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source: CONFIG/UNIFORM/v5/LMDZORINCA_v5/GENERAL/DRIVER/lmdz.driver @ 1923

Last change on this file since 1923 was 1923, checked in by jgipsl, 12 years ago
Corrected bug affecting create_etat0_limit for leap calendar.
File size: 24.7 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"
[1783]	8
	9	# Test if the fichier exist
	10	if [ ! -f ${1} ] ; then
	11	echo "WARNING : ${1} file does not exist. Following will not be done : LMDZ_sed : ${1} ${2} ${3}"
	12	return
	13	fi
[894]	14
[911]	15	sed -e "s/^${2}\ =./${2}= ${3}/" ${1} > ${1}.tmp
[894]	16	RET=$?
	17	echo "LMDZ_sed : ${1} ${2} ${3}"
	18	\mv ${1}.tmp ${1}
	19
	20	IGCM_debug_PopStack "LMDZ_sed"
	21	return $RET
	22	}
[1690]	23	function LMDZ_sed_default
	24	{
	25	# Usage : LMDZ_sed_default filedef var_name
	26	# In file filedef modify the line "var_name=xxx DEFAULT= myvalue"
	27	# into "var_name=myvalue"
	28	IGCM_debug_PushStack "LMDZ_sed_default"
[894]	29
[1690]	30	DefValue=$( grep ${2} ${1} \| awk -F"DEFAULT.=*" '{print $2}')
	31
	32	LMDZ_sed ${1} ${2} $DefValue
	33	IGCM_debug_PopStack "LMDZ_sed_default"
	34	return $RET
	35	}
	36
	37
[396]	38	function ATM_Initialize
	39	{
	40	IGCM_debug_PushStack "ATM_Initialize"
	41
[671]	42	RESOL_ATM=$( echo $RESOL \| awk "-Fx" '{print $2}' \| awk "-F-" '{print $1}')
[396]	43
[659]	44	[ -f ${SUBMIT_DIR}/../.resol ] && eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol) \|\| RESOL_ATM_3D=96x95x19
[396]	45
[659]	46	RESOL_ATM_Z=$( echo ${RESOL_ATM_3D} \| awk "-Fx" '{print $3}' )
[1802]	47	RESOL_ATM_X=$( echo ${RESOL_ATM_3D} \| awk "-Fx" '{print $1}' )
	48	RESOL_ATM_Y=$( echo ${RESOL_ATM_3D} \| awk "-Fx" '{print $2}' )
	49	RESOL_ATM_XY="${RESOL_ATM_X}x${RESOL_ATM_Y}"
[649]	50
[1923]	51	##-- Calendar type for LMDZ and create_etat0_limit
[697]	52	case ${config_UserChoices_CalendarType} in
	53	leap\|gregorian)
[1923]	54	CalendarTypeForLmdz=earth_366d
	55	CalendarTypeForCreate=gregorian;;
[697]	56	noleap)
[1923]	57	CalendarTypeForLmdz=earth_365d
	58	CalendarTypeForCreate=${CalendarTypeForLmdz};;
[697]	59	360d)
[1923]	60	CalendarTypeForLmdz=earth_360d
	61	CalendarTypeForCreate=${CalendarTypeForLmdz};;
[697]	62	*)
	63	CalendarTypeForLmdz=earth_360d
[1923]	64	CalendarTypeForCreate=${CalendarTypeForLmdz}
[697]	65	esac
	66
[1541]	67	##- LMDZ physics version
	68	## Read LMDZ_Physics option in lmdz.card, if not present take default value AP (old physics)
	69	if [ ! X${lmdz_UserChoices_LMDZ_Physics} = X ] ; then
	70	LMDZ_Physics=${lmdz_UserChoices_LMDZ_Physics}
	71	else
	72	LMDZ_Physics=AP
	73	fi
	74	echo LMDZ physics version : ${LMDZ_Physics}
	75
[1643]	76	##- Create_etat0_limit version
[1782]	77	## Define variable CREATE only if it is set in lmdz.card section UserChoices.
	78	## This variable is only used in lmdz.card to choose input files.
	79	if [ ! X${lmdz_UserChoices_CREATE} = X ] ; then
	80	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices CREATE
	81	CREATE=${lmdz_UserChoices_CREATE}
	82	echo create_etat0_limit version : ${CREATE}
	83	fi
[1643]	84
[1782]	85
[1550]	86	## - LMDZ choice of config.def file
	87	## ConfType must be set in lmdz.card
	88	ConfType=${lmdz_UserChoices_ConfType}
[1541]	89
[1550]	90	##- LMDZ output level, to be set in lmdz.card
	91	if [ X${lmdz_UserChoices_OutLevel} = X ] ; then
	92	# OutLevel is not set. Take default value low.
	93	OutLevel=low
	94	else
	95	OutLevel=${lmdz_UserChoices_OutLevel}
	96	fi
	97
[1539]	98	##-- Output frequency purpose ....
[396]	99	##-- Initialisation ....
[1539]	100	ok_mensuel=n
	101	ok_journe=n
[396]	102	ok_hf=n
[1539]	103	ok_hf3h=n
	104	ok_hf3hm=n
	105	ok_stn=n
[396]	106
	107	case ${config_UserChoices_PeriodLength} in
[1539]	108	1Y\|1y\|1M\|1m) ok_mensuel=y ;;
	109	5D\|5d\|1D\|1d) ok_journe=y ;;
[396]	110	esac
	111
	112	for frequency in ${config_ATM_WriteFrequency} ; do
	113	case ${frequency} in
[1539]	114	1M\|1m) ok_mensuel=y ;;
[396]	115	esac
	116	case ${frequency} in
[1539]	117	5D\|5d\|1D\|1d) ok_journe=y ;;
	118	esac
	119	case ${frequency} in
[396]	120	HF\|hf) ok_hf=y ;;
	121	esac
[1539]	122	case ${frequency} in
	123	HF3h\|hf3h) ok_hf3h=y ;;
	124	esac
	125	case ${frequency} in
	126	HF3hm\|hf3hm) ok_hf3hm=y ;;
	127	esac
	128	case ${frequency} in
	129	STN\|stn) ok_stn=y ;;
	130	esac
[396]	131	done
	132
[902]	133	## Read LMDZ_NbPeriod_adjust option in lmdz.card
[1688]	134	if [ X"${lmdz_UserChoices_LMDZ_NbPeriod_adjust}" = X"" ] ; then
	135	# The variable is not in lmdz.card, set default value
	136	LMDZ_NbPeriod_adjust=0
	137	else
	138	LMDZ_NbPeriod_adjust=${lmdz_UserChoices_LMDZ_NbPeriod_adjust}
	139	fi
[396]	140
[815]	141	if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
[1688]	142	LMDZ_Bands_file_name=${lmdz_UserChoices_LMDZ_Bands_file_name}
[815]	143	fi
	144
[912]	145
[1783]	146	## Read LMDZ_COSP_OK in lmdz.card
	147	if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ] ; then
	148	LMDZ_COSP_OK=${lmdz_UserChoices_LMDZ_COSP_OK}
	149	else
	150	LMDZ_COSP_OK=n
	151	fi
	152	## Read LMDZ_COSP_monthly in lmdz.card
	153	if [ ! X${lmdz_UserChoices_LMDZ_COSP_monthly} = X ] ; then
	154	LMDZ_COSP_monthly=${lmdz_UserChoices_LMDZ_COSP_monthly}
	155	else
	156	LMDZ_COSP_monthly=n
	157	fi
	158	## Read LMDZ_COSP_daily in lmdz.card
	159	if [ ! X${lmdz_UserChoices_LMDZ_COSP_daily} = X ] ; then
	160	LMDZ_COSP_daily=${lmdz_UserChoices_LMDZ_COSP_daily}
	161	else
	162	LMDZ_COSP_daily=n
	163	fi
	164	## Read LMDZ_COSP_hf in lmdz.card
	165	if [ ! X${lmdz_UserChoices_LMDZ_COSP_hf} = X ] ; then
	166	LMDZ_COSP_hf=${lmdz_UserChoices_LMDZ_COSP_hf}
	167	else
	168	LMDZ_COSP_hf=n
	169	fi
[1000]	170
[1783]	171	## Read LMDZ_NMC_monthly in lmdz.card
	172	if [ ! X${lmdz_UserChoices_LMDZ_NMC_monthly} = X ] ; then
	173	LMDZ_NMC_monthly=${lmdz_UserChoices_LMDZ_NMC_monthly}
	174	else
	175	LMDZ_NMC_monthly=n
	176	fi
[1000]	177
[1783]	178	## Read LMDZ_NMC_daily in lmdz.card
	179	if [ ! X${lmdz_UserChoices_LMDZ_NMC_daily} = X ] ; then
	180	LMDZ_NMC_daily=${lmdz_UserChoices_LMDZ_NMC_daily}
	181	else
	182	LMDZ_NMC_daily=n
	183	fi
	184
	185	## Read LMDZ_NMC_hf in lmdz.card
	186	if [ ! X${lmdz_UserChoices_LMDZ_NMC_hf} = X ] ; then
	187	LMDZ_NMC_hf=${lmdz_UserChoices_LMDZ_NMC_hf}
	188	else
	189	LMDZ_NMC_hf=n
	190	fi
	191
	192
[396]	193	IGCM_debug_PopStack "ATM_Initialize"
	194	}
	195
	196	#-----------------------------------------------------------------
	197	function ATM_Update
	198	{
	199	IGCM_debug_PushStack "ATM_Update"
	200
[1537]	201
[749]	202	case ${config_UserChoices_PeriodLength} in
	203	Y\|y)
	204	LMDZ_ecrit_ISCCP=30.
	205	LMDZ_periodav=30.
[755]	206	if [ "${config_UserChoices_CalendarType}" != "360d" ] ; then
[1649]	207	echo Do not consider following warning if your running create_etat0_limit :
[1650]	208	echo WARNING !!! For lmdz : calendartype in config.card. PeriodLength=1Y allowed only for CalendarType=360d
[1649]	209	fi
[749]	210	;;
	211	*)
	212	LMDZ_ecrit_ISCCP=${PeriodLengthInDays}.
	213	LMDZ_periodav=${PeriodLengthInDays}.
	214	;;
	215	esac
[1546]	216
[396]	217	##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
	218	if [ ${CumulPeriod} -eq 1 ] ; then
	219	RAZ_DATE=1
	220	else
	221	RAZ_DATE=0
	222	fi
	223
[1892]	224	## Algorithme for special treatment for Bands_xxx file
	225	## For CumulPeriod=1 ;
	226	## IF NbPeriod_Adjust = 0 ; set LMDZ_adjust=n
	227	## IF LMDZ_Bands_file_name was given in lmdz.card THEN Get Bands file directly from server. Store it later with _0 suffix.
	228	## IF no LMDZ_Bands_file_name was given, start without Bands file. Store it later with _0 suffix.
	229	## ELSE set LMDZ_adjust=y ; start without Bands file ; Store it later in PARAM/ directory in submit directory with suffix _1 ;
	230	##
	231	## For CumulPeriod=2 to LMDZ_NbPeriod_adjust ;
	232	## Get Bands file from PARAM/ in submit directory (CumulPeriod-1) ; set LMDZ_adjust=y ; Store Bands file in PARAM/ ;
	233	##
	234	## For CumulPeriod > LMDZ_NbPeriod_adjust ; LMDZ_adjust=n ; Get Bands file from PARAM/ ; Do not store ;
[815]	235
	236	if [ ${CumulPeriod} -eq 1 ] ; then
	237	if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
[1778]	238	if [ ! X${LMDZ_Bands_file_name} = X ] ; then
[1688]	239	IGCM_sys_Get ${LMDZ_Bands_file_name} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
	240	IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
	241	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"
	242	fi
[815]	243	fi
	244	fi
	245
[743]	246	LMDZ_adjust=n
	247	[ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && LMDZ_adjust=y
	248
[815]	249	RefPeriod=${LMDZ_NbPeriod_adjust} #0 to use a Bands file from Restart
	250	[ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && (( RefPeriod = ${CumulPeriod} - 1 ))
[743]	251
[1897]	252	# Get Bands file from PARAM directory if file exist
	253	if [ ${CumulPeriod} -gt 1 && -f ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${RefPeriod} ] ; then
[1894]	254	IGCM_sys_Cp ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${RefPeriod} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
[1892]	255	IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
	256	fi
[743]	257
[1535]	258	##-- GHG forcing :
[1546]	259	## If forcing file exist in run directory, read values for the current year and modify config.def
[1535]	260	if [ -f SOLARANDVOLCANOES.txt ] ; then
	261	IPCC_SOLAR=`grep Annee_${year} SOLARANDVOLCANOES.txt \| awk -F= '{print $2}'`
[1546]	262	LMDZ_sed config.def solaire ${IPCC_SOLAR}
[1690]	263	else
	264	LMDZ_sed_default config.def solaire
[1535]	265	fi
	266	if [ -f CO2.txt ] ; then
	267	IPCC_CO2=`grep Annee_${year} CO2.txt \| awk -F= '{print $2}'`
[1546]	268	LMDZ_sed config.def co2_ppm ${IPCC_CO2}
[1690]	269	else
	270	LMDZ_sed_default config.def co2_ppm
[1535]	271	fi
[1690]	272
	273
[1535]	274	if [ -f CH4.txt ] ; then
	275	IPCC_CH4=`grep Annee_${year} CH4.txt \| awk -F= '{print $2}'`
[1546]	276	LMDZ_sed config.def CH4_ppb ${IPCC_CH4}
[1690]	277	else
	278	LMDZ_sed_default config.def CH4_ppb
[1535]	279	fi
	280	if [ -f N2O.txt ] ; then
	281	IPCC_N2O=`grep Annee_${year} N2O.txt \| awk -F= '{print $2}'`
[1546]	282	LMDZ_sed config.def N2O_ppb ${IPCC_N2O}
[1690]	283	else
	284	LMDZ_sed_default config.def N2O_ppb
[1535]	285	fi
	286	if [ -f CFC11.txt ] ; then
	287	IPCC_CFC11=`grep Annee_${year} CFC11.txt \| awk -F= '{print $2}'`
[1546]	288	LMDZ_sed config.def CFC11_ppt ${IPCC_CFC11}
[1690]	289	else
	290	LMDZ_sed_default config.def CFC11_ppt
[1535]	291	fi
	292	if [ -f CFC12.txt ] ; then
	293	IPCC_CFC12=`grep Annee_${year} CFC12.txt \| awk -F= '{print $2}'`
[1546]	294	LMDZ_sed config.def CFC12_ppt ${IPCC_CFC12}
[1690]	295	else
	296	LMDZ_sed_default config.def CFC12_ppt
[1535]	297	fi
	298
[1780]	299
	300	##-- Add special treatement for CARBON CYCLE
[1546]	301	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
[1780]	302	ATM_Carbon_Update
	303	fi
[1537]	304
	305
[1538]	306	##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
	307	## COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
	308	if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] && [ ${year} -ge 1979 ]) ; then
	309	LMDZ_COSP_daily=y
	310	fi
[1537]	311
[1538]	312
[1540]	313	## output.def parameters
[1546]	314	# columns in phys_output_filekeys refer to the filenames given in phys_out_filenames in output.def :
[1539]	315	# histmth histday histhf histfh3h histhf3hm histstn
[1546]	316	LMDZ_sed output.def phys_out_filekeys "${ok_mensuel} ${ok_journe} ${ok_hf} ${ok_hf3h} ${ok_hf3hm} ${ok_stn}"
[1540]	317	LMDZ_sed output.def ecrit_ISCCP ${LMDZ_ecrit_ISCCP}
	318	LMDZ_sed output.def ok_cosp ${LMDZ_COSP_OK}
	319	LMDZ_sed output.def ok_mensuelCOSP ${LMDZ_COSP_monthly}
	320	LMDZ_sed output.def ok_journeCOSP ${LMDZ_COSP_daily}
	321	LMDZ_sed output.def ok_hfCOSP ${LMDZ_COSP_hf}
[1783]	322	LMDZ_sed output.def ok_histNMC "${LMDZ_NMC_monthly} ${LMDZ_NMC_daily} ${LMDZ_NMC_hf}"
[396]	323
[1544]	324	## gcm.def parameters :
	325	# Modification only for new physics
[1750]	326	if [ X${LMDZ_Physics} = X"NPv3.1" ] ; then
[1544]	327	LMDZ_sed gcm.def iphysiq 5
[1690]	328	else
	329	LMDZ_sed_default gcm.def iphysiq
[1544]	330	fi
[396]	331
[1544]	332
[911]	333	## run.def parameters
	334	LMDZ_sed run.def dayref ${InitDay}
	335	LMDZ_sed run.def nday ${PeriodLengthInDays}
	336	LMDZ_sed run.def raz_date ${RAZ_DATE}
	337	LMDZ_sed run.def periodav ${LMDZ_periodav}
	338	LMDZ_sed run.def adjust ${LMDZ_adjust}
[396]	339
[1804]	340	# Set anneeref different for gcm and ce0l
[1923]	341	# Variable calend is different for a run with create_etat0_limit and the gcm
[1804]	342	# Test if executable create_etat0_limit is present and lmdz.x is not present
	343	if [ -f create_etat0_limit* ] \|\| [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
	344	# for case ce0l : always take current year
	345	LMDZ_sed run.def anneeref ${year}
[1923]	346	LMDZ_sed run.def calend ${CalendarTypeForCreate}
[1804]	347	else
	348	# for case gcm : take first year of simulation
	349	LMDZ_sed run.def anneeref ${InitYear}
[1923]	350	LMDZ_sed run.def calend ${CalendarTypeForLmdz}
[1804]	351	fi
[1643]	352
[1804]	353	# Activate creation of file grilles_gcm.nc only at first period
	354	if [ ${CumulPeriod} -eq 1 ] ; then
	355	LMDZ_sed run.def grilles_gcm_netcdf y
	356	else
	357	LMDZ_sed run.def grilles_gcm_netcdf n
	358	fi
	359
[1650]	360	## Determine from the variable ListOfComponents in config.card coupling to external models
	361	## and set corresponding parameters in run.def
	362	echo ListOfComponents now running : ${config_ListOfComponents[*]}
	363
	364	if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
	365	echo "Activate ORCHIDEE, set VEGET=y in run.def"
	366	LMDZ_sed run.def VEGET y
	367	else
	368	echo "No ORCHIDEE, set VEGET=n in run.def"
	369	LMDZ_sed run.def VEGET n
	370	fi
	371
	372	if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
	373	echo "Activate coupling to ocean, set type_ocean=couple in run.def"
	374	LMDZ_sed run.def type_ocean couple
	375	else
	376	echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
	377	LMDZ_sed run.def type_ocean force
	378	fi
	379
	380	if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
	381	echo "Activate coupling to INCA, set type_trac=inca in run.def"
[1666]	382	LMDZ_sed run.def type_trac inca
[1650]	383	elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
	384	echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
[1666]	385	LMDZ_sed run.def type_trac repr
[1779]	386	LMDZ_sed run.def config_inca none
[1650]	387	else
	388	echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
[1666]	389	LMDZ_sed run.def type_trac lmdz
[1779]	390	LMDZ_sed run.def config_inca none
[1650]	391	fi
	392
	393
[1686]	394	# config.def : If running with Reprobus, desactivate ok_ade, ok_aie and read_climoz
[1816]	395	if [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
[1686]	396	LMDZ_sed config.def ok_ade n
	397	LMDZ_sed config.def ok_aie n
[1816]	398	LMDZ_sed config.def aerosol_couple n
[1686]	399	LMDZ_sed config.def read_climoz 0
[1816]	400	elif [ X${config_ListOfComponents_CHM} = Xinca ]; then
	401	case ${CHEM} in
	402	AER)
	403	LMDZ_sed config.def ok_ade y
	404	LMDZ_sed config.def ok_aie n
	405	LMDZ_sed config.def aerosol_couple y
	406	LMDZ_sed config.def read_climoz 0
	407	;;
	408	NMHC_AER)
	409	LMDZ_sed config.def ok_ade y
	410	LMDZ_sed config.def ok_aie n
	411	LMDZ_sed config.def aerosol_couple y
	412	LMDZ_sed config.def read_climoz 0
	413	;;
	414	GES)
	415	LMDZ_sed config.def ok_ade n
	416	LMDZ_sed config.def ok_aie n
	417	LMDZ_sed config.def aerosol_couple n
	418	LMDZ_sed config.def read_climoz 0
	419	esac
	420
[1686]	421	else
	422	LMDZ_sed config.def ok_ade y
	423	LMDZ_sed config.def ok_aie y
[1816]	424	LMDZ_sed config.def aerosol_couple n
[1686]	425	LMDZ_sed config.def read_climoz 2
	426	fi
	427
[1690]	428	# guide.def : Activate nudging if ok_guide=y set in lmdz.card
[1643]	429	if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
	430	LMDZ_sed guide.def ok_guide ${lmdz_UserChoices_ok_guide}
[1690]	431	else
	432	LMDZ_sed guide.def ok_guide n
[1643]	433	fi
	434
[902]	435	## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
[1172]	436	ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
[1688]	437	if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
[396]	438	awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
	439	IGCM_sys_Mv gcm.def.tmp gcm.def
	440	echo
	441	IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
	442	echo
	443	cat gcm.def
	444	ByPass_hgardfou_teta=n
[902]	445	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
[396]	446	fi
	447
[902]	448	## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
[1172]	449	ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
[1688]	450	if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
[396]	451	sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
	452	IGCM_sys_Mv gcm.def.tmp gcm.def
	453	echo
	454	IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
	455	echo
	456	cat gcm.def
	457	ByPass_hgardfou_mats=n
[902]	458	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
[396]	459	fi
	460
	461	if ( ${FirstInitialize} ) ; then
[1643]	462	if [ -f start.nc ] && [ -f startphy.nc ] ; then
	463	# The restart files already exist. They have been copied from a previous run or from a CREATE job
	464	echo "Restart files for LMDZ have been copied from a previous run"
[1778]	465	elif [ -f create_etat0_limit* ] \|\| [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
[1649]	466	# Do nothing because it is the program for creating restart files that is running and not LMDZ
	467	echo "create_etat0_limit.e will create initial start files"
[1643]	468	else
	469	# Restart files have to be created
	470	echo "Run create_etat0_limit.e to create restart files start.nc and startphy.nc for LMDZ"
[396]	471	if [ ${DRYRUN} -le 2 ] ; then
[894]	472	##-- suppression of ozone file construction --
[1643]	473	cp config.def config.def.save
	474	LMDZ_sed config.def read_climoz 0
[396]	475	IGCM_sys_Cp ${R_EXE}/create_etat0_limit.e ${RUN_DIR}/.
	476	if [ ${DRYRUN} -le 1 ] ; then
[908]	477	${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e
[1643]	478	IGCM_sys_Put_Out start.nc ${R_OUT_ATM_R}/${config_UserChoices_JobName}_${PeriodDateBegin}_start.nc
	479	IGCM_sys_Put_Out startphy.nc ${R_OUT_ATM_R}/${config_UserChoices_JobName}_${PeriodDateBegin}_startphy.nc
[396]	480	fi
[1643]	481	IGCM_sys_Mv config.def.save config.def
[396]	482	else
[908]	483	echo "EXECUTION of ${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e simulated"
	484	echo "EXECUTION of ${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e simulated for DRYRUN = " $DRYRUN >> stack
[396]	485	fi
	486	fi
	487	fi
	488
	489	IGCM_debug_PopStack "ATM_Update"
	490	}
	491
	492	#-----------------------------------
	493	function ATM_Finalize
	494	{
	495	IGCM_debug_PushStack "ATM_Finalize"
	496
[1897]	497	# If the file exist, copy Bands_ file to PARAM/ in submit directory. This file will be used for the simulation.
[1892]	498	# Copy also the same file into ATM/Restart at ARCHIVE directory for backup.
[1897]	499	if [ -f Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ] ; then
	500	if [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] ; then
	501	IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${CumulPeriod}
	502	IGCM_sys_Put_Out Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${R_OUT_ATM_R}/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${CumulPeriod}
	503	elif [ ${CumulPeriod} -eq 1 ] && [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
	504	# Special case : first period and no adjust => Save bands file with suffix _0
	505	IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0
	506	IGCM_sys_Put_Out Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${R_OUT_ATM_R}/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0
	507	fi
[1892]	508	fi
[396]	509
[1537]	510	# Add special treatement for CARBON CYCLE
[1546]	511	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
[1780]	512	ATM_Carbon_Finalize
	513	fi
[1537]	514
[1780]	515	echo FINALIZE ATM !
[1537]	516
[1780]	517	IGCM_debug_PopStack "ATM_Finalize"
	518	}
[1537]	519
	520
	521
[1780]	522	function ATM_Carbon_Update
	523	{
	524	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
[1537]	525
[1780]	526	IGCM_debug_PushStack "ATM_Carbon_Update"
	527
	528	typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
	529	typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
	530	typeset PathCO2log
	531	typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
	532
	533	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
	534	##--Initialization of fluxes to an undefined value at the first run
	535	UndefinedValueCo2=-9999
	536	InitPeriodCo2=0
	537	InitDateBeginCo2=${UndefinedValueCo2}
	538	InitYearCo2=$(( ${year} - 1 ))
	539	InitDateEndCo2=${InitYearCo2}1231
	540	fCO2_ff=${UndefinedValueCo2}
	541	CO2SBG=${UndefinedValueCo2}
	542	CO2LU=${UndefinedValueCo2}
	543	CO2MBG=${UndefinedValueCo2}
	544	CO2_ppm_prec=${UndefinedValueCo2}
	545	# Get the initial value of atmosp. pco2
	546	CO2_ppm=${lmdz_UserChoices_co2_init}
	547
	548	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
	549	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
	550
[1537]	551	# Save CO2 values in ExeCpuLog variable contents 5 fields
[1780]	552	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
[1537]	553	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
[1780]	554	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	555
	556	# Get the path where the log file co2.log is
	557	PathCO2log=${SUBMIT_DIR}
	558	# Get Previous line in co2.log
	559	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
	560
	561	else
	562
	563	# NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
	564	# !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
	565	#SubmitRestartPath=
	566	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
	567	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
	568	PathCO2log=${config_ATM_SubmitRestartPath}
	569	Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
	570	PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
	571
	572	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
	573	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
	574
	575	# Save Last Line of control in new co2.log file
	576	InitPeriodCo2=0
	577	InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $2}' )
	578	InitDateEndCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $3}' )
	579	fCO2_ff=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $6}' )
	580	CO2SBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $8}' )
	581	CO2LU=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $9}' )
	582	CO2MBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $7}' )
	583	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $5}' )
	584	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	585
	586	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
	587	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
	588	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	589	else
	590	# Get restart line in co2.log
	591	PathCO2log=${SUBMIT_DIR}
	592	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
	593	# Get the value of atmosp. pco2 in co2.log
	594	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	595	fi
	596
[1537]	597	fi
[1780]	598
	599	if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
	600	# Modify co2_ppm in config.def only for historical run
	601	# If not historical run, keep co2_ppm value set earlier by LMDZ_sed
	602	LMDZ_sed config.def co2_ppm ${CO2_ppm}
	603	fi
	604	IGCM_debug_PopStack "ATM_Carbon_Update"
	605	}
[1537]	606
[396]	607
[1780]	608	function ATM_Carbon_Finalize
	609	{
	610	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
	611
	612	IGCM_debug_PushStack "ATM_Carbon_Finalize"
	613
	614	typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
	615
	616	# Fossil fuel emission
	617	if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
	618	# For Control, no fossil fuel emission :
	619	fCO2_ff=0
	620	echo "Fossil Fuel for control run :" ${fCO2_ff}
	621	else
	622	# For historical, get the fossile fuel file :
	623	fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
	624	echo "Fossil Fuel for historical run :" ${fCO2_ff}
	625	fi
	626
	627	# Get the value of ocean carbon flux
	628	CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
	629	CO2MBG=$( echo ${CO2MBG} \| sed -e "s/ *//" )
	630	echo "Ocean carbon flux :" ${CO2MBG}
	631
	632	# Get the value of land fluxes
	633	set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
	634	CO2SRF=$( echo ${CO2SBG_3V[0]} \| sed -e "s/ *//" )
	635	CO2LU=$( echo ${CO2SBG_3V[1]} \| sed -e "s/ *//" )
	636	CO2SBG=$( echo ${CO2SBG_3V[2]} \| sed -e "s/ *//" )
	637	echo "Land carbon flux (NEP) :" ${CO2SRF}
	638	echo "LU flux (FLUC) :" ${CO2LU}
	639	echo "Total Land carbon flux (NBP) :" ${CO2SBG}
	640
	641	# Previous CO2
	642	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	643	echo "Previous CO2 :" ${CO2_ppm_prec}
	644
	645	# Formula
	646	CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" \| bc -l )
	647	echo "New CO2 :" ${CO2_ppm}
	648
	649	# Save CO2 values in ExeCpuLog variable contents 5 fields
	650	echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
	651	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
	652	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	653
	654	IGCM_debug_PopStack "ATM_Carbon_Finalize"
[396]	655	}

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