Merge remote-tracking branch 'emc/develop' into feature/machine_res

.gitignore

@@ -166,6 +166,14 @@ scripts/exemcsfc_global_sfc_prep.sh
 scripts/exgdas_global_marine_analysis_ecen.py
 scripts/exglobal_prep_ocean_obs.py
 # ush symlinks
+ush/bufr2ioda_insitu_profile_argo.py
+ush/bufr2ioda_insitu_profile_bathy.py
+ush/bufr2ioda_insitu_profile_glider.py
+ush/bufr2ioda_insitu_profile_marinemammal.py
+ush/bufr2ioda_insitu_profile_tesac.py
+ush/bufr2ioda_insitu_profile_xbtctd.py
+ush/bufr2ioda_insitu_surface_altkob.py
+ush/bufr2ioda_insitu_surface_trkob.py
 ush/chgres_cube.sh
 ush/emcsfc_ice_blend.sh
 ush/emcsfc_snow.sh

ci/cases/yamls/gfs_extended_ci.yaml

@@ -10,3 +10,4 @@ base:
   DO_NPOESS: "YES"
   DO_GENESIS_FSU: "NO"
   FHMAX_GFS: 384
+  FHMAX_HF_GFS: 120

jobs/JGDAS_ENKF_ARCHIVE

@@ -11,8 +11,8 @@ export CDUMP=${RUN/enkf}
 
 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_TOP
 MEMDIR="ensstat" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-  COM_ATMOS_ANALYSIS_ENSSTAT:COM_ATMOS_ANALYSIS_TMPL \
-  COM_ATMOS_HISTORY_ENSSTAT:COM_ATMOS_HISTORY_TMPL
+  COMIN_ATMOS_ANALYSIS_ENSSTAT:COM_ATMOS_ANALYSIS_TMPL \
+  COMIN_ATMOS_HISTORY_ENSSTAT:COM_ATMOS_HISTORY_TMPL
 
 ###############################################################
 # Run archive script

jobs/JGLOBAL_ARCHIVE

@@ -9,21 +9,45 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "arch" -c "base arch"
 ##############################################
 export CDUMP=${RUN/enkf}
 
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_ATMOS_ANALYSIS COM_ATMOS_BUFR COM_ATMOS_GEMPAK \
-  COM_ATMOS_GENESIS COM_ATMOS_HISTORY COM_ATMOS_INPUT COM_ATMOS_MASTER COM_ATMOS_RESTART \
-  COM_ATMOS_TRACK COM_ATMOS_WMO \
-  COM_CHEM_HISTORY COM_CHEM_ANALYSIS\
-  COM_MED_RESTART \
-  COM_SNOW_ANALYSIS \
-  COM_ICE_HISTORY COM_ICE_INPUT COM_ICE_RESTART COM_ICE_GRIB \
-  COM_OBS COM_TOP \
-  COM_OCEAN_HISTORY COM_OCEAN_RESTART COM_OCEAN_GRIB COM_OCEAN_NETCDF \
-  COM_OCEAN_ANALYSIS \
-  COM_WAVE_GRID COM_WAVE_HISTORY COM_WAVE_STATION COM_WAVE_RESTART \
-  COM_ATMOS_OZNMON COM_ATMOS_RADMON COM_ATMOS_MINMON COM_CONF
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+	COMIN_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
+	COMIN_ATMOS_BUFR:COM_ATMOS_BUFR_TMPL \
+	COMIN_ATMOS_GEMPAK:COM_ATMOS_GEMPAK_TMPL \
+	COMIN_ATMOS_GENESIS:COM_ATMOS_GENESIS_TMPL \
+	COMIN_ATMOS_HISTORY:COM_ATMOS_HISTORY_TMPL \
+	COMIN_ATMOS_INPUT:COM_ATMOS_INPUT_TMPL \
+	COMIN_ATMOS_MASTER:COM_ATMOS_MASTER_TMPL \
+	COMIN_ATMOS_RESTART:COM_ATMOS_RESTART_TMPL \
+	COMIN_ATMOS_TRACK:COM_ATMOS_TRACK_TMPL \
+	COMIN_ATMOS_WMO:COM_ATMOS_WMO_TMPL \
+	COMIN_CHEM_HISTORY:COM_CHEM_HISTORY_TMPL \
+	COMIN_CHEM_ANALYSIS:COM_CHEM_ANALYSIS_TMPL \
+	COMIN_MED_RESTART:COM_MED_RESTART_TMPL \
+	COMIN_SNOW_ANALYSIS:COM_SNOW_ANALYSIS_TMPL \
+	COMIN_ICE_HISTORY:COM_ICE_HISTORY_TMPL \
+	COMIN_ICE_INPUT:COM_ICE_INPUT_TMPL \
+	COMIN_ICE_RESTART:COM_ICE_RESTART_TMPL \
+	COMIN_ICE_GRIB:COM_ICE_GRIB_TMPL \
+	COMIN_OBS:COM_OBS_TMPL \
+	COMIN_TOP:COM_TOP_TMPL \
+	COMIN_OCEAN_HISTORY:COM_OCEAN_HISTORY_TMPL \
+	COMIN_OCEAN_RESTART:COM_OCEAN_RESTART_TMPL \
+	COMIN_OCEAN_GRIB:COM_OCEAN_GRIB_TMPL \
+	COMIN_OCEAN_NETCDF:COM_OCEAN_NETCDF_TMPL \
+	COMIN_OCEAN_ANALYSIS:COM_OCEAN_ANALYSIS_TMPL \
+	COMIN_WAVE_GRID:COM_WAVE_GRID_TMPL \
+	COMIN_WAVE_HISTORY:COM_WAVE_HISTORY_TMPL \
+	COMIN_WAVE_STATION:COM_WAVE_STATION_TMPL \
+	COMIN_WAVE_RESTART:COM_WAVE_RESTART_TMPL \
+	COMIN_ATMOS_OZNMON:COM_ATMOS_OZNMON_TMPL \
+	COMIN_ATMOS_RADMON:COM_ATMOS_RADMON_TMPL \
+	COMIN_ATMOS_MINMON:COM_ATMOS_MINMON_TMPL \
+	COMIN_CONF:COM_CONF_TMPL \
+	COMOUT_ATMOS_TRACK:COM_ATMOS_TRACK_TMPL
 
 for grid in "0p25" "0p50" "1p00"; do
-  YMD=${PDY} HH=${cyc} GRID=${grid} declare_from_tmpl -rx "COM_ATMOS_GRIB_${grid}:COM_ATMOS_GRIB_GRID_TMPL"
+    YMD=${PDY} HH=${cyc} GRID=${grid} declare_from_tmpl -rx \
+       "COMIN_ATMOS_GRIB_${grid}:COM_ATMOS_GRIB_GRID_TMPL"
 done
 
 ###############################################################

jobs/rocoto/atmos_ensstat.sh

@@ -15,21 +15,11 @@ if (( status != 0 )); then exit "${status}"; fi
 export job="atmos_ensstat"
 export jobid="${job}.$$"
 
-###############################################################
-# shellcheck disable=SC2153,SC2001
-IFS='_' read -ra fhrs <<< "${FHRLST//f}" # strip off the 'f's and convert to array
+export FORECAST_HOUR=$(( 10#${FHR3} ))
 
-#---------------------------------------------------------------
+###############################################################
 # Execute the JJOB
-for fhr in "${fhrs[@]}"; do
-    # The analysis fhr is -001.  Performing math on negative, leading 0 integers is tricky.
-    # The negative needs to be in front of "10#", so do some regex magic to make it happen.
-    fhr="10#${fhr}"
-    fhr=${fhr//10\#-/-10\#}
-    export FORECAST_HOUR=$(( fhr ))
-    "${HOMEgfs}/jobs/JGLOBAL_ATMOS_ENSSTAT"
-    status=$?
-    if (( status != 0 )); then exit "${status}"; fi
-done
+###############################################################
+"${HOMEgfs}/jobs/JGLOBAL_ATMOS_ENSSTAT"
 
-exit 0
+exit $?

jobs/rocoto/atmos_products.sh

@@ -15,21 +15,13 @@ if (( status != 0 )); then exit "${status}"; fi
 export job="atmos_products"
 export jobid="${job}.$$"
 
-###############################################################
-# shellcheck disable=SC2153,SC2001
-IFS='_' read -ra fhrs <<< "${FHRLST//f}" # strip off the 'f's and convert to array
+# Negatation needs to be before the base
+fhr3_base="10#${FHR3}"
+export FORECAST_HOUR=$(( ${fhr3_base/10#-/-10#} ))
 
-#---------------------------------------------------------------
+###############################################################
 # Execute the JJOB
-for fhr in "${fhrs[@]}"; do
-    # The analysis fhr is -001.  Performing math on negative, leading 0 integers is tricky.
-    # The negative needs to be in front of "10#", so do some regex magic to make it happen.
-    fhr="10#${fhr}"
-    fhr=${fhr//10\#-/-10\#}
-    export FORECAST_HOUR=$(( fhr ))
-    "${HOMEgfs}/jobs/JGLOBAL_ATMOS_PRODUCTS"
-    status=$?
-    if (( status != 0 )); then exit "${status}"; fi
-done
+###############################################################
+"${HOMEgfs}/jobs/JGLOBAL_ATMOS_PRODUCTS"
 
-exit 0
+exit $?

jobs/rocoto/oceanice_products.sh

@@ -21,17 +21,11 @@ export PYTHONPATH
 export job="oceanice_products"
 export jobid="${job}.$$"
 
-###############################################################
-# shellcheck disable=SC2153,SC2001
-IFS='_' read -ra fhrs <<< "${FHRLST//f}" # strip off the 'f's and convert to array
+export FORECAST_HOUR=$(( 10#${FHR3} ))
 
-#---------------------------------------------------------------
+###############################################################
 # Execute the JJOB
-for fhr in "${fhrs[@]}"; do
-    export FORECAST_HOUR=$(( 10#${fhr} ))
-    "${HOMEgfs}/jobs/JGLOBAL_OCEANICE_PRODUCTS"
-    status=$?
-    if (( status != 0 )); then exit "${status}"; fi
-done
-
-exit 0
+###############################################################
+"${HOMEgfs}/jobs/JGLOBAL_OCEANICE_PRODUCTS"
+
+exit $?

jobs/rocoto/upp.sh

@@ -44,16 +44,11 @@ export PYTHONPATH
 export job="upp"
 export jobid="${job}.$$"
 
-###############################################################
-# shellcheck disable=SC2153,SC2001
-IFS='_' read -ra fhrs <<< "${FHRLST//f}" # strip off the 'f's convert to array
+export FORECAST_HOUR=$(( 10#${FHR3} ))
 
+###############################################################
 # Execute the JJOB
-for fhr in "${fhrs[@]}"; do
-    export FORECAST_HOUR=$(( 10#${fhr} ))
-    "${HOMEgfs}/jobs/JGLOBAL_ATMOS_UPP"
-    status=$?
-    if (( status != 0 )); then exit "${status}"; fi
-done
-
-exit 0
+###############################################################
+"${HOMEgfs}/jobs/JGLOBAL_ATMOS_UPP"
+
+exit $?

parm/archive/arcdir.yaml.j2

@@ -15,41 +15,41 @@ Deterministic: &deterministic
         copy:
             # Cyclone forecasts, produced for both gdas and gfs cycles
             ## Only created if tracking is on and there were systems to track
-            {% if path_exists(COM_ATMOS_TRACK ~ "/atcfunix." ~ RUN ~ "." ~ cycle_YMDH) %}
-            - ["{{ COM_ATMOS_TRACK }}/atcfunix.{{ RUN }}.{{ cycle_YMDH }}", "{{ ARCDIR }}/atcfunix.{{ RUN }}.{{ cycle_YMDH }}"]
-            - ["{{ COM_ATMOS_TRACK }}/atcfunixp.{{ RUN }}.{{ cycle_YMDH }}", "{{ ARCDIR }}/atcfunixp.{{ RUN }}.{{ cycle_YMDH }}"]
+            {% if path_exists(COMIN_ATMOS_TRACK ~ "/atcfunix." ~ RUN ~ "." ~ cycle_YMDH) %}
+            - ["{{ COMIN_ATMOS_TRACK }}/atcfunix.{{ RUN }}.{{ cycle_YMDH }}", "{{ ARCDIR }}/atcfunix.{{ RUN }}.{{ cycle_YMDH }}"]
+            - ["{{ COMIN_ATMOS_TRACK }}/atcfunixp.{{ RUN }}.{{ cycle_YMDH }}", "{{ ARCDIR }}/atcfunixp.{{ RUN }}.{{ cycle_YMDH }}"]
             {% endif %}
 
             # Cyclone tracking data
             {% for basin in ["epac", "natl"] %}
-                {% if path_exists(COM_ATMOS_TRACK + "/" + basin) %}
-            - ["{{ COM_ATMOS_TRACK }}/{{ basin }}", "{{ ARCDIR }}/{{ basin }}"]
+                {% if path_exists(COMIN_ATMOS_TRACK + "/" + basin) %}
+            - ["{{ COMIN_ATMOS_TRACK }}/{{ basin }}", "{{ ARCDIR }}/{{ basin }}"]
                 {% endif %}
             {% endfor %}
 
     {% if MODE == "cycled" %}
     analysis:
         copy:
             # Analysis data (if we are running in cycled mode)
-            - ["{{ COM_ATMOS_GRIB_1p00 }}/{{ head }}pgrb2.1p00.anl", "{{ ARCDIR }}/pgbanl.{{ RUN }}.{{ cycle_YMDH }}.grib2"]
+            - ["{{ COMIN_ATMOS_GRIB_1p00 }}/{{ head }}pgrb2.1p00.anl", "{{ ARCDIR }}/pgbanl.{{ RUN }}.{{ cycle_YMDH }}.grib2"]
 
             {% if DO_JEDIATMVAR %}
-            - ["{{ COM_ATMOS_ANALYSIS }}/{{ head }}atmstat", "{{ ARCDIR }}/atmstat.{{ RUN }}.{{ cycle_YMDH }}"]
+            - ["{{ COMIN_ATMOS_ANALYSIS }}/{{ head }}atmstat", "{{ ARCDIR }}/atmstat.{{ RUN }}.{{ cycle_YMDH }}"]
             {% else %}
-            - ["{{ COM_ATMOS_ANALYSIS }}/{{ head }}gsistat", "{{ ARCDIR }}/gsistat.{{ RUN }}.{{ cycle_YMDH }}"]
+            - ["{{ COMIN_ATMOS_ANALYSIS }}/{{ head }}gsistat", "{{ ARCDIR }}/gsistat.{{ RUN }}.{{ cycle_YMDH }}"]
             {% endif %}
 
             {% if DO_JEDISNOWDA %}
-            - ["{{ COM_SNOW_ANALYSIS }}/{{ head }}snowstat.tgz", "{{ ARCDIR }}/snowstat.{{ RUN }}.{{ cycle_YMDH }}.tgz"]
+            - ["{{ COMIN_SNOW_ANALYSIS }}/{{ head }}snowstat.tgz", "{{ ARCDIR }}/snowstat.{{ RUN }}.{{ cycle_YMDH }}.tgz"]
             {% endif %}
 
             {% if AERO_ANL_CDUMP == RUN or AERO_ANL_CDUMP == "both" %}
-            - ["{{ COM_CHEM_ANALYSIS }}/{{ head }}aerostat", "{{ ARCDIR }}/aerostat.{{ RUN }}.{{ cycle_YMDH }}"]
+            - ["{{ COMIN_CHEM_ANALYSIS }}/{{ head }}aerostat", "{{ ARCDIR }}/aerostat.{{ RUN }}.{{ cycle_YMDH }}"]
             {% endif %}
 
             {% if DO_PREP_OBS_AERO %}
-            - ["{{ COM_OBS }}/{{ head }}aeroobs", "{{ ARCDIR }}/aeroobs.{{ RUN }}.{{ cycle_YMDH }}"]
-            - ["{{ COM_OBS }}/{{ head }}aerorawobs", "{{ ARCDIR }}/aerorawobs.{{ RUN }}.{{ cycle_YMDH }}"]
+            - ["{{ COMIN_OBS }}/{{ head }}aeroobs", "{{ ARCDIR }}/aeroobs.{{ RUN }}.{{ cycle_YMDH }}"]
+            - ["{{ COMIN_OBS }}/{{ head }}aerorawobs", "{{ ARCDIR }}/aerorawobs.{{ RUN }}.{{ cycle_YMDH }}"]
             {% endif %}
 
     {% endif %}
@@ -62,18 +62,18 @@ gfs:  # GFS specific
     gfs:
         copy:
             {% for fhr in range(0, FHMAX_GFS + 1, FHOUT_GFS) %}
-            - ["{{ COM_ATMOS_GRIB_1p00 }}/{{ head }}pgrb2.1p00.f{{ '%03d' % fhr }}", "{{ ARCDIR }}/pgbf{{ '%02d' % fhr }}.{{ RUN }}.{{ cycle_YMDH }}.grib2"]
+            - ["{{ COMIN_ATMOS_GRIB_1p00 }}/{{ head }}pgrb2.1p00.f{{ '%03d' % fhr }}", "{{ ARCDIR }}/pgbf{{ '%02d' % fhr }}.{{ RUN }}.{{ cycle_YMDH }}.grib2"]
             {% endfor %}
 
             # Cyclone genesis data (only present if there are storms)
-            {% if path_exists(COM_ATMOS_GENESIS ~ "/storms.gfso.atcf_gen." ~ cycle_YMDH) %}
-            - ["{{ COM_ATMOS_GENESIS }}/storms.gfso.atcf_gen.{{ cycle_YMDH }}", "{{ ARCDIR }}/storms.gfso.atcf_gen.{{ cycle_YMDH }}"]
-            - ["{{ COM_ATMOS_GENESIS }}/storms.gfso.atcf_gen.altg.{{ cycle_YMDH }}", "{{ ARCDIR }}/storms.gfso.atcf_gen.altg.{{ cycle_YMDH }}"]
+            {% if path_exists(COMIN_ATMOS_GENESIS ~ "/storms.gfso.atcf_gen." ~ cycle_YMDH) %}
+            - ["{{ COMIN_ATMOS_GENESIS }}/storms.gfso.atcf_gen.{{ cycle_YMDH }}", "{{ ARCDIR }}/storms.gfso.atcf_gen.{{ cycle_YMDH }}"]
+            - ["{{ COMIN_ATMOS_GENESIS }}/storms.gfso.atcf_gen.altg.{{ cycle_YMDH }}", "{{ ARCDIR }}/storms.gfso.atcf_gen.altg.{{ cycle_YMDH }}"]
             {% endif %}
 
-            {% if path_exists(COM_ATMOS_GENESIS ~ "/trak.gfso.atcfunix." ~ cycle_YMDH) %}
-            - ["{{ COM_ATMOS_GENESIS }}/trak.gfso.atcfunix.{{ cycle_YMDH }}", "{{ ARCDIR }}/trak.gfso.atcfunix.{{ cycle_YMDH }}"]
-            - ["{{ COM_ATMOS_GENESIS }}/trak.gfso.atcfunix.altg.{{ cycle_YMDH }}", "{{ ARCDIR }}/trak.gfso.atcfunix.altg.{{ cycle_YMDH }}"]
+            {% if path_exists(COMIN_ATMOS_GENESIS ~ "/trak.gfso.atcfunix." ~ cycle_YMDH) %}
+            - ["{{ COMIN_ATMOS_GENESIS }}/trak.gfso.atcfunix.{{ cycle_YMDH }}", "{{ ARCDIR }}/trak.gfso.atcfunix.{{ cycle_YMDH }}"]
+            - ["{{ COMIN_ATMOS_GENESIS }}/trak.gfso.atcfunix.altg.{{ cycle_YMDH }}", "{{ ARCDIR }}/trak.gfso.atcfunix.altg.{{ cycle_YMDH }}"]
             {% endif %}
 
     {% if DO_FIT2OBS %}
@@ -87,8 +87,8 @@ gfs:  # GFS specific
             {% for fhr in range(0, FHMAX_FITS + 1, 6) %}
                 {% set sfcfile = "/" + head + "sfcf" + '%03d'|format(fhr) + ".nc" %}
                 {% set sigfile = "/" + head + "atmf" + '%03d'|format(fhr) + ".nc" %}
-            - ["{{COM_ATMOS_HISTORY}}/{{ sfcfile }}", "{{ VFYARC }}/{{ RUN }}.{{ cycle_YMD }}/{{ cycle_HH }}/{{ sfcfile }}"]
-            - ["{{COM_ATMOS_HISTORY}}/{{ sigfile }}", "{{ VFYARC }}/{{ RUN }}.{{ cycle_YMD }}/{{ cycle_HH }}/{{ sigfile }}"]
+            - ["{{COMIN_ATMOS_HISTORY}}/{{ sfcfile }}", "{{ VFYARC }}/{{ RUN }}.{{ cycle_YMD }}/{{ cycle_HH }}/{{ sfcfile }}"]
+            - ["{{COMIN_ATMOS_HISTORY}}/{{ sigfile }}", "{{ VFYARC }}/{{ RUN }}.{{ cycle_YMD }}/{{ cycle_HH }}/{{ sigfile }}"]
             {% endfor %}
 
     {% endif %}
@@ -101,7 +101,7 @@ gdas:  # GDAS specific
     gdas:
         copy:
             {% for fhr in range(0, FHMAX + 1, FHOUT) %}
-            - ["{{ COM_ATMOS_GRIB_1p00 }}/{{ head }}pgrb2.1p00.f{{ '%03d' % fhr }}", "{{ ARCDIR }}/pgbf{{ '%02d' % fhr }}.{{ RUN }}.{{ cycle_YMDH }}.grib2"]
+            - ["{{ COMIN_ATMOS_GRIB_1p00 }}/{{ head }}pgrb2.1p00.f{{ '%03d' % fhr }}", "{{ ARCDIR }}/pgbf{{ '%02d' % fhr }}.{{ RUN }}.{{ cycle_YMDH }}.grib2"]
             {% endfor %}
 {% endif %}
 
@@ -110,11 +110,11 @@ Ensemble: &ensemble # ENKFGDAS or ENKFGFS
         copy:
             # Copy ensemble analyses
             {% if DO_JEDIATMENS %}
-            - ["{{ COM_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}atmensstat", "{{ ARCDIR }}/atmensstat.{{ RUN }}.{{ cycle_YMDH }}"]
-            - ["{{ COM_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}atminc.ensmean.nc", "{{ ARCDIR }}/atmensstat.{{ RUN }}.{{ cycle_YMDH }}.ensmean.nc"]
+            - ["{{ COMIN_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}atmensstat", "{{ ARCDIR }}/atmensstat.{{ RUN }}.{{ cycle_YMDH }}"]
+            - ["{{ COMIN_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}atminc.ensmean.nc", "{{ ARCDIR }}/atmensstat.{{ RUN }}.{{ cycle_YMDH }}.ensmean.nc"]
             {% else %}
-            - ["{{ COM_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}enkfstat", "{{ ARCDIR }}/enkfstat.{{ RUN }}.{{ cycle_YMDH }}"]
-            - ["{{ COM_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}gsistat.ensmean", "{{ ARCDIR }}/gsistat.{{ RUN }}.{{ cycle_YMDH }}.ensmean"]
+            - ["{{ COMIN_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}enkfstat", "{{ ARCDIR }}/enkfstat.{{ RUN }}.{{ cycle_YMDH }}"]
+            - ["{{ COMIN_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}gsistat.ensmean", "{{ ARCDIR }}/gsistat.{{ RUN }}.{{ cycle_YMDH }}.ensmean"]
             {% endif %}
 
 {% if "enkf" in RUN %}

parm/archive/chem.yaml.j2

@@ -4,4 +4,4 @@ chem:
     target: "{{ ATARDIR }}/{{ cycle_YMDH }}/chem.tar"
     required:
         # TODO explicitize this set
-        - "{{ COM_CHEM_HISTORY | relpath(ROTDIR) }}/{{ head }}*"
+        - "{{ COMIN_CHEM_HISTORY | relpath(ROTDIR) }}/{{ head }}*"

parm/archive/enkf.yaml.j2

@@ -34,10 +34,10 @@ enkf:
 
         # Ensemble mean and spread
         {% for fhr in range(3, fhmax + 1, 3) %}
-        - "{{ COM_ATMOS_HISTORY_ENSSTAT | relpath(ROTDIR) }}/{{ head }}atmf{{ '%03d' % fhr }}.ensmean.nc"
-        - "{{ COM_ATMOS_HISTORY_ENSSTAT | relpath(ROTDIR) }}/{{ head }}sfcf{{ '%03d' % fhr }}.ensmean.nc"
+        - "{{ COMIN_ATMOS_HISTORY_ENSSTAT | relpath(ROTDIR) }}/{{ head }}atmf{{ '%03d' % fhr }}.ensmean.nc"
+        - "{{ COMIN_ATMOS_HISTORY_ENSSTAT | relpath(ROTDIR) }}/{{ head }}sfcf{{ '%03d' % fhr }}.ensmean.nc"
         {% if ENKF_SPREAD %}
-        - "{{ COM_ATMOS_HISTORY_ENSSTAT | relpath(ROTDIR) }}/{{ head }}atmf{{ '%03d' % fhr }}.ensspread.nc"
+        - "{{ COMIN_ATMOS_HISTORY_ENSSTAT | relpath(ROTDIR) }}/{{ head }}atmf{{ '%03d' % fhr }}.ensspread.nc"
         {% endif %}
         {% endfor %}
 
@@ -54,15 +54,15 @@ enkf:
                            "atmensstat"] %}
         {% endif %}
         {% for file in da_files %}
-        - "{{ COM_ATMOS_ANALYSIS_ENSSTAT | relpath(ROTDIR) }}/{{ head }}{{ file }}"
+        - "{{ COMIN_ATMOS_ANALYSIS_ENSSTAT | relpath(ROTDIR) }}/{{ head }}{{ file }}"
         {% endfor %}
 
         # Ensemble mean analyses/increments
         # 6-hr analysis/increment
         {% if do_calc_increment %}
-        - "{{ COM_ATMOS_ANALYSIS_ENSSTAT | relpath(ROTDIR) }}/{{ head }}atmanl.ensmean.nc"
+        - "{{ COMIN_ATMOS_ANALYSIS_ENSSTAT | relpath(ROTDIR) }}/{{ head }}atmanl.ensmean.nc"
         {% else %}
-        - "{{ COM_ATMOS_ANALYSIS_ENSSTAT | relpath(ROTDIR) }}/{{ head }}atminc.ensmean.nc"
+        - "{{ COMIN_ATMOS_ANALYSIS_ENSSTAT | relpath(ROTDIR) }}/{{ head }}atminc.ensmean.nc"
         {% endif %}
 
         {% if DOIAU %}
@@ -71,10 +71,10 @@ enkf:
         {% for fhr in iaufhrs if fhr != 6 %}
         {% if do_calc_increment %}
         # Store analyses instead of increments
-        - "{{ COM_ATMOS_ANALYSIS_ENSSTAT | relpath(ROTDIR) }}/{{ head }}atma{{ '%03d' % fhr }}.ensmean.nc"
+        - "{{ COMIN_ATMOS_ANALYSIS_ENSSTAT | relpath(ROTDIR) }}/{{ head }}atma{{ '%03d' % fhr }}.ensmean.nc"
         {% else %}
         # Store increments
-        - "{{ COM_ATMOS_ANALYSIS_ENSSTAT | relpath(ROTDIR) }}/{{ head }}atmi{{ '%03d' % fhr }}.ensmean.nc"
+        - "{{ COMIN_ATMOS_ANALYSIS_ENSSTAT | relpath(ROTDIR) }}/{{ head }}atmi{{ '%03d' % fhr }}.ensmean.nc"
         {% endif %}
         {% endfor %}
 

parm/archive/enkf_grp.yaml.j2

@@ -5,25 +5,25 @@ enkf_grp:
         {% for mem in range(first_group_mem, last_group_mem + 1) %}
         {% set imem = mem - first_group_mem %}
         # Construct member COM directories
-        {% set COM_ATMOS_ANALYSIS_MEM = COM_ATMOS_ANALYSIS_MEM_list[imem] %}
-        {% set COM_ATMOS_HISTORY_MEM = COM_ATMOS_HISTORY_MEM_list[imem] %}
-        {% set COM_ATMOS_RESTART_MEM = COM_ATMOS_RESTART_MEM_list[imem] %}
+        {% set COMIN_ATMOS_ANALYSIS_MEM = COMIN_ATMOS_ANALYSIS_MEM_list[imem] %}
+        {% set COMIN_ATMOS_HISTORY_MEM = COMIN_ATMOS_HISTORY_MEM_list[imem] %}
+        {% set COMIN_ATMOS_RESTART_MEM = COMIN_ATMOS_RESTART_MEM_list[imem] %}
 
         # Forecast data
         {% for fhr in range(3, 10, 3) %}
-        - "{{ COM_ATMOS_HISTORY_MEM | relpath(ROTDIR) }}/{{ head }}atmf{{ "%03d" % fhr }}.nc"
+        - "{{ COMIN_ATMOS_HISTORY_MEM | relpath(ROTDIR) }}/{{ head }}atmf{{ "%03d" % fhr }}.nc"
         {% endfor %}
 
         # Only store the 6-hour surface forecast
-        - "{{ COM_ATMOS_HISTORY_MEM | relpath(ROTDIR) }}/{{ head }}sfcf006.nc"
+        - "{{ COMIN_ATMOS_HISTORY_MEM | relpath(ROTDIR) }}/{{ head }}sfcf006.nc"
 
         # Store the individual member analysis data
         {% if not lobsdiag_forenkf %}
-        - "{{ COM_ATMOS_RESTART_MEM | relpath(ROTDIR) }}/{{ head }}gsistat"
+        - "{{ COMIN_ATMOS_RESTART_MEM | relpath(ROTDIR) }}/{{ head }}gsistat"
         {% endif %}
         {% if do_calc_increment %}
-        - "{{ COM_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ head }}atmanl.nc"
+        - "{{ COMIN_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ head }}atmanl.nc"
         {% else %}
-        - "{{ COM_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ head }}ratminc.nc"
+        - "{{ COMIN_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ head }}ratminc.nc"
         {% endif %}
         {% endfor %}  # first_group_mem to last_group_mem