add VALGLO plot

FILTERS/filter_grid-T

@@ -1 +1 @@
---cnk_dmn deptht,1 --cnk_dmn time_counter,1 --cnk_dmn x,200 --cnk_dmn y,200 -v (^thetao$)+,(^votemper$),(^so$)+,(^vosaline$)+,(^zos$)+,(^sossheig$)+,(^somxzint1$)+,(^sokaraml$)+
+--cnk_dmn deptht,1 --cnk_dmn time_counter,1 --cnk_dmn x,200 --cnk_dmn y,200 -v (^thetao$)+,(^votemper$),(^so$)+,(^vosaline$)+,(^zos$)+,(^sossheig$)+,(^somxzint1$)+,(^sokaraml$)+,(^hfds$)+,(^sohefldo$)+,(^soicecov$)+

SCRIPT/common.bash

@@ -6,7 +6,9 @@ if [ ! -d $DATPATH ]; then mkdir -p $DATPATH ; fi
 
 # check mesh mask
 cd ${DATPATH}
-if [ ! -L mesh.nc     ] ; then ln -sf ${MSKPATH}/mesh_mask_${CONFIG}-GO6.nc mesh.nc ; fi
-if [ ! -L mask.nc     ] ; then ln -sf ${MSKPATH}/mesh_mask_${CONFIG}-GO6.nc mask.nc ; fi
+if [ ! -L mesh.nc     ] ; then ln -s ${MSKPATH}/mesh_mask_${CONFIG}-GO6.nc mesh.nc ; fi
+if [ ! -L mask.nc     ] ; then ln -s ${MSKPATH}/mesh_mask_${CONFIG}-GO6.nc mask.nc ; fi
+if [ ! -L subbasin.nc ] ; then ln -s ${MSKPATH}/subbasins_${CONFIG}-GO6.nc subbasin.nc ; fi
 if [ ! -L mesh.nc     ] ; then echo "mesh.nc is missing; exit"; exit 1 ; fi
 if [ ! -L mask.nc     ] ; then echo "mask.nc is missing; exit"; exit 1 ; fi
+if [ ! -L subbasin.nc ] ; then echo "subbasin.nc is missing; exit"; exit 1 ; fi

SCRIPT/get_data.bash

@@ -21,11 +21,13 @@ if   [ $FREQ == '5d' ]; then CRUM_FREQ=ond;
 elif [ $FREQ == '1m' ]; then CRUM_FREQ=onm;
 elif [ $FREQ == '1s' ]; then CRUM_FREQ=ons;
 elif [ $FREQ == '1y' ]; then CRUM_FREQ=ony;
+elif [ $FREQ == 'i1m' ]; then CRUM_FREQ=inm;
 else echo '$FREQ frequency is not supported'; exit 1
 fi
 
-if   [ $FREQ == '5d' ]; then FILE_LST=`moo ls moose:/crum/$RUNID/${CRUM_FREQ}.nc.file/*o_${FREQ}_${GRID}_${TAG}.nc`
-else FILE_LST=`moo ls moose:/crum/$RUNID/${CRUM_FREQ}.nc.file/*o_${FREQ}_${TAG}_${GRID}.nc`;
+if   [ $FREQ == '5d'  ]; then FILE_LST=`moo ls moose:/crum/$RUNID/${CRUM_FREQ}.nc.file/*_${FREQ}_${GRID}_${TAG}.nc`
+elif [ $FREQ == 'i1m' ]; then FILE_LST=`moo ls moose:/crum/$RUNID/${CRUM_FREQ}.nc.file/*_1m_${TAG}.nc`
+else FILE_LST=`moo ls moose:/crum/$RUNID/${CRUM_FREQ}.nc.file/*_${FREQ}_${TAG}_${GRID}.nc`;
 fi
 
 for MFILE in `echo ${FILE_LST}`; do

SCRIPT/mk_hfds.bash

@@ -0,0 +1,40 @@
+#!/bin/bash
+#SBATCH --mem=1G
+#SBATCH --time=10
+#SBATCH --ntasks=1
+
+if [[ $# -ne 4 ]]; then echo 'mk_hfds.bash [CONFIG (eORCA12, eORCA025 ...)] [RUNID (mi-aa000)] [TAG (19991201_20061201_ANN)] [FREQ (1y)]'; exit 1 ; fi
+
+CONFIG=$1
+RUNID=$2
+TAG=$3
+FREQ=$4
+GRID='T'
+
+# load path and mask
+. param.bash
+. ${SCRPATH}/common.bash
+
+cd $DATPATH/
+
+# name
+RUN_NAME=${RUNID#*-}
+
+# download data if needed
+#${SCRPATH}/get_data.bash $RUNID $FREQ $TAG grid-${GRID}
+
+# check presence of input file
+FILE=nemo_${RUN_NAME}o_${FREQ}_${TAG}_grid-${GRID}.nc
+if [ ! -f $FILE ] ; then echo "$FILE is missing; exit"; echo "E R R O R in : ./mk_hfds.bash $@ (see SLURM/${CONFIG}/${RUNID}/hfds_${TAG}.out)" >> ${EXEPATH}/ERROR.txt ; exit 1 ; fi
+
+# make mxl
+FILEOUT=GLO_hfds_nemo_${RUN_NAME}o_${FREQ}_${TAG}_grid-${GRID}.nc
+if [ $CONFIG == 'eORCA025' ] ; then $CDFPATH/cdfmean -f $FILE -v '|sohefldo|hfds|' -p T -minmax -o tmp_$FILEOUT ; fi
+
+# mv output file
+if [[ $? -eq 0 ]]; then 
+   mv tmp_$FILEOUT $FILEOUT
+else 
+   echo "error when running cdfmean; exit"; echo "E R R O R in : ./mk_hfds.bash $@ (see SLURM/${CONFIG}/${RUNID}/hfds_${TAG}.out)" >> ${EXEPATH}/ERROR.txt ; exit 1
+fi
+#

SCRIPT/mk_mht.bash

@@ -0,0 +1,42 @@
+#!/bin/bash
+#SBATCH --mem=1G
+#SBATCH --time=10
+#SBATCH --ntasks=1
+
+if [[ $# -ne 4 ]]; then echo 'mk_mht.bash [CONFIG (eORCA12, eORCA025 ...)] [RUNID (mi-aa000)] [TAG (19991201_20061201_ANN)] [FREQ (1y)]'; exit 1 ; fi
+
+CONFIG=$1
+RUNID=$2
+TAG=$3
+FREQ=$4
+
+# load path and mask
+. param.bash
+. ${SCRPATH}/common.bash
+
+cd $DATPATH/
+
+# name
+RUN_NAME=${RUNID#*-}
+
+# download data if needed
+#${SCRPATH}/get_data.bash $RUNID $FREQ $TAG grid-V
+
+# check presence of input file
+FILEV=nemo_${RUN_NAME}o_${FREQ}_${TAG}_grid-V.nc
+if [ ! -f $FILEV ] ; then echo "$FILEV is missing; exit"; echo "E R R O R in : ./mk_mht.bash $@ (see SLURM/${CONFIG}/${RUNID}/mht_${TAG}.out)" >> ${EXEPATH}/ERROR.txt ; exit 1 ; fi
+
+# make mht
+set -x
+FILEOUT=nemo_${RUN_NAME}o_${FREQ}_${TAG}_mht.nc
+$CDFPATH/cdfmhst -vt $FILEV -vvl -o tmp_$FILEOUT
+
+# mv output file
+if [[ $? -eq 0 ]]; then 
+   mv tmp_$FILEOUT $FILEOUT
+else 
+   echo "error when running cdfmht; exit"; echo "E R R O R in : ./mk_mht.bash $@ (see SLURM/${CONFIG}/${RUNID}/mht_${TAG}.out)" >> ${EXEPATH}/ERROR.txt ; exit 1
+fi
+
+# extract only 26.5
+ncks -d y,793,793 $FILEOUT nemo_${RUN_NAME}o_${FREQ}_${TAG}_mht_265.nc

SCRIPT/mk_moc.bash

@@ -0,0 +1,47 @@
+#!/bin/bash
+#SBATCH --mem=1G
+#SBATCH --time=10
+#SBATCH --ntasks=1
+
+if [[ $# -ne 4 ]]; then echo 'mk_moc.bash [CONFIG (eORCA12, eORCA025 ...)] [RUNID (mi-aa000)] [TAG (19991201_20061201_ANN)] [FREQ (1y)]'; exit 1 ; fi
+
+CONFIG=$1
+RUNID=$2
+TAG=$3
+FREQ=$4
+
+# load path and mask
+. param.bash
+. ${SCRPATH}/common.bash
+
+cd $DATPATH/
+
+# name
+RUN_NAME=${RUNID#*-}
+
+# download data if needed
+#${SCRPATH}/get_data.bash $RUNID $FREQ $TAG grid-V
+#${SCRPATH}/get_data.bash $RUNID $FREQ $TAG grid-U
+
+# check presence of input file
+FILEV=nemo_${RUN_NAME}o_${FREQ}_${TAG}_grid-V.nc
+FILEU=nemo_${RUN_NAME}o_${FREQ}_${TAG}_grid-U.nc
+FILET=nemo_${RUN_NAME}o_${FREQ}_${TAG}_grid-T.nc
+FILES=nemo_${RUN_NAME}o_${FREQ}_${TAG}_grid-T.nc
+if [ ! -f $FILEV ] ; then echo "$FILEV is missing; exit"; echo "E R R O R in : ./mk_moc.bash $@ (see SLURM/${CONFIG}/${RUNID}/moc_${TAG}.out)" >> ${EXEPATH}/ERROR.txt ; exit 1 ; fi
+if [ ! -f $FILEU ] ; then echo "$FILEU is missing; exit"; echo "E R R O R in : ./mk_moc.bash $@ (see SLURM/${CONFIG}/${RUNID}/moc_${TAG}.out)" >> ${EXEPATH}/ERROR.txt ; exit 1 ; fi
+if [ ! -f $FILET ] ; then echo "$FILET is missing; exit"; echo "E R R O R in : ./mk_moc.bash $@ (see SLURM/${CONFIG}/${RUNID}/moc_${TAG}.out)" >> ${EXEPATH}/ERROR.txt ; exit 1 ; fi
+if [ ! -f $FILES ] ; then echo "$FILES is missing; exit"; echo "E R R O R in : ./mk_moc.bash $@ (see SLURM/${CONFIG}/${RUNID}/moc_${TAG}.out)" >> ${EXEPATH}/ERROR.txt ; exit 1 ; fi
+
+# make moc
+set -x
+FILEOUT=nemo_${RUN_NAME}o_${FREQ}_${TAG}_moc.nc
+$CDFPATH/cdfmoc -v $FILEV -u $FILEU -t $FILET -s $FILES -rapid -vvl -o tmp_$FILEOUT
+
+# mv output file
+if [[ $? -eq 0 ]]; then 
+   mv rapid_tmp_$FILEOUT rapid_$FILEOUT
+else 
+   echo "error when running cdfmoc; exit"; echo "E R R O R in : ./mk_moc.bash $@ (see SLURM/${CONFIG}/${RUNID}/moc_${TAG}.out)" >> ${EXEPATH}/ERROR.txt ; exit 1
+fi
+

SCRIPT/mk_sie.bash

@@ -0,0 +1,39 @@
+#!/bin/bash
+#SBATCH --mem=1G
+#SBATCH --time=10
+#SBATCH --ntasks=1
+
+if [[ $# -ne 4 ]]; then echo 'mk_sie.bash [CONFIG (eORCA12, eORCA025 ...)] [RUNID (mi-aa000)] [TAG (19991201_20061201_ANN)] [FREQ (1y)]'; exit 1 ; fi
+
+CONFIG=$1
+RUNID=$2
+TAG=$3
+FREQ=$4
+GRID='T'
+
+# load path and mask
+. param.bash
+. ${SCRPATH}/common.bash
+
+cd $DATPATH/
+
+# name
+RUN_NAME=${RUNID#*-}
+
+# download data if needed
+#${SCRPATH}/get_data.bash $RUNID $FREQ $TAG grid-${GRID}
+
+# check presence of input file
+FILE=nemo_${RUN_NAME}o_${FREQ}_${TAG}_grid-T.nc
+if [ ! -f $FILE ] ; then echo "$FILE is missing; exit"; echo "E R R O R in : ./mk_sie.bash $@ (see SLURM/${CONFIG}/${RUNID}/sie_${TAG}.out)" >> ${EXEPATH}/ERROR.txt ; exit 1 ; fi
+
+# make sie
+FILEOUT=ARC_sie_nemo_${RUN_NAME}o_${FREQ}_${TAG}.nc
+if [ $CONFIG == 'eORCA025' ] ; then $CDFPATH/cdficediags -i $FILE -o tmp_$FILEOUT ; fi
+
+# mv output file
+if [[ $? -eq 0 ]]; then 
+   mv tmp_$FILEOUT $FILEOUT
+else 
+   echo "error when running cdficediags; exit"; echo "E R R O R in : ./mk_sie.bash $@ (see SLURM/${CONFIG}/${RUNID}/sie_${TAG}.out)" >> ${EXEPATH}/ERROR.txt ; exit 1
+fi

SCRIPT/mk_sst.bash

@@ -0,0 +1,49 @@
+#!/bin/bash
+#SBATCH --mem=1G
+#SBATCH --time=10
+#SBATCH --ntasks=1
+
+if [[ $# -ne 4 ]]; then echo 'mk_sst.bash [CONFIG (eORCA12, eORCA025 ...)] [RUNID (mi-aa000)] [TAG (19991201_20061201_ANN)] [FREQ (1y)]'; exit 1 ; fi
+
+CONFIG=$1
+RUNID=$2
+TAG=$3
+FREQ=$4
+GRID='T'
+
+# load path and mask
+. param.bash
+. ${SCRPATH}/common.bash
+
+cd $DATPATH/
+
+# name
+RUN_NAME=${RUNID#*-}
+
+# download data if needed
+#${SCRPATH}/get_data.bash $RUNID $FREQ $TAG grid-${GRID}
+
+# check presence of input file
+FILE=nemo_${RUN_NAME}o_${FREQ}_${TAG}_grid-${GRID}.nc
+if [ ! -f $FILE ] ; then echo "$FILE is missing; exit"; echo "E R R O R in : ./mk_sst.bash $@ (see SLURM/${CONFIG}/${RUNID}/sst_${TAG}.out)" >> ${EXEPATH}/ERROR.txt ; exit 1 ; fi
+
+# make sst
+FILEOUT=SO_sst_nemo_${RUN_NAME}o_${FREQ}_${TAG}_grid-${GRID}.nc
+if [ $CONFIG == 'eORCA025' ] ; then $CDFPATH/cdfmean -f $FILE -v '|thetao|votemper|' -surf -w 0 0 384 510 1 1 -p T -minmax -o tmp_$FILEOUT ; fi
+
+# mv output file
+if [[ $? -eq 0 ]]; then 
+   mv tmp_$FILEOUT $FILEOUT
+else 
+   echo "error when running cdfmean; exit"; echo "E R R O R in : ./mk_sst.bash $@ (see SLURM/${CONFIG}/${RUNID}/sst_${TAG}.out)" >> ${EXEPATH}/ERROR.txt ; exit 1
+fi
+
+FILEOUT=NWC_sst_nemo_${RUN_NAME}o_${FREQ}_${TAG}_grid-${GRID}.nc
+if [ $CONFIG == 'eORCA025' ] ; then $CDFPATH/cdfmean -f $FILE -surf -v '|thetao|votemper|' -w 950 1020 870 940 1 1 -p T -minmax -o tmp_$FILEOUT ; fi
+
+#mv output file
+if [[ $? -eq 0 ]]; then 
+   mv tmp_$FILEOUT $FILEOUT
+else 
+   echo "error when running cdfmean; exit"; echo "E R R O R in : ./mk_sst.bash $@ (see SLURM/${CONFIG}/${RUNID}/sst_${TAG}.out)" >> ${EXEPATH}/ERROR.txt ; exit 1
+fi

SCRIPT/plot_box_VALGLO.py

@@ -0,0 +1,103 @@
+import matplotlib
+import netCDF4 as nc
+#matplotlib.use('GTKAgg') 
+import numpy as np
+from numpy import ma
+import os
+import argparse
+import cartopy
+import matplotlib.pyplot as plt
+import matplotlib as matplotlib
+import matplotlib.colors as colors
+from matplotlib.colors import Normalize
+import cartopy.crs as ccrs
+import sys
+import re
+from cartopy.feature import LAND
+
+# ============================ plot utility ========================================
+def add_land_features(ax,cfeature_lst):
+# get isf groiunding line, ice shelf front and coastline
+    for ifeat,cfeat in enumerate(cfeature_lst):
+        if cfeat=='isf':
+            #feature = cartopy.feature.NaturalEarthFeature('physical', 'antarctic_ice_shelves_polys', '50m',facecolor='0.75',edgecolor='k') # global plot
+            feature = cartopy.feature.NaturalEarthFeature('physical', 'antarctic_ice_shelves_polys', '50m',facecolor='none',edgecolor='k')
+        elif cfeat=='lakes':
+            feature = cartopy.feature.NaturalEarthFeature('physical', 'lakes'                      , '50m',facecolor='none',edgecolor='k')
+        elif cfeat=='coast':
+            feature = cartopy.feature.NaturalEarthFeature('physical', 'coastline'                  , '50m',facecolor='0.75',edgecolor='k')
+        elif cfeat=='land':
+            feature = cartopy.feature.NaturalEarthFeature('physical', 'land'                       , '50m',facecolor='0.75',edgecolor='k')
+        elif cfeat=='bathy_z1000':
+            feature = cartopy.feature.NaturalEarthFeature('physical', 'bathymetry_J_1000'          , '10m',facecolor='none',edgecolor='k')
+        elif cfeat=='bathy_z2000':
+            feature = cartopy.feature.NaturalEarthFeature('physical', 'bathymetry_I_2000'          , '10m',facecolor='none',edgecolor='k')
+        elif cfeat=='bathy_z3000':
+            feature = cartopy.feature.NaturalEarthFeature('physical', 'bathymetry_H_3000'          , '10m',facecolor='none',edgecolor='k')
+        else:
+            print 'feature unknown : '+cfeat
+            sys.exit(42)
+        ax.add_feature(feature,linewidth=0.5)
+
+class box(object):
+    def __init__(self,corner,name):
+        self.xmin=corner[0]-1
+        self.xmax=corner[1]-1
+        self.ymin=corner[2]-1
+        self.ymax=corner[3]-1
+        self.name=name
+
+cfile='/data/cr1/pmathiot/MESH_MASK/bathymetry_eORCA025-GO6.nc'
+ncid   = nc.Dataset(cfile)
+bathy = ncid.variables['Bathymetry'][0:-2,:]
+ncid.close()
+cfile='/data/cr1/pmathiot/MESH_MASK/mesh_mask_eORCA025-GO6.nc'
+ncid   = nc.Dataset(cfile)
+lon = ncid.variables['nav_lon'][0:-2,:]
+lat = ncid.variables['nav_lat'][0:-2,:]
+delta_lon=np.abs(np.diff(lon))
+j_lst,i_lst=np.nonzero(delta_lon>180)
+print j_lst.shape, i_lst.shape
+for idx in range(0,len(j_lst)):
+    lon[j_lst[idx], i_lst[idx]+1:] += 360
+print lon.shape, lat.shape, bathy.shape
+
+box_lst=[None]*1
+box_lst[0]=box([950,1020,870,940],'NWC')
+
+mask=np.zeros(shape=bathy.shape)
+for box in box_lst:
+    mask[box.ymin:box.ymax,box.xmin:box.xmax] = 1.0
+
+proj=cartopy.crs.Robinson(); # ccrs.Stereographic(central_latitude=-90.0, central_longitude=0.0)
+XY_lim=[-180, 180, -90, 90]
+plt.figure(figsize=np.array([210, 210]) / 25.4)
+ax=plt.subplot(1, 1, 1, projection=proj, axisbg='0.75')
+#ax=plt.subplot(1, 1, 1)
+add_land_features(ax,['isf','lakes','land'])
+print np.max(bathy), np.min(bathy)
+ax.pcolormesh(lon,lat,bathy,cmap='Blues',vmin=0,vmax=7000,transform=ccrs.PlateCarree(),rasterized=True)
+
+ax.contour(lon,lat,mask,levels=[0.99, 2.0],transform=ccrs.PlateCarree(),colors='k',rasterized=True,linewidths=2)
+
+# ACC section
+ax.plot([lon[420,874], lon[332,899]],[lat[420,874], lat[332,899]],transform=ccrs.PlateCarree(),color='k',linewidth=2,rasterized=True)
+ax.text(lon[420,874]+5,lat[420,874]+2,'Drake',transform=ccrs.PlateCarree(),color='k',fontweight='bold',fontsize=16)
+
+# 26.5 north section
+ax.plot([-80.63, -13],[26.5, 26.5],transform=ccrs.PlateCarree(),color='k',linewidth=2,rasterized=True)
+box=box_lst[0]; ax.text(-60, 15, '26.5 N',transform=ccrs.PlateCarree(),color='k',fontweight='bold',fontsize=16)
+
+# SO box
+ax.plot([-180, 180],[-60, -60],transform=ccrs.PlateCarree(),color='k',linewidth=2,rasterized=True)
+ax.plot([-180, 180],[-40, -40],transform=ccrs.PlateCarree(),color='k',linewidth=2,rasterized=True)
+ax.text(0, -55,'SO',transform=ccrs.PlateCarree(),color='k',fontweight='bold',fontsize=16)
+
+# NWC box
+box=box_lst[0]; ax.text(lon[box.ymin+50,box.xmax+50], lat[box.ymin+50,box.xmin+50],box.name,transform=ccrs.PlateCarree(),color='k',fontweight='bold',fontsize=16)
+
+#pcol=ax.pcolormesh(lon,lat,bathy)
+#ax.set_extent(XY_lim, ccrs.PlateCarree())
+plt.savefig('box_VALGLO.png', format='png', dpi=150)
+plt.show()
+