source: TOOLS/MOSAIX/CreateOasisGrids.bash @ 4172

Last change on this file since 4172 was 4172, checked in by omamce, 4 years ago

O.M. :

  • More documentation
  • Update run-off weights computation
  • Update calving weights computation
  • Property svn:executable set to *
  • Property svn:keywords set to Date Revision HeadURL Author Id
File size: 18.8 KB
Line 
1#!/bin/bash
2### ===========================================================================
3###
4### Creates grids.nc, masks.nc and areas.nc for OASIS-MCT
5###
6### ===========================================================================
7##
8##  Warning, to install, configure, run, use any of Olivier Marti's
9##  software or to read the associated documentation you'll need at least
10##  one (1) brain in a reasonably working order. Lack of this implement
11##  will void any warranties (either express or implied).
12##  O. Marti assumes no responsability for errors, omissions,
13##  data loss, or any other consequences caused directly or indirectly by
14##  the usage of his software by incorrectly or partially configured
15##  personal.
16##
17###
18### Documentation : https://forge.ipsl.jussieu.fr/igcmg/wiki/IPSLCM6/MOSAIX
19###
20## SVN information
21#  $Author$
22#  $Date$
23#  $Revision$
24#  $Id$
25#  $HeadURL$
26
27set +vx
28
29echo ${Titre}"Starting CreateOasisGrids.bash"${Norm}
30
31##
32echo ${Titre}"Default configuration (may be overrided by command line parameters)"${Norm}
33## ===========================================================================
34OCE=ORCA2.3
35# OCE=eORCA1.2
36ATM=ICO30
37#ATM=ICO40
38#ATM=ICO450
39#ATM=LMD144142
40#ATM=LMD9695
41
42## ===========================================================================
43##
44## You should not change anything below this line ....
45##
46## ===========================================================================
47
48echo ${Titre}"Defines computer"${Norm}
49# ================
50if [[ $(hostname) = curie* ]]    ; then arch=curie ; center=tgcc ; fi
51if [[ $(hostname) = irene* ]]    ; then arch=irene ; center=tgcc ; fi
52if [[ $(hostname) = lsce3005* ]] ; then arch=spip  ; center=spip ; fi
53
54PROGRAM=$(basename ${0})
55
56case ${arch} in
57    ( curie | irene )
58    set +vx
59    module unload cdo nco ferret
60    module unload netcdf hdf5
61    module load python # /2.7.12
62    module load netcdf/4.3.3.1_hdf5_parallel # Version for XIOS
63    module load nco
64    R_IN=$(ccc_home -u igcmg --cccwork)/IGCM
65    TMPDIR=${SCRATCHDIR}/TMP
66    SUBMIT_DIR=${BRIDGE_MSUB_PWD:-${SUBMIT_DIR}}
67    ;;
68    ( spip )
69    R_IN=${HOME}/Scratch/IGCM
70    TMPDIR=${HOME}/Scratch/TMP
71    SUBMIT_DIR=$(pwd)
72    MPIRUN=/opt/local/bin/mpirun-openmpi-gcc49 -n 2
73    ;;
74    ( * ) exit -1 ;;
75esac
76
77##
78echo ${Titre}"Command line parameters"${Norm}
79## ===========================================================================
80set -e
81set -o verbose
82set -o xtrace
83
84while [[ ${1} = -* ]] ; do
85    case ${1} in
86        ( -- ) shift ; break ;;
87        ( -o=* | --oce=*    ) OCE=${1##*=}     ; echo OCE:${OCE}    ;;
88        ( -o   | --oce      ) shift ; OCE=${1} ; echo OCE:${OCE}    ;;
89        ( -a=* | --atm=*    ) ATM=${1##*=}     ; echo ATM:${ATM}    ;;
90        ( -a   | --atm      ) shift ; ATM=${1} ; echo ATM:${ATM}    ;;
91        ( -v | --verbose    ) set -o verbose   ;;
92        ( -x | --xtrace     ) set -o xtrace    ;;
93        ( -e                ) set -e           ;;
94        ( -V | --noverbose  ) set +o verbose   ;;
95        ( -X | --noxtrace   ) set +o xtrace    ;;
96        ( -E                ) set +e           ;;
97        ( -* ) echo ${Bold}"Unknown option : ${1}"${Norm} ; return 1 ;;
98    esac
99    shift
100done
101
102##
103echo ${Titre}"Short names (grid names in Oasis)"${Norm}
104## ===========================================================================
105case ${OCE} in
106    ( *ORC*) oce=orc ;;
107esac
108case ${ATM} in
109    ( *ICO*         ) atm=ico ;;
110    ( *dynamico*    ) atm=ico ;;
111    ( *lmd* | *LMD* ) atm=lmd ;;
112esac
113
114CplModel=${OCE}x${ATM}
115
116##
117echo ${Titre}"Get input files"${Norm}
118## ===========================================================================
119[[ -f ${OCE}_coordinates_mask.nc ]] || cp ${R_IN}/OCE/NEMO/${OCE}/${OCE}_coordinates_mask.nc  .
120[[ -f ${ATM}_grid.nc             ]] || cp ${R_IN}/ATM/GRID/${ATM}_grid.nc                   .
121
122#
123echo ${Titre}"Format for OASIS-MCT files : should be NetCDF3 classic or NetCDF3 64 bits"${Norm}
124# ---------------------------------------------------------------------------
125FL_FMT3=64bit
126
127#
128echo ${Titre}"Cleaning"${Norm}
129# ----------------------------------------------------------------------------
130rm -f grids_${CplModel}.nc masks_${CplModel}.nc areas_${CplModel}.nc
131rm  -f *_tmp.nc
132
133#
134echo ${Titre}"Creates NetCDF3 version of input files"${Norm}
135# ----------------------------------------------------------------------------
136ncks --overwrite --fl_fmt=${FL_FMT} --history ${OCE}_coordinates_mask.nc      ${OCE}_coordinates_mask_${FL_FMT3}.nc
137ncks --overwrite --fl_fmt=${FL_FMT} --history ${ATM}_grid_maskFrom_${OCE}.nc  ${ATM}_grid_maskFrom_${OCE}_${FL_FMT3}.nc
138
139
140#
141echo ${Titre}"Creates ocean fields"${Norm}
142# ----------------------------------------------------------------------------
143for OCEGRID in T U V ; do
144    ncks --fl_fmt=${FL_FMT3} -C --history --append --variable nav_lon_grid_${OCEGRID},nav_lat_grid_${OCEGRID},bounds_lon_grid_${OCEGRID},bounds_lat_grid_${OCEGRID} ${OCE}_coordinates_mask_${FL_FMT3}.nc grids_${CplModel}.nc
145    ncks --fl_fmt=${FL_FMT3} -C --history --append --variable area_grid_${OCEGRID} ${OCE}_coordinates_mask_${FL_FMT3}.nc areas_${CplModel}.nc
146    # Inverts mask values and switch to integer
147    ncks --fl_fmt=${FL_FMT33} --history -C --variable mask_${OCEGRID} ${OCE}_coordinates_mask_${FL_FMT3}.nc mask_${OCEGRID}_tmp.nc
148    ncatted --history \
149            --attribute coordinates,mask_${OCEGRID},d,,         \
150            --attribute online_operation,mask_${OCEGRID},d,,    \
151            --attribute cell_measures,mask_${OCEGRID},d,,       \
152    mask_${OCEGRID}_tmp.nc
153   
154    ncap2 --fl_fmt=${FL_FMT3} --history --append --script "mask_${OCEGRID}=int(1-mask_${OCEGRID});"    mask_${OCEGRID}_tmp.nc masks_${CplModel}.nc
155    rm mask_${OCEGRID}_tmp.nc
156    ncatted --history \
157            --attribute long_name,mask_${OCEGRID},o,c,"Land-sea mask" \
158            --attribute units,mask_${OCEGRID},o,c,"Land:1, Ocean:0"    masks_${CplModel}.nc
159    # Change order of dimensions
160    mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc
161    ncpdq --permute nvertex_grid_${OCEGRID},y_grid_${OCEGRID},x_grid_${OCEGRID} grids_${CplModel}_tmp.nc grids_${CplModel}.nc
162    rm grids_${CplModel}_tmp.nc
163done
164
165ncks --history --append --variable lon,lat ${ATM}_grid_maskFrom_${OCE}_${FL_FMT3}.nc grids_${CplModel}.nc
166 
167#
168echo ${Titre}"We need to have different names for dimensions and variables"${Norm}
169# ----------------------------------------------------------------------------
170ncrename --history --variable lon,alon   grids_${CplModel}.nc
171ncrename --history --variable lat,alat   grids_${CplModel}.nc
172
173if [[ ${ATM} = dynamico* || ${ATM} = ICO* ]] ; then
174    ncks --fl_fmt=${FL_FMT3} --history --append --variable bounds_lon,bounds_lat ${ATM}_grid_maskFrom_${OCE}_${FL_FMT3}.nc grids_${CplModel}.nc
175fi
176
177ncks --fl_fmt=${FL_FMT3} --history -C --append --variable aire   ${ATM}_grid_maskFrom_${OCE}_${FL_FMT3}.nc areas_${CplModel}.nc
178ncatted --history --attribute coordinates,aire,d,,     \
179        --attribute _FillValue,aire,d,,                \
180        --attribute missing_value,aire,d,,             \
181        --attribute online_operation,aire,d,,          \
182        --attribute units,aire,o,c,"m2"                \
183        --attribute standard_name,aire,o,c,"cell_area" \
184        areas_${CplModel}.nc
185
186ncks --fl_fmt=${FL_FMT3} --history -C --variable OceMask         ${ATM}_grid_maskFrom_${OCE}_${FL_FMT3}.nc OceMask_tmp.nc
187ncatted --history \
188        --attribute coordinates,OceMask,d,,         \
189        --attribute online_operation,OceMask,d,,    \
190        --attribute _FillValue,OceMask,d,,          \
191        --attribute missing_value,OceMask,d,,       \
192        OceMask_tmp.nc
193ncap2 --fl_fmt=${FL_FMT3} --history --append --script "OceMask=int(1-OceMask)"            OceMask_tmp.nc masks_${CplModel}.nc # For OASIS, ocean=0, land=1
194rm OceMask_tmp.nc
195ncatted --history \
196        --attribute long_name,OceMask,o,c,"Land-sea mask"   \
197        --attribute units,OceMask,o,c,"Land:1, Ocean:0"  masks_${CplModel}.nc
198
199ncatted --history --attribute history,global,d,, grids_${CplModel}.nc
200ncatted --history --attribute history,global,d,, masks_${CplModel}.nc
201ncatted --history --attribute history,global,d,, areas_${CplModel}.nc
202
203if [[ ${atm} = *dynamico* || ${atm} = ico* ]] ; then
204    ncrename --history --dimension cell,ycell grids_${CplModel}.nc
205    ncrename --history --dimension cell,ycell areas_${CplModel}.nc
206    ncrename --history --dimension cell,ycell masks_${CplModel}.nc
207fi
208# if [[ ${atm} = *lmd* ]] ; then
209#     ncrename --dimension lon,tlmdlon  grids_${CplModel}.nc
210#     ncrename --dimension lat,tlmdlat  grids_${CplModel}.nc
211#     ncrename --dimension lon,tlmdlon  masks_${CplModel}.nc
212#     ncrename --dimension lat,tlmdlat  masks_${CplModel}.nc
213#     ncrename --dimension lon,tlmdlon  areas_${CplModel}.nc
214#     ncrename --dimension lat,tlmdlat  areas_${CplModel}.nc
215# fi
216
217#
218echo ${Titre}"DYNAMICO grids : 1) Set correct order of dimensions, 2) Add a dimension"${Norm}
219# ----------------------------------------------------------------------------
220if [[ ${atm} = dynamico* || ${atm} = ico* ]] ; then
221    mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc
222    ncpdq --permute nvertex,ycell,xcell  grids_${CplModel}_tmp.nc grids_${CplModel}.nc
223   
224    mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc
225    cat <<EOF >add_dim.nco
226//
227defdim("xcell",1) ;
228alat               [ycell,xcell] = alat       ;
229alon               [ycell,xcell] = alon       ;
230bounds_lat [nvertex,ycell,xcell] = bounds_lat ;
231bounds_lon [nvertex,ycell,xcell] = bounds_lon ;
232//
233EOF
234   
235    ncap2 --fl_fmt=${FL_FMT3} --history --append --script-file add_dim.nco  grids_${CplModel}_tmp.nc grids_${CplModel}.nc
236   
237    mv masks_${CplModel}.nc masks_${CplModel}_tmp.nc
238    ncap2 --fl_fmt=${FL_FMT3} --history --append --script 'defdim("xcell",1) ; OceMask[time_counter,ycell,xcell]=OceMask(:,:)'  masks_${CplModel}_tmp.nc masks_${CplModel}.nc
239
240    mv areas_${CplModel}.nc areas_${CplModel}_tmp.nc
241    ncap2 --fl_fmt=${FL_FMT3} --history --append --script 'defdim("xcell",1) ; aire[ycell,xcell]=aire(:) ; '                    areas_${CplModel}_tmp.nc areas_${CplModel}.nc
242
243    rm -f grids_${CplModel}_tmp.nc areas_${CplModel}_tmp.nc masks_${CplModel}_tmp.nc
244fi
245
246#
247echo ${Titre}"Some changes specific to LMDZ lon/lat grid"${Norm}
248# ----------------------------------------------------------------------------
249if [[ ${atm} = lmd* ]] ; then
250    echo ${Titre}"Spreads lon and lat to get 2D fields"${Norm}
251    # -----------------------------------------------------------------------
252    mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc
253    ncap2 --fl_fmt=${FL_FMT3} --history --append --script "alon[lat,lon]=alon; alat[lat,lon]=alat"  grids_${CplModel}_tmp.nc grids_${CplModel}.nc
254    rm -f grids_${CplModel}_tmp.nc
255    ncatted --history \
256            --attribute long_name,alon,o,c,"Longitude"    \
257            --attribute long_name,alat,o,c,"Latitude"     \
258            --attribute units,alon,o,c,"degrees_east"     \
259            --attribute units,alat,o,c,"degrees_north"    \
260            --attribute grid_type,alon,o,c,"P"            \
261            --attribute grid_type,alat,o,c,"P"            \
262            --attribute overlap,alon,o,i,0                \
263            --attribute overlap,alat,o,i,0                grids_${CplModel}.nc
264   
265    echo ${Titre}"Generates cell corners"${Norm}
266    # -----------------------------------------------------------------------
267cat <<EOF > add_bounds.nco
268defdim ("nvertex_lmd", 4) ;
269*delta_x = alon(0,1) - alon(0,0) ;
270*delta_y = alat(1,0) - alat(0,0) ;
271//
272bounds_lon[nvertex_lmd,lat,lon] = 0.0 ;
273bounds_lat[nvertex_lmd,lat,lon] = 0.0 ;
274//
275bounds_lon (0,:,:) = alon + delta_x*0.5 ;
276bounds_lat (0,:,:) = alat + delta_y*0.5 ;
277bounds_lon (1,:,:) = alon + delta_x*0.5 ;
278bounds_lat (1,:,:) = alat - delta_y*0.5 ;
279bounds_lon (2,:,:) = alon - delta_x*0.5 ;
280bounds_lat (2,:,:) = alat - delta_y*0.5 ;
281bounds_lon (3,:,:) = alon - delta_x*0.5 ;
282bounds_lat (3,:,:) = alat + delta_y*0.5 ;
283//
284where (bounds_lat >  90.0 ) bounds_lat =  90.0 ;;
285where (bounds_lat < -90.0 ) bounds_lat = -90.0 ;;
286//
287EOF
288    mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc
289    ncap2 --fl_fmt=${FL_FMT3} --history --script-file add_bounds.nco -O grids_${CplModel}_tmp.nc grids_${CplModel}.nc
290    rm grids_${CplModel}_tmp.nc
291fi
292
293#
294echo ${Titre}"Generates grid o${atm}, 'o' meaning 'one'"${Norm}
295# same as t${atm} grid, with surfaces set to 1
296# and mask to 0 (ocean everywhere, to compute integral over the whole grid))
297# This grid is used when field are quantities instead of fluxes (i.e river flow)
298# ----------------------------------------------------------------------------
299mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc
300ncap2 --fl_fmt=${FL_FMT3} --history --script "o${atm}_lon=alon; o${atm}_lat=alat; bounds_o${atm}_lon=bounds_lon; bounds_o${atm}_lat=bounds_lat; " grids_${CplModel}_tmp.nc grids_${CplModel}.nc
301
302mv areas_${CplModel}.nc areas_${CplModel}_tmp.nc
303ncap2 --fl_fmt=${FL_FMT3} --history --script "o${atm}_aire=aire*0.0d+1.0d; "   areas_${CplModel}_tmp.nc areas_${CplModel}.nc
304
305mv masks_${CplModel}.nc masks_${CplModel}_tmp.nc
306ncap2 --fl_fmt=${FL_FMT3} --history --script "o${atm}_mask=int(OceMask)*0+0; " masks_${CplModel}_tmp.nc masks_${CplModel}.nc
307
308rm grids_${CplModel}_tmp.nc areas_${CplModel}_tmp.nc masks_${CplModel}_tmp.nc
309
310#
311echo ${Titre}"Final renaming"${Norm}
312# ----------------------------------------------------------------------------
313for OCEGRID in T U V
314do
315    ocegrid=${OCEGRID~} # To lowercase
316    ncrename --history --variable nav_lon_grid_${OCEGRID},${ocegrid}${oce}.lon     grids_${CplModel}.nc
317    ncrename --history --variable nav_lat_grid_${OCEGRID},${ocegrid}${oce}.lat     grids_${CplModel}.nc
318    ncrename --history --variable bounds_lon_grid_${OCEGRID},${ocegrid}${oce}.clo  grids_${CplModel}.nc
319    ncrename --history --variable bounds_lat_grid_${OCEGRID},${ocegrid}${oce}.cla  grids_${CplModel}.nc
320    ncrename --history --variable mask_${OCEGRID},${ocegrid}${oce}.msk             masks_${CplModel}.nc
321    ncrename --history --variable area_grid_${OCEGRID},${ocegrid}${oce}.srf        areas_${CplModel}.nc
322   
323    ncatted --history \
324            --attribute bounds,${ocegrid}${oce}.lon,m,c,"${ocegrid}${oce}.clo"  \
325            --attribute bounds,${ocegrid}${oce}.lat,m,c,"${ocegrid}${oce}.cla"  \
326            --attribute units,${ocegrid}${oce}.clo,o,c,"degrees_east"        \
327            --attribute units,${ocegrid}${oce}.clo,o,c,"degrees_north" grids_${CplModel}.nc
328done
329
330ncrename --history --variable alon,t${atm}.lon                grids_${CplModel}.nc
331ncrename --history --variable alat,t${atm}.lat                grids_${CplModel}.nc
332ncrename --history --variable o${atm}_lon,o${atm}.lon         grids_${CplModel}.nc
333ncrename --history --variable o${atm}_lat,o${atm}.lat         grids_${CplModel}.nc
334ncrename --history --variable OceMask,t${atm}.msk             masks_${CplModel}.nc
335ncrename --history --variable o${atm}_mask,o${atm}.msk        masks_${CplModel}.nc
336ncrename --history --variable aire,t${atm}.srf                areas_${CplModel}.nc
337ncrename --history --variable o${atm}_aire,o${atm}.srf        areas_${CplModel}.nc
338
339ncrename --history --variable bounds_lon,t${atm}.clo          grids_${CplModel}.nc
340ncrename --history --variable bounds_lat,t${atm}.cla          grids_${CplModel}.nc
341ncrename --history --variable bounds_o${atm}_lon,o${atm}.clo  grids_${CplModel}.nc
342ncrename --history --variable bounds_o${atm}_lat,o${atm}.cla  grids_${CplModel}.nc
343
344for atmgrid in t o ; do
345    ncatted --history \
346            --attribute bounds,${atmgrid}${atm}.lon,c,c,"${atmgrid}${atm}.clo"   \
347            --attribute bounds,${atmgrid}${atm}.lat,c,c,"${atmgrid}${atm}.cla"   \
348            --attribute units,${atmgrid}${atm}.clo,o,c,"degrees_east"            \
349            --attribute units,${atmgrid}${atm}.cla,o,c,"degrees_north"        grids_${CplModel}.nc
350done
351
352##
353echo ${Titre}"Change all NetCDF files to NetCDF 3 format"${Norm}
354## ===========================================================================
355for InFile in areas_${CplModel}.nc grids_${CplModel}.nc masks_${CplModel}.nc ; do
356    if [[ $(ncdump -k ${InFile}) = *netCDF-4* ]] ; then
357        mv ${InFile} tmp_${InFile}
358        ncks --fl_fmt=${FL_FMT3} --history  tmp_${InFile} ${InFile}
359        rm tmp_${InFile}
360    fi
361done
362
363##
364echo ${Titre}"Add some useful information in NetCDF headers"${Norm}
365## ===========================================================================
366UUID=$(uuid)
367NCO=$(ncks --version |& tail -1|sed 's/ncks //')
368for type in areas masks grids ; do
369    ncatted --history \
370            --attribute nco_openmp_thread_number,global,d,,            \
371            --attribute uuid,global,d,,                                \
372            --attribute LongName,global,d,,                            \
373            --attribute NCO,global,o,c,"NCO netCDF Operator ${NCO} http://nco.sourceforge.net" \
374            --attribute Conventions,global,o,c,"CF-1.6"                \
375            --attribute source,global,o,c,"IPSL Earth system model"    \
376            --attribute group,global,o,c,"ICMC IPSL Climate Modelling Center" \
377            --attribute production,global,o,c,"$(finger ${LOGNAME} | head -1 | awk '{print $4, $5}') " \
378            --attribute Institution,global,o,c,"IPSL https://www.ipsl.fr" \
379            --attribute Ocean,global,o,c,"${OCE} https://www.nemo-ocean.eu"  \
380            --attribute Atmosphere,global,o,c,"${ATM} http://lmdz.lmd.jussieu.fr" \
381            --attribute HOSTNAME,global,o,c,"$(hostname)"              \
382            --attribute LOGNAME,global,o,c,"$(whoami)"                 \
383            --attribute Program,global,o,c,"Generated by ${0}"         \
384            --attribute name,global,o,c,"${type}_${CplModel}.nc"       \
385            --attribute directory,global,o,c,"$(pwd)"                  \
386            --attribute description,global,o,c,"Fields needed by OASIS-MCT" \
387            --attribute title,global,o,c,"${type}_${CplModel}.nc"      \
388            --attribute timeStamp,global,o,c,"$(date)"                 \
389            --attribute associatedFiles,global,o,c,"grids_${CplModel}.nc areas_${CplModel}.nc masks_${CplModel}.nc" \
390            --attribute originalFiles,global,o,c,"${OCE}_coordinates_mask.nc ${ATM}_grid_mask.nc"\
391            --attribute uuid,global,o,c,"${UUID}"                      \
392            --attribute OS,global,o,c,"$(uname -o)"                    \
393            --attribute release,global,o,c,"$(uname -r)"               \
394            --attribute hardware,global,o,c,"$(uname -i)"              \
395            --attribute SVN_Author,global,o,c,"$Author$"      \
396            --attribute SVN_Date,global,o,c,"$Date$" \
397            --attribute SVN_Revision,global,o,c,"$Revision$"                    \
398            --attribute SVN_Id,global,o,c,"$Id$" \
399            --attribute SVN_HeardURL,global,o,c,"$HeadURL $" \
400            ${type}_${CplModel}.nc
401done
402
403
404exit
405#
406echo ${Titre}"Name of the dimensions ?"${Norm} 
407# ----------------------------------------------------------------------------
408for OCEGRID in T U V ; do
409    ocegrid=${OCEGRID~} # Downcase name of grids
410    ncrename --history --dimension  x_grid_${OCEGRID},x${ocegrid}${oce}         grids_${CplModel}.nc
411    ncrename --history --dimension  y_grid_${OCEGRID},y${ocegrid}${oce}         grids_${CplModel}.nc
412    ncrename --history --dimension  nvertex_grid_${OCEGRID},crn${ocegrid}${oce} grids_${CplModel}.nc
413done
414
415## ===========================================================================
416echo ${Titre}"exit from CreateOasisGrids "${Norm}
417
418## ===========================================================================
419##
420echo ${Titre}"                  That's all folk's !!!   "${Norm}
421##
422## ===========================================================================
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