From 2ae84dc18e3dfa9185df9419e5adcf8aa4fb473c Mon Sep 17 00:00:00 2001
From: vsicardi <vsicardi@bsc.es>
Date: Tue, 2 Jul 2019 10:47:34 +0200
Subject: [PATCH 01/16] interpolation nudging files tool was added

---
 interpolation_nudging/compute_density.py      |  36 ++
 interpolation_nudging/compute_density.pyc     | Bin 0 -> 1219 bytes
 interpolation_nudging/interp_fc01_s4.sh       |  83 ++++
 interpolation_nudging/interp_fc02_s4.sh       |  83 ++++
 interpolation_nudging/interp_fc03_s4.sh       |  83 ++++
 interpolation_nudging/interp_fc04_s4.sh       |  83 ++++
 interpolation_nudging/interp_s4.sh            |  83 ++++
 .../library_interp_extrap.py                  | 400 ++++++++++++++++++
 .../library_interp_extrap.pyc                 | Bin 0 -> 12477 bytes
 interpolation_nudging/prep_restart_interp.py  | 188 ++++++++
 10 files changed, 1039 insertions(+)
 create mode 100644 interpolation_nudging/compute_density.py
 create mode 100644 interpolation_nudging/compute_density.pyc
 create mode 100755 interpolation_nudging/interp_fc01_s4.sh
 create mode 100755 interpolation_nudging/interp_fc02_s4.sh
 create mode 100755 interpolation_nudging/interp_fc03_s4.sh
 create mode 100755 interpolation_nudging/interp_fc04_s4.sh
 create mode 100755 interpolation_nudging/interp_s4.sh
 create mode 100644 interpolation_nudging/library_interp_extrap.py
 create mode 100644 interpolation_nudging/library_interp_extrap.pyc
 create mode 100644 interpolation_nudging/prep_restart_interp.py

diff --git a/interpolation_nudging/compute_density.py b/interpolation_nudging/compute_density.py
new file mode 100644
index 0000000..438bbd0
--- /dev/null
+++ b/interpolation_nudging/compute_density.py
@@ -0,0 +1,36 @@
+import numpy as np
+from numpy import ma as ma
+def compute_density(ptemp, psal):
+    """Compute the density using the Jackett and McDougall (1994) equation of state
+    (adapted from fortran routine eosbn2 from NEMO 3.3)
+    by C. Prodhomme -- 2016
+    Arguments:
+    ptemp: numpy array of potential temperature
+    psal: numpy array of potential salinity
+    Output:
+    zrhop: numpy array of density
+    """
+
+    #???
+    rau0 = 1035 
+
+    zrau0r = 1.e0 / rau0
+    #square root salinity
+    psalr = np.sqrt( np.absolute(psal))
+
+
+    # compute volumic mass pure water at atm pressure
+    zr1= ( ( ( ( 6.536332e-9*ptemp-1.120083e-6 )*ptemp+1.001685e-4 )*ptemp
+            -9.095290e-3 )*ptemp+6.793952e-2 )*ptemp+999.842594
+    # seawater volumic mass atm pressure
+    zr2= ( ( ( 5.3875e-9*ptemp-8.2467e-7 )*ptemp+7.6438e-5 ) *ptemp   
+           -4.0899e-3 ) *ptemp+0.824493
+    zr3= ( -1.6546e-6*ptemp+1.0227e-4 )*ptemp-5.72466e-3
+    zr4= 4.8314e-4
+
+    # potential volumic mass (reference to the surface)
+    zrhop= ( zr4*psal + zr3*psalr + zr2 ) *psal + zr1
+    
+    return(zrhop)
+  
+    
diff --git a/interpolation_nudging/compute_density.pyc b/interpolation_nudging/compute_density.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..2d0b997adf94c7c22b2f4acace94341148b1e2eb
GIT binary patch
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diff --git a/interpolation_nudging/interp_fc01_s4.sh b/interpolation_nudging/interp_fc01_s4.sh
new file mode 100755
index 0000000..e77471d
--- /dev/null
+++ b/interpolation_nudging/interp_fc01_s4.sh
@@ -0,0 +1,83 @@
+#!/bin/ksh
+#SBATCH -n 1
+#SBATCH -t 78:00:00
+#SBATCH -J interpORAS4
+#SBATCH -o interp-oras4-%j.log   
+set -exv
+#module load netCDF-Fortran/4.2-foss-2015a
+# This script download the s4 restarts from ECMWF 
+# and launch the interpolation of the files toward 
+# the target resolution
+# History : Chloe Prodhomme - Initial version                           2016 
+#         : Valentina Sicardi - Changes to interpolate nudging files to ORCA1L75
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#                                Arguments
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+YEARI=2017 # first years of the restarts to be intepolated
+YEARF=2018 # Last year to be interpolated
+MEMBER_LST="01 02 03 04" # List of members to interpolate
+MON_LST2="0228 0331 0430 0531 0630 0731 0831 0930 1031 1130 1231" #"0131 0228 0331 0430 0531 0630 0731 0831 1031 1130 1231" # List of months to intepolate in formate MMDD
+MON_LST1="0201 0301 0401 0501 0601 0701 0801 0901 1001 1101 1201" #"0131 0228 0331 0430 0531 0630 0731 0831 1031 1130 1231" # 
+month="01 02 03 04 05 06 07 08 09 10 11 12"
+config=1L75 #target resolution for the output grid
+modelversion="Ec3.2" 
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+workdir=/scratch/Earth/$USER/ORAS4/
+tmpdir=/scratch/Earth/$USER/interp/
+rm -f /scratch/Earth/$USER/ORAS4/*
+mkdir -p $workdir
+mkdir -p $tmpdir
+cp *.py $workdir
+cp *.nc $workdir
+cd $workdir
+
+
+#loop over the members
+for mem in $MEMBER_LST ; do
+    #loop over the month
+	#loop over the years
+	for YEAR in `seq $YEARI $YEARF`; do
+            for MON1 in  $MON_LST1; do
+                for MON2 in $MON_LST2; do 
+                    for mon in ${month}; do
+            #DATASOURCE="/esarchive/recon/ecmwf/nemovar_system4/monthly_mean/thetao/thetao_Omon_ORAS4_opa1_20180201-20180228.nc" # HERE should go the input file 
+            DATASOURCE="/esarchive/recon/ecmwf/nemovar_system4/monthly_mean/so/so_Omon_ORAS4_opa4_${YEAR}${MON1}-${YEAR}${MON2}.nc" # HERE should go the input file 
+
+            #fileto_interp=s4_fc00_201802.nc # the file DATASOURCE should be renamed something like: s4_MEMBER_YEARMONTH.nc" s4_fc00_201801.nc
+            fileto_interp=s4_fc${mem}_${YEAR}${mon}.nc # the file DATASOURCE should be renamed something like: s4_MEMBER_YEARMONTH.nc" s4_fc00_201801.nc
+            echo ${fileto_interp}
+	   # cp $DATASOURCE ${localdir}/$fileto_interp
+             cp $DATASOURCE ${workdir}/$fileto_interp
+             echo ${fileto_interp}
+            #before the interpolation the file shoudl be modified as follow:
+             ncrename -d time,t    ${workdir}/${fileto_interp}                  #s4_fc00_201802.nc
+             ncrename -d olevel,z    ${workdir}/${fileto_interp}
+             ncrename -v olevel,z   ${workdir}/${fileto_interp}  
+             ncrename -v z,nav_lev  ${workdir}/${fileto_interp}    #$fileto_interp
+             ncrename -v time,time_counter ${workdir}/${fileto_interp}
+             ncrename -v latitude,nav_lat ${workdir}/${fileto_interp}
+             ncrename -v  longitude,nav_lon ${workdir}/${fileto_interp}
+             
+            #fileout=s4_fc0_YEAR.nc ####  the final interpolated file, should be 12 months file. with thethao renamed to votemper and so renamed to vosaline 
+            # fileout=s4_fc${mem}_${YEAR}.nc
+            echo $(pwd) 
+            #echo ${fileout}
+	    #Launch the interpolation toward the target resolution
+            echo ${fileto_interp}
+	    python prep_restart_interp.py ${fileto_interp} /esnas/autosubmit/con_files/mesh_mask_nemo.nemovar_O1L42.nc $config $modelversion
+	    # remove the local files
+           done 
+	done #loop year
+    done #loop month
+  done 
+done #loop member
+       #   ncrename -v  thetao,votemper ${fileto_interp}               #s4_fc00_201802.nc
+         ncrename -v  so,vosaline ${fileto_interp}         
+
+         # merge all interpolated files s4_MEMBER_YEARMONTH.nc in one 12 months file: s4_fc00_YEAR.nc . and they should go in:
+         #/esarchive/releases/nudging/ocean/s4/ORCA1L75/MEMBER 
+
+     
+                  
+
diff --git a/interpolation_nudging/interp_fc02_s4.sh b/interpolation_nudging/interp_fc02_s4.sh
new file mode 100755
index 0000000..78af761
--- /dev/null
+++ b/interpolation_nudging/interp_fc02_s4.sh
@@ -0,0 +1,83 @@
+#!/bin/ksh
+#SBATCH -n 1
+#SBATCH -t 78:00:00
+#SBATCH -J interpORAS4
+#SBATCH -o interp-oras4-%j.log   
+set -exv
+#module load netCDF-Fortran/4.2-foss-2015a
+# This script download the s4 restarts from ECMWF 
+# and launch the interpolation of the files toward 
+# the target resolution
+# History : Chloe Prodhomme - Initial version                           2016 
+#         : Valentina Sicardi - Changes to interpolate nudging files to ORCA1L75
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#                                Arguments
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+YEARI=2017 # first years of the restarts to be intepolated
+YEARF=2018 # Last year to be interpolated
+MEMBER_LST="02 03 04" # List of members to interpolate
+MON_LST2="0228 0331 0430 0531 0630 0731 0831 0930 1031 1130 1231" #"0131 0228 0331 0430 0531 0630 0731 0831 1031 1130 1231" # List of months to intepolate in formate MMDD
+MON_LST1="0201 0301 0401 0501 0601 0701 0801 0901 1001 1101 1201" #"0131 0228 0331 0430 0531 0630 0731 0831 1031 1130 1231" # 
+month="01 02 03 04 05 06 07 08 09 10 11 12"
+config=1L75 #target resolution for the output grid
+modelversion="Ec3.2" 
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+workdir=/scratch/Earth/$USER/ORAS4/
+tmpdir=/scratch/Earth/$USER/interp/
+rm -f /scratch/Earth/$USER/ORAS4/*
+mkdir -p $workdir
+mkdir -p $tmpdir
+cp *.py $workdir
+cp *.nc $workdir
+cd $workdir
+
+
+#loop over the members
+for mem in $MEMBER_LST ; do
+    #loop over the month
+	#loop over the years
+	for YEAR in `seq $YEARI $YEARF`; do
+            for MON1 in  $MON_LST1; do
+                for MON2 in $MON_LST2; do 
+                    for mon in ${month}; do
+            #DATASOURCE="/esarchive/recon/ecmwf/nemovar_system4/monthly_mean/thetao/thetao_Omon_ORAS4_opa1_20180201-20180228.nc" # HERE should go the input file 
+            DATASOURCE="/esarchive/recon/ecmwf/nemovar_system4/monthly_mean/so/so_Omon_ORAS4_opa2_${YEAR}${MON1}-${YEAR}${MON2}.nc" # HERE should go the input file 
+
+            #fileto_interp=s4_fc00_201802.nc # the file DATASOURCE should be renamed something like: s4_MEMBER_YEARMONTH.nc" s4_fc00_201801.nc
+            fileto_interp=s4_fc${mem}_${YEAR}${mon}.nc # the file DATASOURCE should be renamed something like: s4_MEMBER_YEARMONTH.nc" s4_fc00_201801.nc
+            echo ${fileto_interp}
+	   # cp $DATASOURCE ${localdir}/$fileto_interp
+             cp $DATASOURCE ${workdir}/$fileto_interp
+             echo ${fileto_interp}
+            #before the interpolation the file shoudl be modified as follow:
+             ncrename -d time,t    ${workdir}/${fileto_interp}                  #s4_fc00_201802.nc
+             ncrename -d olevel,z    ${workdir}/${fileto_interp}
+             ncrename -v olevel,z   ${workdir}/${fileto_interp}  
+             ncrename -v z,nav_lev  ${workdir}/${fileto_interp}    #$fileto_interp
+             ncrename -v time,time_counter ${workdir}/${fileto_interp}
+             ncrename -v latitude,nav_lat ${workdir}/${fileto_interp}
+             ncrename -v  longitude,nav_lon ${workdir}/${fileto_interp}
+             
+            #fileout=s4_fc0_YEAR.nc ####  the final interpolated file, should be 12 months file. with thethao renamed to votemper and so renamed to vosaline 
+            # fileout=s4_fc${mem}_${YEAR}.nc
+            echo $(pwd) 
+            #echo ${fileout}
+	    #Launch the interpolation toward the target resolution
+            echo ${fileto_interp}
+	    python prep_restart_interp.py ${fileto_interp} /esnas/autosubmit/con_files/mesh_mask_nemo.nemovar_O1L42.nc $config $modelversion
+	    # remove the local files
+           done 
+	done #loop year
+    done #loop month
+  done 
+done #loop member
+       #   ncrename -v  thetao,votemper ${fileto_interp}               #s4_fc00_201802.nc
+         ncrename -v  so,vosaline  ${fileto_interp}          
+
+         # merge all interpolated files s4_MEMBER_YEARMONTH.nc in one 12 months file: s4_fc00_YEAR.nc . and they should go in:
+         #/esarchive/releases/nudging/ocean/s4/ORCA1L75/MEMBER 
+
+     
+                  
+
diff --git a/interpolation_nudging/interp_fc03_s4.sh b/interpolation_nudging/interp_fc03_s4.sh
new file mode 100755
index 0000000..300b9eb
--- /dev/null
+++ b/interpolation_nudging/interp_fc03_s4.sh
@@ -0,0 +1,83 @@
+#!/bin/ksh
+#SBATCH -n 1
+#SBATCH -t 78:00:00
+#SBATCH -J interpORAS4
+#SBATCH -o interp-oras4-%j.log   
+set -exv
+#module load netCDF-Fortran/4.2-foss-2015a
+# This script download the s4 restarts from ECMWF 
+# and launch the interpolation of the files toward 
+# the target resolution
+# History : Chloe Prodhomme - Initial version                           2016 
+#         : Valentina Sicardi - Changes to interpolate nudging files to ORCA1L75
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#                                Arguments
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+YEARI=2017 # first years of the restarts to be intepolated
+YEARF=2018 # Last year to be interpolated
+MEMBER_LST="03 04" # List of members to interpolate
+MON_LST2="0228 0331 0430 0531 0630 0731 0831 0930 1031 1130 1231" #"0131 0228 0331 0430 0531 0630 0731 0831 1031 1130 1231" # List of months to intepolate in formate MMDD
+MON_LST1="0201 0301 0401 0501 0601 0701 0801 0901 1001 1101 1201" #"0131 0228 0331 0430 0531 0630 0731 0831 1031 1130 1231" # 
+month="01 02 03 04 05 06 07 08 09 10 11 12"
+config=1L75 #target resolution for the output grid
+modelversion="Ec3.2" 
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+workdir=/scratch/Earth/$USER/ORAS4/
+tmpdir=/scratch/Earth/$USER/interp/
+rm -f /scratch/Earth/$USER/ORAS4/*
+mkdir -p $workdir
+mkdir -p $tmpdir
+cp *.py $workdir
+cp *.nc $workdir
+cd $workdir
+
+
+#loop over the members
+for mem in $MEMBER_LST ; do
+    #loop over the month
+	#loop over the years
+	for YEAR in `seq $YEARI $YEARF`; do
+            for MON1 in  $MON_LST1; do
+                for MON2 in $MON_LST2; do 
+                    for mon in ${month}; do
+            #DATASOURCE="/esarchive/recon/ecmwf/nemovar_system4/monthly_mean/thetao/thetao_Omon_ORAS4_opa1_20180201-20180228.nc" # HERE should go the input file 
+            DATASOURCE="/esarchive/recon/ecmwf/nemovar_system4/monthly_mean/so/so_Omon_ORAS4_opa3_${YEAR}${MON1}-${YEAR}${MON2}.nc" # HERE should go the input file 
+
+            #fileto_interp=s4_fc00_201802.nc # the file DATASOURCE should be renamed something like: s4_MEMBER_YEARMONTH.nc" s4_fc00_201801.nc
+            fileto_interp=s4_fc${mem}_${YEAR}${mon}.nc # the file DATASOURCE should be renamed something like: s4_MEMBER_YEARMONTH.nc" s4_fc00_201801.nc
+            echo ${fileto_interp}
+	   # cp $DATASOURCE ${localdir}/$fileto_interp
+             cp $DATASOURCE ${workdir}/$fileto_interp
+             echo ${fileto_interp}
+            #before the interpolation the file shoudl be modified as follow:
+             ncrename -d time,t    ${workdir}/${fileto_interp}                  #s4_fc00_201802.nc
+             ncrename -d olevel,z    ${workdir}/${fileto_interp}
+             ncrename -v olevel,z   ${workdir}/${fileto_interp}  
+             ncrename -v z,nav_lev  ${workdir}/${fileto_interp}    #$fileto_interp
+             ncrename -v time,time_counter ${workdir}/${fileto_interp}
+             ncrename -v latitude,nav_lat ${workdir}/${fileto_interp}
+             ncrename -v  longitude,nav_lon ${workdir}/${fileto_interp}
+             
+            #fileout=s4_fc0_YEAR.nc ####  the final interpolated file, should be 12 months file. with thethao renamed to votemper and so renamed to vosaline 
+            # fileout=s4_fc${mem}_${YEAR}.nc
+            echo $(pwd) 
+            #echo ${fileout}
+	    #Launch the interpolation toward the target resolution
+            echo ${fileto_interp}
+	    python prep_restart_interp.py ${fileto_interp} /esnas/autosubmit/con_files/mesh_mask_nemo.nemovar_O1L42.nc $config $modelversion
+	    # remove the local files
+           done 
+	done #loop year
+    done #loop month
+  done 
+done #loop member
+       #   ncrename -v  thetao,votemper ${fileto_interp}               #s4_fc00_201802.nc
+         ncrename -v  so,vosaline ${fileto_interp}          
+
+         # merge all interpolated files s4_MEMBER_YEARMONTH.nc in one 12 months file: s4_fc00_YEAR.nc . and they should go in:
+         #/esarchive/releases/nudging/ocean/s4/ORCA1L75/MEMBER 
+
+     
+                  
+
diff --git a/interpolation_nudging/interp_fc04_s4.sh b/interpolation_nudging/interp_fc04_s4.sh
new file mode 100755
index 0000000..90cf835
--- /dev/null
+++ b/interpolation_nudging/interp_fc04_s4.sh
@@ -0,0 +1,83 @@
+#!/bin/ksh
+#SBATCH -n 1
+#SBATCH -t 78:00:00
+#SBATCH -J interpORAS4
+#SBATCH -o interp-oras4-%j.log   
+set -exv
+#module load netCDF-Fortran/4.2-foss-2015a
+# This script download the s4 restarts from ECMWF 
+# and launch the interpolation of the files toward 
+# the target resolution
+# History : Chloe Prodhomme - Initial version                           2016 
+#         : Valentina Sicardi - Changes to interpolate nudging files to ORCA1L75
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#                                Arguments
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+YEARI=2017 # first years of the restarts to be intepolated
+YEARF=2018 # Last year to be interpolated
+MEMBER_LST="04" # List of members to interpolate
+MON_LST2="0228 0331 0430 0531 0630 0731 0831 0930 1031 1130 1231" #"0131 0228 0331 0430 0531 0630 0731 0831 1031 1130 1231" # List of months to intepolate in formate MMDD
+MON_LST1="0201 0301 0401 0501 0601 0701 0801 0901 1001 1101 1201" #"0131 0228 0331 0430 0531 0630 0731 0831 1031 1130 1231" # 
+month="01 02 03 04 05 06 07 08 09 10 11 12"
+config=1L75 #target resolution for the output grid
+modelversion="Ec3.2" 
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+workdir=/scratch/Earth/$USER/ORAS4/
+tmpdir=/scratch/Earth/$USER/interp/
+rm -f /scratch/Earth/$USER/ORAS4/*
+mkdir -p $workdir
+mkdir -p $tmpdir
+cp *.py $workdir
+cp *.nc $workdir
+cd $workdir
+
+
+#loop over the members
+for mem in $MEMBER_LST ; do
+    #loop over the month
+	#loop over the years
+	for YEAR in `seq $YEARI $YEARF`; do
+            for MON1 in  $MON_LST1; do
+                for MON2 in $MON_LST2; do 
+                    for mon in ${month}; do
+            #DATASOURCE="/esarchive/recon/ecmwf/nemovar_system4/monthly_mean/thetao/thetao_Omon_ORAS4_opa1_20180201-20180228.nc" # HERE should go the input file 
+            DATASOURCE="/esarchive/recon/ecmwf/nemovar_system4/monthly_mean/so/so_Omon_ORAS4_opa4_${YEAR}${MON1}-${YEAR}${MON2}.nc" # HERE should go the input file 
+
+            #fileto_interp=s4_fc00_201802.nc # the file DATASOURCE should be renamed something like: s4_MEMBER_YEARMONTH.nc" s4_fc00_201801.nc
+            fileto_interp=s4_fc${mem}_${YEAR}${mon}.nc # the file DATASOURCE should be renamed something like: s4_MEMBER_YEARMONTH.nc" s4_fc00_201801.nc
+            echo ${fileto_interp}
+	   # cp $DATASOURCE ${localdir}/$fileto_interp
+             cp $DATASOURCE ${workdir}/$fileto_interp
+             echo ${fileto_interp}
+            #before the interpolation the file shoudl be modified as follow:
+             ncrename -d time,t    ${workdir}/${fileto_interp}                  #s4_fc00_201802.nc
+             ncrename -d olevel,z    ${workdir}/${fileto_interp}
+             ncrename -v olevel,z   ${workdir}/${fileto_interp}  
+             ncrename -v z,nav_lev  ${workdir}/${fileto_interp}    #$fileto_interp
+             ncrename -v time,time_counter ${workdir}/${fileto_interp}
+             ncrename -v latitude,nav_lat ${workdir}/${fileto_interp}
+             ncrename -v  longitude,nav_lon ${workdir}/${fileto_interp}
+             
+            #fileout=s4_fc0_YEAR.nc ####  the final interpolated file, should be 12 months file. with thethao renamed to votemper and so renamed to vosaline 
+            # fileout=s4_fc${mem}_${YEAR}.nc
+            echo $(pwd) 
+            #echo ${fileout}
+	    #Launch the interpolation toward the target resolution
+            echo ${fileto_interp}
+	    python prep_restart_interp.py ${fileto_interp} /esnas/autosubmit/con_files/mesh_mask_nemo.nemovar_O1L42.nc $config $modelversion
+	    # remove the local files
+           done 
+	done #loop year
+    done #loop month
+  done 
+done #loop member
+       #   ncrename -v  thetao,votemper ${fileto_interp}               #s4_fc00_201802.nc
+        ncrename -v  so,vosaline ${fileto_interp}          
+
+         # merge all interpolated files s4_MEMBER_YEARMONTH.nc in one 12 months file: s4_fc00_YEAR.nc . and they should go in:
+         #/esarchive/releases/nudging/ocean/s4/ORCA1L75/MEMBER 
+
+     
+                  
+
diff --git a/interpolation_nudging/interp_s4.sh b/interpolation_nudging/interp_s4.sh
new file mode 100755
index 0000000..43e2ae7
--- /dev/null
+++ b/interpolation_nudging/interp_s4.sh
@@ -0,0 +1,83 @@
+#!/bin/ksh
+#SBATCH -n 1
+#SBATCH -t 78:00:00
+#SBATCH -J interpORAS4
+#SBATCH -o interp-oras4-%j.log   
+set -exv
+#module load netCDF-Fortran/4.2-foss-2015a
+# This script download the s4 restarts from ECMWF 
+# and launch the interpolation of the files toward 
+# the target resolution
+# History : Chloe Prodhomme - Initial version                           2016 
+#         : Valentina Sicardi - Changes to interpolate nudging files to ORCA1L75
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#                                Arguments
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+YEARI=2018 # first years of the restarts to be intepolated
+YEARF=2019 # Last year to be interpolated
+MEMBER_LST="00 01 02 03 04" # List of members to interpolate
+MON_LST2="0228 0331 0430 0531 0630 0731 0831 0930 1031 1130 1231" #"0131 0228 0331 0430 0531 0630 0731 0831 1031 1130 1231" # List of months to intepolate in formate MMDD
+MON_LST1="0201 0301 0401 0501 0601 0701 0801 0901 1001 1101 1201" #"0131 0228 0331 0430 0531 0630 0731 0831 1031 1130 1231" # 
+month="01 02 03 04 05 06 07 08 09 10 11 12"
+config=1L75 #target resolution for the output grid
+modelversion="Ec3.2" 
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+workdir=/scratch/Earth/$USER/ORAS4/
+tmpdir=/scratch/Earth/$USER/interp/
+rm -f /scratch/Earth/$USER/ORAS4/*
+mkdir -p $workdir
+mkdir -p $tmpdir
+cp *.py $workdir
+cp *.nc $workdir
+cd $workdir
+
+
+#loop over the members
+for mem in $MEMBER_LST ; do
+    #loop over the month
+	#loop over the years
+	for YEAR in `seq $YEARI $YEARF`; do
+            for MON1 in  $MON_LST1; do
+                for MON2 in $MON_LST2; do 
+                    for mon in ${month}; do
+            #DATASOURCE="/esarchive/recon/ecmwf/nemovar_system4/monthly_mean/thetao/thetao_Omon_ORAS4_opa1_20180201-20180228.nc" # HERE should go the input file 
+            DATASOURCE="/esarchive/recon/ecmwf/nemovar_system4/monthly_mean/so/so_Omon_ORAS4_opa0_${YEAR}${MON1}-${YEAR}${MON2}.nc" # HERE should go the input file 
+
+            #fileto_interp=s4_fc00_201802.nc # the file DATASOURCE should be renamed something like: s4_MEMBER_YEARMONTH.nc" s4_fc00_201801.nc
+            fileto_interp=s4_fc${mem}_${YEAR}${mon}.nc # the file DATASOURCE should be renamed something like: s4_MEMBER_YEARMONTH.nc" s4_fc00_201801.nc
+            echo ${fileto_interp}
+	   # cp $DATASOURCE ${localdir}/$fileto_interp
+             cp $DATASOURCE ${workdir}/$fileto_interp
+             echo ${fileto_interp}
+            #before the interpolation the file shoudl be modified as follow:
+             ncrename -d time,t    ${workdir}/${fileto_interp}                  #s4_fc00_201802.nc
+             ncrename -d olevel,z    ${workdir}/${fileto_interp}
+             ncrename -v olevel,z   ${workdir}/${fileto_interp}  
+             ncrename -v z,nav_lev  ${workdir}/${fileto_interp}    #$fileto_interp
+             ncrename -v time,time_counter ${workdir}/${fileto_interp}
+             ncrename -v latitude,nav_lat ${workdir}/${fileto_interp}
+             ncrename -v  longitude,nav_lon ${workdir}/${fileto_interp}
+             
+            #fileout=s4_fc0_YEAR.nc ####  the final interpolated file, should be 12 months file. with thethao renamed to votemper and so renamed to vosaline 
+            # fileout=s4_fc${mem}_${YEAR}.nc
+            echo $(pwd) 
+            #echo ${fileout}
+	    #Launch the interpolation toward the target resolution
+            echo ${fileto_interp}
+	    python prep_restart_interp.py ${fileto_interp} /esnas/autosubmit/con_files/mesh_mask_nemo.nemovar_O1L42.nc $config $modelversion
+	    # remove the local files
+           done 
+	done #loop year
+    done #loop month
+  done 
+done #loop member
+      #    ncrename -v  thetao,votemper ${fileto_interp}               #s4_fc00_201802.nc
+         ncrename -v  so,vosaline ${fileto_interp}         
+
+         # merge all interpolated files s4_MEMBER_YEARMONTH.nc in one 12 months file: s4_fc00_YEAR.nc . and they should go in:
+         #/esarchive/releases/nudging/ocean/s4/ORCA1L75/MEMBER 
+
+     
+                  
+
diff --git a/interpolation_nudging/library_interp_extrap.py b/interpolation_nudging/library_interp_extrap.py
new file mode 100644
index 0000000..b19cd17
--- /dev/null
+++ b/interpolation_nudging/library_interp_extrap.py
@@ -0,0 +1,400 @@
+import numpy as np
+from numpy import ma as ma
+from netCDF4 import Dataset as nc
+import sys
+from scipy.spatial import ckdtree
+from glob import glob
+import shutil
+import gzip
+
+def getvarmask(varin):
+    """define if the name of the mask corresponding to each variable
+    input:
+    varin: name of the input variables
+    output:
+    mask: name of the corresponding mask variables
+    varlon: name of the longitude variable
+    varlat: name of the latitude variables"""
+
+    if varin in ['avmu','un','ub','gru','gsu','gtu','ssu_m','u_io']:
+        mask='umask' ; varlon='glamu' ; varlat='gphiu' 
+    elif varin in ['avmv','vn','vb','grv','gsv','gtv','ssv_m','v_io']:
+        mask='vmask' ; varlon='glamv' ; varlat='gphiv'  
+    elif varin in ['rotb','rotn']:
+        mask='fmask' ; varlon='glamf' ; varlat='gphif' 
+    elif varin in ['avt','avmt','en','dissl','hdivb','hdivn','rhop','so','thetao','sb','tb','gcx','gcxb','gcxbfs','ssh_m','sshb','sshn','sss_m','sst_m','alb_ice','sst_io','sss_io']:
+        mask='tmask' ; varlon='glamt' ; varlat='gphit' 
+    else:
+        print("variable not found")
+        sys.exit(1)
+    return(mask, varlon, varlat)
+    
+def read_files(fin, varin, fmin, fmout):
+    """This function is reading the variables needed for the interpolation
+    process from the input files
+    Arguments:
+    filein: Input restart type netcdf (already open)
+    varin: Variable to interpolate
+    varmask: name of the mask variable corresponding to varin 
+            (tmask, umask, vmask, fmask)
+    fmin: Input maskfile type netcdf (already open) 
+    fmout: Output mask file type netcdf (already open)
+    Outputs:
+    fieldin: Field to interpolate
+    depthin: 3D depth corresponding to fieldin
+    thickin: 3D thichness corresponding to the fieldin
+    thickout: 3D thickness toward which the interpolation 
+              has to be performed
+    depthout: 3D depth toward which the interpolation 
+              has to be performed
+    """
+    
+    #get the mask variable corresponding to varin
+    varmask, varlon, varlat =getvarmask(varin)
+
+    
+    #read the input mask (needed because original s4 not masked)
+    maskin=np.array(fmin.variables[varmask][:].squeeze())
+    #generate a masked array to mask the land
+    maskin=ma.array(maskin>=1,mask=maskin<0.5)
+    #read the thickness
+    thickin=np.array(fmin.variables["e3t_0"][:].squeeze())
+    #read the depth
+    depthin=np.array(fmin.variables["gdept_0"][:].squeeze())
+    #read the longitude
+    lonin=np.array(fmin.variables[varlon][:].squeeze())
+    #read the latitude
+    latin=np.array(fmin.variables[varlat][:].squeeze())
+
+    
+    fieldin=np.array(fin.variables[varin][:].squeeze())
+    #diemnsion name
+    dimnames=list(fin.variables[varin].dimensions)
+
+    
+
+    #if the last level of the input field is fully masked ()
+    #or almost fully masked (less than 20points)
+    #remove it
+    #check if the variable is 2D or 3D:
+    if len(fieldin.shape)==3:
+        lastlev=maskin.shape[0]-1
+        if (np.sum(maskin[lastlev,:,:])<=20) or (ma.sum(maskin[lastlev,:,:]).mask):
+            maskin=maskin[0:lastlev,:,:]
+            fieldin=np.array(fieldin[0:lastlev,:,:])
+            thickin=thickin[0:lastlev]
+            depthin=depthin[0:lastlev]
+
+
+    #read the mask field
+    maskout=np.array(fmout.variables[varmask][:].squeeze())
+    #thickness
+    thickout=np.array(fmout.variables["e3t_0"][:].squeeze())
+    #depth
+    depthout=np.array(fmout.variables["gdept_0"][:].squeeze())
+    #read the longitude
+    lonout=np.array(fmout.variables[varlon][:].squeeze())
+    #read the latitude
+    latout=np.array(fmout.variables[varlat][:].squeeze())
+    #generate a masked array to mask the land
+    maskout=ma.array(maskout,mask=maskout<0.5)
+
+    #permute the dimensions if needed
+    # not take into account t dimension (size 1)
+    if len(fieldin.shape)==3:
+        correctdimorder=(u'z', u'y', u'x')
+    else:
+        correctdimorder=(u'y', u'x')
+
+    dimnames.remove(u't')
+    #the correctdimension order
+    for idim,dimname in enumerate(dimnames):
+        if dimname!=correctdimorder[idim]:
+            print("Dimension"+dimname+"permuted")
+            fieldin=moveaxis(fieldin, idim, 
+                         correctdimorder.index(dimname))
+    
+    # extend the input depth in 3D 
+    #(needed because from Nemo 3.6 both vary with time ans space)
+    lz0, ly0, lx0 = maskin.shape
+    lzout, lyout, lxout = maskout.shape
+    if len(depthin.shape)==1:
+        depthin.shape=(lz0,1,1)
+        depthin=np.repeat(np.repeat(depthin,ly0, axis=1), lx0, axis=2)
+    if len(depthout.shape)==1:
+        depthout.shape=(lzout,1,1)
+        depthout=np.repeat(np.repeat(depthout, ly0, axis=1), lx0, axis=2)
+    # extend the input thickness in 3D
+    if len(thickin.shape)==1:
+        thickin.shape=(lz0,1,1)
+        thickin=np.repeat(np.repeat(thickin,ly0, axis=1), lx0, axis=2)
+    if len(thickout.shape)==1:
+        thickout.shape=(lzout,1,1)
+        thickout=np.repeat(np.repeat(thickout,ly0, axis=1), lx0, axis=2)
+
+
+    #construct mask and thickness for 2D variables
+    if len(fieldin.shape)==2:
+        ly0,lx0=fieldin.shape
+        maskin=maskin[0,:,:]
+        thickin=np.zeros((ly0,lx0),'d')
+        depthin=np.zeros((ly0,lx0),'d')
+        thickout=np.zeros((ly0,lx0),'d')
+        depthout=np.zeros((ly0,lx0),'d')
+        maskout=maskout[0,:,:]
+
+    #check that the mask corresponds to the input file
+    #(in s4 restarts continents are filled with 0)
+    
+    if (fieldin[np.where(maskin.mask)]!=0).any():
+        print("the variable: "+varmask)
+        print("the input mask:")
+        print(fmin.filepath())
+        print("does not corespond to the input file:")
+        print(fin.filepath())
+        print("for the variable:"+varin)
+        sys.exit(1)
+
+    #apply the mask
+    fieldin=ma.array(fieldin,mask=1-maskin)
+
+    #check that the field is not empty
+    if  (np.sum(fieldin)==0):
+        print("The field written from the file: "+f)
+        print("for the variable"+varin)
+        print("mask with the file: "+fmask)
+        print("seems to be empty")
+        print("Please check your input")
+        sys.exit(1)
+    
+    return(fieldin, thickin, depthin, lonin, latin, 
+           maskout, thickout, depthout, lonout, latout)
+
+def interp_vert(fieldin, thick_in, thick_out):
+    """This function interpolates vertically a (x,y,z) field using the
+    conservative method.
+    Arguments:
+    fieldin: Input Field type mask array
+    thick_int: input thickness thickness of the level 
+    thick_out: output thickness of the level 
+    History : Chloe Prodhomme - Initial version adpated
+              from Cfutools extrap_vert function
+              written by V. Guemas - 2016"""
+
+    (lz0,ly0,lx0)=fieldin.shape
+    (lz1,ly1,lx1)=thick_out.shape
+
+    var0_a=np.array(fieldin)
+    var0=np.array(fieldin)
+    var0=ma.masked_array(var0,mask=None,fill_value=None)
+
+    var0=var0.astype('d')
+
+    mask_in=1-fieldin.mask
+    
+    var1=np.zeros((lz1,ly0,lx0),'d')
+    thick_jk1=np.zeros((ly0,lx0),'d')
+    mask_out=np.zeros((lz1,ly0,lx0),'d')
+    thick_bis=np.zeros((ly0,lx0),'d')
+
+    jk0=0
+    for jk1 in np.arange(lz1) :
+        while ( (jk0 <= (lz0-1)) & ((np.add.reduce(thick_in[0:(jk0+1)]) <= np.add.reduce(thick_out[0:(jk1+1)])) ).any()) :
+            thick_bis=np.multiply(np.minimum(thick_in[jk0],np.add.reduce(thick_in[0:(jk0+1)])-np.add.reduce(thick_out[0:jk1])),mask_in[jk0,:,:])
+            var1[jk1,:,:]=var1[jk1,:,:]+np.multiply(var0[jk0,:,:],thick_bis)
+            thick_jk1=thick_jk1+thick_bis
+            jk0=jk0+1
+        if True: #( jk0 <= (lz0-1)) :
+            jk0in=min(jk0,lz0-1)
+            thick_bis=np.multiply(np.minimum(thick_out[jk1],np.add.reduce(thick_out[0:(jk1+1)])-np.add.reduce(thick_in[0:jk0])),mask_in[jk0in,:,:])
+            var1[jk1,:,:]=var1[jk1,:,:]+np.multiply(var0[jk0in,:,:],thick_bis)
+            thick_jk1=thick_jk1+thick_bis
+        mask_out[jk1,:,:]=np.where(thick_jk1>0.01,False,True)
+        thick_jk1=np.where(thick_jk1==0.,1.,thick_jk1)
+        var1[jk1,:,:]=var1[jk1,:,:]/thick_jk1
+        thick_jk1[:,:]=0
+    #mask the output field
+    fieldout=ma.array(var1, mask=mask_out)
+    
+    return(fieldout)
+
+
+def lon_lat_to_cartesian(lon, lat, R=1):
+    """calculates lon, lat coordinates of a point on a sphere with
+    radius R
+    """
+    lon_r = np.radians(lon)
+    lat_r = np.radians(lat)
+    x = R * np.cos(lat_r) * np.cos(lon_r)
+    y = R * np.cos(lat_r) * np.sin(lon_r)
+    z = R * np.sin(lat_r)
+    return x, y, z
+
+
+def extrap(fieldin,lonin,latin,maskout):
+    """This function extrapolates horizontally each level of a (x,y,z)
+    field using the nearest neighbour method.
+    Argument:
+    fieldin: Input field (ma.array type)
+    lonin: 2d longitude
+    latin: 2d longitude
+    maskout: mask of the field after extrapolation
+    Output:
+    fieldout: output field (ma.array)
+    """
+    #add a dimension of size 1 for 2d field
+    if len(fieldin.shape)==2:
+        fieldin.shape=(1,)+fieldin.shape
+
+    #construct points to fill
+    Pfill=ma.array((fieldin.mask)&(maskout!=0), mask=1-maskout)
+
+    # fieldout intitialization
+    fieldout=np.array(fieldin)
+    
+    
+    #each level has a different mask, loop over the levels
+    lz0=fieldin.shape[0]
+        
+    for lev in np.arange(lz0):
+        newvar = ma.array(fieldin[lev,:,:], 
+                          mask=fieldin.mask[lev,:,:])
+        Pfilllev = Pfill[lev,:,:] 
+        
+        #not masked coordinates for the present level
+        nomlon = lonin[np.where(newvar.mask==False)]
+        nomlat = latin[np.where(newvar.mask==False)]
+        #cartesian coordinates of not masked points
+        levxs, levys, levzs = lon_lat_to_cartesian(nomlon, nomlat)
+        levkdt = ckdtree.cKDTree(np.array([levxs, levys, levzs]).T)
+        #points to extrapolate at the current level
+        newindexes = np.where(Pfilllev==1)
+        latidxs = newindexes[0]
+        lonidxs = newindexes[1]
+        #print(newindexes)
+        exlon = lonin[latidxs, lonidxs]
+        exlat = latin[latidxs, lonidxs]
+        #print(newvar[levkdt.data[0,0], levkdt.data[0,1]])
+               
+        #cartesian coordinates of the points to extrapolate
+        xt, yt, zt = lon_lat_to_cartesian(exlon, exlat)
+        #calculates distances and indexes of the nearest neighbours
+        dist, idx = levkdt.query(np.array([xt, yt, zt]).T, k=1, p=2)
+
+        #assign to the result matrix the found values
+        fieldout[lev,latidxs, lonidxs] = newvar[np.where(newvar.mask==False)].flatten()[idx]
+
+    #mask field out
+    fieldout=fieldout*maskout
+    fieldout=ma.array(fieldout,mask=1-maskout)
+    return(fieldout)
+
+
+
+def vertinterp_extrap(filein, varin, fmask, fmaskout, month="", modvers=""):
+    """read and interpolate verticaly and extrapolate horizontal the given variable
+    from a restart file
+    Arguments:
+    filein: Input restart file
+    varin: name of the variable to extrapolate
+    fmask: mask file corresponding to varin
+    fmaskout: mask to define the grid toward which the extrapolation if done
+    month: starting month of the restart
+           (needed only if there are points to fill in the caspienne sea)
+    modelvers: name of the model version to find the climatology to fill the caspienne
+          (needed only if there are points to fill in the caspienne sea)  
+   
+    """
+    
+    #read files and define variables needed for the rest of the process
+    (fieldin, thickin, depthin, lonin, latin, 
+     maskout, 
+     thickout, depthout, 
+     lonout, latout) = read_files(filein, 
+                                varin, fmask, fmaskout)
+
+    #check if the variable is 2D or 3D:
+    if len(fieldin.shape)==3:
+        #perform the vertical extrapolation
+        fieldin=interp_vert(fieldin, thickin,thickout)
+    
+    #construct points to fill
+    Pfill=ma.array((fieldin.mask)&(maskout!=0), mask=1-maskout)
+    
+    #find if the caspienne sea need to be filled
+    caspbox=np.where((lonin>45)&(lonin<56)&(latin>35)&(latin<50))
+    #longitude and latitude boundary of the caspienne sea
+    loncasp1,loncasp2=caspbox[0].min(),caspbox[0].max()
+    latcasp1,latcasp2=caspbox[1].min(),caspbox[1].max()
+    #check is there are points to fill in the caspienne sea
+    if len(fieldin.shape)==2:
+        casptest=np.sum(Pfill[loncasp1:loncasp2,latcasp1:latcasp2], 
+                            axis=(0,1))!=0
+    else: 
+        casptest=np.sum(Pfill[:,loncasp1:loncasp2,latcasp1:latcasp2], 
+                            axis=(0,1,2))!=0
+    #If there are points to be filled
+    if  casptest:
+
+        #if ((varin=="so")|(varin=="so"))|((varin=="thetao")|(varin=="thetao")):
+        if ((varin=="so")|(varin=="thetao")):
+
+        #Ugly solution, to be improve would need levitus file at all resolution
+            if modvers=="Ec3.1":
+                pathclim="/esnas/releases/ic/ocean/ORCA1L46/levitus_clim/"
+                if ((varin=="tn")|(varin=="tb")):
+                    #name of the file
+                    varclim="votemper"
+                    fileclim=pathclim+"temperature_m%02d.nc"%month
+            
+                if ((varin=="sn")|(varin=="sb")):
+                    #open climatological files
+                    varclim="vosaline"
+                    fileclim=pathclim+"salinity_m%02d.nc"%month  
+
+            elif modvers=="Ec2.3":
+                #in this case we use an old restart for the climatology
+                fileclim=glob("/esnas/releases/ic/ocean/ORCA1/s4/s4_fc0_1993%02d*_restart.nc.gz"%month)
+                print(fileclim)
+                shutil.copy(fileclim[0], "fileclim.nc.gz")
+                fileclim="fileclim.nc"
+                inF = gzip.open('fileclim.nc.gz', 'rb')
+                outF = open(fileclim, 'wb')
+                outF.write( inF.read() )
+                inF.close()
+                outF.close()
+                varclim=varin
+            else:
+                print("no climatology is available for this model version to fill the caspienne sea:")
+                print(modvers)
+                sys.exit(1)
+
+            #open the file
+            print(fileclim)
+            fclim=nc(fileclim, "r")
+            #read variable for the given month
+            clim=np.array(fclim.variables[varclim][:].squeeze())
+
+            #add the caspienne sea
+            fieldin[:,caspbox[0],caspbox[1]]=clim[:,caspbox[0],caspbox[1]]
+        else:
+            print(fieldin.shape)
+            print(caspbox[1].min())
+            print(caspbox[1].max())
+            print(caspbox[0].min())
+            print(caspbox[0].max())
+            if (len(fieldin.shape)==3):
+                fieldin[:,caspbox[0],caspbox[1]]=0
+            elif  (len(fieldin.shape)==2):
+                fieldin[caspbox[0],caspbox[1]]=0
+            else:
+                print("vertinterp_extrap function can handle only 2 and 3d arrays")
+                sys.exit(1)
+    
+    #horizontal extrapolation
+    fieldout=extrap(fieldin,lonin,latin,maskout)
+    return(fieldout)
+
+
+    
+    
diff --git a/interpolation_nudging/library_interp_extrap.pyc b/interpolation_nudging/library_interp_extrap.pyc
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diff --git a/interpolation_nudging/prep_restart_interp.py b/interpolation_nudging/prep_restart_interp.py
new file mode 100644
index 0000000..470839a
--- /dev/null
+++ b/interpolation_nudging/prep_restart_interp.py
@@ -0,0 +1,188 @@
+from library_interp_extrap import *
+from compute_density import compute_density
+from glob import glob
+import os
+import shutil
+import gzip
+#This fonction generate a restart interpolated verticaly on the output grid
+###########
+#Arguments#
+###########
+#filein: input restart file
+#fmask: input mask corresponding to the input file 
+#ex: fmask="/esnas/autosubmit/con_files/mesh_mask_nemo.nemovar_O1L42.nc"
+#resout: output resolution ex: resout="1L75"
+#versout: corresponding model version ex:versout="Ec3.2"
+
+
+#  Input arguments
+filein=sys.argv[1]
+fmask=sys.argv[2]
+resout=sys.argv[3]
+versout=sys.argv[4]
+
+#go in the working directory
+#workdir="/scratch/Earth/"+os.environ["USER"]+"/restart_"+resout+"_"+versout
+#if (not os.path.isdir(workdir)):
+#    os.makedirs(workdir)
+#os.chdir(workdir)
+
+# mask file describing the output grid
+fmaskout="/esarchive/autosubmit/con_files/mesh_mask_nemo."+versout+"_O"+resout+".nc"
+
+#dirout="/esnas/releases/ic/ocean/ORCA"+resout+"/s4"
+dirout="/esarchive/scratch/Earth/vsicardi/ORAS_interp"
+#print("before entering in the loop")
+#check if the output file is already there
+if len(glob(os.path.join(dirout, filein+".gz")))==0:
+    #print("enter agin in the loop")
+    #copy the file from the /esnas into the 
+    dirin,fileinloc=os.path.split(filein)
+    if dirin!="":
+        shutil.copy(filein, fileinloc)
+    
+    #copy the mask from the /esnas into the 
+    dirmask,fmaskloc=os.path.split(fmask)
+    if dirmask!="":
+        shutil.copy(fmask, fmaskloc)
+
+    #temporary output file
+    fileout=filein.replace(".nc","_new.nc")
+    
+    #define the variable name of longitude latitude depth
+    #to be copied from the mask
+    vardim=["nav_lon", "nav_lat", "nav_lev"]
+
+    #variable copied with no interpolation
+    varnointerp=["time_counter"]
+
+    lstfieldout=[]
+
+    #Open the output file
+    fin=nc(fileinloc, "r")
+    print(fin)
+    fmout=nc(fmaskout, "r")
+    fmin=nc(fmaskloc, "r")
+    fout=nc(fileout, "w", format="NETCDF3_CLASSIC")
+    nlev=fmout.dimensions["z"].size
+    #print(fileout)
+   
+    #copy all th dimension for fin except the level
+    for name, dimension in fin.dimensions.iteritems():
+        if name != "z":
+            fout.createDimension(str(name), len(dimension) if not dimension.isunlimited() else None)
+    #create the level dimension
+    fout.createDimension("z", nlev)
+    #print(fileout)
+
+    #write the variable corresponding to the dimension (from the input mask)
+    for name in vardim:
+        variable=fmout.variables[name]
+       # print(fileout)
+       #print(fout)
+        fout.createVariable(name, variable.datatype, variable.dimensions)
+        fout.variables[name][:]=variable[:]
+        #print("after writting dimension variable")
+            
+        listdens=[]
+        listdens_varname=[]
+       # print(fin.variables)
+    
+    
+    for varin, variable in fin.variables.iteritems():
+        print ('print1') 
+        print (varin) 
+        ##take out the variable nav_lev, lon ,lat
+        if not(varin in vardim):
+            print ('print2') 
+            print (varin)
+            ##for the variable which no need interpolation copy them
+            if varin in varnointerp:
+                print ('print3') 
+                print (varin) 
+                #print(variable.datatype)
+                #print(variable.dimensions)
+                #print(fout)
+                var=fout.createVariable(varin, variable.datatype, variable.dimensions)
+                var[:]=variable[:]
+                #print("after writting variable:")
+                #print(varin)
+            else:
+                month=int(fileinloc.split("_")[2][4:6])
+                ##perform the interpolation vertical y horizontal
+                print ('print4') 
+                print (varin) 
+                print ("test") 
+                fieldout=vertinterp_extrap(fin, varin, fmin, fmout, 
+                                           month=month, modvers=versout)
+                ##add the temporal dimension
+                shapeout=(1,)+fieldout.shape
+                fieldout.shape=shapeout
+                print(varin)
+                if varin in ["so","sn"]:
+                    print("Iam here")
+                    listdens.append(fieldout)
+                    listdens_varname.append(varin)
+                ##put 0 for mask value (only by converting from ma into np array)
+                fieldout=np.array(fieldout)
+                print("before defining variable")
+                print(varin)
+                #print(variable.datatype)
+                #print(variable.dimensions)
+                #print(fout)
+                #add a test to avoid negative values in en
+                if varin =="en":
+                    fieldout[fieldout<0]=0
+                    print("negative values removed from en")
+                var=fout.createVariable(varin, variable.datatype, variable.dimensions)
+                var[:]=fieldout                  
+                #print("after writting variable:")
+                print(varin)
+                #get temperature
+    print(listdens_varname)
+    #ptemp=listdens[listdens_varname.index("thetao")]
+    #get salinity
+    psal=listdens[listdens_varname.index("so")]
+
+    #print("rhop")
+    #rhop=compute_density(ptemp, psal) 
+    #convert into numpy array (0 instead of mask)
+    #rhop=np.array(rhop)
+    #write density into the output file
+    #print("before writting variable:")
+    #print(rhop)
+    #var=fout.createVariable("rhop", 
+    #                        fin.variables["tn"].datatype, 
+    #                        fin.variables["tn"].dimensions)
+    ##print("after defining  rhop in the file")
+
+    #var[:]=rhop
+    #print("after writting rhop")
+    
+           
+    fin.close()
+    #print("after closing fin")
+    fout.close()
+    #print("after closing fout")
+    fmin.close()
+    #print("after closing fmin")
+    fmout.close()
+    #print("after closing fmout")
+
+    #gzip the files
+    
+    #print("before gzip:  "+ fileout)
+    with open(fileout, 'rb') as f_in, gzip.open(fileout+'.gz', 'wb') as f_out:
+        shutil.copyfileobj(f_in, f_out)
+    #print("after gzip")
+    #copy the output file into /esnas
+    shutil.copy(fileout+'.gz', os.path.join(dirout,fileinloc+'.gz'))
+    print("the interpolated file has been created and copied into:")
+    print(os.path.join(dirout,fileinloc+'.gz'))
+
+    #remove the local files
+    os.remove(fileinloc)
+    os.remove(fileout+'.gz')
+    os.remove(fileout)
+    
+    print("local files have been removed")
-- 
GitLab


From 385bb97fbf36b1d2aadbbac6d1ae41afb326c2ff Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Sun, 8 Mar 2020 21:08:42 +0100
Subject: [PATCH 02/16] Add new file

---
 interpolation/Interp_ORAS5.sh | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 interpolation/Interp_ORAS5.sh

diff --git a/interpolation/Interp_ORAS5.sh b/interpolation/Interp_ORAS5.sh
new file mode 100644
index 0000000..3df2940
--- /dev/null
+++ b/interpolation/Interp_ORAS5.sh
@@ -0,0 +1,13 @@
+#!/bin/ksh
+#SBATCH -n 1
+#SBATCH -t 78:00:00
+#SBATCH -J remaporas5
+#SBATCH -o remaporas5-%j.log   
+
+
+set -exv
+
+year1=1991
+year2=1999
+for year in `seq $year1  $year2` ; do 
+cdo remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -fillmiss2 -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc /esarchive/releases/nudging/ocean/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc00/s5_fc0_${year}b.nc ;  done
\ No newline at end of file
-- 
GitLab


From 3c4916abd57ecbe982a0f8404f967c519147e0d0 Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Mon, 9 Mar 2020 11:51:02 +0100
Subject: [PATCH 03/16] Update Interp_ORAS5.sh

---
 interpolation/Interp_ORAS5.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interpolation/Interp_ORAS5.sh b/interpolation/Interp_ORAS5.sh
index 3df2940..2707101 100644
--- a/interpolation/Interp_ORAS5.sh
+++ b/interpolation/Interp_ORAS5.sh
@@ -10,4 +10,4 @@ set -exv
 year1=1991
 year2=1999
 for year in `seq $year1  $year2` ; do 
-cdo remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -fillmiss2 -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc /esarchive/releases/nudging/ocean/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc00/s5_fc0_${year}b.nc ;  done
\ No newline at end of file
+cdo setmisstoc,0 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -fillmiss2 -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc /esarchive/releases/nudging/ocean/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc00/s5_fc0_${year}b.nc ;  done
\ No newline at end of file
-- 
GitLab


From af26ebe93280bd962aa8ee482dfb3f68ed468785 Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Mon, 9 Mar 2020 11:51:18 +0100
Subject: [PATCH 04/16] Delete Interp_ORAS5.sh

---
 interpolation/Interp_ORAS5.sh | 13 -------------
 1 file changed, 13 deletions(-)
 delete mode 100644 interpolation/Interp_ORAS5.sh

diff --git a/interpolation/Interp_ORAS5.sh b/interpolation/Interp_ORAS5.sh
deleted file mode 100644
index 2707101..0000000
--- a/interpolation/Interp_ORAS5.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/bin/ksh
-#SBATCH -n 1
-#SBATCH -t 78:00:00
-#SBATCH -J remaporas5
-#SBATCH -o remaporas5-%j.log   
-
-
-set -exv
-
-year1=1991
-year2=1999
-for year in `seq $year1  $year2` ; do 
-cdo setmisstoc,0 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -fillmiss2 -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc /esarchive/releases/nudging/ocean/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc00/s5_fc0_${year}b.nc ;  done
\ No newline at end of file
-- 
GitLab


From 7c0edfc99a14d75c48cfea712a68a1aafe7da27b Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Mon, 9 Mar 2020 11:51:54 +0100
Subject: [PATCH 05/16] Add new file

---
 interpolation_nudging/Interp_ORAS5.nc | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 interpolation_nudging/Interp_ORAS5.nc

diff --git a/interpolation_nudging/Interp_ORAS5.nc b/interpolation_nudging/Interp_ORAS5.nc
new file mode 100644
index 0000000..2436684
--- /dev/null
+++ b/interpolation_nudging/Interp_ORAS5.nc
@@ -0,0 +1,14 @@
+#!/bin/ksh
+#SBATCH -n 1
+#SBATCH -t 78:00:00
+#SBATCH -J remaporas5
+#SBATCH -o remaporas5-%j.log   
+
+
+set -exv
+
+year1=1991
+year2=1999
+for year in `seq $year1  $year2` ; do 
+cdo setmisstoc,0 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -fillmiss2 -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc /esarchive/releases/nudging/ocean/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc00/s5_fc0_${year}b.nc ;  
+done
-- 
GitLab


From ae0a01b8e5d66d5731088f4d6cd8fd8ae17fa1c8 Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Mon, 9 Mar 2020 11:54:20 +0100
Subject: [PATCH 06/16] Update Interp_ORAS5.nc

---
 interpolation_nudging/{Interp_ORAS5.nc => Interp_ORAS5.sh} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename interpolation_nudging/{Interp_ORAS5.nc => Interp_ORAS5.sh} (100%)

diff --git a/interpolation_nudging/Interp_ORAS5.nc b/interpolation_nudging/Interp_ORAS5.sh
similarity index 100%
rename from interpolation_nudging/Interp_ORAS5.nc
rename to interpolation_nudging/Interp_ORAS5.sh
-- 
GitLab


From e9d3697a38079680769f244671ea14be246a3099 Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Mon, 9 Mar 2020 12:20:51 +0100
Subject: [PATCH 07/16] Update Interp_ORAS5.sh

---
 interpolation_nudging/Interp_ORAS5.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interpolation_nudging/Interp_ORAS5.sh b/interpolation_nudging/Interp_ORAS5.sh
index 2436684..83d9097 100644
--- a/interpolation_nudging/Interp_ORAS5.sh
+++ b/interpolation_nudging/Interp_ORAS5.sh
@@ -10,5 +10,5 @@ set -exv
 year1=1991
 year2=1999
 for year in `seq $year1  $year2` ; do 
-cdo setmisstoc,0 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -fillmiss2 -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc /esarchive/releases/nudging/ocean/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc00/s5_fc0_${year}b.nc ;  
+cdo setmisstoc,0 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -fillmiss2 -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc /esarchive/releases/nudging/ocean/ORCA025L75/fc00/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc00/s5_fc0_${year}b.nc ;  
 done
-- 
GitLab


From ff6b3c49eec721de926ee691b73676ca6f371460 Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Thu, 12 Nov 2020 14:56:13 +0100
Subject: [PATCH 08/16] Update Interp_ORAS5.sh

---
 interpolation_nudging/Interp_ORAS5.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/interpolation_nudging/Interp_ORAS5.sh b/interpolation_nudging/Interp_ORAS5.sh
index 83d9097..fde90a1 100644
--- a/interpolation_nudging/Interp_ORAS5.sh
+++ b/interpolation_nudging/Interp_ORAS5.sh
@@ -7,8 +7,8 @@
 
 set -exv
 
-year1=1991
-year2=1999
+year1=1990
+year2=2019
 for year in `seq $year1  $year2` ; do 
-cdo setmisstoc,0 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -fillmiss2 -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc /esarchive/releases/nudging/ocean/ORCA025L75/fc00/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc00/s5_fc0_${year}b.nc ;  
+cdo setmisstoc,0 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -fillmiss2 -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc  /esarchive/releases/nudging/ocean/s5/ORCA025L75_ORAS5/fc00/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc0/s5_fc0_${year}.nc ;  
 done
-- 
GitLab


From 2f4ab43d5989d400c42a3ef18846d6fb31aff940 Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Thu, 12 Nov 2020 14:59:40 +0100
Subject: [PATCH 09/16] Add new file

---
 interpolation_nudging/Interp_ORAS5_ORCA025 | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 interpolation_nudging/Interp_ORAS5_ORCA025

diff --git a/interpolation_nudging/Interp_ORAS5_ORCA025 b/interpolation_nudging/Interp_ORAS5_ORCA025
new file mode 100644
index 0000000..d39bfab
--- /dev/null
+++ b/interpolation_nudging/Interp_ORAS5_ORCA025
@@ -0,0 +1,14 @@
+#!/bin/ksh
+#SBATCH -n 1
+#SBATCH -t 78:00:00
+#SBATCH -J remaporas5
+#SBATCH -o remaporas5-%j.log   
+
+
+set -exv
+
+year1=1990
+year2=2019
+for year in `seq $year1  $year2` ; do 
+cdo setmisstoc,0 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc -fillmiss2 -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc  /esarchive/releases/nudging/ocean/s5/ORCA025L75_ORAS5/fc00/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc0/s5_fc0_${year}.nc ;  
+done
-- 
GitLab


From a0faa1ea8cf2dc96be792b311d137a2640741549 Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Thu, 12 Nov 2020 15:00:29 +0100
Subject: [PATCH 10/16] Update Interp_ORAS5_ORCA025

---
 interpolation_nudging/Interp_ORAS5_ORCA025 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interpolation_nudging/Interp_ORAS5_ORCA025 b/interpolation_nudging/Interp_ORAS5_ORCA025
index d39bfab..a8a4669 100644
--- a/interpolation_nudging/Interp_ORAS5_ORCA025
+++ b/interpolation_nudging/Interp_ORAS5_ORCA025
@@ -10,5 +10,5 @@ set -exv
 year1=1990
 year2=2019
 for year in `seq $year1  $year2` ; do 
-cdo setmisstoc,0 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc -fillmiss2 -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc  /esarchive/releases/nudging/ocean/s5/ORCA025L75_ORAS5/fc00/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc0/s5_fc0_${year}.nc ;  
+cdo setmisstoc,0 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc -fillmiss2 -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc  /esarchive/releases/nudging/ocean/s5/ORCA025L75_ORAS5/fc00/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA025L75/fc0/s5_fc0_${year}.nc ;  
 done
-- 
GitLab


From 5e4b1acd25ea1acd599958286e0083cef8e8bf67 Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Thu, 12 Nov 2020 15:02:55 +0100
Subject: [PATCH 11/16] Update Interp_ORAS5_ORCA025

---
 interpolation_nudging/Interp_ORAS5_ORCA025 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interpolation_nudging/Interp_ORAS5_ORCA025 b/interpolation_nudging/Interp_ORAS5_ORCA025
index a8a4669..e64af75 100644
--- a/interpolation_nudging/Interp_ORAS5_ORCA025
+++ b/interpolation_nudging/Interp_ORAS5_ORCA025
@@ -10,5 +10,5 @@ set -exv
 year1=1990
 year2=2019
 for year in `seq $year1  $year2` ; do 
-cdo setmisstoc,0 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc -fillmiss2 -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc  /esarchive/releases/nudging/ocean/s5/ORCA025L75_ORAS5/fc00/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA025L75/fc0/s5_fc0_${year}.nc ;  
+cdo setmisstoc,0 -fillmiss2 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc  /esarchive/releases/nudging/ocean/s5/ORCA025L75_ORAS5/fc00/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA025L75/fc0/s5_fc0_${year}.nc ;  
 done
-- 
GitLab


From d587b0b0669bdc5b536d1226fe9f14f76831823e Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Thu, 12 Nov 2020 15:03:24 +0100
Subject: [PATCH 12/16] Update Interp_ORAS5.sh

---
 interpolation_nudging/Interp_ORAS5.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interpolation_nudging/Interp_ORAS5.sh b/interpolation_nudging/Interp_ORAS5.sh
index fde90a1..d8fa6e0 100644
--- a/interpolation_nudging/Interp_ORAS5.sh
+++ b/interpolation_nudging/Interp_ORAS5.sh
@@ -10,5 +10,5 @@ set -exv
 year1=1990
 year2=2019
 for year in `seq $year1  $year2` ; do 
-cdo setmisstoc,0 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -fillmiss2 -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc  /esarchive/releases/nudging/ocean/s5/ORCA025L75_ORAS5/fc00/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc0/s5_fc0_${year}.nc ;  
+cdo setmisstoc,0 -fillmiss2  -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc  /esarchive/releases/nudging/ocean/s5/ORCA025L75_ORAS5/fc00/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc0/s5_fc0_${year}.nc ;  
 done
-- 
GitLab


From 67cf7356a13d12757d29b7e08369e4d0dc514d52 Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Thu, 12 Nov 2020 15:13:14 +0100
Subject: [PATCH 13/16] Update Interp_ORAS5_ORCA025

---
 .../{Interp_ORAS5_ORCA025 => Interp_ORAS5_ORCA025.sh}             | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename interpolation_nudging/{Interp_ORAS5_ORCA025 => Interp_ORAS5_ORCA025.sh} (100%)

diff --git a/interpolation_nudging/Interp_ORAS5_ORCA025 b/interpolation_nudging/Interp_ORAS5_ORCA025.sh
similarity index 100%
rename from interpolation_nudging/Interp_ORAS5_ORCA025
rename to interpolation_nudging/Interp_ORAS5_ORCA025.sh
-- 
GitLab


From a8b341db9a420cf23e1f09625152bfa6703344b8 Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Thu, 25 Feb 2021 16:01:54 +0100
Subject: [PATCH 14/16] Update Interp_ORAS5.sh

---
 interpolation_nudging/Interp_ORAS5.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interpolation_nudging/Interp_ORAS5.sh b/interpolation_nudging/Interp_ORAS5.sh
index d8fa6e0..00519fe 100644
--- a/interpolation_nudging/Interp_ORAS5.sh
+++ b/interpolation_nudging/Interp_ORAS5.sh
@@ -10,5 +10,5 @@ set -exv
 year1=1990
 year2=2019
 for year in `seq $year1  $year2` ; do 
-cdo setmisstoc,0 -fillmiss2  -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc  /esarchive/releases/nudging/ocean/s5/ORCA025L75_ORAS5/fc00/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc0/s5_fc0_${year}.nc ;  
+cdo setmisstoc,0 -fillmiss2  -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc  /esarchive/releases/nudging/ocean/s5/ORCA025L75_ORAS5/fc0/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc00/s5_fc0_${year}.nc ;  
 done
-- 
GitLab


From 50ab1acfa3fec5ecedda10983d25c05bb64515a4 Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Thu, 25 Feb 2021 16:02:17 +0100
Subject: [PATCH 15/16] Update Interp_ORAS5.sh

---
 interpolation_nudging/Interp_ORAS5.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interpolation_nudging/Interp_ORAS5.sh b/interpolation_nudging/Interp_ORAS5.sh
index 00519fe..049f484 100644
--- a/interpolation_nudging/Interp_ORAS5.sh
+++ b/interpolation_nudging/Interp_ORAS5.sh
@@ -10,5 +10,5 @@ set -exv
 year1=1990
 year2=2019
 for year in `seq $year1  $year2` ; do 
-cdo setmisstoc,0 -fillmiss2  -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc  /esarchive/releases/nudging/ocean/s5/ORCA025L75_ORAS5/fc0/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc00/s5_fc0_${year}.nc ;  
+cdo setmisstoc,0 -fillmiss2  -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA1.nc -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc  /esarchive/releases/nudging/ocean/s5/ORCA025L75_ORAS5/fc0/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA1L75/fc00/s5_fc00_${year}.nc ;  
 done
-- 
GitLab


From 4f831c585e87caa09bb3ab9a0e00a0fbda8a9953 Mon Sep 17 00:00:00 2001
From: Juan <juan.acosta@bsc.es>
Date: Wed, 4 Aug 2021 18:08:30 +0000
Subject: [PATCH 16/16] Update Interp_ORAS5_ORCA025.sh

---
 interpolation_nudging/Interp_ORAS5_ORCA025.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interpolation_nudging/Interp_ORAS5_ORCA025.sh b/interpolation_nudging/Interp_ORAS5_ORCA025.sh
index e64af75..b9be890 100644
--- a/interpolation_nudging/Interp_ORAS5_ORCA025.sh
+++ b/interpolation_nudging/Interp_ORAS5_ORCA025.sh
@@ -10,5 +10,5 @@ set -exv
 year1=1990
 year2=2019
 for year in `seq $year1  $year2` ; do 
-cdo setmisstoc,0 -fillmiss2 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc -setctomiss,0 -setgrid,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc  /esarchive/releases/nudging/ocean/s5/ORCA025L75_ORAS5/fc00/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA025L75/fc0/s5_fc0_${year}.nc ;  
+cdo setmisstoc,0 -fillmiss2 -remapbil,/esarchive/scratch/jacosta/TMP/bathy_meter_ORCA025.nc -setctomiss,0 /esarchive/releases/nudging/ocean/s5/ORCA025L75_ORAS5/fc0/s5_fc0_${year}.nc /esarchive/releases/nudging/ocean/s5/ORCA025L75/fc0/s5_fc0_${year}.nc ;  
 done
-- 
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