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source: TOOLS/MOSAIX/CreateWeightsMask.bash @ 4317

Last change on this file since 4317 was 4317, checked in by omamce, 5 years ago
O.M: Mosaix. Correct NEMO mask to use maskutil
Property svn:executable set to ``* Property svn:keywords set to `Date Revision HeadURL Author Id`
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Rev	Line
[3620]	1	#!/bin/bash
[3719]	2	#MSUB -r WeightsMask # Job name
	3	#MSUB -o Out_WeightsMask # Standard output
	4	#MSUB -e Out_WeightsMask # Error output
[4159]	5	#MSUB -n 16 # Number of processors
[4186]	6	#MSUB -T 7200 # Time limit (seconds)
[3966]	7	#MSUB -q skylake
	8	#MSUB -p gen2212
	9	#MSUB -m work
[3620]	10
	11	### ===========================================================================
	12	###
[3719]	13	### Creates interpolation weights between ORCA and atmosphere grids.
[3620]	14	### Interpolates ORCA mask to atmosphere grid.
	15	### Weight files are at OASIS-MCT format.
	16	###
	17	### Atmosphere grid may be lon/lat LMDZ or DYNAMICO icosahedron
[3627]	18	###
	19	### Documentation : https://forge.ipsl.jussieu.fr/igcmg/wiki/IPSLCM6/MOSAIX
[3620]	20	### ===========================================================================
	21	##
	22	## Warning, to install, configure, run, use any of Olivier Marti's
	23	## software or to read the associated documentation you'll need at least
	24	## one (1) brain in a reasonably working order. Lack of this implement
	25	## will void any warranties (either express or implied).
	26	## O. Marti assumes no responsability for errors, omissions,
	27	## data loss, or any other consequences caused directly or indirectly by
	28	## the usage of his software by incorrectly or partially configured
	29	## personal.
	30	##
[3623]	31	## SVN information
[3665]	32	# $Author$
	33	# $Date$
	34	# $Revision$
	35	# $Id$
[3632]	36	# $HeadURL$
[4090]	37	#
[4317]	38	# CplModel=eORCA1.2xLMD144142 ; qsub -r ${CplModel} -o Out_${CplModel} -e Out_${CplModel} CreateWeightsMask.bash
	39	# CplModel=ORCA2.3xLMD9695
	40	# CplModel=ORCA2.3xICO30
	41	# CplModel=ORCA2.3xICO40
	42	# CplModel=eORCA1.2xICO40
	43	# CplModel=eORCA1.2xLMD256256
	44	# CplModel=eORCA1.2xICO450
	45	# CplModel=eORCA025.1xLMD256256
[4195]	46	#
	47
[4172]	48	set +vx
[3901]	49	export Bold=$(tput bold)
	50	export Unde=$(tput smul) ; export OffUnde=$(tput rmul)
	51	export Stou=$(tput smso) ; export OffStou=$(tput rmso)
	52	export Reve=$(tput rev )
	53	couleurs=( "Black" "Blue" "Green" "Cyan" "Red" "Magenta" "Yellow" "White" )
[4259]	54	for i in $(seq 0 7) ; do eval "export ${couleurs[$i]}=$(tput setf ${i})" ; done
[4186]	55	export Norm=$(tput sgr0)
[4172]	56	export Titre=${Bold}${Blue}
[3620]	57
	58	##
	59	## Configuration
	60	## ===========================================================================
[4159]	61	set -e
[3620]	62
	63	#
[4317]	64	echo ${Titre}"Defines model"${Norm}
	65	# =================================
	66	#CplModel=ORCA2.3xLMD9695
	67	#CplModel=ORCA2.3xICO30
	68	#CplModel=ORCA2.3xICO40
	69	CplModel=eORCA1.2xLMD144142
	70	#CplModel=eORCA1.2xLMD256256
	71	#CplModel=eORCA1.2xICO40
	72	#CplModel=eORCA1.2xICO450
	73	#CplModel=eORCA025.1xLMD256256
[3620]	74
[4317]	75	Version="v3" ; Comment="Preliminary attempt - Do not trust !"
[3620]	76
[4317]	77	# If available, get model name from job name
[4195]	78	if [[ X${SLURM_JOB_NAME} = XORC \|\| X${SLURM_JOB_NAME} = XLMD \|\| X${SLURM_JOB_NAME} = XICO ]] ; then
[4317]	79	CplModel=${SLURM_JOB_NAME} ;
[4195]	80	fi
[4317]	81	OCE=${CplModel//x} ; ATM=${CplModel##x}
[4195]	82
[4186]	83	echo ${Titre}"ATM model : ${ATM}"${Norm}
	84	echo ${Titre}"OCE model : ${OCE}"${Norm}
[4195]	85	echo ${Titre}"Cpl model : ${CplModel}"${Norm}
[4172]	86
[4186]	87	# Runoff parameter. atmCoastWidth and oceCoastWidth in grid points, searchRadius in km
	88	atmCoastWidth=2 ; oceCoastWidth=2 ; searchRadius=600.0
[4298]	89	runOff_atmQuantity=Quantity ; runOff_oceQuantity=Surfacic
[4172]	90
[4298]	91	[[ ${ATM} = ICO* ]] && atmCoastWidth=0 # Parameter relevant for LMD rectilinear grid only
	92	[[ ${ATM} = LMD* ]] && atmCoastWidth=2
	93	[[ ${OCE} = ORCA2.3 ]] && oceCoastWidth=1
	94	[[ ${OCE} = eORCA1.2 ]] && oceCoastWidth=3
	95	[[ ${OCE} = eORCA025* ]] && oceCoastWidth=1
[4186]	96
[4153]	97	# Default values, used to create ocean fraction on atmospheric grid
[4186]	98	DefaultValues=( Direction=o2a,oceGrid=t,atmGrid=t,Order=1st,Quantity=false,Renormalize=false,useArea=false,maskSrc=true,maskDst=false,Name=OceFrac )
[3620]	99
[4172]	100	## List of weights to build
	101	## ====================================================================================================================================
	102	#
	103	# Each item in CommandList describes the properties of interpolation weights to generate.
[4159]	104	# White spaces separate analysis. No spaces in any analysis.
	105	#
[4172]	106	# Specific commands : 'Runoff', 'Calving'
	107	#
[4159]	108	# Keywords :
[4298]	109	# Direction : o2a for ocean to atmosphere, a2o for atmosphere to ocean.
	110	# Order : 1st or 2nd.
[4159]	111	# Quantity : true if integrated quantity over a grid box, false for flux (quantity / m^2)
[4298]	112	# or intensive value (temperature, salinity, sea-ice fraction, ...).
	113	# Renormalize : used when source grid is masked, to use values on non masked points only.
	114	# oceGrid : t, u or v point for NEMO C grid.
	115	# atmGrid : up to know, only t grid used in the atmosphere.
	116	# useArea : if true area from the model metrics is used. If false, areas are computed by XIOS from grid corners.
	117	# maskSrc : true to use the source grid mask, false to used all grid points.
	118	# maskDst : true to use the destination grid mask, false to use all grid points.
[4159]	119	#
[4259]	120	## Classic cases for IPSLCM6
	121	AtmOceFluxes=" Direction=a2o,Order=1st,Quantity=false,Renormalize=false,atmGrid=t,oceGrid=t,useArea=true,maskSrc=true,maskDst=true,Name=HeatWaterFluxes" # Heat and water fluxes
	122	OceAtmTemp=" Direction=o2a,Order=1st,Quantity=false,Renormalize=true,oceGrid=t,atmGrid=t,useArea=false,maskSrc=true,maskDst=true,Name=TempIceAlb" # Temperature, sea-ice fraction, albedo
	123	OceAtmTemp2nd=" Direction=o2a,Order=2nd,Quantity=false,Renormalize=true,oceGrid=t,atmGrid=t,useArea=false,maskSrc=true,maskDst=true,Name=TempIceAlb" # Temperature, sea-ice fraction, albedo
	124	AtmOceStressU=" Direction=a2o,Order=2nd,Quantity=false,Renormalize=false,atmGrid=t,oceGrid=u,useArea=true,maskSrc=true,maskDst=true,Name=WindStress" # Wind stress to NEMO U point
	125	AtmOceStressV=" Direction=a2o,Order=2nd,Quantity=false,Renormalize=false,atmGrid=t,oceGrid=v,useArea=true,maskSrc=true,maskDst=true,Name=WindStress" # Wind stress to NEMO V point
	126	AtmOceQuantity=" Direction=a2o,Order=1st,Quantity=true,Renormalize=false,atmGrid=t,oceGrid=t,useArea=false,maskSrc=true,maskDst=true,Name=Quantity" # e.g. runoff
[4298]	127	# For new parameterization
	128	AtmOceTemp=" Direction=o2a,Order=1st,Quantity=false,Renormalize=true,oceGrid=t,atmGrid=t,useArea=false,maskSrc=true,maskDst=true,Name=OceTemp" # e.g. T and S correction from DWL parametrization
[4259]	129	OceAtmFluxes=" Direction=o2a,Order=1st,Quantity=false,Renormalize=false,atmGrid=t,oceGrid=t,useArea=true,maskSrc=true,maskDst=true,Name=OceAtmFluxes" # e.g. CO2 fluxes
[4298]	130	# Test to do with 2nd order
	131	AtmOceFluxes2nd="Direction=a2o,Order=2nd,Quantity=false,Renormalize=false,atmGrid=t,oceGrid=t,useArea=true,maskSrc=true,maskDst=true,Name=HeatWaterFluxes" # Heat and water fluxes
[4259]	132	OceAtmFluxes2nd="Direction=o2a,Order=2nd,Quantity=false,Renormalize=false,atmGrid=t,oceGrid=t,useArea=true,maskSrc=true,maskDst=true,Name=OceAtmFluxes" # e.g. CO2 fluxes
[4317]	133	AtmOceTemp2nd=" Direction=o2a,Order=2nd,Quantity=false,Renormalize=true,oceGrid=t,atmGrid=t,useArea=false,maskSrc=true,maskDst=true,Name=OceTemp" # e.g. T and S correction from DWL parametrization
[4159]	134
[4259]	135	## Creates the list
	136
[4186]	137	# Standard list for IPSLCM6
	138	#CommandList=( ${AtmOceFluxes} ${OceAtmTemp} ${AtmOceStressU} ${AtmOceStressV} ${OceAtmFluxes} Runoff Calving Grids )
[4172]	139
[4259]	140	# More comprehensive list for IPSLCM6 with new features
[4317]	141	#CommandList=( ${AtmOceFluxes} ${OceAtmTemp} ${AtmOceStressU} ${AtmOceStressV} ${OceAtmFluxes} ${AtmOceTemp} Runoff Calving Grids )
[4172]	142
[4259]	143	# With 2nd order
[4317]	144	CommandList=( ${AtmOceFluxes} ${AtmOceFluxes2nd} ${OceAtmTemp} ${OceAtmTemp2nd} ${AtmOceStressU} ${AtmOceStressV} ${OceAtmFluxes} ${OceAtmFluxes2nd} ${AtmOceTemp} ${AtmOceTemp2nd} Runoff Calving Grids )
[4259]	145
[4186]	146	# Debugs
	147	#CommandList=( ${AtmOceFluxes} ${OceAtmTemp} Runoff Calving Grids )
[4199]	148	#CommandList=( ${AtmOceFluxes} Runoff Calving Grids )
[4317]	149	#CommandList=( ${AtmOceFluxes} ${OceAtmTemp} )
[4259]	150	#CommandList=( Runoff )
	151	#CommandList=( Runoff Calving Grids )
[4186]	152	#CommandList=( Calving )
	153	#CommandList=( Grids )
[4172]	154
[3620]	155	## ===========================================================================
	156	##
	157	## You should not change anything below this line ....
	158	##
	159	## ===========================================================================
[4199]	160	Tag="MOSAIX"
[3620]	161	SUBMIT_DIR=$(pwd)
[4259]	162	FMT_XIOS=netcdf4
[4159]	163
	164	# Functions to handle command parameters
	165	# ======================================
[4153]	166	function read_Command {
	167	# Decipher the command line to set bash variables
	168	local l_Debug="no" l_Element
	169	while [[ ${1} = -* ]] ; do
	170	case ${1} in
	171	( -- ) shift ; break ;;
	172	( -d \| --debug ) l_Debug="true" ; shift ;;
	173	esac
	174	done
	175	local l_Command=${1}
[4159]	176	for l_Element in $(echo ${l_Command} \| tr "," "\n" ) ; do
[4153]	177	[[ "X${l_Debug}" = "Xtrue" ]] && echo ${l_Element}
	178	eval export ${l_Element}
	179	done
	180	}
[3620]	181
[4153]	182	function setValues {
[4317]	183	# Set default values
[4186]	184	read_Command "Direction=None,Order=None,Quantity=None,Renormalize=None,atmGrid=None,oceGrid=None,useArea=None,maskSrc=None,maskDst=None"
[4317]	185	# Read command line
[4186]	186	read_Command ${1}
	187	#
[4317]	188	oceGrid=${oceGrid,,} ; atmGrid=${atmGrid,,} # Model names to lower case
	189	OCEGRID=${oceGrid^^} ; ATMGRID=${atmGrid^^} # Model names to upper case
[4153]	190
	191	case ${Order} in
	192	( 1st ) numOrder=1 ;;
	193	( 2nd ) numOrder=2 ;;
	194	esac
	195	case ${Renormalize} in
	196	( true ) NormName=Normalized ;;
	197	( false ) NormName=UnNormalized ;;
	198	esac
	199	case ${Quantity} in
	200	( true ) QuantName=Integrated ;;
	201	( false ) QuantName=Surfacic ;;
	202	esac
	203	case ${useArea} in
	204	( true ) AreaName=Area ;;
	205	( false ) AreaName=NoArea ;;
	206	esac
	207
[4186]	208	if [[ "${Name}" != "None" ]] ; then
[4259]	209	FullName=${Name}_${Order}Order
[4186]	210	else
[4199]	211	FullName=${Order}Order_${NormName}_${QuantName}_${AreaName}
[4186]	212	fi
	213
[4153]	214	case ${Direction} in
	215	( o2a )
[4159]	216	src=${oce} ; SRC=${OCE} ; srcGrid=${oceGrid} ; srcDomainType=${oceDomainType} ; SRCGRID=${OCEGRID} ; srcArea=area_grid_${OCEGRID}
	217	dst=${atm} ; DST=${ATM} ; dstGrid=${atmGrid} ; dstDomainType=${atmDomainType} ; DSTGRID=${ATMGRID} ; dstArea=aire
[4153]	218	;;
	219	( a2o )
[4159]	220	src=${atm} ; SRC=${ATM} ; srcGrid=${atmGrid} ; srcDomainType=${atmDomainType} ; SRCGRID=${ATMGRID} ; srcArea=aire
	221	dst=${oce} ; DST=${OCE} ; dstGrid=${oceGrid} ; dstDomainType=${oceDomainType} ; DSTGRID=${OCEGRID} ; dstArea=area_grid_${OCEGRID}
[4153]	222	;;
	223	esac
[4186]	224	echo ${Green}"${SRC} ${SRCGRID} toward ${DST} ${DSTGRID} - ${Order} Order - Normalize: ${Renormalize} - Quantity: ${QuantName} - Area: ${AreaName} "${Norm}
[4199]	225	echo ${Green}"FullName : ${FullName}"${Norm}
[4153]	226	}
[4186]	227
[3620]	228	#
	229	# Defines computer
	230	# ================
[3901]	231	if [[ $(hostname) = irene* ]] ; then arch=irene ; center=tgcc ; fi
[4153]	232	if [[ $(hostname) = lsce* ]] ; then arch=spip ; center=spip ; fi
[3734]	233
[3620]	234	PROGRAM=$(basename ${0})
	235
	236	case ${arch} in
[4153]	237	( irene )
[3620]	238	set +vx
[4259]	239	set +e
[3966]	240	R_IN=$(ccc_home -u igcmg --cccwork)/IGCM
	241	TMPDIR=${CCCWORKDIR}/TMP
	242	SUBMIT_DIR=${BRIDGE_MSUB_PWD:-${SUBMIT_DIR}}
	243	PROGRAM=${BRIDGE_MSUB_REQNAME}
[4172]	244	MpiRun="time ccc_mprun"
[4195]	245	PyRun="time ccc_mprun -n 1" # Needed to force python to run on one process only
[4259]	246	#module purge
	247	source $(ccc_home -u igcmg)/MachineEnvironment/irene/env_irene
[4153]	248	source ${SUBMIT_DIR}/arch.env
[4259]	249	#module load nco
[4172]	250	module load python3
[4153]	251	module load datadir/igcmg
[3966]	252	module list
[4259]	253	set -e
[3966]	254	;;
[3734]	255	( spip )
	256	R_IN=${HOME}/Scratch/IGCM
	257	TMPDIR=${HOME}/Scratch/TMP
	258	SUBMIT_DIR=$(pwd)
[4172]	259	MpiRun="/opt/local/bin/mpirun -n 4"
	260	PyRun="time"
[3734]	261	;;
[3901]	262	( * ) exit -1 ;;
[3620]	263	esac
	264
	265	set -x ; set -e
	266
[4195]	267	mkdir -p ${TMPDIR}/${CplModel} \|\| exit 1
	268	cd ${TMPDIR}/${CplModel} \|\| exit 1
[4146]	269	rm -fr *
[3620]	270
	271	#
	272	# Suffixes
	273	# ---------------------------------------------------------------------------
	274
	275	case ${OCE} in
[4153]	276	( ORC ) oce=orc ; oceDomainType=curvilinear ;;
[3620]	277	esac
[4159]	278
[3620]	279	case ${ATM} in
[4153]	280	( dynamico ) atm=ico ; atmDomainType=unstructured ;;
	281	( ICO ) atm=ico ; atmDomainType=unstructured ;;
	282	( lmd \| LMD ) atm=lmd ; atmDomainType=rectilinear ;;
[3620]	283	esac
	284
[4159]	285	case ${OCE} in # Periodicity type of ORCA grid
[4298]	286	( ORCA2* ) OcePerio=4 ;;
[4172]	287	( ORCA1* \| eORCA1* ) OcePerio=6 ;;
[4298]	288	( ORCA025* \| eORCA025* ) OcePerio=6 ;;
[3723]	289	esac
[3620]	290	#
	291
[4195]	292	cp ${SUBMIT_DIR}/bin/interpol.exe .
	293	cp ${SUBMIT_DIR}/*.py .
[4153]	294	cp ${SUBMIT_DIR}/iodef_atm_to_oce.xml .
	295	cp ${SUBMIT_DIR}/iodef_oce_to_atm.xml .
[3620]	296
	297	cp ${R_IN}/OCE/NEMO/${OCE}/${OCE}_coordinates_mask.nc .
[3639]	298	cp ${R_IN}/ATM/GRID/${ATM}_grid.nc .
[3620]	299
[4317]	300	# Soucis a corriger plus tard
	301	if [[ ${ATM} = LMD9695 ]] ; then
	302	cat <<EOF > toDouble.nco
	303	lat = double (lat) ;
	304	lon = double (lon) ;
	305	aire = double (aire) ;
	306	fract_oce = double (fract_oce) ;
	307	fract_sic = double (fract_sic) ;
	308	fract_oce_plus_sic = double (fract_oce_plus_sic) ;
	309	EOF
	310	ncap2 --history --overwrite --script-file toDouble.nco ${ATM}_grid.nc tmp_${ATM}_grid.nc
	311	mv tmp_${ATM}_grid.nc ${ATM}_grid.nc
	312	fi
[3620]	313
[3912]	314
[3901]	315	##
[4172]	316	echo ${Titre}"NEMO T point towards ATM - 1st order"${Norm}
[3901]	317	## ===========================================================================
[4153]	318	echo "Command parameters : ${Command}"
[4186]	319	setValues ${DefaultValues}
[3620]	320
[4153]	321	cp iodef_oce_to_atm.xml iodef.xml
	322
[4172]	323	python3 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
	324	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/file_definition/file[@id="file_src"]/field[@id="area_src"]' -k name -v area_grid_T
	325	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/domain_definition/domain[@id="domain_src"]' -k type -v ${srcDomainType}
	326	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/domain_definition/domain[@id="domain_dst"]' -k type -v ${dstDomainType}
	327	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k order -v 1
	328	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k quantity -v false
	329	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k renormalize -v false
	330	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k use_area -v false
	331	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="file_src"]/field[@id="mask_source"]' -k name -v maskutil_T
	332	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="file_src"]/field[@id="area_source"]' -k name -v area_grid_T
[4199]	333	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]' -k name -v dia_${srcGrid}${src}_to_${dstGrid}${dst}_${FullName}
[4172]	334	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="title"]' -t "${SRC} mask interpolated to ${DST}"
	335	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="source_grid"]' -t ${srcDomainType}
	336	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="dest_grid"]' -t ${dstDomainType}
	337	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="order"]' -t 1
	338	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_src"]' -k type -v ${srcDomainType}
	339	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]' -k type -v ${dstDomainType}
[4199]	340	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k weight_filename -v rmp_${srcGrid}${src}_to_${dstGrid}${dst}_${FullName}.nc
[4172]	341	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k order -v 1
	342	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="normalization"]' -t false
	343	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="quantity"]' -t false
	344	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="use_area"]' -t false
	345	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k renormalize -v false
	346	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k quantity -v false
	347	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k use_area -v false
[3620]	348
[4199]	349	cp iodef.xml iodef_${srcGrid}${src}_to_${dstGrid}${dst}_${FullName}.xml
[3901]	350	ln -fs ${OCE}_coordinates_mask.nc oce_grid.nc
	351	ln -fs ${ATM}_grid.nc atm_grid.nc
[3620]	352
[4172]	353	${MpiRun} ./interpol.exe --mask_src=${maskSrc} --mask_dst=${maskDst} --use_area=${useArea}
	354
[3620]	355	##
[4172]	356	echo ${Titre}"Correct spurious values (extremes)"${Norm}
[3620]	357	## ===========================================================================
	358	cat <<EOF > correction_masque.nco
	359	where (OceFrac < 0.00001 ) OceFrac=OceFrac.get_miss() ;
	360	where (OceFrac > 0.99999 ) OceFrac=1.0 ;
	361	OceFrac.delete_miss() ;
	362	// Fill masked values to land values
	363	where (OceFrac > 1.0 ) OceFrac=0.0 ;
	364	where (OceFrac < 0.0 ) OceFrac=0.0 ;
[4298]	365	OceMask = OceFrac ;
[3620]	366	EOF
[4199]	367	ncap2 --history --overwrite --script-file correction_masque.nco dia_t${oce}_to_t${atm}_${FullName}.nc tmp_dia_t${oce}_to_t${atm}_${FullName}.nc ; mv tmp_dia_t${oce}_to_t${atm}_${FullName}.nc dia_t${oce}_to_t${atm}_${FullName}.nc
	368	ncatted --history -a missing_value,OceFrac,d,,"" -a _FillValue,OceFrac,d,,"" dia_t${oce}_to_t${atm}_${FullName}.nc
[4298]	369	ncatted --history -a missing_value,OceMask,d,,"" -a _FillValue,OceMask,d,,"" dia_t${oce}_to_t${atm}_${FullName}.nc
	370
[3620]	371	##
[4298]	372	echo ${Titre}"Creates mask on ATM grid"${Norm}
[3620]	373	## ===========================================================================
[4199]	374	cp dia_t${oce}_to_t${atm}_${FullName}.nc dia_t${oce}_to_t${atm}_${FullName}_mask.nc
[4298]	375	ncks --alphabetize --history --overwrite --variable OceFrac dia_t${oce}_to_t${atm}_${FullName}_mask.nc ${ATM}_grid_maskFrom_${OCE}.nc
[4317]	376	ncatted --history --attribute name,global,m,c,"${ATM}_grid_maskFrom_${OCE}.nc" ${ATM}_grid_maskFrom_${OCE}.nc
[3620]	377
	378	cat <<EOF > creation_masque.nco
[4298]	379	Oce2AtmMask = OceMask ;
	380	where (OceMask > 0.0 ) Oce2AtmMask=1 ;
	381	where (OceMask <= 0.0 ) Oce2AtmMask=0 ;
[3620]	382	EOF
[4081]	383
[4298]	384	ncap2 --history --overwrite --script-file creation_masque.nco dia_t${oce}_to_t${atm}_${FullName}.nc tmp_dia_${ATM}_grid_maskFrom_${OCE}.nc
	385	ncks --overwrite --history --variable OceMask,OceFrac,Oce2AtmMask tmp_dia_${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}.nc
[3620]	386
[4081]	387	if [[ $(ncdump -h ${ATM}_grid_maskFrom_${OCE}.nc \| grep domain_dst \| wc -l) -gt 0 ]] ; then
[4317]	388	echo "Change dimension names, and some attributes accordingly"
	389	## ===========================================================
[4081]	390	case ${atm} in
	391	( ico )
[4088]	392	ncrename --history --dimension cell_domain_dst,cell ${ATM}_grid_maskFrom_${OCE}.nc
	393	ncrename --history --dimension nvertex_domain_dst,nvertex ${ATM}_grid_maskFrom_${OCE}.nc
	394	ncrename --history --variable lat_domain_dst,lat ${ATM}_grid_maskFrom_${OCE}.nc
	395	ncrename --history --variable lon_domain_dst,lon ${ATM}_grid_maskFrom_${OCE}.nc
	396	ncrename --history --variable bounds_lat_domain_dst,bounds_lat ${ATM}_grid_maskFrom_${OCE}.nc
	397	ncrename --history --variable bounds_lon_domain_dst,bounds_lon ${ATM}_grid_maskFrom_${OCE}.nc
	398	ncatted --history --attribute bounds,lat,m,c,"bounds_lat" ${ATM}_grid_maskFrom_${OCE}.nc
	399	ncatted --history --attribute bounds,lon,m,c,"bounds_lon" ${ATM}_grid_maskFrom_${OCE}.nc
[4081]	400	;;
[4317]	401	( lmd )
	402	ncrename --history --variabl lon_domain_dst,lon ${ATM}_grid_maskFrom_${OCE}.nc
	403	ncrename --history --variable lat_domain_dst,lat ${ATM}_grid_maskFrom_${OCE}.nc
	404	ncrename --history --dimension lon_domain_dst,lon ${ATM}_grid_maskFrom_${OCE}.nc
	405	ncrename --history --dimension lat_domain_dst,lat ${ATM}_grid_maskFrom_${OCE}.nc
[4081]	406	;;
	407	esac
	408	ncatted --history --attribute coordinates,OceFrac,m,c,"lat lon" ${ATM}_grid_maskFrom_${OCE}.nc
	409	ncatted --history --attribute coordinates,OceMask,m,c,"lat lon" ${ATM}_grid_maskFrom_${OCE}.nc
[4298]	410	ncatted --history --attribute coordinates,Oce2AtmMask,m,c,"lat lon" ${ATM}_grid_maskFrom_${OCE}.nc
[4317]	411
	412	ncatted --history --attribute long_name,OceFrac,c,c,"fraction of ocean in a grid cell" ${ATM}_grid_maskFrom_${OCE}.nc
	413	ncatted --history --attribute units,OceFrac,c,c,"[0,1]" ${ATM}_grid_maskFrom_${OCE}.nc
	414	ncatted --history --attribute long_name,OceMask,c,c,"fraction of ocean in a grid cell" ${ATM}_grid_maskFrom_${OCE}.nc
	415	ncatted --history --attribute units,OceMask,c,c,"[0,1]" ${ATM}_grid_maskFrom_${OCE}.nc
	416	ncatted --history --attribute long_name,Oce2AtmMask,c,c,"land mask" ${ATM}_grid_maskFrom_${OCE}.nc
	417	ncatted --history --attribute units,Oce2AtmMask,c,c,"Land:0, Ocean:1" ${ATM}_grid_maskFrom_${OCE}.nc
[4088]	418
[4081]	419	fi
	420
[4317]	421	ncks --history --alphabetize --append --variable aire atm_grid.nc ${ATM}_grid_maskFrom_${OCE}.nc
	422	ncatted --history --attribute units,aire,m,c,"m^2" ${ATM}_grid_maskFrom_${OCE}.nc
	423
[4081]	424	[[ ${atm} = ico ]] && ncks --alphabetize --history --append --variable bounds_lon,bounds_lat atm_grid.nc ${ATM}_grid_maskFrom_${OCE}.nc
	425
[4298]	426
	427	##
[4199]	428	#echo ${Titre}"Creates mask of coastal OCE points"${Norm}
[3901]	429	## ===========================================================================
[4199]	430	#${PyRun} python3 -u ComputeNemoCoast.py -n ${OcePerio} -i ${OCE}_coordinates_mask.nc # Creates OceCoastal
[4172]	431
[3901]	432	##
[4199]	433	#echo ${Titre}"Creates mask of coastal ATM points"${Norm}
[3901]	434	## ===========================================================================
[4199]	435	#cat <<EOF > coastal.nco
	436	#AtmCoastal = OceFrac * 0.0 ;
	437	#where (OceFrac > 0.0 && OceFrac < 1.0 ) AtmCoastal = 1.0 ;
	438	#EOF
	439	#ncap2 --history --overwrite --script-file coastal.nco ${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_coastal_maskFrom_${OCE}.nc
	440	#ncks --history --append --variable AtmCoastal ${ATM}_coastal_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}.nc
	441	#rm ${ATM}_coastal_maskFrom_${OCE}.nc
[4081]	442
[3901]	443	##
[4172]	444	echo ${Titre}"Other weights files"${Norm}
[3718]	445	## ===========================================================================
[4153]	446	# Loop on commands
	447	for Command in ${CommandList[@]}
	448	do
	449	echo "Command parameters : ${Command}"
[4186]	450	setValues ${Command}
[4172]	451	if [[ ${Command} = "Runoff" ]] ; then okRunoff=yes ; continue ; fi
	452	if [[ ${Command} = "Calving" ]] ; then okCalving=yes ; continue ; fi
[4186]	453	if [[ ${Command} = "Grids" ]] ; then okGrids=yes ; continue ; fi
[4172]	454
[4153]	455	ln -fs ${OCE}_coordinates_mask.nc oce_grid.nc
[4298]	456	#ln -fs ${ATM}_grid.nc atm_grid.nc
	457	ln -fs ${ATM}_grid_maskFrom_${OCE}.nc atm_grid.nc
[4153]	458
	459	case ${Direction} in
	460	( o2a )
	461	cp iodef_oce_to_atm.xml iodef.xml
[4082]	462
[4317]	463	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/file_definition/file[@id="file_src"]/field[@id="mask_src"]' -k name -v maskutil_${DSTGRID}
[4298]	464	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/file_definition/file[@id="file_dst"]/field[@id="mask_dst"]' -k name -v Oce2AtmMask
[4082]	465
[4172]	466	python3 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_${SRCGRID}
	467	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="file_src"]/field[@id="area_source"]' -k name -v area_grid_${SRCGRID}
[4298]	468	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="file_dst"]/field[@id="mask_dest"]' -k name -v Oce2AtmMask
[4172]	469	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="file_dst"]/field[@id="area_dest"]' -k name -v aire
[4153]	470	;;
	471	( a2o )
	472	cp iodef_atm_to_oce.xml iodef.xml
[4082]	473
[4298]	474	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/file_definition/file[@id="file_src"]/field[@id="mask_src"]' -k name -v Oce2AtmMask
[4172]	475	python3 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_${DSTGRID}
[4082]	476
[4298]	477	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="file_src"]/field[@id="mask_source"]' -k name -v Oce2AtmMask
[4172]	478	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="file_src"]/field[@id="area_source"]' -k name -v aire
	479	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="file_dst"]/field[@id="mask_dest"]' -k name -v mask_${DSTGRID}
	480	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="file_dst"]/field[@id="area_dest"]' -k name -v area_grid_${DSTGRID}
[4153]	481	;;
	482	esac
	483
[4172]	484	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/domain_definition/domain[@id="domain_dst"]' -k type -v ${dstDomainType}
	485	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_read"]/domain_definition/domain[@id="domain_src"]' -k type -v ${srcDomainType}
[4153]	486
[4172]	487	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_src"]' -k type -v ${srcDomainType}
	488	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]' -k type -v ${dstDomainType}
[4153]	489
[4199]	490	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k weight_filename -v rmp_${srcGrid}${src}_to_${dstGrid}${dst}_${FullName}.nc
[4172]	491	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k order -v ${numOrder}
	492	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k quantity -v ${Quantity}
	493	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k renormalize -v ${Renormalize}
	494	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/domain_definition/domain[@id="domain_dst"]/interpolate_domain' -k use_area -v ${useArea}
[4153]	495
[4199]	496	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]' -k name -v dia_${srcGrid}${src}_to_${dstGrid}${dst}_${FullName}
[4172]	497	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="title"]' -t "${SRC} mask interpolated to ${DST}"
	498	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="dest_grid"]' -t ${dstDomainType}
	499	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="source_grid"]' -t ${srcDomainType}
	500	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="normalization"]' -t ${Renormalize}
	501	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="order"]' -t ${numOrder}
	502	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="quantity"]' -t ${Quantity}
	503	python3 update_xml.py -i iodef.xml -n 'context[@id="interpol_run"]/file_definition/file[@id="dia"]/variable[@name="use_area"]' -t ${useArea}
[4153]	504
[4199]	505	cp iodef.xml iodef_${srcGrid}${src}_to_${dstGrid}${dst}_${FullName}.xml
[4172]	506	${MpiRun} ./interpol.exe --mask_src=${maskSrc} --mask_dst=${maskDst} --use_area=${useArea}
[3719]	507	done
[4153]	508
[3620]	509	##
[4172]	510	echo ${Titre}"Add some metadata in file headers"${Norm}
[3620]	511	## ===========================================================================
	512
	513	NCO="$(ncks --version \|& tail -1\|sed 's/ncks //')"
[4172]	514	PYTHON_VER=$( python3 -c "import sys ; print (sys.version.split(' ')[0])" )
[4199]	515	for InFile in $(ls ${oce}_to_${atm}_.nc ${atm}_to_${oce}_.nc ${ATM}_grid_maskFrom_${OCE}.nc 2> /dev/null) ; do
[3639]	516	ncatted --history \
[3620]	517	--attribute LongName,global,d,, \
	518	--attribute nco_openmp_thread_number,global,d,, \
	519	--attribute Conventions,global,o,c,"CF-1.6" \
	520	--attribute source,global,o,c,"IPSL Earth system model" \
	521	--attribute group,global,o,c,"ICMC IPSL Climate Modelling Center" \
	522	--attribute Institution,global,o,c,"IPSL https://www.ipsl.fr" \
	523	--attribute Ocean,global,o,c,"${OCE} https://www.nemo-ocean.eu" \
	524	--attribute Atmosphere,global,o,c,"${ATM} http://lmdz.lmd.jussieu.fr" \
	525	--attribute production,global,o,c,"$(finger ${LOGNAME} \| head -1 \| awk '{print $4, $5}') " \
	526	--attribute originalFiles,global,o,c,"${OCE}_coordinates_mask.nc ${ATM}_grid_mask.nc" \
[4195]	527	--attribute associatedFiles,global,o,c,"grids_${CplModel}.nc areas_${CplModel}.nc masks_${CplModel}.nc" \
[3620]	528	--attribute directory,global,o,c,"$(pwd)" \
	529	--attribute description,global,o,c,"Fields needed by OASIS-MCT" \
	530	--attribute title,global,o,c,"${InFile}.nc" \
	531	--attribute Program,global,o,c,"Generated by ${PROGRAM}" \
	532	--attribute timeStamp,global,o,c,"$(date)" \
	533	--attribute HOSTNAME,global,o,c,"$(hostname)" \
	534	--attribute LOGNAME,global,o,c,"$(whoami)" \
	535	--attribute NCO,global,o,c,"NCO netCDF Operator ${NCO} http://nco.sourceforge.net" \
[4172]	536	--attribute Python,global,o,c,"Python3 version ${PYTHON_VER}" \
[3620]	537	--attribute OS,global,o,c,"$(uname -o)" \
	538	--attribute release,global,o,c,"$(uname -r)" \
	539	--attribute directory,global,o,c,"$(pwd)" \
[3624]	540	--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" \
[4090]	541	--attribute SVN_Author,global,o,c,'$Author$' \
	542	--attribute SVN_Date,global,o,c,'$Date$' \
	543	--attribute SVN_Revision,global,o,c,'$Revision$' \
	544	--attribute SVN_Id,global,o,c,'$Id$' \
[3620]	545	${InFile}
	546	done
	547	##
[4172]	548	echo ${Titre}"Update and complete weight files to fit OASIS requested format"${Norm}
[3620]	549	## ===========================================================================
	550	cat <<EOF > add_dim.nco
	551	defdim("num_wgts",1) ;
	552	weight[n_weight, num_wgts] = weight ;
	553	EOF
	554
[3719]	555	for rmpFile in rmp_*.nc ; do
[4199]	556	mv ${rmpFile} tmp_${rmpFile}
	557	ncap2 --history --script-file add_dim.nco tmp_${rmpFile} ${rmpFile} ; rm tmp_${rmpFile}
[3620]	558
[3719]	559	ncrename --history --dimension n_weight,num_links ${rmpFile}
	560	ncrename --history --variable src_idx,src_address ${rmpFile}
	561	ncrename --history --variable dst_idx,dst_address ${rmpFile}
	562	ncrename --history --variable weight,remap_matrix ${rmpFile}
	563	case ${rmpFile} in
[4082]	564	( 1storder ) ncatted --history --attribute map_method,global,o,c,"Conservative Remapping - 1st order" ${rmpFile} ;;
	565	( 2ndorder ) ncatted --history --attribute map_method,global,o,c,"Conservative Remapping - 2nd order" ${rmpFile} ;;
[3620]	566	esac
[3719]	567	case ${rmpFile} in
[4082]	568	( _Normalized ) ncatted --history --attribute map_method,global,o,c,"Normalization: true" ${rmpFile} ;;
	569	( _UnNormalized ) ncatted --history --attribute map_method,global,o,c,"Normalization: false" ${rmpFile} ;;
[3719]	570	esac
[4082]	571	case ${rmpFile} in
	572	( Integrated ) ncatted --history --attribute map_method,global,o,c,"Quantity: true" ${rmpFile} ;;
	573	( Surfacic ) ncatted --history --attribute map_method,global,o,c,"Quantity: false" ${rmpFile} ;;
	574	esac
[3719]	575	ncatted --history --attribute conventions,global,o,c,"SCRIP" ${rmpFile}
	576	ncatted --history --attribute normalization,global,o,c,"none" ${rmpFile}
[3620]	577
[3719]	578	case ${rmpFile} in
[3620]	579	( rmp_${oce}_to_t${atm}_ )
[3639]	580	ncatted --history \
[3620]	581	--attribute title,global,o,c,"Weights ${OCE} to ${ATM}" \
[4153]	582	--attribute source_grid,global,o,c,"${oceDomainType}" \
	583	--attribute dest_grid,global,o,c,"${atmDomainType}" \
[3719]	584	${rmpFile}
[3620]	585	;;
	586	( rmp_${atm}_to_${oce}_* )
[3639]	587	ncatted --history \
[3620]	588	--attribute title,global,o,c,"Weights ${ATM} to ${OCE}" \
[4153]	589	--attribute source_grid,global,o,c,"${atmDomainType}" \
	590	--attribute dest_grid,global,o,c,"${oceDomainType}" \
[3719]	591	${rmpFile}
[3620]	592	;;
	593	esac
	594	done
	595
[4186]	596	ls
[3620]	597	##
[4172]	598	echo ${Titre}"Add missing variables in rmp files"${Norm}
[3639]	599	## ===========================================================================
[4259]	600	for rmpFile in $(ls rmp_?${atm}_to_[tuv]${oce}_.nc rmp_[tuv]${oce}_to_t${atm}_.nc 2> /dev/null ) ; do
[3901]	601	echo ${rmpFile}
[3719]	602	a_to_o=false ; o_to_a=false
	603	case ${rmpFile} in
	604	( rmp_?${oce}_to_?${atm}_*.nc ) o_to_a=true ;;
	605	( rmp_?${atm}_to_?${oce}_*.nc ) a_to_o=true ;;
	606	esac
	607
[3901]	608	for Grid in t u v o c ; do # Identify grids
	609	[[ ${rmpFile} = rmp_${Grid}${oce}_to_?${atm}_*.nc ]] && ogrid=${Grid}
	610	[[ ${rmpFile} = rmp_?${oce}_to_${Grid}${atm}_*.nc ]] && agrid=${Grid}
	611	[[ ${rmpFile} = rmp_${Grid}${atm}_to_?${oce}_*.nc ]] && agrid=${Grid}
	612	[[ ${rmpFile} = rmp_?${atm}_to_${Grid}${oce}_*.nc ]] && ogrid=${Grid}
[3719]	613	done
	614	OGRID=${ogrid^}
	615	AGRID=${agrid^}
[3639]	616
[3719]	617	cat <<EOF >add_varoce.nco
[3639]	618	defdim ("src_grid_size" , \$x_grid_${OGRID}.size*\$y_grid_${OGRID}.size) ;
	619	defdim ("src_grid_corners", 4) ;
	620	defdim ("src_grid_rank" , 2) ;
	621	//
	622	src_grid_dims[src_grid_rank] = { \$y_grid_${OGRID}.size, \$x_grid_${OGRID}.size } ;
	623	//
	624	src_grid_center_lat [src_grid_size] = 0.0d ;
	625	src_grid_center_lon [src_grid_size] = 0.0d ;
	626	src_grid_center_lat (:) = nav_lat_grid_${OGRID}(:,:) ;
	627	src_grid_center_lon (:) = nav_lon_grid_${OGRID}(:,:) ;
	628	//
	629	src_grid_corner_lat [src_grid_size, src_grid_corners] = 0.0d ;
	630	src_grid_corner_lon [src_grid_size, src_grid_corners] = 0.0d ;
	631	src_grid_corner_lat(:,:) = bounds_lat_grid_${OGRID}(:,:,:) ;
	632	src_grid_corner_lon(:,:) = bounds_lon_grid_${OGRID}(:,:,:) ;
	633	//
	634	src_grid_imask [src_grid_size] = 0 ;
	635	src_grid_area [src_grid_size] = 0.0d ;
	636	src_grid_frac [src_grid_size] = 1.0d ;
	637	src_grid_imask (:) = 1 - mask_${OGRID}(:,:) ;
	638	src_grid_imask.int() ;
	639	src_grid_area (:) = area_grid_${OGRID}(:,:) ;
	640	EOF
	641
[4146]	642	cp add_varoce.nco add_varoce_$(basename ${rmpFile} .nc)_o_to_a.nco
[4199]	643	[[ ${o_to_a} = true ]] && ncap2 --history --append --script-file add_varoce_$(basename ${rmpFile} .nc)_o_to_a.nco ${OCE}_coordinates_mask.nc ${rmpFile}
[3719]	644	sed --in-place "s/src_/dst_/g" add_varoce.nco
[4146]	645	cp add_varoce.nco add_varoce_$(basename ${rmpFile} .nc)_a_to_o.nco
[4199]	646	[[ ${a_to_o} = true ]] && ncap2 --history --append --script-file add_varoce_$(basename ${rmpFile} .nc)_a_to_o.nco ${OCE}_coordinates_mask.nc ${rmpFile}
[3719]	647
	648	if [[ ${atm} = ico ]] ; then
	649	cat <<EOF >add_varatm.nco
[3639]	650	defdim ("dst_grid_size" , \$cell.size) ;
	651	defdim ("dst_grid_corners", 6) ;
	652	defdim ("dst_grid_rank" , 2) ;
	653	//
	654	dst_grid_dims[dst_grid_rank] = { \$cell.size, 1 } ;
	655	//
	656	dst_grid_center_lat [dst_grid_size] = 0.0d ;
	657	dst_grid_center_lon [dst_grid_size] = 0.0d ;
	658	dst_grid_center_lat (:) = lat(:) ;
	659	dst_grid_center_lon (:) = lon(:) ;
	660	//
	661	dst_grid_corner_lat [dst_grid_size, dst_grid_corners] = 0.0d ;
	662	dst_grid_corner_lon [dst_grid_size, dst_grid_corners] = 0.0d ;
	663	dst_grid_corner_lat(:,:) = bounds_lat(:,:) ;
	664	dst_grid_corner_lon(:,:) = bounds_lon(:,:) ;
	665	//
	666	dst_grid_imask [dst_grid_size] = 0 ;
	667	dst_grid_area [dst_grid_size] = 0.0d ;
	668	dst_grid_frac [dst_grid_size] = 1.0d ;
[4298]	669	dst_grid_imask (:) = 1 - Oce2AtmMask(:) ;
[3639]	670	dst_grid_imask.int() ;
	671	dst_grid_area (:) = aire(:) ;
[4259]	672	dst_grid_frac (:) = OceFrac(:) ;
[3639]	673	EOF
[4146]	674	cp add_varatm.nco add_varatm_$(basename ${rmpFile} .nc)_o_to_a.nco
[3719]	675	if [[ ${o_to_a} = true ]] ; then
[4199]	676	ncap2 --history --append --script-file add_varatm_$(basename ${rmpFile} .nc)_o_to_a.nco ${ATM}_grid_maskFrom_${OCE}.nc ${rmpFile}
[3719]	677	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
	678	mv rmp_tmp.nc ${rmpFile}
	679	fi
[3718]	680
[3719]	681	sed --in-place "s/dst_/src_/g" add_varatm.nco
[4146]	682	cp add_varatm.nco add_varatm_$(basename ${rmpFile} .nc)_a_to_o.nco
[3719]	683	if [[ ${a_to_o} = true ]] ; then
[4199]	684	ncap2 --history --append --script-file add_varatm_$(basename ${rmpFile} .nc)_a_to_o.nco ${ATM}_grid_maskFrom_${OCE}.nc ${rmpFile}
[3719]	685	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
	686	mv rmp_tmp.nc ${rmpFile}
	687	fi
	688	fi
[3966]	689
[3719]	690	if [[ ${atm} = lmd ]] ; then
	691	cat <<EOF >add_varatm.nco
[3639]	692	defdim ("dst_grid_size" , \$lon.size*\$lat.size) ;
	693	defdim ("dst_grid_corners", 4) ;
	694	defdim ("dst_grid_rank" , 2) ;
	695	//
	696	dst_grid_dims[dst_grid_rank] = { \$lat.size, \$lon.size } ;
	697	//
	698	dst_grid_center_lat [dst_grid_size] = 0.0d ;
	699	dst_grid_center_lon [dst_grid_size] = 0.0d ;
	700	lat0lon[lat,lon] = lat(:)+0*lon(:) ;
	701	lon0lat[lat,lon] = lon(:)+0*lat(:) ;
	702	dst_grid_center_lat (:) = lat0lon(:,:) ;
	703	dst_grid_center_lon (:) = lon0lat(:,:) ;
	704	//
	705	//dst_grid_corner_lat [dst_grid_size, dst_grid_corners] = 0.0d ; // Not available for LMDZ lon/lat grid
	706	//dst_grid_corner_lon [dst_grid_size, dst_grid_corners] = 0.0d ;
	707	//dst_grid_corner_lat(:,:) = bounds_lat(:,:) ;
	708	//dst_grid_corner_lon(:,:) = bounds_lon(:,:) ;
	709	//
	710	dst_grid_imask [dst_grid_size] = 0 ;
	711	dst_grid_area [dst_grid_size] = 0.0d ;
	712	dst_grid_frac [dst_grid_size] = 1.0d ;
[4298]	713	dst_grid_imask (:) = 1 - Oce2AtmMask(:,:) ;
[3639]	714	dst_grid_imask.int() ;
	715	dst_grid_area (:) = aire(:,:) ;
[4259]	716	dst_grid_frac (:) = OceFrac(:,:) ;
[3639]	717	EOF
[4146]	718	cp add_varatm.nco add_varatm_$(basename ${rmpFile} .nc)_o_to_a.nco
[3719]	719	if [[ ${o_to_a} = true ]] ; then
[4199]	720	ncap2 --history --append --script-file add_varatm_$(basename ${rmpFile} .nc)_o_to_a.nco ${ATM}_grid_maskFrom_${OCE}.nc ${rmpFile}
[3719]	721	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
	722	mv rmp_tmp.nc ${rmpFile}
	723	fi
	724
	725	sed --in-place "s/dst/src/g" add_varatm.nco
[4146]	726	cp add_varatm.nco add_varatm_$(basename ${rmpFile} .nc)_a_to_o.nco
[3719]	727	if [[ ${a_to_o} = true ]] ; then
[4199]	728	ncap2 --history --append --script-file add_varatm_$(basename ${rmpFile} .nc)_a_to_o.nco ${ATM}_grid_maskFrom_${OCE}.nc ${rmpFile}
[3719]	729	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
	730	mv rmp_tmp.nc ${rmpFile}
	731	fi
	732	fi
[3639]	733	done
[3901]	734	ls -al ${OCE}_coordinates_mask.nc
[4097]	735
[3639]	736	##
[4186]	737	## ============================================================================
[4172]	738	echo ${Titre}"Creates and save auxiliary files for OASIS : grids.nc, areas.nc and masks.nc"${Norm}
[4186]	739	cp ${SUBMIT_DIR}/CreateOasisGrids.bash .
	740	bash CreateOasisGrids.bash --oce ${OCE} --atm ${ATM}
[4097]	741
	742
	743	##
[4172]	744	echo ${Titre}"Runoff weights"${Norm}
[4097]	745	## ===========================================================================
[4186]	746	if [[ "X${okRunoff}" = "Xyes" ]] ; then
[4195]	747	${PyRun} python3 -u RunoffWeights.py --oce=${OCE} --atm=${ATM} \
[4172]	748	--atmCoastWidth=${atmCoastWidth} --oceCoastWidth=${oceCoastWidth} --searchRadius=${searchRadius} \
[4195]	749	--grids=grids_${CplModel}.nc --areas=areas_${CplModel}.nc --masks=masks_${CplModel}.nc \
[4199]	750	--o2a=${ATM}_grid_maskFrom_${OCE}.nc --output=rmp_t${atm}_to_t${oce}_runoff_${runOff_atmQuantity}_to_${runOff_oceQuantity}.nc \
	751	--fmt=${FMT_XIOS} \
[4186]	752	--atmQuantity=${runOff_atmQuantity} --oceQuantity=${runOff_oceQuantity}
[4172]	753	fi
[4097]	754
	755	##
[4172]	756	echo ${Titre}"Calving weights"${Norm}
[3620]	757	## ===========================================================================
[4172]	758	if [[ "X${okCalving}" = "Xyes" ]] ; then
	759	case ${OCE} in
[4298]	760	( eORCA025* )
[4186]	761	cp /ccc/work/cont003/gencmip6/deshayej/eORCA_R025_runoff_v1.2.nc .
[4199]	762	${PyRun} python3 -u CalvingWeights.py --output=rmp_t${atm}_to_t${oce}_calving_nosouth.nc --fmt=${FMT_XIOS} \
[4186]	763	--oce=${OCE} --atm=${ATM} --type=nosouth --dir=.
[4199]	764	${PyRun} python3 -u CalvingWeights.py --output=rmp_t${atm}_to_t${oce}_calving_iceberg.nc --fmt=${FMT_XIOS} \
[4186]	765	--oce=${OCE} --atm=${ATM} --type=iceberg --dir=. --repartition_file=eORCA_R025_runoff_v1.2.nc --repartition_var=Icb_flux
[4199]	766	${PyRun} python3 -u CalvingWeights.py --output=rmp_t${atm}_to_t${oce}_calving_iceshelf.nc --fmt=${FMT_XIOS} \
[4186]	767	--oce=${OCE} --atm=${ATM} --type=iceshelf --dir=. --repartition_file=eORCA_R025_runoff_v1.2.nc --repartition_var=sornfisf
[4172]	768	;;
	769
	770	( eORCA1.2 )
	771	cp ${R_IN}/OCE/NEMO/ORCA1_LIM3_PISCES/v3.6_stable/runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc .
[4199]	772	${PyRun} python3 -u CalvingWeights.py --output=rmp_t${atm}_to_t${oce}_calving_nosouth.nc --fmt=${FMT_XIOS}\
[4172]	773	--oce=${OCE} --atm=${ATM} --type=nosouth --dir=.
[4199]	774	${PyRun} python3 -u CalvingWeights.py --output=rmp_t${atm}_to_t${oce}_calving_iceberg.nc --fmt=${FMT_XIOS}\
[4172]	775	--oce=${OCE} --atm=${ATM} --type=iceberg --dir=. --repartition_file=runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc --repartition_var=Icb_flux
[4199]	776	${PyRun} python3 -u CalvingWeights.py --output=rmp_t${atm}_to_t${oce}_calving_iceshelf.nc --fmt=${FMT_XIOS}\
[4172]	777	--oce=${OCE} --atm=${ATM} --type=iceshelf --dir=. --repartition_file=runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc --repartition_var=sornfisf
	778	;;
	779
	780	( * )
[4199]	781	${PyRun} python3 -u CalvingWeights.py --output=rmp_t${atm}_to_t${oce}_calving_full.nc --fmt=${FMT_XIOS} \
[4172]	782	--oce=${OCE} --atm=${ATM} --type=full --dir=.
	783	;;
	784
	785	esac
	786	fi
	787
	788	##
[4199]	789	echo ${Titre}"Simplifies headers, add version and comment"${Norm}
[4172]	790	## ===========================================================================
[4199]	791	for File in $(ls dia_.nc rmp_.nc ${ATM}_grid_maskFrom_${OCE}.nc areas_${OCE}x${ATM}.nc grids_${OCE}x${ATM}.nc masks_${OCE}x${ATM}.nc 2> /dev/null ) ; do
[4037]	792	ncatted --history --attribute history_of_appended_files,global,d,c,"" ${File}
[4199]	793	ncatted --history --attribute history,global,d,c,"" ${File}
[4172]	794	[[ "X${Comment}" != "X" ]] && ncatted --history --attribute Comment,global,o,c,"${Comment}" ${File}
	795	[[ "X${Version}" != "X" ]] && ncatted --history --attribute Version,global,o,c,"${Version}" ${File}
[4199]	796	[[ "X${Tag}" != "X" ]] && ncatted --history --attribute Version,global,o,c,"${Tag}" ${File}
	797	done
	798
	799	##
	800	echo ${Titre}"Rename rmp and dia files"${Norm}
	801	## ===========================================================================
[4259]	802	for File in $(ls ${oce}${atm}* ${atm}${oce}* 2> /dev/null ); do
[3719]	803	NewFile=$(echo ${File} \| sed -e "s/${atm}/${ATM}/" -e "s/${oce}/${OCE}/" )
[4259]	804	mv ${File} ${NewFile}
[3620]	805	done
	806
[4199]	807	##
	808	echo ${Titre}"Add Tag"${Norm}
	809	## ===========================================================================
	810	if [[ "X${Tag}" != "X" ]] ; then
	811	for File in $(ls dia_.nc rmp_.nc ${ATM}_grid_maskFrom_${OCE}.nc areas_${OCE}x${ATM}.nc grids_${OCE}x${ATM}.nc masks_${OCE}x${ATM}.nc 2> /dev/null ) ; do
	812	mv ${File} $(basename ${File} .nc)_${Tag}.nc
	813	done
[4186]	814	fi
[4199]	815	##
	816	echo ${Titre}"Add Version"${Norm}
	817	## ===========================================================================
	818	if [[ "X${Version}" != "X" ]] ; then
	819	for File in $(ls dia_.nc rmp_.nc ${ATM}_grid_maskFrom_${OCE}.nc areas_${OCE}x${ATM}.nc grids_${OCE}x${ATM}.nc masks_${OCE}x${ATM}.nc 2> /dev/null ) ; do
	820	mv ${File} $(basename ${File} .nc)_${Version}.nc
	821	done
	822	fi
	823
	824	## ===========================================================================
	825	echo ${Titre}"Save results"${Norm}
	826	## ===========================================================================
	827	for File in $(ls dia_.nc rmp_.nc ${ATM}_grid_maskFrom_${OCE}.nc areas_${OCE}x${ATM}.nc grids_${OCE}x${ATM}.nc masks_${OCE}x${ATM}.nc 2> /dev/null ) ; do
	828	cp ${File} ${SUBMIT_DIR}
	829	done
[4172]	830
[4199]	831
[3620]	832	##
[4172]	833	echo ${Titre}"Creates a README.txt file"${Norm}
[4090]	834	## ===========================================================================
	835	[[ -f README.txt ]] && rm README.txt
[4298]	836	UUID=$(uuid)
[3620]	837
[4090]	838	cat <<EOF > README.txt
	839	Files produced by CreateWeightsMask.bash and CreateOasisGrids.bash
	840
	841	rmp_* are weights files
	842	dia_* are diagnostic files not needed for the coupler
[4195]	843	grids_${CplModel}.nc areas_${CplModel}.nc masks_${CplModel}.nc are auxiliary file needed by OASIS-MCT
[4090]	844	All files have the same uuid in the global attributes
	845
	846	Description : Weigths and auxiliary files for coupling ${OCE} and ${ATM} needed by OASIS-MCT
	847	Conventions : CF-1.6
	848	source : IPSL Earth system model
	849	group : ICMC IPSL Climate Modelling Center
	850	Institution : IPSL https://www.ipsl.fr
	851	Ocean : ${OCE} https://www.nemo-ocean.eu
	852	Atmosphere : ${ATM} http://lmdz.lmd.jussieu.fr
	853	production : $(finger ${LOGNAME} \| head -1 \| awk '{print $4, $5}')
	854	originalFiles : ${OCE}_coordinates_mask.nc ${ATM}_grid_mask.nc
[4195]	855	associatedFiles : grids_${CplModel}.nc areas_${CplModel}.nc masks_${CplModel}.nc
[4090]	856	directory : $(pwd)
	857	timeStamp : $(date)
	858	uuid : ${UUID}
	859	HOSTNAME : $(hostname)
	860	LOGNAME : $(whoami)
	861	NCO : NCO netCDF Operator ${NCO} http://nco.sourceforge.net
	862	Python version : ${PYTHON_VER}
	863	OS : $(uname -o)
	864	release : $(uname -r)
	865	hardware : $(uname -i)
[4091]	866	EOF
[4090]	867
[4091]	868	echo 'SVN Information : ' >> README.txt
	869	echo '$Author$ ' >> README.txt
	870	echo '$Date$ ' >> README.txt
	871	echo '$Revision$ ' >> README.txt
	872	echo '$Id$ ' >> README.txt
	873	echo '$HeadURL$ ' >> README.txt
[4090]	874
[4172]	875	echo ${Titre}"Compute checksums and add them to README"${Norm}
[4199]	876	# ------------------------------------------------------------
[4091]	877	cat << EOF >> README.txt
[4090]	878
[4159]	879	Files produced, with checksum produced by Unix command shasum (version $(shasum --version)) with default algorithm
[4090]	880
	881	EOF
	882
[4199]	883	for file in $(ls dia_.nc rmp_.nc ${ATM}_grid_maskFrom_${OCE}.nc areas_${OCE}x${ATM}.nc grids_${OCE}x${ATM}.nc masks_${OCE}x${ATM}.nc 2> /dev/null ) ; do
[4298]	884	ncatted --attribute uuid,global,o,c,"${UUID}" ${file}
[4090]	885	echo "$(shasum ${file})" >> README.txt
	886	done
	887
	888	cat <<EOF >> README.txt
	889
	890	================= That's all folk's ! ========================
	891	EOF
	892
[4259]	893	if [[ "X${Version}" != "X" ]] ; then
	894	cp README.txt ${SUBMIT_DIR}/README_${CplModel}_MOSAIX_${Version}.txt
	895	else
	896	cp README.txt ${SUBMIT_DIR}/README_${CplModel}_MOSAIX.txt
	897	fi
[3620]	898	## ===========================================================================
	899	##
[4172]	900	echo ${Titre}" That's all folk's !!! "${Norm}
[3620]	901	##
	902	## ===========================================================================
	903

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