Merge pull request NOAA-EMC#26 from zhanglikate/feature/chem

Feature/chem
jkhender · Mar 31, 2021 · 87724f9 · 87724f9
2 parents 909c321 + 04975e7
commit 87724f9
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diff --git a/jobs/rocoto/calcinc.sh b/jobs/rocoto/calcinc.sh
@@ -2,7 +2,7 @@
 
 ###############################################################
 ## Abstract:
-## Calculate increment of Met. fields for FV3-CHEM
+## Create biomass burning emissions for FV3-CHEM
 ## RUN_ENVIR : runtime environment (emc | nco)
 ## HOMEgfs   : /full/path/to/workflow
 ## EXPDIR : /full/path/to/config/files
@@ -18,73 +18,24 @@ status=$?
 
 ###############################################################
 # Source relevant configs
-configs="base calcinc"
+configs="base"
 for config in $configs; do
     . $EXPDIR/config.${config}
     status=$?
     [[ $status -ne 0 ]] && exit $status
 done
-
-# Source machine runtime environment
-. $BASE_ENV/${machine}.env calcinc
-status=$?
-[[ $status -ne 0 ]] && exit $status
 ###############################################################
-CALCINCEXEC=${CALCINCEXEC:-$HOMEgfs/exec/calc_increment_ens.x}
-NTHREADS_CALCINC=${NTHREADS_CALCINC:-1}
-ncmd=${ncmd:-1}
-imp_physics=${imp_physics:-99}
-INCREMENTS_TO_ZERO=${INCREMENTS_TO_ZERO:-"'NONE'"}
-DO_CALC_INCREMENT=${DO_CALC_INCREMENT:-"YES"}
-export ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
-
-TMPDAY=`$NDATE -24 $PDY$cyc`
-HISDAY=`echo $TMPDAY | cut -c1-8`
-
-if [ $DO_CALC_INCREMENT = "YES" ]; then
-
-export DATA="$RUNDIR/$CDATE/$CDUMP"
-
-[[ ! -d $DATA ]] && mkdir -p $DATA
-
-cd $DATA
-mkdir -p calcinc
-cd calcinc
-
-#     $NLN sigf06 atmges_mem001 ; $NLN siganl atmanl_mem001 ; 
-
-  export OMP_NUM_THREADS=$NTHREADS_CALCINC
-  $NCP $CALCINCEXEC .
-  $NLN $OUTDIR/$CDUMP.$HISDAY/00/$CDUMP.t00z.atmf024.nemsio atmges_mem001
-  $NLN ../regrid/atmanl.$PDY$cyc atmanl_mem001
-  $NLN atminc.nc atminc_mem001
-  rm calc_increment.nml
-  cat > calc_increment.nml << EOF
-&setup
-  datapath = './'
-  analysis_filename = 'atmanl'
-  firstguess_filename = 'atmges'
-  increment_filename = 'atminc'
-  debug = .false.
-  nens = $ncmd
-  imp_physics = $imp_physics
-/
-&zeroinc
-  incvars_to_zero = $INCREMENTS_TO_ZERO
-/
-EOF
-  cat calc_increment.nml
+if [ $CDATE -ge "2021030100" ]; then
+    $HOMEgfs/jobs/rocoto/calcinc_gfsv16.sh
+else
+    $HOMEgfs/jobs/rocoto/calcinc_gfsv15.sh
+fi
+echo "error regrid $rc "
+     exit $rc
 
-  APRUN=$(eval echo $APRUN_CALCINC)
-  $APRUN $(basename $CALCINCEXEC)
-  rc=$?
 
-  export ERR=$rc
-  export err=$ERR
-  $ERRSCRIPT || exit 3
-fi
-
 ###############################################################
 
 ###############################################################
 # Exit cleanly
+
diff --git a/jobs/rocoto/calcinc.sh_rt → jobs/rocoto/calcinc_gfsv15.sh b/jobs/rocoto/calcinc.sh_rt → jobs/rocoto/calcinc_gfsv15.sh
diff --git a/jobs/rocoto/calcinc_gfsv15.sh-retro b/jobs/rocoto/calcinc_gfsv15.sh-retro
@@ -0,0 +1,90 @@
+#!/bin/ksh -x
+
+###############################################################
+## Abstract:
+## Calculate increment of Met. fields for FV3-CHEM
+## RUN_ENVIR : runtime environment (emc | nco)
+## HOMEgfs   : /full/path/to/workflow
+## EXPDIR : /full/path/to/config/files
+## CDATE  : current date (YYYYMMDDHH)
+## CDUMP  : cycle name (gdas / gfs)
+## PDY    : current date (YYYYMMDD)
+## cyc    : current cycle (HH)
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# Source relevant configs
+configs="base calcinc"
+for config in $configs; do
+    . $EXPDIR/config.${config}
+    status=$?
+    [[ $status -ne 0 ]] && exit $status
+done
+
+# Source machine runtime environment
+. $BASE_ENV/${machine}.env calcinc
+status=$?
+[[ $status -ne 0 ]] && exit $status
+###############################################################
+CALCINCEXEC=${CALCINCEXEC:-$HOMEgfs/exec/calc_increment_ens.x}
+NTHREADS_CALCINC=${NTHREADS_CALCINC:-1}
+ncmd=${ncmd:-1}
+imp_physics=${imp_physics:-99}
+INCREMENTS_TO_ZERO=${INCREMENTS_TO_ZERO:-"'NONE'"}
+DO_CALC_INCREMENT=${DO_CALC_INCREMENT:-"YES"}
+export ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
+
+TMPDAY=`$NDATE -24 $PDY$cyc`
+HISDAY=`echo $TMPDAY | cut -c1-8`
+
+if [ $DO_CALC_INCREMENT = "YES" ]; then
+
+export DATA="$RUNDIR/$CDATE/$CDUMP"
+
+[[ ! -d $DATA ]] && mkdir -p $DATA
+
+cd $DATA
+mkdir -p calcinc
+cd calcinc
+
+#     $NLN sigf06 atmges_mem001 ; $NLN siganl atmanl_mem001 ; 
+
+  export OMP_NUM_THREADS=$NTHREADS_CALCINC
+  $NCP $CALCINCEXEC .
+  $NLN $OUTDIR/$CDUMP.$HISDAY/00/$CDUMP.t00z.atmf024.nemsio atmges_mem001
+  $NLN ../regrid/atmanl.$PDY$cyc atmanl_mem001
+  $NLN atminc.nc atminc_mem001
+  rm calc_increment.nml
+  cat > calc_increment.nml << EOF
+&setup
+  datapath = './'
+  analysis_filename = 'atmanl'
+  firstguess_filename = 'atmges'
+  increment_filename = 'atminc'
+  debug = .false.
+  nens = $ncmd
+  imp_physics = $imp_physics
+/
+&zeroinc
+  incvars_to_zero = $INCREMENTS_TO_ZERO
+/
+EOF
+  cat calc_increment.nml
+
+  APRUN=$(eval echo $APRUN_CALCINC)
+  $APRUN $(basename $CALCINCEXEC)
+  rc=$?
+
+  export ERR=$rc
+  export err=$ERR
+  $ERRSCRIPT || exit 3
+fi
+
+###############################################################
+
+###############################################################
+# Exit cleanly
diff --git a/jobs/rocoto/calcinc_gfsv16.sh b/jobs/rocoto/calcinc_gfsv16.sh
@@ -0,0 +1,93 @@
+#!/bin/ksh -x
+
+###############################################################
+## Abstract:
+## Calculate increment of Met. fields for FV3-CHEM
+## RUN_ENVIR : runtime environment (emc | nco)
+## HOMEgfs   : /full/path/to/workflow
+## EXPDIR : /full/path/to/config/files
+## CDATE  : current date (YYYYMMDDHH)
+## CDUMP  : cycle name (gdas / gfs)
+## PDY    : current date (YYYYMMDD)
+## cyc    : current cycle (HH)
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs16_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# Source relevant configs
+configs="base calcinc"
+for config in $configs; do
+    . $EXPDIR/config.${config}
+    status=$?
+    [[ $status -ne 0 ]] && exit $status
+done
+
+# Source machine runtime environment
+. $BASE_ENV/${machine}.env calcinc
+status=$?
+[[ $status -ne 0 ]] && exit $status
+###############################################################
+#CALCINCEXEC=${CALCINCEXEC:-$HOMEgfs/exec/calc_increment_ens_gsdchem.x}
+CALCINCEXEC=${CALCINCEXEC:-$HOMEgfs/exec/calc_increment_ens_ncio.x}
+NTHREADS_CALCINC=${NTHREADS_CALCINC:-1}
+ncmd=${ncmd:-1}
+imp_physics=${imp_physics:-99}
+INCREMENTS_TO_ZERO=${INCREMENTS_TO_ZERO:-"'NONE'"}
+DO_CALC_INCREMENT=${DO_CALC_INCREMENT:-"YES"}
+export ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
+
+TMPDAY=`$NDATE -24 $PDY$cyc`
+HISDAY=`echo $TMPDAY | cut -c1-8`
+
+#convert nemsio to netcdf
+#$EXECgfs/nemsioatm2nc $OUTDIR/$CDUMP.$HISDAY/00/$CDUMP.t00z.atmf024.nemsio $CDUMP.t00z.atmf024.nc
+
+if [ $DO_CALC_INCREMENT = "YES" ]; then
+
+cd $DATA
+mkdir -p calcinc
+cd calcinc
+
+#convert nemsio to netcdf
+$EXECgfs/nemsioatm2nc $OUTDIR/$CDUMP.$HISDAY/00/$CDUMP.t00z.atmf024.nemsio $CDUMP.t00z.atmf024.nc
+#     $NLN sigf06 atmges_mem001 ; $NLN siganl atmanl_mem001 ; 
+
+  export OMP_NUM_THREADS=$NTHREADS_CALCINC
+  $NCP $CALCINCEXEC .
+#  $NLN $OUTDIR/$CDUMP.$HISDAY/00/$CDUMP.t00z.atmf024.nemsio atmges_mem001
+  $NLN $CDUMP.t00z.atmf024.nc atmges_mem001  
+  $NLN ../regrid/atmanl.$PDY$cyc.nc atmanl_mem001  
+  $NLN atminc.nc atminc_mem001
+  rm calc_increment.nml
+  cat > calc_increment.nml << EOF
+&setup
+  datapath = './'
+  analysis_filename = 'atmanl'
+  firstguess_filename = 'atmges'
+  increment_filename = 'atminc'
+  debug = .false.
+  nens = $ncmd
+  imp_physics = $imp_physics
+/
+&zeroinc
+  incvars_to_zero = $INCREMENTS_TO_ZERO
+/
+EOF
+  cat calc_increment.nml
+
+  APRUN=$(eval echo $APRUN_CALCINC)
+  $APRUN $(basename $CALCINCEXEC)
+  rc=$?
+
+  export ERR=$rc
+  export err=$ERR
+  $ERRSCRIPT || exit 3
+fi
+
+###############################################################
+
+###############################################################
+# Exit cleanly
diff --git a/jobs/rocoto/fv3ic.sh b/jobs/rocoto/fv3ic.sh
@@ -2,16 +2,14 @@
 
 ###############################################################
 ## Abstract:
-## Create FV3 initial conditions from GFS intitial conditions
+## Create biomass burning emissions for FV3-CHEM
 ## RUN_ENVIR : runtime environment (emc | nco)
 ## HOMEgfs   : /full/path/to/workflow
 ## EXPDIR : /full/path/to/config/files
 ## CDATE  : current date (YYYYMMDDHH)
 ## CDUMP  : cycle name (gdas / gfs)
 ## PDY    : current date (YYYYMMDD)
 ## cyc    : current cycle (HH)
-###############################################################
-
 ###############################################################
 # Source FV3GFS workflow modules
 . $HOMEgfs/ush/load_fv3gfs_modules.sh
@@ -20,47 +18,24 @@ status=$?
 
 ###############################################################
 # Source relevant configs
-configs="base fv3ic"
+configs="base"
 for config in $configs; do
     . $EXPDIR/config.${config}
     status=$?
     [[ $status -ne 0 ]] && exit $status
 done
-
 ###############################################################
-# Source machine runtime environment
-. $BASE_ENV/${machine}.env fv3ic
-status=$?
-[[ $status -ne 0 ]] && exit $status
-
-# Temporary runtime directory
-export DATA="$RUNDIR/$CDATE/$CDUMP/fv3ic$$"
-[[ -d $DATA ]] && rm -rf $DATA
-
-# Input GFS initial condition directory
-export INIDIR="$ICSDIR/$CDATE/$CDUMP/$CDUMP.$PDY/$cyc"
-
-# Output FV3 initial condition directory
-export OUTDIR="$ICSDIR/$CDATE/$CDUMP/$CASE/INPUT"
-
-export OMP_NUM_THREADS_CH=$NTHREADS_CHGRES
-export APRUNC=$APRUN_CHGRES
-
-# Call global_chgres_driver.sh
-$HOMEgfs/ush/global_chgres_driver.sh
-status=$?
-if [ $status -ne 0 ]; then
-    echo "global_chgres_driver.sh returned with a non-zero exit code, ABORT!"
-    exit $status
+if [ $CDATE -ge "2021030100" ]; then
+    $HOMEgfs/jobs/rocoto/fv3ic_gfsv16.sh
+else
+    $HOMEgfs/jobs/rocoto/fv3ic_gfsv15.sh
 fi
+echo "error fv3ic $rc "
+     exit $rc
 
-# Stage the FV3 initial conditions to ROTDIR
-COMOUT="$ROTDIR/$CDUMP.$PDY/$cyc"
-[[ ! -d $COMOUT ]] && mkdir -p $COMOUT
-cd $COMOUT || exit 99
-rm -rf INPUT
-$NLN $OUTDIR .
+
+###############################################################
 
 ###############################################################
 # Exit cleanly
-exit 0
+