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source: CONFIG/UNIFORM/v6/LMDZOR_v6/GENERAL/DRIVER/lmdz.driver @ 4164

Last change on this file since 4164 was 4108, checked in by jgipsl, 6 years ago
If file context_input_lmdz.xml or context_input_orchidee.xml exit, include it in iodef.xml.
File size: 27.6 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
[3505]	56
[396]	57	case ${config_UserChoices_PeriodLength} in
[2605]	58	1Y\|1y\|1M\|1m) ok_mensuel=.TRUE. ;;
	59	5D\|5d\|1D\|1d) ok_journe=.TRUE. ;;
[396]	60	esac
	61
	62	for frequency in ${config_ATM_WriteFrequency} ; do
	63	case ${frequency} in
[2605]	64	1M\|1m) ok_mensuel=.TRUE. ;;
[396]	65	esac
	66	case ${frequency} in
[2605]	67	5D\|5d\|1D\|1d) ok_journe=.TRUE. ;;
[1539]	68	esac
	69	case ${frequency} in
[2605]	70	HF\|hf) ok_hf=.TRUE. ;;
[396]	71	esac
[1539]	72	case ${frequency} in
[2605]	73	HF3h\|hf3h) ok_hf3h=.TRUE. ;;
[1539]	74	esac
	75	case ${frequency} in
[2605]	76	HF3hm\|hf3hm) ok_hf3hm=.TRUE. ;;
[1539]	77	esac
	78	case ${frequency} in
[2605]	79	STN\|stn) ok_stn=.TRUE. ;;
[1539]	80	esac
[396]	81	done
	82
[3505]	83
	84	## Read LMDZ_COSP_OK in lmdz.card
[2600]	85	if [ X${lmdz_UserChoices_LMDZ_COSP_OK} = Xy ] ; then
	86	## LMDZ_COSP_OK=y, now read all other COSP variables
	87	## Read LMDZ_COSP_monthly in lmdz.card
	88	if [ X${lmdz_UserChoices_LMDZ_COSP_monthly} = Xy ] ; then
[2605]	89	LMDZ_COSP_monthly=.TRUE.
[2600]	90	else
[2605]	91	LMDZ_COSP_monthly=.FALSE.
[2600]	92	fi
	93	## Read LMDZ_COSP_daily in lmdz.card
	94	if [ X${lmdz_UserChoices_LMDZ_COSP_daily} = Xy ] ; then
[2605]	95	LMDZ_COSP_daily=.TRUE.
[2600]	96	else
[2605]	97	LMDZ_COSP_daily=.FALSE.
[2600]	98	fi
	99	## Read LMDZ_COSP_hf in lmdz.card
	100	if [ X${lmdz_UserChoices_LMDZ_COSP_hf} = Xy ] ; then
[2605]	101	LMDZ_COSP_hf=.TRUE.
[2600]	102	else
[2605]	103	LMDZ_COSP_hf=.FALSE.
[2600]	104	fi
[1783]	105	else
[2600]	106	# LMDZ_COSP_OK=n : All cosp output are deactivated
[2605]	107	LMDZ_COSP_monthly=.FALSE.
	108	LMDZ_COSP_daily=.FALSE.
	109	LMDZ_COSP_hf=.FALSE.
[2600]	110	fi
[1000]	111
[1783]	112	## Read LMDZ_NMC_monthly in lmdz.card
[2600]	113	if [ X${lmdz_UserChoices_LMDZ_NMC_monthly} = Xy ] ; then
[2605]	114	LMDZ_NMC_monthly=.TRUE.
[1783]	115	else
[2605]	116	LMDZ_NMC_monthly=.FALSE.
[1783]	117	fi
[2600]	118
[1783]	119	## Read LMDZ_NMC_daily in lmdz.card
[2600]	120	if [ X${lmdz_UserChoices_LMDZ_NMC_daily} = Xy ] ; then
[2605]	121	LMDZ_NMC_daily=.TRUE.
[1783]	122	else
[2605]	123	LMDZ_NMC_daily=.FALSE.
[1783]	124	fi
	125
	126	## Read LMDZ_NMC_hf in lmdz.card
[2600]	127	if [ X${lmdz_UserChoices_LMDZ_NMC_hf} = Xy ] ; then
[2605]	128	LMDZ_NMC_hf=.TRUE.
[1783]	129	else
[2605]	130	LMDZ_NMC_hf=.FALSE.
[1783]	131	fi
[2600]	132
[1783]	133
[396]	134	IGCM_debug_PopStack "ATM_Initialize"
	135	}
	136
	137	#-----------------------------------------------------------------
	138	function ATM_Update
	139	{
	140	IGCM_debug_PushStack "ATM_Update"
	141
[1535]	142	##-- GHG forcing :
[2321]	143	## If forcing file exist in run directory, read values for the current year
	144	## and set in config.def. If not use the default value set in config.def
[2333]	145
	146	# Read value for solaire from file SOLARANDVOLCANOES.txt. If file not existing, take DEFAULT value from file.
[3127]	147	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)"
	148	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]	149	if [ -f SOLARANDVOLCANOES.txt ] ; then
[2333]	150	value=`grep Annee_${year} SOLARANDVOLCANOES.txt \| awk -F= '{print $2}'`
	151	if [ X"${value}" = X ] ; then
[2321]	152	# The grep returned empty variable, stop execution
	153	IGCM_debug_Exit "The file SOLARANDVOLCANOES.txt do not contain the current year."
	154	IGCM_debug_Verif_Exit
	155	fi
[1690]	156	else
[2333]	157	value=DEFAULT
[1535]	158	fi
[2333]	159	IGCM_comp_modifyDefFile nonblocker config.def solaire $value
[2321]	160
[3771]	161	# Read value for eccentricity from file Eccentricity.txt. If file not existing, take DEFAULT value from file.
	162	if [ -f Eccentricity.txt ] ; then
	163	value=`grep Annee_${year} Eccentricity.txt \| awk -F= '{print $2}'`
	164	if [ X"${value}" = X ] ; then
	165	# The grep returned empty variable, stop execution
	166	IGCM_debug_Exit "The file Eccentricity.txt do not contain the current year."
	167	IGCM_debug_Verif_Exit
	168	fi
	169	else
	170	value=DEFAULT
	171	fi
	172	IGCM_comp_modifyDefFile nonblocker config.def R_ecc $value
[2333]	173
[3771]	174	# Read value for obliquity from file Obliquity.txt. If file not existing, take DEFAULT value from file.
	175	if [ -f Obliquity.txt ] ; then
	176	value=`grep Annee_${year} Obliquity.txt \| awk -F= '{print $2}'`
	177	if [ X"${value}" = X ] ; then
	178	# The grep returned empty variable, stop execution
	179	IGCM_debug_Exit "The file Obliquity.txt do not contain the current year."
	180	IGCM_debug_Verif_Exit
	181	fi
	182	else
	183	value=DEFAULT
	184	fi
	185	IGCM_comp_modifyDefFile nonblocker config.def R_incl $value
	186
	187	# Read value for perihelie from file Perihelie.txt. If file not existing, take DEFAULT value from file.
	188	if [ -f Perihelie.txt ] ; then
	189	value=`grep Annee_${year} Perihelie.txt \| awk -F= '{print $2}'`
	190	if [ X"${value}" = X ] ; then
	191	# The grep returned empty variable, stop execution
	192	IGCM_debug_Exit "The file Perihelie.txt do not contain the current year."
	193	IGCM_debug_Verif_Exit
	194	fi
	195	else
	196	value=DEFAULT
	197	fi
	198	IGCM_comp_modifyDefFile nonblocker config.def R_peri $value
	199
[2333]	200	# Read value for co2_ppm from file CO2.txt. If file not existing, take DEFAULT value from file.
[3568]	201	# Calculate co2_ppm_per as co2_ppm*4.
[1535]	202	if [ -f CO2.txt ] ; then
[2333]	203	value=`grep Annee_${year} CO2.txt \| awk -F= '{print $2}'`
	204	if [ X"${value}" = X ] ; then
[2321]	205	# The grep returned empty variable, stop execution
	206	IGCM_debug_Exit "The file CO2.txt do not contain the current year."
	207	IGCM_debug_Verif_Exit
	208	fi
[3568]	209	value4=`grep Annee_${year} CO2.txt \| awk -F= '{print $2 * 4}'`
[1690]	210	else
[2333]	211	value=DEFAULT
[3568]	212	value4=DEFAULT
[1535]	213	fi
[2333]	214	IGCM_comp_modifyDefFile nonblocker config.def co2_ppm $value
[3568]	215	IGCM_comp_modifyDefFile nonblocker config.def co2_ppm_per $value4
[1690]	216
[2333]	217
	218	# Read value for CH4_ppb from file CH4.txt. If file not existing, take DEFAULT value from file.
[1535]	219	if [ -f CH4.txt ] ; then
[2333]	220	value=`grep Annee_${year} CH4.txt \| awk -F= '{print $2}'`
	221	if [ X"${value}" = X ] ; then
[2321]	222	# The grep returned empty variable, stop execution
	223	IGCM_debug_Exit "The file CH4.txt do not contain the current year."
	224	IGCM_debug_Verif_Exit
	225	fi
[2333]	226	else
	227	value=DEFAULT
[1535]	228	fi
[2333]	229	IGCM_comp_modifyDefFile nonblocker config.def CH4_ppb $value
[2321]	230
[2333]	231
	232	# Read value for N2O_ppb from file N2O.txt. If file not existing, take DEFAULT value from file.
[1535]	233	if [ -f N2O.txt ] ; then
[2333]	234	value=`grep Annee_${year} N2O.txt \| awk -F= '{print $2}'`
	235	if [ X"${value}" = X ] ; then
[2321]	236	# The grep returned empty variable, stop execution
	237	IGCM_debug_Exit "The file N2O.txt do not contain the current year."
	238	IGCM_debug_Verif_Exit
	239	fi
[1690]	240	else
[2333]	241	value=DEFAULT
[1535]	242	fi
[2333]	243	IGCM_comp_modifyDefFile nonblocker config.def N2O_ppb $value
[2321]	244
[2333]	245	# Read value for CFC11_ppt from file CFC11.txt. If file not existing, take DEFAULT value from file.
[1535]	246	if [ -f CFC11.txt ] ; then
[2333]	247	value=`grep Annee_${year} CFC11.txt \| awk -F= '{print $2}'`
	248	if [ X"${value}" = X ] ; then
[2321]	249	# The grep returned empty variable, stop execution
	250	IGCM_debug_Exit "The file CFC11.txt do not contain the current year."
	251	IGCM_debug_Verif_Exit
	252	fi
[1690]	253	else
[2333]	254	value=DEFAULT
[1535]	255	fi
[2333]	256	IGCM_comp_modifyDefFile nonblocker config.def CFC11_ppt $value
[2321]	257
[2333]	258
	259	# Read value for CFC12_ppt from file CFC12.txt. If file not existing, take DEFAULT value from file.
[1535]	260	if [ -f CFC12.txt ] ; then
[2333]	261	value=`grep Annee_${year} CFC12.txt \| awk -F= '{print $2}'`
	262	if [ X"${value}" = X ] ; then
[2321]	263	# The grep returned empty variable, stop execution
	264	IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
	265	IGCM_debug_Verif_Exit
	266	fi
[1690]	267	else
[2333]	268	value=DEFAULT
[1535]	269	fi
[2333]	270	IGCM_comp_modifyDefFile nonblocker config.def CFC12_ppt $value
[1535]	271
[1780]	272
[2336]	273	## Coupling Time Step : Take value of FreqCoupling set in oasis.card or if it is not set, take default value 86400
	274	LMDZ_t_coupl=${oasis_UserChoices_FreqCoupling:-86400}
[2332]	275	IGCM_debug_Print 3 "LMDZ_t_coupl " ${LMDZ_t_coupl}
[2333]	276	IGCM_comp_modifyDefFile nonblocker config.def t_coupl ${LMDZ_t_coupl}
[2332]	277
[1780]	278	##-- Add special treatement for CARBON CYCLE
[1546]	279	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
[1780]	280	ATM_Carbon_Update
	281	fi
[1537]	282
	283
[1538]	284	##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
	285	## COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
	286	if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] && [ ${year} -ge 1979 ]) ; then
[2605]	287	LMDZ_COSP_daily=.TRUE.
[1538]	288	fi
[1537]	289
[2600]	290	## Modifiy
[2605]	291	IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled ${ok_mensuel}
	292
	293	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled ${ok_journe}
	294
[2600]	295	if [ X${OutLevel} = Xlow ] \|\| [ X${OutLevel} = Xmedium ] ; then
	296	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 2
	297	else
	298	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 5
	299	fi
	300
[2605]	301	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled ${ok_hf}
	302
[2600]	303	if [ X${OutLevel} = Xlow ] ; then
	304	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 5
	305	elif [ X${OutLevel} = Xmedium ] ; then
	306	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 6
	307	elif [ X${OutLevel} = Xhigh ] ; then
	308	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 7
[2582]	309	fi
[2600]	310
[2755]	311	IGCM_comp_modifyXmlFile nonblocker file_def_histhf3h_lmdz.xml histhf3h enabled ${ok_hf3h}
	312	IGCM_comp_modifyXmlFile nonblocker file_def_histhf3hm_lmdz.xml histhf3hm enabled ${ok_hf3hm}
[2605]	313
	314	IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled ${ok_stn}
[2600]	315
[2605]	316	IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled ${LMDZ_NMC_monthly}
	317	IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled ${LMDZ_NMC_daily}
	318	IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled ${LMDZ_NMC_hf}
[2600]	319
[2605]	320	IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled ${LMDZ_COSP_monthly}
	321	IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled ${LMDZ_COSP_daily}
	322	IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled ${LMDZ_COSP_hf}
[2332]	323
[3104]	324	# Activate the histstrataer output file only for configuration with interactive stratospheric aersols
	325	# done by setting the key word LMDZ_strataero=y in lmdz.card
	326	if [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
	327	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .TRUE.
	328	else
	329	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .FALSE.
	330	fi
[396]	331
[3104]	332
[911]	333	## run.def parameters
[2598]	334
	335
	336	##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
	337	if [ ${CumulPeriod} -eq 1 ] ; then
	338	IGCM_comp_modifyDefFile blocker run.def raz_date 1
	339	else
	340	IGCM_comp_modifyDefFile blocker run.def raz_date 0
	341	fi
	342
	343	##-- Calendar type for LMDZ and create_etat0_limit
	344	case ${config_UserChoices_CalendarType} in
	345	leap\|gregorian)
	346	IGCM_comp_modifyDefFile blocker run.def calend gregorian ;;
	347	noleap)
	348	IGCM_comp_modifyDefFile blocker run.def calend earth_365d ;;
	349	360d)
	350	IGCM_comp_modifyDefFile blocker run.def calend earth_360d ;;
	351	*)
	352	IGCM_comp_modifyDefFile blocker run.def calend earth_360d ;;
	353	esac
	354
[2582]	355	IGCM_comp_modifyDefFile blocker run.def dayref ${InitDay}
	356	IGCM_comp_modifyDefFile blocker run.def nday ${PeriodLengthInDays}
[396]	357
[1804]	358	# Set anneeref different for gcm and ce0l
	359	# Test if executable create_etat0_limit is present and lmdz.x is not present
	360	if [ -f create_etat0_limit* ] \|\| [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
	361	# for case ce0l : always take current year
[2333]	362	IGCM_comp_modifyDefFile blocker run.def anneeref ${year}
[2480]	363
	364	# Temporary, set use_filtre_fft=n because we now use dyn3d for ce0l version where fft is not implemented.
	365	# In more recent versions of LMDZ, this will not be needed.
	366	IGCM_comp_modifyDefFile force run.def use_filtre_fft n
[1804]	367	else
	368	# for case gcm : take first year of simulation
[2333]	369	IGCM_comp_modifyDefFile blocker run.def anneeref ${InitYear}
[1804]	370	fi
[1643]	371
[1650]	372	## Determine from the variable ListOfComponents in config.card coupling to external models
	373	## and set corresponding parameters in run.def
	374	echo ListOfComponents now running : ${config_ListOfComponents[*]}
	375
	376	if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
	377	echo "Activate ORCHIDEE, set VEGET=y in run.def"
[2333]	378	IGCM_comp_modifyDefFile blocker run.def VEGET y
[1650]	379	else
	380	echo "No ORCHIDEE, set VEGET=n in run.def"
[2333]	381	IGCM_comp_modifyDefFile blocker run.def VEGET n
[1650]	382	fi
	383
	384	if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
	385	echo "Activate coupling to ocean, set type_ocean=couple in run.def"
[2333]	386	IGCM_comp_modifyDefFile blocker run.def type_ocean couple
[1650]	387	else
	388	echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
[3935]	389	IGCM_comp_modifyDefFile nonblocker run.def type_ocean force
[1650]	390	fi
	391
	392	if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
	393	echo "Activate coupling to INCA, set type_trac=inca in run.def"
[2333]	394	IGCM_comp_modifyDefFile blocker run.def type_trac inca
[1650]	395	elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
	396	echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
[2333]	397	IGCM_comp_modifyDefFile blocker run.def type_trac repr
	398	IGCM_comp_modifyDefFile blocker run.def config_inca none
[1650]	399	else
	400	echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
[2333]	401	IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
	402	IGCM_comp_modifyDefFile blocker run.def config_inca none
[1650]	403	fi
	404
	405
[4020]	406	# run.def : Activate the call to phytrac
	407	if [ ! X${lmdz_UserChoices_iflag_phytrac} = X ]; then
	408	IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac ${lmdz_UserChoices_iflag_phytrac}
	409	else
	410	IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac 0
	411	fi
	412
	413	# physiq.def : Activate the call to phytrac
	414	if [ ! X${lmdz_UserChoices_ok_bug_cv_trac} = X ]; then
	415	IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac ${lmdz_UserChoices_ok_bug_cv_trac}
	416	else
	417	IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac n
	418	fi
	419
[2015]	420	# config.def : Activate direct radiative effect if ok_ade=y
	421	if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
[2333]	422	IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
[2015]	423	else
[2333]	424	IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
[2015]	425	fi
	426
	427	# config.def : Activate indirect radiative effect if ok_aie=y
	428	if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
[2333]	429	IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
[2015]	430	else
[2333]	431	IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
[2015]	432	fi
[1816]	433
[2015]	434	# config.def : Activate online aerosol coupled model if aerosol_couple=y
	435	if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
[2333]	436	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
[1686]	437	else
[2333]	438	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
[2015]	439	fi
[1686]	440
[4020]	441	# config.def : Activate online Ozone chemistry coupled model if chemistry_couple=y
	442	if [ ! X${lmdz_UserChoices_chemistry_couple} = X ]; then
	443	IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple ${lmdz_UserChoices_chemistry_couple}
	444	else
	445	IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple n
	446	fi
	447
[2015]	448	# config.def : Activate reading of ozone in climatology if read_climoz=2
	449	if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
[2333]	450	IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
[2015]	451	else
[2333]	452	IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0
[2015]	453	fi
	454
	455	# config.def : Choose aerosol use in radiative effect
	456	# type of coupled aerosol =1 (default) =2 => bc only =3 => pom only =4 => seasalt only
	457	# =5 => dust only =6 => all aerosol
	458	if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
[2333]	459	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
[2015]	460	else
[2333]	461	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
[2015]	462	fi
	463
	464	# config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
	465	if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
[2333]	466	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
[2015]	467	else
[2333]	468	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
[2015]	469	fi
	470
[2893]	471	# config.def : Activate COSP
	472	if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ]; then
	473	IGCM_comp_modifyDefFile nonblocker config.def ok_cosp ${lmdz_UserChoices_LMDZ_COSP_OK}
	474	else
	475	IGCM_comp_modifyDefFile nonblocker config.def ok_cosp n
	476	fi
	477
[2911]	478	# config.def : Modify parameter pmagic if it is set in lmdz.card
	479	if [ ! X${lmdz_UserChoices_pmagic} = X ]; then
	480	IGCM_comp_modifyDefFile nonblocker config.def pmagic ${lmdz_UserChoices_pmagic}
	481	else
	482	# Take default value set in config.def
	483	IGCM_comp_modifyDefFile nonblocker config.def pmagic DEFAULT
	484	fi
[2893]	485
[3868]	486	# physiq.def : Modify parameter tau_gl if it is set in lmdz.card
	487	if [ ! X${lmdz_UserChoices_tau_gl} = X ]; then
	488	IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl ${lmdz_UserChoices_tau_gl}
	489	else
	490	# Take default value set in physiq.def
[4038]	491	IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl DEFAULT
[3868]	492	fi
	493
	494
[1690]	495	# guide.def : Activate nudging if ok_guide=y set in lmdz.card
[1643]	496	if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
[2333]	497	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide ${lmdz_UserChoices_ok_guide}
[1690]	498	else
[2333]	499	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
[1643]	500	fi
	501
[3868]	502
[902]	503	## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
[1172]	504	ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
[1688]	505	if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
[396]	506	awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
	507	IGCM_sys_Mv gcm.def.tmp gcm.def
	508	echo
	509	IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
	510	echo
	511	cat gcm.def
	512	ByPass_hgardfou_teta=n
[902]	513	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
[396]	514	fi
	515
[902]	516	## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
[1172]	517	ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
[1688]	518	if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
[396]	519	sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
	520	IGCM_sys_Mv gcm.def.tmp gcm.def
	521	echo
	522	IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
	523	echo
	524	cat gcm.def
	525	ByPass_hgardfou_mats=n
[902]	526	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
[396]	527	fi
	528
[2904]	529	# Add include of LMDZ context in iodef.xml
[4108]	530	# In iodef.xml add on the next line after "COMPONENT CONTEXT"
[2904]	531	echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
[4108]	532	# Add inclusion of file context_input_lmdz.xml if this file exists
	533	if [ -f context_input_lmdz.xml ] ; then
	534	echo '<context id="LMDZ" src="./context_input_lmdz.xml"/>' >> add.tmp
	535	fi
	536	# Include xml files for output configuration if running with workflow CMIP6
[3505]	537	if [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] ; then
	538	echo '<context id="LMDZ" src="./ping_lmdz.xml"/>' >> add.tmp
	539	echo '<context id="LMDZ" src="./dr2xml_lmdz.xml"/>' >> add.tmp
	540	fi
[2904]	541	cp iodef.xml iodef.xml.tmp
	542	sed -e "/COMPONENT CONTEXT/r add.tmp" iodef.xml.tmp > iodef.xml
	543	rm iodef.xml.tmp add.tmp
[2476]	544
[2904]	545	#Long Name as global attribute (if LongName is not empty)
	546	if [ ! "X${config_UserChoices_LongName}" = "X" ] ; then
	547	listfile=$(ls file_def*lmdz.xml)
	548	echo "<variable id=\"LongName\" type=\"string\">${config_UserChoices_LongName}</variable>" > add.tmp
	549	for file in ${listfile}
	550	do
	551	cp ${file} ${file}.tmp
	552	sed -e "/<file id/r add.tmp" \
	553	${file}.tmp > ${file}
	554	rm ${file}.tmp
	555	done
	556	rm add.tmp
[2332]	557	fi
[2904]	558
[396]	559	IGCM_debug_PopStack "ATM_Update"
	560	}
	561
	562	#-----------------------------------
	563	function ATM_Finalize
	564	{
	565	IGCM_debug_PushStack "ATM_Finalize"
	566
[1537]	567	# Add special treatement for CARBON CYCLE
[1546]	568	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
[1780]	569	ATM_Carbon_Finalize
	570	fi
[1537]	571
[1780]	572	echo FINALIZE ATM !
[1537]	573
[1780]	574	IGCM_debug_PopStack "ATM_Finalize"
	575	}
[1537]	576
	577
	578
[1780]	579	function ATM_Carbon_Update
	580	{
	581	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
[1537]	582
[1780]	583	IGCM_debug_PushStack "ATM_Carbon_Update"
	584
	585	typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
	586	typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
	587	typeset PathCO2log
	588	typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
	589
	590	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
	591	##--Initialization of fluxes to an undefined value at the first run
	592	UndefinedValueCo2=-9999
	593	InitPeriodCo2=0
	594	InitDateBeginCo2=${UndefinedValueCo2}
	595	InitYearCo2=$(( ${year} - 1 ))
	596	InitDateEndCo2=${InitYearCo2}1231
	597	fCO2_ff=${UndefinedValueCo2}
	598	CO2SBG=${UndefinedValueCo2}
	599	CO2LU=${UndefinedValueCo2}
	600	CO2MBG=${UndefinedValueCo2}
	601	CO2_ppm_prec=${UndefinedValueCo2}
	602	# Get the initial value of atmosp. pco2
	603	CO2_ppm=${lmdz_UserChoices_co2_init}
	604
	605	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
	606	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
	607
[1537]	608	# Save CO2 values in ExeCpuLog variable contents 5 fields
[1780]	609	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
[1537]	610	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
[1780]	611	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	612
	613	# Get the path where the log file co2.log is
	614	PathCO2log=${SUBMIT_DIR}
	615	# Get Previous line in co2.log
	616	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
	617
	618	else
	619
	620	# NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
	621	# !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
	622	#SubmitRestartPath=
	623	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
	624	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
	625	PathCO2log=${config_ATM_SubmitRestartPath}
	626	Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
	627	PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
	628
	629	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
	630	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
	631
	632	# Save Last Line of control in new co2.log file
	633	InitPeriodCo2=0
	634	InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $2}' )
	635	InitDateEndCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $3}' )
	636	fCO2_ff=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $6}' )
	637	CO2SBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $8}' )
	638	CO2LU=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $9}' )
	639	CO2MBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $7}' )
	640	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $5}' )
	641	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	642
	643	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
	644	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
	645	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	646	else
	647	# Get restart line in co2.log
	648	PathCO2log=${SUBMIT_DIR}
	649	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
	650	# Get the value of atmosp. pco2 in co2.log
	651	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	652	fi
	653
[1537]	654	fi
[1780]	655
	656	if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
[2841]	657	# Modify co2_ppm in config.def only for historical run
	658	# If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
	659	IGCM_comp_modifyDefFile force config.def co2_ppm ${CO2_ppm}
[1780]	660	fi
	661	IGCM_debug_PopStack "ATM_Carbon_Update"
	662	}
[1537]	663
[396]	664
[1780]	665	function ATM_Carbon_Finalize
	666	{
	667	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
	668
	669	IGCM_debug_PushStack "ATM_Carbon_Finalize"
	670
	671	typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
	672
	673	# Fossil fuel emission
	674	if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
	675	# For Control, no fossil fuel emission :
	676	fCO2_ff=0
	677	echo "Fossil Fuel for control run :" ${fCO2_ff}
	678	else
	679	# For historical, get the fossile fuel file :
	680	fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
	681	echo "Fossil Fuel for historical run :" ${fCO2_ff}
	682	fi
	683
	684	# Get the value of ocean carbon flux
	685	CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
	686	CO2MBG=$( echo ${CO2MBG} \| sed -e "s/ *//" )
	687	echo "Ocean carbon flux :" ${CO2MBG}
	688
	689	# Get the value of land fluxes
	690	set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
	691	CO2SRF=$( echo ${CO2SBG_3V[0]} \| sed -e "s/ *//" )
	692	CO2LU=$( echo ${CO2SBG_3V[1]} \| sed -e "s/ *//" )
	693	CO2SBG=$( echo ${CO2SBG_3V[2]} \| sed -e "s/ *//" )
	694	echo "Land carbon flux (NEP) :" ${CO2SRF}
	695	echo "LU flux (FLUC) :" ${CO2LU}
	696	echo "Total Land carbon flux (NBP) :" ${CO2SBG}
	697
	698	# Previous CO2
	699	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
	700	echo "Previous CO2 :" ${CO2_ppm_prec}
	701
	702	# Formula
	703	CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" \| bc -l )
	704	echo "New CO2 :" ${CO2_ppm}
	705
	706	# Save CO2 values in ExeCpuLog variable contents 5 fields
	707	echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
	708	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
	709	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	710
	711	IGCM_debug_PopStack "ATM_Carbon_Finalize"
[396]	712	}

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