diff --git a/.gitignore b/.gitignore
index 79607e39fd..e73b9f2e05 100644
--- a/.gitignore
+++ b/.gitignore
@@ -129,6 +129,7 @@ ush/global_chgres.sh
 ush/global_chgres_driver.sh
 ush/global_cycle.sh
 ush/global_cycle_driver.sh
+ush/jediinc2fv3.py
 ush/mkwfsgbl.sh
 ush/ufsda
 ush/wafs_blending.sh
diff --git a/env/CONTAINER.env b/env/CONTAINER.env
index 48014ab313..d06ca91a9b 100755
--- a/env/CONTAINER.env
+++ b/env/CONTAINER.env
@@ -4,8 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanalrun atmensanalrun"
-    echo "aeroanlrun"
+    echo "atmanlrun atmensanalrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
diff --git a/env/HERA.env b/env/HERA.env
index 3fa6288200..7960f604ba 100755
--- a/env/HERA.env
+++ b/env/HERA.env
@@ -4,8 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanalrun atmensanalrun"
-    echo "aeroanlrun"
+    echo "atmanlrun atmensanalrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -49,22 +48,16 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
     export wavempexec=${launcher}
     export wave_mpmd=${mpmd_opt}
 
-elif [[ "${step}" = "atmanalrun" ]]; then
+elif [[ "${step}" = "atmanlrun" ]]; then
 
-    export CFP_MP=${CFP_MP:-"YES"}
-    export USE_CFP=${USE_CFP:-"YES"}
-    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
+    nth_max=$((npe_node_max / npe_node_atmanlrun))
 
-    nth_max=$((npe_node_max / npe_node_atmanalrun))
-
-    export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
-    [[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
-    export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"
+    export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
+    [[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
+    export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"
 
 elif [[ "${step}" = "atmensanalrun" ]]; then
 
-    export CFP_MP=${CFP_MP:-"YES"}
-    export USE_CFP=${USE_CFP:-"YES"}
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
     nth_max=$((npe_node_max / npe_node_atmensanalrun))
diff --git a/env/JET.env b/env/JET.env
index 73c5031a68..e5fd85aaa3 100755
--- a/env/JET.env
+++ b/env/JET.env
@@ -4,7 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanalrun atmensanalrun aeroanlrun"
+    echo "atmanlrun atmensanalrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -47,17 +47,13 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
     export wavempexec=${launcher}
     export wave_mpmd=${mpmd_opt}
 
-elif [[ "${step}" = "atmanalrun" ]]; then
+elif [[ "${step}" = "atmanlrun" ]]; then
 
-    export CFP_MP=${CFP_MP:-"YES"}
-    export USE_CFP=${USE_CFP:-"YES"}
-    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-
-    nth_max=$((npe_node_max / npe_node_atmanalrun))
+    nth_max=$((npe_node_max / npe_node_atmanlrun))
 
-    export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
-    [[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
-    export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"
+    export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
+    [[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
+    export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"
 
 elif [[ "${step}" = "atmensanalrun" ]]; then
 
diff --git a/env/ORION.env b/env/ORION.env
index 43aa24689d..1ef58c82bc 100755
--- a/env/ORION.env
+++ b/env/ORION.env
@@ -4,8 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanalrun atmensanalrun"
-    echo "aeroanlrun"
+    echo "atmanlrun atmensanalrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -49,17 +48,13 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
     export wavempexec=${launcher}
     export wave_mpmd=${mpmd_opt}
 
-elif [[ "${step}" = "atmanalrun" ]]; then
+elif [[ "${step}" = "atmanlrun" ]]; then
 
-    export CFP_MP=${CFP_MP:-"YES"}
-    export USE_CFP=${USE_CFP:-"YES"}
-    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-
-    nth_max=$((npe_node_max / npe_node_atmanalrun))
+    nth_max=$((npe_node_max / npe_node_atmanlrun))
 
-    export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
-    [[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
-    export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"
+    export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
+    [[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
+    export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"
 
 elif [[ "${step}" = "atmensanalrun" ]]; then
 
diff --git a/env/S4.env b/env/S4.env
index 4933fb989e..9a62d515a4 100755
--- a/env/S4.env
+++ b/env/S4.env
@@ -4,8 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanalrun atmensanalrun"
-    echo "aeroanlrun"
+    echo "atmanlrun atmensanalrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -47,17 +46,13 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
     export wavempexec=${launcher}
     export wave_mpmd=${mpmd_opt}
 
-elif [[ "${step}" = "atmanalrun" ]]; then
+elif [[ "${step}" = "atmanlrun" ]]; then
 
-    export CFP_MP=${CFP_MP:-"YES"}
-    export USE_CFP=${USE_CFP:-"YES"}
-    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-
-    nth_max=$((npe_node_max / npe_node_atmanalrun))
+    nth_max=$((npe_node_max / npe_node_atmanlrun))
 
-    export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
-    [[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
-    export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"
+    export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
+    [[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
+    export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"
 
 elif [[ "${step}" = "atmensanalrun" ]]; then
 
diff --git a/env/WCOSS2.env b/env/WCOSS2.env
index 44f8dbc994..8110b94b5b 100755
--- a/env/WCOSS2.env
+++ b/env/WCOSS2.env
@@ -4,8 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanalrun atmensanalrun"
-    echo "aeroanlrun"
+    echo "atmanlrun atmensanalrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen esfc efcs epos"
     echo "postsnd awips gempak"
@@ -36,17 +35,13 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
     export wavempexec="${launcher} -np"
     export wave_mpmd=${mpmd_opt}
 
-elif [[ "${step}" = "atmanalrun" ]]; then
+elif [[ "${step}" = "atmanlrun" ]]; then
 
-    export CFP_MP=${CFP_MP:-"YES"}
-    export USE_CFP=${USE_CFP:-"YES"}
-    export APRUNCFP="${launcher} -np \$ncmd ${mpmd_opt}"
-
-    nth_max=$((npe_node_max / npe_node_atmanalrun))
+    nth_max=$((npe_node_max / npe_node_atmanlrun))
 
-    export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
-    [[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
-    export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"
+    export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
+    [[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
+    export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"
 
 elif [[ "${step}" = "atmensanalrun" ]]; then
 
diff --git a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_POST b/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_POST
deleted file mode 100755
index e44e607581..0000000000
--- a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_POST
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/bin/bash
-
-source "${HOMEgfs}/ush/preamble.sh"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "atmanalpost" -c "base atmanal atmanalpost"
-
-
-##############################################
-# Set variables used in the script
-##############################################
-export CDATE=${CDATE:-${PDY}${cyc}}
-export CDUMP=${CDUMP:-${RUN:-"gfs"}}
-export COMPONENT="atmos"
-
-##############################################
-# Begin JOB SPECIFIC work
-##############################################
-
-export GDATE=$(date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - ${assim_freq} hours")
-gPDY=${GDATE:0:8}
-export gcyc=${GDATE:8:2}
-export GDUMP=${GDUMP:-"gdas"}
-
-export OPREFIX="${CDUMP}.t${cyc}z."
-export GPREFIX="${GDUMP}.t${gcyc}z."
-export APREFIX="${CDUMP}.t${cyc}z."
-
-export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}}
-
-mkdir -p ${COMOUT}
-
-# COMIN_GES and COMIN_GES_ENS are used in script
-export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/${COMPONENT}"
-export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${gPDY}/${gcyc}/${COMPONENT}"
-
-# Add UFSDA to PYTHONPATH
-export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush/:${PYTHONPATH}
-
-###############################################################
-# Run relevant script
-
-EXSCRIPT=${GDASPOSTPY:-${HOMEgfs}/scripts/exgdas_global_atmos_analysis_post.py}
-${EXSCRIPT}
-status=$?
-[[ ${status} -ne 0 ]] && exit ${status}
-
-##############################################
-# End JOB SPECIFIC work
-##############################################
-
-##############################################
-# Final processing
-##############################################
-if [ -e "${pgmout}" ] ; then
-  cat ${pgmout}
-fi
-
-##########################################
-# Remove the Temporary working directory
-##########################################
-cd ${DATAROOT}
-[[ ${KEEPDATA} = "NO" ]] && rm -rf ${DATA}
-
-exit 0
diff --git a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_PREP b/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_PREP
deleted file mode 100755
index 093fccdd5a..0000000000
--- a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_PREP
+++ /dev/null
@@ -1,62 +0,0 @@
-#!/bin/bash
-
-source "${HOMEgfs}/ush/preamble.sh"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "atmanalprep" -c "base atmanal atmanalprep"
-
-
-##############################################
-# Set variables used in the script
-##############################################
-export CDATE=${CDATE:-${PDY}${cyc}}
-export CDUMP=${CDUMP:-${RUN:-"gfs"}}
-export COMPONENT="atmos"
-
-##############################################
-# Begin JOB SPECIFIC work
-##############################################
-
-export GDATE=$(date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - ${assim_freq} hours")
-gPDY=${GDATE:0:8}
-export gcyc=${GDATE:8:2}
-export GDUMP=${GDUMP:-"gdas"}
-
-export OPREFIX="${CDUMP}.t${cyc}z."
-export GPREFIX="${GDUMP}.t${gcyc}z."
-export APREFIX="${CDUMP}.t${cyc}z."
-
-export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}}
-
-mkdir -p ${COMOUT}
-
-# COMIN_GES and COMIN_GES_ENS are used in script
-export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/${COMPONENT}"
-export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${gPDY}/${gcyc}/${COMPONENT}"
-
-# Add UFSDA to PYTHONPATH
-export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush/:${PYTHONPATH}
-
-###############################################################
-# Run relevant script
-EXSCRIPT=${GDASPREPPY:-${HOMEgfs}/scripts/exgdas_global_atmos_analysis_prep.py}
-${EXSCRIPT}
-status=$?
-[[ ${status} -ne 0 ]] && exit ${status}
-
-##############################################
-# End JOB SPECIFIC work
-##############################################
-
-##############################################
-# Final processing
-##############################################
-if [ -e "${pgmout}" ] ; then
-  cat ${pgmout}
-fi
-
-##########################################
-# Remove the Temporary working directory
-##########################################
-cd ${DATAROOT}
-[[ ${KEEPDATA} = "NO" ]] && rm -rf ${DATA}
-
-exit 0
diff --git a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_RUN b/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_RUN
deleted file mode 100755
index 876598ff7e..0000000000
--- a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_RUN
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/bin/bash
-
-source "${HOMEgfs}/ush/preamble.sh"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "atmanalrun" -c "base atmanal atmanalrun"
-
-
-##############################################
-# Set variables used in the script
-##############################################
-export CDATE=${CDATE:-${PDY}${cyc}}
-export CDUMP=${CDUMP:-${RUN:-"gfs"}}
-export COMPONENT="atmos"
-
-##############################################
-# Begin JOB SPECIFIC work
-##############################################
-
-export GDATE=$(date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - ${assim_freq} hours")
-gPDY=${GDATE:0:8}
-export gcyc=${GDATE:8:2}
-export GDUMP=${GDUMP:-"gdas"}
-
-export OPREFIX="${CDUMP}.t${cyc}z."
-export GPREFIX="${GDUMP}.t${gcyc}z."
-export APREFIX="${CDUMP}.t${cyc}z."
-
-export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}}
-
-mkdir -p ${COMOUT}
-
-# COMIN_GES and COMIN_GES_ENS are used in script
-export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/${COMPONENT}"
-export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${gPDY}/${gcyc}/${COMPONENT}"
-
-# Add UFSDA to PYTHONPATH
-export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush/:${PYTHONPATH}
-
-###############################################################
-# Run relevant script
-
-EXSCRIPT=${GDASRUNSH:-${HOMEgfs}/scripts/exgdas_global_atmos_analysis_run.sh}
-${EXSCRIPT}
-status=$?
-[[ ${status} -ne 0 ]] && exit ${status}
-
-##############################################
-# End JOB SPECIFIC work
-##############################################
-
-##############################################
-# Final processing
-##############################################
-if [ -e "${pgmout}" ] ; then
-  cat ${pgmout}
-fi
-
-##########################################
-# Remove the Temporary working directory
-##########################################
-cd ${DATAROOT}
-[[ ${KEEPDATA} = "NO" ]] && rm -rf ${DATA}
-
-exit 0
diff --git a/jobs/JGLOBAL_ATM_ANALYSIS_FINALIZE b/jobs/JGLOBAL_ATM_ANALYSIS_FINALIZE
new file mode 100755
index 0000000000..1719b18580
--- /dev/null
+++ b/jobs/JGLOBAL_ATM_ANALYSIS_FINALIZE
@@ -0,0 +1,51 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+export WIPE_DATA="NO"
+export DATA=${DATA:-${DATAROOT}/${RUN}atmanl_${cyc}}
+source "${HOMEgfs}/ush/jjob_header.sh" -e "atmanlfinal" -c "base atmanl atmanlfinal"
+
+##############################################
+# Set variables used in the script
+##############################################
+GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+GDUMP="gdas"
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+export COMOUT=${COMOUT:-${ROTDIR}/${RUN}.${PDY}/${cyc}/atmos}
+mkdir -p "${COMOUT}"
+
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="${ROTDIR}/${GDUMP}.${GDATE:0:8}/${GDATE:8:2}/atmos"
+export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${GDATE:0:8}/${GDATE:8:2}/atmos"
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASATMFINALPY:-${HOMEgfs}/scripts/exglobal_atm_analysis_finalize.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd "${DATAROOT}" || ( echo "FATAL ERROR: ${DATAROOT} does not exist, ABORT!"; exit 1 )
+[[ ${KEEPDATA} = "NO" ]] && rm -rf "${DATA}"
+
+exit 0
diff --git a/jobs/JGLOBAL_ATM_ANALYSIS_INITIALIZE b/jobs/JGLOBAL_ATM_ANALYSIS_INITIALIZE
new file mode 100755
index 0000000000..8fc7c249b3
--- /dev/null
+++ b/jobs/JGLOBAL_ATM_ANALYSIS_INITIALIZE
@@ -0,0 +1,44 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+export DATA=${DATA:-${DATAROOT}/${RUN}atmanl_${cyc}}
+source "${HOMEgfs}/ush/jjob_header.sh" -e "atmanlinit" -c "base atmanl atmanlinit"
+
+##############################################
+# Set variables used in the script
+##############################################
+GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+GDUMP="gdas"
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+export COMOUT=${COMOUT:-${ROTDIR}/${RUN}.${PDY}/${cyc}/atmos}
+mkdir -p "${COMOUT}"
+
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="${ROTDIR}/${GDUMP}.${GDATE:0:8}/${GDATE:8:2}/atmos"
+export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${GDATE:0:8}/${GDATE:8:2}/atmos"
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASATMINITPY:-${HOMEgfs}/scripts/exglobal_atm_analysis_initialize.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+exit 0
diff --git a/jobs/JGLOBAL_ATM_ANALYSIS_RUN b/jobs/JGLOBAL_ATM_ANALYSIS_RUN
new file mode 100755
index 0000000000..b04c70e209
--- /dev/null
+++ b/jobs/JGLOBAL_ATM_ANALYSIS_RUN
@@ -0,0 +1,44 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+export WIPE_DATA="NO"
+export DATA=${DATA:-${DATAROOT}/${RUN}atmanl_${cyc}}
+source "${HOMEgfs}/ush/jjob_header.sh" -e "atmanlrun" -c "base atmanl atmanlrun"
+
+##############################################
+# Set variables used in the script
+##############################################
+GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+GDUMP="gdas"
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+export COMOUT=${COMOUT:-${ROTDIR}/${RUN}.${PDY}/${cyc}/atmos}
+mkdir -p "${COMOUT}"
+
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="${ROTDIR}/${GDUMP}.${GDATE:0:8}/${GDATE:8:2}/atmos"
+export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${GDATE:0:8}/${GDATE:8:2}/atmos"
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASATMRUNSH:-${HOMEgfs}/scripts/exglobal_atm_analysis_run.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+exit 0
diff --git a/jobs/rocoto/atmanalpost.sh b/jobs/rocoto/atmanalpost.sh
deleted file mode 100755
index 71ace70c8b..0000000000
--- a/jobs/rocoto/atmanalpost.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-#! /usr/bin/env bash
-
-export STRICT="NO"
-source "${HOMEgfs}/ush/preamble.sh"
-export STRICT="YES"
-
-###############################################################
-# Source UFSDA workflow modules
-. ${HOMEgfs}/ush/load_ufsda_modules.sh
-status=$?
-[[ ${status} -ne 0 ]] && exit ${status}
-
-export job="atmanalpost"
-export jobid="${job}.$$"
-
-###############################################################
-# Execute the JJOB
-${HOMEgfs}/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_POST
-status=$?
-exit ${status}
diff --git a/jobs/rocoto/atmanalprep.sh b/jobs/rocoto/atmanalprep.sh
deleted file mode 100755
index d5b729194a..0000000000
--- a/jobs/rocoto/atmanalprep.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-#! /usr/bin/env bash
-
-export STRICT="NO"
-source "${HOMEgfs}/ush/preamble.sh"
-export STRICT="YES"
-
-###############################################################
-# Source UFSDA workflow modules
-. ${HOMEgfs}/ush/load_ufsda_modules.sh
-status=$?
-[[ ${status} -ne 0 ]] && exit ${status}
-
-export job="atmanalprep"
-export jobid="${job}.$$"
-
-###############################################################
-# Execute the JJOB
-${HOMEgfs}/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_PREP
-status=$?
-exit ${status}
diff --git a/jobs/rocoto/atmanalrun.sh b/jobs/rocoto/atmanalrun.sh
deleted file mode 100755
index 63aa08c184..0000000000
--- a/jobs/rocoto/atmanalrun.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-#! /usr/bin/env bash
-
-export STRICT="NO"
-source "${HOMEgfs}/ush/preamble.sh"
-export STRICT="YES"
-
-###############################################################
-# Source UFSDA workflow modules
-. ${HOMEgfs}/ush/load_ufsda_modules.sh
-status=$?
-[[ ${status} -ne 0 ]] && exit ${status}
-
-export job="atmanalrun"
-export jobid="${job}.$$"
-
-###############################################################
-# Execute the JJOB
-${HOMEgfs}/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_RUN
-status=$?
-exit ${status}
diff --git a/jobs/rocoto/atmanlfinal.sh b/jobs/rocoto/atmanlfinal.sh
new file mode 100755
index 0000000000..3c75c52cb0
--- /dev/null
+++ b/jobs/rocoto/atmanlfinal.sh
@@ -0,0 +1,23 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source UFSDA workflow modules
+. "${HOMEgfs}/ush/load_ufsda_modules.sh"
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+export job="atmanlfinal"
+export jobid="${job}.$$"
+
+###############################################################
+# setup python path for workflow utilities and tasks
+pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+export PYTHONPATH
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_FINALIZE"
+status=$?
+exit "${status}"
diff --git a/jobs/rocoto/atmanlinit.sh b/jobs/rocoto/atmanlinit.sh
new file mode 100755
index 0000000000..7bb2587f0b
--- /dev/null
+++ b/jobs/rocoto/atmanlinit.sh
@@ -0,0 +1,24 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source UFSDA workflow modules
+. "${HOMEgfs}/ush/load_ufsda_modules.sh"
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+export job="atmanlinit"
+export jobid="${job}.$$"
+
+###############################################################
+# setup python path for workflow utilities and tasks
+pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+export PYTHONPATH
+
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_INITIALIZE"
+status=$?
+exit "${status}"
diff --git a/jobs/rocoto/atmanlrun.sh b/jobs/rocoto/atmanlrun.sh
new file mode 100755
index 0000000000..aad80e0b06
--- /dev/null
+++ b/jobs/rocoto/atmanlrun.sh
@@ -0,0 +1,24 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source UFSDA workflow modules
+. "${HOMEgfs}/ush/load_ufsda_modules.sh"
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+export job="atmanlrun"
+export jobid="${job}.$$"
+
+###############################################################
+# setup python path for workflow utilities and tasks
+pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+export PYTHONPATH
+
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_RUN"
+status=$?
+exit "${status}"
diff --git a/parm/config/config.atmanalpost b/parm/config/config.atmanalpost
deleted file mode 100644
index fd5f3bbbcc..0000000000
--- a/parm/config/config.atmanalpost
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/bash -x
-
-########## config.atmanalpost ##########
-# Post Atm Analysis specific
-
-echo "BEGIN: config.atmanalpost"
-
-# Get task specific resources
-. $EXPDIR/config.resources atmanalpost
-echo "END: config.atmanalpost"
diff --git a/parm/config/config.atmanalprep b/parm/config/config.atmanalprep
deleted file mode 100644
index 0014520f5f..0000000000
--- a/parm/config/config.atmanalprep
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/bash -x
-
-########## config.atmanalprep ##########
-# Pre Atm Analysis specific
-
-echo "BEGIN: config.atmanalprep"
-
-# Get task specific resources
-. $EXPDIR/config.resources atmanalprep
-echo "END: config.atmanalprep"
diff --git a/parm/config/config.atmanalrun b/parm/config/config.atmanalrun
deleted file mode 100644
index 5aaac6a01d..0000000000
--- a/parm/config/config.atmanalrun
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/bin/bash -x
-
-########## config.atmanalrun ##########
-# Atm Analysis specific
-
-echo "BEGIN: config.atmanalrun"
-
-# Get task specific resources
-. $EXPDIR/config.resources atmanalrun
-
-# Task specific variables
-export JEDIVAREXE=$HOMEgfs/exec/fv3jedi_var.x
-
-echo "END: config.atmanalrun"
diff --git a/parm/config/config.atmanal b/parm/config/config.atmanl
similarity index 52%
rename from parm/config/config.atmanal
rename to parm/config/config.atmanl
index 2e36ffa603..719018d1fd 100644
--- a/parm/config/config.atmanal
+++ b/parm/config/config.atmanl
@@ -1,25 +1,25 @@
-#!/bin/bash -x
+#! /usr/bin/env bash
 
-########## config.atmanal ##########
-# configuration common to all atm analysis tasks
+########## config.atmanl ##########
+# configuration common to all atm var analysis tasks
 
-echo "BEGIN: config.atmanal"
+echo "BEGIN: config.atmanl"
 
 export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/atm/obs/config/
-export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/atm/obs/lists/gdas_prototype.yaml
+export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/atm/obs/lists/gdas_prototype_3d.yaml
 export ATMVARYAML=${HOMEgfs}/sorc/gdas.cd/parm/atm/variational/3dvar_dripcg.yaml
-export STATICB_TYPE="identity"
+export STATICB_TYPE="gsibec"
 export BERROR_YAML=${HOMEgfs}/sorc/gdas.cd/parm/atm/berror/staticb_${STATICB_TYPE}.yaml
 export FV3JEDI_FIX=${HOMEgfs}/fix/gdas
-export R2D2_OBS_DB='ufsda_test'
-export R2D2_OBS_DUMP='oper_gdas'
-export R2D2_OBS_SRC='ncdiag'
-export R2D2_BC_SRC='gsi'
-export R2D2_BC_DUMP='oper_gdas'
-export R2D2_ARCH_DB='local'
 export INTERP_METHOD='barycentric'
 
+export layout_x=1
+export layout_y=1
+
 export io_layout_x=1
 export io_layout_y=1
 
-echo "END: config.atmanal"
+export JEDIVAREXE=${HOMEgfs}/exec/fv3jedi_var.x
+export crtm_VERSION="2.3.0"
+
+echo "END: config.atmanl"
diff --git a/parm/config/config.atmanlfinal b/parm/config/config.atmanlfinal
new file mode 100644
index 0000000000..a6b714f7fc
--- /dev/null
+++ b/parm/config/config.atmanlfinal
@@ -0,0 +1,10 @@
+#! /usr/bin/env bash
+
+########## config.atmanlfinal ##########
+# Post Atm Var Analysis specific
+
+echo "BEGIN: config.atmanlfinal"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" atmanlfinal
+echo "END: config.atmanlfinal"
diff --git a/parm/config/config.atmanlinit b/parm/config/config.atmanlinit
new file mode 100644
index 0000000000..bc95ef4962
--- /dev/null
+++ b/parm/config/config.atmanlinit
@@ -0,0 +1,10 @@
+#! /usr/bin/env bash
+
+########## config.atmanlinit ##########
+# Pre Atm Var Analysis specific
+
+echo "BEGIN: config.atmanlinit"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" atmanlinit
+echo "END: config.atmanlinit"
diff --git a/parm/config/config.atmanlrun b/parm/config/config.atmanlrun
new file mode 100644
index 0000000000..68b7615718
--- /dev/null
+++ b/parm/config/config.atmanlrun
@@ -0,0 +1,11 @@
+#! /usr/bin/env bash
+
+########## config.atmanlrun ##########
+# Atm Var Analysis specific
+
+echo "BEGIN: config.atmanlrun"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" atmanlrun
+
+echo "END: config.atmanlrun"
diff --git a/parm/config/config.resources b/parm/config/config.resources
index 31b871da61..b1ca57e5cb 100644
--- a/parm/config/config.resources
+++ b/parm/config/config.resources
@@ -9,7 +9,7 @@ if [[ $# -ne 1 ]]; then
     echo "Must specify an input task argument to set resource variables!"
     echo "argument can be any one of the following:"
     echo "getic init coupled_ic aerosol_init"
-    echo "atmanalprep atmanalrun atmanalpost"
+    echo "atmanlinit atmanlrun atmanlfinal"
     echo "atmensanalprep atmensanalrun atmensanalpost"
     echo "aeroanlinit aeroanlrun aeroanlfinal"
     echo "anal sfcanl analcalc analdiag gldas fcst post vrfy fit2obs metp arch echgres"
@@ -167,39 +167,39 @@ elif [[ ${step} = "waveawipsgridded" ]]; then
     export NTASKS=${npe_waveawipsgridded}
     export memory_waveawipsgridded_gfs="1GB"
 
-elif [[ "${step}" = "atmanalprep" ]]; then
+elif [[ "${step}" = "atmanlinit" ]]; then
 
-    export wtime_atmanalprep="00:10:00"
-    export npe_atmanalprep=1
-    export nth_atmanalprep=1
-    npe_node_atmanalprep=$(echo "${npe_node_max} / ${nth_atmanalprep}" | bc)
-    export npe_node_atmanalprep
-    export memory_atmanalprep="3072M"
+    export wtime_atmanlinit="00:10:00"
+    export npe_atmanlinit=1
+    export nth_atmanlinit=1
+    npe_node_atmanlinit=$(echo "${npe_node_max} / ${nth_atmanlinit}" | bc)
+    export npe_node_atmanlinit
+    export memory_atmanlinit="3072M"
 
-elif [[ "${step}" = "atmanalrun" ]]; then
+elif [[ "${step}" = "atmanlrun" ]]; then
 
     # make below case dependent later
     export layout_x=1
     export layout_y=1
 
-    export wtime_atmanalrun="00:30:00"
-    npe_atmanalrun=$(echo "${layout_x} * ${layout_y} * 6" | bc)
-    export npe_atmanalrun
-    npe_atmanalrun_gfs=$(echo "${layout_x} * ${layout_y} * 6" | bc)
-    export npe_atmanalrun_gfs
-    export nth_atmanalrun=1
-    export nth_atmanalrun_gfs=${nth_atmanalrun}
-    npe_node_atmanalrun=$(echo "${npe_node_max} / ${nth_atmanalrun}" | bc)
-    export npe_node_atmanalrun
+    export wtime_atmanlrun="00:30:00"
+    npe_atmanlrun=$(echo "${layout_x} * ${layout_y} * 6" | bc)
+    export npe_atmanlrun
+    npe_atmanlrun_gfs=$(echo "${layout_x} * ${layout_y} * 6" | bc)
+    export npe_atmanlrun_gfs
+    export nth_atmanlrun=1
+    export nth_atmanlrun_gfs=${nth_atmanlrun}
+    npe_node_atmanlrun=$(echo "${npe_node_max} / ${nth_atmanlrun}" | bc)
+    export npe_node_atmanlrun
     export is_exclusive=True
 
-elif [[ "${step}" = "atmanalpost" ]]; then
+elif [[ "${step}" = "atmanlfinal" ]]; then
 
-    export wtime_atmanalpost="00:30:00"
-    export npe_atmanalpost=${npe_node_max}
-    export nth_atmanalpost=1
-    npe_node_atmanalpost=$(echo "${npe_node_max} / ${nth_atmanalpost}" | bc)
-    export npe_node_atmanalpost
+    export wtime_atmanlfinal="00:30:00"
+    export npe_atmanlfinal=${npe_node_max}
+    export nth_atmanlfinal=1
+    npe_node_atmanlfinal=$(echo "${npe_node_max} / ${nth_atmanlfinal}" | bc)
+    export npe_node_atmanlfinal
     export is_exclusive=True
 
 elif [[ "${step}" = "aeroanlinit" ]]; then
diff --git a/parm/parm_gdas/atm_crtm_coeff.yaml b/parm/parm_gdas/atm_crtm_coeff.yaml
new file mode 100644
index 0000000000..8e8d433b06
--- /dev/null
+++ b/parm/parm_gdas/atm_crtm_coeff.yaml
@@ -0,0 +1,178 @@
+mkdir:
+- $(DATA)/crtm
+copy:
+# Emissivity files
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/NPOESS.VISice.EmisCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/NPOESS.VISland.EmisCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/NPOESS.VISsnow.EmisCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/NPOESS.VISwater.EmisCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/NPOESS.IRice.EmisCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/NPOESS.IRland.EmisCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/NPOESS.IRsnow.EmisCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/Nalli.IRwater.EmisCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/FASTEM6.MWwater.EmisCoeff.bin, $(DATA)/crtm]
+# Aerosol and Cloud files
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/AerosolCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/CloudCoeff.bin, $(DATA)/crtm]
+##- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/CloudCoeff.GFDLFV3.-109z-1.bin, $(DATA)/crtm]
+# Satellite_Sensor specific Tau and Spc coefficient files
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/abi_g16.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/abi_g16.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/abi_g17.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/abi_g17.TauCoeff.bin, $(DATA)/crtm]
+##- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/abi_g18.SpcCoeff.bin, $(DATA)/crtm]
+##- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/abi_g18.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ahi_himawari8.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ahi_himawari8.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ahi_himawari9.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ahi_himawari9.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/airs_aqua.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/airs_aqua.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsr2_gcom-w1.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsr2_gcom-w1.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsre_aqua.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsre_aqua.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_aqua.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_aqua.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_metop-a.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_metop-a.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_metop-b.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_metop-b.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_metop-c.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_metop-c.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_n15.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_n15.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_n18.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_n18.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_n19.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_n19.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsub_n17.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsub_n17.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/atms_n20.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/atms_n20.TauCoeff.bin, $(DATA)/crtm]
+##- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/atms_n21.SpcCoeff.bin, $(DATA)/crtm]
+##- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/atms_n21.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/atms_npp.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/atms_npp.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/avhrr3_metop-a.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/avhrr3_metop-a.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/avhrr3_metop-b.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/avhrr3_metop-b.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/avhrr3_metop-c.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/avhrr3_metop-c.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/avhrr3_n18.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/avhrr3_n18.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/avhrr3_n19.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/avhrr3_n19.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/cris-fsr_n20.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/cris-fsr_n20.TauCoeff.bin, $(DATA)/crtm]
+##- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/cris-fsr_n21.SpcCoeff.bin, $(DATA)/crtm]
+##- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/cris-fsr_n21.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/cris-fsr_npp.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/cris-fsr_npp.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/gmi_gpm.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/gmi_gpm.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/hirs3_n17.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/hirs3_n17.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/hirs4_metop-a.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/hirs4_metop-a.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/hirs4_metop-b.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/hirs4_metop-b.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/hirs4_n19.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/hirs4_n19.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/iasi_metop-a.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/iasi_metop-a.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/iasi_metop-b.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/iasi_metop-b.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/iasi_metop-c.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/iasi_metop-c.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/imgr_g11.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/imgr_g11.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/imgr_g12.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/imgr_g12.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/imgr_g13.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/imgr_g13.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/imgr_g14.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/imgr_g14.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/imgr_g15.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/imgr_g15.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/mhs_metop-a.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/mhs_metop-a.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/mhs_metop-b.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/mhs_metop-b.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/mhs_metop-c.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/mhs_metop-c.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/mhs_n18.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/mhs_n18.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/mhs_n19.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/mhs_n19.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/saphir_meghat.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/saphir_meghat.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/seviri_m08.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/seviri_m08.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/seviri_m09.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/seviri_m09.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/seviri_m10.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/seviri_m10.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/seviri_m11.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/seviri_m11.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD1_g11.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD1_g11.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD1_g12.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD1_g12.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD1_g13.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD1_g13.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD1_g14.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD1_g14.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD1_g15.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD1_g15.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD2_g11.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD2_g11.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD2_g12.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD2_g12.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD2_g13.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD2_g13.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD2_g14.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD2_g14.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD2_g15.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD2_g15.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD3_g11.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD3_g11.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD3_g12.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD3_g12.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD3_g13.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD3_g13.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD3_g14.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD3_g14.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD3_g15.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD3_g15.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD4_g11.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD4_g11.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD4_g12.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD4_g12.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD4_g13.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD4_g13.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD4_g14.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD4_g14.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD4_g15.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/sndrD4_g15.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ssmi_f15.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ssmi_f15.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ssmis_f16.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ssmis_f16.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ssmis_f17.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ssmis_f17.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ssmis_f18.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ssmis_f18.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ssmis_f19.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ssmis_f19.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ssmis_f20.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/ssmis_f20.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/viirs-m_j1.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/viirs-m_j1.TauCoeff.bin, $(DATA)/crtm]
+##- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/viirs-m_j2.SpcCoeff.bin, $(DATA)/crtm]
+##- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/viirs-m_j2.TauCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/viirs-m_npp.SpcCoeff.bin, $(DATA)/crtm]
+- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/viirs-m_npp.TauCoeff.bin, $(DATA)/crtm]
+# Special Spc files
+##- [$(HOMEgfs)/fix/gdas/crtm/$(crtm_VERSION)/amsua_metop-a_v2.SpcCoeff.bin, $(DATA)/crtm]
diff --git a/parm/parm_gdas/atm_jedi_fix.yaml b/parm/parm_gdas/atm_jedi_fix.yaml
new file mode 100644
index 0000000000..07b0fe49f1
--- /dev/null
+++ b/parm/parm_gdas/atm_jedi_fix.yaml
@@ -0,0 +1,7 @@
+mkdir:
+- $(DATA)/fv3jedi
+copy:
+- [$(HOMEgfs)/fix/gdas/fv3jedi/fv3files/akbk$(npz).nc4, $(DATA)/fv3jedi/akbk.nc4]
+- [$(HOMEgfs)/fix/gdas/fv3jedi/fv3files/fmsmpp.nml, $(DATA)/fv3jedi/fmsmpp.nml]
+- [$(HOMEgfs)/fix/gdas/fv3jedi/fv3files/field_table_gfdl, $(DATA)/fv3jedi/field_table]
+- [$(HOMEgfs)/fix/gdas/fv3jedi/fieldmetadata/gfs-restart.yaml, $(DATA)/fv3jedi/gfs-restart.yaml]
diff --git a/parm/parm_gdas/atmanl_inc_vars.yaml b/parm/parm_gdas/atmanl_inc_vars.yaml
new file mode 100644
index 0000000000..cb6718ce9f
--- /dev/null
+++ b/parm/parm_gdas/atmanl_inc_vars.yaml
@@ -0,0 +1 @@
+incvars: ['ua', 'va', 't', 'sphum', 'liq_wat', 'ice_wat', 'o3mr']
diff --git a/scripts/exgdas_global_atmos_analysis_post.py b/scripts/exgdas_global_atmos_analysis_post.py
deleted file mode 100755
index 2f17ee4aea..0000000000
--- a/scripts/exgdas_global_atmos_analysis_post.py
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/usr/bin/env python3
-################################################################################
-#  UNIX Script Documentation Block
-#                      .                                             .
-# Script name:         exgdas_global_atmos_analysis_post.py
-# Script description:  Post atmospheric analysis script.
-#
-# Author: Cory Martin      Org: NCEP/EMC     Date: 2021-12-29
-#
-# Abstract: This script runs after the atmospheric analysis and
-#           archives each diagnostic file into the R2D2 local user database.
-#
-# $Id$
-#
-# Attributes:
-#   Language: Python3
-#
-################################################################################
-
-# import os and sys to add ush to path
-import logging
-import os
-import sys
-
-# set up logger
-logging.basicConfig(format='%(asctime)s:%(levelname)s:%(message)s', level=logging.INFO, datefmt='%Y-%m-%d %H:%M:%S')
-
-# get absolute path of ush/ directory either from env or relative to this file
-my_dir = os.path.dirname(__file__)
-my_home = os.path.dirname(os.path.dirname(my_dir))
-gdas_home = os.path.join(os.environ['HOMEgfs'], 'sorc', 'gdas.cd')
-sys.path.append(os.path.join(os.getenv('HOMEgfs', my_home), 'ush'))
-logging.info(f"sys.path={sys.path}")
-
-# import UFSDA utilities
-import ufsda
-
-# get configuration based on environment variables
-config = ufsda.misc_utils.get_env_config(component='atm')
-config['DIAG_DIR'] = os.path.join(os.environ['COMOUT'], 'diags')
-config['BIAS_OUT_DIR'] = os.path.join(os.environ['COMOUT'], 'bc')
-config['provider'] = 'ncdiag'
-
-# use R2D2 to archive diags and bias correction coefficient files
-ufsda.archive.atm_diags(config)
diff --git a/scripts/exgdas_global_atmos_analysis_prep.py b/scripts/exgdas_global_atmos_analysis_prep.py
deleted file mode 100755
index 65c77cd903..0000000000
--- a/scripts/exgdas_global_atmos_analysis_prep.py
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/usr/bin/env python3
-################################################################################
-#  UNIX Script Documentation Block
-#                      .                                             .
-# Script name:         exgdas_global_atmos_analysis_prep.py
-# Script description:  Stages files and generates YAML for Global Atmosphere Analysis
-#
-# Author: Cory Martin      Org: NCEP/EMC     Date: 2021-12-21
-#
-# Abstract: This script stages necessary input files and produces YAML
-#           configuration input file for FV3-JEDI executable(s) needed
-#           to produce a UFS Global Atmospheric Analysis.
-#
-# $Id$
-#
-# Attributes:
-#   Language: Python3
-#
-################################################################################
-
-# import os and sys to add ush to path
-import logging
-import os
-import sys
-
-# set up logger
-logging.basicConfig(format='%(asctime)s:%(levelname)s:%(message)s', level=logging.INFO, datefmt='%Y-%m-%d %H:%M:%S')
-
-# get absolute path of ush/ directory either from env or relative to this file
-my_dir = os.path.dirname(__file__)
-my_home = os.path.dirname(os.path.dirname(my_dir))
-gdas_home = os.path.join(os.environ['HOMEgfs'], 'sorc', 'gdas.cd')
-sys.path.append(os.path.join(os.getenv('HOMEgfs', my_home), 'ush'))
-logging.info(f"sys.path={sys.path}")
-
-# import UFSDA utilities
-import ufsda
-from ufsda.stage import atm_obs, bias_obs
-
-# get configuration based on environment variables
-config = ufsda.misc_utils.get_env_config(component='atm')
-
-# use R2D2 to stage obs and bias correction coefficient files
-ufsda.stage.atm_obs(config)
-ufsda.stage.bias_obs(config)
diff --git a/scripts/exgdas_global_atmos_analysis_run.sh b/scripts/exgdas_global_atmos_analysis_run.sh
deleted file mode 100755
index 45ccdf525b..0000000000
--- a/scripts/exgdas_global_atmos_analysis_run.sh
+++ /dev/null
@@ -1,182 +0,0 @@
-#!/bin/bash
-################################################################################
-####  UNIX Script Documentation Block
-#                      .                                             .
-# Script name:         exgdas_global_atmos_analysis_run.sh
-# Script description:  Runs the global atmospheric analysis with FV3-JEDI
-#
-# Author: Cory Martin        Org: NCEP/EMC     Date: 2021-12-28
-#
-# Abstract: This script makes a global model atmospheric analysis using FV3-JEDI
-#           and also (for now) updates increment files using a python ush utility
-#
-# $Id$
-#
-# Attributes:
-#   Language: POSIX shell
-#   Machine: Orion
-#
-################################################################################
-
-#  Set environment.
-source "$HOMEgfs/ush/preamble.sh"
-
-#  Directories
-pwd=$(pwd)
-
-#  Utilities
-export NLN=${NLN:-"/bin/ln -sf"}
-export INCPY=${INCPY:-"$HOMEgfs/sorc/gdas.cd/ush/jediinc2fv3.py"}
-export GENYAML=${GENYAML:-"$HOMEgfs/sorc/gdas.cd/ush/genYAML"}
-export GETOBSYAML=${GETOBSYAML:-"$HOMEgfs/sorc/gdas.cd/ush/get_obs_list.py"}
-
-################################################################################
-# make subdirectories
-mkdir -p $DATA/fv3jedi
-mkdir -p $DATA/obs
-mkdir -p $DATA/diags
-mkdir -p $DATA/bc
-mkdir -p $DATA/anl
-
-################################################################################
-# generate YAML file
-cat > $DATA/temp.yaml << EOF
-template: ${ATMVARYAML}
-output: $DATA/fv3jedi_var.yaml
-config:
-  atm: true
-  BERROR_YAML: $BERROR_YAML
-  OBS_DIR: obs
-  DIAG_DIR: diags
-  CRTM_COEFF_DIR: crtm
-  BIAS_IN_DIR: obs
-  BIAS_OUT_DIR: bc
-  OBS_PREFIX: $OPREFIX
-  BIAS_PREFIX: $GPREFIX
-  OBS_LIST: $OBS_LIST
-  OBS_YAML_DIR: $OBS_YAML_DIR
-  BKG_DIR: bkg
-  fv3jedi_staticb_dir: berror
-  fv3jedi_fix_dir: fv3jedi
-  fv3jedi_fieldset_dir: fv3jedi
-  fv3jedi_fieldmetadata_dir: fv3jedi
-  OBS_DATE: '$CDATE'
-  BIAS_DATE: '$GDATE'
-  ANL_DIR: anl/
-  NMEM_ENKF: '$NMEM_ENKF'
-  INTERP_METHOD: '$INTERP_METHOD'
-EOF
-$GENYAML --config $DATA/temp.yaml
-
-################################################################################
-# link observations to $DATA
-$GETOBSYAML --config $DATA/fv3jedi_var.yaml --output $DATA/${OPREFIX}obsspace_list
-files=$(cat $DATA/${OPREFIX}obsspace_list)
-for file in $files; do
-  basefile=$(basename $file)
-  $NLN $COMOUT/$basefile $DATA/obs/$basefile
-done
-
-# link backgrounds to $DATA
-# linking FMS RESTART files for now
-# change to (or make optional) for cube sphere history later
-$NLN ${COMIN_GES}/RESTART $DATA/bkg
-
-
-# optionally link ensemble backgrounds to $DATA
-if [ $DOHYBVAR = "YES" ]; then
-   mkdir -p $DATA/ens
-   fhrs="06"
-   if [ $l4densvar = ".true." ]; then
-      fhrs="03 04 05 06 07 08 09"
-   fi
-
-   for imem in $(seq 1 $NMEM_ENKF); do
-      memchar="mem"$(printf %03i $imem)
-      for fhr in $fhrs; do
-         $NLN ${COMIN_GES_ENS}/$memchar/atmos/RESTART $DATA/ens/$memchar
-      done
-   done
-
-fi
-
-################################################################################
-# link fix files to $DATA
-# static B
-CASE_BERROR=${CASE_BERROR:-${CASE_ANL:-${CASE}}}
-if [[ (${STATICB_TYPE} = "bump") || (${STATICB_TYPE} = "gsibec") ]] ; then
-    ${NLN} "${FV3JEDI_FIX}/${STATICB_TYPE}/${CASE_BERROR}/" "${DATA}/berror"
-fi
-
-# vertical coordinate
-LAYERS=$(expr $LEVS - 1)
-$NLN $FV3JEDI_FIX/fv3jedi/fv3files/akbk${LAYERS}.nc4 $DATA/fv3jedi/akbk.nc4
-
-# other FV3-JEDI fix files
-$NLN $FV3JEDI_FIX/fv3jedi/fv3files/fmsmpp.nml $DATA/fv3jedi/fmsmpp.nml
-$NLN $FV3JEDI_FIX/fv3jedi/fv3files/field_table_gfdl $DATA/fv3jedi/field_table
-
-# fieldmetadata
-$NLN $FV3JEDI_FIX/fv3jedi/fieldmetadata/gfs-restart.yaml $DATA/fv3jedi/gfs-restart.yaml
-
-# fieldsets
-fieldsets="dynamics.yaml ufo.yaml"
-for fieldset in $fieldsets; do
-  $NLN $FV3JEDI_FIX/fv3jedi/fieldsets/$fieldset $DATA/fv3jedi/$fieldset
-done
-
-# CRTM coeffs
-${NLN} "${FV3JEDI_FIX}/crtm/2.3.0" "${DATA}/crtm"
-
-#  Link executable to $DATA
-$NLN $JEDIVAREXE $DATA/fv3jedi_var.x
-
-################################################################################
-# run executable
-export OMP_NUM_THREADS=$NTHREADS_ATMANAL
-export pgm=$JEDIVAREXE
-. prep_step
-$APRUN_ATMANAL $DATA/fv3jedi_var.x $DATA/fv3jedi_var.yaml 1>&1 2>&2
-export err=$?; err_chk
-
-################################################################################
-# translate FV3-JEDI increment to FV3 readable format
-if [[ "${CASE_BERROR}" = "${CASE}" ]]; then
-    atmges_fv3=${COMIN_GES}/${GPREFIX}atmf006.nc
-else
-    atmges_fv3=${COMIN_GES}/${GPREFIX}atmf006.ensres.nc
-fi
-atminc_jedi=${DATA}/anl/atminc.${PDY}_${cyc}0000z.nc4
-atminc_fv3=${COMOUT}/${CDUMP}.${cycle}.atminc.nc
-if [ -s $atminc_jedi ]; then
-    $INCPY $atmges_fv3 $atminc_jedi $atminc_fv3
-    export err=$?
-else
-    echo "***WARNING*** missing $atminc_jedi   ABORT"
-    export err=99
-fi
-err_chk
-
-################################################################################
-# Create log file noting creating of analysis increment file
-echo "$CDUMP $CDATE atminc and tiled sfcanl done at $(date)" > $COMOUT/${CDUMP}.${cycle}.loginc.txt
-
-################################################################################
-# Copy diags and YAML to $COMOUT
-cp -r $DATA/fv3jedi_var.yaml $COMOUT/${CDUMP}.${cycle}.fv3jedi_var.yaml
-cp -rf $DATA/diags $COMOUT/
-cp -rf $DATA/bc $COMOUT/
-
-# ***WARNING*** PATCH
-# Copy abias, abias_pc, and abias_air from previous cycle to current cycle
-# Deterministic abias used in enkf cycle
-alist="abias abias_air abias_int abias_pc"
-for abias in $alist; do
-    cp "${COMIN_GES}/${GPREFIX}${abias}" "${COMOUT}/${APREFIX}${abias}"
-done
-
-################################################################################
-
-exit ${err}
-
-################################################################################
diff --git a/scripts/exglobal_atm_analysis_finalize.py b/scripts/exglobal_atm_analysis_finalize.py
new file mode 100755
index 0000000000..cd6938e210
--- /dev/null
+++ b/scripts/exglobal_atm_analysis_finalize.py
@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+# exgdas_global_atm_analysis_finalize.py
+# This script creates an AtmAnalysis class
+# and runs the finalize method
+# which perform post-processing and clean up activities
+# for a global atm variational analysis
+import os
+
+from pygw.logger import Logger
+from pygw.configuration import cast_strdict_as_dtypedict
+from pygfs.task.atm_analysis import AtmAnalysis
+
+
+# Initialize root logger
+logger = Logger(level='DEBUG', colored_log=True)
+
+
+if __name__ == '__main__':
+
+    # Take configuration from environment and cast it as python dictionary
+    config = cast_strdict_as_dtypedict(os.environ)
+
+    # Instantiate the atm analysis task
+    AtmAnl = AtmAnalysis(config)
+    AtmAnl.finalize()
diff --git a/scripts/exglobal_atm_analysis_initialize.py b/scripts/exglobal_atm_analysis_initialize.py
new file mode 100755
index 0000000000..b003d98c00
--- /dev/null
+++ b/scripts/exglobal_atm_analysis_initialize.py
@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+# exgdas_global_atm_analysis_initialize.py
+# This script creates an AtmAnalysis class
+# and runs the initialize method
+# which create and stage the runtime directory
+# and create the YAML configuration
+# for a global atm variational analysis
+import os
+
+from pygw.logger import Logger
+from pygw.configuration import cast_strdict_as_dtypedict
+from pygfs.task.atm_analysis import AtmAnalysis
+
+# Initialize root logger
+logger = Logger(level='DEBUG', colored_log=True)
+
+
+if __name__ == '__main__':
+
+    # Take configuration from environment and cast it as python dictionary
+    config = cast_strdict_as_dtypedict(os.environ)
+
+    # Instantiate the atm analysis task
+    AtmAnl = AtmAnalysis(config)
+    AtmAnl.initialize()
diff --git a/scripts/exglobal_atm_analysis_run.py b/scripts/exglobal_atm_analysis_run.py
new file mode 100755
index 0000000000..e1f44208c9
--- /dev/null
+++ b/scripts/exglobal_atm_analysis_run.py
@@ -0,0 +1,23 @@
+#!/usr/bin/env python3
+# exgdas_global_atm_analysis_run.py
+# This script creates an AtmAnalysis object
+# and runs the execute method
+# which executes the global atm variational analysis
+import os
+
+from pygw.logger import Logger
+from pygw.configuration import cast_strdict_as_dtypedict
+from pygfs.task.atm_analysis import AtmAnalysis
+
+# Initialize root logger
+logger = Logger(level='DEBUG', colored_log=True)
+
+
+if __name__ == '__main__':
+
+    # Take configuration from environment and cast it as python dictionary
+    config = cast_strdict_as_dtypedict(os.environ)
+
+    # Instantiate the atm analysis task
+    AtmAnl = AtmAnalysis(config)
+    AtmAnl.execute()
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 379d19387b..2872fdab42 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -187,6 +187,7 @@ fi
 if [[ -d "${script_dir}/gdas.cd" ]]; then
   cd "${top_dir}/ush" || exit 1
     ${LINK} "${script_dir}/gdas.cd/ush/ufsda"                              .
+    ${LINK} "${script_dir}/gdas.cd/ush/jediinc2fv3.py"                     .
 fi
 
 
diff --git a/ush/python/pygfs/task/atm_analysis.py b/ush/python/pygfs/task/atm_analysis.py
new file mode 100644
index 0000000000..a632e318d9
--- /dev/null
+++ b/ush/python/pygfs/task/atm_analysis.py
@@ -0,0 +1,445 @@
+#!/usr/bin/env python3
+
+import os
+import glob
+import gzip
+import tarfile
+from logging import getLogger
+from typing import Dict, List, Any
+
+from pygw.attrdict import AttrDict
+from pygw.file_utils import FileHandler
+from pygw.timetools import add_to_datetime, to_fv3time, to_timedelta, to_YMDH
+from pygw.fsutils import rm_p, chdir
+from pygw.yaml_file import parse_yamltmpl, parse_j2yaml, save_as_yaml
+from pygw.logger import logit
+from pygw.executable import Executable
+from pygw.exceptions import WorkflowException
+from pygfs.task.analysis import Analysis
+
+logger = getLogger(__name__.split('.')[-1])
+
+
+class AtmAnalysis(Analysis):
+    """
+    Class for global atm analysis tasks
+    """
+    @logit(logger, name="AtmAnalysis")
+    def __init__(self, config):
+        super().__init__(config)
+
+        _res = int(self.config.CASE[1:])
+        _res_anl = int(self.config.CASE_ANL[1:])
+        _window_begin = add_to_datetime(self.runtime_config.current_cycle, -to_timedelta(f"{self.config.assim_freq}H") / 2)
+        _fv3jedi_yaml = os.path.join(self.runtime_config.DATA, f"{self.runtime_config.CDUMP}.t{self.runtime_config.cyc:02d}z.atmvar.yaml")
+
+        # Create a local dictionary that is repeatedly used across this class
+        local_dict = AttrDict(
+            {
+                'npx_ges': _res + 1,
+                'npy_ges': _res + 1,
+                'npz_ges': self.config.LEVS - 1,
+                'npz': self.config.LEVS - 1,
+                'npx_anl': _res_anl + 1,
+                'npy_anl': _res_anl + 1,
+                'npz_anl': self.config.LEVS - 1,
+                'ATM_WINDOW_BEGIN': _window_begin,
+                'ATM_WINDOW_LENGTH': f"PT{self.config.assim_freq}H",
+                'comin_ges_atm': self.config.COMIN_GES,
+                'OPREFIX': f"{self.runtime_config.CDUMP}.t{self.runtime_config.cyc:02d}z.",  # TODO: CDUMP is being replaced by RUN
+                'APREFIX': f"{self.runtime_config.CDUMP}.t{self.runtime_config.cyc:02d}z.",  # TODO: CDUMP is being replaced by RUN
+                'GPREFIX': f"gdas.t{self.runtime_config.previous_cycle.hour:02d}z.",
+                'fv3jedi_yaml': _fv3jedi_yaml,
+            }
+        )
+
+        # task_config is everything that this task should need
+        self.task_config = AttrDict(**self.config, **self.runtime_config, **local_dict)
+
+    @logit(logger)
+    def initialize(self: Analysis) -> None:
+        """Initialize a global atm analysis
+
+        This method will initialize a global atm analysis using JEDI.
+        This includes:
+        - staging CRTM fix files
+        - staging FV3-JEDI fix files
+        - staging B error files
+        - staging model backgrounds
+        - generating a YAML file for the JEDI executable
+        - linking the JEDI executable (TODO make it copyable, requires JEDI fix)
+        - creating output directories
+        """
+        super().initialize()
+
+        # stage CRTM fix files
+        crtm_fix_list_path = os.path.join(self.task_config.HOMEgfs, 'parm', 'parm_gdas', 'atm_crtm_coeff.yaml')
+        logger.debug(f"Staging CRTM fix files from {crtm_fix_list_path}")
+        crtm_fix_list = parse_yamltmpl(crtm_fix_list_path, self.task_config)
+        FileHandler(crtm_fix_list).sync()
+
+        # stage fix files
+        jedi_fix_list_path = os.path.join(self.task_config.HOMEgfs, 'parm', 'parm_gdas', 'atm_jedi_fix.yaml')
+        logger.debug(f"Staging JEDI fix files from {jedi_fix_list_path}")
+        jedi_fix_list = parse_yamltmpl(jedi_fix_list_path, self.task_config)
+        FileHandler(jedi_fix_list).sync()
+
+        # stage berror files
+        # copy static background error files, otherwise it will assume ID matrix
+        logger.debug(f"Stage files for STATICB_TYPE {self.task_config.STATICB_TYPE}")
+        FileHandler(self.get_berror_dict(self.task_config)).sync()
+
+        # stage backgrounds
+        FileHandler(self.get_bkg_dict(AttrDict(self.task_config))).sync()
+
+        # generate variational YAML file
+        logger.debug(f"Generate variational YAML file: {self.task_config.fv3jedi_yaml}")
+        varda_yaml = parse_j2yaml(self.task_config.ATMVARYAML, self.task_config)
+        save_as_yaml(varda_yaml, self.task_config.fv3jedi_yaml)
+        logger.info(f"Wrote variational YAML to: {self.task_config.fv3jedi_yaml}")
+
+        # link executable to DATA/ directory
+        exe_src = self.task_config.JEDIVAREXE
+        logger.debug(f"Link executable {exe_src} to DATA/")  # TODO: linking is not permitted per EE2.  Needs work in JEDI to be able to copy the exec.
+        exe_dest = os.path.join(self.task_config.DATA, os.path.basename(exe_src))
+        if os.path.exists(exe_dest):
+            rm_p(exe_dest)
+        os.symlink(exe_src, exe_dest)
+
+        # need output dir for diags and anl
+        logger.debug("Create empty output [anl, diags] directories to receive output from executable")
+        newdirs = [
+            os.path.join(self.task_config.DATA, 'anl'),
+            os.path.join(self.task_config.DATA, 'diags'),
+        ]
+        FileHandler({'mkdir': newdirs}).sync()
+
+    @logit(logger)
+    def execute(self: Analysis) -> None:
+
+        chdir(self.task_config.DATA)
+
+        exec_cmd = Executable(self.task_config.APRUN_ATMANL)
+        exec_name = os.path.join(self.task_config.DATA, 'fv3jedi_var.x')
+        exec_cmd.add_default_arg(exec_name)
+        exec_cmd.add_default_arg(self.task_config.fv3jedi_yaml)
+
+        try:
+            logger.debug(f"Executing {exec_cmd}")
+            exec_cmd()
+        except OSError:
+            raise OSError(f"Failed to execute {exec_cmd}")
+        except Exception:
+            raise WorkflowException(f"An error occured during execution of {exec_cmd}")
+
+        pass
+
+    @logit(logger)
+    def finalize(self: Analysis) -> None:
+        """Finalize a global atm analysis
+
+        This method will finalize a global atm analysis using JEDI.
+        This includes:
+        - tar output diag files and place in ROTDIR
+        - copy the generated YAML file from initialize to the ROTDIR
+        - copy the updated bias correction files to ROTDIR
+        - write UFS model readable atm incrment file
+
+        """
+        # ---- tar up diags
+        # path of output tar statfile
+        atmstat = os.path.join(self.task_config.COMOUTatmos, f"{self.task_config.APREFIX}atmstat")
+
+        # get list of diag files to put in tarball
+        diags = glob.glob(os.path.join(self.task_config.DATA, 'diags', 'diag*nc4'))
+
+        logger.info(f"Compressing {len(diags)} diag files to {atmstat}.gz")
+
+        # gzip the files first
+        logger.debug(f"Gzipping {len(diags)} diag files")
+        for diagfile in diags:
+            with open(diagfile, 'rb') as f_in, gzip.open(f"{diagfile}.gz", 'wb') as f_out:
+                f_out.writelines(f_in)
+
+        # open tar file for writing
+        logger.debug(f"Creating tar file {atmstat} with {len(diags)} gzipped diag files")
+        with tarfile.open(atmstat, "w") as archive:
+            for diagfile in diags:
+                diaggzip = f"{diagfile}.gz"
+                archive.add(diaggzip, arcname=os.path.basename(diaggzip))
+
+        # copy full YAML from executable to ROTDIR
+        logger.info(f"Copying {self.task_config.fv3jedi_yaml} to {self.task_config.COMOUTatmos}")
+        src = os.path.join(self.task_config.DATA, f"{self.task_config.CDUMP}.t{self.task_config.cyc:02d}z.atmvar.yaml")
+        dest = os.path.join(self.task_config.COMOUTatmos, f"{self.task_config.CDUMP}.t{self.task_config.cyc:02d}z.atmvar.yaml")
+        logger.debug(f"Copying {src} to {dest}")
+        yaml_copy = {
+            'mkdir': [self.task_config.COMOUTatmos],
+            'copy': [[src, dest]]
+        }
+        FileHandler(yaml_copy).sync()
+
+        # copy bias correction files to ROTDIR
+        logger.info("Copy bias correction files from DATA/ to COM/")
+        biasdir = os.path.join(self.task_config.DATA, 'bc')
+        biasls = os.listdir(biasdir)
+        biaslist = []
+        for bfile in biasls:
+            src = os.path.join(biasdir, bfile)
+            dest = os.path.join(self.task_config.COMOUTatmos, bfile)
+            biaslist.append([src, dest])
+
+        gprefix = f"{self.task_config.GPREFIX}"
+        gsuffix = f"{to_YMDH(self.task_config.previous_cycle)}" + ".txt"
+        aprefix = f"{self.task_config.APREFIX}"
+        asuffix = f"{to_YMDH(self.task_config.current_cycle)}" + ".txt"
+
+        logger.info(f"Copying {gprefix}*{gsuffix} from DATA/ to COM/ as {aprefix}*{asuffix}")
+        obsdir = os.path.join(self.task_config.DATA, 'obs')
+        obsls = os.listdir(obsdir)
+        for ofile in obsls:
+            if ofile.endswith(".txt"):
+                src = os.path.join(obsdir, ofile)
+                tfile = ofile.replace(gprefix, aprefix)
+                tfile = tfile.replace(gsuffix, asuffix)
+                dest = os.path.join(self.task_config.COMOUTatmos, tfile)
+                biaslist.append([src, dest])
+
+        bias_copy = {
+            'mkdir': [self.task_config.COMOUTatmos],
+            'copy': biaslist,
+        }
+        FileHandler(bias_copy).sync()
+
+        # Create UFS model readable atm increment file from UFS-DA atm increment
+        logger.info("Create UFS model readable atm increment file from UFS-DA atm increment")
+        self.jedi2fv3inc()
+
+    def clean(self):
+        super().clean()
+
+    @logit(logger)
+    def get_bkg_dict(self, task_config: Dict[str, Any]) -> Dict[str, List[str]]:
+        """Compile a dictionary of model background files to copy
+
+        This method constructs a dictionary of FV3 RESTART files (coupler, core, tracer)
+        that are needed for global atm DA and returns said dictionary for use by the FileHandler class.
+
+        Parameters
+        ----------
+        task_config: Dict
+            a dictionary containing all of the configuration needed for the task
+
+        Returns
+        ----------
+        bkg_dict: Dict
+            a dictionary containing the list of model background files to copy for FileHandler
+        """
+        # NOTE for now this is FV3 RESTART files and just assumed to be fh006
+
+        # get FV3 RESTART files, this will be a lot simpler when using history files
+        rst_dir = os.path.join(task_config.comin_ges_atm, 'RESTART')  # for now, option later?
+        run_dir = os.path.join(task_config.DATA, 'bkg')
+
+        # Start accumulating list of background files to copy
+        bkglist = []
+
+        # atm DA needs coupler
+        basename = f'{to_fv3time(task_config.current_cycle)}.coupler.res'
+        bkglist.append([os.path.join(rst_dir, basename), os.path.join(run_dir, basename)])
+
+        # atm DA needs core, srf_wnd, tracer, phy_data, sfc_data
+        for ftype in ['core', 'srf_wnd', 'tracer']:
+            template = f'{to_fv3time(self.task_config.current_cycle)}.fv_{ftype}.res.tile{{tilenum}}.nc'
+            for itile in range(1, task_config.ntiles + 1):
+                basename = template.format(tilenum=itile)
+                bkglist.append([os.path.join(rst_dir, basename), os.path.join(run_dir, basename)])
+
+        for ftype in ['phy_data', 'sfc_data']:
+            template = f'{to_fv3time(self.task_config.current_cycle)}.{ftype}.tile{{tilenum}}.nc'
+            for itile in range(1, task_config.ntiles + 1):
+                basename = template.format(tilenum=itile)
+                bkglist.append([os.path.join(rst_dir, basename), os.path.join(run_dir, basename)])
+
+        bkg_dict = {
+            'mkdir': [run_dir],
+            'copy': bkglist,
+        }
+        return bkg_dict
+
+    @logit(logger)
+    def get_berror_dict(self, config: Dict[str, Any]) -> Dict[str, List[str]]:
+        """Compile a dictionary of background error files to copy
+
+        This method will construct a dictionary of either bump of gsibec background
+        error files for global atm DA and return said dictionary for use by the
+        FileHandler class.
+
+        Parameters
+        ----------
+        config: Dict
+            a dictionary containing all of the configuration needed
+
+        Returns
+        ----------
+        berror_dict: Dict
+            a dictionary containing the list of atm background error files to copy for FileHandler
+        """
+        SUPPORTED_BERROR_STATIC_MAP = {'identity': self._get_berror_dict_identity,
+                                       'bump': self._get_berror_dict_bump,
+                                       'gsibec': self._get_berror_dict_gsibec}
+
+        try:
+            berror_dict = SUPPORTED_BERROR_STATIC_MAP[config.STATICB_TYPE](config)
+        except KeyError:
+            raise KeyError(f"{config.STATICB_TYPE} is not a supported background error type.\n" +
+                           f"Currently supported background error types are:\n" +
+                           f'{" | ".join(SUPPORTED_BERROR_STATIC_MAP.keys())}')
+
+        return berror_dict
+
+    @staticmethod
+    @logit(logger)
+    def _get_berror_dict_identity(config: Dict[str, Any]) -> Dict[str, List[str]]:
+        """Identity BE does not need any files for staging.
+
+        This is a private method and should not be accessed directly.
+
+        Parameters
+        ----------
+        config: Dict
+            a dictionary containing all of the configuration needed
+        Returns
+        ----------
+        berror_dict: Dict
+            Empty dictionary [identity BE needs not files to stage]
+        """
+        logger.info(f"Identity background error does not use staged files.  Return empty dictionary")
+        return {}
+
+    @staticmethod
+    @logit(logger)
+    def _get_berror_dict_bump(config: Dict[str, Any]) -> Dict[str, List[str]]:
+        """Compile a dictionary of atm bump background error files to copy
+
+        This method will construct a dictionary of atm bump background error
+        files for global atm DA and return said dictionary to the parent
+
+        This is a private method and should not be accessed directly.
+
+        Parameters
+        ----------
+        config: Dict
+            a dictionary containing all of the configuration needed
+
+        Returns
+        ----------
+        berror_dict: Dict
+            a dictionary of atm bump background error files to copy for FileHandler
+        """
+        # BUMP atm static-B needs nicas, cor_rh, cor_rv and stddev files.
+        b_dir = config.BERROR_DATA_DIR
+        b_datestr = to_fv3time(config.BERROR_DATE)
+        berror_list = []
+        for ftype in ['cor_rh', 'cor_rv', 'stddev']:
+            coupler = f'{b_datestr}.{ftype}.coupler.res'
+            berror_list.append([
+                os.path.join(b_dir, coupler), os.path.join(config.DATA, 'berror', coupler)
+            ])
+
+            template = '{b_datestr}.{ftype}.fv_tracer.res.tile{{tilenum}}.nc'
+            for itile in range(1, config.ntiles + 1):
+                tracer = template.format(tilenum=itile)
+                berror_list.append([
+                    os.path.join(b_dir, tracer), os.path.join(config.DATA, 'berror', tracer)
+                ])
+
+        nproc = config.ntiles * config.layout_x * config.layout_y
+        for nn in range(1, nproc + 1):
+            berror_list.append([
+                os.path.join(b_dir, f'nicas_aero_nicas_local_{nproc:06}-{nn:06}.nc'),
+                os.path.join(config.DATA, 'berror', f'nicas_aero_nicas_local_{nproc:06}-{nn:06}.nc')
+            ])
+
+        # create dictionary of background error files to stage
+        berror_dict = {
+            'mkdir': [os.path.join(config.DATA, 'berror')],
+            'copy': berror_list,
+        }
+        return berror_dict
+
+    @staticmethod
+    @logit(logger)
+    def _get_berror_dict_gsibec(config: Dict[str, Any]) -> Dict[str, List[str]]:
+        """Compile a dictionary of atm gsibec background error files to copy
+
+        This method will construct a dictionary of atm gsibec background error
+        files for global atm DA and return said dictionary to the parent
+
+        This is a private method and should not be accessed directly.
+
+        Parameters
+        ----------
+        config: Dict
+            a dictionary containing all of the configuration needed
+
+        Returns
+        ----------
+        berror_dict: Dict
+            a dictionary of atm gsibec background error files to copy for FileHandler
+        """
+        # GSI atm static-B needs namelist and coefficient files.
+        b_dir = os.path.join(config.HOMEgfs, 'fix', 'gdas', 'gsibec', config.CASE_ANL)
+        berror_list = []
+        for ftype in ['gfs_gsi_global.nml', 'gsi-coeffs-gfs-global.nc4']:
+            berror_list.append([
+                os.path.join(b_dir, ftype),
+                os.path.join(config.DATA, 'berror', ftype)
+            ])
+
+        # create dictionary of background error files to stage
+        berror_dict = {
+            'mkdir': [os.path.join(config.DATA, 'berror')],
+            'copy': berror_list,
+        }
+        return berror_dict
+
+    @logit(logger)
+    def jedi2fv3inc(self: Analysis) -> None:
+        """Generate UFS model readable analysis increment
+
+        This method writes a UFS DA atm increment in UFS model readable format.
+        This includes:
+        - write UFS-DA atm increments using variable names expected by UFS model
+        - compute and write delp increment
+        - compute and write hydrostatic delz increment
+
+        Please note that some of these steps are temporary and will be modified
+        once the modle is able to directly read atm increments.
+
+        """
+        # Select the atm guess file based on the analysis and background resolutions
+        # Fields from the atm guess are used to compute the delp and delz increments
+        case_anl = int(self.task_config.CASE_ANL[1:])
+        case = int(self.task_config.CASE[1:])
+
+        file = f"{self.task_config.GPREFIX}" + "atmf006" + f"{'' if case_anl == case else '.ensres'}" + ".nc"
+        atmges_fv3 = os.path.join(self.task_config.comin_ges_atm, file)
+
+        # Set the path/name to the input UFS-DA atm increment file (atminc_jedi)
+        # and the output UFS model atm increment file (atminc_fv3)
+        cdate = to_fv3time(self.task_config.current_cycle)
+        cdate_inc = cdate.replace('.', '_')
+        atminc_jedi = os.path.join(self.task_config.DATA, 'anl', f'atminc.{cdate_inc}z.nc4')
+        atminc_fv3 = os.path.join(self.task_config.COMOUTatmos, f"{self.task_config.CDUMP}.t{self.task_config.cyc:02d}z.atminc.nc")
+
+        # Reference the python script which does the actual work
+        incpy = os.path.join(self.task_config.HOMEgfs, 'ush/jediinc2fv3.py')
+
+        # Execute incpy to create the UFS model atm increment file
+        cmd = Executable(incpy)
+        cmd.add_default_arg(atmges_fv3)
+        cmd.add_default_arg(atminc_jedi)
+        cmd.add_default_arg(atminc_fv3)
+        logger.debug(f"Executing {cmd}")
+        cmd(output='stdout', error='stderr')
diff --git a/workflow/applications.py b/workflow/applications.py
index 34746e613e..82ef576ed9 100644
--- a/workflow/applications.py
+++ b/workflow/applications.py
@@ -107,7 +107,7 @@ def __init__(self, conf: Configuration) -> None:
         self.do_vrfy = _base.get('DO_VRFY', True)
         self.do_fit2obs = _base.get('DO_FIT2OBS', True)
         self.do_metp = _base.get('DO_METP', False)
-        self.do_jedivar = _base.get('DO_JEDIVAR', False)
+        self.do_jediatmvar = _base.get('DO_JEDIVAR', False)
         self.do_jediens = _base.get('DO_JEDIENS', False)
         self.do_jediocnvar = _base.get('DO_JEDIOCNVAR', False)
 
@@ -177,8 +177,8 @@ def _cycled_configs(self):
 
         configs = ['prep']
 
-        if self.do_jedivar:
-            configs += ['atmanalprep', 'atmanalrun', 'atmanalpost']
+        if self.do_jediatmvar:
+            configs += ['atmanlinit', 'atmanlrun', 'atmanlfinal']
         else:
             configs += ['anal', 'analdiag']
 
@@ -354,8 +354,8 @@ def _get_cycled_task_names(self):
 
         gdas_gfs_common_cleanup_tasks = ['arch']
 
-        if self.do_jedivar:
-            gdas_gfs_common_tasks_before_fcst += ['atmanalprep', 'atmanalrun', 'atmanalpost']
+        if self.do_jediatmvar:
+            gdas_gfs_common_tasks_before_fcst += ['atmanlinit', 'atmanlrun', 'atmanlfinal']
         else:
             gdas_gfs_common_tasks_before_fcst += ['anal']
 
@@ -384,7 +384,7 @@ def _get_cycled_task_names(self):
 
         # Collect all "gdas" cycle tasks
         gdas_tasks = gdas_gfs_common_tasks_before_fcst.copy()
-        if not self.do_jedivar:
+        if not self.do_jediatmvar:
             gdas_tasks += ['analdiag']
 
         if self.do_gldas:
diff --git a/workflow/rocoto/workflow_tasks.py b/workflow/rocoto/workflow_tasks.py
index 370f27f771..2cc50cde86 100644
--- a/workflow/rocoto/workflow_tasks.py
+++ b/workflow/rocoto/workflow_tasks.py
@@ -12,7 +12,7 @@ class Tasks:
     SERVICE_TASKS = ['arch', 'earc', 'getic']
     VALID_TASKS = ['aerosol_init', 'coupled_ic', 'getic', 'init',
                    'prep', 'anal', 'sfcanl', 'analcalc', 'analdiag', 'gldas', 'arch',
-                   'atmanalprep', 'atmanalrun', 'atmanalpost',
+                   'atmanlinit', 'atmanlrun', 'atmanlfinal',
                    'ocnanalprep', 'ocnanalbmat', 'ocnanalrun', 'ocnanalpost',
                    'earc', 'ecen', 'echgres', 'ediag', 'efcs',
                    'eobs', 'eomg', 'epos', 'esfc', 'eupd',
@@ -352,8 +352,8 @@ def anal(self):
     def sfcanl(self):
 
         deps = []
-        if self.app_config.do_jedivar:
-            dep_dict = {'type': 'task', 'name': f'{self.cdump}atmanalrun'}
+        if self.app_config.do_jediatmvar:
+            dep_dict = {'type': 'task', 'name': f'{self.cdump}atmanlfinal'}
         else:
             dep_dict = {'type': 'task', 'name': f'{self.cdump}anal'}
         deps.append(rocoto.add_dependency(dep_dict))
@@ -367,8 +367,8 @@ def sfcanl(self):
     def analcalc(self):
 
         deps = []
-        if self.app_config.do_jedivar:
-            dep_dict = {'type': 'task', 'name': f'{self.cdump}atmanalrun'}
+        if self.app_config.do_jediatmvar:
+            dep_dict = {'type': 'task', 'name': f'{self.cdump}atmanlfinal'}
         else:
             dep_dict = {'type': 'task', 'name': f'{self.cdump}anal'}
         deps.append(rocoto.add_dependency(dep_dict))
@@ -396,59 +396,45 @@ def analdiag(self):
 
         return task
 
-    def atmanalprep(self):
-
-        dump_suffix = self._base["DUMP_SUFFIX"]
-        gfs_cyc = self._base["gfs_cyc"]
-        dmpdir = self._base["DMPDIR"]
-        do_gfs_enkf = True if self.app_config.do_hybvar and 'gfs' in self.app_config.eupd_cdumps else False
-
+    def atmanlinit(self):
         deps = []
-        dep_dict = {'type': 'metatask', 'name': 'gdaspost', 'offset': '-06:00:00'}
-        deps.append(rocoto.add_dependency(dep_dict))
-        data = f'&ROTDIR;/gdas.@Y@m@d/@H/atmos/gdas.t@Hz.atmf009.nc'
-        dep_dict = {'type': 'data', 'data': data, 'offset': '-06:00:00'}
-        deps.append(rocoto.add_dependency(dep_dict))
-        data = f'{dmpdir}/{self.cdump}{dump_suffix}.@Y@m@d/@H/atmos/{self.cdump}.t@Hz.updated.status.tm00.bufr_d'
-        dep_dict = {'type': 'data', 'data': data}
+        dep_dict = {'type': 'task', 'name': f'{self.cdump}prep'}
         deps.append(rocoto.add_dependency(dep_dict))
-        dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
-
-        cycledef = self.cdump
-        if self.cdump in ['gfs'] and do_gfs_enkf and gfs_cyc != 4:
-            cycledef = 'gdas'
+        if self.app_config.do_hybvar:
+            dep_dict = {'type': 'metatask', 'name': 'enkfgdasepmn', 'offset': '-06:00:00'}
+            deps.append(rocoto.add_dependency(dep_dict))
+            dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
+        else:
+            dependencies = rocoto.create_dependency(dep=deps)
 
-        resources = self.get_resource('atmanalprep')
-        task = create_wf_task('atmanalprep', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies,
+        cycledef = "gdas"
+        resources = self.get_resource('atmanlinit')
+        task = create_wf_task('atmanlinit', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies,
                               cycledef=cycledef)
+
         return task
 
-    def atmanalrun(self):
+    def atmanlrun(self):
 
         deps = []
-        dep_dict = {'type': 'task', 'name': f'{self.cdump}atmanalprep'}
+        dep_dict = {'type': 'task', 'name': f'{self.cdump}atmanlinit'}
         deps.append(rocoto.add_dependency(dep_dict))
-        if self.app_config.do_hybvar:
-            dep_dict = {'type': 'metatask', 'name': 'enkfgdasepmn', 'offset': '-06:00:00'}
-            deps.append(rocoto.add_dependency(dep_dict))
-            dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
-        else:
-            dependencies = rocoto.create_dependency(dep=deps)
+        dependencies = rocoto.create_dependency(dep=deps)
 
-        resources = self.get_resource('atmanalrun')
-        task = create_wf_task('atmanalrun', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies)
+        resources = self.get_resource('atmanlrun')
+        task = create_wf_task('atmanlrun', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies)
 
         return task
 
-    def atmanalpost(self):
+    def atmanlfinal(self):
 
         deps = []
-        dep_dict = {'type': 'task', 'name': f'{self.cdump}atmanalrun'}
+        dep_dict = {'type': 'task', 'name': f'{self.cdump}atmanlrun'}
         deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
 
-        resources = self.get_resource('atmanalpost')
-        task = create_wf_task('atmanalpost', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies)
+        resources = self.get_resource('atmanlfinal')
+        task = create_wf_task('atmanlfinal', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies)
 
         return task