#!/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}

    ##- LMDZ output level, to be set in lmdz.card
    if [ X${lmdz_UserChoices_OutLevel} = X ] ; then
	# OutLevel is not set. Take default value low.
	OutLevel=low
    else
	OutLevel=${lmdz_UserChoices_OutLevel}
    fi

    ##-- Output frequency purpose ....
    ##--  Initialisation  ....
    ok_mensuel=.FALSE.
    ok_journe=.FALSE.
    ok_hf=.FALSE.
    ok_hf3h=.FALSE.
    ok_hf3hm=.FALSE.
    ok_stn=.FALSE.


    case ${config_UserChoices_PeriodLength} in
	1Y|1y|1M|1m) ok_mensuel=.TRUE. ;;
	5D|5d|1D|1d) ok_journe=.TRUE. ;;
    esac

    for frequency in ${config_ATM_WriteFrequency} ; do
	case ${frequency} in
	    1M|1m) ok_mensuel=.TRUE. ;;
	esac
	case ${frequency} in
	    5D|5d|1D|1d) ok_journe=.TRUE. ;;
	esac
	case ${frequency} in
	    HF|hf) ok_hf=.TRUE. ;;
	esac
	case ${frequency} in 
	    HF3h|hf3h) ok_hf3h=.TRUE. ;;
	esac
	case ${frequency} in 
	    HF3hm|hf3hm) ok_hf3hm=.TRUE. ;;
	esac
	case ${frequency} in
	    STN|stn) ok_stn=.TRUE. ;;
	esac
    done


##  Read LMDZ_COSP_OK in lmdz.card
    if [ X${lmdz_UserChoices_LMDZ_COSP_OK} = Xy ] ; then
	##  LMDZ_COSP_OK=y, now read all other COSP variables
	##  Read LMDZ_COSP_monthly in lmdz.card
	if [ X${lmdz_UserChoices_LMDZ_COSP_monthly} = Xy ] ; then
	    LMDZ_COSP_monthly=.TRUE.
	else
	    LMDZ_COSP_monthly=.FALSE.
	fi
        ##  Read LMDZ_COSP_daily in lmdz.card
	if [ X${lmdz_UserChoices_LMDZ_COSP_daily} = Xy ] ; then
	    LMDZ_COSP_daily=.TRUE.
	else
	    LMDZ_COSP_daily=.FALSE.
	fi
        ##  Read LMDZ_COSP_hf in lmdz.card
	if [ X${lmdz_UserChoices_LMDZ_COSP_hf} = Xy ] ; then
	    LMDZ_COSP_hf=.TRUE.
	else
	    LMDZ_COSP_hf=.FALSE.
	fi
    else
	# LMDZ_COSP_OK=n : All cosp output are deactivated
	LMDZ_COSP_monthly=.FALSE.
	LMDZ_COSP_daily=.FALSE.
	LMDZ_COSP_hf=.FALSE.
    fi	

    ##  Read LMDZ_NMC_monthly in lmdz.card
    if [ X${lmdz_UserChoices_LMDZ_NMC_monthly} = Xy ] ; then
	LMDZ_NMC_monthly=.TRUE.
    else
	LMDZ_NMC_monthly=.FALSE.
    fi
    
    ## Read LMDZ_NMC_daily in lmdz.card
    if [ X${lmdz_UserChoices_LMDZ_NMC_daily} = Xy ] ; then
	LMDZ_NMC_daily=.TRUE.
    else
	LMDZ_NMC_daily=.FALSE.
    fi
    
    ## Read LMDZ_NMC_hf in lmdz.card
    if [ X${lmdz_UserChoices_LMDZ_NMC_hf} = Xy ] ; then
	LMDZ_NMC_hf=.TRUE.
    else
	LMDZ_NMC_hf=.FALSE.
    fi

    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} 

    ##-- Add special treatement for CARBON CYCLE
    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
	ATM_Carbon_Update
    fi


    ##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate 
    ##   COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
    if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] &&  [ ${year} -ge 1979 ]) ; then
	LMDZ_COSP_daily=.TRUE.
    fi

    ## Modifiy 
    IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled ${ok_mensuel}
    
    IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled ${ok_journe}
    
    if [ X${OutLevel} = Xlow ] || [ X${OutLevel} = Xmedium ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 2
    else
	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 5
    fi
    
    IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled ${ok_hf}
    
    if [ X${OutLevel} = Xlow ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 5
    elif [ X${OutLevel} = Xmedium ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 6
    elif [ X${OutLevel} = Xhigh ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 7
    fi
    	
    IGCM_comp_modifyXmlFile nonblocker file_def_histhf3h_lmdz.xml histhf3h enabled ${ok_hf3h}
    IGCM_comp_modifyXmlFile nonblocker file_def_histhf3hm_lmdz.xml histhf3hm enabled ${ok_hf3hm}

    IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled ${ok_stn}

    IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled ${LMDZ_NMC_monthly}
    IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled ${LMDZ_NMC_daily}
    IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled ${LMDZ_NMC_hf}
    
    IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled ${LMDZ_COSP_monthly}
    IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled ${LMDZ_COSP_daily}
    IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled ${LMDZ_COSP_hf}

    # Activate the histstrataer output file only for configuration with interactive stratospheric aersols 
    # done by setting the key word LMDZ_strataero=y in lmdz.card
    if [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .TRUE.
    else
	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .FALSE.
    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${config_ListOfComponents_CHM} = Xinca ] ; then
	echo "Activate coupling to INCA, set type_trac=inca in run.def"
	IGCM_comp_modifyDefFile blocker run.def type_trac inca
    elif [ X${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
    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
    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
    fi


    # run.def : Activate the call to phytrac 
    if [ ! X${lmdz_UserChoices_iflag_phytrac} = X ]; then 
	IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac ${lmdz_UserChoices_iflag_phytrac}
    elif [ X${config_UserChoices_ConfigType} = XESMCO2 ] ; then
	IGCM_comp_modifyDefFile blocker run.def iflag_phytrac 1  
    else
	IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac DEFAULT
    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

    # 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"

    # Add special treatement for CARBON CYCLE
    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
	ATM_Carbon_Finalize
    fi

    echo FINALIZE ATM !

    IGCM_debug_PopStack "ATM_Finalize"
}



function ATM_Carbon_Update
{
    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card

    IGCM_debug_PushStack "ATM_Carbon_Update"

    typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
    typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
    typeset PathCO2log 
    typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
    
    if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
        ##--Initialization of fluxes to an undefined value at the first run
	UndefinedValueCo2=-9999
	InitPeriodCo2=0
	InitDateBeginCo2=${UndefinedValueCo2}
	InitYearCo2=$(( ${year} - 1 )) 
	InitDateEndCo2=${InitYearCo2}1231
	fCO2_ff=${UndefinedValueCo2} 
	CO2SBG=${UndefinedValueCo2}
	CO2LU=${UndefinedValueCo2}
	CO2MBG=${UndefinedValueCo2}
	CO2_ppm_prec=${UndefinedValueCo2}
        # Get the initial value of atmosp. pco2 
	CO2_ppm=${lmdz_UserChoices_co2_init}
	
	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
	
        # Save CO2 values in ExeCpuLog variable contents 5 fields
	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
	    gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	
        # Get the path where the log file co2.log is
	PathCO2log=${SUBMIT_DIR} 
        # Get Previous line in co2.log
	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
	
    else
	
	# NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
        # !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
	#SubmitRestartPath=
	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
	    IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
	    PathCO2log=${config_ATM_SubmitRestartPath}
	    Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
	    PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
	    
	    IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
	    IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
	    
            # Save Last Line of control in new co2.log file
	    InitPeriodCo2=0   
	    InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $2}' )
	    InitDateEndCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $3}' )
	    fCO2_ff=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $6}' )
	    CO2SBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $8}' )
	    CO2LU=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $9}' )
	    CO2MBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $7}' )
	    CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $5}' )
	    CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
	    
	    echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
		gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
	else
           # Get restart line in co2.log
	    PathCO2log=${SUBMIT_DIR}
	    PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
           # Get the value of atmosp. pco2 in co2.log
	    CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
	fi
	
    fi
    
    if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
	# Modify co2_ppm in config.def only for historical run
	# If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
	IGCM_comp_modifyDefFile force config.def co2_ppm     ${CO2_ppm}
    fi
    IGCM_debug_PopStack "ATM_Carbon_Update"
}


function ATM_Carbon_Finalize
{
    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card

    IGCM_debug_PushStack "ATM_Carbon_Finalize"

    typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
    
	# Fossil fuel emission
    if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
            # For Control, no fossil fuel emission :
	fCO2_ff=0
	echo "Fossil Fuel for control run  :" ${fCO2_ff}
    else
            # For historical, get the fossile fuel file :
	fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
	echo "Fossil Fuel for historical run  :" ${fCO2_ff}
    fi
    
        # Get the value of ocean carbon flux
    CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
    CO2MBG=$( echo ${CO2MBG} | sed -e "s/ *//" )
    echo "Ocean carbon flux  :" ${CO2MBG}
    
        # Get the value of land fluxes
    set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
    CO2SRF=$( echo ${CO2SBG_3V[0]} | sed -e "s/ *//" )
    CO2LU=$( echo ${CO2SBG_3V[1]} | sed -e "s/ *//" )
    CO2SBG=$( echo ${CO2SBG_3V[2]} | sed -e "s/ *//" )
    echo "Land carbon flux (NEP)         :" ${CO2SRF}
    echo "LU flux          (FLUC)        :" ${CO2LU}
    echo "Total Land carbon flux (NBP)   :" ${CO2SBG}
    
        # Previous CO2
    CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
    echo "Previous CO2  :" ${CO2_ppm_prec}
    
        # Formula
    CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" | bc -l )
    echo "New CO2  :" ${CO2_ppm}
    
        # Save CO2 values in ExeCpuLog variable contents 5 fields
    echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
	gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
                           $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
    
    IGCM_debug_PopStack "ATM_Carbon_Finalize"
}
