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source: TOOLS/MOSAIX/CreateWeightsMask.bash @ 3901

Last change on this file since 3901 was 3901, checked in by omamce, 6 years ago

O.M. : add weight for coastal points only, to prepare computation

of weights for river run-off

Property svn:executable set to *
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1	#!/bin/bash
2	#MSUB -r WeightsMask # Job name
3	#MSUB -o Out_WeightsMask # Standard output
4	#MSUB -e Out_WeightsMask # Error output
5	#MSUB -eo
6	#MSUB -n 4 # Number of processors
7	#MSUB -T 1800 # Time limit (seconds)
8	#MSUB -q standard
9	#MSUB -Q test
10	#MSUB -p devcmip6
11
12	### ===========================================================================
13	###
14	### Creates interpolation weights between ORCA and atmosphere grids.
15	### Interpolates ORCA mask to atmosphere grid.
16	### Weight files are at OASIS-MCT format.
17	###
18	### Atmosphere grid may be lon/lat LMDZ or DYNAMICO icosahedron
19	###
20	### Documentation : https://forge.ipsl.jussieu.fr/igcmg/wiki/IPSLCM6/MOSAIX
21	### ===========================================================================
22	##
23	## Warning, to install, configure, run, use any of Olivier Marti's
24	## software or to read the associated documentation you'll need at least
25	## one (1) brain in a reasonably working order. Lack of this implement
26	## will void any warranties (either express or implied).
27	## O. Marti assumes no responsability for errors, omissions,
28	## data loss, or any other consequences caused directly or indirectly by
29	## the usage of his software by incorrectly or partially configured
30	## personal.
31	##
32	## SVN information
33	# $Author$
34	# $Date$
35	# $Revision$
36	# $Id$
37	# $HeadURL$
38	export Bold=$(tput bold)
39	export Unde=$(tput smul) ; export OffUnde=$(tput rmul)
40	export Stou=$(tput smso) ; export OffStou=$(tput rmso)
41	export Reve=$(tput rev )
42	couleurs=( "Black" "Blue" "Green" "Cyan" "Red" "Magenta" "Yellow" "White" )
43	for i in $(seq 0 7 ) ; do eval "export ${couleurs[$i]}=$(tput setf $i)" ; done
44	export Norm=$(tput sgr0 )
45
46	##
47	## Configuration
48	## ===========================================================================
49
50	#
51	# Defines models
52	# ==============
53	OCE=ORCA2.3
54	#OCE=eORCA1.2
55	#OCE=ORCA025
56
57	#ATM=ICO30
58	#ATM=ICO40
59	#ATM=ICO450
60	ATM=LMD9695
61	#ATM=LMD144X142
62
63	#
64	# Defines OCE grids to handle
65	# ===========================
66	ListOCEGRID="T U V"
67	ListOrder="1st" # 2nd"
68	ListNormalize="false true"
69
70	## ===========================================================================
71	##
72	## You should not change anything below this line ....
73	##
74	## ===========================================================================
75	SUBMIT_DIR=$(pwd)
76
77	#
78	# Defines computer
79	# ================
80	if [[ $(hostname) = curie* ]] ; then arch=curie ; center=tgcc ; fi
81	if [[ $(hostname) = irene* ]] ; then arch=irene ; center=tgcc ; fi
82	if [[ $(hostname) = lsce3005* ]] ; then arch=spip ; center=spip ; fi
83
84	PROGRAM=$(basename ${0})
85
86	case ${arch} in
87	( curie \| irene )
88	set +vx
89	module purge
90	source /ccc/cont003/home/dsm/p86ipsl/.env_intel17.0.2_curie;
91	source /ccc/cont003/home/dsm/p86ipsl/.env_netcdf4.3.3.1_curie
92	R_IN=$(ccc_home -u igcmg --cccwork)/IGCM
93	TMPDIR=${SCRATCHDIR}/TMP
94	SUBMIT_DIR=${BRIDGE_MSUB_PWD:-${SUBMIT_DIR}}
95	PROGRAM=${BRIDGE_MSUB_REQNAME}
96	MPIRUN=ccc_mprun
97	;;
98	( spip )
99	R_IN=${HOME}/Scratch/IGCM
100	TMPDIR=${HOME}/Scratch/TMP
101	SUBMIT_DIR=$(pwd)
102	MPIRUN=/opt/local/bin/mpirun-openmpi-gcc49 -n 2
103	;;
104	( * ) exit -1 ;;
105	esac
106
107	set -x ; set -e
108
109	mkdir -p ${TMPDIR}/${OCE}x${ATM} \|\| exit 1
110	cd ${TMPDIR}/${OCE}x${ATM} \|\| exit 1
111	rm -f *
112
113	#
114	# Suffixes
115	# ---------------------------------------------------------------------------
116	Listocegrid=${ListOCEGRID,,}
117
118	case ${OCE} in
119	( ORC ) oce=orc ; oce_domain_type=curvilinear ;;
120	esac
121	case ${ATM} in
122	( dynamico ) atm=ico ; atm_domain_type=unstructured ;;
123	( ICO ) atm=ico ; atm_domain_type=unstructured ;;
124	( lmd \| LMD ) atm=lmd ; atm_domain_type=rectilinear ;;
125	esac
126
127	case ${OCE} in
128	( ORCA2.3* ) OcePerio=4 ;;
129	( ORCA1* \| eORCA1* ) OcePerio=6 ;;
130	esac
131	#
132	# Format for OASIS files : should be NetCDF3 classic or NetCDF3 64 bits
133	# ---------------------------------------------------------------------------
134	FMT_OASIS=64bit
135	FMT_XIOS=netcdf4
136
137
138	cp ${SUBMIT_DIR}/bin/interpol.exe .
139	cp ${SUBMIT_DIR}/*.py .
140
141
142	cp ${R_IN}/OCE/NEMO/${OCE}/${OCE}_coordinates_mask.nc .
143	cp ${R_IN}/ATM/GRID/${ATM}_grid.nc .
144
145	ncks --overwrite --fl_fmt=${FMT_OASIS} --history ${OCE}_coordinates_mask.nc ${OCE}_coordinates_mask_${FMT_OASIS}.nc
146	ncks --overwrite --fl_fmt=${FMT_OASIS} --history ${ATM}_grid.nc ${ATM}_grid_${FMT_OASIS}.nc
147	#
148	# Creates OCEAN C grid : redundant point removed to compute proper integrals # A passer dans CreateWeights
149	# ----------------------------------------------------------------------------
150	cat <<EOF >add_c_grid.nco
151	nav_lon_grid_C = nav_lon_grid_T ;
152	nav_lat_grid_C = nav_lat_grid_T ;
153	bounds_lon_grid_C = bounds_lon_grid_T ;
154	bounds_lat_grid_C = bounds_lat_grid_T ;
155	area_grid_C = area_grid_T ;
156	mask_C = maskutil_T ;
157	EOF
158
159	ncap2 --overwrite --history --script-file add_c_grid.nco ${OCE}_coordinates_mask.nc tmp_${OCE}_coordinates_mask.nc
160	ncks --overwrite --variable nav_lon_grid_C,nav_lat_grid_C,bounds_lon_grid_C,bounds_lat_grid_C,area_grid_C,mask_C tmp_${OCE}_coordinates_mask.nc C_${OCE}_coordinates_mask.nc
161	rm tmp_${OCE}_coordinates_mask_${FMT_OASIS}.nc
162	ncrename --dimension x_grid_T,x_grid_C C_${OCE}_coordinates_mask.nc
163	ncrename --dimension y_grid_T,y_grid_C C_${OCE}_coordinates_mask.nc
164	ncrename --dimension nvertex_grid_T,nvertex_grid_C C_${OCE}_coordinates_mask.nc
165	ncks --append C_${OCE}_coordinates_mask.nc ${OCE}_coordinates_mask.nc
166	rm C_${OCE}_coordinates_mask.nc
167
168	ncks --overwrite --fl_fmt=${FMT_OASIS} --history {OCE}_coordinates_mask.nc ${OCE}_coordinates_mask_${FMT_OASIS}.nc
169
170	ls -al
171
172	##
173	## NEMO T point towards ATM - 1st order
174	## ===========================================================================
175	echo ${Green}"${OCE} T toward ${ATM} - 1storder"${Norm}
176	cp ${SUBMIT_DIR}/iodef_oce_to_atm.xml iodef.xml
177
178	python update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/file_definition/file[@id="file_src"]/field[@id="mask_src"]' -k name -v maskutil_T
179	python update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/domain_definition/domain[@id="domain_src"]' -k type -v ${oce_domain_type}
180	python update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/domain_definition/domain[@id="domain_dst"]' -k type -v ${atm_domain_type}
181	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="file_src"]/field[@id="mask_source"]' -k name -v maskutil_T
182	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]' -k name -v dia_t${oce}_to_t${atm}_1storder_false
183	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="title"]' -t "${OCE} mask interpolated to ${ATM}"
184	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="source_grid"]' -t ${oce_domain_type}
185	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="dest_grid"]' -t ${atm_domain_type}
186	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="order"]' -t 1
187	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_src"]' -k type -v ${oce_domain_type}
188	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]' -k type -v ${atm_domain_type}
189	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k weight_filename -v rmp_t${oce}_to_t${atm}_1storder_false.nc
190	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k order -v 1
191	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="normalization"]' -t false
192	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k renormalize -v false
193
194	cp iodef.xml iodef_t${oce}_to_t${atm}_1storder_false.xml
195	ln -fs ${OCE}_coordinates_mask.nc oce_grid.nc
196	ln -fs ${ATM}_grid.nc atm_grid.nc
197
198	time /usr/bin/time ${MPIRUN} ./interpol.exe --mask_src=yes --mask_dst=no
199
200	##
201	## Correct spurious values (extremes)
202	## ===========================================================================
203	cat <<EOF > correction_masque.nco
204	where (OceFrac < 0.00001 ) OceFrac=OceFrac.get_miss() ;
205	where (OceFrac > 0.99999 ) OceFrac=1.0 ;
206	OceFrac.delete_miss() ;
207	// Fill masked values to land values
208	where (OceFrac > 1.0 ) OceFrac=0.0 ;
209	where (OceFrac < 0.0 ) OceFrac=0.0 ;
210	EOF
211	ncap2 --history --overwrite --script-file correction_masque.nco dia_t${oce}_to_t${atm}_1storder_false.nc tmp_dia_t${oce}_to_t${atm}_1storder_false.nc ; mv tmp_dia_t${oce}_to_t${atm}_1storder_false.nc dia_t${oce}_to_t${atm}_1storder_false.nc
212	ncatted --history -a missing_value,OceFrac,d,,"" -a _FillValue,OceFrac,d,,"" dia_t${oce}_to_t${atm}_1storder_false.nc
213
214	##
215	## Creates mask on ATM grid
216	## ===========================================================================
217	cp dia_t${oce}_to_t${atm}_1storder_false.nc dia_t${oce}_to_t${atm}_1storder_false_mask.nc
218	ncks --alphabetize --history --overwrite --variable OceFrac dia_t${oce}_to_t${atm}_1storder_false_mask.nc ${ATM}_grid_maskFrom_${OCE}.nc
219	ncks --alphabetize --history --append --variable aire atm_grid.nc ${ATM}_grid_maskFrom_${OCE}.nc
220	[[ ${atm} = ico ]] && ncks --alphabetize --history --append --variable bounds_lon,bounds_lat atm_grid.nc ${ATM}_grid_maskFrom_${OCE}.nc
221
222	cat <<EOF > creation_masque.nco
223	where (OceFrac > 0.0 ) OceFrac=1 ;
224	where (OceFrac <= 0.0 ) OceFrac=0 ;
225	EOF
226	ncap2 --history --overwrite --script-file creation_masque.nco dia_t${oce}_to_t${atm}_1storder_false_mask.nc tmp_dia_t${oce}_to_t${atm}_1storder_false_mask.nc ; mv tmp_dia_t${oce}_to_t${atm}_1storder_false_mask.nc dia_t${oce}_to_t${atm}_1storder_false_mask.nc
227	ncrename --history --variable OceFrac,OceMask dia_t${oce}_to_t${atm}_1storder_false_mask.nc
228
229	ncks --alphabetize --history --append --variable OceMask dia_t${oce}_to_t${atm}_1storder_false_mask.nc ${ATM}_grid_maskFrom_${OCE}.nc
230	rm dia_t${oce}_to_t${atm}_1storder_false_mask.nc
231
232
233
234	##
235	## NEMO, other case, towards ATM
236	## ===========================================================================
237	for order in ${ListOrder} ; do
238	case ${order} in
239	( 1st ) num_order=1 ;;
240	( 2nd ) num_order=2 ;;
241	esac
242	for normalize in ${ListNormalize} ; do
243	for OCEGRID in ${ListOCEGRID} ; do
244	ocegrid=${OCEGRID,,}
245
246	if [[ ! -f rmp_${ocegrid}${oce}_to_t${atm}_${order}order_${normalize}.nc ]] ; then
247
248	echo ${Green}"${OCE} ${OCEGRID} toward ${ATM} - ${order}order - normalize: ${normalize}"${Norm}
249
250	python update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/file_definition/file[@id="file_src"]/field[@id="mask_src"]' -k name -v maskutil_${OCEGRID}
251	python update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/domain_definition/domain[@id="domain_src"]' -k type -v ${oce_domain_type}
252	python update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/domain_definition/domain[@id="domain_dst"]' -k type -v ${atm_domain_type}
253	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="file_src"]/field[@id="mask_source"]' -k name -v maskutil_${OCEGRID}
254	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]' -k name -v dia_${ocegrid}${oce}_to_t${atm}_${order}order_${normalize}
255	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="title"]' -t "${OCE} mask interpolated to ${ATM}"
256	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="source_grid"]' -t ${oce_domain_type}
257	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="dest_grid"]' -t ${atm_domain_type}
258	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="order"]' -t ${num_order}
259	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="normalization"]' -t ${normalize}
260	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_src"]' -k type -v ${oce_domain_type}
261	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]' -k type -v ${atm_domain_type}
262	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k order -v ${num_order}
263	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k weight_filename -v rmp_${ocegrid}${oce}_to_t${atm}_${order}order_${normalize}.nc
264	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k renormalize -v ${normalize}
265
266	cp iodef.xml iodef_${ocegrid}${oce}_t${atm}_${order}order_${normalize}.xml
267
268	ln -fs ${OCE}_coordinates_mask.nc oce_grid.nc
269	ln -fs ${ATM}_grid.nc atm_grid.nc
270	time /usr/bin/time ${MPIRUN} ./interpol.exe --mask_src=yes --mask_dst=yes
271	fi
272
273	done
274	done
275	done
276
277	##
278	## ATM towards NEMO points
279	## ===========================================================================
280	cp ${SUBMIT_DIR}/iodef_atm_to_oce.xml iodef.xml
281
282	python update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/domain_definition/domain[@id="domain_src"]' -k type -v ${atm_domain_type}
283	python update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/domain_definition/domain[@id="domain_dst"]' -k type -v ${oce_domain_type}
284	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="title"]' -t "${ATM} mask interpolated to ${OCE}"
285	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="source_grid"]' -t ${atm_domain_type}
286	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="dest_grid"]' -t ${oce_domain_type}
287	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_src"]' -k type -v ${atm_domain_type}
288	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]' -k type -v ${oce_domain_type}
289
290	for order in ${ListOrder} ; do
291	case ${order} in
292	( 1st ) num_order=1 ;;
293	( 2nd ) num_order=2 ;;
294	esac
295	for normalize in ${ListNormalize} ; do
296	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k order -v ${num_order}
297	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="order"]' -t ${num_order}
298	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="normalization"]' -t ${normalize}
299	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k renormalize -v ${normalize}
300
301	for OCEGRID in ${ListOCEGRID} ; do
302	ocegrid=${OCEGRID,,}
303
304	echo ${Green}"${ATM} toward ${OCE} ${OCEGRID} - ${order}order - normalize: ${normalize}"${Norm}
305	python update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/file_definition/file[@id="file_dst"]/field[@id="mask_dst"]' -k name -v mask_${OCEGRID}
306	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="file_dst"]/field[@id="mask_dest"]' -k name -v mask_${OCEGRID}
307	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]' -k name -v dia_t${atm}_to_${ocegrid}${oce}_${order}order_${normalize}
308	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k weight_filename -v rmp_t${atm}_to_${ocegrid}${oce}_${order}order_${normalize}.nc
309	cp iodef.xml iodef_t${atm}_to_${ocegrid}${oce}_${order}order_${normalize}.xml
310
311	ln -fs ${OCE}_coordinates_mask.nc oce_grid.nc
312	ln -fs ${ATM}_grid.nc atm_grid.nc
313	time /usr/bin/time ${MPIRUN} ./interpol.exe --mask_src=yes --mask_dst=yes
314
315	done
316	done
317	done
318
319	##
320	## Creates mask of coastal OCE points
321	## ===========================================================================
322	python ComputeNemoCoast.py -n ${OcePerio} -i ${OCE}_coordinates_mask.nc # Creates OceCoastal
323	##
324	## Creates mask of coastal ATM points
325	## ===========================================================================
326	cat <<EOF > coastal.nco
327	AtmCoastal = OceFrac * 0.0 ;
328	where (OceFrac > 0.0 && OceFrac < 1.0 ) AtmCoastal = 1.0 ;
329	EOF
330	ncap2 --history --overwrite --script-file coastal.nco ${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_coastal_maskFrom_${OCE}.nc
331	ncks --history --append --variable AtmCoastal ${ATM}_coastal_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}.nc
332	rm ${ATM}_coastal_maskFrom_${OCE}.nc
333	ncks --alphabetize --history --overwrite --fl_fmt=${FMT_OASIS} ${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}_${FMT_OASIS}.nc
334	##
335	## ATM towards NEMO points - runoff
336	## ===========================================================================
337	cp ${SUBMIT_DIR}/iodef_atm_to_oce.xml iodef.xml
338	for normalize in ${ListNormalize} ; do
339	python update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/domain_definition/domain[@id="domain_src"]' -k type -v ${atm_domain_type}
340	python update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/domain_definition/domain[@id="domain_dst"]' -k type -v ${oce_domain_type}
341	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="title"]' -t "${ATM} coastal mask interpolated to ${OCE}"
342	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="source_grid"]' -t ${atm_domain_type}
343	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="dest_grid"]' -t ${oce_domain_type}
344	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_src"]' -k type -v ${atm_domain_type}
345	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]' -k type -v ${oce_domain_type}
346	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k order -v 1
347	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="order"]' -t 1
348	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="normalization"]' -t ${normalize}
349	python update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/file_definition/file[@id="file_src"]' -k name -v ${ATM}_grid_maskFrom_${OCE}
350	python update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/file_definition/file[@id="file_src"]/field[@id="mask_src"]' -k name -v AtmCoastal
351	python update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/file_definition/file[@id="file_dst"]/field[@id="mask_dst"]' -k name -v OceCoastal
352	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]' -k name -v dia_o${atm}_to_c${oce}_1storder_${normalize}
353	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k weight_filename -v rmp_o${atm}_to_c${oce}_1storder_${normalize}.nc
354	python update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k renormalize -v ${normalize}
355
356	cp iodef.xml iodef_o${atm}_to_c${oce}_1storder_${normalize}.xml
357
358	ln -fs ${OCE}_coordinates_mask.nc oce_grid.nc
359	ln -fs ${ATM}_grid.nc atm_grid.nc
360	time /usr/bin/time ${MPIRUN} ./interpol.exe --mask_src=yes --mask_dst=yes
361
362	# Now we should divide weight par source (atm) grid area : run-off is a quantity/s integrated on the grid mox, not a flux
363	done
364	##
365	## Copy all NetCDF files to NetCDF 3 format (needed for OASIS)
366	## ===========================================================================
367	for InFile in *.nc ; do
368	OuFile=$(basename ${InFile} .nc)_${FMT_OASIS}.nc
369	if [[ ! -f ${OuFile} ]] ; then
370	ncks --alphabetize --history --fl_fmt=${FMT_OASIS} ${InFile} ${OuFile}
371	fi
372	done
373
374	##
375	## Add time axis and coordinates information
376	## (needed if files need to be read by XIOS)
377	## ===========================================================================
378	#ncatted --history -a coordinates,aire,m,c,"lat lon" ${ATM}_grid_maskFrom_${OCE}.nc
379	ncap2 --overwrite --history --script 'defdim("time_counter",1) ;' ${ATM}_grid_maskFrom_${OCE}.nc tmp_${ATM}_grid_maskFrom_${OCE}.nc ; mv tmp_${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}.nc
380	ncks --alphabetize --history --overwrite --fl_fmt=${FMT_OASIS} ${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}_${FMT_OASIS}.nc
381
382	if [[ ${atm} = ico ]] ; then
383	cat <<EOF > add_time.nco
384	OceFrac [time_counter,cell] = OceFrac (:) ;
385	OceMask [time_counter,cell] = OceMask (:) ;
386	AtmCoastal [time_counter,cell] = AtmCoastal (:) ;
387	EOF
388	ncap2 --overwrite --history --script-file add_time.nco ${ATM}_grid_maskFrom_${OCE}.nc tmp_${ATM}_grid_maskFrom_${OCE}.nc ; mv tmp_${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}.nc
389	ncatted --history \
390	-a coordinates,OceFrac,c,c,"time_counter cell" \
391	-a coordinates,OceMask,c,c,"time_counter cell" \
392	-a coordinates,AtmCoastal,c,c,"time_counter cell" \
393	-a coordinates,aire,c,c,"cell" \
394	${ATM}_grid_maskFrom_${OCE}.nc
395	fi
396	ncks --alphabetize --history --overwrite --fl_fmt=${FMT_OASIS} ${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}_${FMT_OASIS}.nc
397
398	if [[ ${atm} = lmd ]] ; then
399	cat <<EOF > add_time.nco
400	OceFrac [time_counter,lat,lon] = OceFrac (:,:) ;
401	OceMask [time_counter,lat,lon] = OceMask (:,:) ;
402	AtmCoastal [time_counter,lat,lon] = AtmCoastal (:,:) ;
403	EOF
404	ncap2 --overwrite --history --script-file add_time.nco ${ATM}_grid_maskFrom_${OCE}.nc tmp_${ATM}_grid_maskFrom_${OCE}.nc ; mv tmp_${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}.nc
405	ncatted --history \
406	-a coordinates,OceFrac,c,c,"time_counter lat lon" \
407	-a coordinates,OceMask,c,c,"time_counter lat lon" \
408	-a coordinates,AtmCoastal,c,c,"time_counter lat lon" \
409	-a coordinates,aire,c,c,"lat lon" \
410	${ATM}_grid_maskFrom_${OCE}.nc
411	fi
412	ncks --alphabetize --overwrite --mk_rec time_counter ${ATM}_grid_maskFrom_${OCE}.nc tmp_${ATM}_grid_maskFrom_${OCE}.nc ; mv tmp_${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}.nc
413	ncks --alphabetize --history --overwrite --fl_fmt=${FMT_OASIS} ${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}_${FMT_OASIS}.nc
414
415	##
416	## Add some metadata in file headers
417	## ===========================================================================
418
419	UUID=$(uuid)
420	NCO="$(ncks --version \|& tail -1\|sed 's/ncks //')"
421	PYTHON_VER=$( python -i -c "import sys ; print (sys.version.split(' ')[0])" )
422	for InFile in ${oce}_to_${atm}_.nc ${atm}_to_${oce}_.nc ${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}_${FMT_OASIS}.nc; do
423	ncatted --history \
424	--attribute uuid,global,d,, \
425	--attribute LongName,global,d,, \
426	--attribute nco_openmp_thread_number,global,d,, \
427	--attribute Conventions,global,o,c,"CF-1.6" \
428	--attribute source,global,o,c,"IPSL Earth system model" \
429	--attribute group,global,o,c,"ICMC IPSL Climate Modelling Center" \
430	--attribute Institution,global,o,c,"IPSL https://www.ipsl.fr" \
431	--attribute Ocean,global,o,c,"${OCE} https://www.nemo-ocean.eu" \
432	--attribute Atmosphere,global,o,c,"${ATM} http://lmdz.lmd.jussieu.fr" \
433	--attribute production,global,o,c,"$(finger ${LOGNAME} \| head -1 \| awk '{print $4, $5}') " \
434	--attribute originalFiles,global,o,c,"${OCE}_coordinates_mask.nc ${ATM}_grid_mask.nc" \
435	--attribute associatedFiles,global,o,c,"grids_${OCE}x${ATM}.nc areas_${OCE}x${ATM}.nc masks_${OCE}x${ATM}.nc" \
436	--attribute directory,global,o,c,"$(pwd)" \
437	--attribute description,global,o,c,"Fields needed by OASIS-MCT" \
438	--attribute title,global,o,c,"${InFile}.nc" \
439	--attribute Program,global,o,c,"Generated by ${PROGRAM}" \
440	--attribute timeStamp,global,o,c,"$(date)" \
441	--attribute uuid,global,o,c,"${UUID}" \
442	--attribute HOSTNAME,global,o,c,"$(hostname)" \
443	--attribute LOGNAME,global,o,c,"$(whoami)" \
444	--attribute NCO,global,o,c,"NCO netCDF Operator ${NCO} http://nco.sourceforge.net" \
445	--attribute Python,global,o,c,"Python version ${PYTHON_VER}" \
446	--attribute OS,global,o,c,"$(uname -o)" \
447	--attribute release,global,o,c,"$(uname -r)" \
448	--attribute hardware,global,o,c,"$(uname -i)" \
449	--attribute directory,global,o,c,"$(pwd)" \
450	--attribute description,global,o,c,"Generated with XIOS http://forge.ipsl.jussieu.fr/ioserver and MOSAIX https://forge.ipsl.jussieu.fr/igcmg/browser/TOOLS/MOSAIX" \
451	--attribute Comment,global,o,c,"Preliminary attempt - Do not trust !" \
452	--attribute SVN_Author,global,o,c,"$Author$" \
453	--attribute SVN_Date,global,o,c,"$Date$" \
454	--attribute SVN_Revision,global,o,c,"$Revision$" \
455	--attribute SVN_Id,global,o,c,"$Id$" \
456	${InFile}
457	done
458
459
460	##
461	## Update and complete weights file to fit OASIS requested format
462	## ===========================================================================
463	cat <<EOF > add_dim.nco
464	defdim("num_wgts",1) ;
465	weight[n_weight, num_wgts] = weight ;
466	EOF
467
468	for rmpFile in rmp_*.nc ; do
469	mv ${rmpFile} xios_${rmpFile}
470	ncap2 --fl_fmt=${FMT_OASIS} --history --script-file add_dim.nco xios_${rmpFile} ${rmpFile}
471
472	ncrename --history --dimension n_weight,num_links ${rmpFile}
473	ncrename --history --variable src_idx,src_address ${rmpFile}
474	ncrename --history --variable dst_idx,dst_address ${rmpFile}
475	ncrename --history --variable weight,remap_matrix ${rmpFile}
476	case ${rmpFile} in
477	( _1storder_.nc ) ncatted --history --attribute map_method,global,o,c,"Conservative Remapping - 1st order" ${rmpFile} ;;
478	( _2ndorder_.nc ) ncatted --history --attribute map_method,global,o,c,"Conservative Remapping - 2nd order" ${rmpFile} ;;
479	esac
480	case ${rmpFile} in
481	( *_true.nc ) ncatted --history --attribute map_method,global,o,c,"Normalization: true" ${rmpFile} ;;
482	( *_false.nc ) ncatted --history --attribute map_method,global,o,c,"Normalization: false" ${rmpFile} ;;
483	esac
484	ncatted --history --attribute conventions,global,o,c,"SCRIP" ${rmpFile}
485	ncatted --history --attribute normalization,global,o,c,"none" ${rmpFile}
486
487	case ${rmpFile} in
488	( rmp_${oce}_to_t${atm}_ )
489	ncatted --history \
490	--attribute title,global,o,c,"Weights ${OCE} to ${ATM}" \
491	--attribute source_grid,global,o,c,"${oce_domain_type}" \
492	--attribute dest_grid,global,o,c,"${atm_domain_type}" \
493	${rmpFile}
494	;;
495	( rmp_${atm}_to_${oce}_* )
496	ncatted --history \
497	--attribute title,global,o,c,"Weights ${ATM} to ${OCE}" \
498	--attribute source_grid,global,o,c,"${atm_domain_type}" \
499	--attribute dest_grid,global,o,c,"${oce_domain_type}" \
500	${rmpFile}
501	;;
502	esac
503	done
504
505	##
506	## Add missing variables in rmp files
507	## ===========================================================================
508	for rmpFile in rmp_* ; do
509	echo ${rmpFile}
510	a_to_o=false ; o_to_a=false
511	case ${rmpFile} in
512	( rmp_?${oce}_to_?${atm}_*.nc ) o_to_a=true ;;
513	( rmp_?${atm}_to_?${oce}_*.nc ) a_to_o=true ;;
514	esac
515
516	for Grid in t u v o c ; do # Identify grids
517	[[ ${rmpFile} = rmp_${Grid}${oce}_to_?${atm}_*.nc ]] && ogrid=${Grid}
518	[[ ${rmpFile} = rmp_?${oce}_to_${Grid}${atm}_*.nc ]] && agrid=${Grid}
519	[[ ${rmpFile} = rmp_${Grid}${atm}_to_?${oce}_*.nc ]] && agrid=${Grid}
520	[[ ${rmpFile} = rmp_?${atm}_to_${Grid}${oce}_*.nc ]] && ogrid=${Grid}
521	done
522	OGRID=${ogrid^}
523	AGRID=${agrid^}
524
525	cat <<EOF >add_varoce.nco
526	defdim ("src_grid_size" , \$x_grid_${OGRID}.size*\$y_grid_${OGRID}.size) ;
527	defdim ("src_grid_corners", 4) ;
528	defdim ("src_grid_rank" , 2) ;
529	//
530	src_grid_dims[src_grid_rank] = { \$y_grid_${OGRID}.size, \$x_grid_${OGRID}.size } ;
531	//
532	src_grid_center_lat [src_grid_size] = 0.0d ;
533	src_grid_center_lon [src_grid_size] = 0.0d ;
534	src_grid_center_lat (:) = nav_lat_grid_${OGRID}(:,:) ;
535	src_grid_center_lon (:) = nav_lon_grid_${OGRID}(:,:) ;
536	//
537	src_grid_corner_lat [src_grid_size, src_grid_corners] = 0.0d ;
538	src_grid_corner_lon [src_grid_size, src_grid_corners] = 0.0d ;
539	src_grid_corner_lat(:,:) = bounds_lat_grid_${OGRID}(:,:,:) ;
540	src_grid_corner_lon(:,:) = bounds_lon_grid_${OGRID}(:,:,:) ;
541	//
542	src_grid_imask [src_grid_size] = 0 ;
543	src_grid_area [src_grid_size] = 0.0d ;
544	src_grid_frac [src_grid_size] = 1.0d ;
545	src_grid_imask (:) = 1 - mask_${OGRID}(:,:) ;
546	src_grid_imask.int() ;
547	src_grid_area (:) = area_grid_${OGRID}(:,:) ;
548	EOF
549
550	[[ ${o_to_a} = true ]] && ncap2 --history --append --script-file add_varoce.nco ${OCE}_coordinates_mask_${FMT_OASIS}.nc ${rmpFile}
551	sed --in-place "s/src_/dst_/g" add_varoce.nco
552	[[ ${a_to_o} = true ]] && ncap2 --history --append --script-file add_varoce.nco ${OCE}_coordinates_mask_${FMT_OASIS}.nc ${rmpFile}
553
554	if [[ ${atm} = ico ]] ; then
555	cat <<EOF >add_varatm.nco
556	defdim ("dst_grid_size" , \$cell.size) ;
557	defdim ("dst_grid_corners", 6) ;
558	defdim ("dst_grid_rank" , 2) ;
559	//
560	dst_grid_dims[dst_grid_rank] = { \$cell.size, 1 } ;
561	//
562	dst_grid_center_lat [dst_grid_size] = 0.0d ;
563	dst_grid_center_lon [dst_grid_size] = 0.0d ;
564	dst_grid_center_lat (:) = lat(:) ;
565	dst_grid_center_lon (:) = lon(:) ;
566	//
567	dst_grid_corner_lat [dst_grid_size, dst_grid_corners] = 0.0d ;
568	dst_grid_corner_lon [dst_grid_size, dst_grid_corners] = 0.0d ;
569	dst_grid_corner_lat(:,:) = bounds_lat(:,:) ;
570	dst_grid_corner_lon(:,:) = bounds_lon(:,:) ;
571	//
572	dst_grid_imask [dst_grid_size] = 0 ;
573	dst_grid_area [dst_grid_size] = 0.0d ;
574	dst_grid_frac [dst_grid_size] = 1.0d ;
575	dst_grid_imask (:) = 1 - OceMask(0,:) ;
576	dst_grid_imask.int() ;
577	dst_grid_area (:) = aire(:) ;
578	EOF
579	if [[ ${o_to_a} = true ]] ; then
580	ncap2 --history --append --script-file add_varatm.nco ${ATM}_grid_maskFrom_${OCE}_${FMT_OASIS}.nc ${rmpFile}
581	ncks --alphabetize --history --overwrite --variable src_address,dst_address,remap_matrix,src_grid_dims,src_grid_center_lat,src_grid_center_lon,src_grid_corner_lon,src_grid_corner_lat,src_grid_area,src_grid_imask,dst_grid_dims,dst_grid_center_lat,dst_grid_center_lon,dst_grid_corner_lon,dst_grid_corner_lat,dst_grid_area,dst_grid_imask ${rmpFile} rmp_tmp.nc
582	mv rmp_tmp.nc ${rmpFile}
583	fi
584
585	sed --in-place "s/dst_/src_/g" add_varatm.nco
586	if [[ ${a_to_o} = true ]] ; then
587	ncap2 --history --append --script-file add_varatm.nco ${ATM}_grid_maskFrom_${OCE}_${FMT_OASIS}.nc ${rmpFile}
588	ncks --alphabetize --history --overwrite --variable src_address,dst_address,remap_matrix,src_grid_dims,src_grid_center_lat,src_grid_center_lon,src_grid_corner_lon,src_grid_corner_lat,src_grid_area,src_grid_imask,dst_grid_dims,dst_grid_center_lat,dst_grid_center_lon,dst_grid_corner_lon,dst_grid_corner_lat,dst_grid_area,dst_grid_imask ${rmpFile} rmp_tmp.nc
589	mv rmp_tmp.nc ${rmpFile}
590	fi
591	fi
592	if [[ ${atm} = lmd ]] ; then
593	cat <<EOF >add_varatm.nco
594	defdim ("dst_grid_size" , \$lon.size*\$lat.size) ;
595	defdim ("dst_grid_corners", 4) ;
596	defdim ("dst_grid_rank" , 2) ;
597	//
598	dst_grid_dims[dst_grid_rank] = { \$lat.size, \$lon.size } ;
599	//
600	dst_grid_center_lat [dst_grid_size] = 0.0d ;
601	dst_grid_center_lon [dst_grid_size] = 0.0d ;
602	lat0lon[lat,lon] = lat(:)+0*lon(:) ;
603	lon0lat[lat,lon] = lon(:)+0*lat(:) ;
604	dst_grid_center_lat (:) = lat0lon(:,:) ;
605	dst_grid_center_lon (:) = lon0lat(:,:) ;
606	//
607	//dst_grid_corner_lat [dst_grid_size, dst_grid_corners] = 0.0d ; // Not available for LMDZ lon/lat grid
608	//dst_grid_corner_lon [dst_grid_size, dst_grid_corners] = 0.0d ;
609	//dst_grid_corner_lat(:,:) = bounds_lat(:,:) ;
610	//dst_grid_corner_lon(:,:) = bounds_lon(:,:) ;
611	//
612	dst_grid_imask [dst_grid_size] = 0 ;
613	dst_grid_area [dst_grid_size] = 0.0d ;
614	dst_grid_frac [dst_grid_size] = 1.0d ;
615	dst_grid_imask (:) = 1 - OceMask(0,:,:) ;
616	dst_grid_imask.int() ;
617	dst_grid_area (:) = aire(:,:) ;
618	dst_grid_frac (:) = OceFrac(0,:,:) ;
619	EOF
620	if [[ ${o_to_a} = true ]] ; then
621	ncap2 --history --append --script-file add_varatm.nco ${ATM}_grid_maskFrom_${OCE}_${FMT_OASIS}.nc ${rmpFile}
622	ncks --alphabetize --history --overwrite --variable src_address,dst_address,remap_matrix,src_grid_dims,src_grid_center_lat,src_grid_center_lon,src_grid_corner_lon,src_grid_corner_lat,src_grid_area,src_grid_imask,dst_grid_dims,dst_grid_center_lat,dst_grid_center_lon,dst_grid_area,dst_grid_imask ${rmpFile} rmp_tmp.nc
623	mv rmp_tmp.nc ${rmpFile}
624	fi
625
626	sed --in-place "s/dst/src/g" add_varatm.nco
627	if [[ ${a_to_o} = true ]] ; then
628	ncap2 --history --append --script-file add_varatm.nco ${ATM}_grid_maskFrom_${OCE}_${FMT_OASIS}.nc ${rmpFile}
629	ncks --alphabetize --history --overwrite --variable src_address,dst_address,remap_matrix,src_grid_dims,src_grid_center_lat,src_grid_center_lon,src_grid_area,src_grid_imask,dst_grid_dims,dst_grid_center_lat,dst_grid_center_lon,dst_grid_corner_lon,dst_grid_corner_lat,dst_grid_area,dst_grid_imask ${rmpFile} rmp_tmp.nc
630	mv rmp_tmp.nc ${rmpFile}
631	fi
632	fi
633	done
634	ls -al ${OCE}_coordinates_mask.nc
635	##
636	## Save results
637	## ===========================================================================
638	cp ${ATM}_grid_maskFrom_${OCE}.nc ${SUBMIT_DIR}
639	for File in dia_.nc rmp_.nc
640	do
641	NewFile=$(echo ${File} \| sed -e "s/${atm}/${ATM}/" -e "s/${oce}/${OCE}/" )
642	cp ${File} ${SUBMIT_DIR}/${NewFile}
643	done
644
645	##
646	## Creates and save auxiliary files for OASIS
647	## ===========================================================================
648	bash ${SUBMIT_DIR}/CreateOasisGrids.bash --oce ${OCE} --atm ${ATM}
649
650	cp areas_${OCE}x${ATM}.nc ${SUBMIT_DIR}
651	cp grids_${OCE}x${ATM}.nc ${SUBMIT_DIR}
652	cp masks_${OCE}x${ATM}.nc ${SUBMIT_DIR}
653
654
655	## ===========================================================================
656	##
657	## That's all folk's !!!
658	##
659	## ===========================================================================
660

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