source: TOOLS/CMIP6_FORCING/SCENARIOS/AER_TROP_EMISSIONS/REGRID/regrid_scen.sh

#--corrected 2080 bug 9/2018, ThL
#--reworked 7/2018 for scenario emissions, ThL
#--updated on 5/2/2018 with new paths, ThL
#--updated on 4/5/2017 with improved Sheng & Zwiers algorithm, ThL
#--corrected some interpolation preprocessing (compared to v4)
#--updated on 5/5/2017 with correction factor (30/46) on NOx vs. NO
#--updated on 9/5/2017 with output separation BB/anthro for SO2, NOx and NH3
#--corrected on 22/6/2017 for BB: undef values zeroed before remapping
#--corrected on 26/09/2017 for NOx units: PNNL dataset is kg NO2, VUA is kg NO. 
#  INCA expects NO in its AER version.
#
#INCA  conc_dms flx_nox flx_bc flx_pom flx_bbbc flx_bbpom flx_so2 flx_so4 flx_h2s flx_nh3
#CMIP6 species  NOx     BC     OC                         SO2                     NH3
# + NMVOC CO

#--INCA example file where dms_conc can be reused
fileINCAex="/home/oboucher/CMIP6/AER_EMISSIONS/INCAfile/sflx_lmdz_phy_1997.nc"

#--input directory for anthropogenic (non-BB) emissions
dirin="/prodigfs/project/input4MIPs/CMIP6/ScenarioMIP/IAMC/"

#--LMDz grid information
grid="144x143"
gridfile="../GRID/grid-lmdz-lonlat_"${grid}
nbpoint=$((144*141+2))

for scen in "ssp119" "ssp126" "ssp245" "ssp370" "ssp434" "ssp460" "ssp534-over" "ssp585"
do

#--output directory
dirout="/data/"${USER}"/CMIP6/AEROSOL/ScenarioMIP/${scen}/v2_correcte/"
if [ ! -d ${dirout} ] ; then mkdir -p ${dirout} ; fi

if [ ${scen} == "ssp119" ] ; then prefix="IMAGE" ; fi
if [ ${scen} == "ssp126" ] ; then prefix="IMAGE" ; fi
if [ ${scen} == "ssp245" ] ; then prefix="MESSAGE-GLOBIOM" ; fi
if [ ${scen} == "ssp370" ] ; then prefix="AIM" ; fi
if [ ${scen} == "ssp434" ] ; then prefix="GCAM4" ; fi
if [ ${scen} == "ssp460" ] ; then prefix="GCAM4" ; fi
if [ ${scen} == "ssp534-over" ] ; then prefix="REMIND-MAGPIE" ; fi
if [ ${scen} == "ssp585" ] ; then prefix="REMIND-MAGPIE" ; fi

#--loop on years
for year in {2015..2100}
do

if [ ${year} -ge "2015" -a ${year} -lt "2020" ]
then
year1=2015
year2=2020
fi
if [ ${year} -ge "2020" -a ${year} -lt "2030" ]
then
year1=2020
year2=2030
fi
if [ ${year} -ge "2030" -a ${year} -lt "2040" ]
then
year1=2030
year2=2040
fi
if [ ${year} -ge "2040" -a ${year} -lt "2050" ]
then
year1=2040
year2=2050
fi
if [ ${year} -ge "2050" -a ${year} -lt "2060" ]
then
year1=2050
year2=2060
fi
if [ ${year} -ge "2060" -a ${year} -lt "2070" ]
then
year1=2060
year2=2070
fi
if [ ${year} -ge "2070" -a ${year} -lt "2080" ]
then
year1=2070
year2=2080
fi
if [ ${year} -ge "2080" -a ${year} -lt "2090" ]
then
year1=2080
year2=2090
fi
if [ ${year} -ge "2090" -a ${year} -lt "2100" ]
then
year1=2090
year2=2100
fi
if [ ${year} == 2100 ]
then
year1=2100
year2=2100
fi
#--weights for linear interpolation
if [ ${year} == 2015 ]
then
pond1="1"
pond2="0"
fi
if [ ${year} == 2016 ]
then
pond1="0.8"
pond2="0.2"
fi
if [ ${year} == 2017 ]
then
pond1="0.6"
pond2="0.4"
fi
if [ ${year} == 2018 ]
then
pond1="0.4"
pond2="0.6"
fi
if [ ${year} == 2019 ]
then
pond1="0.2"
pond2="0.8"
fi
if [ ${year} == 2020 -o ${year} == 2030 -o ${year} == 2040 -o ${year} == 2050 -o ${year} == 2060 -o ${year} == 2070 -o ${year} == 2080 -o ${year} == 2090 ]
then
pond1="1"
pond2="0"
fi
if [ ${year} == 2021 -o ${year} == 2031 -o ${year} == 2041 -o ${year} == 2051 -o ${year} == 2061 -o ${year} == 2071 -o ${year} == 2081 -o ${year} == 2091 ]
then
pond1="0.9"
pond2="0.1"
fi
if [ ${year} == 2022 -o ${year} == 2032 -o ${year} == 2042 -o ${year} == 2052 -o ${year} == 2062 -o ${year} == 2072 -o ${year} == 2082 -o ${year} == 2092 ]
then
pond1="0.8"
pond2="0.2"
fi
if [ ${year} == 2023 -o ${year} == 2033 -o ${year} == 2043 -o ${year} == 2053 -o ${year} == 2063 -o ${year} == 2073 -o ${year} == 2083 -o ${year} == 2093 ]
then
pond1="0.7"
pond2="0.3"
fi
if [ ${year} == 2024 -o ${year} == 2034 -o ${year} == 2044 -o ${year} == 2054 -o ${year} == 2064 -o ${year} == 2074 -o ${year} == 2084 -o ${year} == 2094 ]
then
pond1="0.6"
pond2="0.4"
fi
if [ ${year} == 2025 -o ${year} == 2035 -o ${year} == 2045 -o ${year} == 2055 -o ${year} == 2065 -o ${year} == 2075 -o ${year} == 2085 -o ${year} == 2095 ]
then
pond1="0.5"
pond2="0.5"
fi
if [ ${year} == 2026 -o ${year} == 2036 -o ${year} == 2046 -o ${year} == 2056 -o ${year} == 2066 -o ${year} == 2076 -o ${year} == 2086 -o ${year} == 2096 ]
then
pond1="0.4"
pond2="0.6"
fi
if [ ${year} == 2027 -o ${year} == 2037 -o ${year} == 2047 -o ${year} == 2057 -o ${year} == 2067 -o ${year} == 2077 -o ${year} == 2087 -o ${year} == 2097 ]
then
pond1="0.3"
pond2="0.7"
fi
if [ ${year} == 2028 -o ${year} == 2038 -o ${year} == 2048 -o ${year} == 2058 -o ${year} == 2068 -o ${year} == 2078 -o ${year} == 2088 -o ${year} == 2098 ]
then
pond1="0.2"
pond2="0.8"
fi
if [ ${year} == 2029 -o ${year} == 2039 -o ${year} == 2049 -o ${year} == 2059 -o ${year} == 2069 -o ${year} == 2079 -o ${year} == 2089 -o ${year} == 2099 ]
then
pond1="0.1"
pond2="0.9"
fi
if [ ${year} == 2100 ]
then
pond1="0"
pond2="1"
fi

#--species 
for species in "BC" "NOx" "OC" "SO2" "NH3"
do

if [ ${species} = "BC"  ] ; then speciesinca="bc"  ; fi
if [ ${species} = "NOx" ] ; then speciesinca="nox" ; fi
if [ ${species} = "OC"  ] ; then speciesinca="pom" ; fi
if [ ${species} = "SO2" ] ; then speciesinca="so2" ; fi
if [ ${species} = "NH3" ] ; then speciesinca="nh3" ; fi

if [ ${species} = "BC"  ] ; then speciesUp="BC"  ; fi
if [ ${species} = "NOx" ] ; then speciesUp="NOX" ; fi
if [ ${species} = "OC"  ] ; then speciesUp="OC" ; fi
if [ ${species} = "SO2" ] ; then speciesUp="SO2" ; fi
if [ ${species} = "NH3" ] ; then speciesUp="NH3" ; fi

#--Dealing with anthro emissions file...

echo "... "${year}" : Dealing with "${species}" anthro input file..."

#--input file anthro (fossil fuel emissions)
filename=${dirin}IAMC-${prefix}-${scen}-1-1/atmos/mon/${species}_em_anthro/gn/v20180628/${species}-em-anthro_input4MIPs_emissions_ScenarioMIP_IAMC-${prefix}-${scen}-1-1_gn_201501-210012.nc

#--two temporary files for interpolation
filetmp1=${dirout}tmp1.nc
filetmp2=${dirout}tmp2.nc

#--output files
filenameout1=${dirout}flux_${speciesinca}_${year}.nc
filenameout1b=${dirout}flux_0_${speciesinca}_${year}.nc
filenameout2=${dirout}flux_lmdz_${speciesinca}_${year}.nc
filenameout3=${dirout}flux_vector_${speciesinca}_${year}.nc

echo ${filename} ${filenameout1} ${filenameout2} ${filenameout3}
rm -f ${filetmp1} ${filetmp2} ${filenameout1} ${filenameout2} ${filenameout3}

#--unfortunately idl not happy with input netcdf files so need to ferretize files
#--I also sum over sectors and I extract the correct years as well
#--first year (start of 5-Y or 10-Y period, for later interpolation)
rm -f rewrite.jnl
cat << eod > rewrite.jnl
use "${filename}"
set region/t=16-jan-${year1}:16-dec-${year1}
save/clobber/file="${filetmp1}" ${speciesUp}_EM_ANTHRO[k=@sum]
eod
#--run ferret script
ferret << eod
go rewrite.jnl
exit
eod
#--second year (end of 5-Y or 10-Y period, for later interpolation)
rm -f rewrite.jnl
cat << eod > rewrite.jnl
use "${filename}"
set region/t=16-jan-${year2}:16-dec-${year2}
save/clobber/file="${filetmp2}" ${speciesUp}_EM_ANTHRO[k=@sum]
eod
#--run ferret script
ferret << eod 
go rewrite.jnl
exit
eod

#--performing time interpolation
cdo add -mulc,${pond1} -selname,${speciesUp}_EM_ANTHRO ${filetmp1} -mulc,${pond2} -selname,${speciesUp}_EM_ANTHRO ${filetmp2} ${filenameout1}

cdo setmisstoc,0.0 ${filenameout1} ${filenameout1b}

#--remap to LMDz grid
#--OC to POM conversion factor
#--otherwise change to capital letters if not (eg NOx)
if [ ${species} == "OC"  ] ; then 
echo cdo remapcon,${gridfile} -chname,`echo ${species}_EM_ANTHRO | awk '{print toupper($0)}'`,flux -mulc,1.4 ${filenameout1b} ${filenameout2}
cdo remapcon,${gridfile} -chname,`echo ${species}_EM_ANTHRO | awk '{print toupper($0)}'`,flux -mulc,1.4 ${filenameout1b} ${filenameout2}
else
echo cdo remapcon,${gridfile} -chname,`echo ${species}_EM_ANTHRO | awk '{print toupper($0)}'`,flux  ${filenameout1b} ${filenameout2}
cdo remapcon,${gridfile} -chname,`echo ${species}_EM_ANTHRO | awk '{print toupper($0)}'`,flux ${filenameout1b} ${filenameout2}
fi

#--Improved Sheng & Zwiers algorithm + transform into vector
rm -f regrid.pro
cat << eod >> regrid.pro
pro regrid
filename='${filenameout2}'
print, filename
NETCDFREAD,filename,'flux',flux,dimflux
NETCDFREAD,filename,'lat',lat,dimlat0
NETCDFREAD,filename,'lon',lon,dimlon0
NETCDFREAD,filename,'TIME',time,dimtime0
dimlat=dimlat0(0)
dimlon=dimlon0(0)
dimtime=dimtime0(0)
print, 'dim flux=', dimflux
A = float([     [3./4., 1./8., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1./8.],$
                [1./8., 3./4., 1./8., 0., 0., 0., 0., 0., 0., 0., 0., 0.],$
                [0., 1./8., 3./4., 1./8., 0., 0., 0., 0., 0., 0., 0., 0.],$
                [0., 0., 1./8., 3./4., 1./8., 0., 0., 0., 0., 0., 0., 0.],$
                [0., 0., 0., 1./8., 3./4., 1./8., 0., 0., 0., 0., 0., 0.],$
                [0., 0., 0., 0., 1./8., 3./4., 1./8., 0., 0., 0., 0., 0.],$
                [0., 0., 0., 0., 0., 1./8., 3./4., 1./8., 0., 0., 0., 0.],$
                [0., 0., 0., 0., 0., 0., 1./8., 3./4., 1./8., 0., 0., 0.],$
                [0., 0., 0., 0., 0., 0., 0., 1./8., 3./4., 1./8., 0., 0.],$
                [0., 0., 0., 0., 0., 0., 0., 0., 1./8., 3./4., 1./8., 0.],$
                [0., 0., 0., 0., 0., 0., 0., 0., 0., 1./8., 3./4., 1./8.],$
                [1./8., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1./8., 3./4.]   ])
fluxinit=flux
flux_check=flux
for lo=0,dimlon-1 do begin
for la=0,dimlat-1 do begin
flux_check(lo,la,*) = invert(A) ## transpose(fluxinit(lo,la,*))
endfor
endfor                  
m_bloq = make_array(dimlon,dimlat,12,value=0)           ; Matrice booléenne "mois à bloquer ou non"
if total(where(flux_check lt 0)) ne -1 then m_bloq(where(flux_check lt 0)) = 1
; Correction/adaptation de la matrice S&Z en fonction du masque booléen m_bloq
for lo=0,dimlon-1 do begin
for la=0,dimlat-1 do begin
whereneg = where(flux_check(lo,la,*) lt 0)              ; (12 pts max) Identification de potentiels points à problÚmes, corrigés négativement
nbannul=n_elements(whereneg)*(total(whereneg) ne -1)
flux_corr=flux_check(lo,la,*)                           ; Création d'un vecteur pour recevoir les valeurs corrigées, initialisé à flux_check au cas où on n'ait rien à faire d'autre qu'une seule itération
A2 = A                                                  ; Je repars de la matrice A initiale, ce pour chaque point de grille
;                                                       ; Potentiellement plusieurs passages pour éliminer toutes les valeurs négatives
while nbannul ne 0 do begin                             ; Si l'on a effectivement des émissions corrigées négativement...
m_bloq(lo,la,whereneg) = 1                              ; Update de la matrice m_bloq
for m=0,11 do begin
if m eq 11 then begin                                   ; Pour plus de facilité, mois précédents et suivants codés ici
p=10
s=0
endif else if m eq 0 then begin
p=11
s=1
endif else begin
p = m-1
s = m+1
endelse
if m_bloq(lo,la,m) then begin                           ; Je traite les mois bloqués en eux-mêmes
A2(p,m) = 0.
A2(m,m) = 1.
A2(s,m) = 0.
endif                                                   ; Fin du cas si l'on est sur un mois bloqué
if ~m_bloq(lo,la,m) then begin                          ; Je traite les mois non bloqués, pour ceux adjacents à un mois bloqué
if m_bloq(lo,la,p) and m_bloq(lo,la,s) then begin               ; Mois encadré de deux mois bloqués
A2(p,m) = 1./4.
A2(m,m) = 1./2.
A2(s,m) = 1./4.
endif else if m_bloq(lo,la,p) and ~m_bloq(lo,la,s) then begin   ; Mois précédent bloqué (uniquement)
A2(p,m) = 2./8.
A2(m,m) = 5./8.
A2(s,m) = 1./8.
endif else if ~m_bloq(lo,la,p) and m_bloq(lo,la,s) then begin   ; Mois suivant bloqué (uniquement)
A2(p,m) = 1./8.
A2(m,m) = 5./8.
A2(s,m) = 2./8.
endif
endif                                                           ; Fin du cas mois non bloqué
endfor                                                          ; Fin de la boucle sur les mois, balayage de la matrice
flux_corr = invert(A2) ## transpose(fluxinit(lo,la,*))          ; Ré-itération de la multiplication matricielle avec la matrice A modifiée (A2)
whereneg = where(flux_corr lt 0)                                ; (12 pts max) Ré-identification de potentiels nouveaux points à problÚmes, corrigés négativement
nbannul=n_elements(whereneg)*(total(whereneg) ne -1)
endwhile                                                        ; Fin du cas où l'on avait des problÚmes d'émissions corrigées négativement
; *** IMPORTANT ! *** Pour signaler les mois bloqués, on prend la convention suivante :
;       valeur négative ou nulle <=> mois bloqué
;       valeur positive <=> mois à interpolation classique
flux(lo,la,*) = flux_corr                                       ; En sortie de la boucle while, normalement flux_corr est complÚtement positif
endfor                                                          ; Fin boucle lat
endfor                                                          ; Fin boucle lon
nbnegtotal = n_elements(where(m_bloq eq 1)) * (total(where(m_bloq eq 1)) ne -1)
if nbnegtotal ne 0 then flux(where(m_bloq eq 1)) = -flux(where(m_bloq eq 1))            ; Je force à des valeurs négatives
;
month_in_year=12
nbpoint=${nbpoint}
flux2=fltarr(nbpoint,month_in_year)
flux2(*,*)=0.0
;
for l=0,month_in_year-1 do begin
flux2(0,l)=TOTAL(flux(*,0,l))/float(dimlon)
flux2(nbpoint-1,l)=TOTAL(flux(*,dimlat-1,l))/float(dimlon)
endfor
;
pt=1
for j=1,dimlat-2  do begin
for i=0,dimlon-1  do begin
for l=0,month_in_year-1 do begin
  flux2(pt,l)=flux(i,j,l)
endfor
pt=pt+1
endfor
endfor
;
;saving netcdf file
;
fluxstruct={vector:fltarr(nbpoint),time:fltarr(month_in_year), $
            flx_${speciesinca}:fltarr(nbpoint,month_in_year) }
;
fluxstruct.vector=float(indgen(nbpoint)+1)
;;fluxstruct.time=float(indgen(month_in_year)+1)
fluxstruct.time=[15, 45, 75, 105, 135, 165, 195, 225, 255, 285, 315, 345]
fluxstruct.flx_${speciesinca}=flux2
;
attributes = {units:strarr(3),long_name:strarr(3)}
attributes.units = ['vector','days since 1960-01-01','flux']
attributes.long_name = ['vector', 'time', 'flux']
;
dimensions = {isdim:intarr(3), links:intarr(2,3)}
       dimensions.isdim =  [1,1,0]  ; (1=dimension, 0=variable)
       dimensions.links = [ [-1,-1],[-1,-1],[0,1]    ]
;
netcdfwrite,'${filenameout3}',fluxstruct,clobber=1, attributes=attributes, dimensions=dimensions
;
end
eod

#
#--calling IDL
#
/opt/idl-6.4/idl/bin/idl << eod
.r netcdf
.r netcdfwrite
.r struct_dims
.r regrid
regrid
exit
eod
#


#--now dealing with BB sources
echo "... "${year}" : Dealing with "${species}" openburning input file..."

filename=${dirin}IAMC-${prefix}-${scen}-1-1/atmos/mon/${species}_em_openburning/gn/v20180628/${species}-em-openburning_input4MIPs_emissions_ScenarioMIP_IAMC-${prefix}-${scen}-1-1_gn_201501-210012.nc

if [ ${species} = "BC"  ] ; then speciesinca="bc"  ; fi
if [ ${species} = "NOx" ] ; then speciesinca="nox" ; fi
if [ ${species} = "OC"  ] ; then speciesinca="pom" ; fi
if [ ${species} = "SO2" ] ; then speciesinca="so2" ; fi
if [ ${species} = "NH3" ] ; then speciesinca="nh3" ; fi

#--two temporary files for interpolation
filetmp1=${dirout}tmp1.nc
filetmp2=${dirout}tmp2.nc

#--output files
filenameout1=${dirout}flux_${speciesinca}bb_${year}.nc
filenameout1b=${dirout}flux_0_${speciesinca}bb_${year}.nc
filenameout2=${dirout}flux_lmdz0_${speciesinca}bb_${year}.nc
filenameout3=${dirout}flux_vector_${speciesinca}bb_${year}.nc

echo ${filename} ${filenameout1} ${filenameout1b} ${filenameout2} ${filenameout3}
rm -f ${filetmp1} ${filetmp2} ${filenameout1} ${filenameout1b} ${filenameout2} ${filenameout3}

#--unfortunately idl not happy with input netcdf files so need to ferretize files
#--I also sum over sectors and I extract the correct years as well
#--first year (start of 5-Y or 10-Y period, for later interpolation)
rm -f rewrite.jnl
cat << eod > rewrite.jnl
use "${filename}"
set region/t=16-jan-${year1}:16-dec-${year1}
save/clobber/file="${filetmp1}" ${speciesUp}_EM_OPENBURNING[k=@sum]
eod
#--run ferret script
ferret << eod
go rewrite.jnl
exit
eod
#--second year (end of 5-Y or 10-Y period, for later interpolation)
rm -f rewrite.jnl
cat << eod > rewrite.jnl
use "${filename}"
set region/t=16-jan-${year2}:16-dec-${year2}
save/clobber/file="${filetmp2}" ${speciesUp}_EM_OPENBURNING[k=@sum]
eod
#--run ferret script
ferret << eod 
go rewrite.jnl
exit
eod

#--performing time interpolation
cdo add -mulc,${pond1} -selname,${speciesUp}_EM_OPENBURNING ${filetmp1} -mulc,${pond2} -selname,${speciesUp}_EM_OPENBURNING ${filetmp2} ${filenameout1}

#--replace undef with 0
cdo setmisstoc,0.0 ${filenameout1} ${filenameout1b}

#--remap to LMDz grid
#--OC to POM conversion factor
#--as ferret returns NOX, treat NOx NOX inconsistency in names by converting to upper case
if [ ${species} != "OC"  ] ; then
echo cdo remapcon,${gridfile} -chname,`echo ${species}_EM_OPENBURNING | awk '{print toupper($0)}'`,flux ${filenameout1b} ${filenameout2}
cdo remapcon,${gridfile} -chname,`echo ${species}_EM_OPENBURNING | awk '{print toupper($0)}'`,flux ${filenameout1b} ${filenameout2}
else
echo cdo remapcon,${gridfile} -chname,${species}_EM_OPENBURNING,flux -mulc,1.4 ${filenameout1b} ${filenameout2}
cdo remapcon,${gridfile} -chname,${species}_EM_OPENBURNING,flux -mulc,1.4 ${filenameout1b} ${filenameout2}
fi

#--Improved Sheng & Zwiers algorithm + transform into vector
rm -f regrid.pro
cat << eod >> regrid.pro
pro regrid
filename='${filenameout2}'
print, filename
NETCDFREAD,filename,'flux',flux,dimflux
NETCDFREAD,filename,'lat',lat,dimlat0
NETCDFREAD,filename,'lon',lon,dimlon0
NETCDFREAD,filename,'TIME',time,dimtime0
dimlat=dimlat0(0)
dimlon=dimlon0(0)
dimtime=dimtime0(0)
print, 'dim flux=', dimflux
A = float([     [3./4., 1./8., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1./8.],$
                [1./8., 3./4., 1./8., 0., 0., 0., 0., 0., 0., 0., 0., 0.],$
                [0., 1./8., 3./4., 1./8., 0., 0., 0., 0., 0., 0., 0., 0.],$
                [0., 0., 1./8., 3./4., 1./8., 0., 0., 0., 0., 0., 0., 0.],$
                [0., 0., 0., 1./8., 3./4., 1./8., 0., 0., 0., 0., 0., 0.],$
                [0., 0., 0., 0., 1./8., 3./4., 1./8., 0., 0., 0., 0., 0.],$
                [0., 0., 0., 0., 0., 1./8., 3./4., 1./8., 0., 0., 0., 0.],$
                [0., 0., 0., 0., 0., 0., 1./8., 3./4., 1./8., 0., 0., 0.],$
                [0., 0., 0., 0., 0., 0., 0., 1./8., 3./4., 1./8., 0., 0.],$
                [0., 0., 0., 0., 0., 0., 0., 0., 1./8., 3./4., 1./8., 0.],$
                [0., 0., 0., 0., 0., 0., 0., 0., 0., 1./8., 3./4., 1./8.],$
                [1./8., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1./8., 3./4.]   ])
fluxinit=flux
flux_check=flux
for lo=0,dimlon-1 do begin
for la=0,dimlat-1 do begin
flux_check(lo,la,*) = invert(A) ## transpose(fluxinit(lo,la,*))
endfor
endfor                  
m_bloq = make_array(dimlon,dimlat,12,value=0)           ; Matrice booléenne "mois à bloquer ou non"
if total(where(flux_check lt 0)) ne -1 then m_bloq(where(flux_check lt 0)) = 1
; Correction/adaptation de la matrice S&Z en fonction du masque booléen m_bloq
for lo=0,dimlon-1 do begin
for la=0,dimlat-1 do begin
whereneg = where(flux_check(lo,la,*) lt 0)              ; (12 pts max) Identification de potentiels points à problÚmes, corrigés négativement
nbannul=n_elements(whereneg)*(total(whereneg) ne -1)
flux_corr=flux_check(lo,la,*)                           ; Création d'un vecteur pour recevoir les valeurs corrigées, initialisé à flux_check au cas où on n'ait rien à faire (à part 1 seule correction matricielle)
A2 = A                                                  ; Je repars de la matrice A initiale, ce pour chaque point de grille
;                                                       ; Potentiellement plusieurs passages pour éliminer toutes les valeurs négatives
while nbannul ne 0 do begin                             ; Si l'on a effectivement des émissions corrigées négativement...
m_bloq(lo,la,whereneg) = 1                              ; Update de la matrice m_bloq
for m=0,11 do begin
if m eq 11 then begin                                   ; Pour plus de facilité, mois précédents et suivants codés ici
p=10
s=0
endif else if m eq 0 then begin
p=11
s=1
endif else begin
p = m-1
s = m+1
endelse
if m_bloq(lo,la,m) then begin                           ; Je traite les mois bloqués en eux-mêmes
A2(p,m) = 0.
A2(m,m) = 1.
A2(s,m) = 0.
endif                                                   ; Fin du cas si l'on est sur un mois bloqué
if ~m_bloq(lo,la,m) then begin                          ; Je traite les mois non bloqués, pour ceux adjacents à un mois bloqué
if m_bloq(lo,la,p) and m_bloq(lo,la,s) then begin               ; Mois encadré de deux mois bloqués
A2(p,m) = 1./4.
A2(m,m) = 1./2.
A2(s,m) = 1./4.
endif else if m_bloq(lo,la,p) and ~m_bloq(lo,la,s) then begin   ; Mois précédent bloqué (uniquement)
A2(p,m) = 2./8.
A2(m,m) = 5./8.
A2(s,m) = 1./8.
endif else if ~m_bloq(lo,la,p) and m_bloq(lo,la,s) then begin   ; Mois suivant bloqué (uniquement)
A2(p,m) = 1./8.
A2(m,m) = 5./8.
A2(s,m) = 2./8.
endif
endif                                                           ; Fin du cas mois non bloqué
endfor                                                          ; Fin de la boucle sur les mois, balayage de la matrice
flux_corr = invert(A2) ## transpose(fluxinit(lo,la,*))          ; Ré-itération de la multiplication matricielle avec la matrice A modifiée (A2)
whereneg = where(flux_corr lt 0)                                ; (12 pts max) Ré-identification de potentiels nouveaux points à problÚmes, corrigés négativement
nbannul=n_elements(whereneg)*(total(whereneg) ne -1)
endwhile                                                        ; Fin du cas où l'on avait des problÚmes d'émissions corrigées négativement
; *** IMPORTANT ! *** Pour signaler les mois bloqués, on prend la convention suivante :
;       valeur négative ou nulle <=> mois bloqué
;       valeur positive <=> mois à interpolation classique
flux(lo,la,*) = flux_corr                                       ; En sortie de la boucle while, normalement flux_corr est complÚtement positif
endfor                                                          ; Fin boucle lat
endfor                                                          ; Fin boucle lon
nbnegtotal = n_elements(where(m_bloq eq 1)) * (total(where(m_bloq eq 1)) ne -1)
if nbnegtotal ne 0 then flux(where(m_bloq eq 1)) = -flux(where(m_bloq eq 1))            ; Je force à des valeurs négatives
;
month_in_year=12
nbpoint=${nbpoint}
flux2=fltarr(nbpoint,month_in_year)
flux2(*,*)=0.0
;
for l=0,month_in_year-1 do begin
flux2(0,l)=TOTAL(flux(*,0,l))/float(dimlon)
flux2(nbpoint-1,l)=TOTAL(flux(*,dimlat-1,l))/float(dimlon)
endfor
;
pt=1
for j=1,dimlat-2  do begin
for i=0,dimlon-1  do begin
for l=0,month_in_year-1 do begin
  flux2(pt,l)=flux(i,j,l)
endfor
pt=pt+1
endfor
endfor
;
;saving netcdf file
;
fluxstruct={vector:fltarr(nbpoint),time:fltarr(month_in_year), $
            flx_bb${speciesinca}:fltarr(nbpoint,month_in_year) }
;
fluxstruct.vector=float(indgen(nbpoint)+1)
;;fluxstruct.time=float(indgen(month_in_year)+1)
fluxstruct.time=[15, 45, 75, 105, 135, 165, 195, 225, 255, 285, 315, 345]
fluxstruct.flx_bb${speciesinca}=flux2
;
attributes = {units:strarr(3),long_name:strarr(3)}
attributes.units = ['vector','days since 1960-01-01','flux']
attributes.long_name = ['vector', 'time', 'flux']
;
dimensions = {isdim:intarr(3), links:intarr(2,3)}
       dimensions.isdim =  [1,1,0]  ; (1=dimension, 0=variable)
       dimensions.links = [ [-1,-1],[-1,-1],[0,1]    ]
;
netcdfwrite,'${filenameout3}',fluxstruct,clobber=1, attributes=attributes, dimensions=dimensions
;
end
eod

#
#--calling IDL
#
/opt/idl-6.4/idl/bin/idl << eod
.r netcdf
.r netcdfwrite
.r struct_dims
.r regrid
regrid
exit
eod
#

#--end loop on species
done

#--cleaning up
rm -f ferret*

#--unfortunately idl use capital letters for variable names so need to change to small letters for now 
rm -f ${dirout}flux_vector_h2s_${year}.nc ${dirout}flux_vector_so4_${year}.nc
cdo expr,'flx_h2s=0.*FLX_SO2' ${dirout}flux_vector_so2_${year}.nc ${dirout}flux_vector_h2s_${year}.nc
cdo expr,'flx_so4=0.*FLX_SO2' ${dirout}flux_vector_so2_${year}.nc ${dirout}flux_vector_so4_${year}.nc

rm -f ${dirout}flux_vector_${year}.nc

#--combining everything into a single file with some final preprocessing
rm -f ${dirout}flux_vector_noxtot_${year}.nc ${dirout}flux_vector_so2tot_${year}.nc ${dirout}flux_vector_nh3tot_${year}.nc

#--deleting output file if already there
rm -f ${dirout}sflx_lmdz_cmip6_${year}.nc
#--merging all files into a single one
#--PNNL NOx is NO2 so 30/46 scaling factor to change to NO 
#--VUA NOx is NO so no change in unit
cdo merge -expr,'flx_bc=FLX_BC' ${dirout}flux_vector_bc_${year}.nc -expr,'flx_bbbc=FLX_BBBC' ${dirout}flux_vector_bcbb_${year}.nc -expr,'flx_pom=FLX_POM' ${dirout}flux_vector_pom_${year}.nc -expr,'flx_bbpom=FLX_BBPOM' ${dirout}flux_vector_pombb_${year}.nc -expr,'flx_nox=30.*FLX_NOX/46.' ${dirout}flux_vector_nox_${year}.nc -expr,'flx_bbnox=FLX_BBNOX;' ${dirout}flux_vector_noxbb_${year}.nc -expr,'flx_so2=FLX_SO2' ${dirout}flux_vector_so2_${year}.nc -expr,'flx_bbso2=FLX_BBSO2' ${dirout}flux_vector_so2bb_${year}.nc -expr,'flx_nh3=FLX_NH3' ${dirout}flux_vector_nh3_${year}.nc -expr,'flx_bbnh3=FLX_BBNH3' ${dirout}flux_vector_nh3bb_${year}.nc  ${dirout}flux_vector_h2s_${year}.nc ${dirout}flux_vector_so4_${year}.nc -selname,conc_dms ${fileINCAex} ${dirout}sflx_lmdz_cmip6_${year}.nc

ncrename -d VECTOR,vector -v VECTOR,vector ${dirout}sflx_lmdz_cmip6_${year}.nc
ncrename -d TIME,time     -v TIME,time     ${dirout}sflx_lmdz_cmip6_${year}.nc

#--cleaning up 
rm -f ${dirout}flux*_${year}.nc
#--to be uncommented in final script

#--end loop on years
done

#--end loop on scenarios
done

#--cleaning the mess
rm -f ferret*
rm -f regrid.pro
rm -f rewrite.jnl