Index: /trunk/LMDZ.GENERIC/README
===================================================================
--- /trunk/LMDZ.GENERIC/README	(revision 3219)
+++ /trunk/LMDZ.GENERIC/README	(revision 3220)
@@ -1841,2 +1841,9 @@
 == 08/02/2024 == EM
 Code cleanup. Remove obsolete "sourceevol" option and related variables.
+
+== 16/02/2024 == EM
+Cleanup in deftank:
+- Update xml files: add missing variable definitions in field_def_physics.xml,
+  extract file_def_physics.xml from context_lmdz_physics.xml (and rename it 
+  context_pcm_physics.xml)
+- remove "executable property" for def files
Index: unk/LMDZ.GENERIC/deftank/context_lmdz_physics.xml
===================================================================
--- /trunk/LMDZ.GENERIC/deftank/context_lmdz_physics.xml	(revision 3219)
+++ 	(revision )
@@ -1,255 +1,0 @@
-<context id="LMDZ">
-
-    <!-- Definition of a calendar is done in code via wxios_set_cal -->
-
-    <!-- Definition of domains and groups of domains -->
-    <domain_definition>
-        <domain_group id="dom_glo" data_dim="1">
-          <domain id="dom_glo" />
-        </domain_group>
-
-    </domain_definition>
-
-    <domain_definition>
-        <domain id="dom_64_48" type="rectilinear" ni_glo="64" nj_glo="48"   >
-          <generate_rectilinear_domain/>
-          <interpolate_domain order="1"/>
-        </domain>
-
-        <domain id="dom_96_95" type="rectilinear"  ni_glo="96" nj_glo="95"  >
-          <generate_rectilinear_domain/>
-          <interpolate_domain order="1"/>
-        </domain>
-
-        <domain id="dom_144_142" type="rectilinear" ni_glo="144" nj_glo="142"   >
-          <generate_rectilinear_domain/>
-          <interpolate_domain order="1"/>
-        </domain>
-
-        <domain id="dom_512_360" type="rectilinear" ni_glo="512" nj_glo="360"   >
-          <generate_rectilinear_domain/>
-          <interpolate_domain order="1"/>
-        </domain>
-
-        <domain id="dom_720_360" type="rectilinear" ni_glo="720" nj_glo="360" >
-          <generate_rectilinear_domain/>
-          <interpolate_domain order="1"/>
-        </domain>
-
-        <domain id="dom_128_96" type="rectilinear" ni_glo="128" nj_glo="96" >
-          <generate_rectilinear_domain/>
-          <interpolate_domain order="1"/>
-        </domain>
-
-        <domain id="dom_256_192" type="rectilinear" ni_glo="256" nj_glo="192" >
-          <generate_rectilinear_domain/>
-          <interpolate_domain order="1"/>
-        </domain>
-
-        <domain id="dom_out" domain_ref="dom_128_96"/>
-    </domain_definition>
-    <!-- <domain_definition src="./domain_def.xml"/> -->
-
-    <!-- Definition of vertical axes 
-                           NB: these must be defined and set in code via
-         xios_output_mod -->
-    <axis_definition>
-        <axis id="presnivs" 
-              standard_name="Pseudo-pressure of model vertical levels" 
-              unit="Pa">
-        </axis>
-        <axis id="altitude" 
-              standard_name="Pseudo-altitude of model vertical levels" 
-              unit="km">
-        </axis>
-        <!--Added for diagspecIR-->
-        <axis id="IR_Wavenumber"
-               standard_name="Band mid frequency in the infrared"
-               unit="cm-1"> 
-        </axis>
-        <!--Added for diagspecVI-->
-        <axis id="VI_Wavenumber"
-              standard_name="Band mid frequency in the visible"
-              unit=
-            "cm-1">
-        </axis>
-
-    </axis_definition>
-
-    <scalar_definition>
-           <scalar id="scalar" />
-    </scalar_definition>
-
-    <grid_definition>
-        <!-- toggle axis id below to change output vertical axis -->
-        <grid id="grid_3D">
-            <domain domain_ref="dom_glo" />
-            <axis axis_ref="altitude" />
-        </grid>
-        <grid id="grid_2D">
-            <domain domain_ref="dom_glo" />
-        </grid>
-        <!--Added for diagspecIR-->
-        <grid id='grid_IR_3D'>
-            <domain domain_ref="dom_glo" />
-            <axis axis_ref='IR_Wavenumber'/>
-        </grid>
-        <!-- Added for diagspecVI-->
-        <grid id="grid_VI_3D">
-          <domain domain_ref="dom_glo" />
-          <axis axis_ref="VI_Wavenumber"/>
-        </grid>
-        <!-- grid for interpolated lon-lat outputs -->
-        <!-- to output scalars -->
-        <grid id="scalarpoint" >
-            <scalar scalar_ref="scalar" />
-        </grid>
-        <!-- output grids -->
-        <grid id="grid_3D_out">
-            <domain domain_ref="dom_out" />
-            <axis axis_ref="altitude" />
-        </grid>
-        <grid id="grid_2D_out">                                                   
-            <domain domain_ref="dom_out" />                                       
-        </grid>
-        <!--added for diagspecIR-->
-        <grid id="grid_IR_3D_out">
-            <domain domain_ref="dom_out"/>
-            <axis axis_ref="IR_Wavenumber"/>
-        </grid>
-        <grid id="grid_IR">
-            <axis axis_ref="IR_Wavenumber"/>
-        </grid>
-        <!--Added for diagspecVI-->
-        <grid id="grid_VI_3D_out">
-            <domain domain_ref="dom_out"/>
-            <axis axis_ref="VI_Wavenumber"/> 
-        </axis>
-        <grid id="grid_VI">
-          <axis axis_ref="VI_Wavenumber"/> 
-        </grid>
-    </grid_definition>                                                            
-                                                                                  
-    <!-- Definition of model variables -->                                        
-    <field_definition src="./field_def_physics.xml" />                            
-                                                                                  
-    <!-- Definition of output files -->                                           
-    <file_definition>                                                             
-                                                                                  
-        <!-- Instantaneous outputs; Here output_freq in physics time steps -->    
-        <!--                                                                      
-           1 ts == 1 physical ts                                     
-           if physical ts is half a day,                                          
-           10ts   below means every 5 days                                        
-           2000ts below means every 1000 days                                     
-        <file id="histins"                                                        
-              name="Xhistins"                                                     
-              output_freq="40ts" sync_freq="40ts"                                 
-              split_freq="2000ts"                                                 
-              type="one_file"                                                     
-              enabled=".true.">                                                   
-        split_freq does not seem to work                                          
-        -->                                                                       
-        <file id="histins"                                                        
-              name="Xhistins"                                                     
-              output_freq="50ts"                                                   
-              type="one_file"                                                     
-              time_units="days"
-              enabled="true">                                                     
-                                                                                  
-                                                                                  
-            <!-- VARS 0D -->                                                      
-            <field_group operation="instant"                                      
-                         grid_ref="scalarpoint"                                   
-                         freq_op="1ts">                                           
-                <field field_ref="ls" />                                          
-            </field_group>                                                        
-                                                                                  
-            <!--<field_group domain_ref="dom_glo"> -->                            
-            <!--<field_group grid_ref="grid_2D_out">-->                           
-            <!-- toggle domain_ref to output on native or lon-lat domain -->      
-                                                                                  
-              <!-- VARS 2D -->                                                    
-              <field_group operation="instant" prec="4"                           
-                           grid_ref="grid_2D_out"                                 
-                           freq_op="1ts">                                         
-                  <field field_ref="area" operation="once" />              
-                  <field field_ref="ps" enabled="true" />                         
-                  <field field_ref="ISR" enabled="true" />                        
-                  <field field_ref="OLR" enabled="true" />
-                  <field field_ref="ASR" enabled="true" />                        
-              </field_group>  
-
-              <!-- VARS 3D -->                                                    
-              <field_group operation="instant"                                    
-                           grid_ref="grid_3D_out"                                 
-                           freq_op="1ts">                                         
-                  <field field_ref="u" />                                         
-                  <field field_ref="v" />                                         
-                  <field field_ref="omega"/>                                      
-                  <field field_ref="temperature" />                               
-
-                  <!--field field_ref="h2o_vap" />
-                  <field field_ref="h2o_ice" />
-                  <field field_ref="w_plm" />
-                  <field field_ref="detr" />
-                  <field field_ref="entr" /-->
-              </field_group>                                                      
-                                                                                  
-            <!--</field_group>-->                                                 
-        </file>   
-       <!--XspecIR-->                                                                 
-      <file id="specIR"
-            name="XspecIR"
-            output_freq="50ts"
-            type="one_file"
-            time_units="days"
-            enabled="true">     
-          <!--Var 1D ?-->
-          <field_group operation="instant"
-                        grid_ref="grid_IR"
-                        freq_op="1ts">
-              <field field_ref="IR_Bandwidth" operation="once"/>
-          </field_group>
-          <!--Var 2D-->
-          <field_group operation="instant" prec="4"
-                        grid_ref="grid_2D_out"
-                        freq_op="1ts">
-              <field field_ref="area" operation="once" />
-          </field_group>
-          <!--Var 3D-->
-          <field_group operation="instant"
-                        grid_ref="grid_IR_3D_out"
-                        freq_op="1ts">
-              <field field_ref="OLR3D" />
-          </field_group>
-      </file>
-       <!--XspecVI-->                                                                 
-      <file id="specVI"
-            name="XspecVI"
-            output_freq="50ts"
-            type="one_file"
-            time_units="days"
-            enabled="true">     
-          <!--Var 1D -->
-          <field_group operation="instant"
-                        grid_ref="grid_VI"
-                        freq_op="1ts">
-              <field field_ref="VI_Bandwidth" operation="once"/>
-          </field_group>
-          <!--Var 2D-->
-          <field_group operation="instant" prec="4"
-                        grid_ref="grid_2D_out"
-                        freq_op="1ts">
-              <field field_ref="area" operation="once" />
-          </field_group>
-          <!--Var 3D-->
-          <field_group operation="instant"
-                        grid_ref="grid_VI_3D_out"
-                        freq_op="1ts">
-              <field field_ref="OSR3D" />
-              <field field_ref="GSR3D" />
-          </field_group>
-      </file>
-    </file_definition>                                                                                                                                     
-</context>  
Index: /trunk/LMDZ.GENERIC/deftank/context_pcm_physics.xml
===================================================================
--- /trunk/LMDZ.GENERIC/deftank/context_pcm_physics.xml	(revision 3220)
+++ /trunk/LMDZ.GENERIC/deftank/context_pcm_physics.xml	(revision 3220)
@@ -0,0 +1,141 @@
+<context id="LMDZ">
+
+    <!-- Definition of a calendar is done in code via wxios_set_cal -->
+
+    <!-- Definition of domains and groups of domains -->
+    <domain_definition>
+        <!-- NB: dom_glo data_dim is 1 for DYNAMICO and 2 for LMDZ.COMMON -->
+        <domain_group id="dom_glo" data_dim="1">
+          <domain id="dom_glo" />
+        </domain_group>
+
+    </domain_definition>
+
+    <domain_definition>
+        <domain id="dom_64_48" type="rectilinear" ni_glo="64" nj_glo="48"   >
+          <generate_rectilinear_domain/>
+          <interpolate_domain order="1"/>
+        </domain>
+
+        <domain id="dom_96_95" type="rectilinear"  ni_glo="96" nj_glo="95"  >
+          <generate_rectilinear_domain/>
+          <interpolate_domain order="1"/>
+        </domain>
+
+        <domain id="dom_144_142" type="rectilinear" ni_glo="144" nj_glo="142"   >
+          <generate_rectilinear_domain/>
+          <interpolate_domain order="1"/>
+        </domain>
+
+        <domain id="dom_512_360" type="rectilinear" ni_glo="512" nj_glo="360"   >
+          <generate_rectilinear_domain/>
+          <interpolate_domain order="1"/>
+        </domain>
+
+        <domain id="dom_720_360" type="rectilinear" ni_glo="720" nj_glo="360" >
+          <generate_rectilinear_domain/>
+          <interpolate_domain order="1"/>
+        </domain>
+
+        <domain id="dom_128_96" type="rectilinear" ni_glo="128" nj_glo="96" >
+          <generate_rectilinear_domain/>
+          <interpolate_domain order="1"/>
+        </domain>
+
+        <domain id="dom_256_192" type="rectilinear" ni_glo="256" nj_glo="192" >
+          <generate_rectilinear_domain/>
+          <interpolate_domain order="1"/>
+        </domain>
+
+        <!-- NB: dom_out data_ref should be "dom_glo" with LMDZ.COMMON -->
+        <domain id="dom_out" domain_ref="dom_128_96"/>
+    </domain_definition>
+
+
+    <!-- Definition of vertical axes 
+                           NB: these must be defined and set in code via
+         xios_output_mod -->
+    <axis_definition>
+        <axis id="presnivs" 
+              standard_name="Pseudo-pressure of model vertical levels" 
+              unit="Pa">
+        </axis>
+        <axis id="altitude" 
+              standard_name="Pseudo-altitude of model vertical levels" 
+              unit="km">
+        </axis>
+        <!--Added for diagspecIR-->
+        <axis id="IR_Wavenumber"
+               standard_name="Band mid frequency in the infrared"
+               unit="cm-1"> 
+        </axis>
+        <!--Added for diagspecVI-->
+        <axis id="VI_Wavenumber"
+              standard_name="Band mid frequency in the visible"
+              unit=
+            "cm-1">
+        </axis>
+
+    </axis_definition>
+
+    <scalar_definition>
+           <scalar id="scalar" />
+    </scalar_definition>
+
+    <grid_definition>
+        <!-- toggle axis id below to change output vertical axis -->
+        <grid id="grid_3D">
+            <domain domain_ref="dom_glo" />
+            <axis axis_ref="altitude" />
+        </grid>
+        <grid id="grid_2D">
+            <domain domain_ref="dom_glo" />
+        </grid>
+        <!--Added for diagspecIR-->
+        <grid id='grid_IR_3D'>
+            <domain domain_ref="dom_glo" />
+            <axis axis_ref='IR_Wavenumber'/>
+        </grid>
+        <!-- Added for diagspecVI-->
+        <grid id="grid_VI_3D">
+          <domain domain_ref="dom_glo" />
+          <axis axis_ref="VI_Wavenumber"/>
+        </grid>
+        <!-- grid for interpolated lon-lat outputs -->
+        <!-- to output scalars -->
+        <grid id="scalarpoint" >
+            <scalar scalar_ref="scalar" />
+        </grid>
+        <!-- output grids -->
+        <grid id="grid_3D_out">
+            <domain domain_ref="dom_out" />
+            <axis axis_ref="altitude" />
+        </grid>
+        <grid id="grid_2D_out">                                                   
+            <domain domain_ref="dom_out" />                                       
+        </grid>
+        <!--added for diagspecIR-->
+        <grid id="grid_IR_3D_out">
+            <domain domain_ref="dom_out"/>
+            <axis axis_ref="IR_Wavenumber"/>
+        </grid>
+        <grid id="grid_IR">
+            <axis axis_ref="IR_Wavenumber"/>
+        </grid>
+        <!--Added for diagspecVI-->
+        <grid id="grid_VI_3D_out">
+            <domain domain_ref="dom_out"/>
+            <axis axis_ref="VI_Wavenumber"/> 
+        </axis>
+        <grid id="grid_VI">
+          <axis axis_ref="VI_Wavenumber"/> 
+        </grid>
+    </grid_definition>                                                            
+                                                                                  
+    <!-- Definition of model variables -->                                        
+    <field_definition src="./field_def_physics.xml" />                            
+                                                                                  
+    <!-- Definition of output files -->
+    <file_definition src="./file_def_physics.xml" />
+
+</context>  
Index: /trunk/LMDZ.GENERIC/deftank/field_def_physics.xml
===================================================================
--- /trunk/LMDZ.GENERIC/deftank/field_def_physics.xml	(revision 3219)
+++ /trunk/LMDZ.GENERIC/deftank/field_def_physics.xml	(revision 3220)
@@ -1,6 +1,7 @@
-<!-- =========================================================================================================== -->
-<!-- field_def_physics.xml                                                                                       -->
-<!-- Definition of all existing variables that can be output from Dynamico physics                               -->
-<!-- =========================================================================================================== -->
+<!-- ============================================================== -->
+<!-- field_def_physics.xml                                          -->
+<!-- Definition of all existing variables that can be outputed
+     from Generic PCM physics                                       -->
+<!-- ============================================================== -->
 
     <field_definition prec="4" 
@@ -66,8 +67,8 @@
                    long_name="H2O ice thickness"
                    unit="kg/m2" />
-            <field id="h2o_cropped"
+            <field id="h2o_layer1"
                    long_name="h2o in the first layer"  
                    unit="kg/kg" />
-            <field id="co2_cropped"
+            <field id="co2_layer1"
                    long_name="co2 in the first layer"  
                    unit="kg/kg" />
@@ -89,9 +90,12 @@
                    long_name="Downward omega velocity" 
                    unit="Pa/s" />
+            <field id="p" 
+                   long_name="Atmospheric pressure" 
+                   unit="Pa" />
             <field id="h2o_vap" 
-                   long_name="Vapor mass mixing ratio" 
+                   long_name="Water vapor mass mixing ratio" 
                    unit="kg/kg" />
             <field id="h2o_ice" 
-                   long_name="Vapor mass mixing ratio" 
+                   long_name="Water ice mass mixing ratio" 
                    unit="kg/kg" />
             <field id="detr" 
@@ -112,4 +116,5 @@
                      unit="W/m^2/cm^-1" />
        </field_group>
+
        <!-- SPectral VI 3D variables-->
        <field_group id="spectral_VI_3D" grid_ref="grid_VI_3D">
Index: /trunk/LMDZ.GENERIC/deftank/file_def_physics.xml
===================================================================
--- /trunk/LMDZ.GENERIC/deftank/file_def_physics.xml	(revision 3220)
+++ /trunk/LMDZ.GENERIC/deftank/file_def_physics.xml	(revision 3220)
@@ -0,0 +1,116 @@
+<!-- =================================================================== -->
+<!-- file_def_physics.xml                                                -->
+<!-- Definition of output files for Generic PCM physics                  -->
+<!-- =================================================================== -->
+
+    <file_definition>                                                             
+                                                                                  
+        <!-- Instantaneous outputs; Here output_freq in physics time steps -->    
+        <!--                                                                      
+           1 ts == 1 physical ts                                     
+           if physical ts is half a day,                                          
+           10ts   below means every 5 days                                        
+           2000ts below means every 1000 days
+          -->                                  
+        <file id="histins"                                                        
+              name="Xhistins"                                                     
+              output_freq="50ts"                                                   
+              type="one_file"                                                     
+              time_units="days"
+              enabled="true">                                                     
+                                                                                  
+                                                                                  
+            <!-- VARS 0D -->                                                      
+            <field_group operation="instant"                                      
+                         grid_ref="scalarpoint"                                   
+                         freq_op="1ts">                                           
+                <field field_ref="ls" />                                          
+            </field_group>                                                        
+                                                                                  
+            <!--<field_group domain_ref="dom_glo"> -->                            
+            <!--<field_group grid_ref="grid_2D_out">-->                           
+            <!-- toggle domain_ref to output on native or lon-lat domain -->      
+                                                                                  
+              <!-- VARS 2D -->                                                    
+              <field_group operation="instant" prec="4"                           
+                           grid_ref="grid_2D_out"                                 
+                           freq_op="1ts">                                         
+                  <field field_ref="area" operation="once" />              
+                  <field field_ref="ps" enabled="true" />                         
+                  <field field_ref="ISR" enabled="true" />                        
+                  <field field_ref="OLR" enabled="true" />
+                  <field field_ref="ASR" enabled="true" />                        
+              </field_group>  
+
+              <!-- VARS 3D -->                                                    
+              <field_group operation="instant"                                    
+                           grid_ref="grid_3D_out"                                 
+                           freq_op="1ts">                                         
+                  <field field_ref="u" />                                         
+                  <field field_ref="v" />                                         
+                  <field field_ref="omega"/>                                      
+                  <field field_ref="temperature" />                               
+
+                  <!--field field_ref="h2o_vap" />
+                  <field field_ref="h2o_ice" />
+                  <field field_ref="w_plm" />
+                  <field field_ref="detr" />
+                  <field field_ref="entr" /-->
+              </field_group>                                                      
+                                                                                  
+            <!--</field_group>-->                                                 
+        </file>   
+       <!--XspecIR-->                                                                 
+      <file id="specIR"
+            name="XspecIR"
+            output_freq="50ts"
+            type="one_file"
+            time_units="days"
+            enabled="true">     
+          <!--Var 1D ?-->
+          <field_group operation="instant"
+                        grid_ref="grid_IR"
+                        freq_op="1ts">
+              <field field_ref="IR_Bandwidth" operation="once"/>
+          </field_group>
+          <!--Var 2D-->
+          <field_group operation="instant" prec="4"
+                        grid_ref="grid_2D_out"
+                        freq_op="1ts">
+              <field field_ref="area" operation="once" />
+          </field_group>
+          <!--Var 3D-->
+          <field_group operation="instant"
+                        grid_ref="grid_IR_3D_out"
+                        freq_op="1ts">
+              <field field_ref="OLR3D" />
+          </field_group>
+      </file>
+       <!--XspecVI-->                                                                 
+      <file id="specVI"
+            name="XspecVI"
+            output_freq="50ts"
+            type="one_file"
+            time_units="days"
+            enabled="true">     
+          <!--Var 1D -->
+          <field_group operation="instant"
+                        grid_ref="grid_VI"
+                        freq_op="1ts">
+              <field field_ref="VI_Bandwidth" operation="once"/>
+          </field_group>
+          <!--Var 2D-->
+          <field_group operation="instant" prec="4"
+                        grid_ref="grid_2D_out"
+                        freq_op="1ts">
+              <field field_ref="area" operation="once" />
+          </field_group>
+          <!--Var 3D-->
+          <field_group operation="instant"
+                        grid_ref="grid_VI_3D_out"
+                        freq_op="1ts">
+              <field field_ref="OSR3D" />
+              <field field_ref="GSR3D" />
+          </field_group>
+      </file>
+    </file_definition>                                                                                                                                     
Index: /trunk/LMDZ.GENERIC/deftank/iodef.xml
===================================================================
--- /trunk/LMDZ.GENERIC/deftank/iodef.xml	(revision 3219)
+++ /trunk/LMDZ.GENERIC/deftank/iodef.xml	(revision 3220)
@@ -26,5 +26,5 @@
         
 
-        <context id="LMDZ" src="./context_lmdz_physics.xml"/>
+        <context id="LMDZ" src="./context_pcm_physics.xml"/>