#!/bin/bash
#
# This script allows to prepare a simulation case in terms of species used,
# specified chemical schemes, number of aerosol bins, bin sizes, boundary conditions.

echo -e "\033[1;47m Preparation of CHEMISTRY files \033[0m"

#-------------------------------------------------------------------------------------------------------
# cut1 and cut2 forced the size distribution to have these values in the middle of the size distribution
cut1=2.5
cut2=10.

# dmin and dmax (micrometers) are used as tuner parameter to adjust the aerosol
# distribution (they are not the min and max cut off diameter !!)
dmin=0.01
dmax=40.

# create families at the end of REACTIONS and separate GASP / AERO models

if [ ${mecachim} = "0" ] ;  then
   mecaj=melchior2
else
   mecaj=${meca}
fi   
if [[ ${seasalt} = "2" && "${meca}" == "saprc" ]] ; then
   mecaj=${meca}.nacl
fi

#================================================
echo "Make non-chemistry dependent files"

\cp -f DEPO_SPEC.${meca}      DEPO_SPEC
\cp -f SEASALT.univ           SEASALT
\cp -f VEGETATION.univ        VEGETATION
\cp -f SEA.univ               SEA
\cp -f DEPO_PARS.univ         DEPO_PARS
\cp -f SEMIVOL.univ           SEMIVOL
\cp -f SOIL.univ              SOIL

# Data for the wet deposition
\cp -f WETD_SPEC.univ         WETD_SPEC

#---------------------------------------------------
# Prepare ascii data files for mineral dust

if [ ${iusedust} -gt 0 ] ;  then


touch MAKEPRI.dust MINERAL.dust FastJ.dust REACTIONS.dust 
touch WETD_SPEC.dust AEROSOL.dust OUTPUT_SPECIES.dust input-fastj_1.txt
\rm MAKEPRI.dust MINERAL.dust FastJ.dust REACTIONS.dust 
\rm WETD_SPEC.dust AEROSOL.dust OUTPUT_SPECIES.dust input-fastj_1.txt

if [ $iusedust == "1" ] ; then
   inputdustfile=DATA_MINERAL.onlyDUST
fi
if [ $iusedust == "2" ] ; then
   inputdustfile=DATA_MINERAL.elements
fi
if [ $iusedust == "3" ] ; then
   inputdustfile=DATA_MINERAL.species
fi

gawk -v iusedust=$iusedust -f chemprep-prepDUSTmineralo.awk -v file=${inputdustfile} ${inputdustfile}

\cp -f MINERAL.dust MINERAL
cat WETD_SPEC.dust    >> WETD_SPEC
cat -s ${chemprepdir}/data_fastj/input-fastj.txt FastJ.dust >> input-fastj_1.txt

fi

touch input-fastj_1.txt

#---------------------------------------------------

# Prepare files in case of use of tracers
if [ ${trc} -eq 1  ] ;  then
   . chemprep-prep-tracer.sh
fi

if [ ${trc} -eq 1 ] ;  then
   cat  DEPO_SPEC.trc >> DEPO_SPEC
   cat  WETD_SPEC.trc >> WETD_SPEC
   cat  FastJ.trc     >> input-fastj_1.txt
fi

#================================================
echo "Make FAMILIES and AEROSOL"

touch ANTHROPIC
if [ ${mecachim} -gt 0 ] ; then
   cat ${chemprepdir}/data/ANTHROPIC.${meca}    >> ANTHROPIC
fi
if [ ${aero} -eq 1 ] ; then
   cat ANTHROPIC.aero                           >> ANTHROPIC
  if [ ${carb} = "0" ] ;  then
     cat ANTHROPIC.tppm                         >> ANTHROPIC
  fi
fi
if [ ${soatyp} -gt 0 ] ;  then
   cat ANTHROPIC.med                            >> ANTHROPIC
fi
if [ ${carb} = "1" ] ;  then
   cat ANTHROPIC.carb                           >> ANTHROPIC
fi

if [ ${trc} -eq 1 ] ;  then
   cat ANTHROPIC.trc                            >> ANTHROPIC
fi

\cp ANTHROPIC FIRES

echo "Make REACTIONS unique file"
touch AEROSOL MAKEPRI REACTIONS
\rm -r AEROSOL MAKEPRI REACTIONS
touch AEROSOL MAKEPRI REACTIONS

if [ ${mecachim} -gt 0 ] ;  then
    cat REACTIONS.univ.${meca}                  >> REACTIONS
    if [ ${aero} = "0" ] ;  then
       cat REACTIONS.univ.other.${meca}         >> REACTIONS
    fi
fi
if [ ${aero} = "1" ] ;  then
   cat AEROSOL.aero.${soa}                      >> AEROSOL
   cat MAKEPRI.aero                             >> MAKEPRI
   cat REACTIONS.univ.aero                      >> REACTIONS
   cat REACTIONS.univ.${meca}.soa-${soa}        >> REACTIONS
fi
if [ ${seasalt} = "1" ] ;  then
   cat REACTIONS.univ.isal                      >> REACTIONS
   cat AEROSOL.isal                             >> AEROSOL
   cat MAKEPRI.isal                             >> MAKEPRI
fi
if [ ${seasalt} = "2" ] ;  then
   if [ "${meca}" == "saprc" ] ; then
      cat REACTIONS.univ.${meca}.nacl          >> REACTIONS
   fi
   cat REACTIONS.univ.nacl                     >> REACTIONS
   cat AEROSOL.nacl                            >> AEROSOL
   cat MAKEPRI.nacl                            >> MAKEPRI
fi
if [ ${iusedust} -gt 0 ] ;  then
   cat REACTIONS.dust                          >> REACTIONS
   cat AEROSOL.dust                            >> AEROSOL
   cat MAKEPRI.dust                            >> MAKEPRI
fi

if [ ${carb} = "1" ] ;  then
   cat REACTIONS.univ.carb                     >> REACTIONS
   cat AEROSOL.carb                            >> AEROSOL
   cat MAKEPRI.carb                            >> MAKEPRI
fi
if [[ ${carb} = "0"  &&  ${aero} = "1"  ]] ;  then
   cat MAKEPRI.tppm                            >> MAKEPRI
fi
if [ ${trc} = "1" ] ;  then
   cat REACTIONS.trc                           >> REACTIONS
   cat AEROSOL.trc                             >> AEROSOL
   cat MAKEPRI.trc                             >> MAKEPRI
fi

# Delete empty lines
sed '/^$/d' MAKEPRI > tmp
mv tmp MAKEPRI

#================================================
echo "Make active species list"

echo "   - gaseous or non-reactive species species"

   gawk -f chemprep.awk REACTIONS
   
# last line for fastJ   
   echo "9999" >> "FJX_j2j.dat"
   
   sort .species | uniq | gawk '{print $0}' > ACTIVE_SPECIES.gas
   cat ACTIVE_SPECIES.gas > tmp
   sort tmp | uniq | gawk '{print NR,$0}' > ACTIVE_SPECIES.gas
   ngasspec=`wc -l ACTIVE_SPECIES.gas  | gawk '{print $1}'`

if [ ${bins} = "1" ] ;  then

echo "   - aerosols species"
   echo "      Building aerosols size distributions: chemprep-distrib program"

   echo ${nbins} ${cut1} ${cut2} ${dmin} ${dmax} > tmpdistrib
   ./chemprep-distrib.e || exit 1
   sort -g -k 2,2 AEROSOL -o tmp

   echo "# Number of sections D(2.5) D(10.0)"                                     > aerobin.univ
   cat .fambound >> aerobin.univ
   \rm .fambound
   echo "# Name of aerosol components, properties (no blank line a the end!)"    >> aerobin.univ
   echo "# NAME          TYPE   Molar mass     Origin [0=bio,1=anth,2=mineral]"  >> aerobin.univ
   cat aerobin.univ tmp > AEROSOL
   \rm aerobin.univ
   echo "====================================="
   echo "AEROSOL file for this simulation:"
   echo "-------------------------------------"
   cat AEROSOL
   echo "   -  Prepare families list"
   ./chemprep-families.e || exit 1

# full active species file
# ACTIVE_SPECIES.aero previously created by chemprep-families.e
# contains list of aerosols species as bins: p01PPM ...

   cat ACTIVE_SPECIES.aero > tmp
   rm -f OUTPUT_SPECIES.aero-bins
   for spec in `awk '{print $1}' ACTIVE_SPECIES.aero` ; do
       mass=`grep -w ${spec:3} AEROSOL | awk '{print $3}'`
       echo "${spec} ${mass}" >>OUTPUT_SPECIES.aero-bins
   done
   gawk '{print NR+"'${ngasspec}'",$0}' tmp > ACTIVE_SPECIES.aero
   \rm tmp

else
   \rm -f PRIMARY AEROSOL MAKEPRI
fi

#================================================
# finalize ACTIVE_SPECIES file

if [ -e ACTIVE_SPECIES.gas ] ; then
   cat ACTIVE_SPECIES.gas > tmp-gas
fi
if [ -e ACTIVE_SPECIES.aero ] ; then
   cat ACTIVE_SPECIES.aero > tmp-aero
fi

touch tmp-gas tmp-aero tmp-cplt ACTIVE_SPECIES
cat tmp-gas tmp-aero > tmp-cplt

# Put value for transport scheme
gawk '{print $0,'$iadv,$iadvv'}' tmp-cplt >  ACTIVE_SPECIES

\rm tmp-*

#================================================
# FAMILIES.auto prepared by chemprep-families.e in case of aerosols

echo "Make families list"

touch .tmp .tmp1 .tmp2
\rm .tmp .tmp1 .tmp2
touch FAMILIES1 FAMILIES2 FAMILIES
\rm FAMILIES1 FAMILIES2 FAMILIES

touch OUTPUT_SPECIES.families
touch tmp_families

if [ ${mecachim} -gt 0 ] ;  then
   cat FAMILIES.gasp.${meca}         > tmp_families
   sed -e s/=/" "/g tmp_families     > .tmp
   sed -e s/+/" "/g .tmp             > .tmp1
   gawk '{print NF-1,$0}' .tmp1      >> FAMILIES1
   cat FAMILIES1 | gawk '{print $2,"0."}' >> OUTPUT_SPECIES.families
   cat FAMILIES1 >>FAMILIES
fi
if [ -e FAMILIES.auto ] ; then
   cat  FAMILIES.auto                > tmp_families
   sed -e s/=/" "/g tmp_families     > .tmp
   sed -e s/+/" "/g .tmp             > .tmp1
   gawk '{print NF-1,$0}' .tmp1      >> FAMILIES2
   cat FAMILIES2 | gawk '{print $2,"100."}' >> OUTPUT_SPECIES.families
   cat FAMILIES2 >>FAMILIES
fi

if [ ${trc} = 1  ] ;  then
   cat FAMILIES.trcgas >> FAMILIES
fi

# Families when several mineral dust species

if [ ${iusedust} -ge 2 ] ;  then

    \rm tmp1 tmp2

    gawk -v nbins=${nbins} '{
       if(FNR==1){printf "pDUST=" > "tmp1"}
       for(i=1;i<=nbins;i++){
          spec=$1
          printf("%-s%.2i%-s%-s","p",i,spec,"+") >> "tmp1"
       }
    }' AEROSOL.dust

   gawk  '{
      long=length($1)-1
      val=substr($1,1,long)
      printf("%-s",val) >> "tmp2"
   }' tmp1
   
   cat tmp2 >> tmp-dust
   sed -e s/=/" "/g tmp-dust  > tmp-dust2
   sed -e s/+/" "/g tmp-dust2 > tmp-dust3
   gawk '{print NF-1,$0}' tmp-dust3 > tmp-dust4
   sed -e s/=/" "/ tmp-dust4 | gawk '{print $2,"100."}' >> OUTPUT_SPECIES.families
   
   cat tmp-dust4 >> FAMILIES
   \rm tmp1 tmp2
   \rm tmp-dust tmp-dust2 tmp-dust3 tmp-dust4

fi

echo "Building output species list"

touch OUTPUT_SPECIES.full OUTPUT_SPECIES.low


if [ ${mecachim} != "0" ] ;  then
   cat OUTPUT_SPECIES_${meca}.gas.full        >> OUTPUT_SPECIES.full
   cat OUTPUT_SPECIES.gas.low                 >> OUTPUT_SPECIES.low
fi

if [ ${aero} = "1" ] ;  then
   cat OUTPUT_SPECIES.aero.${soa}             >> OUTPUT_SPECIES.full
fi
if [ ${seasalt} = "1" ] ;  then
   cat OUTPUT_SPECIES.isal                    >> OUTPUT_SPECIES.full
fi
if [ ${seasalt} = "2" ] ;  then
   cat OUTPUT_SPECIES.nacl                    >> OUTPUT_SPECIES.full
   if [ "${meca}" == "saprc" ] ; then
       cat OUTPUT_SPECIES_saprc.nacl           >> OUTPUT_SPECIES.full
   fi

fi
if [ ${iusedust} -gt 0 ] ;  then
   cat OUTPUT_SPECIES.dust                    >> OUTPUT_SPECIES.full
fi
if [ ${carb} = "1" ] ;  then
   cat OUTPUT_SPECIES.carb                    >> OUTPUT_SPECIES.full
fi

if [ ${trc} = "1" ] ;  then
   cat OUTPUT_SPECIES.trc                     >> OUTPUT_SPECIES.low
   cat OUTPUT_SPECIES.trc                     >> OUTPUT_SPECIES.full
fi

if [ ${bins} = "1" ] ;  then
   cat OUTPUT_SPECIES.aero-bins               >> OUTPUT_SPECIES.full
fi

# Add families: always included in the output species file

cat OUTPUT_SPECIES.families                   >> OUTPUT_SPECIES.full
cat OUTPUT_SPECIES.families                   >> OUTPUT_SPECIES.low

#---------------------------------------------------------------------
# Copy fastJX input data files

\cp input-fastj_1.txt	                            ${chemprepfic}/input-fastj.txt

\cp ${chemprepdir}/data_fastj/FJX_spec_${mecaj}.dat ${chemprepfic}/FJX_spec.dat
\cp ${chemprepdir}/data_fastj/FJX_scat-cld.dat	    ${chemprepfic}
\cp ${chemprepdir}/data_fastj/FJX_scat-UMa.dat	    ${chemprepfic}
\cp ${chemprepdir}/data_fastj/atmos_std.dat	    ${chemprepfic}


\rm tmp* .tmp*
\rm input-fastj_1.txt