Index: NEMO/branches/2019/dev_r11643_ENHANCE-11_CEthe_Shaconemo_diags/cfgs/ORCA2_ICE_PISCES/EXPREF/axis_def_nemo.xml
===================================================================
--- NEMO/branches/2019/dev_r11643_ENHANCE-11_CEthe_Shaconemo_diags/cfgs/ORCA2_ICE_PISCES/EXPREF/axis_def_nemo.xml	(revision 11998)
+++ NEMO/branches/2019/dev_r11643_ENHANCE-11_CEthe_Shaconemo_diags/cfgs/ORCA2_ICE_PISCES/EXPREF/axis_def_nemo.xml	(revision 11998)
@@ -0,0 +1,1 @@
+link ../../SHARED/axis_def_nemo.xml
Index: NEMO/branches/2019/dev_r11643_ENHANCE-11_CEthe_Shaconemo_diags/cfgs/ORCA2_ICE_PISCES/EXPREF/context_nemo.xml
===================================================================
--- NEMO/branches/2019/dev_r11643_ENHANCE-11_CEthe_Shaconemo_diags/cfgs/ORCA2_ICE_PISCES/EXPREF/context_nemo.xml	(revision 11644)
+++ NEMO/branches/2019/dev_r11643_ENHANCE-11_CEthe_Shaconemo_diags/cfgs/ORCA2_ICE_PISCES/EXPREF/context_nemo.xml	(revision 11998)
@@ -5,46 +5,38 @@
 -->
 <context id="nemo">
-<!-- $id$ -->
+    <!-- $id$ -->
     <variable_definition>
-    <!-- Year of time origin for NetCDF files; defaults to 1800 -->
-       <variable id="ref_year" type="int"   > 1800 </variable>
-       <variable id="rau0"     type="float" > 1026.0 </variable>
-       <variable id="cpocean"  type="float" > 3991.86795711963 </variable>
-       <variable id="convSpsu" type="float" > 0.99530670233846  </variable>
-       <variable id="rhoic"    type="float" > 917.0 </variable>
-       <variable id="rhosn"    type="float" > 330.0 </variable>
-       <variable id="missval"  type="float" > 1.e20 </variable>
+       <!-- Year/Month/Day of time origin for NetCDF files; defaults to 1800-01-01 -->
+       <variable id="ref_year"  type="int"> 1900 </variable>
+       <variable id="ref_month" type="int"> 01 </variable>
+       <variable id="ref_day"   type="int"> 01 </variable>
+       <variable id="rau0"      type="float" > 1026.0 </variable>
+       <variable id="cpocean"   type="float" > 3991.86795711963 </variable>
+       <variable id="convSpsu"  type="float" > 0.99530670233846  </variable>
+       <variable id="rhoic"     type="float" > 917.0 </variable>
+       <variable id="rhosn"     type="float" > 330.0 </variable>
+       <variable id="missval"   type="float" > 1.e20 </variable>
     </variable_definition>
+
 <!-- Fields definition -->
-    <field_definition src="./field_def_nemo-oce.xml"/>    <!--  NEMO ocean dynamics     --> 
-    <field_definition src="./field_def_nemo-ice.xml"/>    <!--  NEMO sea-ice model      --> 
-    <field_definition src="./field_def_nemo-pisces.xml"/> <!--  NEMO ocean biology      --> 
+    <field_definition src="./field_def_nemo-oce.xml"/>    <!--  NEMO ocean dynamics     -->
+    <field_definition src="./field_def_nemo-ice.xml"/>    <!--  NEMO sea-ice model      -->
+    <field_definition src="./field_def_nemo-pisces.xml"/> <!--  NEMO ocean biology      -->
 
 <!-- Files definition -->
-    <file_definition src="./file_def_nemo-oce.xml"/>     <!--  NEMO ocean dynamics      --> 
-    <file_definition src="./file_def_nemo-ice.xml"/>     <!--  NEMO sea-ice model       --> 
-    <file_definition src="./file_def_nemo-pisces.xml"/>  <!--  NEMO ocean biology       --> 
-    <!-- 
-============================================================================================================
-= grid definition = = DO NOT CHANGE =
-============================================================================================================
-    -->
-    
-    <axis_definition>
-      <axis id="deptht"  long_name="Vertical T levels" unit="m" positive="down" />
-      <axis id="depthu"  long_name="Vertical U levels" unit="m" positive="down" />
-      <axis id="depthv"  long_name="Vertical V levels" unit="m" positive="down" />
-      <axis id="depthw"  long_name="Vertical W levels" unit="m" positive="down" />
-      <axis id="profsed" long_name="Vertical S levels" unit="cm" positive="down"/>
-      <axis id="nfloat"  long_name="Float number"      unit="-"                 />
-      <axis id="icbcla"  long_name="Iceberg class"     unit="1"                 />
-      <axis id="ncatice" long_name="Ice category"      unit="1"                 />
-      <axis id="iax_20C" long_name="20 degC isotherm"  unit="degC"              />
-      <axis id="iax_28C" long_name="28 degC isotherm"  unit="degC"              />
-    </axis_definition>
+    <file_definition src="./file_def_nemo-oce.xml"/>     <!--  NEMO ocean dynamics      -->
+    <file_definition src="./file_def_nemo-ice.xml"/>     <!--  NEMO sea-ice model       -->
+    <file_definition src="./file_def_nemo-pisces.xml"/>  <!--  NEMO ocean biology       -->
+
+
+<!-- Axis definition -->
+    <axis_definition src="./axis_def_nemo.xml"/>
  
+<!-- Domain definition -->
     <domain_definition src="./domain_def_nemo.xml"/>
+
+<!-- Grids definition -->
+    <grid_definition   src="./grid_def_nemo.xml"/>
   
-    <grid_definition src="./grid_def_nemo.xml"/>
-    
+
 </context>
Index: NEMO/branches/2019/dev_r11643_ENHANCE-11_CEthe_Shaconemo_diags/cfgs/ORCA2_ICE_PISCES/EXPREF/file_def_nemo-ice.xml
===================================================================
--- NEMO/branches/2019/dev_r11643_ENHANCE-11_CEthe_Shaconemo_diags/cfgs/ORCA2_ICE_PISCES/EXPREF/file_def_nemo-ice.xml	(revision 11644)
+++ NEMO/branches/2019/dev_r11643_ENHANCE-11_CEthe_Shaconemo_diags/cfgs/ORCA2_ICE_PISCES/EXPREF/file_def_nemo-ice.xml	(revision 11998)
@@ -123,6 +123,18 @@
    <file_group id="3h"  output_freq="3h"  output_level="10" enabled=".TRUE."/> <!-- 3h files -->     
    <file_group id="4h"  output_freq="4h"  output_level="10" enabled=".TRUE."/> <!-- 4h files -->
-   <file_group id="6h"  output_freq="6h"  output_level="10" enabled=".TRUE."/> <!-- 6h files -->        
-   <file_group id="1m"  output_freq="1mo" output_level="10" enabled=".TRUE."/> <!-- real monthly files -->
+   <file_group id="6h"  output_freq="6h"  output_level="10" enabled=".TRUE."/> <!-- 6h files -->      
+
+   <file_group id="1m"  output_freq="1mo" output_level="10" enabled=".TRUE."> <!-- real monthly files -->
+
+     <!-- To compute transport through straits : need to read ice mask at ice iteration at freq_offset = 1mo - nn_fsbc
+      <file id="file23" name_suffix="_strait_ice" description="transport variables through straits" >
+          <field field_ref="strait_mifl"      name="simassacrossline"  freq_offset="1mo-4ts" />
+          <field field_ref="strait_msfl"      name="snmassacrossline"  freq_offset="1mo-4ts" />
+          <field field_ref="strait_arfl"      name="siareaacrossline"  freq_offset="1mo-4ts" />
+        </file>
+     -->
+
+    </file_group>
+
    <file_group id="2m"  output_freq="2mo" output_level="10" enabled=".TRUE."/> <!-- real 2m files -->
    <file_group id="3m"  output_freq="3mo" output_level="10" enabled=".TRUE."/> <!-- real 3m files -->
@@ -133,5 +145,12 @@
    <file_group id="5y"  output_freq="5y"  output_level="10" enabled=".TRUE."/> <!-- real 5y files -->
    <file_group id="10y" output_freq="10y" output_level="10" enabled=".TRUE."/> <!-- real 10y files -->
-   
+ 
+   <!-- To compute transport through straits : need to read ice mask at ice iteration at freq_offset = - nn_fsbc + 1
+   <file id="maskMFO" name="maskMFO" enabled="true" mode="read" output_freq="1mo" cyclic="true"  >
+      <field id="maskMFO_u_ice" operation="instant"  freq_offset="-3ts"  grid_ref="grid_U_4strait_ice" />
+      <field id="maskMFO_v_ice" operation="instant"  freq_offset="-3ts"  grid_ref="grid_V_4strait_ice" />
+   </file>
+
+     -->
  </file_definition>
  
Index: NEMO/branches/2019/dev_r11643_ENHANCE-11_CEthe_Shaconemo_diags/cfgs/ORCA2_ICE_PISCES/EXPREF/file_def_nemo-oce.xml
===================================================================
--- NEMO/branches/2019/dev_r11643_ENHANCE-11_CEthe_Shaconemo_diags/cfgs/ORCA2_ICE_PISCES/EXPREF/file_def_nemo-oce.xml	(revision 11644)
+++ NEMO/branches/2019/dev_r11643_ENHANCE-11_CEthe_Shaconemo_diags/cfgs/ORCA2_ICE_PISCES/EXPREF/file_def_nemo-oce.xml	(revision 11998)
@@ -93,5 +93,12 @@
           <field field_ref="bgfrctem"     name="bgfrctem"    />
           <field field_ref="bgfrchfx"     name="bgfrchfx"    />
-          <field field_ref="bgfrcsal"     name="bgfrcsal"    />
+	  <field field_ref="bgfrcsal"     name="bgfrcsal"    />
+
+	  <field field_ref="masstot"      name="masso"  />
+          <field field_ref="voltot"       name="volo"  />
+          <field field_ref="sshthster"    name="zostoga"  />
+          <field field_ref="temptot"      name="bigthetaoga"  />
+          <field field_ref="saltot"       name="soga"  />
+          <field field_ref="ssttot"       name="tosga"  />
         </file>
 
@@ -100,9 +107,50 @@
 
       <file_group id="1m" output_freq="1mo" output_level="10" enabled=".TRUE."> <!-- real monthly files -->
+
+        <file id="file16" name_suffix="_diaptr2D" description="zonal mean variables" >
+          <field field_ref="sophtove"    name="htovovrt"      grid_ref="grid_ptr_T_2D"  />
+          <field field_ref="sopstove"    name="sltovovrt"     grid_ref="grid_ptr_T_2D"  />
+          <field field_ref="sophtgyre"   name="htovgyre"      grid_ref="grid_ptr_T_2D"  />
+          <field field_ref="sopstgyre"   name="sltogyre"      grid_ref="grid_ptr_T_2D"  />
+          <field field_ref="sophtbtr"    name="htbtr"         grid_ref="grid_ptr_T_2D"  />
+          <field field_ref="sopstbtr"    name="sltbtr"        grid_ref="grid_ptr_T_2D"  />
+          <field field_ref="sophtadv"    name="htadv"         grid_ref="grid_ptr_T_2D"  />
+          <field field_ref="sopstadv"    name="sltadv"        grid_ref="grid_ptr_T_2D"  />
+          <field field_ref="sophtldf"    name="htldf"         grid_ref="grid_ptr_T_2D"  />
+          <field field_ref="sopstldf"    name="sltldf"        grid_ref="grid_ptr_T_2D"  />
+          <field field_ref="sophtvtr"    name="hfbasin"       grid_ref="grid_ptr_T_2D"  />
+          <field field_ref="sopstvtr"    name="sltbasin"      grid_ref="grid_ptr_T_2D"  />
+          <field field_ref="sophteiv"    name="hfbasinpmadv"  grid_ref="grid_ptr_T_2D"  />
+          <field field_ref="sopsteiv"    name="sltbasinpmadv" grid_ref="grid_ptr_T_2D"  />
+        </file>
+
+
+         <file id="file17" name_suffix="_diaptr3D" description="zonal mean variables" >
+          <field field_ref="zomsf"       name="msftyz"        grid_ref="grid_ptr_W_3D"  />
+          <field field_ref="zotem"       name="znltem"        grid_ref="grid_ptr_T_3D"  />
+          <field field_ref="zosal"       name="znlsal"        grid_ref="grid_ptr_T_3D"  />
+          <field field_ref="zosrf"       name="znlsrf"        grid_ref="grid_ptr_T_3D"  />
+        </file>
+
+      <!--  
+         <file id="file18" name_suffix="_strait_oce" description="transport variables through straits" >
+           <field field_ref="masstr_strait"        name="mfo"               />
+         </file>	   
+      -->
+
       </file_group>
 
       <file_group id="1y"  output_freq="1y" output_level="10" enabled=".TRUE."> <!-- real yearly files -->
       </file_group>
-	
+
+      <!--  To compute transport through straits : need to read mask file ( every month is the best otherwise costly )
+
+      <file id="maskMFO"  name="maskMFO" enabled="true" mode="read" output_freq="1mo" cyclic="true"  >
+        <field id="maskMFO_u" operation="instant" freq_offset="1mo" grid_ref="grid_U_4strait" />
+        <field id="maskMFO_v" operation="instant" freq_offset="1mo" grid_ref="grid_V_4strait" />
+      </file>
+
+    -->
+
       
       <file_group id="1ts" output_freq="1ts" output_level="10" enabled=".TRUE."/> <!-- 1 time step files -->
