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source: CONFIG/UNIFORM/v6/LMDZORSTRATAER_v6/GENERAL/DRIVER/lmdz.driver @ 3146

Last change on this file since 3146 was 3146, checked in by jgipsl, 7 years ago
Modifications in STRATAER config
File size: 24.3 KB

Rev	Line
[396]	1	#!/bin/ksh
	2	#-----------------------------------------------------------------
	3	function ATM_Initialize
	4	{
	5	IGCM_debug_PushStack "ATM_Initialize"
	6
[671]	7	RESOL_ATM=$( echo $RESOL \| awk "-Fx" '{print $2}' \| awk "-F-" '{print $1}')
[396]	8
[2321]	9	[ -f ${SUBMIT_DIR}/../.resol ] && eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol) \|\| RESOL_ATM_3D=96x95x39
[396]	10
[659]	11	RESOL_ATM_Z=$( echo ${RESOL_ATM_3D} \| awk "-Fx" '{print $3}' )
[1802]	12	RESOL_ATM_X=$( 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${RESOL_ATM_Y}"
[649]	15
[1541]	16	##- LMDZ physics version
	17	## Read LMDZ_Physics option in lmdz.card, if not present take default value AP (old physics)
	18	if [ ! X${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 : ${LMDZ_Physics}
	24
[1643]	25	##- Create_etat0_limit version
[1782]	26	## Define variable CREATE only if it is set in lmdz.card section UserChoices.
	27	## This variable is only used in lmdz.card to choose input files.
	28	if [ ! X${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 : ${CREATE}
	32	fi
[1643]	33
[1782]	34
[1550]	35	## - LMDZ choice of config.def file
	36	## ConfType must be set in lmdz.card
	37	ConfType=${lmdz_UserChoices_ConfType}
[1541]	38
[1550]	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
[1539]	47	##-- Output frequency purpose ....
[396]	48	##-- Initialisation ....
[2605]	49	ok_mensuel=.FALSE.
	50	ok_journe=.FALSE.
	51	ok_hf=.FALSE.
	52	ok_hf3h=.FALSE.
	53	ok_hf3hm=.FALSE.
	54	ok_stn=.FALSE.
[396]	55
	56	case ${config_UserChoices_PeriodLength} in
[2605]	57	1Y\|1y\|1M\|1m) ok_mensuel=.TRUE. ;;
	58	5D\|5d\|1D\|1d) ok_journe=.TRUE. ;;
[396]	59	esac
	60
	61	for frequency in ${config_ATM_WriteFrequency} ; do
	62	case ${frequency} in
[2605]	63	1M\|1m) ok_mensuel=.TRUE. ;;
[396]	64	esac
	65	case ${frequency} in
[2605]	66	5D\|5d\|1D\|1d) ok_journe=.TRUE. ;;
[1539]	67	esac
	68	case ${frequency} in
[2605]	69	HF\|hf) ok_hf=.TRUE. ;;
[396]	70	esac
[1539]	71	case ${frequency} in
[2605]	72	HF3h\|hf3h) ok_hf3h=.TRUE. ;;
[1539]	73	esac
	74	case ${frequency} in
[2605]	75	HF3hm\|hf3hm) ok_hf3hm=.TRUE. ;;
[1539]	76	esac
	77	case ${frequency} in
[2605]	78	STN\|stn) ok_stn=.TRUE. ;;
[1539]	79	esac
[396]	80	done
	81
[1783]	82	## Read LMDZ_COSP_OK in lmdz.card
[2600]	83	if [ X${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${lmdz_UserChoices_LMDZ_COSP_monthly} = Xy ] ; then
[2605]	87	LMDZ_COSP_monthly=.TRUE.
[2600]	88	else
[2605]	89	LMDZ_COSP_monthly=.FALSE.
[2600]	90	fi
	91	## Read LMDZ_COSP_daily in lmdz.card
	92	if [ X${lmdz_UserChoices_LMDZ_COSP_daily} = Xy ] ; then
[2605]	93	LMDZ_COSP_daily=.TRUE.
[2600]	94	else
[2605]	95	LMDZ_COSP_daily=.FALSE.
[2600]	96	fi
	97	## Read LMDZ_COSP_hf in lmdz.card
	98	if [ X${lmdz_UserChoices_LMDZ_COSP_hf} = Xy ] ; then
[2605]	99	LMDZ_COSP_hf=.TRUE.
[2600]	100	else
[2605]	101	LMDZ_COSP_hf=.FALSE.
[2600]	102	fi
[1783]	103	else
[2600]	104	# LMDZ_COSP_OK=n : All cosp output are deactivated
[2605]	105	LMDZ_COSP_monthly=.FALSE.
	106	LMDZ_COSP_daily=.FALSE.
	107	LMDZ_COSP_hf=.FALSE.
[2600]	108	fi
[1000]	109
[1783]	110	## Read LMDZ_NMC_monthly in lmdz.card
[2600]	111	if [ X${lmdz_UserChoices_LMDZ_NMC_monthly} = Xy ] ; then
[2605]	112	LMDZ_NMC_monthly=.TRUE.
[1783]	113	else
[2605]	114	LMDZ_NMC_monthly=.FALSE.
[1783]	115	fi
[2600]	116
[1783]	117	## Read LMDZ_NMC_daily in lmdz.card
[2600]	118	if [ X${lmdz_UserChoices_LMDZ_NMC_daily} = Xy ] ; then
[2605]	119	LMDZ_NMC_daily=.TRUE.
[1783]	120	else
[2605]	121	LMDZ_NMC_daily=.FALSE.
[1783]	122	fi
	123
	124	## Read LMDZ_NMC_hf in lmdz.card
[2600]	125	if [ X${lmdz_UserChoices_LMDZ_NMC_hf} = Xy ] ; then
[2605]	126	LMDZ_NMC_hf=.TRUE.
[1783]	127	else
[2605]	128	LMDZ_NMC_hf=.FALSE.
[1783]	129	fi
[2600]	130
[1783]	131
[396]	132	IGCM_debug_PopStack "ATM_Initialize"
	133	}
	134
	135	#-----------------------------------------------------------------
	136	function ATM_Update
	137	{
	138	IGCM_debug_PushStack "ATM_Update"
	139
[1535]	140	##-- GHG forcing :
[2321]	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
[2333]	143
	144	# Read value for solaire from file SOLARANDVOLCANOES.txt. If file not existing, take DEFAULT value from file.
[1535]	145	if [ -f SOLARANDVOLCANOES.txt ] ; then
[2333]	146	value=`grep Annee_${year} SOLARANDVOLCANOES.txt \| awk -F= '{print $2}'`
	147	if [ X"${value}" = X ] ; then
[2321]	148	# The grep returned empty variable, stop execution
	149	IGCM_debug_Exit "The file SOLARANDVOLCANOES.txt do not contain the current year."
	150	IGCM_debug_Verif_Exit
	151	fi
[1690]	152	else
[2333]	153	value=DEFAULT
[1535]	154	fi
[2333]	155	IGCM_comp_modifyDefFile nonblocker config.def solaire $value
[2321]	156
[2333]	157
	158	# Read value for co2_ppm from file CO2.txt. If file not existing, take DEFAULT value from file.
[1535]	159	if [ -f CO2.txt ] ; then
[2333]	160	value=`grep Annee_${year} CO2.txt \| awk -F= '{print $2}'`
	161	if [ X"${value}" = X ] ; then
[2321]	162	# The grep returned empty variable, stop execution
	163	IGCM_debug_Exit "The file CO2.txt do not contain the current year."
	164	IGCM_debug_Verif_Exit
	165	fi
[1690]	166	else
[2333]	167	value=DEFAULT
[1535]	168	fi
[2333]	169	IGCM_comp_modifyDefFile nonblocker config.def co2_ppm $value
[1690]	170
[2333]	171
	172	# Read value for CH4_ppb from file CH4.txt. If file not existing, take DEFAULT value from file.
[1535]	173	if [ -f CH4.txt ] ; then
[2333]	174	value=`grep Annee_${year} CH4.txt \| awk -F= '{print $2}'`
	175	if [ X"${value}" = X ] ; then
[2321]	176	# The grep returned empty variable, stop execution
	177	IGCM_debug_Exit "The file CH4.txt do not contain the current year."
	178	IGCM_debug_Verif_Exit
	179	fi
[2333]	180	else
	181	value=DEFAULT
[1535]	182	fi
[2333]	183	IGCM_comp_modifyDefFile nonblocker config.def CH4_ppb $value
[2321]	184
[2333]	185
	186	# Read value for N2O_ppb from file N2O.txt. If file not existing, take DEFAULT value from file.
[1535]	187	if [ -f N2O.txt ] ; then
[2333]	188	value=`grep Annee_${year} N2O.txt \| awk -F= '{print $2}'`
	189	if [ X"${value}" = X ] ; then
[2321]	190	# The grep returned empty variable, stop execution
	191	IGCM_debug_Exit "The file N2O.txt do not contain the current year."
	192	IGCM_debug_Verif_Exit
	193	fi
[1690]	194	else
[2333]	195	value=DEFAULT
[1535]	196	fi
[2333]	197	IGCM_comp_modifyDefFile nonblocker config.def N2O_ppb $value
[2321]	198
[2333]	199	# Read value for CFC11_ppt from file CFC11.txt. If file not existing, take DEFAULT value from file.
[1535]	200	if [ -f CFC11.txt ] ; then
[2333]	201	value=`grep Annee_${year} CFC11.txt \| awk -F= '{print $2}'`
	202	if [ X"${value}" = X ] ; then
[2321]	203	# The grep returned empty variable, stop execution
	204	IGCM_debug_Exit "The file CFC11.txt do not contain the current year."
	205	IGCM_debug_Verif_Exit
	206	fi
[1690]	207	else
[2333]	208	value=DEFAULT
[1535]	209	fi
[2333]	210	IGCM_comp_modifyDefFile nonblocker config.def CFC11_ppt $value
[2321]	211
[2333]	212
	213	# Read value for CFC12_ppt from file CFC12.txt. If file not existing, take DEFAULT value from file.
[1535]	214	if [ -f CFC12.txt ] ; then
[2333]	215	value=`grep Annee_${year} CFC12.txt \| awk -F= '{print $2}'`
	216	if [ X"${value}" = X ] ; then
[2321]	217	# The grep returned empty variable, stop execution
	218	IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
	219	IGCM_debug_Verif_Exit
	220	fi
[1690]	221	else
[2333]	222	value=DEFAULT
[1535]	223	fi
[2333]	224	IGCM_comp_modifyDefFile nonblocker config.def CFC12_ppt $value
[1535]	225
[1780]	226
[2336]	227	## Coupling Time Step : Take value of FreqCoupling set in oasis.card or if it is not set, take default value 86400
	228	LMDZ_t_coupl=${oasis_UserChoices_FreqCoupling:-86400}
[2332]	229	IGCM_debug_Print 3 "LMDZ_t_coupl " ${LMDZ_t_coupl}
[2333]	230	IGCM_comp_modifyDefFile nonblocker config.def t_coupl ${LMDZ_t_coupl}
[2332]	231
[1780]	232	##-- Add special treatement for CARBON CYCLE
[1546]	233	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
[1780]	234	ATM_Carbon_Update
	235	fi
[1537]	236
	237
[1538]	238	##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
	239	## COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
	240	if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] && [ ${year} -ge 1979 ]) ; then
[2605]	241	LMDZ_COSP_daily=.TRUE.
[1538]	242	fi
[1537]	243
[2600]	244	## Modifiy
[2605]	245	IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled ${ok_mensuel}
	246
	247	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled ${ok_journe}
	248
[2600]	249	if [ X${OutLevel} = Xlow ] \|\| [ X${OutLevel} = Xmedium ] ; then
	250	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 2
	251	else
	252	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 5
	253	fi
	254
[2605]	255	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled ${ok_hf}
	256
[2600]	257	if [ X${OutLevel} = Xlow ] ; then
	258	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 5
	259	elif [ X${OutLevel} = Xmedium ] ; then
	260	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 6
	261	elif [ X${OutLevel} = Xhigh ] ; then
	262	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 7
[2582]	263	fi
[2600]	264
[2755]	265	IGCM_comp_modifyXmlFile nonblocker file_def_histhf3h_lmdz.xml histhf3h enabled ${ok_hf3h}
	266	IGCM_comp_modifyXmlFile nonblocker file_def_histhf3hm_lmdz.xml histhf3hm enabled ${ok_hf3hm}
[2605]	267
	268	IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled ${ok_stn}
[2600]	269
[2605]	270	IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled ${LMDZ_NMC_monthly}
	271	IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled ${LMDZ_NMC_daily}
	272	IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled ${LMDZ_NMC_hf}
[2600]	273
[2605]	274	IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled ${LMDZ_COSP_monthly}
	275	IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled ${LMDZ_COSP_daily}
	276	IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled ${LMDZ_COSP_hf}
[2332]	277
[3106]	278	# Activate the histstrataer output file only for configuration with interactive stratospheric aersols
[3107]	279	# done by setting the key word LMDZ_strataer=y in lmdz.card
	280	if [ X${lmdz_UserChoices_LMDZ_strataer} = Xy ] ; then
[3106]	281	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .TRUE.
	282	else
	283	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .FALSE.
	284	fi
[396]	285
[3106]	286
[911]	287	## run.def parameters
[2598]	288
	289
	290	##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
	291	if [ ${CumulPeriod} -eq 1 ] ; then
	292	IGCM_comp_modifyDefFile blocker run.def raz_date 1
	293	else
	294	IGCM_comp_modifyDefFile blocker run.def raz_date 0
	295	fi
	296
	297	##-- Calendar type for LMDZ and create_etat0_limit
	298	case ${config_UserChoices_CalendarType} in
	299	leap\|gregorian)
	300	IGCM_comp_modifyDefFile blocker run.def calend gregorian ;;
	301	noleap)
	302	IGCM_comp_modifyDefFile blocker run.def calend earth_365d ;;
	303	360d)
	304	IGCM_comp_modifyDefFile blocker run.def calend earth_360d ;;
	305	*)
	306	IGCM_comp_modifyDefFile blocker run.def calend earth_360d ;;
	307	esac
	308
[2582]	309	IGCM_comp_modifyDefFile blocker run.def dayref ${InitDay}
	310	IGCM_comp_modifyDefFile blocker run.def nday ${PeriodLengthInDays}
[396]	311
[1804]	312	# Set anneeref different for gcm and ce0l
	313	# Test if executable create_etat0_limit is present and lmdz.x is not present
	314	if [ -f create_etat0_limit* ] \|\| [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
	315	# for case ce0l : always take current year
[2333]	316	IGCM_comp_modifyDefFile blocker run.def anneeref ${year}
[2480]	317
	318	# Temporary, set use_filtre_fft=n because we now use dyn3d for ce0l version where fft is not implemented.
	319	# In more recent versions of LMDZ, this will not be needed.
	320	IGCM_comp_modifyDefFile force run.def use_filtre_fft n
[1804]	321	else
	322	# for case gcm : take first year of simulation
[2333]	323	IGCM_comp_modifyDefFile blocker run.def anneeref ${InitYear}
[1804]	324	fi
[1643]	325
[1650]	326	## Determine from the variable ListOfComponents in config.card coupling to external models
	327	## and set corresponding parameters in run.def
	328	echo ListOfComponents now running : ${config_ListOfComponents[*]}
	329
	330	if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
	331	echo "Activate ORCHIDEE, set VEGET=y in run.def"
[2333]	332	IGCM_comp_modifyDefFile blocker run.def VEGET y
[1650]	333	else
	334	echo "No ORCHIDEE, set VEGET=n in run.def"
[2333]	335	IGCM_comp_modifyDefFile blocker run.def VEGET n
[1650]	336	fi
	337
	338	if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
	339	echo "Activate coupling to ocean, set type_ocean=couple in run.def"
[2333]	340	IGCM_comp_modifyDefFile blocker run.def type_ocean couple
[1650]	341	else
	342	echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
[2333]	343	IGCM_comp_modifyDefFile blocker run.def type_ocean force
[1650]	344	fi
	345
	346	if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
	347	echo "Activate coupling to INCA, set type_trac=inca in run.def"
[2333]	348	IGCM_comp_modifyDefFile blocker run.def type_trac inca
[1650]	349	elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
	350	echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
[2333]	351	IGCM_comp_modifyDefFile blocker run.def type_trac repr
	352	IGCM_comp_modifyDefFile blocker run.def config_inca none
[1650]	353	else
[3107]	354	if [ X${lmdz_UserChoices_LMDZ_strataer} = Xy ] ; then
[3146]	355	echo "No coupling to chemistry model but it is a LMDZ STRATAER configuration, set type_trac=coag in run.def"
	356	IGCM_comp_modifyDefFile blocker run.def type_trac coag
[3107]	357	IGCM_comp_modifyDefFile blocker run.def config_inca none
	358	else
	359	echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
	360	IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
	361	IGCM_comp_modifyDefFile blocker run.def config_inca none
	362	fi
[1650]	363	fi
	364
	365
[2015]	366	# config.def : Activate direct radiative effect if ok_ade=y
	367	if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
[2333]	368	IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
[2015]	369	else
[2333]	370	IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
[2015]	371	fi
	372
	373	# config.def : Activate indirect radiative effect if ok_aie=y
	374	if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
[2333]	375	IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
[2015]	376	else
[2333]	377	IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
[2015]	378	fi
[1816]	379
[2015]	380	# config.def : Activate online aerosol coupled model if aerosol_couple=y
	381	if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
[2333]	382	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
[1686]	383	else
[2333]	384	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
[2015]	385	fi
[1686]	386
[2015]	387	# config.def : Activate reading of ozone in climatology if read_climoz=2
	388	if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
[2333]	389	IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
[2015]	390	else
[2333]	391	IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0
[2015]	392	fi
	393
	394	# config.def : Choose aerosol use in radiative effect
	395	# type of coupled aerosol =1 (default) =2 => bc only =3 => pom only =4 => seasalt only
	396	# =5 => dust only =6 => all aerosol
	397	if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
[2333]	398	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
[2015]	399	else
[2333]	400	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
[2015]	401	fi
	402
	403	# config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
	404	if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
[2333]	405	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
[2015]	406	else
[2333]	407	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
[2015]	408	fi
	409
[2893]	410	# config.def : Activate COSP
	411	if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ]; then
	412	IGCM_comp_modifyDefFile nonblocker config.def ok_cosp ${lmdz_UserChoices_LMDZ_COSP_OK}
	413	else
	414	IGCM_comp_modifyDefFile nonblocker config.def ok_cosp n
	415	fi
	416
[2911]	417	# config.def : Modify parameter pmagic if it is set in lmdz.card
	418	if [ ! X${lmdz_UserChoices_pmagic} = X ]; then
	419	IGCM_comp_modifyDefFile nonblocker config.def pmagic ${lmdz_UserChoices_pmagic}
	420	else
	421	# Take default value set in config.def
	422	IGCM_comp_modifyDefFile nonblocker config.def pmagic DEFAULT
	423	fi
[2893]	424
[1690]	425	# guide.def : Activate nudging if ok_guide=y set in lmdz.card
[1643]	426	if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
[2333]	427	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide ${lmdz_UserChoices_ok_guide}
[1690]	428	else
[2333]	429	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
[1643]	430	fi
	431
[902]	432	## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
[1172]	433	ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
[1688]	434	if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
[396]	435	awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
	436	IGCM_sys_Mv gcm.def.tmp gcm.def
	437	echo
	438	IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
	439	echo
	440	cat gcm.def
	441	ByPass_hgardfou_teta=n
[902]	442	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
[396]	443	fi
	444
[902]	445	## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
[1172]	446	ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
[1688]	447	if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
[396]	448	sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
	449	IGCM_sys_Mv gcm.def.tmp gcm.def
	450	echo
	451	IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
	452	echo
	453	cat gcm.def
	454	ByPass_hgardfou_mats=n
[902]	455	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
[396]	456	fi
	457
[2904]	458	# Add include of LMDZ context in iodef.xml
	459	# In iodef.xml add on next line after "COMPONENT CONTEXT"
	460	# <context id="LMDZ" src="./context_lmdz.xml"/>
	461	echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
	462	cp iodef.xml iodef.xml.tmp
	463	sed -e "/COMPONENT CONTEXT/r add.tmp" iodef.xml.tmp > iodef.xml
	464	rm iodef.xml.tmp add.tmp
[2476]	465
[2904]	466	#Long Name as global attribute (if LongName is not empty)
	467	if [ ! "X${config_UserChoices_LongName}" = "X" ] ; then
	468	listfile=$(ls file_def*lmdz.xml)
	469	echo "<variable id=\"LongName\" type=\"string\">${config_UserChoices_LongName}</variable>" > add.tmp
	470	for file in ${listfile}
	471	do
	472	cp ${file} ${file}.tmp
	473	sed -e "/<file id/r add.tmp" \
	474	${file}.tmp > ${file}
	475	rm ${file}.tmp
	476	done
	477	rm add.tmp
[2332]	478	fi
[2904]	479
[396]	480	IGCM_debug_PopStack "ATM_Update"
	481	}
	482
	483	#-----------------------------------
	484	function ATM_Finalize
	485	{
	486	IGCM_debug_PushStack "ATM_Finalize"
	487
[1537]	488	# Add special treatement for CARBON CYCLE
[1546]	489	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
[1780]	490	ATM_Carbon_Finalize
	491	fi
[1537]	492
[1780]	493	echo FINALIZE ATM !
[1537]	494
[1780]	495	IGCM_debug_PopStack "ATM_Finalize"
	496	}
[1537]	497
	498
	499
[1780]	500	function ATM_Carbon_Update
	501	{
	502	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
[1537]	503
[1780]	504	IGCM_debug_PushStack "ATM_Carbon_Update"
	505
	506	typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
	507	typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
	508	typeset PathCO2log
	509	typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
	510
	511	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
	512	##--Initialization of fluxes to an undefined value at the first run
	513	UndefinedValueCo2=-9999
	514	InitPeriodCo2=0
	515	InitDateBeginCo2=${UndefinedValueCo2}
	516	InitYearCo2=$(( ${year} - 1 ))
	517	InitDateEndCo2=${InitYearCo2}1231
	518	fCO2_ff=${UndefinedValueCo2}
	519	CO2SBG=${UndefinedValueCo2}
	520	CO2LU=${UndefinedValueCo2}
	521	CO2MBG=${UndefinedValueCo2}
	522	CO2_ppm_prec=${UndefinedValueCo2}
	523	# Get the initial value of atmosp. pco2
	524	CO2_ppm=${lmdz_UserChoices_co2_init}
	525
	526	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
	527	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
	528
[1537]	529	# Save CO2 values in ExeCpuLog variable contents 5 fields
[1780]	530	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
[1537]	531	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
[1780]	532	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	533
	534	# Get the path where the log file co2.log is
	535	PathCO2log=${SUBMIT_DIR}
	536	# Get Previous line in co2.log
	537	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
	538
	539	else
	540
	541	# NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
	542	# !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
	543	#SubmitRestartPath=
	544	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
	545	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
	546	PathCO2log=${config_ATM_SubmitRestartPath}
	547	Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
	548	PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
	549
	550	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
	551	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
	552
	553	# Save Last Line of control in new co2.log file
	554	InitPeriodCo2=0
	555	InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $2}' )
	556	InitDateEndCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $3}' )
	557	fCO2_ff=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $6}' )
	558	CO2SBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $8}' )
	559	CO2LU=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $9}' )
	560	CO2MBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $7}' )
	561	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $5}' )
	562	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	563
	564	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
	565	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
	566	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	567	else
	568	# Get restart line in co2.log
	569	PathCO2log=${SUBMIT_DIR}
	570	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
	571	# Get the value of atmosp. pco2 in co2.log
	572	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	573	fi
	574
[1537]	575	fi
[1780]	576
	577	if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
[2841]	578	# Modify co2_ppm in config.def only for historical run
	579	# If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
	580	IGCM_comp_modifyDefFile force config.def co2_ppm ${CO2_ppm}
[1780]	581	fi
	582	IGCM_debug_PopStack "ATM_Carbon_Update"
	583	}
[1537]	584
[396]	585
[1780]	586	function ATM_Carbon_Finalize
	587	{
	588	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
	589
	590	IGCM_debug_PushStack "ATM_Carbon_Finalize"
	591
	592	typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
	593
	594	# Fossil fuel emission
	595	if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
	596	# For Control, no fossil fuel emission :
	597	fCO2_ff=0
	598	echo "Fossil Fuel for control run :" ${fCO2_ff}
	599	else
	600	# For historical, get the fossile fuel file :
	601	fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
	602	echo "Fossil Fuel for historical run :" ${fCO2_ff}
	603	fi
	604
	605	# Get the value of ocean carbon flux
	606	CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
	607	CO2MBG=$( echo ${CO2MBG} \| sed -e "s/ *//" )
	608	echo "Ocean carbon flux :" ${CO2MBG}
	609
	610	# Get the value of land fluxes
	611	set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
	612	CO2SRF=$( echo ${CO2SBG_3V[0]} \| sed -e "s/ *//" )
	613	CO2LU=$( echo ${CO2SBG_3V[1]} \| sed -e "s/ *//" )
	614	CO2SBG=$( echo ${CO2SBG_3V[2]} \| sed -e "s/ *//" )
	615	echo "Land carbon flux (NEP) :" ${CO2SRF}
	616	echo "LU flux (FLUC) :" ${CO2LU}
	617	echo "Total Land carbon flux (NBP) :" ${CO2SBG}
	618
	619	# Previous CO2
	620	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	621	echo "Previous CO2 :" ${CO2_ppm_prec}
	622
	623	# Formula
	624	CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" \| bc -l )
	625	echo "New CO2 :" ${CO2_ppm}
	626
	627	# Save CO2 values in ExeCpuLog variable contents 5 fields
	628	echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
	629	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
	630	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	631
	632	IGCM_debug_PopStack "ATM_Carbon_Finalize"
[396]	633	}

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