Sea-ice analysis insertion (#2584)

Allows cycling and restarting CICE with the sea-ice analysis if the
marine DA is switched on.

Resolves #2568 
Resolves NOAA-EMC/GDASApp#1103

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST

@@ -13,9 +13,10 @@ export CDATE=${CDATE:-${PDY}${cyc}}
 export GDUMP=${GDUMP:-"gdas"}
 
 # Generate COM variables from templates
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OCEAN_ANALYSIS COM_ICE_RESTART
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OCEAN_ANALYSIS COM_ICE_ANALYSIS COM_ICE_RESTART
 
 mkdir -p "${COM_OCEAN_ANALYSIS}"
+mkdir -p "${COM_ICE_ANALYSIS}"
 mkdir -p "${COM_ICE_RESTART}"
 
 ##############################################

jobs/JGLOBAL_FORECAST

@@ -36,7 +36,7 @@ declare -rx gcyc="${GDATE:8:2}"
 
 # Construct COM variables from templates (see config.com)
 YMD="${PDY}" HH="${cyc}" declare_from_tmpl -rx COM_ATMOS_RESTART COM_ATMOS_INPUT COM_ATMOS_ANALYSIS \
-  COM_ATMOS_HISTORY COM_ATMOS_MASTER COM_TOP COM_CONF
+  COM_ICE_ANALYSIS COM_ATMOS_HISTORY COM_ATMOS_MASTER COM_TOP COM_CONF
 
 RUN="${rCDUMP}" YMD="${gPDY}" HH="${gcyc}" declare_from_tmpl -rx \
   COM_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL

parm/config/gfs/config.com

@@ -84,6 +84,7 @@ declare -rx COM_OCEAN_NETCDF_TMPL=${COM_BASE}'/products/ocean/netcdf'
 declare -rx COM_OCEAN_GRIB_TMPL=${COM_BASE}'/products/ocean/grib2'
 declare -rx COM_OCEAN_GRIB_GRID_TMPL=${COM_OCEAN_GRIB_TMPL}'/${GRID}'
 
+declare -rx COM_ICE_ANALYSIS_TMPL=${COM_BASE}'/analysis/ice'
 declare -rx COM_ICE_INPUT_TMPL=${COM_BASE}'/model_data/ice/input'
 declare -rx COM_ICE_HISTORY_TMPL=${COM_BASE}'/model_data/ice/history'
 declare -rx COM_ICE_RESTART_TMPL=${COM_BASE}'/model_data/ice/restart'

ush/forecast_postdet.sh

@@ -253,15 +253,15 @@ FV3_out() {
   # Copy the final restart files at the end of the forecast segment
   # The final restart written at the end of the forecast does not include the valid date
   # TODO: verify the above statement since RM found that it did!
-  # TODO: For other components, this is only for gfs/gefs - check to see if this should also have this 
-  if [[ "${COPY_FINAL_RESTARTS}" == "YES" ]]; then 
+  # TODO: For other components, this is only for gfs/gefs - check to see if this should also have this
+  if [[ "${COPY_FINAL_RESTARTS}" == "YES" ]]; then
     echo "Copying FV3 restarts for 'RUN=${RUN}' at the end of the forecast segment: ${forecast_end_cycle}"
     for fv3_restart_file in "${fv3_restart_files[@]}"; do
       restart_file="${forecast_end_cycle:0:8}.${forecast_end_cycle:8:2}0000.${fv3_restart_file}"
       ${NCP} "${DATArestart}/FV3_RESTART/${restart_file}" \
              "${COM_ATMOS_RESTART}/${restart_file}"
     done
-  fi 
+  fi
   echo "SUB ${FUNCNAME[0]}: Output data for FV3 copied"
 }
 
@@ -499,7 +499,7 @@ MOM6_out() {
         ${NCP} "${DATArestart}/MOM6_RESTART/${restart_file}" \
                "${COM_OCEAN_RESTART}/${restart_file}"
       done
-    fi 
+    fi
   fi
 
   # Copy restarts for the next cycle for RUN=gdas|enkfgdas|enkfgfs
@@ -527,6 +527,9 @@ CICE_postdet() {
   else  # "${RERUN}" == "NO"
     restart_date="${model_start_date_current_cycle}"
     cice_restart_file="${COM_ICE_RESTART_PREV}/${restart_date:0:8}.${restart_date:8:2}0000.cice_model.res.nc"
+    if [[ "${DO_JEDIOCNVAR:-NO}" == "YES" ]]; then
+      cice_restart_file="${COM_ICE_ANALYSIS}/${restart_date:0:8}.${restart_date:8:2}0000.cice_model_anl.res.nc"
+    fi
   fi
 
   # Copy CICE ICs
@@ -592,7 +595,7 @@ CICE_out() {
       target_file="${forecast_end_cycle:0:8}.${forecast_end_cycle:8:2}0000.cice_model.res.nc"
       ${NCP} "${DATArestart}/CICE_RESTART/${source_file}" \
              "${COM_ICE_RESTART}/${target_file}"
-    fi 
+    fi
   fi
 
   # Copy restarts for next cycle for RUN=gdas|enkfgdas|enkfgfs
@@ -728,7 +731,7 @@ CMEPS_out() {
     else
       echo "Mediator restart '${DATArestart}/CMEPS_RESTART/${source_file}' not found."
     fi
-  fi 
+  fi
 
   # Copy restarts for the next cycle to COM for RUN=gdas|enkfgdas|enkfgfs
   if [[ "${RUN}" =~ "gdas" || "${RUN}" == "enkfgfs" ]]; then

workflow/setup_expt.py

@@ -96,6 +96,7 @@ def fill_ROTDIR_cycled(host, inputs):
     dst_ocn_rst_dir = os.path.join('model_data', 'ocean', 'restart')
     dst_ocn_anl_dir = os.path.join('analysis', 'ocean')
     dst_ice_rst_dir = os.path.join('model_data', 'ice', 'restart')
+    dst_ice_anl_dir = os.path.join('analysis', 'ice')
     dst_atm_anl_dir = os.path.join('analysis', 'atmos')
 
     if flat_structure:
@@ -111,13 +112,15 @@ def fill_ROTDIR_cycled(host, inputs):
         src_ocn_rst_dir = os.path.join('ocean', 'RESTART')
         src_ocn_anl_dir = 'ocean'
         src_ice_rst_dir = os.path.join('ice', 'RESTART')
+        src_ice_anl_dir = dst_ice_anl_dir
         src_atm_anl_dir = 'atmos'
     else:
         src_atm_dir = dst_atm_dir
         src_med_dir = dst_med_dir
         src_ocn_rst_dir = dst_ocn_rst_dir
         src_ocn_anl_dir = dst_ocn_anl_dir
         src_ice_rst_dir = dst_ice_rst_dir
+        src_ice_anl_dir = dst_ice_anl_dir
         src_atm_anl_dir = dst_atm_anl_dir
 
     def link_files_from_src_to_dst(src_dir, dst_dir):
@@ -203,8 +206,9 @@ def link_files_from_src_to_dst(src_dir, dst_dir):
 
     # Link ice files
     if do_ice:
-        dst_dir = os.path.join(rotdir, previous_cycle_dir, dst_ice_rst_dir)
-        src_dir = os.path.join(inputs.icsdir, previous_cycle_dir, src_ice_rst_dir)
+        # First 1/2 cycle needs a CICE6 analysis restart
+        src_dir = os.path.join(inputs.icsdir, current_cycle_dir, src_ice_anl_dir)
+        dst_dir = os.path.join(rotdir, current_cycle_dir, src_ice_anl_dir)
         makedirs_if_missing(dst_dir)
         link_files_from_src_to_dst(src_dir, dst_dir)