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source: CONFIG/UNIFORM/v6/LMDZORINCA_v6/GENERAL/DRIVER/lmdz.driver @ 3304

Last change on this file since 3304 was 3158, checked in by acosce, 7 years ago
update LMDZORINCA with LMDZ physics 6.0.8
File size: 24.3 KB

Rev	Line
[2330]	1	#!/bin/ksh
	2	#-----------------------------------------------------------------
	3	function ATM_Initialize
	4	{
	5	IGCM_debug_PushStack "ATM_Initialize"
	6
	7	RESOL_ATM=$( echo $RESOL \| awk "-Fx" '{print $2}' \| awk "-F-" '{print $1}')
	8
	9	[ -f ${SUBMIT_DIR}/../.resol ] && eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol) \|\| RESOL_ATM_3D=96x95x39
	10
	11	RESOL_ATM_Z=$( echo ${RESOL_ATM_3D} \| awk "-Fx" '{print $3}' )
	12	RESOL_ATM_X=$( echo ${RESOL_ATM_3D} \| awk "-Fx" '{print $1}' )
	13	RESOL_ATM_Y=$( echo ${RESOL_ATM_3D} \| awk "-Fx" '{print $2}' )
	14	RESOL_ATM_XY="${RESOL_ATM_X}x${RESOL_ATM_Y}"
	15
	16	##- LMDZ physics version
	17	## Read LMDZ_Physics option in lmdz.card, if not present take default value AP (old physics)
	18	if [ ! X${lmdz_UserChoices_LMDZ_Physics} = X ] ; then
	19	LMDZ_Physics=${lmdz_UserChoices_LMDZ_Physics}
	20	else
	21	LMDZ_Physics=AP
	22	fi
	23	echo LMDZ physics version : ${LMDZ_Physics}
	24
	25	##- Create_etat0_limit version
	26	## Define variable CREATE only if it is set in lmdz.card section UserChoices.
	27	## This variable is only used in lmdz.card to choose input files.
	28	if [ ! X${lmdz_UserChoices_CREATE} = X ] ; then
	29	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices CREATE
	30	CREATE=${lmdz_UserChoices_CREATE}
	31	echo create_etat0_limit version : ${CREATE}
	32	fi
	33
	34
	35	## - LMDZ choice of config.def file
	36	## ConfType must be set in lmdz.card
	37	ConfType=${lmdz_UserChoices_ConfType}
	38
	39	##- LMDZ output level, to be set in lmdz.card
	40	if [ X${lmdz_UserChoices_OutLevel} = X ] ; then
	41	# OutLevel is not set. Take default value low.
	42	OutLevel=low
	43	else
	44	OutLevel=${lmdz_UserChoices_OutLevel}
	45	fi
	46
	47	##-- Output frequency purpose ....
	48	##-- Initialisation ....
[2694]	49	ok_mensuel=.FALSE.
	50	ok_journe=.FALSE.
	51	ok_hf=.FALSE.
	52	ok_hf3h=.FALSE.
	53	ok_hf3hm=.FALSE.
	54	ok_stn=.FALSE.
[2330]	55
	56	case ${config_UserChoices_PeriodLength} in
[2694]	57	1Y\|1y\|1M\|1m) ok_mensuel=.TRUE. ;;
	58	5D\|5d\|1D\|1d) ok_journe=.TRUE. ;;
[2330]	59	esac
	60
	61	for frequency in ${config_ATM_WriteFrequency} ; do
	62	case ${frequency} in
[2694]	63	1M\|1m) ok_mensuel=.TRUE. ;;
[2330]	64	esac
	65	case ${frequency} in
[2694]	66	5D\|5d\|1D\|1d) ok_journe=.TRUE. ;;
[2330]	67	esac
	68	case ${frequency} in
[2694]	69	HF\|hf) ok_hf=.TRUE. ;;
[2330]	70	esac
	71	case ${frequency} in
[2694]	72	HF3h\|hf3h) ok_hf3h=.TRUE. ;;
[2330]	73	esac
	74	case ${frequency} in
[2694]	75	HF3hm\|hf3hm) ok_hf3hm=.TRUE. ;;
[2330]	76	esac
	77	case ${frequency} in
[2694]	78	STN\|stn) ok_stn=.TRUE. ;;
[2330]	79	esac
	80	done
	81
	82	## Read LMDZ_COSP_OK in lmdz.card
[2694]	83	if [ X${lmdz_UserChoices_LMDZ_COSP_OK} = Xy ] ; then
	84	## LMDZ_COSP_OK=y, now read all other COSP variables
	85	## Read LMDZ_COSP_monthly in lmdz.card
	86	if [ X${lmdz_UserChoices_LMDZ_COSP_monthly} = Xy ] ; then
	87	LMDZ_COSP_monthly=.TRUE.
	88	else
	89	LMDZ_COSP_monthly=.FALSE.
	90	fi
	91	## Read LMDZ_COSP_daily in lmdz.card
	92	if [ X${lmdz_UserChoices_LMDZ_COSP_daily} = Xy ] ; then
	93	LMDZ_COSP_daily=.TRUE.
	94	else
	95	LMDZ_COSP_daily=.FALSE.
	96	fi
	97	## Read LMDZ_COSP_hf in lmdz.card
	98	if [ X${lmdz_UserChoices_LMDZ_COSP_hf} = Xy ] ; then
	99	LMDZ_COSP_hf=.TRUE.
	100	else
	101	LMDZ_COSP_hf=.FALSE.
	102	fi
[2330]	103	else
[2694]	104	# LMDZ_COSP_OK=n : All cosp output are deactivated
	105	LMDZ_COSP_monthly=.FALSE.
	106	LMDZ_COSP_daily=.FALSE.
	107	LMDZ_COSP_hf=.FALSE.
	108	fi
[2330]	109
	110	## Read LMDZ_NMC_monthly in lmdz.card
[2694]	111	if [ X${lmdz_UserChoices_LMDZ_NMC_monthly} = Xy ] ; then
	112	LMDZ_NMC_monthly=.TRUE.
[2330]	113	else
[2694]	114	LMDZ_NMC_monthly=.FALSE.
[2330]	115	fi
[2694]	116
[2330]	117	## Read LMDZ_NMC_daily in lmdz.card
[2694]	118	if [ X${lmdz_UserChoices_LMDZ_NMC_daily} = Xy ] ; then
	119	LMDZ_NMC_daily=.TRUE.
[2330]	120	else
[2694]	121	LMDZ_NMC_daily=.FALSE.
[2330]	122	fi
	123
	124	## Read LMDZ_NMC_hf in lmdz.card
[2694]	125	if [ X${lmdz_UserChoices_LMDZ_NMC_hf} = Xy ] ; then
	126	LMDZ_NMC_hf=.TRUE.
[2330]	127	else
[2694]	128	LMDZ_NMC_hf=.FALSE.
[2330]	129	fi
[2694]	130
[2330]	131
	132	IGCM_debug_PopStack "ATM_Initialize"
	133	}
	134
	135	#-----------------------------------------------------------------
	136	function ATM_Update
	137	{
	138	IGCM_debug_PushStack "ATM_Update"
	139
	140	##-- GHG forcing :
	141	## If forcing file exist in run directory, read values for the current year
	142	## and set in config.def. If not use the default value set in config.def
[2346]	143
	144	# Read value for solaire from file SOLARANDVOLCANOES.txt. If file not existing, take DEFAULT value from file.
[3158]	145	IGCM_debug_Print 1 "Note that the solaire parameter is here below changed but it is only used by LMDZ for old physics(AP and NPv3.2)"
	146	IGCM_debug_Print 1 "For newer physics with iflag_rrtm=1 and ok_suntime_rrtm=y, the solar constant is instead taken from solarforcing.nc file"
[2330]	147	if [ -f SOLARANDVOLCANOES.txt ] ; then
[2346]	148	value=`grep Annee_${year} SOLARANDVOLCANOES.txt \| awk -F= '{print $2}'`
	149	if [ X"${value}" = X ] ; then
[2330]	150	# The grep returned empty variable, stop execution
	151	IGCM_debug_Exit "The file SOLARANDVOLCANOES.txt do not contain the current year."
	152	IGCM_debug_Verif_Exit
	153	fi
	154	else
[2346]	155	value=DEFAULT
[2330]	156	fi
[2346]	157	IGCM_comp_modifyDefFile nonblocker config.def solaire $value
[2330]	158
[2346]	159
	160	# Read value for co2_ppm from file CO2.txt. If file not existing, take DEFAULT value from file.
[2330]	161	if [ -f CO2.txt ] ; then
[2346]	162	value=`grep Annee_${year} CO2.txt \| awk -F= '{print $2}'`
	163	if [ X"${value}" = X ] ; then
[2330]	164	# The grep returned empty variable, stop execution
	165	IGCM_debug_Exit "The file CO2.txt do not contain the current year."
	166	IGCM_debug_Verif_Exit
	167	fi
	168	else
[2346]	169	value=DEFAULT
[2330]	170	fi
[2346]	171	IGCM_comp_modifyDefFile nonblocker config.def co2_ppm $value
[2330]	172
[2346]	173
	174	# Read value for CH4_ppb from file CH4.txt. If file not existing, take DEFAULT value from file.
[2330]	175	if [ -f CH4.txt ] ; then
[2346]	176	value=`grep Annee_${year} CH4.txt \| awk -F= '{print $2}'`
	177	if [ X"${value}" = X ] ; then
[2330]	178	# The grep returned empty variable, stop execution
	179	IGCM_debug_Exit "The file CH4.txt do not contain the current year."
	180	IGCM_debug_Verif_Exit
	181	fi
[2346]	182	else
	183	value=DEFAULT
[2330]	184	fi
[2346]	185	IGCM_comp_modifyDefFile nonblocker config.def CH4_ppb $value
[2330]	186
[2346]	187
	188	# Read value for N2O_ppb from file N2O.txt. If file not existing, take DEFAULT value from file.
[2330]	189	if [ -f N2O.txt ] ; then
[2346]	190	value=`grep Annee_${year} N2O.txt \| awk -F= '{print $2}'`
	191	if [ X"${value}" = X ] ; then
[2330]	192	# The grep returned empty variable, stop execution
	193	IGCM_debug_Exit "The file N2O.txt do not contain the current year."
	194	IGCM_debug_Verif_Exit
	195	fi
	196	else
[2346]	197	value=DEFAULT
[2330]	198	fi
[2346]	199	IGCM_comp_modifyDefFile nonblocker config.def N2O_ppb $value
[2330]	200
[2346]	201	# Read value for CFC11_ppt from file CFC11.txt. If file not existing, take DEFAULT value from file.
[2330]	202	if [ -f CFC11.txt ] ; then
[2346]	203	value=`grep Annee_${year} CFC11.txt \| awk -F= '{print $2}'`
	204	if [ X"${value}" = X ] ; then
[2330]	205	# The grep returned empty variable, stop execution
	206	IGCM_debug_Exit "The file CFC11.txt do not contain the current year."
	207	IGCM_debug_Verif_Exit
	208	fi
	209	else
[2346]	210	value=DEFAULT
[2330]	211	fi
[2346]	212	IGCM_comp_modifyDefFile nonblocker config.def CFC11_ppt $value
[2330]	213
[2346]	214
	215	# Read value for CFC12_ppt from file CFC12.txt. If file not existing, take DEFAULT value from file.
[2330]	216	if [ -f CFC12.txt ] ; then
[2346]	217	value=`grep Annee_${year} CFC12.txt \| awk -F= '{print $2}'`
	218	if [ X"${value}" = X ] ; then
[2330]	219	# The grep returned empty variable, stop execution
	220	IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
	221	IGCM_debug_Verif_Exit
	222	fi
	223	else
[2346]	224	value=DEFAULT
[2330]	225	fi
[2346]	226	IGCM_comp_modifyDefFile nonblocker config.def CFC12_ppt $value
[2330]	227
	228
[2346]	229	## Coupling Time Step : Take value of FreqCoupling set in oasis.card or if it is not set, take default value 86400
	230	LMDZ_t_coupl=${oasis_UserChoices_FreqCoupling:-86400}
	231	IGCM_debug_Print 3 "LMDZ_t_coupl " ${LMDZ_t_coupl}
	232	IGCM_comp_modifyDefFile nonblocker config.def t_coupl ${LMDZ_t_coupl}
	233
[2330]	234	##-- Add special treatement for CARBON CYCLE
	235	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
	236	ATM_Carbon_Update
	237	fi
	238
	239
	240	##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
	241	## COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
	242	if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] && [ ${year} -ge 1979 ]) ; then
[2694]	243	LMDZ_COSP_daily=.TRUE.
[2330]	244	fi
	245
[2694]	246	## Modifiy
	247	IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled ${ok_mensuel}
	248
	249	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled ${ok_journe}
	250
	251	if [ X${OutLevel} = Xlow ] \|\| [ X${OutLevel} = Xmedium ] ; then
	252	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 2
	253	else
	254	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 5
	255	fi
	256
	257	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled ${ok_hf}
	258
	259	if [ X${OutLevel} = Xlow ] ; then
	260	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 5
	261	elif [ X${OutLevel} = Xmedium ] ; then
	262	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 6
	263	elif [ X${OutLevel} = Xhigh ] ; then
	264	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 7
	265	fi
	266
[2770]	267	IGCM_comp_modifyXmlFile nonblocker file_def_histhf3h_lmdz.xml histhf3h enabled ${ok_hf3h}
	268	IGCM_comp_modifyXmlFile nonblocker file_def_histhf3hm_lmdz.xml histhf3hm enabled ${ok_hf3hm}
[2330]	269
[2694]	270	IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled ${ok_stn}
[2480]	271
[2694]	272	IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled ${LMDZ_NMC_monthly}
	273	IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled ${LMDZ_NMC_daily}
	274	IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled ${LMDZ_NMC_hf}
	275
	276	IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled ${LMDZ_COSP_monthly}
	277	IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled ${LMDZ_COSP_daily}
	278	IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled ${LMDZ_COSP_hf}
[2512]	279
[3117]	280	# Activate the histstrataer output file only for configuration with interactive stratospheric aersols
	281	# done by setting the key word LMDZ_strataero=y in lmdz.card
	282	if [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
	283	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .TRUE.
	284	else
	285	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .FALSE.
	286	fi
[2330]	287
[3117]	288
[2330]	289	## run.def parameters
	290
[2694]	291
	292	##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
	293	if [ ${CumulPeriod} -eq 1 ] ; then
	294	IGCM_comp_modifyDefFile blocker run.def raz_date 1
	295	else
	296	IGCM_comp_modifyDefFile blocker run.def raz_date 0
	297	fi
	298
	299	##-- Calendar type for LMDZ and create_etat0_limit
	300	case ${config_UserChoices_CalendarType} in
	301	leap\|gregorian)
	302	IGCM_comp_modifyDefFile blocker run.def calend gregorian ;;
	303	noleap)
	304	IGCM_comp_modifyDefFile blocker run.def calend earth_365d ;;
	305	360d)
	306	IGCM_comp_modifyDefFile blocker run.def calend earth_360d ;;
	307	*)
	308	IGCM_comp_modifyDefFile blocker run.def calend earth_360d ;;
	309	esac
	310
	311	IGCM_comp_modifyDefFile blocker run.def dayref ${InitDay}
	312	IGCM_comp_modifyDefFile blocker run.def nday ${PeriodLengthInDays}
	313
[2330]	314	# Set anneeref different for gcm and ce0l
	315	# Test if executable create_etat0_limit is present and lmdz.x is not present
	316	if [ -f create_etat0_limit* ] \|\| [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
	317	# for case ce0l : always take current year
[2346]	318	IGCM_comp_modifyDefFile blocker run.def anneeref ${year}
[2480]	319
	320	# Temporary, set use_filtre_fft=n because we now use dyn3d for ce0l version where fft is not implemented.
	321	# In more recent versions of LMDZ, this will not be needed.
	322	IGCM_comp_modifyDefFile force run.def use_filtre_fft n
[2330]	323	else
	324	# for case gcm : take first year of simulation
[2346]	325	IGCM_comp_modifyDefFile blocker run.def anneeref ${InitYear}
[2330]	326	fi
	327
	328	## Determine from the variable ListOfComponents in config.card coupling to external models
	329	## and set corresponding parameters in run.def
	330	echo ListOfComponents now running : ${config_ListOfComponents[*]}
	331
	332	if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
	333	echo "Activate ORCHIDEE, set VEGET=y in run.def"
[2346]	334	IGCM_comp_modifyDefFile blocker run.def VEGET y
[2330]	335	else
	336	echo "No ORCHIDEE, set VEGET=n in run.def"
[2346]	337	IGCM_comp_modifyDefFile blocker run.def VEGET n
[2330]	338	fi
	339
	340	if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
	341	echo "Activate coupling to ocean, set type_ocean=couple in run.def"
[2346]	342	IGCM_comp_modifyDefFile blocker run.def type_ocean couple
[2330]	343	else
	344	echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
[2346]	345	IGCM_comp_modifyDefFile blocker run.def type_ocean force
[2330]	346	fi
	347
	348	if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
	349	echo "Activate coupling to INCA, set type_trac=inca in run.def"
[2346]	350	IGCM_comp_modifyDefFile blocker run.def type_trac inca
[2330]	351	elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
	352	echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
[2346]	353	IGCM_comp_modifyDefFile blocker run.def type_trac repr
	354	IGCM_comp_modifyDefFile blocker run.def config_inca none
[2330]	355	else
	356	echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
[2346]	357	IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
	358	IGCM_comp_modifyDefFile blocker run.def config_inca none
[2330]	359	fi
	360
	361
	362	# config.def : Activate direct radiative effect if ok_ade=y
	363	if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
[2346]	364	IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
[2330]	365	else
[2346]	366	IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
[2330]	367	fi
	368
	369	# config.def : Activate indirect radiative effect if ok_aie=y
	370	if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
[2346]	371	IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
[2330]	372	else
[2346]	373	IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
[2330]	374	fi
	375
	376	# config.def : Activate online aerosol coupled model if aerosol_couple=y
	377	if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
[2346]	378	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
[2330]	379	else
[2346]	380	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
[2330]	381	fi
	382
	383	# config.def : Activate reading of ozone in climatology if read_climoz=2
	384	if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
[2346]	385	IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
[2330]	386	else
[2346]	387	IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0
[2330]	388	fi
	389
	390	# config.def : Choose aerosol use in radiative effect
	391	# type of coupled aerosol =1 (default) =2 => bc only =3 => pom only =4 => seasalt only
	392	# =5 => dust only =6 => all aerosol
	393	if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
[2346]	394	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
[2330]	395	else
[2346]	396	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
[2330]	397	fi
	398
	399	# config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
	400	if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
[2346]	401	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
[2330]	402	else
[2346]	403	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
[2330]	404	fi
	405
[2954]	406	# config.def : Activate COSP
	407	if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ]; then
	408	IGCM_comp_modifyDefFile nonblocker config.def ok_cosp ${lmdz_UserChoices_LMDZ_COSP_OK}
	409	else
	410	IGCM_comp_modifyDefFile nonblocker config.def ok_cosp n
	411	fi
	412
	413	# config.def : Modify parameter pmagic if it is set in lmdz.card
	414	if [ ! X${lmdz_UserChoices_pmagic} = X ]; then
	415	IGCM_comp_modifyDefFile nonblocker config.def pmagic ${lmdz_UserChoices_pmagic}
	416	else
	417	# Take default value set in config.def
	418	IGCM_comp_modifyDefFile nonblocker config.def pmagic DEFAULT
	419	fi
	420
[2330]	421	# guide.def : Activate nudging if ok_guide=y set in lmdz.card
	422	if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
[2346]	423	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide ${lmdz_UserChoices_ok_guide}
[2330]	424	else
[2346]	425	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
[2330]	426	fi
	427
	428	## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
	429	ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
	430	if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
	431	awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
	432	IGCM_sys_Mv gcm.def.tmp gcm.def
	433	echo
	434	IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
	435	echo
	436	cat gcm.def
	437	ByPass_hgardfou_teta=n
	438	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
	439	fi
	440
	441	## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
	442	ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
	443	if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
	444	sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
	445	IGCM_sys_Mv gcm.def.tmp gcm.def
	446	echo
	447	IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
	448	echo
	449	cat gcm.def
	450	ByPass_hgardfou_mats=n
	451	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
	452	fi
	453
[2954]	454	# Add include of LMDZ context in iodef.xml
	455	# In iodef.xml add on next line after "COMPONENT CONTEXT"
	456	# <context id="LMDZ" src="./context_lmdz.xml"/>
	457	echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
	458	cp iodef.xml iodef.xml.tmp
	459	sed -e "/COMPONENT CONTEXT/r add.tmp" iodef.xml.tmp > iodef.xml
	460	rm iodef.xml.tmp add.tmp
[2477]	461
[2954]	462	#Long Name as global attribute (if LongName is not empty)
	463	if [ ! "X${config_UserChoices_LongName}" = "X" ] ; then
	464	listfile=$(ls file_def*lmdz.xml)
	465	echo "<variable id=\"LongName\" type=\"string\">${config_UserChoices_LongName}</variable>" > add.tmp
	466	for file in ${listfile}
	467	do
	468	cp ${file} ${file}.tmp
	469	sed -e "/<file id/r add.tmp" \
	470	${file}.tmp > ${file}
	471	rm ${file}.tmp
	472	done
	473	rm add.tmp
[2346]	474	fi
[2954]	475
[2330]	476	IGCM_debug_PopStack "ATM_Update"
	477	}
	478
	479	#-----------------------------------
	480	function ATM_Finalize
	481	{
	482	IGCM_debug_PushStack "ATM_Finalize"
	483
	484	# Add special treatement for CARBON CYCLE
	485	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
	486	ATM_Carbon_Finalize
	487	fi
	488
	489	echo FINALIZE ATM !
	490
	491	IGCM_debug_PopStack "ATM_Finalize"
	492	}
	493
	494
	495
	496	function ATM_Carbon_Update
	497	{
	498	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
	499
	500	IGCM_debug_PushStack "ATM_Carbon_Update"
	501
	502	typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
	503	typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
	504	typeset PathCO2log
	505	typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
	506
	507	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
	508	##--Initialization of fluxes to an undefined value at the first run
	509	UndefinedValueCo2=-9999
	510	InitPeriodCo2=0
	511	InitDateBeginCo2=${UndefinedValueCo2}
	512	InitYearCo2=$(( ${year} - 1 ))
	513	InitDateEndCo2=${InitYearCo2}1231
	514	fCO2_ff=${UndefinedValueCo2}
	515	CO2SBG=${UndefinedValueCo2}
	516	CO2LU=${UndefinedValueCo2}
	517	CO2MBG=${UndefinedValueCo2}
	518	CO2_ppm_prec=${UndefinedValueCo2}
	519	# Get the initial value of atmosp. pco2
	520	CO2_ppm=${lmdz_UserChoices_co2_init}
	521
	522	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
	523	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
	524
	525	# Save CO2 values in ExeCpuLog variable contents 5 fields
	526	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
	527	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
	528	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	529
	530	# Get the path where the log file co2.log is
	531	PathCO2log=${SUBMIT_DIR}
	532	# Get Previous line in co2.log
	533	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
	534
	535	else
	536
	537	# NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
	538	# !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
	539	#SubmitRestartPath=
	540	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
	541	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
	542	PathCO2log=${config_ATM_SubmitRestartPath}
	543	Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
	544	PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
	545
	546	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
	547	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
	548
	549	# Save Last Line of control in new co2.log file
	550	InitPeriodCo2=0
	551	InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $2}' )
	552	InitDateEndCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $3}' )
	553	fCO2_ff=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $6}' )
	554	CO2SBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $8}' )
	555	CO2LU=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $9}' )
	556	CO2MBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $7}' )
	557	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $5}' )
	558	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	559
	560	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
	561	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
	562	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	563	else
	564	# Get restart line in co2.log
	565	PathCO2log=${SUBMIT_DIR}
	566	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
	567	# Get the value of atmosp. pco2 in co2.log
	568	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	569	fi
	570
	571	fi
	572
	573	if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
[2841]	574	# Modify co2_ppm in config.def only for historical run
	575	# If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
	576	IGCM_comp_modifyDefFile force config.def co2_ppm ${CO2_ppm}
[2330]	577	fi
	578	IGCM_debug_PopStack "ATM_Carbon_Update"
	579	}
	580
	581
	582	function ATM_Carbon_Finalize
	583	{
	584	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
	585
	586	IGCM_debug_PushStack "ATM_Carbon_Finalize"
	587
	588	typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
	589
	590	# Fossil fuel emission
	591	if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
	592	# For Control, no fossil fuel emission :
	593	fCO2_ff=0
	594	echo "Fossil Fuel for control run :" ${fCO2_ff}
	595	else
	596	# For historical, get the fossile fuel file :
	597	fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
	598	echo "Fossil Fuel for historical run :" ${fCO2_ff}
	599	fi
	600
	601	# Get the value of ocean carbon flux
	602	CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
	603	CO2MBG=$( echo ${CO2MBG} \| sed -e "s/ *//" )
	604	echo "Ocean carbon flux :" ${CO2MBG}
	605
	606	# Get the value of land fluxes
	607	set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
	608	CO2SRF=$( echo ${CO2SBG_3V[0]} \| sed -e "s/ *//" )
	609	CO2LU=$( echo ${CO2SBG_3V[1]} \| sed -e "s/ *//" )
	610	CO2SBG=$( echo ${CO2SBG_3V[2]} \| sed -e "s/ *//" )
	611	echo "Land carbon flux (NEP) :" ${CO2SRF}
	612	echo "LU flux (FLUC) :" ${CO2LU}
	613	echo "Total Land carbon flux (NBP) :" ${CO2SBG}
	614
	615	# Previous CO2
	616	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	617	echo "Previous CO2 :" ${CO2_ppm_prec}
	618
	619	# Formula
	620	CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" \| bc -l )
	621	echo "New CO2 :" ${CO2_ppm}
	622
	623	# Save CO2 values in ExeCpuLog variable contents 5 fields
	624	echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
	625	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
	626	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	627
	628	IGCM_debug_PopStack "ATM_Carbon_Finalize"
	629	}

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