Add Preporcessing Scripts and a README to the sponges tools

tools/sponge/README.md

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+## Sponges
+
+This folder contains tools for creating temperature and salinity sponges for use in MOM6 based on the GLORYS reanalysis.
+
+## preproc_scripts
+
+Scripts to subset, average, and fill the GLORYS data on the uda to preprocess it for the python scripts.
+
+# Regional Subsetting
+
+Regional subsets of the GLORYS reanalysis are created using `ncks` in `get_so_monthly.sh` and `get_thetao_monthly.sh`. 
+You should adjust the regional subset in the script to match the region of interest.
+
+For example:
+```
+ncks -d latitude,40.,90. -d longitude,0.,360 filein.nc fileout.nc
+```
+
+# Scripts
+
+As written these preprocessing scripts must be run in three stages.
+1. First, subset the temperature and salinity and create monthly averages
+```
+sbatch get_thetao_monthly.sh <YEAR> <MONTH>
+sbatch get_so_monthly.sh <YEAR> <MONTH>
+```
+
+2. Next, fill the data
+```
+sbatch fill_glorys_nn_monthly.sh <YEAR> <MONTH>
+```
+
+3. Finally, once the filled data for every month in a given yeas have been created, the merge script can be used.
+```
+sbatch merge_so_thetao_year.sh <YEAR>
+```
+
+This should produce data that is compatible with `write_nudging_data.py`
+
+## Using these files in MOM6
+
+To use the sponges generated by these scripts in MOM6 we reccomend the following settings:
+```
+#override SPONGE = True
+#override SPONGE_UV = False
+#override SPONGE_DAMPING_FILE = "damping_full_t_90d.nc"
+#override SPONGE_IDAMP_VAR = "Idamp"
+#override SPONGE_STATE_FILE = "glorys_sponge_monthly_bnd_${fyear}.nc"
+#override SPONGE_PTEMP_VAR = "thetao"
+#override SPONGE_SALT_VAR = "so"
+#override SPONGE_ETA_VAR = "depth"
+#override INTERPOLATE_SPONGE_TIME_SPACE = True
+#override SPONGE_DATA_ONGRID = True
+```
+These should be added to `MOM_override` in the experiment of the xml.
+
+In the xml, the paths to the files needed for sponges so that they are include in the `INPUT` directory.
+```
+<!-- Two new files for the nudging: -->
+<dataFile label="input" target="INPUT/" chksum="" size="" timestamp="">
+  <dataSource site="ncrc">$(YOUR_PATH)/damping_full_t_90d.nc</dataSource>
+</dataFile>
+<dataFile label="input" target="INPUT/" chksum="" size="" timestamp="">
+  <dataSource site="ncrc">$(YOUR_PATH)/glorys_sponge_monthly_${fyear}.nc</dataSource>
+</dataFile>
+```
+

tools/sponge/preproc_scripts/fill_glorys_nn_monthly.csh

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+#!/bin/tcsh
+#SBATCH --ntasks=1
+#SBATCH --job-name=fill_glorys_arctic
+#SBATCH --time=2880
+#SBATCH --partition=batch
+
+# Usage: sbatch fill_glorys_nn_monthly.sh <YEAR> <MONTH>
+# Original Author: Andrew Ross, modified by Theresa Morrison
+
+module load cdo
+module load nco/5.0.1
+module load gcp
+
+set year=$1
+set month=`printf "%02d" $2`
+
+set apath='/archive/Theresa.Morrison/datasets/glorys/GLOBAL_MULTIYEAR_PHY_001_030/monthly'
+
+# Regionally-slice and convert daily to monthly GLORYS reanalysis on archive beforehand.
+
+# dmget all of the files for this month from archive.
+dmget ${apath}/so/GLORYS_so_arctic_${year}_${month}.nc ${apath}/thetao/GLORYS_thetao_arctic_${year}_${month}.nc
+
+# copy from archive to vftmp for speed?
+#gcp /archive/acr/datasets/glorys/GLOBAL_MULTIYEAR_PHY_001_030/daily/GLORYS_REANALYSIS_${year}-${month}-*.nc $TMPDIR
+gcp /archive/tnm/datasets/glorys/GLOBAL_MULTIYEAR_PHY_001_030/monthly/so/GLORYS_so_arctic_${year}_${month}.nc $TMPDIR
+gcp /archive/tnm/datasets/glorys/GLOBAL_MULTIYEAR_PHY_001_030/monthly/thetao/GLORYS_thetao_arctic_${year}_${month}.nc $TMPDIR
+
+# create a directory to store the filled files.
+mkdir $TMPDIR/filled
+
+# look for all of the daily files. 
+# loop over them, using cdo setmisstonn to fill the missing data
+# and then ncks to compress the resulting file.
+find ${TMPDIR}/GLORYS_so_arctic_${year}_${month}.nc -type f -exec sh -c 'file="$1"; filename="${file##*/}"; cdo setmisstonn "$1" "${TMPDIR}/filled/${filename}"; ncks -4 -L 5 "${TMPDIR}/filled/${filename}" -O "${TMPDIR}/filled/${filename}"' find-sh {} \;
+find ${TMPDIR}/GLORYS_thetao_arctic_${year}_${month}.nc -type f -exec sh -c 'file="$1"; filename="${file##*/}"; cdo setmisstonn "$1" "${TMPDIR}/filled/${filename}"; ncks -4 -L 5 "${TMPDIR}/filled/${filename}" -O "${TMPDIR}/filled/${filename}"' find-sh {} \;
+
+# copy the filled data for this month to /work.
+gcp $TMPDIR/filled/*.nc /work/tnm/datasets/glorys/GLOBAL_MULTIYEAR_PHY_001_030/monthly/filled

tools/sponge/preproc_scripts/get_so_monthly.csh

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+#!/bin/tcsh
+#SBATCH --ntasks=1
+#SBATCH --job-name=fill_glorys_arctic
+#SBATCH --time=2880
+#SBATCH --partition=batch
+
+# Usage: sbatch get_so_monthly.csh <YEAR> <MONTH>
+
+module load cdo
+module load nco/5.0.1
+module load gcp
+
+set year=$1
+set month=`printf "%02d" $2`
+set var='so'
+set apath='/archive/Theresa.Morrison/datasets/glorys/GLOBAL_MULTIYEAR_PHY_001_030/monthly/'${var}
+# create a directory to store the filled files.
+mkdir $TMPDIR/${var}_${year}_${month}
+
+set day=1
+foreach filename (/uda/Global_Ocean_Physics_Reanalysis/global/daily/${var}/${year}/${var}_mercatorglorys12v1_gl12_mean_${year}${month}*.nc)
+  echo $filename 
+  set short_name=${var}'_arctic_'$day
+  ncks -d latitude,39.,91. --mk_rec_dmn time $filename $TMPDIR/${var}_${year}_${month}/${short_name}'_bd.nc'
+  cdo -setreftime,1993-01-01,00:00:00,1day $TMPDIR/${var}_${year}_${month}/${short_name}'_bd.nc' $TMPDIR/${var}_${year}_${month}/${short_name}'.nc'
+  set day = `expr $day + 1`
+  echo $day
+end
+ncra -O $TMPDIR/${var}_${year}_${month}/${var}_arctic_*.nc ${apath}/GLORYS_${var}_arctic_${year}_${month}.nc

tools/sponge/preproc_scripts/get_thetao_monthly.csh

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+#!/bin/tcsh
+#SBATCH --ntasks=1
+#SBATCH --job-name=fill_glorys_arctic
+#SBATCH --time=2880
+#SBATCH --partition=batch
+
+# Usage: sbatch get_thetao_monthly.csh <YEAR> <MONTH>
+
+module load cdo
+module load nco/5.0.1
+module load gcp
+
+set year=$1
+set month=`printf "%02d" $2`
+set var='thetao'
+set apath='/archive/Theresa.Morrison/datasets/glorys/GLOBAL_MULTIYEAR_PHY_001_030/monthly/'${var}
+# create a directory to store the filled files.
+mkdir $TMPDIR/${var}_${year}_${month}
+
+set day=1
+foreach filename (/uda/Global_Ocean_Physics_Reanalysis/global/daily/${var}/${year}/${var}_mercatorglorys12v1_gl12_mean_${year}${month}*.nc)
+  echo $filename 
+  set short_name=${var}'_arctic_'$day
+  ncks -d latitude,39.,91. --mk_rec_dmn time $filename $TMPDIR/${var}_${year}_${month}/${short_name}'_bd.nc'
+  cdo -setreftime,1993-01-01,00:00:00,1day $TMPDIR/${var}_${year}_${month}/${short_name}'_bd.nc' $TMPDIR/${var}_${year}_${month}/${short_name}'.nc'
+  set day = `expr $day + 1`
+  echo $day
+end
+ncra -O $TMPDIR/${var}_${year}_${month}/${var}_arctic_*.nc ${apath}/GLORYS_${var}_arctic_${year}_${month}.nc

tools/sponge/preproc_scripts/merge_so_thetao_year.csh

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+#!/bin/tcsh
+#SBATCH --ntasks=1
+#SBATCH --job-name=fill_glorys_arctic
+#SBATCH --time=2880
+#SBATCH --partition=batch
+
+# Usage: sbatch fill_glorys_nn_monthly.sh <YEAR> <MONTH>
+
+module load cdo
+module load nco/5.0.1
+module load gcp
+
+set year=$1
+
+set wpath='/work/Theresa.Morrison/datasets/glorys/GLOBAL_MULTIYEAR_PHY_001_030/monthly/filled' 
+
+# Concatenate monthly averages into single file
+ncrcat -O ${wpath}/GLORYS_thetao_arctic_${year}_*.nc ${wpath}/GLORYS_thetao_arctic_${year}.nc
+ncrcat -O ${wpath}/GLORYS_so_arctic_${year}_*.nc ${wpath}/GLORYS_so_arctic_${year}.nc
+
+# Copy salt file to name for final file
+cp -f ${wpath}/GLORYS_so_arctic_${year}.nc ${wpath}/GLORYS_arctic_${year}.nc
+
+# Append temperature data to renamed salinity data 
+ncks -A  ${wpath}/GLORYS_thetao_arctic_${year}.nc ${wpath}/GLORYS_arctic_${year}.nc
+