id="grid_T_3D_zoom" domain_ref="zoomT" axis_ref="deptht"/> 
    172      <grid id="grid_U_3D_zoom" domain_ref="zoomU" axis_ref="depthu"/> 
    173      <grid id="grid_V_3D_zoom" domain_ref="zoomV" axis_ref="depthv"/> 
    174      <grid id="gznl_T_2D" domain_ref="gznl"/> 
    175      <grid id="gznl_T_3D" domain_ref="gznl" axis_ref="deptht"/> 
    176      <grid id="gznl_W_3D" domain_ref="gznl" axis_ref="depthw"/> 
    177     </grid_definition>    
     352    <grid_definition> 
     353        <!--  --> 
     354       <grid id="grid_T_2D" > 
     355         <domain id="grid_T" /> 
     356       </grid> 
     357        <!--  --> 
     358       <grid id="grid_T_3D_ncatice" > 
     359         <domain id="grid_T" /> 
     360         <axis id="ncatice" /> 
     361       </grid> 
     362        <!--  --> 
     363       <grid id="grid_T_3D" > 
     364         <domain id="grid_T" /> 
     365         <axis id="deptht" /> 
     366       </grid> 
     367        <!--  --> 
     368       <grid id="grid_U_2D" > 
     369         <domain id="grid_U" /> 
     370       </grid> 
     371        <!--  --> 
     372       <grid id="grid_U_3D" > 
     373         <domain id="grid_U" /> 
     374         <axis id="depthu" /> 
     375       </grid> 
     376        <!--  --> 
     377       <grid id="grid_V_2D" > 
     378         <domain id="grid_V" /> 
     379       </grid> 
     380        <!--  --> 
     381       <grid id="grid_V_3D" > 
     382         <domain id="grid_V" /> 
     383         <axis id="depthv" /> 
     384       </grid> 
     385        <!--  --> 
     386       <grid id="grid_W_2D" > 
     387         <domain id="grid_W" /> 
     388       </grid> 
     389        <!--  --> 
     390       <grid id="grid_W_3D" > 
     391         <domain id="grid_W" /> 
     392         <axis id="depthw" /> 
     393       </grid> 
     394        <!--  --> 
     395       <grid id="grid_1point" > 
     396         <domain id="1point"/> 
     397       </grid> 
     398        <!--  --> 
     399       <grid id="grid_T_nfloat" > 
     400         <domain id="grid_T" /> 
     401         <axis id="nfloat" /> 
     402       </grid> 
     403        <!--  --> 
     404       <grid id="grid_EqT" > 
     405         <domain id="EqT" /> 
     406       </grid> 
     407        <!--  --> 
     408       <grid id="gznl_T_2D"> 
     409         <domain id="ptr" /> 
     410       </grid> 
     411        <!--  --> 
     412       <grid id="gznl_T_3D"> 
     413         <domain id="ptr" /> 
     414         <axis id="deptht" /> 
     415       </grid> 
     416        <!--  --> 
     417       <grid id="gznl_W_2D"> 
     418         <domain id="ptr" /> 
     419       </grid> 
     420        <!--  --> 
     421       <grid id="gznl_W_3D"> 
     422         <domain id="ptr" /> 
     423         <axis id="depthw" /> 
     424       </grid> 
     425        <!--  --> 
     426       <grid id="grid_T_surface_extract"> 
     427         <domain domain_ref="grid_T" /> 
     428         <axis   axis_ref="deptht_surface" /> 
     429       </grid> 
     430 
     431    </grid_definition> 
    178432  </context> 
    179433   
     
    183437      <variable_definition> 
    184438    
    185      <!--  
    186         We must have buffer_size > jpi*jpj*jpk*8 (with jpi and jpj the subdomain size) 
    187 --> 
    188      <variable id="buffer_size"               type="integer">30000000</variable> 
    189      <variable id="buffer_server_factor_size" type="integer">2</variable> 
    190      <variable id="info_level"                type="integer">0</variable> 
    191      <variable id="using_server"              type="boolean">true</variable> 
    192      <variable id="using_oasis"               type="boolean">true</variable> 
    193      <variable id="oasis_codes_id"            type="string" >toyoce</variable> 
     439     <variable id="info_level"            type="int">0</variable> 
     440     <variable id="using_server"          type="bool">false</variable> 
     441     <variable id="using_oasis"           type="bool">true</variable> 
     442     <variable id="oasis_codes_id"        type="string" >toyoce</variable> 
    194443    
    195444      </variable_definition> 
  • branches/NERC/dev_r5518_NOC_MEDUSA_Stable/NEMOGCM/NEMO/TOP_SRC/MEDUSA/sms_medusa.F90

    r6810 r7766  
    445445      !!---------------------------------------------------------------------- 
    446446      USE lib_mpp , ONLY: ctl_warn 
    447       INTEGER ::   ierr(7)        ! Local variables 
     447      INTEGER ::   ierr(8)        ! Local variables 
    448448      !!---------------------------------------------------------------------- 
    449449      ierr(:) = 0 
  • branches/NERC/dev_r5518_NOC_MEDUSA_Stable/NEMOGCM/NEMO/TOP_SRC/MEDUSA/trcbio_medusa.F90

    r7703 r7766  
    533533      foxy_cons(:,:) = 0.0      !! oxygen consumption 
    534534      foxy_anox(:,:) = 0.0      !! unrealised oxygen consumption 
     535      !! 
    535536# endif 
    536537      ftot_n(:,:)   = 0.0       !! N inventory  
     
    571572      f_riv_c(:,:)   = 0.0      !! riverine C   input  
    572573      f_riv_alk(:,:) = 0.0      !! riverine alk input  
     574      !!  
     575      !! Jpalm -- 06-03-2017 -- Forgotten var to init 
     576      f_omarg(:,:) = 0.0        !! 
     577      f_omcal(:,:) = 0.0  
     578      xFree(:,:) = 0.0          !! state variables for iron-ligand system 
     579      fcomm_resp(:,:) = 0.0  
     580      fprn_ml(:,:) = 0.0        !! mixed layer PP diagnostics 
     581      fprd_ml(:,:) = 0.0        !! mixed layer PP diagnostics 
     582 
    573583      !! 
    574584      !! allocate and initiate 2D diag 
     
    724734         ENDIF      
    725735!! 
    726 !! skip FDT_XXXX, RG_XXXXF, FDS_XXXX, RGSXXXXF diagnostics here 
     736!! skip FDT_XXXX, RG_XXXXF, FDS_XXXX, RGS_XXXXF diagnostics here 
    727737!! 
    728738         IF( med_diag%REMINN%dgsave ) THEN 
  • branches/NERC/dev_r5518_NOC_MEDUSA_Stable/NEMOGCM/NEMO/TOP_SRC/MEDUSA/trcdms_medusa.F90

    r6719 r7766  
    55   !!====================================================================== 
    66   !! History : 
    7    !!  -   !  2014-08  (J. Palmiéri - A. Yool)    added for UKESM1 project 
     7   !!  -   !  2014-08  (J. Palmieri - A. Yool)    added for UKESM1 project 
    88   !!---------------------------------------------------------------------- 
    99#if defined key_medusa && defined key_roam 
     
    4444      !! 
    4545      !! Title  : Calculates DMS ocean surface concentration 
    46       !! Author : Julien Palmiéri and Andrew Yool 
     46      !! Author : Julien Palmieri and Andrew Yool 
    4747      !! Date   : 08/08/14  
    4848      !! 
     
    118118! 
    119119! AXY (13/03/15): Simo & Dachs (2002) 
    120         fq1 = (-1 * log(mld)) + 5.7 
     120        fq1 = (-1.0 * log(mld)) + 5.7 
    121121        fq2 = (55.8 * cmr) + 0.6 
    122122        if (cmr < 0.02) then 
     
    136136!         
    137137! AXY (13/03/15): Halloran et al. (2010) 
    138         fq1 = (-1 * log(mld)) + 5.7 
     138        fq1 = (-1.0 * log(mld)) + 5.7 
    139139        fq2 = (55.8 * cmr) + 0.6 
    140140        fq3 = (90.0 / mld) 
     
    179179 
    180180 
     181 
  • branches/NERC/dev_r5518_NOC_MEDUSA_Stable/NEMOGCM/NEMO/TOP_SRC/MEDUSA/trcnam_medusa.F90

    r7709 r7766  
    8484      &    xburial,                                           & 
    8585      &  jriver_n,jriver_si,jriver_c,jriver_alk,jriver_dep,   & 
    86       &    friver_dep,                                        & 
    8786      &  xsdiss,                                              & 
    88       &  vsed,xhr,                                            & 
    8987      &  sedlam,sedlostpoc,jpkb,jdms,jdms_input,jdms_model 
    9088#if defined key_roam 
    9189      NAMELIST/natroam/ xthetaphy,xthetazoo,xthetanit,        & 
    92       &    xthetarem,xo2min,                                  & 
    93       &    f3_pH,f3_h2co3,f3_hco3,f3_co3,f3_omcal,f3_omarg,   & 
    94       &    f2_ccd_cal,f2_ccd_arg 
     90      &    xthetarem,xo2min  
    9591#endif 
    9692      NAMELIST/natopt/xkg0,xkr0,xkgp,xkrp,xlg,xlr,rpig 
  • branches/NERC/dev_r5518_NOC_MEDUSA_Stable/NEMOGCM/NEMO/TOP_SRC/MEDUSA/trcopt_medusa.F90

    r5841 r7766  
    156156 
    157157      ! Euphotic layer depth 
     158      !! Jpalm -- 06-03-2017 -- add init xze, to avoid halo problems within the 
     159      !!                        writing process 
     160      xze(:,:) = 0.0 
    158161      DO jj = 1, jpj 
    159162         DO ji = 1, jpi 
  • branches/NERC/dev_r5518_NOC_MEDUSA_Stable/NEMOGCM/NEMO/TOP_SRC/MEDUSA/trcsed_medusa.F90

    r6844 r7766  
    4141 
    4242   PUBLIC   trc_sed_medusa     ! called in ??? 
    43    PUBLIC   trc_sed_medusa_sbc       
     43   PUBLIC   trc_sed_medusa_sbc      
     44   PUBLIC   trc_sed_medusa_dust  
    4445 
    4546   !! * Module variables 
     
    126127 
    127128      !! AXY (20/11/14): alter this to report on first MEDUSA call 
    128       !! IF( kt == nit000 ) THEN 
    129129      IF( kt == nittrc000 ) THEN 
    130130         IF(lwp) WRITE(numout,*) 
     
    133133    IF(lwp) WRITE(numout,*) ' kt =',kt 
    134134      ENDIF 
    135  
    136       !! AXY (04/11/13): replace this with a call in trc_ini_medusa 
    137       !! AXY (25/02/10) 
    138       !! call routine for populating CCD array if this is the first time-step 
    139       !! IF( kt == nittrc000 ) CALL medusa_ccd( kt ) 
    140  
    141       !! AXY (04/11/13): replace this with a call in trc_ini_medusa 
    142       !! AXY (26/01/12) 
    143       !! call routine for populating river arrays if this is the first time-step 
    144       !! IF( kt == nittrc000 ) CALL medusa_river( kt ) 
    145  
    146       !! AXY (10/02/09) 
    147       !!IF( (jnt == 1) .and. (bdustfer) )  CALL trc_sed_medusa_sbc( kt ) 
    148  
    149       !! JPALM -- 31-03-2016 -- rewrite trc_sed_medusa_sbc. 
    150       !! IF (kt == nittrc000 ) CALL trc_sed_medusa_sbc  
    151  
    152       !! JPALM -- 20-07-2016 -- adapt dust forcing fields reading and conversion 
    153       !!                     To read dust dep in kg-dust/m2/s instead of g-Fe/m2/month  
    154       !!                     So all forcings and coupling dust dep are in the same SI units 
    155       !!                     and then convert in mmol-Fe/m2/day 
    156  
    157       IF( bdustfer ) THEN 
    158         !! IF( kt == nittrc000 .OR. ( kt /= nittrc000 .AND. ntimes_dust > 1 ) ) THEN 
    159             CALL fld_read( kt, 1, sf_dust ) 
    160             dust(:,:) = sf_dust(1)%fnow(:,:,1) 
    161          !! ENDIF 
    162       ELSEIF (lk_oasis) THEN 
    163          dust = Dust_in_cpl 
    164       ELSE 
    165          dust(:,:) = 0.0 
    166       ENDIF 
    167       !! 
    168       zirondep(:,:) = 0.e0     !! Initialisation of deposition variables 
    169       zirondep(:,:) = dust(:,:) * Fe_dust_mratio / xfe_mass * 1.e6 * 86400.  !! mmol-Fe/m2/d 
    170        
    171       !! JPALM -- 20-07-2016 -- Zirondep and zsidep are not used. 
    172       !!                     So comment out the following lines. but keep them 
    173       !!                     as we may want to used them later on 
    174       !!================================================      
    175       !! 
    176       !! zirondep(:,:,:) = 0.e0     !! Initialisation of deposition variables 
    177       !! zsidep  (:,:)   = 0.e0 
    178       !! 
    179       !! Iron and Si deposition at the surface 
    180       !! ------------------------------------- 
    181       !! 
    182       !! DO jj = 1, jpj 
    183       !!    DO ji = 1, jpi 
    184       !!       zirondep(ji,jj,1) = (dustsolub * dust(ji,jj) / (55.85 * rmtss) + 3.e-10 / ryyss) & 
    185       !!       & * rfact2 / fse3t(ji,jj,1) 
    186       !!       zsidep  (ji,jj)   = 8.8 * 0.075 * dust(ji,jj) * rfact2 / & 
    187       !!       & (fse3t(ji,jj,1) * 28.1 * rmtss) 
    188       !!    END DO 
    189       !! END DO 
    190135 
    191136      ! sedimentation of detrital nitrogen : upstream scheme 
     
    412357   END SUBROUTINE trc_sed_medusa_sbc 
    413358 
     359   !! ====================================================================== 
     360   !! ====================================================================== 
     361   !! ====================================================================== 
     362 
     363   !! AXY & JPALM (28/02/17) 
     364 
     365   SUBROUTINE trc_sed_medusa_dust( kt ) 
     366      !!--------------------------------------------------------------------- 
     367      !!                     ***  ROUTINE trc_sed_medusa_dust  *** 
     368      !! 
     369      !! ** Purpose : compute current dust *before* trc_bio_medusa call 
     370      !! 
     371      !! ** Method  : does what it says on the tin 
     372      !!--------------------------------------------------------------------- 
     373      INTEGER, INTENT( in ) ::   kt      ! ocean time-step index       
     374 
     375      !! AXY (20/11/14): alter this to report on first MEDUSA call 
     376      IF( kt == nittrc000 ) THEN 
     377         IF(lwp) WRITE(numout,*) 
     378         IF(lwp) WRITE(numout,*) ' trc_sed_medusa_dust: MEDUSA dust timestep' 
     379         IF(lwp) WRITE(numout,*) ' ~~~~~~~' 
     380    IF(lwp) WRITE(numout,*) ' kt =',kt 
     381      ENDIF 
     382 
     383      !! AXY (04/11/13): replace this with a call in trc_ini_medusa 
     384      !! AXY (25/02/10) 
     385      !! call routine for populating CCD array if this is the first time-step 
     386      !! IF( kt == nittrc000 ) CALL medusa_ccd( kt ) 
     387 
     388      !! AXY (04/11/13): replace this with a call in trc_ini_medusa 
     389      !! AXY (26/01/12) 
     390      !! call routine for populating river arrays if this is the first time-step 
     391      !! IF( kt == nittrc000 ) CALL medusa_river( kt ) 
     392 
     393      !! AXY (10/02/09) 
     394      !! IF( (jnt == 1) .and. (bdustfer) )  CALL trc_sed_medusa_sbc( kt ) 
     395 
     396      !! JPALM -- 31-03-2016 -- rewrite trc_sed_medusa_sbc. 
     397      !! IF (kt == nittrc000 ) CALL trc_sed_medusa_sbc  
     398 
     399      !! JPALM -- 20-07-2016 -- adapt dust forcing fields reading and conversion 
     400      !!                     To read dust dep in kg-dust/m2/s instead of g-Fe/m2/month  
     401      !!                     So all forcings and coupling dust dep are in the same SI units 
     402      !!                     and then convert in mmol-Fe/m2/day 
     403 
     404      IF( bdustfer ) THEN 
     405            CALL fld_read( kt, 1, sf_dust ) 
     406            dust(:,:) = sf_dust(1)%fnow(:,:,1) 
     407      ELSEIF (lk_oasis) THEN 
     408         dust = Dust_in_cpl 
     409      ELSE 
     410         dust(:,:) = 0.0 
     411      ENDIF 
     412      !! 
     413      zirondep(:,:) = 0.e0     !! Initialisation of deposition variables 
     414      zirondep(:,:) = dust(:,:) * Fe_dust_mratio / xfe_mass * 1.e6 * 86400.  !! mmol-Fe/m2/d 
     415       
     416      !! JPALM -- 20-07-2016 -- Zirondep and zsidep are not used. 
     417      !!                     So comment out the following lines. but keep them 
     418      !!                     as we may want to used them later on 
     419      !!================================================      
     420      !! 
     421      !! zirondep(:,:,:) = 0.e0     !! Initialisation of deposition variables 
     422      !! zsidep  (:,:)   = 0.e0 
     423      !! 
     424      !! Iron and Si deposition at the surface 
     425      !! ------------------------------------- 
     426      !! 
     427      !! DO jj = 1, jpj 
     428      !!    DO ji = 1, jpi 
     429      !!       zirondep(ji,jj,1) = (dustsolub * dust(ji,jj) / (55.85 * rmtss) + 3.e-10 / ryyss) & 
     430      !!       & * rfact2 / fse3t(ji,jj,1) 
     431      !!       zsidep  (ji,jj)   = 8.8 * 0.075 * dust(ji,jj) * rfact2 / & 
     432      !!       & (fse3t(ji,jj,1) * 28.1 * rmtss) 
     433      !!    END DO 
     434      !! END DO 
     435 
     436   END SUBROUTINE trc_sed_medusa_dust 
     437 
    414438#else 
    415439   !!====================================================================== 
     
    425449   !!====================================================================== 
    426450END MODULE  trcsed_medusa 
     451 
  • branches/NERC/dev_r5518_NOC_MEDUSA_Stable/NEMOGCM/NEMO/TOP_SRC/MEDUSA/trcsms_medusa.F90

    r5841 r7766  
    5858      ENDIF 
    5959 
    60       CALL trc_avg_medusa( kt )   ! rolling average module 
     60      CALL trc_avg_medusa( kt ) ! rolling average module 
    6161# if defined key_debug_medusa 
    62          IF(lwp) WRITE(numout,*) ' MEDUSA done trc_avg_medusa' 
    63          CALL flush(numout) 
     62      IF(lwp) WRITE(numout,*) ' MEDUSA done trc_avg_medusa' 
     63      CALL flush(numout) 
     64# endif 
     65       
     66      CALL trc_opt_medusa( kt ) ! optical model 
     67# if defined key_debug_medusa 
     68      IF(lwp) WRITE(numout,*) ' MEDUSA done trc_opt_medusa' 
     69      CALL flush(numout) 
    6470# endif 
    6571 
    66       CALL trc_opt_medusa( kt )   ! optical model 
     72      !! AXY & JPALM (28/02/17): call dust before trc_bio_medusa (because of coupling) 
     73      CALL trc_sed_medusa_dust( kt ) ! dust submodel 
    6774# if defined key_debug_medusa 
    68          IF(lwp) WRITE(numout,*) ' MEDUSA done trc_opt_medusa' 
    69          CALL flush(numout) 
     75      IF(lwp) WRITE(numout,*) ' MEDUSA done trc_sed_medusa_dust' 
     76      CALL flush(numout) 
    7077# endif 
    7178 
     
    7582      CALL flush(numout) 
    7683# else 
    77       CALL trc_bio_medusa( kt )   ! biological model 
    78 # if defined key_debug_medusa 
    79          IF(lwp) WRITE(numout,*) ' MEDUSA done trc_bio_medusa' 
    80          CALL flush(numout) 
    81 # endif 
    82  
    83       CALL trc_sed_medusa( kt )   ! sedimentation model 
    84 # if defined key_debug_medusa 
    85          IF(lwp) WRITE(numout,*) ' MEDUSA done trc_sed_medusa' 
    86          CALL flush(numout) 
    87 # endif 
     84      CALL trc_bio_medusa( kt ) ! biological model 
     85#  if defined key_debug_medusa 
     86      IF(lwp) WRITE(numout,*) ' MEDUSA done trc_bio_medusa' 
     87      CALL flush(numout) 
     88#  endif 
     89       
     90      CALL trc_sed_medusa( kt ) ! sedimentation model 
     91#  if defined key_debug_medusa 
     92      IF(lwp) WRITE(numout,*) ' MEDUSA done trc_sed_medusa' 
     93      CALL flush(numout) 
     94#  endif 
    8895# endif 
    8996 
     
    103110   !!====================================================================== 
    104111END MODULE trcsms_medusa 
     112 
  • branches/NERC/dev_r5518_NOC_MEDUSA_Stable/NEMOGCM/NEMO/TOP_SRC/trcrst.F90

    r7498 r7766  
    686686      !!---------------------------------------------------------------------- 
    687687      INTEGER  :: jk, jn 
    688       REAL(wp) :: ztraf, zmin, zmax, zmean, zdrift 
     688      REAL(wp) :: ztraf, zmin, zmax, zmean, zdrift, areasf 
    689689      REAL(wp), DIMENSION(jpi,jpj) :: zvol 
    690690      !!---------------------------------------------------------------------- 
     
    696696      ENDIF 
    697697      ! 
    698          zvol(:,:) = e1e2t(:,:) * fse3t_a(:,:,1) * tmask(:,:,1) 
     698      zvol(:,:) = e1e2t(:,:) * fse3t_a(:,:,1) * tmask(:,:,1) 
     699      areasf = glob_sum(zvol(:,:)) 
    699700      DO jn = 1, jptra 
    700701         ztraf = glob_sum( tra(:,:,1,jn) * zvol(:,:) ) 
     
    705706            CALL mpp_max( zmax )      ! max over the global domain 
    706707         END IF 
    707          zmean  = ztraf / areatot 
     708         zmean  = ztraf / areasf 
    708709         IF(lwp) WRITE(numout,9001) jn, TRIM( ctrcnm(jn) ), zmean, zmin, zmax 
    709710      END DO 
     
    734735      zvol(:,:) = e1e2t(:,:) * fse3t_a(:,:,1) * tmask(:,:,1) 
    735736      ztraf = glob_sum( dgtr(:,:) * zvol(:,:) ) 
    736       areasf = glob_sum(e1e2t(:,:) * tmask(:,:,1) ) 
     737      !! areasf = glob_sum(e1e2t(:,:) * tmask(:,:,1) ) 
     738      areasf = glob_sum(zvol(:,:)) 
    737739      zmin  = MINVAL( dgtr(:,:), mask= ((tmask(:,:,1).NE.0.)) ) 
    738740      zmax  = MAXVAL( dgtr(:,:), mask= ((tmask(:,:,1).NE.0.)) ) 
     
    741743         CALL mpp_max( zmax )      ! max over the global domain 
    742744      END IF 
    743       zmean  = ztraf / areatot 
     745      zmean  = ztraf / areasf 
    744746      IF(lwp) WRITE(numout,9002) TRIM( names ), zmean, zmin, zmax 
    745747      ! 
  • branches/NERC/dev_r5518_NOC_MEDUSA_Stable/NEMOGCM/NEMO/TOP_SRC/trcstp.F90

    r7709 r7766  
    146146            ztrai = ztrai + glob_sum( trn(:,:,:,jn) * cvol(:,:,:)   ) 
    147147         END DO 
    148          IF( lwp ) WRITE(numstr,9300) kt,  ztrai / areatot 
     148         IF( numstr /= -1 ) WRITE(numstr,9300) kt,  ztrai / areatot 
    1491499300     FORMAT(i10,e18.10) 
    150150      ENDIF 
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