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source: CONFIG/UNIFORM/v6/LMDZOR_v6.2/GENERAL/DRIVER/lmdz.driver @ 4722

Last change on this file since 4722 was 4722, checked in by jgipsl, 5 years ago
Update LMDZOR_v6.2 with changes done in IPSLCM6.2 and other way around.
File size: 30.4 KB

Rev	Line
[396]	1	#!/bin/ksh
	2	#-----------------------------------------------------------------
	3	function ATM_Initialize
	4	{
	5	IGCM_debug_PushStack "ATM_Initialize"
	6
[4463]	7	# Read the resolution from the variables ResolAtm set in config.card UserChoices section or from .resol file
	8	if [ X$ResolAtm != X ] ; then
	9	# ResolAtm is set in config.card
	10	RESOL_ATM_3D=${ResolAtm}
	11	elif [ -f ${SUBMIT_DIR}/../.resol ] ; then
	12	# ResolAtm was not set in config.card, try to read .resol file
	13	eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol) \|\| RESOL_ATM_3D=96x95x39
	14	else
	15	IGCM_debug_Exit "ResolAtm is not set in config.card and the .resol file does not exist."
	16	IGCM_debug_Verif_Exit
	17	fi
	18
	19	IGCM_debug_Print 1 "The atomsopheric resolution is ${RESOL_ATM_3D} "
[396]	20
[659]	21	RESOL_ATM_Z=$( echo ${RESOL_ATM_3D} \| awk "-Fx" '{print $3}' )
[1802]	22	RESOL_ATM_X=$( echo ${RESOL_ATM_3D} \| awk "-Fx" '{print $1}' )
	23	RESOL_ATM_Y=$( echo ${RESOL_ATM_3D} \| awk "-Fx" '{print $2}' )
	24	RESOL_ATM_XY="${RESOL_ATM_X}x${RESOL_ATM_Y}"
[4635]	25	RESOL_ATM=LMD${RESOL_ATM_X}${RESOL_ATM_Y}
[649]	26
[1541]	27	##- LMDZ physics version
	28	## Read LMDZ_Physics option in lmdz.card, if not present take default value AP (old physics)
	29	if [ ! X${lmdz_UserChoices_LMDZ_Physics} = X ] ; then
	30	LMDZ_Physics=${lmdz_UserChoices_LMDZ_Physics}
	31	else
	32	LMDZ_Physics=AP
	33	fi
	34	echo LMDZ physics version : ${LMDZ_Physics}
	35
[1643]	36	##- Create_etat0_limit version
[1782]	37	## Define variable CREATE only if it is set in lmdz.card section UserChoices.
	38	## This variable is only used in lmdz.card to choose input files.
	39	if [ ! X${lmdz_UserChoices_CREATE} = X ] ; then
	40	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices CREATE
	41	CREATE=${lmdz_UserChoices_CREATE}
	42	echo create_etat0_limit version : ${CREATE}
	43	fi
[1643]	44
[1782]	45
[1550]	46	## - LMDZ choice of config.def file
	47	## ConfType must be set in lmdz.card
	48	ConfType=${lmdz_UserChoices_ConfType}
[1541]	49
[1550]	50	##- LMDZ output level, to be set in lmdz.card
	51	if [ X${lmdz_UserChoices_OutLevel} = X ] ; then
	52	# OutLevel is not set. Take default value low.
	53	OutLevel=low
	54	else
	55	OutLevel=${lmdz_UserChoices_OutLevel}
	56	fi
	57
[1539]	58	##-- Output frequency purpose ....
[396]	59	##-- Initialisation ....
[2605]	60	ok_mensuel=.FALSE.
	61	ok_journe=.FALSE.
	62	ok_hf=.FALSE.
	63	ok_hf3h=.FALSE.
	64	ok_hf3hm=.FALSE.
	65	ok_stn=.FALSE.
[396]	66
[3505]	67
[396]	68	case ${config_UserChoices_PeriodLength} in
[2605]	69	1Y\|1y\|1M\|1m) ok_mensuel=.TRUE. ;;
	70	5D\|5d\|1D\|1d) ok_journe=.TRUE. ;;
[396]	71	esac
	72
	73	for frequency in ${config_ATM_WriteFrequency} ; do
	74	case ${frequency} in
[2605]	75	1M\|1m) ok_mensuel=.TRUE. ;;
[396]	76	esac
	77	case ${frequency} in
[2605]	78	5D\|5d\|1D\|1d) ok_journe=.TRUE. ;;
[1539]	79	esac
	80	case ${frequency} in
[2605]	81	HF\|hf) ok_hf=.TRUE. ;;
[396]	82	esac
[1539]	83	case ${frequency} in
[2605]	84	HF3h\|hf3h) ok_hf3h=.TRUE. ;;
[1539]	85	esac
	86	case ${frequency} in
[2605]	87	HF3hm\|hf3hm) ok_hf3hm=.TRUE. ;;
[1539]	88	esac
	89	case ${frequency} in
[2605]	90	STN\|stn) ok_stn=.TRUE. ;;
[1539]	91	esac
[396]	92	done
	93
[3505]	94
	95	## Read LMDZ_COSP_OK in lmdz.card
[2600]	96	if [ X${lmdz_UserChoices_LMDZ_COSP_OK} = Xy ] ; then
	97	## LMDZ_COSP_OK=y, now read all other COSP variables
	98	## Read LMDZ_COSP_monthly in lmdz.card
	99	if [ X${lmdz_UserChoices_LMDZ_COSP_monthly} = Xy ] ; then
[2605]	100	LMDZ_COSP_monthly=.TRUE.
[2600]	101	else
[2605]	102	LMDZ_COSP_monthly=.FALSE.
[2600]	103	fi
	104	## Read LMDZ_COSP_daily in lmdz.card
	105	if [ X${lmdz_UserChoices_LMDZ_COSP_daily} = Xy ] ; then
[2605]	106	LMDZ_COSP_daily=.TRUE.
[2600]	107	else
[2605]	108	LMDZ_COSP_daily=.FALSE.
[2600]	109	fi
	110	## Read LMDZ_COSP_hf in lmdz.card
	111	if [ X${lmdz_UserChoices_LMDZ_COSP_hf} = Xy ] ; then
[2605]	112	LMDZ_COSP_hf=.TRUE.
[2600]	113	else
[2605]	114	LMDZ_COSP_hf=.FALSE.
[2600]	115	fi
[1783]	116	else
[2600]	117	# LMDZ_COSP_OK=n : All cosp output are deactivated
[2605]	118	LMDZ_COSP_monthly=.FALSE.
	119	LMDZ_COSP_daily=.FALSE.
	120	LMDZ_COSP_hf=.FALSE.
[2600]	121	fi
[1000]	122
[1783]	123	## Read LMDZ_NMC_monthly in lmdz.card
[2600]	124	if [ X${lmdz_UserChoices_LMDZ_NMC_monthly} = Xy ] ; then
[2605]	125	LMDZ_NMC_monthly=.TRUE.
[1783]	126	else
[2605]	127	LMDZ_NMC_monthly=.FALSE.
[1783]	128	fi
[2600]	129
[1783]	130	## Read LMDZ_NMC_daily in lmdz.card
[2600]	131	if [ X${lmdz_UserChoices_LMDZ_NMC_daily} = Xy ] ; then
[2605]	132	LMDZ_NMC_daily=.TRUE.
[1783]	133	else
[2605]	134	LMDZ_NMC_daily=.FALSE.
[1783]	135	fi
	136
	137	## Read LMDZ_NMC_hf in lmdz.card
[2600]	138	if [ X${lmdz_UserChoices_LMDZ_NMC_hf} = Xy ] ; then
[2605]	139	LMDZ_NMC_hf=.TRUE.
[1783]	140	else
[2605]	141	LMDZ_NMC_hf=.FALSE.
[1783]	142	fi
	143
[396]	144	IGCM_debug_PopStack "ATM_Initialize"
	145	}
	146
	147	#-----------------------------------------------------------------
	148	function ATM_Update
	149	{
	150	IGCM_debug_PushStack "ATM_Update"
	151
[1535]	152	##-- GHG forcing :
[2321]	153	## If forcing file exist in run directory, read values for the current year
	154	## and set in config.def. If not use the default value set in config.def
[2333]	155
	156	# Read value for solaire from file SOLARANDVOLCANOES.txt. If file not existing, take DEFAULT value from file.
[3127]	157	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)"
	158	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"
[1535]	159	if [ -f SOLARANDVOLCANOES.txt ] ; then
[2333]	160	value=`grep Annee_${year} SOLARANDVOLCANOES.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 SOLARANDVOLCANOES.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 solaire $value
[2321]	170
[3771]	171	# Read value for eccentricity from file Eccentricity.txt. If file not existing, take DEFAULT value from file.
	172	if [ -f Eccentricity.txt ] ; then
	173	value=`grep Annee_${year} Eccentricity.txt \| awk -F= '{print $2}'`
	174	if [ X"${value}" = X ] ; then
	175	# The grep returned empty variable, stop execution
	176	IGCM_debug_Exit "The file Eccentricity.txt do not contain the current year."
	177	IGCM_debug_Verif_Exit
	178	fi
	179	else
	180	value=DEFAULT
	181	fi
	182	IGCM_comp_modifyDefFile nonblocker config.def R_ecc $value
[2333]	183
[3771]	184	# Read value for obliquity from file Obliquity.txt. If file not existing, take DEFAULT value from file.
	185	if [ -f Obliquity.txt ] ; then
	186	value=`grep Annee_${year} Obliquity.txt \| awk -F= '{print $2}'`
	187	if [ X"${value}" = X ] ; then
	188	# The grep returned empty variable, stop execution
	189	IGCM_debug_Exit "The file Obliquity.txt do not contain the current year."
	190	IGCM_debug_Verif_Exit
	191	fi
	192	else
	193	value=DEFAULT
	194	fi
	195	IGCM_comp_modifyDefFile nonblocker config.def R_incl $value
	196
	197	# Read value for perihelie from file Perihelie.txt. If file not existing, take DEFAULT value from file.
	198	if [ -f Perihelie.txt ] ; then
	199	value=`grep Annee_${year} Perihelie.txt \| awk -F= '{print $2}'`
	200	if [ X"${value}" = X ] ; then
	201	# The grep returned empty variable, stop execution
	202	IGCM_debug_Exit "The file Perihelie.txt do not contain the current year."
	203	IGCM_debug_Verif_Exit
	204	fi
	205	else
	206	value=DEFAULT
	207	fi
	208	IGCM_comp_modifyDefFile nonblocker config.def R_peri $value
	209
[2333]	210	# Read value for co2_ppm from file CO2.txt. If file not existing, take DEFAULT value from file.
[3568]	211	# Calculate co2_ppm_per as co2_ppm*4.
[1535]	212	if [ -f CO2.txt ] ; then
[2333]	213	value=`grep Annee_${year} CO2.txt \| awk -F= '{print $2}'`
	214	if [ X"${value}" = X ] ; then
[2321]	215	# The grep returned empty variable, stop execution
	216	IGCM_debug_Exit "The file CO2.txt do not contain the current year."
	217	IGCM_debug_Verif_Exit
	218	fi
[3568]	219	value4=`grep Annee_${year} CO2.txt \| awk -F= '{print $2 * 4}'`
[1690]	220	else
[2333]	221	value=DEFAULT
[3568]	222	value4=DEFAULT
[1535]	223	fi
[2333]	224	IGCM_comp_modifyDefFile nonblocker config.def co2_ppm $value
[3568]	225	IGCM_comp_modifyDefFile nonblocker config.def co2_ppm_per $value4
[1690]	226
[2333]	227
	228	# Read value for CH4_ppb from file CH4.txt. If file not existing, take DEFAULT value from file.
[1535]	229	if [ -f CH4.txt ] ; then
[2333]	230	value=`grep Annee_${year} CH4.txt \| awk -F= '{print $2}'`
	231	if [ X"${value}" = X ] ; then
[2321]	232	# The grep returned empty variable, stop execution
	233	IGCM_debug_Exit "The file CH4.txt do not contain the current year."
	234	IGCM_debug_Verif_Exit
	235	fi
[2333]	236	else
	237	value=DEFAULT
[1535]	238	fi
[2333]	239	IGCM_comp_modifyDefFile nonblocker config.def CH4_ppb $value
[2321]	240
[2333]	241
	242	# Read value for N2O_ppb from file N2O.txt. If file not existing, take DEFAULT value from file.
[1535]	243	if [ -f N2O.txt ] ; then
[2333]	244	value=`grep Annee_${year} N2O.txt \| awk -F= '{print $2}'`
	245	if [ X"${value}" = X ] ; then
[2321]	246	# The grep returned empty variable, stop execution
	247	IGCM_debug_Exit "The file N2O.txt do not contain the current year."
	248	IGCM_debug_Verif_Exit
	249	fi
[1690]	250	else
[2333]	251	value=DEFAULT
[1535]	252	fi
[2333]	253	IGCM_comp_modifyDefFile nonblocker config.def N2O_ppb $value
[2321]	254
[2333]	255	# Read value for CFC11_ppt from file CFC11.txt. If file not existing, take DEFAULT value from file.
[1535]	256	if [ -f CFC11.txt ] ; then
[2333]	257	value=`grep Annee_${year} CFC11.txt \| awk -F= '{print $2}'`
	258	if [ X"${value}" = X ] ; then
[2321]	259	# The grep returned empty variable, stop execution
	260	IGCM_debug_Exit "The file CFC11.txt do not contain the current year."
	261	IGCM_debug_Verif_Exit
	262	fi
[1690]	263	else
[2333]	264	value=DEFAULT
[1535]	265	fi
[2333]	266	IGCM_comp_modifyDefFile nonblocker config.def CFC11_ppt $value
[2321]	267
[2333]	268
	269	# Read value for CFC12_ppt from file CFC12.txt. If file not existing, take DEFAULT value from file.
[1535]	270	if [ -f CFC12.txt ] ; then
[2333]	271	value=`grep Annee_${year} CFC12.txt \| awk -F= '{print $2}'`
	272	if [ X"${value}" = X ] ; then
[2321]	273	# The grep returned empty variable, stop execution
	274	IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
	275	IGCM_debug_Verif_Exit
	276	fi
[1690]	277	else
[2333]	278	value=DEFAULT
[1535]	279	fi
[2333]	280	IGCM_comp_modifyDefFile nonblocker config.def CFC12_ppt $value
[1535]	281
[1780]	282
[2336]	283	## Coupling Time Step : Take value of FreqCoupling set in oasis.card or if it is not set, take default value 86400
	284	LMDZ_t_coupl=${oasis_UserChoices_FreqCoupling:-86400}
[2332]	285	IGCM_debug_Print 3 "LMDZ_t_coupl " ${LMDZ_t_coupl}
[2333]	286	IGCM_comp_modifyDefFile nonblocker config.def t_coupl ${LMDZ_t_coupl}
[2332]	287
[1780]	288	##-- Add special treatement for CARBON CYCLE
[1546]	289	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
[1780]	290	ATM_Carbon_Update
	291	fi
[1537]	292
	293
[1538]	294	##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
	295	## COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
	296	if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] && [ ${year} -ge 1979 ]) ; then
[2605]	297	LMDZ_COSP_daily=.TRUE.
[1538]	298	fi
[1537]	299
[2600]	300	## Modifiy
[2605]	301	IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled ${ok_mensuel}
	302
	303	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled ${ok_journe}
	304
[2600]	305	if [ X${OutLevel} = Xlow ] \|\| [ X${OutLevel} = Xmedium ] ; then
	306	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 2
	307	else
	308	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 5
	309	fi
	310
[2605]	311	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled ${ok_hf}
	312
[2600]	313	if [ X${OutLevel} = Xlow ] ; then
	314	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 5
	315	elif [ X${OutLevel} = Xmedium ] ; then
	316	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 6
	317	elif [ X${OutLevel} = Xhigh ] ; then
	318	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 7
[2582]	319	fi
[2600]	320
[2755]	321	IGCM_comp_modifyXmlFile nonblocker file_def_histhf3h_lmdz.xml histhf3h enabled ${ok_hf3h}
	322	IGCM_comp_modifyXmlFile nonblocker file_def_histhf3hm_lmdz.xml histhf3hm enabled ${ok_hf3hm}
[2605]	323
	324	IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled ${ok_stn}
[2600]	325
[2605]	326	IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled ${LMDZ_NMC_monthly}
	327	IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled ${LMDZ_NMC_daily}
	328	IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled ${LMDZ_NMC_hf}
[2600]	329
[2605]	330	IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled ${LMDZ_COSP_monthly}
	331	IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled ${LMDZ_COSP_daily}
	332	IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled ${LMDZ_COSP_hf}
[2332]	333
[3104]	334	# Activate the histstrataer output file only for configuration with interactive stratospheric aersols
	335	# done by setting the key word LMDZ_strataero=y in lmdz.card
	336	if [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
	337	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .TRUE.
[4722]	338	IGCM_comp_modifyXmlFile nonblocker file_def_histdaystrataer_lmdz.xml histdaystrataer enabled .TRUE.
[3104]	339	else
	340	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .FALSE.
[4722]	341	IGCM_comp_modifyXmlFile nonblocker file_def_histdaystrataer_lmdz.xml histdaystrataer enabled .FALSE.
[3104]	342	fi
[396]	343
[3104]	344
[911]	345	## run.def parameters
[2598]	346
	347
	348	##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
	349	if [ ${CumulPeriod} -eq 1 ] ; then
	350	IGCM_comp_modifyDefFile blocker run.def raz_date 1
	351	else
	352	IGCM_comp_modifyDefFile blocker run.def raz_date 0
	353	fi
	354
	355	##-- Calendar type for LMDZ and create_etat0_limit
	356	case ${config_UserChoices_CalendarType} in
	357	leap\|gregorian)
	358	IGCM_comp_modifyDefFile blocker run.def calend gregorian ;;
	359	noleap)
	360	IGCM_comp_modifyDefFile blocker run.def calend earth_365d ;;
	361	360d)
	362	IGCM_comp_modifyDefFile blocker run.def calend earth_360d ;;
	363	*)
	364	IGCM_comp_modifyDefFile blocker run.def calend earth_360d ;;
	365	esac
	366
[2582]	367	IGCM_comp_modifyDefFile blocker run.def dayref ${InitDay}
	368	IGCM_comp_modifyDefFile blocker run.def nday ${PeriodLengthInDays}
[396]	369
[1804]	370	# Set anneeref different for gcm and ce0l
	371	# Test if executable create_etat0_limit is present and lmdz.x is not present
	372	if [ -f create_etat0_limit* ] \|\| [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
	373	# for case ce0l : always take current year
[2333]	374	IGCM_comp_modifyDefFile blocker run.def anneeref ${year}
[2480]	375
	376	# Temporary, set use_filtre_fft=n because we now use dyn3d for ce0l version where fft is not implemented.
	377	# In more recent versions of LMDZ, this will not be needed.
	378	IGCM_comp_modifyDefFile force run.def use_filtre_fft n
[1804]	379	else
	380	# for case gcm : take first year of simulation
[2333]	381	IGCM_comp_modifyDefFile blocker run.def anneeref ${InitYear}
[1804]	382	fi
[1643]	383
[1650]	384	## Determine from the variable ListOfComponents in config.card coupling to external models
	385	## and set corresponding parameters in run.def
	386	echo ListOfComponents now running : ${config_ListOfComponents[*]}
	387
	388	if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
	389	echo "Activate ORCHIDEE, set VEGET=y in run.def"
[2333]	390	IGCM_comp_modifyDefFile blocker run.def VEGET y
[1650]	391	else
	392	echo "No ORCHIDEE, set VEGET=n in run.def"
[2333]	393	IGCM_comp_modifyDefFile blocker run.def VEGET n
[1650]	394	fi
	395
	396	if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
	397	echo "Activate coupling to ocean, set type_ocean=couple in run.def"
[2333]	398	IGCM_comp_modifyDefFile blocker run.def type_ocean couple
[1650]	399	else
	400	echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
[3935]	401	IGCM_comp_modifyDefFile nonblocker run.def type_ocean force
[1650]	402	fi
	403
	404	if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
	405	echo "Activate coupling to INCA, set type_trac=inca in run.def"
[2333]	406	IGCM_comp_modifyDefFile blocker run.def type_trac inca
[1650]	407	elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
	408	echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
[2333]	409	IGCM_comp_modifyDefFile blocker run.def type_trac repr
	410	IGCM_comp_modifyDefFile blocker run.def config_inca none
[4635]	411	elif [ X${config_UserChoices_ConfigType} = XESMCO2 ] ; then
	412	echo "ESM config, set type_trac=co2i in run.def"
	413	IGCM_comp_modifyDefFile blocker run.def type_trac co2i
	414	IGCM_comp_modifyDefFile blocker run.def config_inca none
[1650]	415	else
	416	echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
[2333]	417	IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
	418	IGCM_comp_modifyDefFile blocker run.def config_inca none
[1650]	419	fi
	420
	421
[4020]	422	# run.def : Activate the call to phytrac
	423	if [ ! X${lmdz_UserChoices_iflag_phytrac} = X ]; then
	424	IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac ${lmdz_UserChoices_iflag_phytrac}
[4635]	425	elif [ X${config_UserChoices_ConfigType} = XESMCO2 ] ; then
	426	IGCM_comp_modifyDefFile blocker run.def iflag_phytrac 1
[4020]	427	else
[4632]	428	IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac DEFAULT
[4020]	429	fi
	430
[4431]	431	# run.def : Activate the new calving
	432	if [ ! X${lmdz_UserChoices_cpl_old_calving} = X ]; then
	433	IGCM_comp_modifyDefFile nonblocker run.def cpl_old_calving ${lmdz_UserChoices_cpl_old_calving}
	434	else
	435	IGCM_comp_modifyDefFile nonblocker run.def cpl_old_calving y
	436	fi
	437
[4020]	438	# physiq.def : Activate the call to phytrac
	439	if [ ! X${lmdz_UserChoices_ok_bug_cv_trac} = X ]; then
	440	IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac ${lmdz_UserChoices_ok_bug_cv_trac}
	441	else
	442	IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac n
	443	fi
	444
[4632]	445	# config.def : Activate aerosol strato
	446	if [ ! X${lmdz_UserChoices_flag_aerosol_strat} = X ]; then
	447	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol_strat ${lmdz_UserChoices_flag_aerosol_strat}
	448	else
	449	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol_strat DEFAULT
	450	fi
	451
[2015]	452	# config.def : Activate direct radiative effect if ok_ade=y
	453	if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
[2333]	454	IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
[2015]	455	else
[2333]	456	IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
[2015]	457	fi
	458
	459	# config.def : Activate indirect radiative effect if ok_aie=y
	460	if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
[2333]	461	IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
[2015]	462	else
[2333]	463	IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
[2015]	464	fi
[1816]	465
[2015]	466	# config.def : Activate online aerosol coupled model if aerosol_couple=y
	467	if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
[2333]	468	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
[1686]	469	else
[2333]	470	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
[2015]	471	fi
[1686]	472
[4020]	473	# config.def : Activate online Ozone chemistry coupled model if chemistry_couple=y
	474	if [ ! X${lmdz_UserChoices_chemistry_couple} = X ]; then
	475	IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple ${lmdz_UserChoices_chemistry_couple}
	476	else
	477	IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple n
	478	fi
	479
[2015]	480	# config.def : Activate reading of ozone in climatology if read_climoz=2
	481	if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
[2333]	482	IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
[2015]	483	else
[2333]	484	IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0
[2015]	485	fi
	486
	487	# config.def : Choose aerosol use in radiative effect
	488	# type of coupled aerosol =1 (default) =2 => bc only =3 => pom only =4 => seasalt only
	489	# =5 => dust only =6 => all aerosol
	490	if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
[2333]	491	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
[2015]	492	else
[2333]	493	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
[2015]	494	fi
	495
	496	# config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
	497	if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
[2333]	498	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
[2015]	499	else
[2333]	500	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
[2015]	501	fi
	502
[2893]	503	# config.def : Activate COSP
	504	if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ]; then
	505	IGCM_comp_modifyDefFile nonblocker config.def ok_cosp ${lmdz_UserChoices_LMDZ_COSP_OK}
	506	else
	507	IGCM_comp_modifyDefFile nonblocker config.def ok_cosp n
	508	fi
	509
[2911]	510	# config.def : Modify parameter pmagic if it is set in lmdz.card
	511	if [ ! X${lmdz_UserChoices_pmagic} = X ]; then
	512	IGCM_comp_modifyDefFile nonblocker config.def pmagic ${lmdz_UserChoices_pmagic}
	513	else
	514	# Take default value set in config.def
	515	IGCM_comp_modifyDefFile nonblocker config.def pmagic DEFAULT
	516	fi
[2893]	517
[4635]	518	if [ X${config_UserChoices_ConfigType} = XESMCO2 ] ; then
	519	# Set carbon cycle parameters according to parmeters in lmdz.card
	520	IGCM_comp_modifyDefFile blocker config.def level_coupling_esm 2
	521	IGCM_comp_modifyDefFile blocker config.def carbon_cycle_cpl ${lmdz_UserChoices_carbon_cycle_cpl}
	522	IGCM_comp_modifyDefFile blocker config.def carbon_cycle_tr ${lmdz_UserChoices_carbon_cycle_tr}
	523	IGCM_comp_modifyDefFile blocker config.def carbon_cycle_rad ${lmdz_UserChoices_carbon_cycle_rad}
	524	else
	525	# Take default value set in config.def
	526	IGCM_comp_modifyDefFile nonblocker config.def level_coupling_esm DEFAULT
	527	IGCM_comp_modifyDefFile nonblocker config.def carbon_cycle_cpl DEFAULT
	528	IGCM_comp_modifyDefFile nonblocker config.def carbon_cycle_tr DEFAULT
	529	IGCM_comp_modifyDefFile nonblocker config.def carbon_cycle_rad DEFAULT
	530	fi
	531
[3868]	532	# physiq.def : Modify parameter tau_gl if it is set in lmdz.card
	533	if [ ! X${lmdz_UserChoices_tau_gl} = X ]; then
	534	IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl ${lmdz_UserChoices_tau_gl}
	535	else
	536	# Take default value set in physiq.def
[4038]	537	IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl DEFAULT
[3868]	538	fi
	539
	540
[1690]	541	# guide.def : Activate nudging if ok_guide=y set in lmdz.card
[1643]	542	if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
[2333]	543	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide ${lmdz_UserChoices_ok_guide}
[1690]	544	else
[2333]	545	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
[1643]	546	fi
	547
[3868]	548
[902]	549	## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
[1172]	550	ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
[1688]	551	if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
[396]	552	awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
	553	IGCM_sys_Mv gcm.def.tmp gcm.def
	554	echo
	555	IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
	556	echo
	557	cat gcm.def
	558	ByPass_hgardfou_teta=n
[902]	559	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
[396]	560	fi
	561
[902]	562	## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
[1172]	563	ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
[1688]	564	if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
[396]	565	sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
	566	IGCM_sys_Mv gcm.def.tmp gcm.def
	567	echo
	568	IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
	569	echo
	570	cat gcm.def
	571	ByPass_hgardfou_mats=n
[902]	572	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
[396]	573	fi
	574
[2904]	575	# Add include of LMDZ context in iodef.xml
[4108]	576	# In iodef.xml add on the next line after "COMPONENT CONTEXT"
[2904]	577	echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
[4108]	578	# Add inclusion of file context_input_lmdz.xml if this file exists
	579	if [ -f context_input_lmdz.xml ] ; then
	580	echo '<context id="LMDZ" src="./context_input_lmdz.xml"/>' >> add.tmp
	581	fi
	582	# Include xml files for output configuration if running with workflow CMIP6
[3505]	583	if [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] ; then
	584	echo '<context id="LMDZ" src="./ping_lmdz.xml"/>' >> add.tmp
	585	echo '<context id="LMDZ" src="./dr2xml_lmdz.xml"/>' >> add.tmp
	586	fi
[2904]	587	cp iodef.xml iodef.xml.tmp
	588	sed -e "/COMPONENT CONTEXT/r add.tmp" iodef.xml.tmp > iodef.xml
	589	rm iodef.xml.tmp add.tmp
[2476]	590
[2904]	591	#Long Name as global attribute (if LongName is not empty)
	592	if [ ! "X${config_UserChoices_LongName}" = "X" ] ; then
	593	listfile=$(ls file_def*lmdz.xml)
	594	echo "<variable id=\"LongName\" type=\"string\">${config_UserChoices_LongName}</variable>" > add.tmp
	595	for file in ${listfile}
	596	do
	597	cp ${file} ${file}.tmp
	598	sed -e "/<file id/r add.tmp" \
	599	${file}.tmp > ${file}
	600	rm ${file}.tmp
	601	done
	602	rm add.tmp
[2332]	603	fi
[4353]	604
	605	#Compression level (if CompressionLevel is not empty)
	606	if [ ! "X${config_UserChoices_CompressionLevel}" = "X" ] ; then
	607	echo "NetCDF output files compression level is " ${config_UserChoices_CompressionLevel}
	608	listfile=$(ls file_def*lmdz.xml)
	609	for file in ${listfile}
	610	do
	611	sed -i -e "s/\(compression_level=\"\)[^\"]*\(\"\)/\1${config_UserChoices_CompressionLevel}\2/" ${file}
	612	done
	613	fi
	614
[2904]	615
[396]	616	IGCM_debug_PopStack "ATM_Update"
	617	}
	618
	619	#-----------------------------------
	620	function ATM_Finalize
	621	{
	622	IGCM_debug_PushStack "ATM_Finalize"
	623
[1537]	624	# Add special treatement for CARBON CYCLE
[1546]	625	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
[1780]	626	ATM_Carbon_Finalize
	627	fi
[1537]	628
[1780]	629	echo FINALIZE ATM !
[1537]	630
[1780]	631	IGCM_debug_PopStack "ATM_Finalize"
	632	}
[1537]	633
	634
	635
[1780]	636	function ATM_Carbon_Update
	637	{
	638	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
[1537]	639
[1780]	640	IGCM_debug_PushStack "ATM_Carbon_Update"
	641
	642	typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
	643	typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
	644	typeset PathCO2log
	645	typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
	646
	647	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
	648	##--Initialization of fluxes to an undefined value at the first run
	649	UndefinedValueCo2=-9999
	650	InitPeriodCo2=0
	651	InitDateBeginCo2=${UndefinedValueCo2}
	652	InitYearCo2=$(( ${year} - 1 ))
	653	InitDateEndCo2=${InitYearCo2}1231
	654	fCO2_ff=${UndefinedValueCo2}
	655	CO2SBG=${UndefinedValueCo2}
	656	CO2LU=${UndefinedValueCo2}
	657	CO2MBG=${UndefinedValueCo2}
	658	CO2_ppm_prec=${UndefinedValueCo2}
	659	# Get the initial value of atmosp. pco2
	660	CO2_ppm=${lmdz_UserChoices_co2_init}
	661
	662	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
	663	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
	664
[1537]	665	# Save CO2 values in ExeCpuLog variable contents 5 fields
[1780]	666	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
[1537]	667	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
[1780]	668	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	669
	670	# Get the path where the log file co2.log is
	671	PathCO2log=${SUBMIT_DIR}
	672	# Get Previous line in co2.log
	673	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
	674
	675	else
	676
	677	# NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
	678	# !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
	679	#SubmitRestartPath=
	680	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
	681	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
	682	PathCO2log=${config_ATM_SubmitRestartPath}
	683	Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
	684	PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
	685
	686	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
	687	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
	688
	689	# Save Last Line of control in new co2.log file
	690	InitPeriodCo2=0
	691	InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $2}' )
	692	InitDateEndCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $3}' )
	693	fCO2_ff=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $6}' )
	694	CO2SBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $8}' )
	695	CO2LU=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $9}' )
	696	CO2MBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $7}' )
	697	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $5}' )
	698	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	699
	700	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
	701	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
	702	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	703	else
	704	# Get restart line in co2.log
	705	PathCO2log=${SUBMIT_DIR}
	706	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
	707	# Get the value of atmosp. pco2 in co2.log
	708	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	709	fi
	710
[1537]	711	fi
[1780]	712
	713	if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
[2841]	714	# Modify co2_ppm in config.def only for historical run
	715	# If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
	716	IGCM_comp_modifyDefFile force config.def co2_ppm ${CO2_ppm}
[1780]	717	fi
	718	IGCM_debug_PopStack "ATM_Carbon_Update"
	719	}
[1537]	720
[396]	721
[1780]	722	function ATM_Carbon_Finalize
	723	{
	724	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
	725
	726	IGCM_debug_PushStack "ATM_Carbon_Finalize"
	727
	728	typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
	729
	730	# Fossil fuel emission
	731	if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
	732	# For Control, no fossil fuel emission :
	733	fCO2_ff=0
	734	echo "Fossil Fuel for control run :" ${fCO2_ff}
	735	else
	736	# For historical, get the fossile fuel file :
	737	fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
	738	echo "Fossil Fuel for historical run :" ${fCO2_ff}
	739	fi
	740
	741	# Get the value of ocean carbon flux
	742	CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
	743	CO2MBG=$( echo ${CO2MBG} \| sed -e "s/ *//" )
	744	echo "Ocean carbon flux :" ${CO2MBG}
	745
	746	# Get the value of land fluxes
	747	set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
	748	CO2SRF=$( echo ${CO2SBG_3V[0]} \| sed -e "s/ *//" )
	749	CO2LU=$( echo ${CO2SBG_3V[1]} \| sed -e "s/ *//" )
	750	CO2SBG=$( echo ${CO2SBG_3V[2]} \| sed -e "s/ *//" )
	751	echo "Land carbon flux (NEP) :" ${CO2SRF}
	752	echo "LU flux (FLUC) :" ${CO2LU}
	753	echo "Total Land carbon flux (NBP) :" ${CO2SBG}
	754
	755	# Previous CO2
	756	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	757	echo "Previous CO2 :" ${CO2_ppm_prec}
	758
	759	# Formula
	760	CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" \| bc -l )
	761	echo "New CO2 :" ${CO2_ppm}
	762
	763	# Save CO2 values in ExeCpuLog variable contents 5 fields
	764	echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
	765	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
	766	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	767
	768	IGCM_debug_PopStack "ATM_Carbon_Finalize"
[396]	769	}

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