#!/bin/ksh
#-----------------------------------------------------------------
function ATM_Initialize
{
    IGCM_debug_PushStack "ATM_Initialize"

    # Read the resolution from the variables ResolAtm set in config.card UserChoices section or from .resol file
    if [ X$ResolAtm != X ] ; then
	# ResolAtm is set in config.card
	RESOL_ATM_3D=${ResolAtm}
    elif [ -f ${SUBMIT_DIR}/../.resol ] ; then
	# ResolAtm was not set in config.card, try to read .resol file
	eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol) || RESOL_ATM_3D=96x95x39
    else
	IGCM_debug_Exit "ResolAtm is not set in config.card and the .resol file does not exist."
	IGCM_debug_Verif_Exit
    fi
    
    IGCM_debug_Print 1 "The atomsopheric resolution is ${RESOL_ATM_3D} " 

    RESOL_ATM_Z=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $3}' )
    RESOL_ATM_X=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $1}' )
    RESOL_ATM_Y=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $2}' )
    RESOL_ATM_XY="${RESOL_ATM_X}x${RESOL_ATM_Y}"
    RESOL_ATM=LMD${RESOL_ATM_X}${RESOL_ATM_Y}

    ##- LMDZ physics version
    ##  Read LMDZ_Physics option in lmdz.card, if not present take default value AP (old physics) 
    if [ ! X${lmdz_UserChoices_LMDZ_Physics} = X ] ; then
	LMDZ_Physics=${lmdz_UserChoices_LMDZ_Physics}
    else
	LMDZ_Physics=AP
    fi
    echo LMDZ physics version : ${LMDZ_Physics}

    ##- Create_etat0_limit version
    ##  Define variable CREATE only if it is set in lmdz.card section UserChoices.
    ##  This variable is only used in lmdz.card to choose input files.
    if [ ! X${lmdz_UserChoices_CREATE} = X ] ; then
	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices CREATE
	CREATE=${lmdz_UserChoices_CREATE}
	echo create_etat0_limit version : ${CREATE}
    fi


    ## - LMDZ choice of config.def file
    ##   ConfType must be set in lmdz.card
    ConfType=${lmdz_UserChoices_ConfType}

    IGCM_debug_PopStack "ATM_Initialize"
}

#-----------------------------------------------------------------
function ATM_Update
{
    IGCM_debug_PushStack "ATM_Update"

    ##-- GHG forcing :
    ##   If forcing file exist in run directory, read values for the current year 
    ##   and set in config.def. If not use the default value set in config.def

    # Read value for solaire from file SOLARANDVOLCANOES.txt. If file not existing, take DEFAULT value from file. 
    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)"
    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"
    if [ -f SOLARANDVOLCANOES.txt ] ; then
	value=`grep Annee_${year} SOLARANDVOLCANOES.txt | awk -F= '{print $2}'`
	if [ X"${value}" = X ] ; then
	    # The grep returned empty variable, stop execution
	    IGCM_debug_Exit "The file SOLARANDVOLCANOES.txt do not contain the current year."
	    IGCM_debug_Verif_Exit
	fi
    else
	value=DEFAULT
    fi
    IGCM_comp_modifyDefFile nonblocker config.def solaire $value

    # Read value for eccentricity from file Eccentricity.txt. If file not existing, take DEFAULT value from file.
    if [ -f Eccentricity.txt ] ; then
	value=`grep Annee_${year} Eccentricity.txt | awk -F= '{print $2}'`
	if [ X"${value}" = X ] ; then
	    # The grep returned empty variable, stop execution
	    IGCM_debug_Exit "The file Eccentricity.txt do not contain the current year."
	    IGCM_debug_Verif_Exit
	fi
    else
	value=DEFAULT
    fi
    IGCM_comp_modifyDefFile nonblocker config.def R_ecc $value

    # Read value for obliquity from file Obliquity.txt. If file not existing, take DEFAULT value from file.
    if [ -f Obliquity.txt ] ; then
	value=`grep Annee_${year} Obliquity.txt | awk -F= '{print $2}'`
	if [ X"${value}" = X ] ; then
	    # The grep returned empty variable, stop execution
	    IGCM_debug_Exit "The file Obliquity.txt do not contain the current year."
	    IGCM_debug_Verif_Exit
	fi
    else
	value=DEFAULT
    fi
    IGCM_comp_modifyDefFile nonblocker config.def R_incl $value

    # Read value for perihelie from file Perihelie.txt. If file not existing, take DEFAULT value from file.
    if [ -f Perihelie.txt ] ; then
	value=`grep Annee_${year} Perihelie.txt | awk -F= '{print $2}'`
	if [ X"${value}" = X ] ; then
	    # The grep returned empty variable, stop execution
	    IGCM_debug_Exit "The file Perihelie.txt do not contain the current year."
	    IGCM_debug_Verif_Exit
	fi
    else
	value=DEFAULT
    fi
    IGCM_comp_modifyDefFile nonblocker config.def R_peri $value

    # Read value for co2_ppm from file CO2.txt. If file not existing, take DEFAULT value from file. 
    # Calculate co2_ppm_per as co2_ppm*4.
    if [ -f CO2.txt ] ; then
       	value=`grep Annee_${year} CO2.txt | awk -F= '{print $2}'`
	if [ X"${value}" = X ] ; then
	    # The grep returned empty variable, stop execution
	    IGCM_debug_Exit "The file CO2.txt do not contain the current year."
	    IGCM_debug_Verif_Exit
	fi
	value4=`grep Annee_${year} CO2.txt | awk -F= '{print $2 * 4}'`
    else
	value=DEFAULT
	value4=DEFAULT
    fi
    IGCM_comp_modifyDefFile nonblocker config.def co2_ppm $value
    IGCM_comp_modifyDefFile nonblocker config.def co2_ppm_per $value4


    # Read value for CH4_ppb from file CH4.txt. If file not existing, take DEFAULT value from file. 
    if [ -f CH4.txt ] ; then
	value=`grep Annee_${year} CH4.txt | awk -F= '{print $2}'`
	if [ X"${value}" = X ] ; then
	    # The grep returned empty variable, stop execution
	    IGCM_debug_Exit "The file CH4.txt do not contain the current year."
	    IGCM_debug_Verif_Exit
	fi
    else
	value=DEFAULT
    fi
    IGCM_comp_modifyDefFile nonblocker config.def CH4_ppb $value


    # Read value for N2O_ppb from file N2O.txt. If file not existing, take DEFAULT value from file. 
    if [ -f N2O.txt ] ; then
	value=`grep Annee_${year} N2O.txt | awk -F= '{print $2}'`
	if [ X"${value}" = X ] ; then
	    # The grep returned empty variable, stop execution
	    IGCM_debug_Exit "The file N2O.txt do not contain the current year."
	    IGCM_debug_Verif_Exit
	fi
    else
	value=DEFAULT
    fi
    IGCM_comp_modifyDefFile nonblocker config.def N2O_ppb $value

    # Read value for CFC11_ppt from file CFC11.txt. If file not existing, take DEFAULT value from file. 
    if [ -f CFC11.txt ] ; then
	value=`grep Annee_${year} CFC11.txt | awk -F= '{print $2}'`
	if [ X"${value}" = X ] ; then
	    # The grep returned empty variable, stop execution
	    IGCM_debug_Exit "The file CFC11.txt do not contain the current year."
	    IGCM_debug_Verif_Exit
	fi
    else
	value=DEFAULT
    fi
    IGCM_comp_modifyDefFile nonblocker config.def CFC11_ppt $value


    # Read value for CFC12_ppt from file CFC12.txt. If file not existing, take DEFAULT value from file. 
    if [ -f CFC12.txt ] ; then
	value=`grep Annee_${year} CFC12.txt | awk -F= '{print $2}'`
	if [ X"${value}" = X ] ; then
	    # The grep returned empty variable, stop execution
	    IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
	    IGCM_debug_Verif_Exit
	fi
    else
	value=DEFAULT
    fi
    IGCM_comp_modifyDefFile nonblocker config.def CFC12_ppt $value


    ## Coupling Time Step : Take value of FreqCoupling set in oasis.card or if it is not set, take default value 86400
    LMDZ_t_coupl=${oasis_UserChoices_FreqCoupling:-86400}
    IGCM_debug_Print 3 "LMDZ_t_coupl "   ${LMDZ_t_coupl}
    IGCM_comp_modifyDefFile nonblocker config.def t_coupl   ${LMDZ_t_coupl} 



    ## Activate diagnostic output files and set output_level for each file

    # histmth
    if [ X${lmdz_UserChoices_output_level_histmth} = X ] || [ X${lmdz_UserChoices_output_level_histmth} = XNONE ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled FALSE
	IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth output_level 0
    else
	IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled TRUE
	IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth output_level ${lmdz_UserChoices_output_level_histmth} 
    fi

    # histday
    if [ X${lmdz_UserChoices_output_level_histday} = X ] || [ X${lmdz_UserChoices_output_level_histday} = XNONE ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled FALSE
	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 0
    else
	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled TRUE
	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level ${lmdz_UserChoices_output_level_histday} 
    fi

    # histhf
    if [ X${lmdz_UserChoices_output_level_histhf} = X ] || [ X${lmdz_UserChoices_output_level_histhf} = XNONE ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled FALSE
	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 0
    else
	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled TRUE
	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level ${lmdz_UserChoices_output_level_histhf} 
    fi

    # histmthNMC
    if [ X${lmdz_UserChoices_output_level_histmthNMC} = X ] || [ X${lmdz_UserChoices_output_level_histmthNMC} = XNONE ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled FALSE
	IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC output_level 0
    else
	IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled TRUE
	IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC output_level ${lmdz_UserChoices_output_level_histmthNMC} 
    fi

    # histdayNMC
    if [ X${lmdz_UserChoices_output_level_histdayNMC} = X ] || [ X${lmdz_UserChoices_output_level_histdayNMC} = XNONE ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled FALSE
	IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC output_level 0
    else
	IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled TRUE
	IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC output_level ${lmdz_UserChoices_output_level_histdayNMC} 
    fi

    # histhfNMC
    if [ X${lmdz_UserChoices_output_level_histhfNMC} = X ] || [ X${lmdz_UserChoices_output_level_histhfNMC} = XNONE ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled FALSE
	IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC output_level 0
    else
	IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled TRUE
	IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC output_level ${lmdz_UserChoices_output_level_histhfNMC} 
    fi

    # histstrataer
    if [ X${lmdz_UserChoices_output_level_histstrataer} = X ] || [ X${lmdz_UserChoices_output_level_histstrataer} = XNONE ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled FALSE
	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer output_level 0
    else
	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled TRUE
	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer output_level ${lmdz_UserChoices_output_level_histstrataer} 
    fi

    # histdaystrataer
    if [ X${lmdz_UserChoices_output_level_histdaystrataer} = X ] || [ X${lmdz_UserChoices_output_level_histdaystrataer} = XNONE ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histdaystrataer_lmdz.xml histdaystrataer enabled FALSE
	IGCM_comp_modifyXmlFile nonblocker file_def_histdaystrataer_lmdz.xml histdaystrataer output_level 0
    else
	IGCM_comp_modifyXmlFile nonblocker file_def_histdaystrataer_lmdz.xml histdaystrataer enabled TRUE
	IGCM_comp_modifyXmlFile nonblocker file_def_histdaystrataer_lmdz.xml histdaystrataer output_level ${lmdz_UserChoices_output_level_histstrataer}
    fi

    # histstn
    if [ X${lmdz_UserChoices_output_level_histstn} = X ] || [ X${lmdz_UserChoices_output_level_histstn} = XNONE ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled FALSE
	IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn output_level 0
    else
	IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled TRUE
	IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn output_level ${lmdz_UserChoices_output_level_histstn} 
    fi


    # histmthCOSP
    if [ X${lmdz_UserChoices_output_level_histmthCOSP} = X ] || [ X${lmdz_UserChoices_output_level_histmthCOSP} = XNONE ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled FALSE
	IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP output_level 0
    else
	IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled TRUE
	IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP output_level ${lmdz_UserChoices_output_level_histmthCOSP} 
    fi


    # histdayCOSP
    if [ X${lmdz_UserChoices_output_level_histdayCOSP} = X ] || [ X${lmdz_UserChoices_output_level_histdayCOSP} = XNONE ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled FALSE
	IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP output_level 0
    else
	IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled TRUE
	IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP output_level ${lmdz_UserChoices_output_level_histdayCOSP} 
    fi


    # histhfCOSP
    if [ X${lmdz_UserChoices_output_level_histhfCOSP} = X ] || [ X${lmdz_UserChoices_output_level_histhfCOSP} = XNONE ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled FALSE
	IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP output_level 0
    else
	IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled TRUE
	IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP output_level ${lmdz_UserChoices_output_level_histhfCOSP} 
    fi


    ## run.def parameters


    ##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
    if [ ${CumulPeriod} -eq 1 ] ; then
	IGCM_comp_modifyDefFile blocker run.def raz_date  1
    else
	IGCM_comp_modifyDefFile blocker run.def raz_date  0
    fi

    ##-- Calendar type for LMDZ and create_etat0_limit
    case ${config_UserChoices_CalendarType} in
        leap|gregorian)
	    IGCM_comp_modifyDefFile blocker run.def calend  gregorian ;;
        noleap)
	    IGCM_comp_modifyDefFile blocker run.def calend  earth_365d ;;
        360d)
	    IGCM_comp_modifyDefFile blocker run.def calend  earth_360d ;;
        *)
	    IGCM_comp_modifyDefFile blocker run.def calend  earth_360d ;;
    esac

    IGCM_comp_modifyDefFile blocker run.def dayref    ${InitDay}
    IGCM_comp_modifyDefFile blocker run.def nday      ${PeriodLengthInDays}

    # Set anneeref different for gcm and ce0l
    # Test if executable create_etat0_limit is present and lmdz.x is not present
    if [ -f create_etat0_limit* ] || [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
	# for case ce0l : always take current year
	IGCM_comp_modifyDefFile blocker run.def anneeref ${year}

        # Temporary, set use_filtre_fft=n because we now use dyn3d for ce0l version where fft is not implemented. 
        # In more recent versions of LMDZ, this will not be needed. 
	IGCM_comp_modifyDefFile force   run.def use_filtre_fft n
    else
	# for case gcm : take first year of simulation
	IGCM_comp_modifyDefFile blocker run.def anneeref ${InitYear}
    fi

    ## Determine from the variable ListOfComponents in config.card coupling to external models 
    ## and set corresponding parameters in run.def
    echo ListOfComponents now running : ${config_ListOfComponents[*]}

    if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
	echo "Activate ORCHIDEE, set VEGET=y in run.def"
	IGCM_comp_modifyDefFile blocker run.def VEGET y
    else
	echo "No ORCHIDEE, set VEGET=n in run.def"
	IGCM_comp_modifyDefFile blocker run.def VEGET n
    fi

    if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
	echo "Activate coupling to ocean, set type_ocean=couple in run.def"
	IGCM_comp_modifyDefFile blocker run.def type_ocean couple
    else
	echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
	IGCM_comp_modifyDefFile nonblocker run.def type_ocean force
    fi

    if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
	echo "Activate coupling to INCA, set type_trac=inca in run.def"
	IGCM_comp_modifyDefFile blocker run.def type_trac inca
	IGCM_comp_modifyDefFile blocker run.def iflag_phytrac 1  
    elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
	echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
	IGCM_comp_modifyDefFile blocker run.def type_trac repr
        IGCM_comp_modifyDefFile blocker run.def config_inca none
	IGCM_comp_modifyDefFile blocker run.def iflag_phytrac 1  
    elif [ X${config_UserChoices_ConfigType} = XESMCO2 ] ; then 
	echo "ESM config, set type_trac=co2i in run.def"
	IGCM_comp_modifyDefFile blocker run.def type_trac co2i
        IGCM_comp_modifyDefFile blocker run.def config_inca none
	IGCM_comp_modifyDefFile blocker run.def iflag_phytrac 1  
    elif [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
        echo "No coupling to chemistry model but it is a LMDZ STRATAER configuration, set type_trac=coag in run.def"
        IGCM_comp_modifyDefFile blocker run.def type_trac coag
        IGCM_comp_modifyDefFile blocker run.def config_inca none
	IGCM_comp_modifyDefFile blocker run.def iflag_phytrac 1  
    else
	echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
	IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
        IGCM_comp_modifyDefFile blocker run.def config_inca none
	IGCM_comp_modifyDefFile blocker run.def iflag_phytrac 0
    fi

    # run.def : Activate the new calving 
    if [ ! X${lmdz_UserChoices_cpl_old_calving} = X ]; then 
	IGCM_comp_modifyDefFile nonblocker run.def cpl_old_calving ${lmdz_UserChoices_cpl_old_calving}
    else
	IGCM_comp_modifyDefFile nonblocker run.def cpl_old_calving y
    fi 

    # physiq.def : Activate the call to phytrac 
    if [ ! X${lmdz_UserChoices_ok_bug_cv_trac} = X ]; then 
	IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac  ${lmdz_UserChoices_ok_bug_cv_trac}
    else
	IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac  n
    fi 

    # config.def : Activate aerosol strato 
    if [ ! X${lmdz_UserChoices_flag_aerosol_strat} = X ]; then 
	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol_strat ${lmdz_UserChoices_flag_aerosol_strat}
    else
	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol_strat DEFAULT
    fi 

    # config.def : Activate direct radiative effect if ok_ade=y
    if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then 
	IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
    else
	IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
    fi 

    # config.def : Activate indirect radiative effect if ok_aie=y
    if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then 
	IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
    else
	IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
    fi 

    # config.def : Activate online aerosol coupled model if aerosol_couple=y
    if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then 
	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
    else
	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
    fi 

    # config.def : Activate online Ozone chemistry coupled model if chemistry_couple=y
    if [ ! X${lmdz_UserChoices_chemistry_couple} = X ]; then 
	IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple ${lmdz_UserChoices_chemistry_couple}
    else
	IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple n
    fi 

    # config.def : Activate reading of ozone in climatology if read_climoz=2
    if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then 
	IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
    else
	IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0	
    fi 

    # config.def : Choose aerosol use in radiative effect 
    #  type of coupled aerosol =1 (default) =2 => bc  only =3 => pom only =4 => seasalt only 
    # =5 => dust only =6 => all aerosol    
    if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then 
	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
    else
	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
    fi 

    # config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
    if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then 
	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
    else
	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n	
    fi 

    # config.def : Activate COSP
    if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ]; then 
	IGCM_comp_modifyDefFile nonblocker config.def ok_cosp ${lmdz_UserChoices_LMDZ_COSP_OK}
    else
	IGCM_comp_modifyDefFile nonblocker config.def ok_cosp n	
    fi 

    # config.def : Modify parameter pmagic if it is set in lmdz.card
    if [ ! X${lmdz_UserChoices_pmagic} = X ]; then 
	IGCM_comp_modifyDefFile nonblocker config.def pmagic ${lmdz_UserChoices_pmagic}
    else
	# Take default value set in config.def
	IGCM_comp_modifyDefFile nonblocker config.def pmagic DEFAULT
    fi 

    if [ X${config_UserChoices_ConfigType} = XESMCO2 ] ; then
	# Set carbon cycle parameters according to parmeters in lmdz.card 
	IGCM_comp_modifyDefFile blocker config.def level_coupling_esm 2 
	IGCM_comp_modifyDefFile blocker config.def carbon_cycle_cpl ${lmdz_UserChoices_carbon_cycle_cpl} 
	IGCM_comp_modifyDefFile blocker config.def carbon_cycle_tr ${lmdz_UserChoices_carbon_cycle_tr}
	IGCM_comp_modifyDefFile blocker config.def carbon_cycle_rad ${lmdz_UserChoices_carbon_cycle_rad}
    else
	# Take default value set in config.def
	IGCM_comp_modifyDefFile nonblocker config.def level_coupling_esm DEFAULT
	IGCM_comp_modifyDefFile nonblocker config.def carbon_cycle_cpl DEFAULT 
	IGCM_comp_modifyDefFile nonblocker config.def carbon_cycle_tr DEFAULT
	IGCM_comp_modifyDefFile nonblocker config.def carbon_cycle_rad DEFAULT
    fi

    # config.def : Modify parameter ok_volcan if ok_volcan=y or LMDZ_strataero=y in lmdz.card
    # Note: ok_volcan is a flag allowing a double-call with/without natural forcing (instead of with/without anthro forcing).
    if [ ! X${lmdz_UserChoices_ok_volcan} = X ] || [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
	IGCM_comp_modifyDefFile nonblocker config.def ok_volcan ${lmdz_UserChoices_ok_volcan}
    else
	# Take default value set in config.def
	IGCM_comp_modifyDefFile nonblocker config.def ok_volcan DEFAULT
    fi

    # physiq.def : Modify parameter tau_gl if it is set in lmdz.card
    if [ ! X${lmdz_UserChoices_tau_gl} = X ]; then 
	IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl ${lmdz_UserChoices_tau_gl}
    else
	# Take default value set in physiq.def
	IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl DEFAULT
    fi
   

    # guide.def : Activate nudging if ok_guide=y set in lmdz.card
    if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide  ${lmdz_UserChoices_ok_guide}
    else
	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
    fi


    ## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
    ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
    if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
	awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
	IGCM_sys_Mv gcm.def.tmp gcm.def
	echo
	IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
	echo
	cat gcm.def
	ByPass_hgardfou_teta=n
	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
    fi

    ## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
    ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
    if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
	sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
        IGCM_sys_Mv gcm.def.tmp gcm.def
        echo
        IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
        echo
        cat gcm.def
        ByPass_hgardfou_mats=n
        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
    fi

    # Add include of LMDZ context in iodef.xml
    # In iodef.xml add on the next line after "COMPONENT CONTEXT"
    echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
    # Add inclusion of file context_input_lmdz.xml if this file exists
    if [ -f context_input_lmdz.xml ] ; then
        echo '<context id="LMDZ" src="./context_input_lmdz.xml"/>' >> add.tmp
    fi
    # Include xml files for output configuration if running with workflow CMIP6
    if [ X"$( echo ${config_UserChoices_ExpType} | grep CMIP6 )" != "X" ] ; then
	echo '<context id="LMDZ" src="./ping_lmdz.xml"/>' >> add.tmp
	echo '<context id="LMDZ" src="./dr2xml_lmdz.xml"/>' >> add.tmp
    fi
    cp iodef.xml iodef.xml.tmp
    sed -e "/COMPONENT CONTEXT/r add.tmp" iodef.xml.tmp > iodef.xml
    rm iodef.xml.tmp add.tmp

    #Long Name as global attribute (if LongName is not empty)
    if [ ! "X${config_UserChoices_LongName}" = "X" ] ; then
	listfile=$(ls file_def*lmdz.xml)
	echo "<variable id=\"LongName\" type=\"string\">${config_UserChoices_LongName}</variable>" > add.tmp
	for file in ${listfile}
	do
	    cp ${file} ${file}.tmp
	    sed -e "/<file id/r add.tmp" \
		${file}.tmp > ${file}
	    rm ${file}.tmp 
	done
	rm add.tmp
    fi

    # Compression level (if CompressionLevel is not empty)
    if [ ! "X${config_UserChoices_CompressionLevel}" = "X" ] ; then
    echo "NetCDF output files compression level is " ${config_UserChoices_CompressionLevel}
    listfile=$(ls file_def*lmdz.xml)
    for file in ${listfile} ; do
        sed -i -e "s/\(compression_level=\"\)[^\"]*\(\"\)/\1${config_UserChoices_CompressionLevel}\2/" ${file}
    done
    fi

            
    IGCM_debug_PopStack "ATM_Update"
}

#-----------------------------------
function ATM_Finalize
{
    IGCM_debug_PushStack "ATM_Finalize"

    IGCM_debug_Print 1 "FINALIZE ATM !"

    IGCM_debug_PopStack "ATM_Finalize"
}