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source: CONFIG/UNIFORM/v5/LMDZORINCA_v5/GENERAL/DRIVER/lmdz.driver @ 1779

Last change on this file since 1779 was 1779, checked in by jgipsl, 12 years ago
Modification to be able to run LMDZ4 with the same run.def as LMDZ5. In LMDZ4 config_inca=none is needed when running without inca. In LMDZ5, type_trac=lmdz is sufficient. NB! LMDZ4 is not possible to use with INCA or REPROBUS.
File size: 20.3 KB

Rev	Line
[396]	1	#!/bin/ksh
	2	#-----------------------------------------------------------------
[894]	3	function LMDZ_sed
	4	{
[1690]	5	# Usage : LMDZ_sed filedef var_name myvalue
	6	# In file filedef modify the line containing var_name=xxx into var_name=myvalue
[894]	7	IGCM_debug_PushStack "LMDZ_sed"
	8
[911]	9	sed -e "s/^${2}\ =./${2}= ${3}/" ${1} > ${1}.tmp
[894]	10	RET=$?
	11	echo "LMDZ_sed : ${1} ${2} ${3}"
	12	\mv ${1}.tmp ${1}
	13
	14	IGCM_debug_PopStack "LMDZ_sed"
	15	return $RET
	16	}
[1690]	17	function LMDZ_sed_default
	18	{
	19	# Usage : LMDZ_sed_default filedef var_name
	20	# In file filedef modify the line "var_name=xxx DEFAULT= myvalue"
	21	# into "var_name=myvalue"
	22	IGCM_debug_PushStack "LMDZ_sed_default"
[894]	23
[1690]	24	DefValue=$( grep ${2} ${1} \| awk -F"DEFAULT.=*" '{print $2}')
	25
	26	LMDZ_sed ${1} ${2} $DefValue
	27	IGCM_debug_PopStack "LMDZ_sed_default"
	28	return $RET
	29	}
	30
	31
[396]	32	function ATM_Initialize
	33	{
	34	IGCM_debug_PushStack "ATM_Initialize"
	35
[671]	36	RESOL_ATM=$( echo $RESOL \| awk "-Fx" '{print $2}' \| awk "-F-" '{print $1}')
[396]	37
[659]	38	[ -f ${SUBMIT_DIR}/../.resol ] && eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol) \|\| RESOL_ATM_3D=96x95x19
[396]	39
[659]	40	RESOL_ATM_Z=$( echo ${RESOL_ATM_3D} \| awk "-Fx" '{print $3}' )
[649]	41
[697]	42	##-- Calendar type for LMDZ
	43	case ${config_UserChoices_CalendarType} in
	44	leap\|gregorian)
	45	CalendarTypeForLmdz=earth_366d;;
	46	noleap)
	47	CalendarTypeForLmdz=earth_365d;;
	48	360d)
	49	CalendarTypeForLmdz=earth_360d;;
	50	*)
	51	CalendarTypeForLmdz=earth_360d
	52	esac
	53
[1541]	54	##- LMDZ physics version
	55	## Read LMDZ_Physics option in lmdz.card, if not present take default value AP (old physics)
	56	if [ ! X${lmdz_UserChoices_LMDZ_Physics} = X ] ; then
	57	LMDZ_Physics=${lmdz_UserChoices_LMDZ_Physics}
	58	else
	59	LMDZ_Physics=AP
	60	fi
	61	echo LMDZ physics version : ${LMDZ_Physics}
	62
[1643]	63	##- Create_etat0_limit version
[1689]	64	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices CREATE
[1643]	65	CREATE=${lmdz_UserChoices_CREATE}
	66	echo create_etat0_limit version : ${CREATE}
	67
[1550]	68	## - LMDZ choice of config.def file
	69	## ConfType must be set in lmdz.card
	70	ConfType=${lmdz_UserChoices_ConfType}
[1541]	71
[1550]	72	##- LMDZ output level, to be set in lmdz.card
	73	if [ X${lmdz_UserChoices_OutLevel} = X ] ; then
	74	# OutLevel is not set. Take default value low.
	75	OutLevel=low
	76	else
	77	OutLevel=${lmdz_UserChoices_OutLevel}
	78	fi
	79
[1539]	80	##-- Output frequency purpose ....
[396]	81	##-- Initialisation ....
[1539]	82	ok_mensuel=n
	83	ok_journe=n
[396]	84	ok_hf=n
[1539]	85	ok_hf3h=n
	86	ok_hf3hm=n
	87	ok_stn=n
[396]	88
	89	case ${config_UserChoices_PeriodLength} in
[1539]	90	1Y\|1y\|1M\|1m) ok_mensuel=y ;;
	91	5D\|5d\|1D\|1d) ok_journe=y ;;
[396]	92	esac
	93
	94	for frequency in ${config_ATM_WriteFrequency} ; do
	95	case ${frequency} in
[1539]	96	1M\|1m) ok_mensuel=y ;;
[396]	97	esac
	98	case ${frequency} in
[1539]	99	5D\|5d\|1D\|1d) ok_journe=y ;;
	100	esac
	101	case ${frequency} in
[396]	102	HF\|hf) ok_hf=y ;;
	103	esac
[1539]	104	case ${frequency} in
	105	HF3h\|hf3h) ok_hf3h=y ;;
	106	esac
	107	case ${frequency} in
	108	HF3hm\|hf3hm) ok_hf3hm=y ;;
	109	esac
	110	case ${frequency} in
	111	STN\|stn) ok_stn=y ;;
	112	esac
[396]	113	done
	114
[902]	115	## Read LMDZ_NbPeriod_adjust option in lmdz.card
[1688]	116	if [ X"${lmdz_UserChoices_LMDZ_NbPeriod_adjust}" = X"" ] ; then
	117	# The variable is not in lmdz.card, set default value
	118	LMDZ_NbPeriod_adjust=0
	119	else
	120	LMDZ_NbPeriod_adjust=${lmdz_UserChoices_LMDZ_NbPeriod_adjust}
	121	fi
[396]	122
[815]	123	if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
[1688]	124	LMDZ_Bands_file_name=${lmdz_UserChoices_LMDZ_Bands_file_name}
[815]	125	fi
	126
[912]	127	## Read LMDZ_Freq_aero and LMDZ_Length_aero in lmdz.card
[1172]	128	LMDZ_Freq_aero=${lmdz_UserChoices_LMDZ_Freq_aero}
	129	LMDZ_Length_aero=${lmdz_UserChoices_LMDZ_Length_aero}
[912]	130
[1000]	131	## Read LMDZ_COSP_monthly LMDZ_COSP_daily and LMDZ_COSP_hf in lmdz.card
[1172]	132	LMDZ_COSP_OK=${lmdz_UserChoices_LMDZ_COSP_OK}
	133	LMDZ_COSP_monthly=${lmdz_UserChoices_LMDZ_COSP_monthly}
	134	LMDZ_COSP_daily=${lmdz_UserChoices_LMDZ_COSP_daily}
	135	LMDZ_COSP_hf=${lmdz_UserChoices_LMDZ_COSP_hf}
[1000]	136
[1003]	137	## Read LMDZ_NMC_monthly LMDZ_NMC_daily and LMDZ_NMC_hf in lmdz.card
[1172]	138	LMDZ_NMC_monthly=${lmdz_UserChoices_LMDZ_NMC_monthly}
	139	LMDZ_NMC_daily=${lmdz_UserChoices_LMDZ_NMC_daily}
	140	LMDZ_NMC_hf=${lmdz_UserChoices_LMDZ_NMC_hf}
[1000]	141
[396]	142	IGCM_debug_PopStack "ATM_Initialize"
	143	}
	144
	145	#-----------------------------------------------------------------
	146	function ATM_Update
	147	{
	148	IGCM_debug_PushStack "ATM_Update"
	149
[1537]	150
[749]	151	case ${config_UserChoices_PeriodLength} in
	152	Y\|y)
	153	LMDZ_ecrit_ISCCP=30.
	154	LMDZ_periodav=30.
[755]	155	if [ "${config_UserChoices_CalendarType}" != "360d" ] ; then
[1649]	156	echo Do not consider following warning if your running create_etat0_limit :
[1650]	157	echo WARNING !!! For lmdz : calendartype in config.card. PeriodLength=1Y allowed only for CalendarType=360d
[1649]	158	fi
[749]	159	;;
	160	*)
	161	LMDZ_ecrit_ISCCP=${PeriodLengthInDays}.
	162	LMDZ_periodav=${PeriodLengthInDays}.
	163	;;
	164	esac
[1546]	165
[396]	166	##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
	167	if [ ${CumulPeriod} -eq 1 ] ; then
	168	RAZ_DATE=1
	169	else
	170	RAZ_DATE=0
	171	fi
	172
[815]	173	## algo : For CumulPeriod=1 ;
	174	## IF NbPeriod_Adjust = 0, Get Bands file directly from server, store it with _0 suffix
	175	## ELSE LMDZ_adjust=y ; save Bands file on file server ;
	176	## For CumulPeriod=2 to LMDZ_NbPeriod_adjust ; Get Bands file from server (CumulPeriod-1) ; LMDZ_adjust=y ; save Bands file on file server ;
	177	## For CumulPeriod > LMDZ_NbPeriod_adjust ; LMDZ_adjust=n ; Get Bands file from server (CumulPeriod=LMDZ_NbPeriod_adjust 0 to force it) ; Use Bands ;
	178
	179	if [ ${CumulPeriod} -eq 1 ] ; then
	180	if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
[1778]	181	if [ ! X${LMDZ_Bands_file_name} = X ] ; then
[1688]	182	IGCM_sys_Get ${LMDZ_Bands_file_name} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
	183	IGCM_sys_Put_Out Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${R_OUT_ATM_D}/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0
	184	IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
	185	IGCM_debug_Print 1 "Bands file forced to ${LMDZ_Bands_file_name} and stored in ${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0"
	186	fi
[815]	187	fi
	188	fi
	189
[743]	190	LMDZ_adjust=n
	191	[ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && LMDZ_adjust=y
	192
[815]	193	RefPeriod=${LMDZ_NbPeriod_adjust} #0 to use a Bands file from Restart
	194	[ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && (( RefPeriod = ${CumulPeriod} - 1 ))
[743]	195
[902]	196	[ ${CumulPeriod} -gt 1 ] && ( IGCM_sys_Get ${R_OUT_ATM_D}/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${RefPeriod} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ; IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat )
[743]	197
[1535]	198	##-- GHG forcing :
[1546]	199	## If forcing file exist in run directory, read values for the current year and modify config.def
[1535]	200	if [ -f SOLARANDVOLCANOES.txt ] ; then
	201	IPCC_SOLAR=`grep Annee_${year} SOLARANDVOLCANOES.txt \| awk -F= '{print $2}'`
[1546]	202	LMDZ_sed config.def solaire ${IPCC_SOLAR}
[1690]	203	else
	204	LMDZ_sed_default config.def solaire
[1535]	205	fi
	206	if [ -f CO2.txt ] ; then
	207	IPCC_CO2=`grep Annee_${year} CO2.txt \| awk -F= '{print $2}'`
[1546]	208	LMDZ_sed config.def co2_ppm ${IPCC_CO2}
[1690]	209	else
	210	LMDZ_sed_default config.def co2_ppm
[1535]	211	fi
[1690]	212
	213
[1535]	214	if [ -f CH4.txt ] ; then
	215	IPCC_CH4=`grep Annee_${year} CH4.txt \| awk -F= '{print $2}'`
[1546]	216	LMDZ_sed config.def CH4_ppb ${IPCC_CH4}
[1690]	217	else
	218	LMDZ_sed_default config.def CH4_ppb
[1535]	219	fi
	220	if [ -f N2O.txt ] ; then
	221	IPCC_N2O=`grep Annee_${year} N2O.txt \| awk -F= '{print $2}'`
[1546]	222	LMDZ_sed config.def N2O_ppb ${IPCC_N2O}
[1690]	223	else
	224	LMDZ_sed_default config.def N2O_ppb
[1535]	225	fi
	226	if [ -f CFC11.txt ] ; then
	227	IPCC_CFC11=`grep Annee_${year} CFC11.txt \| awk -F= '{print $2}'`
[1546]	228	LMDZ_sed config.def CFC11_ppt ${IPCC_CFC11}
[1690]	229	else
	230	LMDZ_sed_default config.def CFC11_ppt
[1535]	231	fi
	232	if [ -f CFC12.txt ] ; then
	233	IPCC_CFC12=`grep Annee_${year} CFC12.txt \| awk -F= '{print $2}'`
[1546]	234	LMDZ_sed config.def CFC12_ppt ${IPCC_CFC12}
[1690]	235	else
	236	LMDZ_sed_default config.def CFC12_ppt
[1535]	237	fi
	238
[1537]	239	# Add special treatement for CARBON CYCLE
[1546]	240	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
[1537]	241
	242	typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
	243	typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
	244	typeset PathCO2log
	245	typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
	246
[1778]	247	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
[1537]	248	##--Initialization of fluxes to an undefined value at the first run
	249	UndefinedValueCo2=-9999
	250	InitPeriodCo2=0
	251	InitDateBeginCo2=${UndefinedValueCo2}
	252	InitYearCo2=$(( ${year} - 1 ))
	253	InitDateEndCo2=${InitYearCo2}1231
	254	fCO2_ff=${UndefinedValueCo2}
	255	CO2SBG=${UndefinedValueCo2}
	256	CO2LU=${UndefinedValueCo2}
	257	CO2MBG=${UndefinedValueCo2}
	258	CO2_ppm_prec=${UndefinedValueCo2}
	259	# Get the initial value of atmosp. pco2
	260	CO2_ppm=${lmdz_UserChoices_co2_init}
	261
	262	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
	263	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
	264
	265	# Save CO2 values in ExeCpuLog variable contents 5 fields
	266	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
	267	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
	268	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	269
	270	# Get the path where the log file co2.log is
	271	PathCO2log=${SUBMIT_DIR}
	272	# Get Previous line in co2.log
	273	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
	274
	275	else
	276
	277	# NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
	278	# !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
	279	#SubmitRestartPath=
[1778]	280	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
[1537]	281	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
	282	PathCO2log=${config_ATM_SubmitRestartPath}
	283	Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
	284	PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
	285
	286	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
	287	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
	288
	289	# Save Last Line of control in new co2.log file
	290	InitPeriodCo2=0
	291	InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $2}' )
	292	InitDateEndCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $3}' )
	293	fCO2_ff=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $6}' )
	294	CO2SBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $8}' )
	295	CO2LU=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $9}' )
	296	CO2MBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $7}' )
	297	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $5}' )
	298	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	299
	300	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
	301	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
	302	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	303	else
	304	# Get restart line in co2.log
	305	PathCO2log=${SUBMIT_DIR}
	306	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
	307	# Get the value of atmosp. pco2 in co2.log
	308	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	309	fi
	310
	311	fi
	312
	313	if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
[1546]	314	# Modify co2_ppm in config.def only for historical run
[1690]	315	# If not historical run, keep co2_ppm value set earlier by LMDZ_sed
[1546]	316	LMDZ_sed config.def co2_ppm ${CO2_ppm}
[1537]	317	fi
	318	fi
	319	# end CARBON_CYCLE
	320
[1538]	321	##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
	322	## COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
	323	if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] && [ ${year} -ge 1979 ]) ; then
	324	LMDZ_COSP_daily=y
	325	fi
[1537]	326
[1538]	327
[1540]	328	## output.def parameters
[1546]	329	# columns in phys_output_filekeys refer to the filenames given in phys_out_filenames in output.def :
[1539]	330	# histmth histday histhf histfh3h histhf3hm histstn
[1546]	331	LMDZ_sed output.def phys_out_filekeys "${ok_mensuel} ${ok_journe} ${ok_hf} ${ok_hf3h} ${ok_hf3hm} ${ok_stn}"
[1540]	332	LMDZ_sed output.def ecrit_ISCCP ${LMDZ_ecrit_ISCCP}
	333	LMDZ_sed output.def ok_cosp ${LMDZ_COSP_OK}
	334	LMDZ_sed output.def ok_mensuelCOSP ${LMDZ_COSP_monthly}
	335	LMDZ_sed output.def ok_journeCOSP ${LMDZ_COSP_daily}
	336	LMDZ_sed output.def ok_hfCOSP ${LMDZ_COSP_hf}
	337	LMDZ_sed output.def ok_histNMC "${LMDZ_NMC_monthly}, ${LMDZ_NMC_daily}, ${LMDZ_NMC_hf}"
[396]	338
[1544]	339	## gcm.def parameters :
	340	# Modification only for new physics
[1750]	341	if [ X${LMDZ_Physics} = X"NPv3.1" ] ; then
[1544]	342	LMDZ_sed gcm.def iphysiq 5
[1690]	343	else
	344	LMDZ_sed_default gcm.def iphysiq
[1544]	345	fi
[396]	346
[1544]	347
[911]	348	## run.def parameters
	349	LMDZ_sed run.def dayref ${InitDay}
	350	LMDZ_sed run.def anneeref ${InitYear}
	351	LMDZ_sed run.def calend ${CalendarTypeForLmdz}
	352	LMDZ_sed run.def nday ${PeriodLengthInDays}
	353	LMDZ_sed run.def raz_date ${RAZ_DATE}
	354	LMDZ_sed run.def periodav ${LMDZ_periodav}
	355	LMDZ_sed run.def adjust ${LMDZ_adjust}
[396]	356
[1643]	357
[1650]	358	## Determine from the variable ListOfComponents in config.card coupling to external models
	359	## and set corresponding parameters in run.def
	360	echo ListOfComponents now running : ${config_ListOfComponents[*]}
	361
	362	if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
	363	echo "Activate ORCHIDEE, set VEGET=y in run.def"
	364	LMDZ_sed run.def VEGET y
	365	else
	366	echo "No ORCHIDEE, set VEGET=n in run.def"
	367	LMDZ_sed run.def VEGET n
	368	fi
	369
	370	if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
	371	echo "Activate coupling to ocean, set type_ocean=couple in run.def"
	372	LMDZ_sed run.def type_ocean couple
	373	else
	374	echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
	375	LMDZ_sed run.def type_ocean force
	376	fi
	377
	378	if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
	379	echo "Activate coupling to INCA, set type_trac=inca in run.def"
[1666]	380	LMDZ_sed run.def type_trac inca
[1650]	381	elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
	382	echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
[1666]	383	LMDZ_sed run.def type_trac repr
[1779]	384	LMDZ_sed run.def config_inca none
[1650]	385	else
	386	echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
[1666]	387	LMDZ_sed run.def type_trac lmdz
[1779]	388	LMDZ_sed run.def config_inca none
[1650]	389	fi
	390
	391
[1686]	392	# config.def : If running with Reprobus, desactivate ok_ade, ok_aie and read_climoz
[1697]	393	if [ X${config_ListOfComponents_CHM} = Xreprobus ] \|\| [ X${config_ListOfComponents_CHM} = Xinca ] ; then
[1686]	394	LMDZ_sed config.def ok_ade n
	395	LMDZ_sed config.def ok_aie n
	396	LMDZ_sed config.def read_climoz 0
	397	else
	398	LMDZ_sed config.def ok_ade y
	399	LMDZ_sed config.def ok_aie y
	400	LMDZ_sed config.def read_climoz 2
	401	fi
	402
[1690]	403	# guide.def : Activate nudging if ok_guide=y set in lmdz.card
[1643]	404	if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
	405	LMDZ_sed guide.def ok_guide ${lmdz_UserChoices_ok_guide}
[1690]	406	else
	407	LMDZ_sed guide.def ok_guide n
[1643]	408	fi
	409
[902]	410	## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
[1172]	411	ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
[1688]	412	if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
[396]	413	awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
	414	IGCM_sys_Mv gcm.def.tmp gcm.def
	415	echo
	416	IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
	417	echo
	418	cat gcm.def
	419	ByPass_hgardfou_teta=n
[902]	420	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
[396]	421	fi
	422
[902]	423	## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
[1172]	424	ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
[1688]	425	if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
[396]	426	sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
	427	IGCM_sys_Mv gcm.def.tmp gcm.def
	428	echo
	429	IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
	430	echo
	431	cat gcm.def
	432	ByPass_hgardfou_mats=n
[902]	433	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
[396]	434	fi
	435
	436	if ( ${FirstInitialize} ) ; then
[1643]	437	if [ -f start.nc ] && [ -f startphy.nc ] ; then
	438	# The restart files already exist. They have been copied from a previous run or from a CREATE job
	439	echo "Restart files for LMDZ have been copied from a previous run"
[1778]	440	elif [ -f create_etat0_limit* ] \|\| [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
[1649]	441	# Do nothing because it is the program for creating restart files that is running and not LMDZ
	442	echo "create_etat0_limit.e will create initial start files"
[1643]	443	else
	444	# Restart files have to be created
	445	echo "Run create_etat0_limit.e to create restart files start.nc and startphy.nc for LMDZ"
[396]	446	if [ ${DRYRUN} -le 2 ] ; then
[894]	447	##-- suppression of ozone file construction --
[1643]	448	cp config.def config.def.save
	449	LMDZ_sed config.def read_climoz 0
[396]	450	IGCM_sys_Cp ${R_EXE}/create_etat0_limit.e ${RUN_DIR}/.
	451	if [ ${DRYRUN} -le 1 ] ; then
[908]	452	${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e
[1643]	453	IGCM_sys_Put_Out start.nc ${R_OUT_ATM_R}/${config_UserChoices_JobName}_${PeriodDateBegin}_start.nc
	454	IGCM_sys_Put_Out startphy.nc ${R_OUT_ATM_R}/${config_UserChoices_JobName}_${PeriodDateBegin}_startphy.nc
[396]	455	fi
[1643]	456	IGCM_sys_Mv config.def.save config.def
[396]	457	else
[908]	458	echo "EXECUTION of ${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e simulated"
	459	echo "EXECUTION of ${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e simulated for DRYRUN = " $DRYRUN >> stack
[396]	460	fi
	461	fi
	462	fi
	463
	464	IGCM_debug_PopStack "ATM_Update"
	465	}
	466
	467	#-----------------------------------
	468	function ATM_Finalize
	469	{
	470	IGCM_debug_PushStack "ATM_Finalize"
	471
[743]	472	[ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && IGCM_sys_Put_Out Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${R_OUT_ATM_D}/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${CumulPeriod}
[396]	473
[1537]	474
	475	# Add special treatement for CARBON CYCLE
[1546]	476	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
[1537]	477	typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
	478
	479	# Fossil fuel emission
	480	if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
	481	# For Control, no fossil fuel emission :
	482	fCO2_ff=0
	483	echo "Fossil Fuel for control run :" ${fCO2_ff}
	484	else
	485	# For historical, get the fossile fuel file :
	486	fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
	487	echo "Fossil Fuel for historical run :" ${fCO2_ff}
	488	fi
	489
	490	# Get the value of ocean carbon flux
	491	CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
	492	CO2MBG=$( echo ${CO2MBG} \| sed -e "s/ *//" )
	493	echo "Ocean carbon flux :" ${CO2MBG}
	494
	495	# Get the value of land fluxes
	496	set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
	497	CO2SRF=$( echo ${CO2SBG_3V[0]} \| sed -e "s/ *//" )
	498	CO2LU=$( echo ${CO2SBG_3V[1]} \| sed -e "s/ *//" )
	499	CO2SBG=$( echo ${CO2SBG_3V[2]} \| sed -e "s/ *//" )
	500	echo "Land carbon flux (NEP) :" ${CO2SRF}
	501	echo "LU flux (FLUC) :" ${CO2LU}
	502	echo "Total Land carbon flux (NBP) :" ${CO2SBG}
	503
	504	# Previous CO2
	505	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	506	echo "Previous CO2 :" ${CO2_ppm_prec}
	507
	508	# Formula
	509	CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" \| bc -l )
	510	echo "New CO2 :" ${CO2_ppm}
	511
	512	# Save CO2 values in ExeCpuLog variable contents 5 fields
	513	echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
	514	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
	515	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	516
	517	fi
	518
[396]	519	echo FINALIZE ATM !
	520
	521	IGCM_debug_PopStack "ATM_Finalize"
	522	}

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