diff --git a/nccf_atm_monthly.sh b/nccf_atm_monthly.sh
index 50477803fbd8a42f8493ec0f3b90ca1dff1c623d..4246f9df2fc12cea6e064f098c8a04d2b3aee9d0 100755
--- a/nccf_atm_monthly.sh
+++ b/nccf_atm_monthly.sh
@@ -46,15 +46,14 @@ function get_leadtime(){
 NMONTH=9999999
 for DIR in $MEM_LST
 do
-  cd ${DATADIR}/${EXPID}/${SDATE}/${DIR}/outputs
+  cd ${DATADIR}/${EXPID}/original_files/${SDATE}/${DIR}/outputs
   NFILE=0
   for file in $( find . -maxdepth 1 -name "MMA*" )
   do
     [[ $( echo $file | cut -f5 -d"_" | cut -f1 -d"-" ) -ge ${LEAD_LIST[0]}${LEAD_LIST[1]}01 ]] && [[ $( echo $file | cut -f5 -d"_" | cut -f1 -d"-" ) -le ${LEAD_LIST[2]}${LEAD_LIST[3]}01 ]] && NFILE=$(( NFILE + 1 ))
   done
  
-# NFILE="$( find . -maxdepth 1 -name "MMA*" | wc -l )"
- for TMPFILE in $( find . -maxdepth 1 -name "MMA*" | sed -e 's/\.\///g' )
+for TMPFILE in $( find . -maxdepth 1 -name "MMA*" | sed -e 's/\.\///g' )
  do
 #   if [[ $( echo $TMPFILE | cut -f5 -d"_" | cut -f1 -d"-" ) -ge ${LEAD_LIST[0]}${LEAD_LIST[1]}01 ]]; then
      NMONTHS_LOC=$(tar tvf $TMPFILE | grep GG | wc -l)
@@ -98,9 +97,6 @@ function header(){
 function rtime(){
  DATE1=$1
  DATE2=$2
-# FACTOR=day # h for hour, d for days
-# echo "NFRP:",$NFRP
-# FACTOR=day # h for hour, d for days
  YEAR1=$(echo $DATE1|cut -c1-4)
  MONTH1=$(echo $DATE1|cut -c5-6)
  DAY1=$(echo $DATE1|cut -c7-8)
@@ -109,14 +105,6 @@ function rtime(){
  DAY2=$(echo $DATE2|cut -c7-8)
  SEC1=$(date --utc --date "${YEAR1}-${MONTH1}-${DAY1}" +%s)
  SEC2=$(date --utc --date "${YEAR2}-${MONTH2}-${DAY2}" +%s)
-# case $FACTOR in 
-#  hour)
-#  FACTOR=3600 # 60*60
-#  ;;
-#  day)
-#  FACTOR=86400 # 60*60*24
-#  ;;
-# esac
  REFTIME_VALUE=$(((SEC2-SEC1)/FACTOR))
 }
 
@@ -156,17 +144,11 @@ function get_hours(){
 
 function extract(){
 
-#typeset var jt
-#typeset var YEAR0
-#typeset var YEARF
-#typeset var MON0
-#typeset var MONF
-
 for MEM in ${MEM_LST[@]}; do
 # untar and unzip MMA SH files and GG files 
 
 if [  -z $( echo ${LEAD_LIST[@]} ) ];then 
- PATH_TO_SEARCH=${DATADIR}/${EXPID}/${SDATE}/$MEM
+ PATH_TO_SEARCH=${DATADIR}/${EXPID}/original_files/${SDATE}/$MEM
  FILE_LIST=$(find $PATH_TO_SEARCH -type f -iname "MMA*" 2> /dev/null)
 else
  export YEAR0=${LEAD_LIST[0]}
@@ -179,9 +161,9 @@ else
  export LTIME0=1
  export LTIMEF=$(( ( ($YEARF - $YEAR0) * 12 + 10#$MONF - 10#$MON0+1 )/$CHUNK_SIZE ))
  jt=$LTIME0
+ FILE_LIST="" 
  while [ $jt -le $((LTIMEF)) ]
   do
-   FILE_LIST="" 
    YEAR1=$(( $YEAR0 +(10#$MON0+($jt-1)*$CHUNK_SIZE - 1 )/ 12 ))
    MON1=$(( ( 10#$MON0 + ( $jt - 1 ) * ($CHUNK_SIZE) ) % 12))
    MON1=$(echo $(printf "%02d" $(( 10#$MON1))) )
@@ -192,9 +174,9 @@ else
    [[ 10#$MON2 -eq 0 ]] && MON2=12
    [[ 10#$MON2 -eq 12 ]] && YEAR2=$(( $YEAR2 - 1 )) 
    jt=$(($jt+1))
-   FILE="$( find ${DATADIR}/${EXPID}/${SDATE}/*/outputs/ -maxdepth 1 -name "MMA_${EXPID}_${SDATE}_${MEM}_${YEAR1}"$(printf "%02d" $((10#$MON1)))"01-${YEAR2}"$(printf "%02d" $((10#$MON2)))"*.tar" )"
+   FILE="$( find ${DATADIR}/${EXPID}/original_files/${SDATE}/*/outputs/ -maxdepth 1 -name "MMA_${EXPID}_${SDATE}_${MEM}_${YEAR1}"$(printf "%02d" $((10#$MON1)))"01-${YEAR2}"$(printf "%02d" $((10#$MON2)))"*.tar" )"
    if [[ -z ${FILE} ]]; then
-    echo "Expected file ${DATADIR}/${EXPID}/${SDATE}/${MEM}/outputs/MMA_${EXPID}_${SDATE}_${MEM}_${YEAR1}${MON1}01-${YEAR2}${MON2}*.tar not found, check your Namelist parameters"
+    echo "Expected file ${DATADIR}/${EXPID}/original_files/${SDATE}/${MEM}/outputs/MMA_${EXPID}_${SDATE}_${MEM}_${YEAR1}${MON1}01-${YEAR2}${MON2}*.tar not found, check your Namelist parameters"
     exit
    fi
    FILE_LIST="$FILE_LIST ${FILE}"
@@ -211,15 +193,7 @@ fi
        tar xvf ${f} ${FILE} ;gunzip -q ${FILE}; mv ${FILE%???} ${FILE%???}.$MEM
       done
     done
-echo "jt ltimef " $jt $((LTIMEF)) 
-if [ $jt -le $((LTIMEF)) ]; then
-  echo le
-else
- echo gt
-fi 
-echo "sortie de extract" $MEM -- ${MEM_LST[@]}
 done
-echo "sortie de extract"
 }
 
 function read_vars(){
@@ -268,7 +242,7 @@ for MEM in ${MEM_LST[@]}; do
   nb_months_asked=$(( ( ($YEARF - $YEAR0) * 12 + 10#$MONF - 10#$MON0+1 ) ))
 
 if  [[ $NLT -ne $nb_months_asked ]];then
- echo "Warning, the number of months in MMA ($nb_files) is different from the number of months you required according to the LEADLIST",$(( ( ($YEARF - $YEAR0) * 12 + $MONF - $MON0+1 )))," check your configfile!"
+ echo "Warning, the number of months in MMA ($nb_files) is different from the number of months you required according to the LEADLIST",$(( ( ($YEARF - $YEAR0) * 12 + 10#$MONF - $MON0+1 )))," check your configfile!"
  exit
 fi
 ####  process each variable  ####
@@ -365,7 +339,6 @@ fi
       esac
   done # loop for VAR
 done # loop for members 
-echo "after loop on members in surface"
 
 
 # finish selecting the variables 
@@ -373,13 +346,11 @@ echo "after loop on members in surface"
  for VAR in ${VAR_LST_2D[@]}; do 
     new_name $VAR
     pathout=${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_f${NFRP}h
-    pathout=${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_f${NFRP}h
     mkdir -m ug+w -m o-w -p $pathout
     LSMBSH="${LISTMEMB[0]}-${LISTMEMB[${#LISTMEMB[@]}-1]}"
 #    PREVIOUS_FILE="$(ls -tr ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly/${varnew}_${SDATE}_*.nc | tail -1)" (if left like this, we have the "no such file" pb. but if we chose the "find" option, we can sort the files and get hte last one edited => have to make a find to be sure there are some previous_files and then, if so, get the actual previous_file with the ls command.
 #savedir 
    PREVIOUS_FILE="$( find  ${pathout} -maxdepth 1 -name "${varnew}_${SDATE}_*.nc" )"
-echo okkkk
     if [ ! -z $( ls $PREVIOUS_FILE ) ] ; then
      PREVIOUS_FILE="$(ls -tr ${pathout}/${varnew}_${SDATE}_*.nc | tail -1)"
      cd ${pathout} 
@@ -403,11 +374,7 @@ echo okkkk
      else
       echo "Some members are going to be treated twice! If you are not adding new lead_times, revise the consistency between your member list and the previously processed files"
      fi
-echo ok2
     fi
-echo ok3
-pwd
-ls
 YRSO=${YEAR0}$(printf "%02d" $(( 10#$MON0)))_${YEARF}$(printf "%02d" $(( 10#$MONF)))
 gather_memb tmp_${varnew}_$SDATE ${varnew}_${SDATE}_fc${LSMBSH}_${YRSO}.nc $varnew $VAR
 
@@ -434,21 +401,17 @@ output=${varnew}_${SDATE}_fc${LSMBSH}_${YRSO}.nc
 #
 #if [[ $idx -ne 40 ]]; then
         for att in units valid_range actual_range code table GRID_TYPE ; do 
-      ncatted -O -h -a ${att},${varnew},d,c, ${output}	
+          ncatted -O -h -a ${att},${varnew},d,c, ${output}	
         done
 #
-# Adding and modifying the {varnew}iable attributes
+# Adding and modifying the variable attributes
 #
         ncatted -O -h -a _FillValue,${varnew},a,f,1.e+12 ${output}
-        ncatted -O -h -a standard_name,${varnew},o,c,"$cfustandard_name" ${output} # {varnew}iable standard name
-        ncatted -O -h -a long_name,${varnew},o,c,"$cfulong_name" ${output}         # {varnew}iable long name
-        ncatted -O -h -a cell_methods,${varnew},o,c,"$cfucell_methods" ${output}   # {varnew}iable cell methods
-        ncatted -O -h -a unit_long,${varnew},o,c,"$cfuunit_long" ${output}         # {varnew}iable long unit name
-        ncatted -O -h -a units,${varnew},o,c,"$cfuunit" ${output}                  # {varnew}iable units
-#fi
-#        ncatted -O -h -a data_type,level_${varnew},o,c,"$cfulevel_type" ${output}  # {varnew}iable level type
-#        ncatted -O -h -a units,level_${varnew},o,c,"$cfulevel_units" ${output}     # {varnew}iable level units
-#        ncatted -O -h -a coordinates,${varnew},o,c,"longitude latitude reftime leadtime time_bnd experiment_id source realization institution level_${varnew}" ${output} # variable coordinates
+        ncatted -O -h -a standard_name,${varnew},o,c,"$cfustandard_name" ${output} # variable standard name
+        ncatted -O -h -a long_name,${varnew},o,c,"$cfulong_name" ${output}         # variable long name
+        ncatted -O -h -a cell_methods,${varnew},o,c,"$cfucell_methods" ${output}   # variable cell methods
+        ncatted -O -h -a unit_long,${varnew},o,c,"$cfuunit_long" ${output}         # variable long unit name
+        ncatted -O -h -a units,${varnew},o,c,"$cfuunit" ${output}                  # variable units
         ncatted -O -h -a coordinates,${varnew},o,c,"longitude latitude reftime leadtime time_bnd experiment_id source realization institution " ${output} # variable coordinates
 #
 # If the NetCDF file had a horizontal axis name different from longitude
@@ -456,7 +419,6 @@ output=${varnew}_${SDATE}_fc${LSMBSH}_${YRSO}.nc
         ncrename -h -d lon,longitude -v lon,longitude  ${output}
        
         [[ ! -z $( ncdump -h ${output} | grep record ) ]] && ncrename -h -d record,ensemble ${output}
-#        [[ ! -z $( ncdump -h ${output} | grep ensemble ) ]] && ncrename -h -d record,ensemble ${output}
 #
 # If the NetCDF file had a vertical axis name different from latitude
 #
@@ -466,25 +428,13 @@ output=${varnew}_${SDATE}_fc${LSMBSH}_${YRSO}.nc
 #
         ncatted -O -h -a axis,longitude,o,c,"X" ${output}       # variable longitude axis
         ncatted -O -h -a axis,latitude,o,c,"Y" ${output}        # variable latitude axis
-#[[ $idx -ne 40 ]] &&
-#   ncatted -O -h -a axis,level_${varnew},o,c,"Z" ${output} # variable level axis
 # modify level information
 # reshape the dimension and make time unlimited 
 
-#        [[ ! -z $( ncdump -h ${output} | grep record ) ]] && ncpdq -O -h -a time,ensemble ${output} ${output}
         [[ ! -z $( ncdump -h ${output} | grep ensemble ) ]] && ncpdq -O -h -a time,ensemble ${output} ${output}
         cp ${output} hhh.nc
         ncks -h -A header.nc ${output}
-#if [[ $idx -ne 40 ]]; then 
        nt=$(cdo ntime ${output})
-#        ncatted -O -h -a standard_name,level_${varnew},c,c,"height" ${output}       # standard name
-#        ncatted -O -h -a long_name,level_${varnew},c,c,"reference height" ${output} # long name
-#        ncatted -O -h -a data_type,level_${varnew},c,c,"float" ${output}            # data type
-#        ncatted -O -h -a units,level_${varnew},c,c,"m" ${output}                    # units
-#        ncatted -O -h -a axis,level_${varnew},c,c,"Z" ${output}                     # axis
-#        ncatted -O -h -a positive,level_${varnew},c,c,"up" ${output}
-#        ncap2 -O -h -s "level_${varnew}=float(${cfulevel_number})" $output $output
-#fi
 # delete history
         ncatted -h -a history,global,d,, $output
 # change institution name
@@ -545,8 +495,6 @@ function new_name(){  #to be rethought: make a match between var_name and xml ta
         idx=28
         ;;
         "SSTK")
-#        "SST")
-#weird...        VAR=SSTK
         varnew=tos
         idx=10
         ;;
@@ -654,7 +602,6 @@ function new_name(){  #to be rethought: make a match between var_name and xml ta
         varnew=cl
         idx=35
 	;;
-#pab!!!! new variables to be added when variable list read directly in outputs, some are missing
         "var78")
         varnew=tclw
         idx=38
@@ -700,8 +647,6 @@ function gather_memb() {
 # Created in May 2012           Author : vguemas@ic3.cat                            
 # Adapted for atmospherical outputs January 2013 pierre-antoine.bretonniere@ic3.cat 
 
-#  OLD_FILE=$(ls ${1}_* || echo "")
-#  NEW_FILES=$(ls "${1}".*)
   OLD_FILE="$( find . -maxdepth 1 -name "${1}_*" | sed -e 's/\.\///g' | sort -u )"
   NEW_FILES="$( find . -maxdepth 1 -name "${1}.*" | sed -e 's/\.\///g'| sort -u )"
   VAR_LOC=$3
@@ -714,20 +659,16 @@ if [[ $( echo $NEW_FILES | wc -w ) -gt 1 ]]; then
   ncecat -O -h tmp_cat.nc tmp_cat2.nc
   ncpdq -O -h -a ensemble,record tmp_cat2.nc tmp_cat2.nc
   ncwa -O -h -a record tmp_cat2.nc tmp_cat2.nc
-  mv tmp_cat2.nc tmp_cat.nc #new
+  mv tmp_cat2.nc tmp_cat.nc 
 else
   mv ${NEW_FILES} tmp_cat.nc
 fi
 
  for var_check in $VAR_LST_3D_GG
   do
-  if [ $VAR_OLD == $var_check ];then
-   ncks -O -h -a -v lon,lat,$VAR_LOC tmp_cat.nc tmp_cat.nc
-#   ncks -O -h -a -v lon,lat,$VAR_LOC tmp_cat2.nc tmp_cat3.nc
-#   mv tmp_cat3.nc tmp_cat.nc
-#  else
-#   mv tmp_cat2.nc tmp_cat.nc
-  fi
+    if [ $VAR_OLD == $var_check ];then
+      ncks -O -h -a -v lon,lat,$VAR_LOC tmp_cat.nc tmp_cat.nc
+    fi
  done
  if [ ! -z $OLD_FILE ] ; then
    ncks -C -O -v longitude,latitude,$VAR_LOC $OLD_FILE tmp_0_${OLD_FILE}
@@ -760,7 +701,6 @@ function save_final_output(){
 # Select variables and levels   
 function combine_3d(){
 for MEM in ${MEM_LST[@]}; do
-#   FILES=$(ls MMA*SH*.nc.$MEM)
    FILES="$(find . -maxdepth 1 -name  "MMA*SH*.nc.$MEM" | sed -e 's/\.\///g' )"
    echo $FILES
    for f in ${FILES}; do   
@@ -771,18 +711,17 @@ for MEM in ${MEM_LST[@]}; do
     done
     rm -f ${f}
    done
-#    FILES=$(ls MMA*GG*.nc.$MEM)
     FILES=$(find . -maxdepth 1 -name  "MMA*GG*.nc.$MEM" | sed -e 's/\.\///g' )
     for f in ${FILES}; do
    for var in ${VAR_LST_3D_GG[@]}; do
         new_name $var
         TMP_OUT=tmp_${varnew}_$f
-     case $var in #pab
+     case $var in 
        Q)  
-        cdo selname,${var} -sellevel,${LEVEL_LST} ${f} ${TMP_OUT} #
+        cdo selname,${var} -sellevel,${LEVEL_LST} ${f} ${TMP_OUT} 
        ;;
        *)
-        cdo selname,${var} ${f} ${TMP_OUT} #pab
+        cdo selname,${var} ${f} ${TMP_OUT} 
         ;;
       esac
     done
@@ -814,7 +753,6 @@ function regrid2x2(){
  done
  for var in ${VAR_LST_3D_GG[@]}; do
    new_name $var
-#   FILES="$(ls ${varnew}_$SDATE.*.nc)"
    FILES=$(find . -maxdepth 1 -name "${varnew}_$SDATE.*.nc" | sed -e 's/\.\///g' )
    for f in ${FILES}; do
  
@@ -826,51 +764,42 @@ function regrid2x2(){
 
 function upper(){
    for var in ${VAR_LST_3D[@]}; do
-    new_name $var
-
-    echo ${LISTMEMB[0]} -- ${#LISTMEMB[@]} -- ${LISTMEMB[${#LISTMEMB[@]}-1]} 
-    LSMBSH="${LISTMEMB[0]}-${LISTMEMB[${#LISTMEMB[@]}-1]}"
-#    PREVIOUS_FILE="$(ls ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly/${varnew}_${SDATE}_*.nc | tail -1)"
-#    PREVIOUS_FILE="$( find . -maxdepth 1 -name  "${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly/${varnew}_${SDATE}_*.nc" | tail -1 | sed -e 's/\.\///g' )"
-#savedir 
-#   PREVIOUS_FILE="$( find  ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly -maxdepth -name  "${varnew}_${SDATE}_*.nc" | tail -1 | sed -e 's/\.\///g' )"
-   PREVIOUS_FILE="$( find  ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_f${NFRP}h -maxdepth -name  "${varnew}_${SDATE}_*.nc" | tail -1 | sed -e 's/\.\///g' )"
-    if [  ! -z $PREVIOUS_FILE ] ; then
-#     cd ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly/; 
-     cd ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_f${NFRP}h/; 
-     FILE_NAME_PREVIOUS="$( find . -maxdepth 1 -name "${varnew}_${SDATE}_*.nc" | tail -1 | sed -e 's/\.\///g' )"; cd -
-     IDX_1ST=$(echo ${varnew}_${SDATE}_ | wc -m )
-     FIRST_MEMBER_PREVIOUS=$(echo $FILE_NAME_PREVIOUS | cut -b$IDX_1ST )
-     IDX_LST=$( expr $IDX_1ST + 2 )
-     LAST_MEMBER_PREVIOUS=$(echo $FILE_NAME_PREVIOUS  | cut -b$IDX_LST )
+     new_name $var
+     LSMBSH="${LISTMEMB[0]}-${LISTMEMB[${#LISTMEMB[@]}-1]}"
+     PREVIOUS_FILE="$( find  ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_f${NFRP}h -maxdepth -name  "${varnew}_${SDATE}_*.nc" | tail -1 | sed -e 's/\.\///g' )"
+     if [  ! -z $PREVIOUS_FILE ] ; then
+       cd ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_f${NFRP}h/; 
+       FILE_NAME_PREVIOUS="$( find . -maxdepth 1 -name "${varnew}_${SDATE}_*.nc" | tail -1 | sed -e 's/\.\///g' )"; cd -
+       IDX_1ST=$(echo ${varnew}_${SDATE}_ | wc -m )
+       FIRST_MEMBER_PREVIOUS=$(echo $FILE_NAME_PREVIOUS | cut -b$IDX_1ST )
+       IDX_LST=$( expr $IDX_1ST + 2 )
+       LAST_MEMBER_PREVIOUS=$(echo $FILE_NAME_PREVIOUS  | cut -b$IDX_LST )
 #security check:
-     if [ $LAST_MEMBER_PREVIOUS -le $(expr ${LISTMEMB[0]} - 1 ) ] ; then
-        cp $PREVIOUS_FILE rg_$FILE_NAME_PREVIOUS
-       if [ $LAST_MEMBER_PREVIOUS -eq $(expr ${LISTMEMB[0]} - 1 ) ] ; then
-        LSMBSH=${FIRST_MEMBER_PREVIOUS}-${LISTMEMB[${#LISTMEMB[@]}-1]}
+       if [ $LAST_MEMBER_PREVIOUS -le $(expr ${LISTMEMB[0]} - 1 ) ] ; then
+         cp $PREVIOUS_FILE rg_$FILE_NAME_PREVIOUS
+         if [ $LAST_MEMBER_PREVIOUS -eq $(expr ${LISTMEMB[0]} - 1 ) ] ; then
+           LSMBSH=${FIRST_MEMBER_PREVIOUS}-${LISTMEMB[${#LISTMEMB[@]}-1]}
+         else
+           echo "Actual list of members does not follow directly the ones already post-processed! Check you did not forget any members at the beginning of your list"
+           MISSING_FIRST=$(expr ${LAST_MEMBER_PREVIOUS} + 1 )
+           MISSING_LAST=$(expr ${LISTMEMB[0]} - 1 )
+           LSMBSH=${FIRST_MEMBER_PREVIOUS}_${LISTMEMB[${#LISTMEMB[@]}-1]}-${MISSING_FIRST}_${MISSING_LAST}
+         fi
        else
-        echo "Actual list of members does not follow directly the ones already post-processed! Check you did not forget any members at the beginning of your list"
-        MISSING_FIRST=$(expr ${LAST_MEMBER_PREVIOUS} + 1 )
-        MISSING_LAST=$(expr ${LISTMEMB[0]} - 1 )
-        LSMBSH=${FIRST_MEMBER_PREVIOUS}_${LISTMEMB[${#LISTMEMB[@]}-1]}-${MISSING_FIRST}_${MISSING_LAST}
-       fi
-     else
-      echo "Some members are going to be treated twice! Revise the consistency between your member list and the previously processed files"
-     fi
+         echo "Some members are going to be treated twice! Revise the consistency between your member list and the previously processed files"
+      fi
     fi
     YRSO=${YEAR0}$(printf "%02d" $(( 10#$MON0)))_${YEARF}$(printf "%02d" $((10#$MONF))).nc
     [[ 10#${MONF} -le 9 ]] && [[ $( echo $MONF | wc -c) -eq 2 ]] && YRSO=${YEAR0}${MON0}_${YEARF}$(printf "%02d" ${MONF}).nc
     gather_memb rg_${varnew}_$SDATE ${varnew}_${SDATE}_fc${LSMBSH}_${YRSO}.nc $varnew $VAR
     output=${varnew}_${SDATE}_fc${LSMBSH}_${YRSO}.nc
-#    gather_memb rg_${varnew}_$SDATE ${varnew}_${SDATE}_${LSMBSH}.nc $varnew $VAR
-#    output=${varnew}_${SDATE}_${LSMBSH}.nc
-	rm -f ${FILES}
-   for CHECK_VAR in $VAR_LST_3D_SH
+    rm -f ${FILES}
+    for CHECK_VAR in $VAR_LST_3D_SH
     do
-    if [ $CHECK_VAR == $var ];then
+      if [ $CHECK_VAR == $var ];then
     	ncrename -h -d lon,longitude -d lat,latitude -d lev,level ${output}
     	ncrename -h -v lon,longitude -v lat,latitude -v lev,level ${output}
-    fi
+      fi
    done
    for CHECK_VAR in $VAR_LST_3D_GG
     do
@@ -879,8 +808,7 @@ function upper(){
       [[ ! -z $( ncdump -h ${output} | grep "mlev =" ) ]] && ncrename -h -d mlev,level -v mlev,level ${output}
       [[ ! -z $( ncdump -h ${output} | grep "lev =" ) ]] && ncrename -h -d lev,level -v lev,level ${output}
       if [[ ! -z $( ncdump -h ${output} | grep "depth =" ) ]]; then
-        ncrename -h -d depth,level ${output}
-        ncrename -h -v depth,level ${output}
+        ncrename -h -d .depth,level -v .depth,level ${output}
       fi
       ncrename -h -v lon,longitude -v lat,latitude ${output}
     fi
@@ -975,15 +903,11 @@ function upper(){
           ncrename -h -O -d record,ensemble $output $output
         fi
         ncpdq -O -h -a time,ensemble ${output} ${output} # reshape the dimension and make time unlimited
-      #  ncks  -h -A $HEAD_DIR/${SDATE}.nc ${output}
         ncks  -h -A header.nc ${output}
         ncrename -O -h -v time,kaka $output # delete time variable 
         ncks -O -h -x -v kaka $output $output # delete time variable
         ncatted -h -a history,global,d,, $output  #delete history
         ncatted -h -a institution,global,m,c,"IC3" $output ## change institution name in global attributes
-#pwd
-#ls
-#exit
 
 # create a script to change the EXPID, insitutution, ensember, source and realiazation 
 	i=0 # index
@@ -997,7 +921,6 @@ EOF
 		i=$((i+1))
 	done
 ##
-#        rm -f ${files}*
         save_final_output $varnew $output
  done # loop over variables 
 }
@@ -1008,7 +931,6 @@ EOF
 function maxmin(){
 for VAR in ${VAR_LST_MXMN[@]}; do
  new_name $VAR
- echo "llll"  $SDATE
  output=${VAR}_${SDATE}.nc
  cp $DATADIR/${EXPID}/daily/$VAR/${VAR}_${SDATE}_*.nc.gz .
  gunzip ${VAR}_${SDATE}_*.nc.gz 
@@ -1048,13 +970,13 @@ for att in GRID_TYPE ; do
  ncatted -O -h -a ${att},${varnew},d,c, ${output}      
 done
 #
-# Adding and modifying the {varnew}iable attributes
+# Adding and modifying the variable attributes
 #
-ncatted -O -h -a standard_name,${varnew},o,c,"$cfustandard_name" ${output} # {varnew}iable standard name
-ncatted -O -h -a long_name,${varnew},o,c,"$cfulong_name" ${output}         # {varnew}iable long name
-ncatted -O -h -a cell_methods,${varnew},o,c,"$cfucell_methods" ${output}   # {varnew}iable cell methods
-ncatted -O -h -a data_type,level_${varnew},o,c,"$cfulevel_type" ${output}  # {varnew}iable level type
-ncatted -O -h -a units,level_${varnew},o,c,"$cfulevel_units" ${output}     # {varnew}iable level units
+ncatted -O -h -a standard_name,${varnew},o,c,"$cfustandard_name" ${output} # variable standard name
+ncatted -O -h -a long_name,${varnew},o,c,"$cfulong_name" ${output}         # variable long name
+ncatted -O -h -a cell_methods,${varnew},o,c,"$cfucell_methods" ${output}   # variable cell methods
+ncatted -O -h -a data_type,level_${varnew},o,c,"$cfulevel_type" ${output}  # variable level type
+ncatted -O -h -a units,level_${varnew},o,c,"$cfulevel_units" ${output}     # variable level units
 ncatted -O -h -a coordinates,${varnew},o,c,"longitude latitude reftime leadtime time_bnd experiment_id source realization institution level_${varnew}" ${output}
 #
 # Adding variable axis
@@ -1107,16 +1029,11 @@ export WORKDIR
 FACTOR=$((NFRP*3600))
 ENSEMBLE=${#MEM_LST[@]}
 if [[ $ENSEMBLE -eq 0 ]]; then
-  MEM_LST=( $( ls ${DATADIR}/${EXPID}/${SDATE} ) ) 
+  MEM_LST=( $( ls ${DATADIR}/${EXPID}/original_files/${SDATE} ) ) 
   ENSEMBLE=${#MEM_LST[@]}
   echo "Warning: you passed an empty member list. By default, it will treat all the available members: " ${MEM_LST[@]}
 fi
 LISTMEMB=( $(echo ${MEM_LST[@]} | sed -e 's/fc//g') ) #member list without "fc"
-echo ${MEM_LST[0]}
-echo $LISTMEMB
-echo  ${LISTMEMB[0]}
-echo ${LISTMEMB[${#LISTMEMB[@]}-1]}
-echo ${#LISTMEMB[@]}
 
 rm -rf ${WORKDIR}
 mkdir -p ${WORKDIR}
@@ -1126,23 +1043,22 @@ fi
 
 cd ${WORKDIR}
 
-if [[ ! -d ${DATADIR}/${EXPID} ]]; then
-  [[ -d /esarchive/exp/ecearth/${EXPID} ]] && DATADIR=/esarchive/exp/ecearth
+if [[ -d /esarchive/exp/ecearth/${EXPID} ]]; then 
+  DATADIR=/esarchive/exp/ecearth
+else
+  DATADIR=/esnas/exp/ecearth
 fi
-base_path=${DATADIR}/${EXPID}/${SDATE}
-mkdir -p ${SAVEDIR}/${EXPID}; # chmod -R 775 $SAVEDIR/${EXPID} 
+base_path=${DATADIR}/${EXPID}/original_files/${SDATE}
+mkdir -p ${SAVEDIR}/${EXPID};  chmod -R 775 $SAVEDIR/${EXPID} 
 
-#exit stop
 get_leadtime
 header $SDATE
 extract
 echo "after extract"
 
 if [ -z ${VAR_LST_2D[@]}  ]; then
-# GG=$(ls *GG* | head -1)
  GG="$(find . -maxdepth 1 -name "*GG*" | head -1 | sed -e 's/\.\///g' )"
  read_vars $GG GG
-# SH=$(ls *SH* | head -1)
  SH="$(find . -maxdepth 1 -name "*SH*" | head -1 | sed -e 's/\.\///g' )"
  read_vars $SH SH
 rm -f /scratch/Earth/${USER}/pp/VAR_LST_2D.txt 
@@ -1188,8 +1104,6 @@ upper
 
 if [[ ${#VAR_LST_MXMN[@]} > 0 ]]; then
  maxmin
-#else 
-# echo "" #empty line to avoid trap issue
 fi
 
 cd ~/; rm -rf $WORKDIR # clean up