Cherry pick de-template COM PR #4555 and resolve conflicts

.gitignore

@@ -187,6 +187,7 @@ ush/python/soca
 ush/python/gen_bufr2ioda_json.py
 ush/python/gen_bufr2ioda_yaml.py
 ush/python/run_bufr2ioda.py
+ush/python/wxflow
 ush/spoc
 # ush log file
 ush/fetch-fix-data.log

dev/job_cards/rocoto/prep.sh

@@ -28,18 +28,16 @@ GDUMP="gdas"
 
 export OPREFIX="${RUN_local}.t${cyc}z."
 
-RUN=${RUN_local} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMIN_OBS:COM_OBS_TMPL \
-    COMOUT_OBS:COM_OBS_TMPL \
-    COMINobsproc:COM_OBSPROC_TMPL \
-    COMINobsforge:COM_OBSFORGE_TMPL \
-    COMIN_TCVITAL:COM_TCVITAL_TMPL \
-    COMOUT_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
-
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-    COMOUT_OBS_PREV:COM_OBS_TMPL \
-    COMINobsproc_PREV:COM_OBSPROC_TMPL \
-    COMOUT_ATMOS_ANALYSIS_PREV:COM_ATMOS_ANALYSIS_TMPL
+declare -rx COMIN_OBS="${ROTDIR}/${RUN_local}.${PDY}/${cyc}/obs"
+declare -rx COMOUT_OBS="${ROTDIR}/${RUN_local}.${PDY}/${cyc}/obs"
+declare -rx COMINobsproc="${DMPDIR}/${RUN}.${PDY}/${cyc}/atmos"
+declare -rx COMINobsforge="${IODADIR}/${RUN_local}.${PDY}/${cyc}"
+declare -rx COMIN_TCVITAL="${DMPDIR}/${RUN_local}.${PDY}/${cyc}/atmos"
+declare -rx COMOUT_ATMOS_ANALYSIS="${ROTDIR}/${RUN_local}.${PDY}/${cyc}/analysis/atmos"
+
+declare -rx COMOUT_OBS_PREV="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/obs"
+declare -rx COMINobsproc_PREV="${DMPDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos"
+declare -rx COMOUT_ATMOS_ANALYSIS_PREV="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/analysis/atmos"
 
 mkdir -p "${COMOUT_OBS}"
 
@@ -136,8 +134,8 @@ rm -f "${COMOUT_OBS}/${OPREFIX}prepbufr"
 rm -f "${COMOUT_OBS}/${OPREFIX}prepbufr.acft_profiles"
 rm -f "${COMOUT_OBS}/${OPREFIX}nsstbufr"
 
-RUN="gdas" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMIN_ATMOS_HISTORY_GDAS:COM_ATMOS_HISTORY_TMPL
-RUN="gfs" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMIN_ATMOS_HISTORY_GFS:COM_ATMOS_HISTORY_TMPL
+declare -rx COMIN_ATMOS_HISTORY_GDAS="${ROTDIR}/gdas.${PDY}/${cyc}/model/atmos/history"
+declare -rx COMIN_ATMOS_HISTORY_GFS="${ROTDIR}/gfs.${PDY}/${cyc}/model/atmos/history"
 
 export job="j${RUN_local}_prep_${cyc}"
 

dev/jobs/JGDAS_AERO_ANALYSIS_GENERATE_BMATRIX

@@ -14,10 +14,10 @@ export PYTHONPATH
 ##############################################
 
 # Generate COM variables from templates
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMIN_OBS:COM_OBS_TMPL \
-    COMOUT_CHEM_BMAT:COM_CHEM_BMAT_TMPL \
-    COMIN_ATMOS_RESTART:COM_ATMOS_RESTART_TMPL \
-    COMOUT_CONF:COM_CONF_TMPL
+declare -rx COMIN_OBS="${ROTDIR}/${RUN}.${PDY}/${cyc}/obs"
+declare -rx COMOUT_CHEM_BMAT="${ROTDIR}/${RUN}.${PDY}/${cyc}/analysis/chem/bmatrix"
+declare -rx COMIN_ATMOS_RESTART="${ROTDIR}/${RUN}.${PDY}/${cyc}/model/atmos/restart"
+declare -rx COMOUT_CONF="${ROTDIR}/${RUN}.${PDY}/${cyc}/conf"
 
 mkdir -p "${COMOUT_CHEM_BMAT}"
 mkdir -p "${COMOUT_CONF}"

dev/jobs/JGDAS_ATMOS_CHGRES_FORENKF

@@ -14,12 +14,10 @@ export DO_CALC_ANALYSIS=${DO_CALC_ANALYSIS:-"YES"}
 export APREFIX="${RUN/enkf/}.t${cyc}z."
 export APREFIX_ENS="${RUN}.t${cyc}z."
 
-RUN=${RUN/enkf/} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMIN_ATMOS_HISTORY:COM_ATMOS_HISTORY_TMPL \
-    COMOUT_ATMOS_HISTORY:COM_ATMOS_HISTORY_TMPL
+declare -rx COMIN_ATMOS_HISTORY="${ROTDIR}/${RUN/enkf/}.${PDY}/${cyc}/model/atmos/history"
+declare -rx COMOUT_ATMOS_HISTORY="${ROTDIR}/${RUN/enkf/}.${PDY}/${cyc}/model/atmos/history"
 
-MEMDIR="mem001" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMIN_ATMOS_HISTORY_MEM:COM_ATMOS_HISTORY_TMPL
+declare -rx COMIN_ATMOS_HISTORY_MEM="${ROTDIR}/${RUN}.${PDY}/${cyc}/mem001/model/atmos/history"
 
 ###############################################################
 # Run relevant script

dev/jobs/JGDAS_ATMOS_GEMPAK

@@ -10,12 +10,12 @@ export DBN_ALERT_TYPE=${DBN_ALERT_TYPE:-GDAS_GEMPAK}
 # Define COM directories
 ##############################################
 for grid in 0p25 1p00; do
-    GRID=${grid} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx "COMOUT_ATMOS_GRIB_${grid}:COM_ATMOS_GRIB_GRID_TMPL"
+    declare -rx "COMIN_ATMOS_GRIB_${grid}"="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/grib2/${grid}"
 done
 
 for grid in 0p25 1p00; do
     prod_dir="COMOUT_ATMOS_GEMPAK_${grid}"
-    GRID=${grid} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx "COMOUT_ATMOS_GEMPAK_${grid}:COM_ATMOS_GEMPAK_TMPL"
+    declare -rx "COMOUT_ATMOS_GEMPAK_${grid}"="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/gempak/${grid}"
 
     if [[ ! -d "${!prod_dir}" ]]; then
         mkdir -m 775 -p "${!prod_dir}"

dev/jobs/JGDAS_ATMOS_GEMPAK_META_NCDC

@@ -30,15 +30,15 @@ export DBN_ALERT_TYPE=GDAS_METAFILE
 ##############################################
 # Define COM directories
 ##############################################
-GRID=1p00 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx "COMIN_ATMOS_GEMPAK_1p00:COM_ATMOS_GEMPAK_TMPL"
+declare -rx COMIN_ATMOS_GEMPAK_1p00="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/gempak/1p00"
 
-GRID="meta" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx "COMOUT_ATMOS_GEMPAK_META:COM_ATMOS_GEMPAK_TMPL"
+declare -rx COMOUT_ATMOS_GEMPAK_META="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/gempak/meta"
 if [[ ! -d "${COMOUT_ATMOS_GEMPAK_META}" ]]; then
     mkdir -m 775 -p "${COMOUT_ATMOS_GEMPAK_META}"
 fi
 
 if ((cyc % 12 == 0)); then
-    GRID="gif" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx "COMOUT_ATMOS_GEMPAK_GIF:COM_ATMOS_GEMPAK_TMPL"
+    declare -rx COMOUT_ATMOS_GEMPAK_GIF="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/gempak/gif"
     if [[ ! -d "${COMOUT_ATMOS_GEMPAK_GIF}" ]]; then
         mkdir -m 775 -p "${COMOUT_ATMOS_GEMPAK_GIF}"
     fi

dev/jobs/JGDAS_ATMOS_VERFOZN

@@ -16,10 +16,8 @@ export gcyc=${GDATE:8:2}
 #---------------------------------------------
 # OZN_TANKDIR - WHERE OUTPUT DATA WILL RESIDE
 #
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMIN_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMOUT_ATMOS_OZNMON:COM_ATMOS_OZNMON_TMPL
+declare -rx COMIN_ATMOS_ANALYSIS="${ROTDIR}/${RUN}.${PDY}/${cyc}/analysis/atmos"
+declare -rx COMOUT_ATMOS_OZNMON="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/oznmon"
 
 export oznstat="${COMIN_ATMOS_ANALYSIS}/gdas.t${cyc}z.oznstat.tar"
 export TANKverf_ozn=${TANKverf_ozn:-${COMOUT_ATMOS_OZNMON}}

dev/jobs/JGDAS_ATMOS_VERFRAD

@@ -17,12 +17,9 @@ export gcyc=${GDATE:8:2}
 # COMOUT - WHERE GSI OUTPUT RESIDES
 # TANKverf - WHERE OUTPUT DATA WILL RESIDE
 #############################################
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMIN_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMOUT_ATMOS_RADMON:COM_ATMOS_RADMON_TMPL
-YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-    COMIN_ATMOS_RADMON_PREV:COM_ATMOS_RADMON_TMPL
+declare -rx COMIN_ATMOS_ANALYSIS="${ROTDIR}/${RUN}.${PDY}/${cyc}/analysis/atmos"
+declare -rx COMOUT_ATMOS_RADMON="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/radmon"
+declare -rx COMIN_ATMOS_RADMON_PREV="${ROTDIR}/${RUN}.${gPDY}/${gcyc}/products/atmos/radmon"
 
 export biascr="${COMIN_ATMOS_ANALYSIS}/gdas.t${cyc}z.abias.txt"
 export radstat="${COMIN_ATMOS_ANALYSIS}/gdas.t${cyc}z.radstat.tar"

dev/jobs/JGDAS_FIT2OBS

@@ -13,8 +13,8 @@ vcyc=${CDATE:8:2}
 
 # These are used by fit2obs, so we can't change them to the standard COM variable names
 # shellcheck disable=SC2153
-YMD=${vday} HH=${vcyc} declare_from_tmpl -rx COMIN_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
-RUN=${RUN/enkf/} YMD=${vday} HH=${vcyc} declare_from_tmpl -rx COMIN_OBS:COM_OBS_TMPL
+declare -rx COMIN_ANALYSIS="${ROTDIR}/${RUN}.${vday}/${vcyc}/analysis/atmos"
+declare -rx COMIN_OBS="${ROTDIR}/${RUN/enkf/}.${vday}/${vcyc}/obs"
 
 export COM_VRFYARCH=${COM_VRFYARCH:-${ROTDIR}/vrfyarch}
 

dev/jobs/JGEFS_WAVE_STAT

@@ -8,14 +8,12 @@ source "${USHgfs}/wave_domain_grid.sh"
 for grid in ${wavepostGRD}; do
     process_grdID "${grid}"
     prod_dir_grid="COMOUT_WAVE_GRID_${grid}"
-    MEMDIR="ensstat" GRID=${grid} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-        "${prod_dir_grid}:COM_WAVE_GRID_TMPL"
+    declare -rx "${prod_dir_grid}"="${ROTDIR}/${RUN}.${PDY}/${cyc}/ensstat/products/wave/gridded"
     if [[ ! -d "${!prod_dir_grid}" ]]; then
         mkdir -m 775 -p "${!prod_dir_grid}"
     fi
 done
-MEMDIR="ensstat" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMOUT_WAVE_STATION_ENS:COM_WAVE_STATION_TMPL
+declare -rx COMOUT_WAVE_STATION_ENS="${ROTDIR}/${RUN}.${PDY}/${cyc}/ensstat/products/wave/station"
 if [[ ! -d "${COMOUT_WAVE_STATION_ENS}" ]]; then
     mkdir -m 775 -p "${COMOUT_WAVE_STATION_ENS}"
 fi

dev/jobs/JGEFS_WAVE_STAT_PNT

@@ -4,8 +4,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "wave_stat_pnt" -c "base wave wave_sta
 
 # Set COM Paths
 
-MEMDIR="ensstat" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMOUT_WAVE_STATION_ENS:COM_WAVE_STATION_TMPL
+declare -rx COMOUT_WAVE_STATION_ENS="${ROTDIR}/${RUN}.${PDY}/${cyc}/ensstat/products/wave/station"
 if [[ ! -d "${COMOUT_WAVE_STATION_ENS}" ]]; then
     mkdir -m 775 -p "${COMOUT_WAVE_STATION_ENS}"
 fi

dev/jobs/JGFS_ATMOS_AWIPS_20KM_1P0DEG

@@ -10,10 +10,8 @@ export COMPONENT="atmos"
 # Define COM directories
 ##############################################
 
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMOUT_ATMOS_WMO:COM_ATMOS_WMO_TMPL
-GRID="0p25" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMIN_ATMOS_GRIB_0p25:COM_ATMOS_GRIB_GRID_TMPL
+declare -rx COMOUT_ATMOS_WMO="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/wmo"
+declare -rx COMIN_ATMOS_GRIB_0p25="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/grib2/0p25"
 
 if [[ ! -d "${COMOUT_ATMOS_WMO}" ]]; then
     mkdir -m 775 -p "${COMOUT_ATMOS_WMO}"

dev/jobs/JGFS_ATMOS_CYCLONE_GENESIS

@@ -10,8 +10,8 @@ export cmodel=${RUN}
 ##############################################
 # Define COM directories
 ##############################################
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMOUT_ATMOS_GENESIS:COM_ATMOS_GENESIS_TMPL
-YMD=${PDY} HH=${cyc} GRID="0p25" declare_from_tmpl -rx COMIN_ATMOS_GRIB_0p25:COM_ATMOS_GRIB_GRID_TMPL
+declare -rx COMOUT_ATMOS_GENESIS="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/cyclone/genesis_vital"
+declare -rx COMIN_ATMOS_GRIB_0p25="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/grib2/0p25"
 
 # The following variables are used by the tracker scripts which are outside
 #   of global-workflow and therefore can't be standardized at this time

dev/jobs/JGFS_ATMOS_CYCLONE_TRACKER

@@ -7,11 +7,9 @@ export COMPONENT="atmos"
 ##############################################
 # Define COM and Data directories
 ##############################################
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMOUT_ATMOS_TRACK:COM_ATMOS_TRACK_TMPL \
-    COMIN_ATMOS_GENESIS:COM_ATMOS_GENESIS_TMPL
-YMD=${PDY} HH=${cyc} GRID="0p25" declare_from_tmpl -rx \
-    COMIN_ATMOS_GRIB_0p25:COM_ATMOS_GRIB_GRID_TMPL
+declare -rx COMOUT_ATMOS_TRACK="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/cyclone/tracks"
+declare -rx COMIN_ATMOS_GENESIS="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/cyclone/genesis_vital"
+declare -rx COMIN_ATMOS_GRIB_0p25="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/grib2/0p25"
 
 if [[ ! -d "${COMOUT_ATMOS_TRACK}" ]]; then mkdir -p "${COMOUT_ATMOS_TRACK}"; fi
 

dev/jobs/JGFS_ATMOS_FBWIND

@@ -13,8 +13,8 @@ export COMPONENT="atmos"
 # Define COM directories
 ##############################################
 
-GRID="0p25" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMIN_ATMOS_GRIB_0p25:COM_ATMOS_GRIB_GRID_TMPL
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMOUT:COM_ATMOS_WMO_TMPL
+declare -rx COMIN_ATMOS_GRIB_0p25="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/grib2/0p25"
+declare -rx COMOUT="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/wmo"
 if [[ ! -d "${COMOUT}" ]]; then
     mkdir -m 775 -p "${COMOUT}"
 fi

dev/jobs/JGFS_ATMOS_FSU_GENESIS

@@ -5,8 +5,8 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "genesis_fsu" -c "base genesis_fsu"
 ##############################################
 # Define COM and Data directories
 ##############################################
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMOUT_ATMOS_GENESIS:COM_ATMOS_GENESIS_TMPL
-YMD=${PDY} HH=${cyc} GRID="0p25" declare_from_tmpl -rx COMIN_ATMOS_GRIB_0p25:COM_ATMOS_GRIB_GRID_TMPL
+declare -rx COMOUT_ATMOS_GENESIS="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/cyclone/genesis_vital"
+declare -rx COMIN_ATMOS_GRIB_0p25="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/grib2/0p25"
 
 # The following variables are used by the tracker scripts which are outside
 #   of global-workflow and therefore can't be standardized at this time

dev/jobs/JGFS_ATMOS_GEMPAK

@@ -16,12 +16,12 @@ export DO_HD_PGRB=${DO_HD_PGRB:-YES}
 # Define COM directories
 ##############################################
 for grid in 0p25 0p50 1p00; do
-    GRID=${grid} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx "COMIN_ATMOS_GRIB_${grid}:COM_ATMOS_GRIB_GRID_TMPL"
+    declare -rx "COMIN_ATMOS_GRIB_${grid}"="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/grib2/${grid}"
 done
 
 for grid in 1p00 0p50 0p25 40km 35km_atl 35km_pac; do
     prod_dir="COMOUT_ATMOS_GEMPAK_${grid}"
-    GRID=${grid} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx "COMOUT_ATMOS_GEMPAK_${grid}:COM_ATMOS_GEMPAK_TMPL"
+    declare -rx "COMOUT_ATMOS_GEMPAK_${grid}"="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/gempak/${grid}"
 
     if [[ ! -d "${!prod_dir}" ]]; then
         mkdir -m 775 -p "${!prod_dir}"

dev/jobs/JGFS_ATMOS_GEMPAK_META

@@ -43,9 +43,9 @@ export COMINukmet=${COMINukmet:-$(compath.py "${envir}/ukmet/${ukmet_ver}")/ukme
 export COMINecmwf=${COMINecmwf:-$(compath.py "${envir}/ecmwf/${ecmwf_ver}")/ecmwf}
 export COMINnam=${COMINnam:-$(compath.py "${envir}/nam/${nam_ver}")/nam}
 
-GRID=1p00 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx "COMIN_ATMOS_GEMPAK_1p00:COM_ATMOS_GEMPAK_TMPL"
+declare -rx COMIN_ATMOS_GEMPAK_1p00="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/gempak/1p00"
 
-GRID="meta" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx "COMOUT_ATMOS_GEMPAK_META:COM_ATMOS_GEMPAK_TMPL"
+declare -rx COMOUT_ATMOS_GEMPAK_META="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/gempak/meta"
 mkdir -m 775 -p "${COMOUT_ATMOS_GEMPAK_META}"
 
 ########################################################

dev/jobs/JGFS_ATMOS_GEMPAK_NCDC_UPAPGIF

@@ -24,18 +24,18 @@ export COMPONENT="atmos"
 ##############################################
 # Define COM directories
 ##############################################
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMIN_OBS:COM_OBS_TMPL
-GRID=1p00 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx "COMIN_ATMOS_GEMPAK_1p00:COM_ATMOS_GEMPAK_TMPL"
+declare -rx COMIN_OBS="${ROTDIR}/${RUN}.${PDY}/${cyc}/obs"
+declare -rx COMIN_ATMOS_GEMPAK_1p00="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/gempak/1p00"
 
 # Declare COMOUT_ATMOS_GEMPAK_GIF and COMOUT_ATMOS_GEMPAK_UPPER_AIR
 for grid in gif upper_air; do
     _GRID="${grid^^}"
     gempak_dir="COMOUT_ATMOS_GEMPAK_${_GRID}"
-    GRID=${grid} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx "${gempak_dir}:COM_ATMOS_GEMPAK_TMPL"
+    declare -rx "${gempak_dir}"="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/gempak/${grid}"
     if [[ ! -d "${!gempak_dir}" ]]; then mkdir -m 775 -p "${!gempak_dir}"; fi
 done
 
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMOUT_ATMOS_WMO:COM_ATMOS_WMO_TMPL
+declare -rx COMOUT_ATMOS_WMO="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/wmo"
 if [[ ! -d "${COMOUT_ATMOS_WMO}" ]]; then mkdir -m 775 -p "${COMOUT_ATMOS_WMO}"; fi
 
 export pgmout=OUTPUT.$$

dev/jobs/JGFS_ATMOS_GEMPAK_PGRB2_SPEC

@@ -8,8 +8,10 @@ export EXT=""
 ##############################################
 # Define COM directories
 ##############################################
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMOUT_ATMOS_GOES:COM_ATMOS_GOES_TMPL
-GRID=0p25 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx "COMOUT_ATMOS_GEMPAK_0p25:COM_ATMOS_GEMPAK_TMPL"
+# shellcheck disable=SC2153
+declare -rx COMIN_ATMOS_GOES="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/goes_sim"
+# shellcheck disable=SC2153
+declare -rx COMOUT_ATMOS_GEMPAK_0p25="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/gempak/0p25"
 if [[ ! -d "${COMOUT_ATMOS_GEMPAK_0p25}" ]]; then
     mkdir -m 775 -p "${COMOUT_ATMOS_GEMPAK_0p25}"
 fi

dev/jobs/JGFS_ATMOS_PGRB2_SPEC_NPOESS

@@ -13,11 +13,9 @@ export OMP_NUM_THREADS=${OMP_NUM_THREADS:-1}
 # Define COM directories
 ##############################################
 
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMIN_ATMOS_MASTER:COM_ATMOS_MASTER_TMPL \
-    COMOUT_ATMOS_GOES:COM_ATMOS_GOES_TMPL
-GRID="0p50" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMIN_ATMOS_GRIB_0p50:COM_ATMOS_GRIB_GRID_TMPL
+declare -rx COMIN_ATMOS_MASTER="${ROTDIR}/${RUN}.${PDY}/${cyc}/model/atmos/master"
+declare -rx COMOUT_ATMOS_GOES="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/goes_sim"
+declare -rx COMIN_ATMOS_GRIB_0p50="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/grib2/0p50"
 
 mkdir -m 775 -p "${COMOUT_ATMOS_GOES}"
 

dev/jobs/JGFS_ATMOS_POSTSND

@@ -10,12 +10,11 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "postsnd" -c "base postsnd"
 # Define COM Directories
 ##############################
 
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMIN_ATMOS_HISTORY:COM_ATMOS_HISTORY_TMPL \
-    COMIN_ATMOS_BUFR:COM_ATMOS_BUFR_TMPL \
-    COMOUT_ATMOS_BUFR:COM_ATMOS_BUFR_TMPL \
-    COMOUT_ATMOS_WMO:COM_ATMOS_WMO_TMPL \
-    COMOUT_ATMOS_GEMPAK:COM_ATMOS_GEMPAK_TMPL
+declare -rx COMIN_ATMOS_HISTORY="${ROTDIR}/${RUN}.${PDY}/${cyc}/model/atmos/history"
+declare -rx COMIN_ATMOS_BUFR="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/bufr"
+declare -rx COMOUT_ATMOS_BUFR="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/bufr"
+declare -rx COMOUT_ATMOS_WMO="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/wmo"
+declare -rx COMOUT_ATMOS_GEMPAK="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/gempak/"
 
 if [[ ! -d "${COMOUT_ATMOS_BUFR}" ]]; then
     mkdir -p "${COMOUT_ATMOS_BUFR}"

dev/jobs/JGFS_ATMOS_VERIFICATION

@@ -22,7 +22,7 @@ export CDATE=${PDY}${cyc}
 # shellcheck disable=SC2041
 for grid in '1p00'; do
     prod_dir="COM_ATMOS_GRIB_${grid}"
-    GRID=${grid} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx "${prod_dir}:COM_ATMOS_GRIB_GRID_TMPL"
+    declare -rx "${prod_dir}"="${ROTDIR}/${RUN}.${PDY}/${cyc}/products/atmos/grib2/${grid}"
 done
 
 # TODO: If none of these are on, why are we running this job?

dev/jobs/JGLOBAL_AERO_ANALYSIS_FINALIZE

@@ -16,10 +16,9 @@ export PYTHONPATH
 ##############################################
 
 # Generate COM variables from templates
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMOUT_CHEM_ANALYSIS:COM_CHEM_ANALYSIS_TMPL \
-    COMOUT_CONF:COM_CONF_TMPL \
-    COMOUT_ATMOS_RESTART:COM_ATMOS_RESTART_TMPL
+declare -rx COMOUT_CHEM_ANALYSIS="${ROTDIR}/${RUN}.${PDY}/${cyc}/analysis/chem"
+declare -rx COMOUT_CONF="${ROTDIR}/${RUN}.${PDY}/${cyc}/conf"
+declare -rx COMOUT_ATMOS_RESTART="${ROTDIR}/${RUN}.${PDY}/${cyc}/model/atmos/restart"
 
 mkdir -m 755 -p "${COMOUT_CHEM_ANALYSIS}"
 mkdir -m 755 -p "${COMOUT_ATMOS_RESTART}"

dev/jobs/JGLOBAL_AERO_ANALYSIS_INITIALIZE

@@ -26,14 +26,12 @@ GDUMP="${GDUMP/gcafs/gcdas}"
 ##############################################
 
 # Generate COM variables from templates
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMIN_OBS:COM_OBS_TMPL \
-    COMOUT_CHEM_ANALYSIS:COM_CHEM_ANALYSIS_TMPL
-
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-    COMIN_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL \
-    COMIN_CHEM_BMAT_PREV:COM_CHEM_BMAT_TMPL \
-    COMIN_CHEM_ANALYSIS_PREV:COM_CHEM_ANALYSIS_TMPL
+declare -rx COMIN_OBS="${ROTDIR}/${RUN}.${PDY}/${cyc}/obs"
+declare -rx COMOUT_CHEM_ANALYSIS="${ROTDIR}/${RUN}.${PDY}/${cyc}/analysis/chem"
+
+declare -rx COMIN_ATMOS_RESTART_PREV="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/model/atmos/restart"
+declare -rx COMIN_CHEM_BMAT_PREV="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/analysis/chem/bmatrix"
+declare -rx COMIN_CHEM_ANALYSIS_PREV="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/analysis/chem"
 
 ###############################################################
 # Run relevant script