From 55da38b2d055d835f8a929bb347f81de050984d7 Mon Sep 17 00:00:00 2001
From: "Jianping.Huang" <Jianping.Huang@noaa.gov>
Date: Fri, 16 Jun 2023 13:27:02 +0000
Subject: [PATCH 1/7] update bias correction scripts and correct airnow data
 path

---
 scripts/exregional_bias_correction_o3.sh   | 59 +++++++++++-----------
 scripts/exregional_bias_correction_pm25.sh | 26 +++++-----
 scripts/exregional_fire_emission.sh        | 24 ++++-----
 ush/config_defaults.yaml                   |  9 ++--
 ush/machine/wcoss2.yaml                    |  7 +--
 5 files changed, 62 insertions(+), 63 deletions(-)

diff --git a/scripts/exregional_bias_correction_o3.sh b/scripts/exregional_bias_correction_o3.sh
index c0206933fc..3fec165b91 100755
--- a/scripts/exregional_bias_correction_o3.sh
+++ b/scripts/exregional_bias_correction_o3.sh
@@ -97,7 +97,7 @@ if [ ${#FCST_LEN_CYCL[@]} -gt 1 ]; then
   cyc_mod=$(( ${cyc} - ${DATE_FIRST_CYCL:8:2} ))
   CYCLE_IDX=$(( ${cyc_mod} / ${INCR_CYCL_FREQ} ))
   FCST_LEN_HRS=${FCST_LEN_CYCL[$CYCLE_IDX]}
-fi
+fi  
 
 #-----------------------------------------------------------------------------
 # STEP 1: Retrieve AIRNOW observation data
@@ -108,10 +108,11 @@ mkdir -p "${DATA}/data"
 if [ -d "${DATA}/data/bcdata.${yyyymm}" ]; then
   rm -rf "${DATA}/data/bcdata.${yyyymm}"
   mkdir -p "${DATA}/data/bcdata.${yyyymm}"
-  cp -rL "${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm}/airnow" "${DATA}/data/bcdata.${yyyymm}"
-  cp -rL "${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm}/interpolated" "${DATA}/data/bcdata.${yyyymm}" 
+  cp -rL "${COMINbicor}/bcdata.${yyyymm}/airnow" "${DATA}/data/bcdata.${yyyymm}"
+  cp -rL "${COMINbicor}/bcdata.${yyyymm}/interpolated" "${DATA}/data/bcdata.${yyyymm}"
 fi
 
+cd ${DATA}
 # Retrieve real-time airnow data for the last three days and convert them into netcdf
 if [ "${DO_REAL_TIME}" = "TRUE" ]; then
   for ipdym in {1..3}; do
@@ -214,31 +215,31 @@ POST_STEP
 
 cp ${DATA}/out/ozone/${yyyy}/*nc ${DATA}/data/bcdata.${yyyymm}/interpolated/ozone/${yyyy}
 
-if [ "${DO_AQM_SAVE_AIRNOW_HIST}" = "TRUE" ]; then
-  mkdir -p ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm}/interpolated/ozone/${yyyy}
-  cp ${DATA}/out/ozone/${yyyy}/*nc ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm}/interpolated/ozone/${yyyy}
+#if [ "${DO_AQM_SAVE_AIRNOW_HIST}" = "TRUE" ]; then
+  mkdir -p ${COMOUTbicor}/bcdata.${yyyymm}/interpolated/ozone/${yyyy}
+  cp ${DATA}/out/ozone/${yyyy}/*nc ${COMOUTbicor}/bcdata.${yyyymm}/interpolated/ozone/${yyyy}
 
   # CSV files
-  mkdir -p ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm}/airnow/csv/${yyyy}/${PDY}
-  mkdir -p ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm_m1}/airnow/csv/${yyyy_m1}/${PDYm1}
-  mkdir -p ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm_m2}/airnow/csv/${yyyy_m2}/${PDYm2}
-  mkdir -p ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm_m3}/airnow/csv/${yyyy_m3}/${PDYm3}
-  cp ${DCOMINairnow}/${PDYm1}/airnow/HourlyAQObs_${PDYm1}*.dat ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm_m1}/airnow/csv/${yyyy_m1}/${PDYm1}  
-  cp ${DCOMINairnow}/${PDYm2}/airnow/HourlyAQObs_${PDYm2}*.dat ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm_m2}/airnow/csv/${yyyy_m2}/${PDYm2}  
-  cp ${DCOMINairnow}/${PDYm3}/airnow/HourlyAQObs_${PDYm3}*.dat ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm_m3}/airnow/csv/${yyyy_m3}/${PDYm3}
+  mkdir -p ${COMOUTbicor}/bcdata.${yyyymm}/airnow/csv/${yyyy}/${PDY}
+  mkdir -p ${COMOUTbicor}/bcdata.${yyyymm_m1}/airnow/csv/${yyyy_m1}/${PDYm1}
+  mkdir -p ${COMOUTbicor}/bcdata.${yyyymm_m2}/airnow/csv/${yyyy_m2}/${PDYm2}
+  mkdir -p ${COMOUTbicor}/bcdata.${yyyymm_m3}/airnow/csv/${yyyy_m3}/${PDYm3}
+  cp ${DCOMINairnow}/${PDYm1}/airnow/HourlyAQObs_${PDYm1}*.dat ${COMOUTbicor}/bcdata.${yyyymm_m1}/airnow/csv/${yyyy_m1}/${PDYm1}  
+  cp ${DCOMINairnow}/${PDYm2}/airnow/HourlyAQObs_${PDYm2}*.dat ${COMOUTbicor}/bcdata.${yyyymm_m2}/airnow/csv/${yyyy_m2}/${PDYm2}  
+  cp ${DCOMINairnow}/${PDYm3}/airnow/HourlyAQObs_${PDYm3}*.dat ${COMOUTbicor}/bcdata.${yyyymm_m3}/airnow/csv/${yyyy_m3}/${PDYm3}
 
   # NetCDF files
-  mkdir -p ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm}/airnow/netcdf/${yyyy}/${PDY}
-  mkdir -p ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm_m1}/airnow/netcdf/${yyyy_m1}/${PDYm1}
-  mkdir -p ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm_m2}/airnow/netcdf/${yyyy_m2}/${PDYm2}
-  mkdir -p ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm_m3}/airnow/netcdf/${yyyy_m3}/${PDYm3}
-  cp ${DATA}/data/bcdata.${yyyymm_m1}/airnow/netcdf/${yyyy_m1}/${PDYm1}/HourlyAQObs.${PDYm1}.nc ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm_m1}/airnow/netcdf/${yyyy_m1}/${PDYm1}  
-  cp ${DATA}/data/bcdata.${yyyymm_m2}/airnow/netcdf/${yyyy_m2}/${PDYm2}/HourlyAQObs.${PDYm2}.nc ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm_m2}/airnow/netcdf/${yyyy_m2}/${PDYm2}  
-  cp ${DATA}/data/bcdata.${yyyymm_m3}/airnow/netcdf/${yyyy_m3}/${PDYm3}/HourlyAQObs.${PDYm3}.nc ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm_m3}/airnow/netcdf/${yyyy_m3}/${PDYm3}
-
-  mkdir -p  ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm}/grid/${cyc}z/${PDY}
-  cp ${COMIN}/${NET}.${cycle}.*sfc*.nc ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm}/grid/${cyc}z/${PDY}
-fi
+  mkdir -p ${COMOUTbicor}/bcdata.${yyyymm}/airnow/netcdf/${yyyy}/${PDY}
+  mkdir -p ${COMOUTbicor}/bcdata.${yyyymm_m1}/airnow/netcdf/${yyyy_m1}/${PDYm1}
+  mkdir -p ${COMOUTbicor}/bcdata.${yyyymm_m2}/airnow/netcdf/${yyyy_m2}/${PDYm2}
+  mkdir -p ${COMOUTbicor}/bcdata.${yyyymm_m3}/airnow/netcdf/${yyyy_m3}/${PDYm3}
+  cp ${DATA}/data/bcdata.${yyyymm_m1}/airnow/netcdf/${yyyy_m1}/${PDYm1}/HourlyAQObs.${PDYm1}.nc ${COMOUTbicor}/bcdata.${yyyymm_m1}/airnow/netcdf/${yyyy_m1}/${PDYm1}  
+  cp ${DATA}/data/bcdata.${yyyymm_m2}/airnow/netcdf/${yyyy_m2}/${PDYm2}/HourlyAQObs.${PDYm2}.nc ${COMOUTbicor}/bcdata.${yyyymm_m2}/airnow/netcdf/${yyyy_m2}/${PDYm2}  
+  cp ${DATA}/data/bcdata.${yyyymm_m3}/airnow/netcdf/${yyyy_m3}/${PDYm3}/HourlyAQObs.${PDYm3}.nc ${COMOUTbicor}/bcdata.${yyyymm_m3}/airnow/netcdf/${yyyy_m3}/${PDYm3}
+
+  mkdir -p  ${COMOUTbicor}/bcdata.${yyyymm}/grid/${cyc}z/${PDY}
+  cp ${COMIN}/${NET}.${cycle}.*sfc*.nc ${COMOUTbicor}/bcdata.${yyyymm}/grid/${cyc}z/${PDY}
+#fi
 
 #-----------------------------------------------------------------------------
 # STEP 4:  Performing Bias Correction for Ozone
@@ -246,7 +247,7 @@ fi
 
 rm -rf ${DATA}/data/bcdata*
 
-ln -sf ${AQM_AIRNOW_HIST_DIR}/bcdata* "${DATA}/data"
+ln -sf ${COMINbicor}/bcdata* "${DATA}/data"
 
 mkdir -p ${DATA}/data/sites
 cp ${PARMaqm_utils}/bias_correction/config.ozone.bias_corr_${id_domain}.${cyc}z ${DATA}
@@ -381,7 +382,7 @@ EOF1
 
     cp ${DATA}/${NET}.${cycle}.max_*hr_o3_bc.*.grib2 ${COMOUT}
    
-    if [ "$SENDDBN" = "TRUE" ]; then
+    if [ "$SENDDBN" = "YES" ]; then
       ${DBNROOT}/bin/dbn_alert MODEL AQM_MAX ${job} ${COMOUT}/${NET}.${cycle}.max_1hr_o3_bc.227.grib2
       ${DBNROOT}/bin/dbn_alert MODEL AQM_MAX ${job} ${COMOUT}/${NET}.${cycle}.max_8hr_o3_bc.227.grib2
     fi
@@ -409,7 +410,7 @@ EOF1
     cp awpaqm.${cycle}.*o3-max-bc.227.grib2 ${COMOUTwmo}
 
     # Distribute Data
-    if [ "${SENDDBN_NTC}" = "TRUE" ] ; then
+    if [ "${SENDDBN_NTC}" = "YES" ] ; then
       ${DBNROOT}/bin/dbn_alert ${DBNALERT_TYPE} ${NET} ${job} ${COMOUTwmo}/awpaqm.${cycle}.1ho3-max-bc.227.grib2
       ${DBNROOT}/bin/dbn_alert ${DBNALERT_TYPE} ${NET} ${job} ${COMOUTwmo}/awpaqm.${cycle}.8ho3-max-bc.227.grib2
     fi
@@ -456,7 +457,7 @@ if [ "${cyc}" = "06" ] || [ "${cyc}" = "12" ]; then
   cp ${NET}.${cycle}.ave_8hr_o3_bc.227.grib2 ${COMOUT}
 fi
 
-if [ "${SENDDBN}" = "TRUE" ] ; then
+if [ "${SENDDBN}" = "YES" ] ; then
    ${DBNROOT}/bin/dbn_alert MODEL AQM_CONC ${job} ${COMOUT}/${NET}.${cycle}.ave_1hr_o3_bc.227.grib2
   if [ "${cyc}" = "06" ] || [ "${cyc}" = "12" ]; then
    ${DBNROOT}/bin/dbn_alert MODEL AQM_CONC ${job} ${COMOUT}/${NET}.${cycle}.ave_8hr_o3_bc.227.grib2
@@ -508,7 +509,7 @@ if [ "${cyc}" = "06" ] || [ "${cyc}" = "12" ]; then
     cp awpaqm.${cycle}.${hr}ho3-max-bc.227.grib2 ${COMOUTwmo}
 
     # Distribute Data
-    if [ "${SENDDBN}" = "TRUE" ]; then
+    if [ "${SENDDBN}" = "YES" ]; then
       ${DBNROOT}/bin/dbn_alert ${DBNALERT_TYPE} ${NET} ${job} ${COMOUTwmo}/awpaqm.${cycle}.${hr}ho3-bc.227.grib2
       ${DBNROOT}/bin/dbn_alert ${DBNALERT_TYPE} ${NET} ${job} ${COMOUTwmo}/awpaqm.${cycle}.${hr}ho3-max-bc.227.grib2
     fi
diff --git a/scripts/exregional_bias_correction_pm25.sh b/scripts/exregional_bias_correction_pm25.sh
index 6924b4dbf8..996249770b 100755
--- a/scripts/exregional_bias_correction_pm25.sh
+++ b/scripts/exregional_bias_correction_pm25.sh
@@ -97,7 +97,7 @@ if [ ${#FCST_LEN_CYCL[@]} -gt 1 ]; then
   cyc_mod=$(( ${cyc} - ${DATE_FIRST_CYCL:8:2} ))
   CYCLE_IDX=$(( ${cyc_mod} / ${INCR_CYCL_FREQ} ))
   FCST_LEN_HRS=${FCST_LEN_CYCL[$CYCLE_IDX]}
-fi
+fi  
 
 #-----------------------------------------------------------------------------
 # STEP 1: Retrieve AIRNOW observation data
@@ -111,9 +111,9 @@ if [ -d "${DATA}/data/bcdata.${yyyymm}" ]; then
   cp -rL "${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm}/airnow" "${DATA}/data/bcdata.${yyyymm}"
   cp -rL "${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm}/interpolated" "${DATA}/data/bcdata.${yyyymm}"
 fi
-
+cd ${DATA}
 # Retrieve real-time airnow data for the last three days
-if [ "${DO_REAL_TIME}" = "TRUE" ]; then
+#if [ "${DO_REAL_TIME}" = "TRUE" ]; then
   for ipdym in {1..3}; do
     case $ipdym in
       1)
@@ -156,7 +156,7 @@ if [ "${DO_REAL_TIME}" = "TRUE" ]; then
     fi
     POST_STEP
   done
-fi
+#fi
 
 #-----------------------------------------------------------------------------
 # STEP 2:  Extracting PM2.5, O3, and met variables from CMAQ input and outputs
@@ -214,10 +214,10 @@ POST_STEP
 
 cp ${DATA}/out/pm25/${yyyy}/*nc ${DATA}/data/bcdata.${yyyymm}/interpolated/pm25/${yyyy}
 
-if [ "${DO_AQM_SAVE_AIRNOW_HIST}" = "TRUE" ]; then
-  mkdir -p  ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm}/interpolated/pm25/${yyyy}
-  cp ${DATA}/out/pm25/${yyyy}/*nc ${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm}/interpolated/pm25/${yyyy}
-fi
+#if [ "${DO_AQM_SAVE_AIRNOW_HIST}" = "TRUE" ]; then
+  mkdir -p  ${COMOUTbicor}/bcdata.${yyyymm}/interpolated/pm25/${yyyy}
+  cp ${DATA}/out/pm25/${yyyy}/*nc ${COMOUTbicor}/bcdata.${yyyymm}/interpolated/pm25/${yyyy}
+#fi
 
 #-----------------------------------------------------------------------
 # STEP 4:  Performing Bias Correction for PM2.5 
@@ -225,7 +225,7 @@ fi
 
 rm -rf ${DATA}/data/bcdata*
 
-ln -sf ${AQM_AIRNOW_HIST_DIR}/bcdata* "${DATA}/data"
+ln -sf ${COMINbicor}/bcdata* "${DATA}/data"
 
 mkdir -p ${DATA}/data/sites
 
@@ -280,7 +280,7 @@ fi
 POST_STEP
 
 cp ${DATA}/${NET}.${cycle}.pm25*bc*.grib2 ${COMOUT}
-if [ "$SENDDBN" = "TRUE" ]; then
+if [ "$SENDDBN" = "YES" ]; then
   $DBNROOT/bin/dbn_alert MODEL AQM_PM ${job} ${COMOUT}
 fi
 
@@ -377,7 +377,7 @@ EOF1
   cp ${NET}.${cycle}.max_1hr_pm25_bc.227.grib2   ${COMOUT}
   cp ${NET}.${cycle}.ave_24hr_pm25_bc.227.grib2  ${COMOUT}
 
-  if [ "${SENDDBN}" = "TRUE" ]; then
+  if [ "${SENDDBN}" = "YES" ]; then
     ${DBNROOT}/bin/dbn_alert MODEL AQM_MAX ${job} ${COMOUT}/${NET}.${cycle}.max_1hr_pm25_bc.227.grib2
     ${DBNROOT}/bin/dbn_alert MODEL AQM_PM ${job} ${COMOUT}/${NET}.${cycle}.ave_24hr_pm25_bc.227.grib2
   fi
@@ -395,7 +395,7 @@ wgrib2 tmpfile_pm25_bc -set_grib_type c3b -new_grid_winds earth -new_grid ${grid
 
 cp tmpfile_pm25_bc ${COMOUT}/${NET}.${cycle}.ave_1hr_pm25_bc.${id_domain}.grib2
 cp ${NET}.${cycle}.grib2_pm25_bc.227 ${COMOUT}/${NET}.${cycle}.ave_1hr_pm25_bc.227.grib2
-if [ "${SENDDBN}" = "TRUE" ]; then
+if [ "${SENDDBN}" = "YES" ]; then
   ${DBNROOT}/bin/dbn_alert MODEL AQM_PM ${job} ${COMOUT}/${NET}.${cycle}.ave_1hr_pm25_bc.227.grib2
 fi
 
@@ -463,7 +463,7 @@ if [ "${cyc}" = "06" ] || [ "${cyc}" = "12" ]; then
   cp awpaqm.${cycle}.24hr-pm25-ave-bc.227.grib2      ${COMOUTwmo}
 
   # Distribute Data
-  if [ "${SENDDBN_NTC}" = "TRUE" ] ; then
+  if [ "${SENDDBN_NTC}" = "YES" ] ; then
     ${DBNROOT}/bin/dbn_alert ${DBNALERT_TYPE} ${NET} ${job} ${COMOUTwmo}/awpaqm.${cycle}.1hpm25-bc.227.grib2
     ${DBNROOT}/bin/dbn_alert ${DBNALERT_TYPE} ${NET} ${job} ${COMOUTwmo}/awpaqm.${cycle}.daily-1hr-pm25-max-bc.227.grib2
     ${DBNROOT}/bin/dbn_alert ${DBNALERT_TYPE} ${NET} ${job} ${COMOUTwmo}/awpaqm.${cycle}.24hr-pm25-ave-bc.227.grib2
diff --git a/scripts/exregional_fire_emission.sh b/scripts/exregional_fire_emission.sh
index 909382d28c..e1d1c913cf 100755
--- a/scripts/exregional_fire_emission.sh
+++ b/scripts/exregional_fire_emission.sh
@@ -56,12 +56,10 @@ data files.
 yyyymmdd=${FIRE_FILE_CDATE:0:8}
 hh=${FIRE_FILE_CDATE:8:2}
 
-CDATE_mh3=$( $DATE_UTIL --utc --date "${yyyymmdd} ${hh} UTC - 3 hours" "+%Y%m%d%H" )
-CDATE_mh2=$( $DATE_UTIL --utc --date "${yyyymmdd} ${hh} UTC - 2 hours" "+%Y%m%d%H" )
 CDATE_mh1=$( $DATE_UTIL --utc --date "${yyyymmdd} ${hh} UTC - 1 hours" "+%Y%m%d%H" )
 
-yyyymmdd_mh3=${CDATE_mh3:0:8}
-hh_mh3=${CDATE_mh3:8:2}
+yyyymmdd_mh1=${CDATE_mh1:0:8}
+hh_mh1=${CDATE_mh1:8:2}
 #
 #-----------------------------------------------------------------------
 #
@@ -76,19 +74,19 @@ if [ -e "${DCOMINfire}/${aqm_fire_file_fn}" ]; then
   cp "${DCOMINfire}/${aqm_fire_file_fn}" "${FIRE_EMISSION_STAGING_DIR}"
 else
   # Copy raw data 
-  for ihr in {0..21}; do
-    download_time=$( $DATE_UTIL --utc --date "${yyyymmdd_mh3} ${hh_mh3} UTC - $ihr hours" "+%Y%m%d%H" )
+  for ihr in {0..23}; do
+    download_time=$( $DATE_UTIL --utc --date "${yyyymmdd_mh1} ${hh_mh1} UTC - $ihr hours" "+%Y%m%d%H" )
     FILE_13km="Hourly_Emissions_13km_${download_time}00_${download_time}00.nc"
     yyyymmdd_dn=${download_time:0:8}
     hh_dn=${download_time:8:2}
     missing_download_time=$( $DATE_UTIL --utc --date "${yyyymmdd_dn} ${hh_dn} UTC - 24 hours" "+%Y%m%d%H" )
     yyyymmdd_dn_md1=${missing_download_time:0:8}
     FILE_13km_md1=Hourly_Emissions_13km_${missing_download_time}00_${missing_download_time}00.nc
-    if [ -e "${DCOMINfire}/RAVE_raw_new/${yyyymmdd_dn}/${FILE_13km}" ]; then
-      ln -sf "${DCOMINfire}/RAVE_raw_new/${yyyymmdd_dn}/${FILE_13km}" .
-    elif [ -e "${DCOMINfire}/RAVE_raw_new/${yyyymmdd_dn_md1}/${FILE_13km_md1}" ]; then
+    if [ -e "${DCOMINfire}/${yyyymmdd_dn}/rave/${FILE_13km}" ]; then
+      cp -p "${DCOMINfire}/${yyyymmdd_dn}/rave/${FILE_13km}" .
+    elif [ -e "${DCOMINfire}/${yyyymmdd_dn_md1}/rave/${FILE_13km_md1}" ]; then
       echo "WARNING: ${FILE_13km} does not exist. Replacing with the file of previous date ..."
-      ln -sf "${DCOMINfire}/RAVE_raw_new/${yyyymmdd_dn_md1}/${FILE_13km_md1}" "${FILE_13km}"
+      cp -p "${DCOMINfire}/${yyyymmdd_dn_md1}/rave/${FILE_13km_md1}" "${FILE_13km}"
     else
       message_txt="Fire Emission RAW data does not exist:
   FILE_13km_md1 = \"${FILE_13km_md1}\"
@@ -97,7 +95,7 @@ else
       if [ "${RUN_ENVIR}" = "community" ]; then
         print_err_msg_exit "${message_txt}"
       else
-        ln -sf  "${DCOMINfire}/Hourly_Emissions_13km_dummy.nc" "${FILE_13km}"
+        cp -p  "${DCOMINfire}/Hourly_Emissions_13km_dummy.nc" "${FILE_13km}"
         message_warning="WARNING: ${message_txt}. Replacing with the dummy file :: AQM RUN SOFT FAILED."
         print_info_msg "${message_warning}"
         if [ ! -z "${maillist}" ]; then
@@ -120,10 +118,6 @@ else
 
   mv temp.nc Hourly_Emissions_13km_${download_time}00_${download_time}00.nc
 
-  # Extra times
-  cp Hourly_Emissions_13km_${CDATE_mh3}00_${CDATE_mh3}00.nc Hourly_Emissions_13km_${CDATE_mh2}00_${CDATE_mh2}00.nc
-  cp Hourly_Emissions_13km_${CDATE_mh3}00_${CDATE_mh3}00.nc Hourly_Emissions_13km_${CDATE_mh1}00_${CDATE_mh1}00.nc
-
   ncrcat -h Hourly_Emissions_13km_*.nc Hourly_Emissions_13km_${yyyymmdd}0000_${yyyymmdd}2300.t${cyc}z.nc
   export err=$?
   if [ $err -ne 0 ]; then
diff --git a/ush/config_defaults.yaml b/ush/config_defaults.yaml
index d72df2cc67..e9b9e46907 100644
--- a/ush/config_defaults.yaml
+++ b/ush/config_defaults.yaml
@@ -2901,8 +2901,10 @@ cpl_aqm_parm:
   # DO_AQM_GEFS_LBCS:
   # Add GEFS aerosol LBCs to chemical LBCs
   #
-  # DO_AQM_SAVE_AIRNOW_HIST:
-  # Save bias-correction airnow training data
+  # COMINbicor 
+  # Read bias-correction training data
+  # COMOUTbicor 
+  # Save bias-correction training data
   #
   # DO_AQM_SAVE_FIRE:
   # Archive fire emission file to HPSS
@@ -3052,4 +3054,5 @@ cpl_aqm_parm:
   DCOMINpt_src_dfv: "/path/to/point/source/base/directory"
 
   DCOMINairnow_dfv: "/path/to/airnow/obaservation/data"
-  AQM_AIRNOW_HIST_DIR: "/path/to/historical/airnow/data/dir"
+  COMINbicor: "/path/to/historical/airnow/data/dir"
+  COMOUTbicor: "/path/to/historical/airnow/data/dir"
diff --git a/ush/machine/wcoss2.yaml b/ush/machine/wcoss2.yaml
index 349c279746..c5cfe44743 100644
--- a/ush/machine/wcoss2.yaml
+++ b/ush/machine/wcoss2.yaml
@@ -42,12 +42,13 @@ cpl_aqm_parm:
   DCOMINbio_dfv: /lfs/h2/emc/lam/noscrub/RRFS_CMAQ/aqm/bio
   DCOMINdust_dfv: /lfs/h2/emc/lam/noscrub/RRFS_CMAQ/FENGSHA
   DCOMINcanopy_dfv: /lfs/h2/emc/lam/noscrub/RRFS_CMAQ/canopy
-  DCOMINfire_dfv: /lfs/h2/emc/physics/noscrub/kai.wang/RAVE_fire/RAVE_NA_NRT
+  DCOMINfire_dfv: /lfs/h1/ops/dev/dcom 
   DCOMINchem_lbcs_dfv: /lfs/h2/emc/lam/noscrub/RRFS_CMAQ/LBCS/AQM_NA13km_AM4_v1
-  DCOMINgefs_dfv: /lfs/h2/emc/lam/noscrub/RRFS_CMAQ/GEFS_DATA
+  DCOMINgefs_dfv: /lfs/h1/ops/prod/com/gefs/v12.3 
   DCOMINpt_src_dfv: /lfs/h2/emc/physics/noscrub/Youhua.Tang/nei2016v1-pt/v2023-01-PT
   DCOMINairnow_dfv: /lfs/h1/ops/prod/dcom
-  AQM_AIRNOW_HIST_DIR: /lfs/h2/emc/physics/noscrub/jianping.huang/Bias_correction/aqmv7.0
+  COMINbicor: /lfs/h2/emc/physics/noscrub/jianping.huang/Bias_correction/aqmv7.0.81
+  COMOUTbicor: /lfs/h2/emc/physics/noscrub/jianping.huang/Bias_correction/aqmv7.0.81
   NEXUS_INPUT_DIR: /lfs/h2/emc/lam/noscrub/RRFS_CMAQ/nexus_emissions
   NEXUS_FIX_DIR: /lfs/h2/emc/lam/noscrub/RRFS_CMAQ/nexus/fix
   NEXUS_GFS_SFC_DIR: /lfs/h2/emc/lam/noscrub/RRFS_CMAQ/GFS_DATA

From cf3b038025774cca796d1e1d3fca2510a041e975 Mon Sep 17 00:00:00 2001
From: "Jianping.Huang" <Jianping.Huang@noaa.gov>
Date: Tue, 20 Jun 2023 17:09:38 +0000
Subject: [PATCH 2/7] update hash numbers for arl_nexus and AQM_utils

---
 Externals.cfg                              |  4 ++--
 scripts/exregional_bias_correction_o3.sh   | 14 +++-----------
 scripts/exregional_bias_correction_pm25.sh | 11 ++---------
 ush/machine/wcoss2.yaml                    |  7 ++++---
 4 files changed, 11 insertions(+), 25 deletions(-)

diff --git a/Externals.cfg b/Externals.cfg
index 75f80c599c..c871f9a3ea 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -30,7 +30,7 @@ protocol = git
 repo_url = https://github.com/noaa-oar-arl/NEXUS
 # Specify either a branch name or a hash but not both.
 #branch = develop
-hash = 3842818
+hash = 732a441
 local_path = sorc/arl_nexus
 required = True
 
@@ -39,7 +39,7 @@ protocol = git
 repo_url = https://github.com/NOAA-EMC/AQM-utils
 # Specify either a branch name or a hash but not both.
 #branch = develop
-hash = 9b2921c
+hash = 694a139 
 local_path = sorc/AQM-utils
 required = True
 
diff --git a/scripts/exregional_bias_correction_o3.sh b/scripts/exregional_bias_correction_o3.sh
index 3fec165b91..c168671648 100755
--- a/scripts/exregional_bias_correction_o3.sh
+++ b/scripts/exregional_bias_correction_o3.sh
@@ -97,24 +97,16 @@ if [ ${#FCST_LEN_CYCL[@]} -gt 1 ]; then
   cyc_mod=$(( ${cyc} - ${DATE_FIRST_CYCL:8:2} ))
   CYCLE_IDX=$(( ${cyc_mod} / ${INCR_CYCL_FREQ} ))
   FCST_LEN_HRS=${FCST_LEN_CYCL[$CYCLE_IDX]}
-fi  
+fi
 
 #-----------------------------------------------------------------------------
 # STEP 1: Retrieve AIRNOW observation data
 #-----------------------------------------------------------------------------
 
-# Link the historical airnow data
 mkdir -p "${DATA}/data"
-if [ -d "${DATA}/data/bcdata.${yyyymm}" ]; then
-  rm -rf "${DATA}/data/bcdata.${yyyymm}"
-  mkdir -p "${DATA}/data/bcdata.${yyyymm}"
-  cp -rL "${COMINbicor}/bcdata.${yyyymm}/airnow" "${DATA}/data/bcdata.${yyyymm}"
-  cp -rL "${COMINbicor}/bcdata.${yyyymm}/interpolated" "${DATA}/data/bcdata.${yyyymm}"
-fi
 
-cd ${DATA}
 # Retrieve real-time airnow data for the last three days and convert them into netcdf
-if [ "${DO_REAL_TIME}" = "TRUE" ]; then
+#if [ "${DO_REAL_TIME}" = "TRUE" ]; then
   for ipdym in {1..3}; do
     case $ipdym in
       1)
@@ -157,7 +149,7 @@ if [ "${DO_REAL_TIME}" = "TRUE" ]; then
     fi
     POST_STEP
   done     
-fi
+#fi
 
 #-----------------------------------------------------------------------------
 # STEP 2:  Extracting PM2.5, O3, and met variables from CMAQ input and outputs
diff --git a/scripts/exregional_bias_correction_pm25.sh b/scripts/exregional_bias_correction_pm25.sh
index 996249770b..850e44e95c 100755
--- a/scripts/exregional_bias_correction_pm25.sh
+++ b/scripts/exregional_bias_correction_pm25.sh
@@ -97,21 +97,14 @@ if [ ${#FCST_LEN_CYCL[@]} -gt 1 ]; then
   cyc_mod=$(( ${cyc} - ${DATE_FIRST_CYCL:8:2} ))
   CYCLE_IDX=$(( ${cyc_mod} / ${INCR_CYCL_FREQ} ))
   FCST_LEN_HRS=${FCST_LEN_CYCL[$CYCLE_IDX]}
-fi  
+fi
 
 #-----------------------------------------------------------------------------
 # STEP 1: Retrieve AIRNOW observation data
 #-----------------------------------------------------------------------------
 
-# Link the historical airnow data
 mkdir -p "${DATA}/data"
-if [ -d "${DATA}/data/bcdata.${yyyymm}" ]; then
-  rm -rf "${DATA}/data/bcdata.${yyyymm}"
-  mkdir -p "${DATA}/data/bcdata.${yyyymm}"
-  cp -rL "${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm}/airnow" "${DATA}/data/bcdata.${yyyymm}"
-  cp -rL "${AQM_AIRNOW_HIST_DIR}/bcdata.${yyyymm}/interpolated" "${DATA}/data/bcdata.${yyyymm}"
-fi
-cd ${DATA}
+
 # Retrieve real-time airnow data for the last three days
 #if [ "${DO_REAL_TIME}" = "TRUE" ]; then
   for ipdym in {1..3}; do
diff --git a/ush/machine/wcoss2.yaml b/ush/machine/wcoss2.yaml
index c5cfe44743..c89242a673 100644
--- a/ush/machine/wcoss2.yaml
+++ b/ush/machine/wcoss2.yaml
@@ -9,9 +9,9 @@ platform:
   MET_BIN_EXEC: bin
   MET_INSTALL_DIR: /apps/ops/para/libs/intel/19.1.3.304/met/10.1.1
   DOMAIN_PREGEN_BASEDIR: /lfs/h2/emc/lam/noscrub/UFS_SRW_App/develop/FV3LAM_pregen
-  QUEUE_DEFAULT: dev
-  QUEUE_FCST: dev
-  QUEUE_HPSS: dev_transfer
+  QUEUE_DEFAULT: devhigh
+  QUEUE_FCST: devhigh
+  QUEUE_HPSS: devhigh
   RUN_CMD_FCST: mpiexec -n ${PE_MEMBER01} -ppn ${PPN_RUN_FCST} --cpu-bind core -depth ${OMP_NUM_THREADS_RUN_FCST}
   RUN_CMD_POST: mpiexec -n ${nprocs}
   RUN_CMD_PRDGEN: mpiexec -n ${nprocs} --cpu-bind core cfp
@@ -47,6 +47,7 @@ cpl_aqm_parm:
   DCOMINgefs_dfv: /lfs/h1/ops/prod/com/gefs/v12.3 
   DCOMINpt_src_dfv: /lfs/h2/emc/physics/noscrub/Youhua.Tang/nei2016v1-pt/v2023-01-PT
   DCOMINairnow_dfv: /lfs/h1/ops/prod/dcom
+  #DCOMINairnow_dfv: /lfs/h2/emc/physics/noscrub/jianping.huang/dcom 
   COMINbicor: /lfs/h2/emc/physics/noscrub/jianping.huang/Bias_correction/aqmv7.0.81
   COMOUTbicor: /lfs/h2/emc/physics/noscrub/jianping.huang/Bias_correction/aqmv7.0.81
   NEXUS_INPUT_DIR: /lfs/h2/emc/lam/noscrub/RRFS_CMAQ/nexus_emissions

From d6e02bad2ffe930929e945ebee52f93f59c33dcb Mon Sep 17 00:00:00 2001
From: "Jianping.Huang" <Jianping.Huang@noaa.gov>
Date: Thu, 22 Jun 2023 02:58:46 +0000
Subject: [PATCH 3/7] update nexus_emis and nexus_post ex-scripts for fix
 biogenic emissions

---
 scripts/exregional_nexus_emission.sh   | 24 +++++++++++++--
 scripts/exregional_nexus_post_split.sh | 42 +++++++++++++-------------
 2 files changed, 42 insertions(+), 24 deletions(-)

diff --git a/scripts/exregional_nexus_emission.sh b/scripts/exregional_nexus_emission.sh
index a41f11d156..43e4d8ed63 100755
--- a/scripts/exregional_nexus_emission.sh
+++ b/scripts/exregional_nexus_emission.sh
@@ -147,10 +147,10 @@ else
   start_del_hr=$(( len_per_split * nspt ))
   start_date=$( $DATE_UTIL --utc --date "${yyyymmdd} ${hh} UTC + ${start_del_hr} hours " "+%Y%m%d%H" )
   if [ "${nsptp}" = "${NUM_SPLIT_NEXUS}" ];then
-    end_date=$( $DATE_UTIL --utc --date "${yyyymmdd} ${hh} UTC + ${FCST_LEN_HRS} hours" "+%Y%m%d%H" )
+    end_date=$( $DATE_UTIL --utc --date "${yyyymmdd} ${hh} UTC + $(expr $FCST_LEN_HRS + 1) hours" "+%Y%m%d%H" )
   else
     end_del_hr=$(( len_per_split * nsptp ))
-    end_date=$( $DATE_UTIL --utc --date "${yyyymmdd} ${hh} UTC + ${end_del_hr} hours" "+%Y%m%d%H" )
+    end_date=$( $DATE_UTIL --utc --date "${yyyymmdd} ${hh} UTC + $(expr $end_del_hr + 1) hours" "+%Y%m%d%H" )
   fi
 fi
 #
@@ -327,6 +327,24 @@ else
   fi
 fi
 POST_STEP
+
+# 
+#-----------------------------------------------------------------------
+#
+# make nexus output pretty and move to INPUT_DATA directory
+#
+#-----------------------------------------------------------------------
+#
+python3 ${ARL_NEXUS_DIR}/utils/python/make_nexus_output_pretty.py --src ${DATA}/NEXUS_Expt_split.nc --grid ${DATA}/grid_spec.nc -o ${INPUT_DATA}/${NET}.${cycle}${dot_ensmem}.NEXUS_Expt_split.${nspt}.nc -t ${DATA}/HEMCO_sa_Time.rc
+export err=$?
+if [ $err -ne 0 ]; then
+  message_txt="Call to python script \"make_nexus_output_pretty.py\" failed."
+  if [ "${RUN_ENVIR}" = "community" ]; then
+    print_err_msg_exit "${message_txt}"
+  else
+    err_exit "${message_txt}"
+  fi
+fi
 #
 #-----------------------------------------------------------------------
 #
@@ -334,7 +352,7 @@ POST_STEP
 #
 #-----------------------------------------------------------------------
 #
-mv ${DATA}/NEXUS_Expt_split.nc ${INPUT_DATA}/${NET}.${cycle}${dot_ensmem}.NEXUS_Expt_split.${nspt}.nc
+#mv ${DATA}/NEXUS_Expt_split.nc ${INPUT_DATA}/${NET}.${cycle}${dot_ensmem}.NEXUS_Expt_split.${nspt}.nc
 
 #
 #-----------------------------------------------------------------------
diff --git a/scripts/exregional_nexus_post_split.sh b/scripts/exregional_nexus_post_split.sh
index f1830092ce..9ac0048649 100755
--- a/scripts/exregional_nexus_post_split.sh
+++ b/scripts/exregional_nexus_post_split.sh
@@ -99,27 +99,27 @@ fi
 #
 #-----------------------------------------------------------------------
 #
-python3 ${ARL_NEXUS_DIR}/utils/python/nexus_time_parser.py -f ${DATA}/HEMCO_sa_Time.rc -s $start_date -e $end_date
-export err=$?
-if [ $err -ne 0 ]; then
-  message_txt="Call to python script \"nexus_time_parser.py\" failed."
-  if [ "${RUN_ENVIR}" = "community" ]; then
-    print_err_msg_exit "${message_txt}"
-  else
-    err_exit "${message_txt}"
-  fi
-fi
+# python3 ${ARL_NEXUS_DIR}/utils/python/nexus_time_parser.py -f ${DATA}/HEMCO_sa_Time.rc -s $start_date -e $end_date
+# export err=$?
+# if [ $err -ne 0 ]; then
+#   message_txt="Call to python script \"nexus_time_parser.py\" failed."
+#   if [ "${RUN_ENVIR}" = "community" ]; then
+#     print_err_msg_exit "${message_txt}"
+#   else
+#     err_exit "${message_txt}"
+#   fi
+# fi
 
-python3 ${ARL_NEXUS_DIR}/utils/python/make_nexus_output_pretty.py --src ${DATA}/NEXUS_Expt_combined.nc --grid ${DATA}/grid_spec.nc -o ${DATA}/NEXUS_Expt_pretty.nc -t ${DATA}/HEMCO_sa_Time.rc
-export err=$?
-if [ $err -ne 0 ]; then
-  message_txt="Call to python script \"make_nexus_output_pretty.py\" failed."
-  if [ "${RUN_ENVIR}" = "community" ]; then
-    print_err_msg_exit "${message_txt}"
-  else
-    err_exit "${message_txt}"
-  fi
-fi
+# python3 ${ARL_NEXUS_DIR}/utils/python/make_nexus_output_pretty.py --src ${DATA}/NEXUS_Expt_combined.nc --grid ${DATA}/grid_spec.nc -o ${DATA}/NEXUS_Expt_pretty.nc -t ${DATA}/HEMCO_sa_Time.rc
+# export err=$?
+# if [ $err -ne 0 ]; then
+#   message_txt="Call to python script \"make_nexus_output_pretty.py\" failed."
+#   if [ "${RUN_ENVIR}" = "community" ]; then
+#     print_err_msg_exit "${message_txt}"
+#   else
+#     err_exit "${message_txt}"
+#   fi
+# fi
 #
 #-----------------------------------------------------------------------
 #
@@ -127,7 +127,7 @@ fi
 #
 #-----------------------------------------------------------------------
 #
-python3 ${ARL_NEXUS_DIR}/utils/combine_ant_bio.py ${DATA}/NEXUS_Expt_pretty.nc ${DATA}/NEXUS_Expt.nc
+python3 ${ARL_NEXUS_DIR}/utils/combine_ant_bio.py "${DATA}/NEXUS_Expt_combined.nc" ${DATA}/NEXUS_Expt.nc
 export err=$?
 if [ $err -ne 0 ]; then
   message_txt="Call to python script \"NEXUS_Expt_pretty.py\" failed."

From 49a692c4d69990d4ca7d62d942923c98dbdc53c9 Mon Sep 17 00:00:00 2001
From: "Jianping.Huang" <Jianping.Huang@noaa.gov>
Date: Fri, 23 Jun 2023 12:47:34 +0000
Subject: [PATCH 4/7] removing uncessary lines with bias-correction ex-scripts

---
 scripts/exregional_bias_correction_o3.sh   | 4 ----
 scripts/exregional_bias_correction_pm25.sh | 8 ++------
 2 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/scripts/exregional_bias_correction_o3.sh b/scripts/exregional_bias_correction_o3.sh
index c168671648..a5190a5494 100755
--- a/scripts/exregional_bias_correction_o3.sh
+++ b/scripts/exregional_bias_correction_o3.sh
@@ -106,7 +106,6 @@ fi
 mkdir -p "${DATA}/data"
 
 # Retrieve real-time airnow data for the last three days and convert them into netcdf
-#if [ "${DO_REAL_TIME}" = "TRUE" ]; then
   for ipdym in {1..3}; do
     case $ipdym in
       1)
@@ -149,7 +148,6 @@ mkdir -p "${DATA}/data"
     fi
     POST_STEP
   done     
-#fi
 
 #-----------------------------------------------------------------------------
 # STEP 2:  Extracting PM2.5, O3, and met variables from CMAQ input and outputs
@@ -207,7 +205,6 @@ POST_STEP
 
 cp ${DATA}/out/ozone/${yyyy}/*nc ${DATA}/data/bcdata.${yyyymm}/interpolated/ozone/${yyyy}
 
-#if [ "${DO_AQM_SAVE_AIRNOW_HIST}" = "TRUE" ]; then
   mkdir -p ${COMOUTbicor}/bcdata.${yyyymm}/interpolated/ozone/${yyyy}
   cp ${DATA}/out/ozone/${yyyy}/*nc ${COMOUTbicor}/bcdata.${yyyymm}/interpolated/ozone/${yyyy}
 
@@ -231,7 +228,6 @@ cp ${DATA}/out/ozone/${yyyy}/*nc ${DATA}/data/bcdata.${yyyymm}/interpolated/ozon
 
   mkdir -p  ${COMOUTbicor}/bcdata.${yyyymm}/grid/${cyc}z/${PDY}
   cp ${COMIN}/${NET}.${cycle}.*sfc*.nc ${COMOUTbicor}/bcdata.${yyyymm}/grid/${cyc}z/${PDY}
-#fi
 
 #-----------------------------------------------------------------------------
 # STEP 4:  Performing Bias Correction for Ozone
diff --git a/scripts/exregional_bias_correction_pm25.sh b/scripts/exregional_bias_correction_pm25.sh
index 850e44e95c..2ae8fb758c 100755
--- a/scripts/exregional_bias_correction_pm25.sh
+++ b/scripts/exregional_bias_correction_pm25.sh
@@ -106,7 +106,6 @@ fi
 mkdir -p "${DATA}/data"
 
 # Retrieve real-time airnow data for the last three days
-#if [ "${DO_REAL_TIME}" = "TRUE" ]; then
   for ipdym in {1..3}; do
     case $ipdym in
       1)
@@ -149,7 +148,6 @@ mkdir -p "${DATA}/data"
     fi
     POST_STEP
   done
-#fi
 
 #-----------------------------------------------------------------------------
 # STEP 2:  Extracting PM2.5, O3, and met variables from CMAQ input and outputs
@@ -207,10 +205,8 @@ POST_STEP
 
 cp ${DATA}/out/pm25/${yyyy}/*nc ${DATA}/data/bcdata.${yyyymm}/interpolated/pm25/${yyyy}
 
-#if [ "${DO_AQM_SAVE_AIRNOW_HIST}" = "TRUE" ]; then
-  mkdir -p  ${COMOUTbicor}/bcdata.${yyyymm}/interpolated/pm25/${yyyy}
-  cp ${DATA}/out/pm25/${yyyy}/*nc ${COMOUTbicor}/bcdata.${yyyymm}/interpolated/pm25/${yyyy}
-#fi
+mkdir -p  ${COMOUTbicor}/bcdata.${yyyymm}/interpolated/pm25/${yyyy}
+cp ${DATA}/out/pm25/${yyyy}/*nc ${COMOUTbicor}/bcdata.${yyyymm}/interpolated/pm25/${yyyy}
 
 #-----------------------------------------------------------------------
 # STEP 4:  Performing Bias Correction for PM2.5 

From 37dab306216b7bc3fb54ad8eb9d219c2cbf4451e Mon Sep 17 00:00:00 2001
From: "Jianping.Huang" <Jianping.Huang@noaa.gov>
Date: Fri, 23 Jun 2023 13:19:39 +0000
Subject: [PATCH 5/7] correct the changes with  in ex-scripts for bias
 correction

---
 scripts/exregional_bias_correction_o3.sh   |  8 +++----
 scripts/exregional_bias_correction_pm25.sh |  8 +++----
 scripts/exregional_nexus_emission.sh       |  9 -------
 scripts/exregional_nexus_post_split.sh     | 28 ----------------------
 ush/config_defaults.yaml                   |  7 ++++--
 ush/machine/wcoss2.yaml                    |  6 ++---
 6 files changed, 16 insertions(+), 50 deletions(-)

diff --git a/scripts/exregional_bias_correction_o3.sh b/scripts/exregional_bias_correction_o3.sh
index a5190a5494..a5de1bbb9e 100755
--- a/scripts/exregional_bias_correction_o3.sh
+++ b/scripts/exregional_bias_correction_o3.sh
@@ -370,7 +370,7 @@ EOF1
 
     cp ${DATA}/${NET}.${cycle}.max_*hr_o3_bc.*.grib2 ${COMOUT}
    
-    if [ "$SENDDBN" = "YES" ]; then
+    if [ "$SENDDBN" = "TRUE" ]; then
       ${DBNROOT}/bin/dbn_alert MODEL AQM_MAX ${job} ${COMOUT}/${NET}.${cycle}.max_1hr_o3_bc.227.grib2
       ${DBNROOT}/bin/dbn_alert MODEL AQM_MAX ${job} ${COMOUT}/${NET}.${cycle}.max_8hr_o3_bc.227.grib2
     fi
@@ -398,7 +398,7 @@ EOF1
     cp awpaqm.${cycle}.*o3-max-bc.227.grib2 ${COMOUTwmo}
 
     # Distribute Data
-    if [ "${SENDDBN_NTC}" = "YES" ] ; then
+    if [ "${SENDDBN_NTC}" = "TRUE" ] ; then
       ${DBNROOT}/bin/dbn_alert ${DBNALERT_TYPE} ${NET} ${job} ${COMOUTwmo}/awpaqm.${cycle}.1ho3-max-bc.227.grib2
       ${DBNROOT}/bin/dbn_alert ${DBNALERT_TYPE} ${NET} ${job} ${COMOUTwmo}/awpaqm.${cycle}.8ho3-max-bc.227.grib2
     fi
@@ -445,7 +445,7 @@ if [ "${cyc}" = "06" ] || [ "${cyc}" = "12" ]; then
   cp ${NET}.${cycle}.ave_8hr_o3_bc.227.grib2 ${COMOUT}
 fi
 
-if [ "${SENDDBN}" = "YES" ] ; then
+if [ "${SENDDBN}" = "TRUE" ] ; then
    ${DBNROOT}/bin/dbn_alert MODEL AQM_CONC ${job} ${COMOUT}/${NET}.${cycle}.ave_1hr_o3_bc.227.grib2
   if [ "${cyc}" = "06" ] || [ "${cyc}" = "12" ]; then
    ${DBNROOT}/bin/dbn_alert MODEL AQM_CONC ${job} ${COMOUT}/${NET}.${cycle}.ave_8hr_o3_bc.227.grib2
@@ -497,7 +497,7 @@ if [ "${cyc}" = "06" ] || [ "${cyc}" = "12" ]; then
     cp awpaqm.${cycle}.${hr}ho3-max-bc.227.grib2 ${COMOUTwmo}
 
     # Distribute Data
-    if [ "${SENDDBN}" = "YES" ]; then
+    if [ "${SENDDBN}" = "TRUE" ]; then
       ${DBNROOT}/bin/dbn_alert ${DBNALERT_TYPE} ${NET} ${job} ${COMOUTwmo}/awpaqm.${cycle}.${hr}ho3-bc.227.grib2
       ${DBNROOT}/bin/dbn_alert ${DBNALERT_TYPE} ${NET} ${job} ${COMOUTwmo}/awpaqm.${cycle}.${hr}ho3-max-bc.227.grib2
     fi
diff --git a/scripts/exregional_bias_correction_pm25.sh b/scripts/exregional_bias_correction_pm25.sh
index 2ae8fb758c..ebefe58002 100755
--- a/scripts/exregional_bias_correction_pm25.sh
+++ b/scripts/exregional_bias_correction_pm25.sh
@@ -269,7 +269,7 @@ fi
 POST_STEP
 
 cp ${DATA}/${NET}.${cycle}.pm25*bc*.grib2 ${COMOUT}
-if [ "$SENDDBN" = "YES" ]; then
+if [ "$SENDDBN" = "TRUE" ]; then
   $DBNROOT/bin/dbn_alert MODEL AQM_PM ${job} ${COMOUT}
 fi
 
@@ -366,7 +366,7 @@ EOF1
   cp ${NET}.${cycle}.max_1hr_pm25_bc.227.grib2   ${COMOUT}
   cp ${NET}.${cycle}.ave_24hr_pm25_bc.227.grib2  ${COMOUT}
 
-  if [ "${SENDDBN}" = "YES" ]; then
+  if [ "${SENDDBN}" = "TRUE" ]; then
     ${DBNROOT}/bin/dbn_alert MODEL AQM_MAX ${job} ${COMOUT}/${NET}.${cycle}.max_1hr_pm25_bc.227.grib2
     ${DBNROOT}/bin/dbn_alert MODEL AQM_PM ${job} ${COMOUT}/${NET}.${cycle}.ave_24hr_pm25_bc.227.grib2
   fi
@@ -384,7 +384,7 @@ wgrib2 tmpfile_pm25_bc -set_grib_type c3b -new_grid_winds earth -new_grid ${grid
 
 cp tmpfile_pm25_bc ${COMOUT}/${NET}.${cycle}.ave_1hr_pm25_bc.${id_domain}.grib2
 cp ${NET}.${cycle}.grib2_pm25_bc.227 ${COMOUT}/${NET}.${cycle}.ave_1hr_pm25_bc.227.grib2
-if [ "${SENDDBN}" = "YES" ]; then
+if [ "${SENDDBN}" = "TRUE" ]; then
   ${DBNROOT}/bin/dbn_alert MODEL AQM_PM ${job} ${COMOUT}/${NET}.${cycle}.ave_1hr_pm25_bc.227.grib2
 fi
 
@@ -452,7 +452,7 @@ if [ "${cyc}" = "06" ] || [ "${cyc}" = "12" ]; then
   cp awpaqm.${cycle}.24hr-pm25-ave-bc.227.grib2      ${COMOUTwmo}
 
   # Distribute Data
-  if [ "${SENDDBN_NTC}" = "YES" ] ; then
+  if [ "${SENDDBN_NTC}" = "TRUE" ] ; then
     ${DBNROOT}/bin/dbn_alert ${DBNALERT_TYPE} ${NET} ${job} ${COMOUTwmo}/awpaqm.${cycle}.1hpm25-bc.227.grib2
     ${DBNROOT}/bin/dbn_alert ${DBNALERT_TYPE} ${NET} ${job} ${COMOUTwmo}/awpaqm.${cycle}.daily-1hr-pm25-max-bc.227.grib2
     ${DBNROOT}/bin/dbn_alert ${DBNALERT_TYPE} ${NET} ${job} ${COMOUTwmo}/awpaqm.${cycle}.24hr-pm25-ave-bc.227.grib2
diff --git a/scripts/exregional_nexus_emission.sh b/scripts/exregional_nexus_emission.sh
index 43e4d8ed63..a2aca2a0ee 100755
--- a/scripts/exregional_nexus_emission.sh
+++ b/scripts/exregional_nexus_emission.sh
@@ -345,15 +345,6 @@ if [ $err -ne 0 ]; then
     err_exit "${message_txt}"
   fi
 fi
-#
-#-----------------------------------------------------------------------
-#
-# Move NEXUS output to INPUT_DATA directory.
-#
-#-----------------------------------------------------------------------
-#
-#mv ${DATA}/NEXUS_Expt_split.nc ${INPUT_DATA}/${NET}.${cycle}${dot_ensmem}.NEXUS_Expt_split.${nspt}.nc
-
 #
 #-----------------------------------------------------------------------
 #
diff --git a/scripts/exregional_nexus_post_split.sh b/scripts/exregional_nexus_post_split.sh
index 9ac0048649..c4f7b9a739 100755
--- a/scripts/exregional_nexus_post_split.sh
+++ b/scripts/exregional_nexus_post_split.sh
@@ -95,34 +95,6 @@ fi
 #
 #-----------------------------------------------------------------------
 #
-# make nexus output pretty
-#
-#-----------------------------------------------------------------------
-#
-# python3 ${ARL_NEXUS_DIR}/utils/python/nexus_time_parser.py -f ${DATA}/HEMCO_sa_Time.rc -s $start_date -e $end_date
-# export err=$?
-# if [ $err -ne 0 ]; then
-#   message_txt="Call to python script \"nexus_time_parser.py\" failed."
-#   if [ "${RUN_ENVIR}" = "community" ]; then
-#     print_err_msg_exit "${message_txt}"
-#   else
-#     err_exit "${message_txt}"
-#   fi
-# fi
-
-# python3 ${ARL_NEXUS_DIR}/utils/python/make_nexus_output_pretty.py --src ${DATA}/NEXUS_Expt_combined.nc --grid ${DATA}/grid_spec.nc -o ${DATA}/NEXUS_Expt_pretty.nc -t ${DATA}/HEMCO_sa_Time.rc
-# export err=$?
-# if [ $err -ne 0 ]; then
-#   message_txt="Call to python script \"make_nexus_output_pretty.py\" failed."
-#   if [ "${RUN_ENVIR}" = "community" ]; then
-#     print_err_msg_exit "${message_txt}"
-#   else
-#     err_exit "${message_txt}"
-#   fi
-# fi
-#
-#-----------------------------------------------------------------------
-#
 # run MEGAN NCO script
 #
 #-----------------------------------------------------------------------
diff --git a/ush/config_defaults.yaml b/ush/config_defaults.yaml
index e9b9e46907..6c3ea6430c 100644
--- a/ush/config_defaults.yaml
+++ b/ush/config_defaults.yaml
@@ -3001,9 +3001,12 @@ cpl_aqm_parm:
   # DCOMINairnow:
   # Path to the directory containing AIRNOW observation data
   #
-  # AQM_AIRNOW_HIST_DIR:
-  # Path to the directory where the historical AIRNOW data are located
+  # COMINbicor:
+  # Path of reading in historical training data for biascorrection 
   #
+  # COMOUTbicor:
+  # Path to save the current cycle's model output and AirNow obs as training data for future use
+  # $COMINbicor and $COMOUTbicor can be distuigshed by the ${yyyy}${mm}$dd under the same location
   #-----------------------------------------------------------------------
   #
   CPL_AQM: false
diff --git a/ush/machine/wcoss2.yaml b/ush/machine/wcoss2.yaml
index c89242a673..ba2baee37f 100644
--- a/ush/machine/wcoss2.yaml
+++ b/ush/machine/wcoss2.yaml
@@ -9,9 +9,9 @@ platform:
   MET_BIN_EXEC: bin
   MET_INSTALL_DIR: /apps/ops/para/libs/intel/19.1.3.304/met/10.1.1
   DOMAIN_PREGEN_BASEDIR: /lfs/h2/emc/lam/noscrub/UFS_SRW_App/develop/FV3LAM_pregen
-  QUEUE_DEFAULT: devhigh
-  QUEUE_FCST: devhigh
-  QUEUE_HPSS: devhigh
+  QUEUE_DEFAULT: dev
+  QUEUE_FCST: dev
+  QUEUE_HPSS: dev_transfer
   RUN_CMD_FCST: mpiexec -n ${PE_MEMBER01} -ppn ${PPN_RUN_FCST} --cpu-bind core -depth ${OMP_NUM_THREADS_RUN_FCST}
   RUN_CMD_POST: mpiexec -n ${nprocs}
   RUN_CMD_PRDGEN: mpiexec -n ${nprocs} --cpu-bind core cfp

From c0b345ad535605a6a41ed9347bfb1b08b534badf Mon Sep 17 00:00:00 2001
From: "Jianping.Huang" <Jianping.Huang@noaa.gov>
Date: Tue, 27 Jun 2023 15:58:11 +0000
Subject: [PATCH 6/7] update nexus harsh number to fix the NEXUS failure with
 concatenate_nexus_post job

---
 Externals.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Externals.cfg b/Externals.cfg
index c871f9a3ea..e619460e32 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -30,7 +30,7 @@ protocol = git
 repo_url = https://github.com/noaa-oar-arl/NEXUS
 # Specify either a branch name or a hash but not both.
 #branch = develop
-hash = 732a441
+hash = 6a7a994
 local_path = sorc/arl_nexus
 required = True
 

From 6adf28eaf1a0d00c6b62ec4f19dbfde84b2b9047 Mon Sep 17 00:00:00 2001
From: "Jianping.Huang" <Jianping.Huang@noaa.gov>
Date: Wed, 28 Jun 2023 16:04:04 +0000
Subject: [PATCH 7/7] adding DO_AQM_SAVE_AIRNOW_HIST back

---
 scripts/exregional_bias_correction_o3.sh   | 4 +++-
 scripts/exregional_bias_correction_pm25.sh | 2 ++
 ush/config_defaults.yaml                   | 6 ++----
 ush/machine/wcoss2.yaml                    | 5 ++---
 4 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/scripts/exregional_bias_correction_o3.sh b/scripts/exregional_bias_correction_o3.sh
index a5de1bbb9e..ed73509a5f 100755
--- a/scripts/exregional_bias_correction_o3.sh
+++ b/scripts/exregional_bias_correction_o3.sh
@@ -205,6 +205,7 @@ POST_STEP
 
 cp ${DATA}/out/ozone/${yyyy}/*nc ${DATA}/data/bcdata.${yyyymm}/interpolated/ozone/${yyyy}
 
+if [ "${DO_AQM_SAVE_AIRNOW_HIST}" = "TRUE" ]; then
   mkdir -p ${COMOUTbicor}/bcdata.${yyyymm}/interpolated/ozone/${yyyy}
   cp ${DATA}/out/ozone/${yyyy}/*nc ${COMOUTbicor}/bcdata.${yyyymm}/interpolated/ozone/${yyyy}
 
@@ -226,8 +227,9 @@ cp ${DATA}/out/ozone/${yyyy}/*nc ${DATA}/data/bcdata.${yyyymm}/interpolated/ozon
   cp ${DATA}/data/bcdata.${yyyymm_m2}/airnow/netcdf/${yyyy_m2}/${PDYm2}/HourlyAQObs.${PDYm2}.nc ${COMOUTbicor}/bcdata.${yyyymm_m2}/airnow/netcdf/${yyyy_m2}/${PDYm2}  
   cp ${DATA}/data/bcdata.${yyyymm_m3}/airnow/netcdf/${yyyy_m3}/${PDYm3}/HourlyAQObs.${PDYm3}.nc ${COMOUTbicor}/bcdata.${yyyymm_m3}/airnow/netcdf/${yyyy_m3}/${PDYm3}
 
-  mkdir -p  ${COMOUTbicor}/bcdata.${yyyymm}/grid/${cyc}z/${PDY}
+  mkdir -p  "${COMOUTbicor}/bcdata.${yyyymm}/grid/${cyc}z/${PDY}"
   cp ${COMIN}/${NET}.${cycle}.*sfc*.nc ${COMOUTbicor}/bcdata.${yyyymm}/grid/${cyc}z/${PDY}
+fi
 
 #-----------------------------------------------------------------------------
 # STEP 4:  Performing Bias Correction for Ozone
diff --git a/scripts/exregional_bias_correction_pm25.sh b/scripts/exregional_bias_correction_pm25.sh
index ebefe58002..b704b214ed 100755
--- a/scripts/exregional_bias_correction_pm25.sh
+++ b/scripts/exregional_bias_correction_pm25.sh
@@ -205,8 +205,10 @@ POST_STEP
 
 cp ${DATA}/out/pm25/${yyyy}/*nc ${DATA}/data/bcdata.${yyyymm}/interpolated/pm25/${yyyy}
 
+if [ "${DO_AQM_SAVE_AIRNOW_HIST}" = "TRUE" ]; then
 mkdir -p  ${COMOUTbicor}/bcdata.${yyyymm}/interpolated/pm25/${yyyy}
 cp ${DATA}/out/pm25/${yyyy}/*nc ${COMOUTbicor}/bcdata.${yyyymm}/interpolated/pm25/${yyyy}
+fi
 
 #-----------------------------------------------------------------------
 # STEP 4:  Performing Bias Correction for PM2.5 
diff --git a/ush/config_defaults.yaml b/ush/config_defaults.yaml
index 6c3ea6430c..ca1f252a8f 100644
--- a/ush/config_defaults.yaml
+++ b/ush/config_defaults.yaml
@@ -2901,10 +2901,8 @@ cpl_aqm_parm:
   # DO_AQM_GEFS_LBCS:
   # Add GEFS aerosol LBCs to chemical LBCs
   #
-  # COMINbicor 
-  # Read bias-correction training data
-  # COMOUTbicor 
-  # Save bias-correction training data
+  # DO_AQM_SAVE_AIRNOW_HIST:
+  # Save bias-correction airnow training data
   #
   # DO_AQM_SAVE_FIRE:
   # Archive fire emission file to HPSS
diff --git a/ush/machine/wcoss2.yaml b/ush/machine/wcoss2.yaml
index ba2baee37f..2d167eef94 100644
--- a/ush/machine/wcoss2.yaml
+++ b/ush/machine/wcoss2.yaml
@@ -47,9 +47,8 @@ cpl_aqm_parm:
   DCOMINgefs_dfv: /lfs/h1/ops/prod/com/gefs/v12.3 
   DCOMINpt_src_dfv: /lfs/h2/emc/physics/noscrub/Youhua.Tang/nei2016v1-pt/v2023-01-PT
   DCOMINairnow_dfv: /lfs/h1/ops/prod/dcom
-  #DCOMINairnow_dfv: /lfs/h2/emc/physics/noscrub/jianping.huang/dcom 
-  COMINbicor: /lfs/h2/emc/physics/noscrub/jianping.huang/Bias_correction/aqmv7.0.81
-  COMOUTbicor: /lfs/h2/emc/physics/noscrub/jianping.huang/Bias_correction/aqmv7.0.81
+  COMINbicor: /lfs/h2/emc/physics/noscrub/jianping.huang/Bias_correction/aqmv7.0
+  COMOUTbicor: /lfs/h2/emc/physics/noscrub/jianping.huang/Bias_correction/aqmv7.0
   NEXUS_INPUT_DIR: /lfs/h2/emc/lam/noscrub/RRFS_CMAQ/nexus_emissions
   NEXUS_FIX_DIR: /lfs/h2/emc/lam/noscrub/RRFS_CMAQ/nexus/fix
   NEXUS_GFS_SFC_DIR: /lfs/h2/emc/lam/noscrub/RRFS_CMAQ/GFS_DATA