Changeset 484 for configs

Timestamp:

09/26/16 14:24:14 (8 years ago)

Author:

ymipsl

Message:

Adapt DCMIP2016 testcases to news output (start/restart files management)

YM

Location:

configs/dcmip2016/RUNS

Files:

• BAROCLINIC_WAVE/dry/field_def.xml (modified) (4 diffs)
• BAROCLINIC_WAVE/dry/filedef_dcmip2016.xml (modified) (3 diffs)
• BAROCLINIC_WAVE/dry/icosa.xml (modified) (4 diffs)
• BAROCLINIC_WAVE/dry/iodef.xml (modified) (1 diff)
• BAROCLINIC_WAVE/dry/run.def (modified) (5 diffs)
• BAROCLINIC_WAVE/dry_variable/field_def.xml (modified) (4 diffs)
• BAROCLINIC_WAVE/dry_variable/filedef_dcmip2016.xml (modified) (1 diff)
• BAROCLINIC_WAVE/dry_variable/icosa.xml (modified) (4 diffs)
• BAROCLINIC_WAVE/moist_full_physiq/field_def.xml (modified) (5 diffs)
• BAROCLINIC_WAVE/moist_full_physiq/filedef_dcmip2016.xml (modified) (1 diff)
• BAROCLINIC_WAVE/moist_full_physiq/icosa.xml (modified) (4 diffs)
• BAROCLINIC_WAVE/moist_full_physiq_0.5deg/field_def.xml (modified) (5 diffs)
• BAROCLINIC_WAVE/moist_full_physiq_0.5deg/filedef_dcmip2016.xml (modified) (1 diff)
• BAROCLINIC_WAVE/moist_full_physiq_0.5deg/icosa.xml (modified) (4 diffs)
• BAROCLINIC_WAVE/moist_full_physiq_0.5deg_1ts/field_def.xml (modified) (5 diffs)
• BAROCLINIC_WAVE/moist_full_physiq_0.5deg_1ts/filedef_dcmip2016.xml (modified) (1 diff)
• BAROCLINIC_WAVE/moist_full_physiq_0.5deg_1ts/icosa.xml (modified) (4 diffs)
• BAROCLINIC_WAVE/moist_full_physiq_0.5deg_2ts/field_def.xml (modified) (5 diffs)
• BAROCLINIC_WAVE/moist_full_physiq_0.5deg_2ts/filedef_dcmip2016.xml (modified) (1 diff)
• BAROCLINIC_WAVE/moist_full_physiq_0.5deg_2ts/icosa.xml (modified) (4 diffs)
• BAROCLINIC_WAVE/moist_full_physiq_30min/field_def.xml (modified) (5 diffs)
• BAROCLINIC_WAVE/moist_full_physiq_30min/filedef_dcmip2016.xml (modified) (1 diff)
• BAROCLINIC_WAVE/moist_full_physiq_30min/icosa.xml (modified) (4 diffs)
• BAROCLINIC_WAVE/moist_kessler/field_def.xml (modified) (5 diffs)
• BAROCLINIC_WAVE/moist_kessler/filedef_dcmip2016.xml (modified) (1 diff)
• BAROCLINIC_WAVE/moist_kessler/icosa.xml (modified) (4 diffs)
• CYCLONE/0125_degree_BRYAN_PBL/field_def.xml (modified) (5 diffs)
• CYCLONE/0125_degree_BRYAN_PBL/filedef_dcmip2016.xml (modified) (1 diff)
• CYCLONE/0125_degree_BRYAN_PBL/icosa.xml (modified) (4 diffs)
• CYCLONE/0125_degree_RJ_PBL/field_def.xml (modified) (5 diffs)
• CYCLONE/0125_degree_RJ_PBL/filedef_dcmip2016.xml (modified) (1 diff)
• CYCLONE/0125_degree_RJ_PBL/icosa.xml (modified) (4 diffs)
• CYCLONE/1over16_degree_BRYAN_PBL/field_def.xml (modified) (5 diffs)
• CYCLONE/1over16_degree_BRYAN_PBL/filedef_dcmip2016.xml (modified) (1 diff)
• CYCLONE/1over16_degree_BRYAN_PBL/icosa.xml (modified) (4 diffs)
• CYCLONE/1over16_degree_RJ_PBL/field_def.xml (modified) (5 diffs)
• CYCLONE/1over16_degree_RJ_PBL/filedef_dcmip2016.xml (modified) (1 diff)
• CYCLONE/1over16_degree_RJ_PBL/icosa.xml (modified) (4 diffs)
• CYCLONE/half_degree_BRYAN_PBL/field_def.xml (modified) (5 diffs)
• CYCLONE/half_degree_BRYAN_PBL/filedef_dcmip2016.xml (modified) (1 diff)
• CYCLONE/half_degree_BRYAN_PBL/icosa.xml (modified) (4 diffs)
• CYCLONE/half_degree_RJ_PBL/field_def.xml (modified) (5 diffs)
• CYCLONE/half_degree_RJ_PBL/filedef_dcmip2016.xml (modified) (1 diff)
• CYCLONE/half_degree_RJ_PBL/icosa.xml (modified) (4 diffs)
• CYCLONE/quarter_degree_BRYAN_PBL/field_def.xml (modified) (5 diffs)
• CYCLONE/quarter_degree_BRYAN_PBL/filedef_dcmip2016.xml (modified) (1 diff)
• CYCLONE/quarter_degree_BRYAN_PBL/icosa.xml (modified) (4 diffs)
• CYCLONE/quarter_degree_RJ_PBL/field_def.xml (modified) (5 diffs)
• CYCLONE/quarter_degree_RJ_PBL/filedef_dcmip2016.xml (modified) (1 diff)
• CYCLONE/quarter_degree_RJ_PBL/icosa.xml (modified) (4 diffs)
• SUPERCELL/1_degree/field_def.xml (modified) (4 diffs)
• SUPERCELL/1_degree/filedef_dcmip2016.xml (modified) (1 diff)
• SUPERCELL/1_degree/icosa.xml (modified) (4 diffs)
• SUPERCELL/2_degree/field_def.xml (modified) (4 diffs)
• SUPERCELL/2_degree/filedef_dcmip2016.xml (modified) (1 diff)
• SUPERCELL/2_degree/icosa.xml (modified) (4 diffs)
• SUPERCELL/4_degree/field_def.xml (modified) (4 diffs)
• SUPERCELL/4_degree/filedef_dcmip2016.xml (modified) (1 diff)
• SUPERCELL/4_degree/icosa.xml (modified) (4 diffs)
• SUPERCELL/half_degree/field_def.xml (modified) (4 diffs)
• SUPERCELL/half_degree/filedef_dcmip2016.xml (modified) (1 diff)
• SUPERCELL/half_degree/icosa.xml (modified) (4 diffs)

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/dry/field_def.xml

@@ -33 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -39 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -49 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -75 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/dry/filedef_dcmip2016.xml

@@ -1 +1 @@
 <file_definition > 
 
-  <file id="output_dcmip2016_native" enabled=".TRUE." output_freq="3h" sync_freq="3h" output_level="10" timeseries="both" description="Dry baroclinic wave" > 
+  <file id="output_dcmip2016_native" convention="CF" enabled="true" output_freq="3h" sync_freq="3h" output_level="10" timeseries="none" description="Dry baroclinic wave" > 
     
     <field_group id="dcmip2016_output_field_once" operation="once" freq_offset="0ts" ts_enabled="true">
@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
       <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+-->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
       <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+-->
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
@@ -56 +60 @@
 
 
-  <file id="output_dcmip2016_regular" enabled=".TRUE." output_freq="3h" sync_freq="3h" output_level="10" description="Dry baroclinic wave" timeseries="both" > 
+  <file id="output_dcmip2016_regular" enabled="false" output_freq="3h" sync_freq="3h" output_level="10" description="Dry baroclinic wave" timeseries="none" > 
     
     <field_group group_ref="dcmip2016_output_field_once"/>

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/dry/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-<!--  <file_definition src="./filedef_debug.xml" /> -->     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read">
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -52 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/dry/iodef.xml

@@ -5 +5 @@
                 <variable_definition>
                 <variable id="print_file" type="bool"> true </variable> 
-                <variable id="min_buffer_size" type="double">1000000</variable> 
                 <variable_group id="buffer">
                 </variable_group>
 
                 <variable_group id="parameters" >
-                        <variable id="using_server" type="bool">true</variable>
+                        <variable id="using_server" type="bool">false</variable>
                         <variable id="info_level" type="int">100</variable>
                 </variable_group>

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/dry/run.def

@@ +1 @@
+mpi_threading_mode=funneled
 INCLUDEDEF = const.def
 
@@ -4 +5 @@
 
 # Number of subdivisions on a main triangle : integer (default=40)
-nbp = 80
+nbp = 40
 
 # Number of vertical layers : integer (default=19)
@@ -14 +15 @@
 
 # Mesh optimisation : number of iterations : integer (default=0)
-optim_it = 2000
+optim_it = 0
 
 # Sub splitting of main rhombus : integer (default=1)
-nsplit_i = 4
-nsplit_j = 4
+nsplit_i = 2
+nsplit_j = 2
 
+omp_level_size=1
 
 #---------------- Numerics ----------------
@@ -49 +51 @@
 # Run length in s : real (default=??)
 #            30 days
-run_length = 2592000
-#run_length = 86400
+#run_length = 2592000
+#run_length = 604800
+run_length = 10800
 
 # Interval in s between two outputs : integer (default=??)
@@ -63 +66 @@
 # Initial state : 
 #   [jablonowsky06|academic|dcmip[1-4]|heldsz|dcmip2_schaer_noshear] (default=jablonowsky06)
-etat0 = dcmip2016_baroclinic_wave
+#etat0 = dcmip2016_baroclinic_wave
+etat0 = start_file
 
+restart_file_name=test_restart
+
+itau_check_conserv=1
 
 itau_physics=3

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/dry_variable/field_def.xml

@@ -33 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -39 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -49 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -75 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/dry_variable/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/dry_variable/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-<!--  <file_definition src="./filedef_debug.xml" /> -->     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read">
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -52 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq/field_def.xml

@@ -15 +15 @@
       <field id="Ai" />
       <field id="phis" />
+      <field id="phi" />
       <field id="precl" />
       <field id="Q1_col_int" />     
@@ -32 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -38 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -48 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -74 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="u850" name="U850"       long_name="Zonal wind at 850 hPa"      unit="m/s"/>
       <field field_ref="v850" name="V850"       long_name="Meridional wind at 850 hPa"   unit="m/s"/>

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-<!--  <file_definition src="./filedef_debug.xml" /> -->     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -52 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq_0.5deg/field_def.xml

@@ -15 +15 @@
       <field id="Ai" />
       <field id="phis" />
+      <field id="phi" />
       <field id="precl" />
       <field id="Q1_col_int" />     
@@ -32 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -38 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -48 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -74 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq_0.5deg/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="u850" name="U850"       long_name="Zonal wind at 850 hPa"      unit="m/s"/>
       <field field_ref="v850" name="V850"       long_name="Meridional wind at 850 hPa"   unit="m/s"/>

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq_0.5deg/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-<!--  <file_definition src="./filedef_debug.xml" /> -->     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -52 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq_0.5deg_1ts/field_def.xml

@@ -15 +15 @@
       <field id="Ai" />
       <field id="phis" />
+      <field id="phi" />
       <field id="precl" />
       <field id="Q1_col_int" />     
@@ -32 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -38 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -48 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -74 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq_0.5deg_1ts/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="u850" name="U850"       long_name="Zonal wind at 850 hPa"      unit="m/s"/>
       <field field_ref="v850" name="V850"       long_name="Meridional wind at 850 hPa"   unit="m/s"/>

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq_0.5deg_1ts/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-<!--  <file_definition src="./filedef_debug.xml" /> -->     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -52 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq_0.5deg_2ts/field_def.xml

@@ -15 +15 @@
       <field id="Ai" />
       <field id="phis" />
+      <field id="phi" />
       <field id="precl" />
       <field id="Q1_col_int" />     
@@ -32 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -38 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -48 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -74 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq_0.5deg_2ts/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="u850" name="U850"       long_name="Zonal wind at 850 hPa"      unit="m/s"/>
       <field field_ref="v850" name="V850"       long_name="Meridional wind at 850 hPa"   unit="m/s"/>

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq_0.5deg_2ts/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-<!--  <file_definition src="./filedef_debug.xml" /> -->     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -52 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq_30min/field_def.xml

@@ -15 +15 @@
       <field id="Ai" />
       <field id="phis" />
+      <field id="phi" />
       <field id="precl" />
       <field id="Q1_col_int" />     
@@ -32 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -38 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -48 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -74 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq_30min/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="u850" name="U850"       long_name="Zonal wind at 850 hPa"      unit="m/s"/>
       <field field_ref="v850" name="V850"       long_name="Meridional wind at 850 hPa"   unit="m/s"/>

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_full_physiq_30min/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-<!--  <file_definition src="./filedef_debug.xml" /> -->     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -52 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_kessler/field_def.xml

@@ -15 +15 @@
       <field id="Ai" />
       <field id="phis" />
+      <field id="phi" />
       <field id="precl" />
       <field id="Q1_col_int" />     
@@ -32 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -38 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -48 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -74 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_kessler/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="u850" name="U850"       long_name="Zonal wind at 850 hPa"      unit="m/s"/>
       <field field_ref="v850" name="V850"       long_name="Meridional wind at 850 hPa"   unit="m/s"/>

configs/dcmip2016/RUNS/BAROCLINIC_WAVE/moist_kessler/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-<!--  <file_definition src="./filedef_debug.xml" /> -->     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -52 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/CYCLONE/0125_degree_BRYAN_PBL/field_def.xml

@@ -15 +15 @@
       <field id="Ai" />
       <field id="phis" />
+      <field id="phi" />
       <field id="precl" />
       <field id="Q1_col_int" />     
@@ -32 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -38 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -48 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -74 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/CYCLONE/0125_degree_BRYAN_PBL/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="u850" name="U850"       long_name="Zonal wind at 850 hPa"      unit="m/s"/>
       <field field_ref="v850" name="V850"       long_name="Meridional wind at 850 hPa"   unit="m/s"/>

configs/dcmip2016/RUNS/CYCLONE/0125_degree_BRYAN_PBL/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-  <file_definition src="./filedef_debug.xml" />     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
-
-     <domain id="regular_0125_degree_zoom" type="rectilinear" ni_glo="800" nj_glo="600" >
-       <generate_rectilinear_domain lon_start="120" lon_end="220" lat_start="-20" lat_end="55"/>
-       <interpolate_domain order="1"/>
-     </domain> 
-
-     <domain id="regular_quarter_degree_zoom" type="rectilinear" ni_glo="400" nj_glo="300" >
-       <generate_rectilinear_domain lon_start="120" lon_end="220" lat_start="-20" lat_end="55"/>
-       <interpolate_domain order="1"/>
-     </domain> 
- 
-     <domain id="regular_quarter_degree" type="rectilinear" ni_glo="1440" nj_glo="720" >
-       <generate_rectilinear_domain />
-       <interpolate_domain order="1"/>
-     </domain> 
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -67 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/CYCLONE/0125_degree_RJ_PBL/field_def.xml

@@ -15 +15 @@
       <field id="Ai" />
       <field id="phis" />
+      <field id="phi" />
       <field id="precl" />
       <field id="Q1_col_int" />     
@@ -32 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -38 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -48 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -74 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/CYCLONE/0125_degree_RJ_PBL/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="u850" name="U850"       long_name="Zonal wind at 850 hPa"      unit="m/s"/>
       <field field_ref="v850" name="V850"       long_name="Meridional wind at 850 hPa"   unit="m/s"/>

configs/dcmip2016/RUNS/CYCLONE/0125_degree_RJ_PBL/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-  <file_definition src="./filedef_debug.xml" />     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
-
-     <domain id="regular_0125_degree_zoom" type="rectilinear" ni_glo="800" nj_glo="600" >
-       <generate_rectilinear_domain lon_start="120" lon_end="220" lat_start="-20" lat_end="55"/>
-       <interpolate_domain order="1"/>
-     </domain> 
-
-     <domain id="regular_quarter_degree_zoom" type="rectilinear" ni_glo="400" nj_glo="300" >
-       <generate_rectilinear_domain lon_start="120" lon_end="220" lat_start="-20" lat_end="55"/>
-       <interpolate_domain order="1"/>
-     </domain> 
- 
-     <domain id="regular_quarter_degree" type="rectilinear" ni_glo="1440" nj_glo="720" >
-       <generate_rectilinear_domain />
-       <interpolate_domain order="1"/>
-     </domain> 
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -67 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/CYCLONE/1over16_degree_BRYAN_PBL/field_def.xml

@@ -15 +15 @@
       <field id="Ai" />
       <field id="phis" />
+      <field id="phi" />
       <field id="precl" />
       <field id="Q1_col_int" />     
@@ -32 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -38 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -48 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -74 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/CYCLONE/1over16_degree_BRYAN_PBL/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="u850" name="U850"       long_name="Zonal wind at 850 hPa"      unit="m/s"/>
       <field field_ref="v850" name="V850"       long_name="Meridional wind at 850 hPa"   unit="m/s"/>

configs/dcmip2016/RUNS/CYCLONE/1over16_degree_BRYAN_PBL/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-  <file_definition src="./filedef_debug.xml" />     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
-
-     <domain id="regular_1over16_degree_zoom" type="rectilinear" ni_glo="1600" nj_glo="1200" >
-       <generate_rectilinear_domain lon_start="120" lon_end="220" lat_start="-20" lat_end="55"/>
-       <interpolate_domain order="1"/>
-     </domain> 
- 
-     <domain id="regular_0125_degree_zoom" type="rectilinear" ni_glo="800" nj_glo="600" >
-       <generate_rectilinear_domain lon_start="120" lon_end="220" lat_start="-20" lat_end="55"/>
-       <interpolate_domain order="1"/>
-     </domain> 
-
-     <domain id="regular_quarter_degree_zoom" type="rectilinear" ni_glo="400" nj_glo="300" >
-       <generate_rectilinear_domain lon_start="120" lon_end="220" lat_start="-20" lat_end="55"/>
-       <interpolate_domain order="1"/>
-     </domain> 
- 
-     <domain id="regular_quarter_degree" type="rectilinear" ni_glo="1440" nj_glo="720" >
-       <generate_rectilinear_domain />
-       <interpolate_domain order="1"/>
-     </domain> 
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -72 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/CYCLONE/1over16_degree_RJ_PBL/field_def.xml

@@ -15 +15 @@
       <field id="Ai" />
       <field id="phis" />
+      <field id="phi" />
       <field id="precl" />
       <field id="Q1_col_int" />     
@@ -32 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -38 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -48 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -74 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/CYCLONE/1over16_degree_RJ_PBL/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="u850" name="U850"       long_name="Zonal wind at 850 hPa"      unit="m/s"/>
       <field field_ref="v850" name="V850"       long_name="Meridional wind at 850 hPa"   unit="m/s"/>

configs/dcmip2016/RUNS/CYCLONE/1over16_degree_RJ_PBL/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-  <file_definition src="./filedef_debug.xml" />     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
-
-     <domain id="regular_1over16_degree_zoom" type="rectilinear" ni_glo="1600" nj_glo="1200" >
-       <generate_rectilinear_domain lon_start="120" lon_end="220" lat_start="-20" lat_end="55"/>
-       <interpolate_domain order="1"/>
-     </domain> 
- 
-     <domain id="regular_0125_degree_zoom" type="rectilinear" ni_glo="800" nj_glo="600" >
-       <generate_rectilinear_domain lon_start="120" lon_end="220" lat_start="-20" lat_end="55"/>
-       <interpolate_domain order="1"/>
-     </domain> 
-
-     <domain id="regular_quarter_degree_zoom" type="rectilinear" ni_glo="400" nj_glo="300" >
-       <generate_rectilinear_domain lon_start="120" lon_end="220" lat_start="-20" lat_end="55"/>
-       <interpolate_domain order="1"/>
-     </domain> 
- 
-     <domain id="regular_quarter_degree" type="rectilinear" ni_glo="1440" nj_glo="720" >
-       <generate_rectilinear_domain />
-       <interpolate_domain order="1"/>
-     </domain> 
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -72 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/CYCLONE/half_degree_BRYAN_PBL/field_def.xml

@@ -15 +15 @@
       <field id="Ai" />
       <field id="phis" />
+      <field id="phi" />
       <field id="precl" />
       <field id="Q1_col_int" />     
@@ -32 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -38 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -48 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -74 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/CYCLONE/half_degree_BRYAN_PBL/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECL"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="u850" name="U850"       long_name="Zonal wind at 850 hPa"      unit="m/s"/>
       <field field_ref="v850" name="V850"       long_name="Meridional wind at 850 hPa"   unit="m/s"/>

configs/dcmip2016/RUNS/CYCLONE/half_degree_BRYAN_PBL/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-  <file_definition src="./filedef_debug.xml" />     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -52 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/CYCLONE/half_degree_RJ_PBL/field_def.xml

@@ -15 +15 @@
       <field id="Ai" />
       <field id="phis" />
+      <field id="phi" />
       <field id="precl" />
       <field id="Q1_col_int" />     
@@ -32 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -38 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -48 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -74 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/CYCLONE/half_degree_RJ_PBL/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECL"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="u850" name="U850"       long_name="Zonal wind at 850 hPa"      unit="m/s"/>
       <field field_ref="v850" name="V850"       long_name="Meridional wind at 850 hPa"   unit="m/s"/>

configs/dcmip2016/RUNS/CYCLONE/half_degree_RJ_PBL/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-  <file_definition src="./filedef_debug.xml" />     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -52 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/CYCLONE/quarter_degree_BRYAN_PBL/field_def.xml

@@ -15 +15 @@
       <field id="Ai" />
       <field id="phis" />
+      <field id="phi" />
       <field id="precl" />
       <field id="Q1_col_int" />     
@@ -32 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -38 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -48 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -74 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/CYCLONE/quarter_degree_BRYAN_PBL/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECL"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="u850" name="U850"       long_name="Zonal wind at 850 hPa"      unit="m/s"/>
       <field field_ref="v850" name="V850"       long_name="Meridional wind at 850 hPa"   unit="m/s"/>

configs/dcmip2016/RUNS/CYCLONE/quarter_degree_BRYAN_PBL/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-  <file_definition src="./filedef_debug.xml" />     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
-
-     <domain id="regular_quarter_degree_zoom" type="rectilinear" ni_glo="400" nj_glo="300" >
-       <generate_rectilinear_domain lon_start="120" lon_end="220" lat_start="-20" lat_end="55"/>
-       <interpolate_domain order="1"/>
-     </domain> 
- 
-     <domain id="regular_quarter_degree" type="rectilinear" ni_glo="1440" nj_glo="720" >
-       <generate_rectilinear_domain />
-       <interpolate_domain order="1"/>
-     </domain> 
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -62 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/CYCLONE/quarter_degree_RJ_PBL/field_def.xml

@@ -15 +15 @@
       <field id="Ai" />
       <field id="phis" />
+      <field id="phi" />
       <field id="precl" />
       <field id="Q1_col_int" />     
@@ -32 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -38 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -48 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -74 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/CYCLONE/quarter_degree_RJ_PBL/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECL"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="u850" name="U850"       long_name="Zonal wind at 850 hPa"      unit="m/s"/>
       <field field_ref="v850" name="V850"       long_name="Meridional wind at 850 hPa"   unit="m/s"/>

configs/dcmip2016/RUNS/CYCLONE/quarter_degree_RJ_PBL/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-  <file_definition src="./filedef_debug.xml" />     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
-
-     <domain id="regular_quarter_degree_zoom" type="rectilinear" ni_glo="400" nj_glo="300" >
-       <generate_rectilinear_domain lon_start="120" lon_end="220" lat_start="-20" lat_end="55"/>
-       <interpolate_domain order="1"/>
-     </domain> 
- 
-     <domain id="regular_quarter_degree" type="rectilinear" ni_glo="1440" nj_glo="720" >
-       <generate_rectilinear_domain />
-       <interpolate_domain order="1"/>
-     </domain> 
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -62 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/SUPERCELL/1_degree/field_def.xml

@@ -33 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -39 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -49 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -75 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/SUPERCELL/1_degree/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 

configs/dcmip2016/RUNS/SUPERCELL/1_degree/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-<!--  <file_definition src="./filedef_debug.xml" /> -->     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -52 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/SUPERCELL/2_degree/field_def.xml

@@ -33 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -39 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -49 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -75 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/SUPERCELL/2_degree/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 

configs/dcmip2016/RUNS/SUPERCELL/2_degree/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-<!--  <file_definition src="./filedef_debug.xml" /> -->     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -52 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/SUPERCELL/4_degree/field_def.xml

@@ -33 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -39 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -49 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -75 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/SUPERCELL/4_degree/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/>  -->
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 

configs/dcmip2016/RUNS/SUPERCELL/4_degree/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-<!--  <file_definition src="./filedef_debug.xml" /> -->     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -52 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>   
   

configs/dcmip2016/RUNS/SUPERCELL/half_degree/field_def.xml

@@ -33 +33 @@
         <field id="omega"/>
         <field id="temp"/>
-        
+
+<!--        
         <field id="q1"/>
         <field id="q2"/>
@@ -39 +40 @@
         <field id="q4"/>
         <field id="q5"/>
-
+-->
+        
         <field id="mass_init" />
         <field id="p_init" />
@@ -49 +51 @@
         <field id="temp_init"/>
         
-        <field id="q_init1"/>
-        <field id="q_init2"/>
-        <field id="q_init3"/>
-        <field id="q_init4"/>
-        <field id="q_init5"/>
       </field_group>
-      
       <field id="u850" />
       <field id="v850" />
@@ -75 +71 @@
       </field_group>
     </field_group> 
-    
+    <field id="q_init" grid_ref="grid_q" />    
+    <field id="q" grid_ref="grid_q" />    
     
     <field_group domain_ref="v" axis_ref="lev">

configs/dcmip2016/RUNS/SUPERCELL/half_degree/filedef_dcmip2016.xml

@@ -23 +23 @@
       <field field_ref="p"  name="P"        standard_name="air_pressure" long_name="Pressure"     unit="Pa"/>
       <field field_ref="temp"  name="T"        standard_name="air_temperature" long_name="Temperature"     unit="K"/>
+<!--
       <field field_ref="q1"  name="Q"        standard_name="specific_humidity"  long_name="Specific humidity"          unit="kg/kg"/>
       <field field_ref="q2"  name="Qc"                                          long_name="Cloud water mixing ration"  unit="kg/kg"/>
-      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/>
+      <field field_ref="q3"  name="Qr"                                          long_name="Rain water mixing ration"  unit="kg/kg"/> -->
       <field field_ref="precl"  name="PRECT"     standard_name="rainfall_rate"  long_name="Large Scale precipitation rate"  unit="m/s"/>
+<!--
       <field field_ref="q4"  name="Q1"      long_name="Single chlorine mixing ratio"  unit="kg/kg"/> 
-      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> 
+      <field field_ref="q5"  name="Q2"      long_name="Chlorine gas mixing ratio"  unit="kg/kg"/> --> 
       <field field_ref="Q1_col_int"  name="Q1_col_int"      long_name="Single chlorine column integrated mixing ratio"  unit="kg/m2"/> 
       <field field_ref="Q2_col_int"  name="Q2_col_int"      long_name="Chlorine gas column integrated mixing ratio"  unit="kg/m2"/> 

configs/dcmip2016/RUNS/SUPERCELL/half_degree/icosa.xml

@@ -4 +4 @@
   <field_definition src="./field_def.xml" />
 
+<!--  <file_definition src="./filedef_debug.xml" /> -->     
   <file_definition src="./filedef_dcmip2016.xml" /> 
-<!--  <file_definition src="./filedef_debug.xml" /> -->     
 
   <file_definition type="one_file" par_access="collective">
@@ -12 +12 @@
       <field_group group_ref="standard_output"/>
     </file>
+
+    <file id="restart" name="restart" enabled="true">
+       <field_group id="group_restart" operation="once"> 
+          <field id="it_restart" name="iteration"  grid_ref="scalar" />
+          <field id="q_restart" name="q"  grid_ref="grid_q" />
+          <field_group domain_ref="i"> 
+             <field id="ps_restart" name="ps" />
+             <field id="phis_restart" name="phis" />
+             <field_group axis_ref="lev" >
+                <field id="theta_rhodz_restart" name="theta_rhodz" />
+                <field id="u_restart" name="u" domain_ref="u"/>
+                <field id="ulon_restart" name="ulon" />
+                <field id="ulat_restart" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
+    <file id="start" name="start" enabled="false" mode="read" >
+       <field_group id="group_start" operation="once"> 
+          <field id="it_start" name="iteration"  grid_ref="scalar" enabled="false"/>
+          <field id="q_start" name="q"  grid_ref="grid_q_read" />
+          <field_group domain_ref="i"> 
+             <field id="ps_start" name="ps" />
+             <field id="phis_start" name="phis" />
+             <field_group axis_ref="lev_read" >
+                <field id="theta_rhodz_start" name="theta_rhodz" />
+                <field id="u_start" name="u" domain_ref="u"/>
+                <field id="ulon_start" name="ulon" />
+                <field id="ulat_start" name="ulat" />
+             </field_group>
+          </field_group>
+       </field_group>
+    </file>
+
     
   </file_definition>
     
   <axis_definition>
-    <axis id="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev" name="lev" positive="down" standard_name="atmopshere_hybrid_sigma_pressure_coordinate" long_name="hybrid level at midpoints" />
+    <axis id="lev_read" />
     <axis id="levp1" name="ilev"  unit="level" positive="down" standard_name="atmopshere_hybride_sigma_pressure_coordinate" long_name="hybrid level at interface" />
     <axis id="lev_pressure" positive="down"  n_glo="2" unit="Pa" value="(0,1)[85000 50000]" >
       <interpolate_axis order="1" coordinate="p" />
     </axis>    
+    <axis id="nq" name="nq" n_glo="5" value="(0,4)[1 2 3 4 5]"/>
   </axis_definition>    
   
@@ -26 +63 @@
     
      <domain_group id="i"> 
-       <domain id="i"/>     
+       <domain id="i" name="mesh"/>     
      </domain_group> 
      
      
      <domain id="v" />
+     <domain id="u" />
      
      <domain id="regular_half_degree" type="rectilinear" ni_glo="720" nj_glo="360" >
@@ -52 +90 @@
     <grid id="scalar">
     </grid>
+    
+    <grid id="grid_q">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev" />
+      <axis axis_ref="nq" />
+    </grid >
+
+    <grid id="grid_q_read">
+      <domain domain_ref="i" />
+      <axis axis_ref="lev_read" />
+      <axis axis_ref="nq" />
+    </grid >
+ 
   </grid_definition>