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

    sed -e "s/^${2}\ *=.*/${2}= ${3}/" ${1} > ${1}.tmp
    RET=$?
    echo "LMDZ_sed : ${1} ${2} ${3}"
    \mv ${1}.tmp ${1}

    IGCM_debug_PopStack "LMDZ_sed"
    return $RET
}

function ATM_Initialize
{
    IGCM_debug_PushStack "ATM_Initialize"

    RESOL_ATM=$( echo $RESOL | awk "-Fx" '{print $2}' | awk "-F-" '{print $1}')

    [ -f ${SUBMIT_DIR}/../.resol ] && eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol) || RESOL_ATM_3D=96x95x19

    RESOL_ATM_Z=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $3}' )

    ##-- Calendar type for LMDZ
    case ${config_UserChoices_CalendarType} in
        leap|gregorian)
            CalendarTypeForLmdz=earth_366d;;
        noleap)
            CalendarTypeForLmdz=earth_365d;;
        360d)
            CalendarTypeForLmdz=earth_360d;;
        *)
            CalendarTypeForLmdz=earth_360d
    esac

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

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

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

    ## Read LMDZ_NbPeriod_adjust option in lmdz.card 
    IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices LMDZ_NbPeriod_adjust
    LMDZ_NbPeriod_adjust=${lmdz_UserChoices_LMDZ_NbPeriod_adjust}

    if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
        IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices LMDZ_Bands_file_name
        LMDZ_Bands_file_name=${lmdz_UserChoices_LMDZ_Bands_file_name}
    fi

    ##  Read LMDZ_Freq_aero and LMDZ_Length_aero in lmdz.card
    LMDZ_Freq_aero=${lmdz_UserChoices_LMDZ_Freq_aero}
    LMDZ_Length_aero=${lmdz_UserChoices_LMDZ_Length_aero}

    ##  Read LMDZ_COSP_monthly  LMDZ_COSP_daily and LMDZ_COSP_hf in lmdz.card
    LMDZ_COSP_OK=${lmdz_UserChoices_LMDZ_COSP_OK}
    LMDZ_COSP_monthly=${lmdz_UserChoices_LMDZ_COSP_monthly}
    LMDZ_COSP_daily=${lmdz_UserChoices_LMDZ_COSP_daily}
    LMDZ_COSP_hf=${lmdz_UserChoices_LMDZ_COSP_hf}

    ##  Read LMDZ_NMC_monthly  LMDZ_NMC_daily and LMDZ_NMC_hf in lmdz.card
    LMDZ_NMC_monthly=${lmdz_UserChoices_LMDZ_NMC_monthly}
    LMDZ_NMC_daily=${lmdz_UserChoices_LMDZ_NMC_daily}
    LMDZ_NMC_hf=${lmdz_UserChoices_LMDZ_NMC_hf}

    IGCM_debug_PopStack "ATM_Initialize"
}

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


    case ${config_UserChoices_PeriodLength} in
        *Y|*y) 
               LMDZ_ecrit_ISCCP=30.
               LMDZ_periodav=30.
               if [ "${config_UserChoices_CalendarType}" != "360d" ] ; then
                  echo Change calendartype in config.card. PeriodLength=1Y allowed only for CalendarType=360d 
                  exit
               fi
               ;;
        *)
               LMDZ_ecrit_ISCCP=${PeriodLengthInDays}.
               LMDZ_periodav=${PeriodLengthInDays}.
               ;;
    esac

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

    ## algo : For CumulPeriod=1 ; 
    ##        IF NbPeriod_Adjust = 0, Get Bands file directly from server, store it with _0 suffix
    ##        ELSE LMDZ_adjust=y ; save Bands file on file server ;
    ##        For CumulPeriod=2 to LMDZ_NbPeriod_adjust ; Get Bands file from server (CumulPeriod-1) ; LMDZ_adjust=y ; save Bands file on file server ;
    ##        For CumulPeriod > LMDZ_NbPeriod_adjust ; LMDZ_adjust=n ; Get Bands file from server (CumulPeriod=LMDZ_NbPeriod_adjust 0 to force it) ; Use Bands ;

    if [ ${CumulPeriod} -eq 1 ] ; then
        if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
            IGCM_sys_Get ${LMDZ_Bands_file_name} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ; IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
            IGCM_sys_Put_Out Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${R_OUT_ATM_D}/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0
            IGCM_debug_Print 1 "Bands file forced to ${LMDZ_Bands_file_name} and stored in ${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0"
        fi
    fi

    LMDZ_adjust=n
    [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && LMDZ_adjust=y

    RefPeriod=${LMDZ_NbPeriod_adjust} #0 to use a Bands file from Restart
    [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && (( RefPeriod = ${CumulPeriod} - 1 )) 

    [ ${CumulPeriod} -gt 1 ] && ( IGCM_sys_Get ${R_OUT_ATM_D}/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${RefPeriod} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ; IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat )

    ##-- GHG forcing :
    ##   If forcing file exist in run directory, read values for the current year and modify physiq.def
    if [ -f SOLARANDVOLCANOES.txt ] ; then
	IPCC_SOLAR=`grep Annee_${year} SOLARANDVOLCANOES.txt | awk -F= '{print $2}'`
	LMDZ_sed physiq.def solaire     ${IPCC_SOLAR}
    fi
    if [ -f CO2.txt ] ; then
	IPCC_CO2=`grep Annee_${year} CO2.txt | awk -F= '{print $2}'`
	LMDZ_sed physiq.def co2_ppm     ${IPCC_CO2}
    fi
    if [ -f CH4.txt ] ; then
	IPCC_CH4=`grep Annee_${year} CH4.txt | awk -F= '{print $2}'`
	LMDZ_sed physiq.def CH4_ppb     ${IPCC_CH4}
    fi
    if [ -f N2O.txt ] ; then
	IPCC_N2O=`grep Annee_${year} N2O.txt | awk -F= '{print $2}'`
	LMDZ_sed physiq.def N2O_ppb     ${IPCC_N2O}
    fi
    if [ -f CFC11.txt ] ; then
	IPCC_CFC11=`grep Annee_${year} CFC11.txt | awk -F= '{print $2}'`
	LMDZ_sed physiq.def CFC11_ppt   ${IPCC_CFC11}
    fi
    if [ -f CFC12.txt ] ; then
	IPCC_CFC12=`grep Annee_${year} CFC12.txt | awk -F= '{print $2}'`
	LMDZ_sed physiq.def CFC12_ppt   ${IPCC_CFC12}
    fi


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

	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 physiq.def only for historical run
	    LMDZ_sed physiq.def co2_ppm     ${CO2_ppm}
	fi
    fi
    # end CARBON_CYCLE

    ##-- 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=y
    fi


    ## physiq.def parameters modified from initial physiq_L${RESOL_ATM_Z}
    #  columns in phys_output_filekeys refer to the filenames given in phys_out_filenames in physiq.def :  
    #                                            histmth       histday        histhf    histfh3h   histhf3hm   histstn
    LMDZ_sed physiq.def phys_out_filekeys        ${ok_mensuel} ${ok_journe}   ${ok_hf}  ${ok_hf3h} ${ok_hf3hm} ${ok_stn}
    LMDZ_sed physiq.def ecrit_ISCCP ${LMDZ_ecrit_ISCCP}
    LMDZ_sed physiq.def ok_cosp     ${LMDZ_COSP_OK}
    LMDZ_sed physiq.def ok_mensuelCOSP  ${LMDZ_COSP_monthly}
    LMDZ_sed physiq.def ok_journeCOSP   ${LMDZ_COSP_daily}
    LMDZ_sed physiq.def ok_hfCOSP   ${LMDZ_COSP_hf}
    LMDZ_sed physiq.def ok_histNMC  "${LMDZ_NMC_monthly}, ${LMDZ_NMC_daily}, ${LMDZ_NMC_hf}"

    ## gcm.def parameters : no change since gcm.def_${RESOL_ATM_3D} is used and already modified

    ## run.def parameters
    LMDZ_sed run.def dayref   ${InitDay}
    LMDZ_sed run.def anneeref ${InitYear}
    LMDZ_sed run.def calend   ${CalendarTypeForLmdz}
    LMDZ_sed run.def nday     ${PeriodLengthInDays}
    LMDZ_sed run.def raz_date ${RAZ_DATE}
    LMDZ_sed run.def periodav ${LMDZ_periodav}
    LMDZ_sed run.def adjust   ${LMDZ_adjust}

    ## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
    IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta
    ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
    if [ ${ByPass_hgardfou_teta} = 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 ]
    IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats
    ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
    if [ ${ByPass_hgardfou_mats} = 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

    if ( ${FirstInitialize} ) ; then

	if ( [ "${config_Restarts_OverRule}" = "n" ] && [ "${config_ATM_Restart}" = "n" ] ); then
	    if [ ${DRYRUN} -le 2 ] ; then
                ##-- suppression of ozone file construction --
                cp physiq.def physiq.def.save
                LMDZ_sed physiq.def read_climoz 0
		IGCM_sys_Cp ${R_EXE}/create_etat0_limit.e ${RUN_DIR}/.
		if [ ${DRYRUN} -le 1 ] ; then
		    ${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e
                    IGCM_sys_Put_Out start.nc    ${R_OUT_ATM_R}/${config_UserChoices_JobName}_${PeriodDateBegin}_start.nc
                    IGCM_sys_Put_Out startphy.nc ${R_OUT_ATM_R}/${config_UserChoices_JobName}_${PeriodDateBegin}_startphy.nc
		fi
                IGCM_sys_Mv physiq.def.save physiq.def
	    else
		echo "EXECUTION of ${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e simulated"
		echo "EXECUTION of ${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e simulated for DRYRUN = " $DRYRUN >> stack
	    fi
	fi

    fi

    IGCM_debug_PopStack "ATM_Update"
}

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

    [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && IGCM_sys_Put_Out Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${R_OUT_ATM_D}/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${CumulPeriod}


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

    fi

    echo FINALIZE ATM !

    IGCM_debug_PopStack "ATM_Finalize"
}