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iodef.xml
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iodef.xml
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<?xml version="1.0"?>
<simulation>
<context id="nemo">
<!-- $id$ -->
<!--
============================================================================================================
= definition of all existing variables =
= DO NOT CHANGE =
============================================================================================================
-->
<field_definition level="1" prec="4" operation="ave(X)" enabled=".TRUE."> <!-- time step automaticaly defined -->
<group id="grid_T" axis_ref="none" grid_ref="grid_T">
<field id="toce" description="temperature" unit="degC" axis_ref="deptht" />
<field id="soce" description="salinity" unit="psu" axis_ref="deptht" />
<field id="somxl010" description="Mixed Layer Depth 0.01 ref.10m" unit="m" />
<field id="soshfldo" description="Shortwave Radiation" unit="W/m2" />
</group>
<group id="grid_W" axis_ref="depthw" grid_ref="grid_W">
<field id="votkeavt" description="Vertical Eddy Diffusivity" unit="m2/s" />
</group>
<!-- ptrc on T grid -->
<group id="ptrc_T" axis_ref="deptht" grid_ref="grid_T">
<field id="DIC" description="Dissolved inorganic Concentration" unit="molC/L" />
<field id="Alkalini" description="Total Alkalinity Concentration" unit="eq/L" />
<field id="O2" description="Oxygen Concentration" unit="molO2/L" />
<field id="CaCO3" description="Calcite Concentration" unit="molC/L" />
<field id="PO4" description="Phosphate Concentration" unit="molC/L" />
<field id="POC" description="Small organic carbon Concentration" unit="molC/L" />
<field id="Si" description="Silicate Concentration" unit="molSi/L" />
<field id="PHY" description="Nanophytoplankton Concentration" unit="molC/L" />
<field id="ZOO" description="Microzooplankton Concentration" unit="molC/L" />
<field id="DOC" description="Dissolved organic Concentration" unit="molC/L" />
<field id="PHY2" description="Diatoms Concentration" unit="molC/L" />
<field id="ZOO2" description="Mesozooplankton Concentration" unit="molC/L" />
<field id="BSi" description="Diatoms Silicate Concentration" unit="molC/L" />
<field id="Fer" description="Dissolved Iron Concentration" unit="molFe/L" />
<field id="BFe" description="Big iron particles Concentration" unit="molFe/L" />
<field id="GOC" description="Big organic carbon Concentration" unit="molC/L" />
<field id="SFe" description="Small iron particles Concentration" unit="molFe/L" />
<field id="DFe" description="Diatoms iron Concentration" unit="molFe/L" />
<field id="DSi" description="Sinking biogenic Silicate Concentration" unit="molC/L" />
<field id="NFe" description="Nano iron Concentration" unit="molC/L" />
<field id="NCHL" description="Nano chlorophyl Concentration" unit="gChl/L" />
<field id="DCHL" description="Diatoms chlorophyl Concentration" unit="gChl/L" />
<field id="NO3" description="Nitrates Concentration" unit="molC/L" />
<field id="NH4" description="Ammonium Concentration" unit="molC/L" />
</group>
<!-- diad on T grid : variables available with key_diatrc -->
<group id="diad_T" axis_ref="none" grid_ref="grid_T">
<field id="PH" description="PH" unit="-" axis_ref="deptht" />
<field id="CO3" description="Bicarbonates" unit="mol/L" axis_ref="deptht" />
<field id="CO3sat" description="CO3 saturation" unit="mol/L" axis_ref="deptht" />
<field id="PAR" description="Photosynthetically Available Radiation" unit="W/m2" axis_ref="deptht" />
<field id="PARmld" description="PAR averaged in the ML" unit="W/m2" axis_ref="deptht" />
<field id="PPPHY" description="Primary production of nanophyto" unit="molC/m3/s" axis_ref="deptht" />
<field id="PPPHY2" description="Primary production of diatoms" unit="molC/m3/s" axis_ref="deptht" />
<field id="PPNEWN" description="New Primary production of nanophyto" unit="molC/m3/s" axis_ref="deptht" />
<field id="PPNEWD" description="New Primary production of diatoms" unit="molC/m3/s" axis_ref="deptht" />
<field id="PBSi" description="Primary production of Si diatoms" unit="molSi/m3/s" axis_ref="deptht" />
<field id="PFeN" description="Primary production of nano iron" unit="molFe/m3/s" axis_ref="deptht" />
<field id="PFeD" description="Primary production of diatoms iron" unit="molFe/m3/s" axis_ref="deptht" />
<field id="PCAL" description="Calcite production" unit="molC/m3/s" axis_ref="deptht" />
<field id="DCAL" description="Calcite dissolution" unit="molC/m3/s" axis_ref="deptht" />
<field id="GRAZ" description="Grazing by zooplankton" unit="molC/m3/s" axis_ref="deptht" />
<field id="Mumax" description="Maximum growth rate" unit="molC/m3/s" axis_ref="deptht" />
<field id="MuN" description="Growth rate Nano" unit="1/s" axis_ref="deptht" />
<field id="MuD" description="Growth rate Dia" unit="1/s" axis_ref="deptht" />
<field id="LNnut" description="Nutrient limitation Nano" unit="-" axis_ref="deptht" />
<field id="LDnut" description="Nutrient Limitation Dia" unit="-" axis_ref="deptht" />
<field id="LNFe" description="Iron limitation Nano" unit="-" axis_ref="deptht" />
<field id="LDFe" description="Iron limiation Dia" unit="-" axis_ref="deptht" />
<field id="LNlight" description="Light limitation Nano" unit="-" axis_ref="deptht" />
<field id="LDlight" description="Light limitation Diatom" unit="-" axis_ref="deptht" />
<field id="GRAZD" description="Total Grazing Loss of Diatoms" unit="molC/m3/s" axis_ref="deptht" />
<field id="GRAZN" description="Total Grazing Loss of Nano" unit="molC/m3/s" axis_ref="deptht" />
<field id="Nfix" description="Nitrogen fixation at surface" unit="molN/m2/s" />
<field id="EPC100" description="Export of carbon particles at 100 m" unit="molC/m2/s" />
<field id="EPFE100" description="Export of biogenic iron at 100 m" unit="molFe/m2/s" />
<field id="EPSI100" description="Export of Silicate at 100 m" unit="molSi/m2/s" />
<field id="EPCAL100" description="Export of Calcite at 100 m" unit="molC/m2/s" />
<field id="Cflx" description="DIC flux" unit="molC/m2/s" />
<field id="Oflx" description="Oxygen flux" unit="molC/m2/s" />
<field id="Kg" description="Gas transfer" unit="molC/m2/s/uatm" />
<field id="Dpco2" description="Delta CO2" unit="uatm" />
<field id="Dpo2" description="Delta O2" unit="uatm" />
<field id="Heup" description="Euphotic layer depth" unit="m" />
<field id="Irondep" description="Iron deposition" unit="molFe/m2/s" />
<field id="PCHLN" description="Chl production of nanophyto" unit="gCHL/m3/s" axis_ref="deptht" />
<field id="PCHLD" description="Chl production of diatoms" unit="gCHL/m3/s" axis_ref="deptht" />
<field id="GmxlN" description="MLD > Heup penalisation for nano" unit="" axis_ref="deptht" />
<field id="GmxlD" description="MLD > Heup penalisation for diatoms" unit="" axis_ref="deptht" />
<field id="GRAZNM" description="Grazing of nano by mesozoo" unit="" axis_ref="deptht" />
<field id="GRAZDM" description="Grazing of diatom by mesozoo" unit="" axis_ref="deptht" />
<field id="GRAZNZ" description="Grazing of nano by microzoo" unit="" axis_ref="deptht" />
<field id="GRAZDZ" description="Grazing of diatom by microzoo" unit="" axis_ref="deptht" />
<field id="mortN" description="Mortality loss of nano" unit="" axis_ref="deptht" />
<field id="mortD" description="Mortality loss of diatoms" unit="" axis_ref="deptht" />
</group>
<group id="trdtrc" axis_ref="deptht" grid_ref="grid_T">
<field id="XAD_Fer" description="Zonal advection Fe trends" unit="molC/m3/s" />
<field id="YAD_Fer" description="Meridional advection Fe trends" unit="molC/s" />
<field id="ZAD_Fer" description="Vertical advection Fe trends" unit="molC/s" />
<field id="LDF_Fer" description="Lateral diffusion Fe trends" unit="molC/s" />
<field id="BBL_Fer" description="Bottom boundary layer" unit="molC/s" />
<field id="ZDF_Fer" description="Vertical diffusion Fe trends" unit="molC/s" />
<field id="DMP_Fer" description="Internal damping" unit="molC/s" />
<field id="FOR_Fer" description="Surface forcing" unit="molC/s" />
<field id="SMS_Fer" description="Source minus sink" unit="molC/s" />
<field id="ATF_Fer" description="Asselin time filter" unit="molC/s" />
<field id="RDB_Fer" description="Before RAD Fe trends" unit="molC/s" />
<field id="RDN_Fer" description="Now RAD Fe trends" unit="molC/s" />
<field id="BACT_Fe" description="Bacterial Fe eq. term" unit="molFe/m3/s" />
<field id="POC_SFe" description="Disaggregation Fe eq. term" unit="molFe/m3/s" />
<field id="SCAV" description="Scavenging Fe eq. term" unit="molFe/m3/s" />
<field id="AGG_Fe" description="Aggregation Fe eq. term" unit="molFe/m3/s" />
<field id="COAG_Fe" description="Coagulation Fe eq. term" unit="molFe/m3/s" />
<field id="GRAFZ" description="1st Fe eq. term. Microzoo" unit="molFe/m3/s" />
<field id="GRAFM" description="2nd Fe eq. term. Mesozoo" unit="molFe/m3/s" />
</group>
<!-- scalar -->
<group id="scalar" axis_ref="none" grid_ref="scalarpoint" zoom_ref="1point" >
</group>
</field_definition>
<!--
============================================================================================================
= output files definition =
= Define your own files =
= put the variables you want... =
============================================================================================================
-->
<file_definition output_level="10" enabled=".TRUE.">
<group id="5d" output_freq="432000" output_level="10" enabled=".TRUE."> <!-- 5d files -->
</group>
<group id="1d" output_freq="86400" output_level="10" enabled=".TRUE."> <!-- 1d files -->
<file id="1d_grid_T" name="auto" description="forcing from gridT" >
<field ref="toce" />
<field ref="soce" />
<field ref="somxl010" />
<field ref="soshfldo" />
</file>
<file id="1d_grid_W" name="auto" description="forcing from gridW" >
<field ref="votkeavt" />
</file>
<file id="1d_ptrc_T" name="auto" description="pisces sms variables" >
<field ref="DIC" />
<field ref="Alkalini" />
<field ref="O2" />
<field ref="CaCO3" />
<field ref="PO4" />
<field ref="POC" />
<field ref="Si" />
<field ref="PHY" />
<field ref="ZOO" />
<field ref="DOC" />
<field ref="PHY2" />
<field ref="ZOO2" />
<field ref="BSi" />
<field ref="Fer" />
<field ref="BFe" />
<field ref="GOC" />
<field ref="SFe" />
<field ref="DFe" />
<field ref="DSi" />
<field ref="NFe" />
<field ref="NCHL" />
<field ref="DCHL" />
<field ref="NO3" />
<field ref="NH4" />
</file>
<file id="1d_diad_T" name="auto" description="additional pisces diagnostics" >
<field ref="PH" />
<field ref="CO3" />
<field ref="CO3sat" />
<field ref="PAR" />
<field ref="PARmld" />
<field ref="PPPHY" />
<field ref="PPPHY2" />
<field ref="PPNEWN" />
<field ref="PPNEWD" />
<field ref="PBSi" />
<field ref="PFeN" />
<field ref="PFeD" />
<field ref="PCAL" />
<field ref="DCAL" />
<field ref="GRAZ" />
<field ref="EPC100" />
<field ref="EPFE100" />
<field ref="EPSI100" />
<field ref="EPCAL100" />
<field ref="Cflx" />
<field ref="Oflx" />
<field ref="Kg" />
<field ref="Dpco2" />
<field ref="Dpo2" />
<field ref="Heup" />
<field ref="Irondep" />
<field ref="Nfix" />
<field ref="Mumax" />
<field ref="MuN" />
<field ref="MuD" />
<field ref="LNnut" />
<field ref="LDnut" />
<field ref="LNFe" />
<field ref="LDFe" />
<field ref="LNlight" />
<field ref="LDlight" />
<field ref="GRAZD" />
<field ref="GRAZN" />
<field ref="PCHLD" />
<field ref="PCHLN" />
<field ref="GmxlD" />
<field ref="GmxlN" />
<field ref="GRAZNM" />
<field ref="GRAZDM" />
<field ref="GRAZNZ" />
<field ref="GRAZDZ" />
<field ref="mortN" />
<field ref="mortD" />
</file>
<file id="1d_trdtrc" name="auto" description="3D iron trends">
<field ref="ZDF_Fer" />
</file>
</group>
<group id="1m" output_freq="-1" output_level="10" enabled=".TRUE."> <!-- real monthly files -->
</group>
<group id="2m" output_freq="-2" output_level="10" enabled=".TRUE."> <!-- real 2m files -->
</group>
<group id="3m" output_freq="-3" output_level="10" enabled=".TRUE."> <!-- real 3m files -->
</group>
<group id="4m" output_freq="-4" output_level="10" enabled=".TRUE."> <!-- real 4m files -->
</group>
<group id="6m" output_freq="-6" output_level="10" enabled=".TRUE."> <!-- real 6m files -->
</group>
<group id="1y" output_freq="-12" output_level="10" enabled=".TRUE."> <!-- real yearly files -->
</group>
<group id="2y" output_freq="-24" output_level="10" enabled=".TRUE."> <!-- real 2y files -->
</group>
<group id="5y" output_freq="-60" output_level="10" enabled=".TRUE."> <!-- real 5y files -->
</group>
<group id="10y" output_freq="-120" output_level="10" enabled=".TRUE."> <!-- real 10y files -->
</group>
</file_definition>
<!--
============================================================================================================
= grid definition =
= DO NOT CHANGE =
============================================================================================================
-->
<axis_definition>
<axis id="deptht" description="Vertical T levels" unit="m" positive=".false." />
<axis id="depthu" description="Vertical U levels" unit="m" positive=".false." />
<axis id="depthv" description="Vertical V levels" unit="m" positive=".false." />
<axis id="depthw" description="Vertical W levels" unit="m" positive=".false." />
<axis id="none" description="axe non defini" unit="none" size="1" />
</axis_definition>
<grid_definition>
<grid id="grid_T" description="grid T" />
<grid id="grid_U" description="grid U" />
<grid id="grid_V" description="grid V" />
<grid id="grid_W" description="grid W" />
<grid id="scalarpoint" description="scalar" >
<zoom id="1point" ibegin="1" jbegin="1" ni="1" nj="1" />
</grid>
</grid_definition>
</context>
</simulation>