added functionality to process a land only case with active glc - no glc yet

postproc/README.md

@@ -3,7 +3,7 @@
 This directory holds subdirectories with scripts that will postprocess model data for use in creating the plots and data used by LIVVkit. There are also scripts to processed observation data useful for any model analysis.
 
 These script environments take raw output from either a stand alone ice sheet model (e.g. cism-albany)
-or a coupled climate model (e.g. cesm1p2, e3sm (in beta testing))
+or a coupled climate model (e.g. cesm1p2, e3sm1p0 (in beta testing))
 
 To enable or update the scripts to work on a given machine, alter the main scripts in the target model 
 subdirectory to load the necessary software.

postproc/e3sm1p0/atm_obs.sh

@@ -18,21 +18,21 @@ for dataset in "${datasets[@]}"
 do
 
 echo "add mask and area variables to annualized daily averages"
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_ANN_climo.nc
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_DJF_climo.nc
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_JJA_climo.nc
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_01_climo.nc
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_02_climo.nc
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_03_climo.nc
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_04_climo.nc
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_05_climo.nc
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_06_climo.nc
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_07_climo.nc
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_08_climo.nc
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_09_climo.nc
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_10_climo.nc
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_11_climo.nc
-ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_12_climo.nc
+ncks -A -v gris_mask,area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_ANN_climo.nc
+ncks -A -v gris_mask,gris_area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_DJF_climo.nc
+ncks -A -v gris_mask,area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_JJA_climo.nc
+ncks -A -v gris_mask,area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_01_climo.nc
+ncks -A -v gris_mask,area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_02_climo.nc
+ncks -A -v gris_mask,area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_03_climo.nc
+ncks -A -v gris_mask,area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_04_climo.nc
+ncks -A -v gris_mask,area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_05_climo.nc
+ncks -A -v gris_mask,area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_06_climo.nc
+ncks -A -v gris_mask,area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_07_climo.nc
+ncks -A -v gris_mask,area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_08_climo.nc
+ncks -A -v gris_mask,area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_09_climo.nc
+ncks -A -v gris_mask,area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_10_climo.nc
+ncks -A -v gris_mask,area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_11_climo.nc
+ncks -A -v gris_mask,area,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_12_climo.nc
 
 echo "average over ice sheet region for cloud data"
 ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_ANN_climo.nc $obspath/${dataset}_ANN_aavg_climo.nc 

postproc/e3sm1p0/lnd.sh

@@ -6,7 +6,7 @@ if [ "$postprocess" = "true" ]; then
 
 # regridding step to regrid to lat lon, currently regrids all years even if not requested
 # this is not needed unless a mask file is needed in the sim output AND analysis of \hist, else regrid after climos made
-if [ "$version" == "e3sm" ]; then
+if [ "$version" == "e3sm_old" ]; then
 
 #uncomment if you have a new mask file with a time dimension
 #ncwa -a -time $outpath/masks/mask_ne30np4_lnd.nc $outpath/masks/mask_ne30np4_lnd_notime.nc 
@@ -40,31 +40,18 @@ if [ "$version" == "cesm1" ]; then
 h0lnd_path=$outpath/lnd/climos
 
 echo "average land monthly climos over ice sheet region"
-ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/lnd/climos/${case}_ANN_climo.nc $outpath/lnd/climos/${case}_ANN_aavg_climo.nc
-ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/lnd/climos/${case}_JJA_climo.nc $outpath/lnd/climos/${case}_JJA_aavg_climo.nc
-ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/lnd/climos/${case}_DJF_climo.nc $outpath/lnd/climos/${case}_DJF_aavg_climo.nc
+ncwa -O -a lat,lon -w gris_area -B "gris_mask == 1" $outpath/lnd/climos/${case}_ANN_climo.nc $outpath/lnd/climos/${case}_ANN_aavg_climo.nc
+ncwa -O -a lat,lon -w gris_area -B "gris_mask == 1" $outpath/lnd/climos/${case}_JJA_climo.nc $outpath/lnd/climos/${case}_JJA_aavg_climo.nc
+ncwa -O -a lat,lon -w gris_area -B "gris_mask == 1" $outpath/lnd/climos/${case}_DJF_climo.nc $outpath/lnd/climos/${case}_DJF_aavg_climo.nc
 
 elif [ "$version" == "e3sm" ]; then
 
-# only needed if no mask in sim output
-#for fl in $outpath/lnd/climos/*.nc; do
-#echo "add mask in original grid to climos in $fl"
-#ncks -A -C -v gris_mask $mask_file $fl
-#done
-
-#echo " remapping these land climo files"
-#climos_path=$outpath/lnd/climo_regrid
-#mkdir -p "$climos_path"
-
-#ls $outpath/lnd/climos/*_climo* 
-#ls $outpath/lnd/climos/*_climo* | ncremap -m $map_file -O $climos_path
-
 climos_path=$outpath/lnd/climos
 
 echo "average land monthly climos over ice sheet region"
-ncwa -O -a lat,lon -w area -B "gris_mask == 1" $climos_path/${case}_ANN_climo.nc $climos_path/${case}_ANN_aavg_climo.nc
-ncwa -O -a lat,lon -w area -B "gris_mask == 1" $climos_path/${case}_JJA_climo.nc $climos_path/${case}_JJA_aavg_climo.nc
-ncwa -O -a lat,lon -w area -B "gris_mask == 1" $climos_path/${case}_DJF_climo.nc $climos_path/${case}_DJF_aavg_climo.nc
+ncwa -O -a lat,lon -w gris_area -B "gris_mask == 1" $climos_path/${case}_ANN_climo.nc $climos_path/${case}_ANN_aavg_climo.nc
+ncwa -O -a lat,lon -w gris_area -B "gris_mask == 1" $climos_path/${case}_JJA_climo.nc $climos_path/${case}_JJA_aavg_climo.nc
+ncwa -O -a lat,lon -w gris_area -B "gris_mask == 1" $climos_path/${case}_DJF_climo.nc $climos_path/${case}_DJF_aavg_climo.nc
 
 fi
 

postproc/e3sm1p0/lnd_obs.sh

@@ -14,7 +14,8 @@ hist_path=$obspath/$casename
 echo "$hist_path"
 lndpath=$hist_path/climos
 outseries=$hist_path/tseries
-mask_file=RACMO23_masks_ZGRN11_latlon.nc 
+#mask_file=RACMO23_masks_ZGRN11_latlon.nc 
+mask_file=RACMO23_masks_ZGRN11.nc 
 gris_pcnt_file=greenland_percent_coverage_latlon.nc
 
 for ivar in "${var[@]}"

postproc/e3sm1p0/main_e3sm.sh

@@ -11,6 +11,7 @@
 # total area of GrIS in model is 1.719e6
 
 postprocess=true
+postprocess_obs=true
 make_plots=false
 
 if [[ $(hostname -s) = rhea* ]]; then
@@ -26,51 +27,35 @@ if [[ $(hostname -s) = rhea* ]]; then
 	outpath=/lustre/atlas1/$project/world-shared/$USER/$case/postproc
 # compute center settings
 	obspath=/lustre/atlas1/cli115/world-shared/4ue/obs_data
-	area_file=/lustre/atlas1/$project/world-shared/$USER/surfdata_0.9x1.25_simyr1850_c110725.nc
 	map_file=/ccs/home/zender/data/maps/map_ne30np4_to_fv129x256_aave.20150901.nc
 	mask_file=/lustre/atlas1/$project/world-shared/4ue/$case/postproc/masks/mask_ne30np4_notime.nc
 	obs_mask_file=/lustre/atlas1/$project/world-shared/4ue/$case/postproc/masks/E3SMv1_ne30.clm2.gris_mask.nc
-	postprocess_obs=false
 
 elif [[ $(hostname -s) = cori* ]]; then
 #user settings
 	project=piscees  
-	case=20180129.DECKv1b_piControl.ne30_oEC.edison
-	year_start=0470
-	year_end=0498
+	case=IGCLM45_MLI_titan
+	year_start=0002
+	year_end=0006
 #need to specify prebase if using data created by someone else until masks are written with sim output
-	prebase=/global/cscratch1/sd/golaz/ACME_simulations
-#	prebase=/global/cscratch1/sd/dcomeau/acme_scratch/edison/archive/$case
-	base=/global/cscratch1/sd/$USER/acme_scratch/edison
+	base=/global/cscratch1/sd/$USER/acme_scratch/titan
 	path=$base/$case
-	outpath=/global/cscratch1/sd/$USER/$case/postproc
-#	outpath=/global/cscratch1/sd/$USER/acme_scratch/edison/$case/postproc
+#	outpath=/global/cscratch1/sd/$USER/$case/postproc
+	outpath=/global/cscratch1/sd/$USER/acme_scratch/titan/$case/postproc
 # compute center settings
 	obspath=/project/projectdirs/piscees/postproc/obs_data
 	area_file=/project/projectdirs/piscees/postproc/surfdata_0.9x1.25_simyr1850_c110725.nc
 	map_file=/project/projectdirs/piscees/postproc/map_ne30np4_to_fv129x256_aave.20150901.nc
 	mask_file=/project/projectdirs/piscees/postproc/mask_ne30np4_notime.nc
 	obs_mask_file=/project/projectdirs/piscees/postproc/E3SMv1_ne30.clm2.gris_mask.nc
-	postprocess_obs=false
 else
   echo "machine not recognized"
 fi
 
-# this copy to local dir can be removed once masks are written with sim output
-#if test -d $prebase/$case; then
-#	echo "Creating user owned target path for output data"
-#	mkdir -p $base/$case/atm/hist
-#	mkdir -p $base/$case/lnd/hist
-#	cp -uvr $prebase/$case/archive/atm/hist/*.04* $path/atm/hist
-#	cp -uvr $prebase/$case/archive/lnd/hist/*.04* $path/atm/hist
-#else
-#	exit 
-#fi
-
 version=e3sm
 atm_vars=("PSL" "CLDLOW" "CLDHGH" "CLDMED" "CLDTOT" "TREFHT" "TS" "TSMX" "TSMN" "PRECC" "PRECL")
-lnd_h0_vars=("FSDS" "QRUNOFF" "QSOIL" "TSA" "RAIN" "SNOW" "FIRA" "FLDS" "FSH" "QSNOMELT")
-#glc_vars=("acab" "thk")
+lnd_h0_vars=("QICE" "QICE_FRZ" "QICE_MELT" "FSDS" "QRUNOFF" "QSOIL" "TSA" "RAIN" "SNOW" "FIRA" "FLDS" "FSH" "QSNOMELT")
+glc_vars=("acab" "thk")
 
 # END OF USER INPUT SECTION
 
@@ -149,32 +134,35 @@ fi
 
 if [ "$postprocess_obs" = "true" ]; then
 
-#if test -a $outpath/masks/${case}.$lnd.gris_mask.nc; then
-#        echo "already created gris_mask and area file, moving on"
-#else
-#        echo "gris_mask file does not exist, creating"
-#
-#	mkdir -p $outpath/masks
-#       	ncks -O -v gris_mask,area $path/lnd/hist/${case}.${lnd}.h0.${year_start}-01.nc $outpath/masks/${case}.${lnd}.gris_mask_time.nc 
-#       	ncwa -a time $outpath/masks/${case}.${lnd}.gris_mask_time.nc $outpath/masks/${case}.${lnd}.gris_mask.nc 
-#
-#fi # if mask file needs to be created
+if test -a $outpath/masks/${case}.$lnd.gris_mask.nc; then
+        echo "already created gris_mask and area file, moving on"
+else
+        echo "gris_mask file does not exist, creating"
+
+	mkdir -p $outpath/masks
+      	ncks -O -v gris_mask,area $path/lnd/hist/${case}.${lnd}.h0.${year_start}-01.nc $outpath/masks/${case}.${lnd}.gris_mask_time.nc 
+       	ncwa -a time $outpath/masks/${case}.${lnd}.gris_mask_time.nc $outpath/masks/${case}.${lnd}.gris_mask.nc 
+
+fi # if mask file needs to be created for use with obs data
 
 echo "process and remap cloud obs"
 . atm_obs.sh 
 echo "process RACMO"
 . lnd_obs.sh 
 
-./remap_RACMO_to_CESM2_inline.sh
+. remap_RACMO_to_E3SM.sh
 
 fi
 
-echo "executing post processing of atm data for validation"
-. atm.sh 
+#echo "executing post processing of atm data for validation"
+#. atm.sh 
 
 echo "executing post processing of lnd data for validation"
 . lnd.sh  
 
+#echo "executing post processing of lnd data for validation"
+#. glc.sh
+
 
 if [ "$make_plots" = "true" ]; then
 echo "make the atmosphere plots"

postproc/e3sm1p0/remap_RACMO_to_E3SM.sh

+#!/bin/bash
+
+# make sure top level call of this script loads ncl and nco/4.6.6 to have weight-generation command ESMF_RegridWeightGen used in ncremap
+
+#run a check, do you have the software to perform the postprocessing?
+#if [[ $(hostname -s) = rhea* ]]; then
+#if [[ $(hostname -s) = titan* ]]; then
+
+#module unload PE-intel # CSZ
+#module load PE-gnu # CSZ
+#module add gsl hdf5
+#module load ncl/6.1.0
+
+#export LD_LIBRARY_PATH='/sw/redhat6/netcdf/4.3.3.1/rhel6.6_gcc4.8.2--with-dap+hdf4/lib:/sw/redhat6/szip/2.1/rhel6.6_gnu4.8.2/lib':${LD_LIBRARY_PATH}
+
+#export PATH='/sw/redhat6/netcdf/4.3.3.1/rhel6.6_gcc4.8.2--with-dap+hdf4/bin':${PATH}
+
+#export LD_LIBRARY_PATH="~zender/lib_rhea":${LD_LIBRARY_PATH}
+#export PATH="~zender/bin_rhea":${PATH}
+
+#module load nco
+#module unload nco/4.6.5
+
+#else
+#  echo "machine not recognized, make sure your path: 
+#        $PATH 
+#        points to a version of nco/4.6.6 or later"
+#
+#fi
+
+#project=$project
+obs_case=racmo23_GRN_monthly
+#case=IGCLM45_MLI_titan
+#path=/lustre/atlas1/$project/world-shared/$USER/$case
+#obspath=/lustre/atlas1/$project/world-shared/$USER/$obs_case
+
+#run a check, is the requested data directory for reampping there?
+#if test -d $path/atm/hist; then
+#        echo "Directory $path/atm/hist exists"
+#else
+#        echo "Target directory $path/atm/hist does not exist"
+#        exit
+#fi
+
+echo $path
+echo $obspath
+
+mkdir -p $obspath/remapped_racmo
+
+seasons=("DJF" "JJA" "ANN")
+field_names=("swsn" "swsd" "lwsn" "lwsd" "senf" "latf" "t2m" "alb" "smb")
+
+for seas in "${seasons[@]}"
+do
+
+for rvar in "${field_names[@]}"
+do
+
+# CHECK whether I need to point to file we will be comparing to
+e3smfile=$path/lnd/hist/${case}.clm2.h0.${year_end}-01.nc
+obsfile=$obspath/${obs_case}/climos/${obs_case}.${rvar}.1980-1999.${seas}.nc 
+tmpfile=$obspath/${obs_case}/remapped_racmo/racmo23_with_latlon_tmpfile.nc
+ReMapFile=$obspath/${obs_case}/remapped_racmo/racmo23_GRN_monthly.${rvar}.1980-1999.remap2e3sm.${seas}.nc 
+
+#------- RACMO lat and lon data ---
+racmolatlon=$obspath/${obs_case}/RACMO23_masks_ZGRN11.nc
+
+## PROCEDURE: remap racmo to have same size as e3sm
+##-first, append lat and lon from racmolatlon file to racmofile
+ncks -C -v lat,lon $racmolatlon -O $tmpfile
+ncks -C -v ${rvar} $obsfile -A $tmpfile
+
+#-- change interpolation algorithm in -a switch causes value difference
+ncremap -i $tmpfile -V TREFHT -a bilinear -d $e3smfile -v ${rvar} -m $obspath/remapped_racmo/RACMO_to_CESM_remap_bilin.nc -o $ReMapFile
+
+done # variables
+done #seasons

postproc/e3sm1p0/tseries_lnd_h0.sh

@@ -7,7 +7,7 @@ echo "make time series of monthly average lnd data for $ivar"
 if [ "$version" == "cesm1" ]; then
 ncrcat -O -v mcdate,time,$ivar $h0lnd_path/${case}.${lnd}.${freq}.*.nc $outpath/lnd/tseries/$case.$lnd.${freq}.$ivar.nc
 elif [ "$version" == "e3sm" ]; then
-ncrcat -O -v mcdate,time,area,$ivar $h0lnd_path/${case}.${lnd}.${freq}.*.nc $outpath/lnd/tseries/$case.$lnd.${freq}.$ivar.nc
+ncrcat -O -v mcdate,time,gris_area,gris_mask,$ivar $h0lnd_path/${case}.${lnd}.${freq}.*.nc $outpath/lnd/tseries/$case.$lnd.${freq}.$ivar.nc
 fi
 
 if test -a $outpath/lnd/tseries/${case}.$lnd.${freq}.$ivar.nc; then
@@ -28,7 +28,7 @@ ncra --mro -O -h -d time,,,12,12 $outpath/lnd/tseries/$case.$lnd.${freq}.$ivar.n
 if [ "$version" == "cesm1" ]; then
 
  echo "add mask and area variables to yearly averaged lnd data for $ivar"
- ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/lnd/tseries/$case.$lnd.${freq}.yrly.$ivar.nc 
+ ncks -A -v gris_mask,gris_area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/lnd/tseries/$case.$lnd.${freq}.yrly.$ivar.nc 
  ncks -A -v PCT_GLC_ICESHEET $base/surfdata_0.9x1.25_lat_lon_simyr1850_c180218.nc $outpath/lnd/tseries/$case.$lnd.${freq}.yrly.$ivar.nc 
  
  ncap2 -O -s 'areaice=PCT_GLC_ICESHEET*0.01*area' $outpath/lnd/tseries/$case.$lnd.${freq}.yrly.$ivar.nc -o $outpath/lnd/tseries/$case.$lnd.${freq}.yrly_ai.$ivar.nc 
@@ -46,12 +46,12 @@ fi
 
 elif [ "$version" == "e3sm" ]; then
 
-for fl in $outpath/lnd/tseries/*clm2.h0.yrly*; do
-ncks -A -C -v gris_mask $mask_file $fl
-done
+#for fl in $outpath/lnd/tseries/*clm2.h0.yrly*; do
+#ncks -A -C -v gris_mask $mask_file $fl
+#done
 
 echo "average over ice sheet region for yearly averaged lnd data for $ivar"
-ncwa -O -a lndgrid -w area -B "gris_mask == 1" $outpath/lnd/tseries/$case.$lnd.${freq}.yrly.$ivar.nc $outpath/lnd/tseries/$case.$lnd.aavg.${freq}.yrly.$ivar.nc
+ncwa -O -a lat,lon -w gris_area -B "gris_mask == 1" $outpath/lnd/tseries/$case.$lnd.${freq}.yrly.$ivar.nc $outpath/lnd/tseries/$case.$lnd.aavg.${freq}.yrly.$ivar.nc
 
 if test -a $outpath/lnd/tseries/${case}.$lnd.aavg.${freq}.yrly.$ivar.nc; then
         echo "Global avg yearly masked $lnd averages of $ivar made"

postproc/e3sm1p0_pre_smb/atm.sh

+#!/bin/bash
+
+# atmosphere
+
+if [ "$postprocess" = "true" ]; then
+
+# regridding step to regrid to lat lon, currently regrids all years even if not requested
+# this block can be removed once mask files are included in sim output
+if [ "$version" == "e3sm" ]; then
+
+#in the event you get a mask file with a time dimension, remove it first
+#ncwa -a -time $outpath/masks/mask_ne30np4.nc tmp.nc 
+#ncks -x -v time tmp.nc $outpath/masks/mask_ne30np4_notime.nc
+
+for fl in $path/atm/hist/*h0*; do
+echo "first add mask in original grid to monthly atm output in $fl"
+ncks --no_tmp_fl -A -C -v gris_mask $mask_file $fl 
+done
+fi
+
+h0atm_path=$outpath/atm/hist_regrid
+mkdir -p "$h0atm_path"
+ls $path/atm/hist/*h0* | ncremap -m $map_file -O $h0atm_path
+
+else
+h0atm_path=$path/atm/hist
+
+fi
+
+#run a check, is the requested data directory there?
+if test -d $h0atm_path; then
+        echo "Directory $h0atm_path exists"
+else
+        echo "Target directory $h0atm_path does not exist, you prob need to activate remapping"
+        exit
+fi
+
+echo "make atm climos"
+mkdir -p $outpath/atm/climos
+ncclimo -a sdd -c ${case} -s ${year_start} -e ${year_end} -m ${atm} -i ${h0atm_path} -o ${outpath}/atm/climos
+
+if test -a $outpath/atm/climos/${case}_ANN_climo.nc; then
+      	echo "File $outpath/atm/climos/${case}_ANN_climo.nc exists"
+else
+      	echo "File $outpath/atm/climos/${case}_ANN_climo.nc does not exist"
+	exit
+fi
+
+if [ "$version" == "cesm1" ]; then
+echo "add mask and area variables to monthly atm climos"
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_ANN_climo.nc
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_DJF_climo.nc
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_JJA_climo.nc
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_01_climo.nc
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_02_climo.nc
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_03_climo.nc
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_04_climo.nc
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_05_climo.nc
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_06_climo.nc
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_07_climo.nc
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_08_climo.nc
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_09_climo.nc
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_10_climo.nc
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_11_climo.nc
+ncks -A -v gris_mask,area $outpath/masks/$case.$lnd.gris_mask.nc $outpath/atm/climos/${case}_12_climo.nc
+fi
+
+echo "average over ice sheet region of atm climos "
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_ANN_climo.nc $outpath/atm/climos/${case}_ANN_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_JJA_climo.nc $outpath/atm/climos/${case}_JJA_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_DJF_climo.nc $outpath/atm/climos/${case}_DJF_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_01_climo.nc $outpath/atm/climos/${case}_01_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_02_climo.nc $outpath/atm/climos/${case}_02_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_03_climo.nc $outpath/atm/climos/${case}_03_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_04_climo.nc $outpath/atm/climos/${case}_04_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_05_climo.nc $outpath/atm/climos/${case}_05_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_06_climo.nc $outpath/atm/climos/${case}_06_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_07_climo.nc $outpath/atm/climos/${case}_07_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_08_climo.nc $outpath/atm/climos/${case}_08_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_09_climo.nc $outpath/atm/climos/${case}_09_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_10_climo.nc $outpath/atm/climos/${case}_10_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_11_climo.nc $outpath/atm/climos/${case}_11_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $outpath/atm/climos/${case}_12_climo.nc $outpath/atm/climos/${case}_12_aavg_climo.nc 
+
+echo "make yearly time series for atm h0 data"
+mkdir -p $outpath/atm/tseries
+
+for ivar in "${atm_vars[@]}"
+do
+
+. tseries_atm_h0.sh 
+
+done
+
+        echo "ATM POSTPROCESSING COMPLETE "
+        echo " "
+
+fi # to postprocess or not
+

postproc/e3sm1p0_pre_smb/atm_obs.sh

+#!/bin/bash
+
+# atmosphere obs data processing
+
+datasets=("CLOUDSAT" "ISCCP")
+
+for dataset in "${datasets[@]}"
+do
+
+# to get this working, need to apply to all climos and using cesm1/e3sm specific mask file that has already been created
+echo "remapping ${dataset} climos onto target grid"
+file_w_data_on_source_grid=$outpath/masks/${case}.clm2.gris_mask.nc
+ncremap -i $file_w_data_on_source_grid -V CLDTOT -a bilinear -d $obspath/${dataset}_01_climo.nc -v gris_mask -o $obspath/$case.gris_mask_${dataset}_grid.nc
+
+done
+
+for dataset in "${datasets[@]}"
+do
+
+echo "add mask and area variables to annualized daily averages"
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_ANN_climo.nc
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_DJF_climo.nc
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_JJA_climo.nc
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_01_climo.nc
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_02_climo.nc
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_03_climo.nc
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_04_climo.nc
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_05_climo.nc
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_06_climo.nc
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_07_climo.nc
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_08_climo.nc
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_09_climo.nc
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_10_climo.nc
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_11_climo.nc
+ncks -A -v gris_mask,gw $obspath/$case.gris_mask_${dataset}_grid.nc $obspath/${dataset}_12_climo.nc
+
+echo "average over ice sheet region for cloud data"
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_ANN_climo.nc $obspath/${dataset}_ANN_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_JJA_climo.nc $obspath/${dataset}_JJA_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_DJF_climo.nc $obspath/${dataset}_DJF_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_01_climo.nc $obspath/${dataset}_01_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_02_climo.nc $obspath/${dataset}_02_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_03_climo.nc $obspath/${dataset}_03_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_04_climo.nc $obspath/${dataset}_04_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_05_climo.nc $obspath/${dataset}_05_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_06_climo.nc $obspath/${dataset}_06_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_07_climo.nc $obspath/${dataset}_07_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_08_climo.nc $obspath/${dataset}_08_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_09_climo.nc $obspath/${dataset}_09_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_10_climo.nc $obspath/${dataset}_10_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_11_climo.nc $obspath/${dataset}_11_aavg_climo.nc 
+ncwa -O -a lat,lon -w area -B "gris_mask == 1" $obspath/${dataset}_12_climo.nc $obspath/${dataset}_12_aavg_climo.nc 
+
+done
+

postproc/e3sm1p0_pre_smb/e3sm_rad_aavg.py

+##On my laptop I installed PyNGL and PyNIO to use Nio and Ngl module for reading *.nc file and for contour plot
+##On titan, I did not install PyNGL and PyNIO, so import Dataset from netCDF4 to read *.nc file
+##probably, I will the following command for contourplot in titan python "from mpl_toolkits.basemap import Basemap"
+
+
+#!/usr/bin/env python3
+
+import numpy as np
+import numpy.ma as ma
+import os
+from netCDF4 import Dataset
+
+
+# ---------------- Data sources ------------------------
+input_file1 = '/lustre/atlas1/cli115/world-shared/4ue/20180215.DECKv1b_H1.ne30_oEC.edison/postproc/lnd/climo_regrid/20180215.DECKv1b_H1.ne30_oEC.edison_JJA_climo.nc'
+input_file3 = '/lustre/atlas1/cli115/world-shared/4ue/20180215.DECKv1b_H1.ne30_oEC.edison/postproc/lnd/climo_regrid/20180215.DECKv1b_H1.ne30_oEC.edison_ANN_climo.nc'
+
+# --------------------------------------------------------------
+# --------------------------------------------------------------
+
+# input_file1 get FLDS (mean downwelling longwave rad),FIRA (mean net IR longwave rad, absorbed)
+# FLDS(0,:,:), FIRA(0,:,:)
+# Matrix gris_area(Greenland ice area) has values 0 and none
+
+# Goal: print out area-weighted average of SW_d(268), SW_net(61), LW_d(235), LW_net(-46), R_net(15), SHF(7), LHF(-8),
+# these variables have size[192,288]
+# FSDS: atmospheric incident solar radiation
+# FSA: absorbed solar radiation
+# FLDS: atmospheric longwave radiation
+# FIRA: net infrared (longwave) radiation
+# FIRE: emitted infrared (longwave) radiation
+# FSH: sensible heat
+# QSOIL: ground evaporation over ice landunits
+
+
+# ---read input_file2, probably get area with ice sheet with nonzero values
+#ncid2 = Dataset(input_file2, mode='r')
+#ices = ncid2.variables['PCT_GLC_ICESHEET'][:] 
+#ncid2.close()
+
+# ---read input_files
+ncid1 = Dataset(input_file1, mode='r')
+#ncid11 = Dataset(input_file11, mode='r')
+ncid3 = Dataset(input_file3, mode='r')
+
+FSDS = ncid1.variables['FSDS'][0,:,:] 
+FSA = ncid1.variables['FSA'][0,:,:] 
+FLDS = ncid1.variables['FLDS'][0,:,:] 
+FIRA = ncid1.variables['FIRA'][0,:,:]
+FSH = ncid1.variables['FSH'][0,:,:] 
+QSOIL = ncid1.variables['QSOIL'][0,:,:] 
+RAIN = ncid3.variables['RAIN'][0,:,:] 
+SNOW = ncid3.variables['SNOW'][0,:,:] 
+QRUNOFF = ncid3.variables['QRUNOFF'][0,:,:] 
+#T2m = ncid11.variables['TREFHT'][0,:,:] 
+T2m = ncid1.variables['TSA'][0,:,:] 
+
+#E3SM
+GrisMask = ncid1.variables['gris_mask'][:,:] 
+
+SW_d  = FSDS 
+SW_net = FSA
+LW_d = FLDS
+LW_net = -1.0 * FIRA
+R_net = FSA-FIRA
+SHF = -1.0 * FSH
+LHF = -1.0 * 2.835e6 * QSOIL
+#SMB = QICE * 3.1567e7
+SMB = RAIN + SNOW - QRUNOFF - QSOIL * 3.1567e7
+T2mC = T2m - 273.15
+
+# ---grid cell area on Greenland. For other regions, the value is 9.999e35.
+area = ncid1.variables['area'][:] 
+
+ncid1.close()
+#ncid11.close()
+ncid3.close()
+
+# # # --- Option I: use greenland mask to mask the area where the ice sheet fraction is zero
+# # # Note: some non-greenland region has non-zero ice sheet fraction.
+Gris_mask = ma.masked_equal(GrisMask,0)
+area_maskice = ma.masked_array(area, mask=Gris_mask.mask)
+
+
+# # # --- Option II: use icesheet fraction mask to mask the area where the ice sheet fraction is zero
+# ices_mask = ma.masked_equal(ices,0)
+# area_maskice = ma.masked_array(area, mask=ices_mask.mask)
+
+
+# # # --- Option III: first multiply area with ices, then use greenland mask to mask the area where the ice sheet fraction is zero
+## -- this option gives the closest results to the Table 1 in the paper.
+#areaices = np.multiply(area,ices)
+#Gris_mask = ma.masked_equal(GrisMask,0)
+#area_maskice = ma.masked_array(areaices, mask=Gris_mask.mask)
+
+
+swdout=(ma.average(SW_d,weights=area_maskice))