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analyse_WMAP3plus.sh
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analyse_WMAP3plus.sh
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#!/bin/bash
# for all the xfrac3d files in the directory given as
# input do the following steps:
# - convert into single precision "0"
# - list the ion redshifts of z in file "ion_redshift" "A1"
# - list the dens redshfits of z in file "dens_redshift""A2"
# - call the program fof_bubbles and write output to file
# fof_HII_z.out and fof_HI_z.out "B"
# - call the program zahn_bubbles and write output to file
# zahn_z.out "C"
# - call the program minkowski and collect outputs in file
# mink_history "D"
# - call the program cc_spherical and write ouput to file
# cc_z.out "E"
# as second input give the directory where output should be
# saved
# to do the cross correltation.
# Some parameters-------------------------------------------
N=256 # number of cells in one direction
h=0.7 #WMAP3+ values as on the group site
# ----------------------------------------------------------
while [ -n "$1" ]; do # as input parameters give a list
# like this: "file" boxsize
# example:
# "100Mpc_f250C_203_new" 100
# Name some directories-------------------------------------
dirneu=/home/martina/WMAP3plus_results/"$1" # this is the dir where the outputs are saved
olddir2="/home/martina/WMAP3plus"/"$1"/results # dir where the xfrac files are
if [ $2 = "114" ]
then olddir="/home/martina/WMAP3plus/114Mpc_densities" # dir where density files are
elif [ $2 = "37" ]
then olddir="/home/martina/WMAP3plus/37Mpc_densities"
fi
mkdir $dirneu
# ----------------------------------------------------------
#---------------------------------------------------------A1
echo $olddir2
for g in "$olddir2"/xfrac3d_*.bin
do
base=`basename "$g" .bin `
z="${base#xfrac3d_}"
echo $z>>$dirneu/redshiftlist_inter
done
mv $dirneu/redshiftlist_inter $dirneu/redshiftlist2
sort -n -r $dirneu/redshiftlist2 > $dirneu/ion_redshift
rm $dirneu/redshiftlist2
#-----------------------------------------------------------
#---------------------------------------------------------A2
for g in "$olddir/"*n_all.dat
do
base=`basename "$g" .dat`
base2="${base%n_all}"
echo $base2 >> $dirneu/redshift_inter
done
mv $dirneu/redshift_inter $dirneu/redshift2
sort -n -r $dirneu/redshift2 > $dirneu/dens_redshift
rm $dirneu/redshift2
#-----------------------------------------------------------
#-----------------------------------------------------------
# read in the whole redshift list from the density files----
count=0
old_IFS=$IFS #to set field seperator variable
IFS=$'\n' # to end of line and set it back later at (!)
allz=($(cat $dirneu/dens_redshift))
#-----------------------------------------------------------
# line by line, assign variables and call the correlation function
while read z1
do
read z2
z3=${allz[$count]}
let count=$count+1
./double2single256 "$olddir2/xfrac3d_"$z1".bin" intermed
#--------------------------------------------------------"E"
cc_spherical "$olddir/${z3}n_all.dat" "intermed" "$dirneu/cc_$z1.out" $N $2 $h
#-----------------------------------------------------------
#--------------------------------------------------------"B"
fof_bubbles "intermed" $dirneu/fof_HII_$z1.out 0.5 0 $2 $h #for HII bubbles
fof_bubbles "intermed" $dirneu/fof_HI_$z1.out 0.5 1 $2 $h #for HI bubbles
#-----------------------------------------------------------
#--------------------------------------------------------"C"
zahn_bubbles "intermed" $dirneu/zahn_$z1.out $N $2 $h
#-----------------------------------------------------------
#--------------------------------------------------------"D"
tail -c 67108868 intermed > "junk" # to cut away the byte-size info from
head -c 67108864 "junk" > "$base" # unformatted fortran output
rm junk
minkowski -x $N -y $N -z $N -b1 -l0.5 -h0.501 -s0 -o $base.mink -i"$base"
echo $z1 >> $base.mink
cat $base.mink >> $dirneu/mink_history_inter
rm $base.mink
rm $base
./redshiftlist "intermed" "$olddir/${z3}n_all.dat" zout #this calc the mass av ion frac
while read a; do
echo -n $a >> zout2
done < zout
echo -n -e ' ' $z1 '\n' >> zout2
cat zout2 >> $dirneu/ionfracs_inter
rm zout
rm zout2
echo end
#-----------------------------------------------------------
###ONLY FOR NEW SIMULATION THAT HAS ONE ION STEP PER DENS STEP
#########################3if [$z3 -gt 9.
#z3=${allz[$count]} # that is for f0.4
#count=$count+1
############################3fi
###
# Now, do the same things again for the second xfrac file that is read for the
# same density file:
sleep 2 # the option with read does not work because I "jump" over two redshifts then
./double2single256 "$olddir2/xfrac3d_"$z2".bin" intermed
cc_spherical "$olddir/${z3}n_all.dat" "intermed" "$dirneu/cc_$z2.out" $N $2 $h
#read -t 2
sleep 1
#--------------------------------------------------------"B"
fof_bubbles "intermed" $dirneu/fof_HII_$z2.out 0.5 0 $2 $h #for HII bubbles
fof_bubbles "intermed" $dirneu/fof_HI_$z2.out 0.5 1 $2 $h #for HI bubbles
#-----------------------------------------------------------
#--------------------------------------------------------"C"
zahn_bubbles "intermed" $dirneu/zahn_$z2.out $N $2 $h
#-----------------------------------------------------------
#--------------------------------------------------------"D"
tail -c 67108868 intermed > "junk"
head -c 67108864 "junk" > "$base"
minkowski -x $N -y $N -z $N -b1 -l0.5 -h0.501 -s0 -o $base.mink -i"$base"
echo $z2 >> $base.mink
cat $base.mink >> $dirneu/mink_history_inter
rm $base.mink
rm junk
rm $base
./redshiftlist "intermed" "$olddir/${z3}n_all.dat" zout
while read a; do
echo -n $a >> zout2
done < zout
echo -n -e ' ' $z2 '\n' >> zout2
cat zout2 >> $dirneu/ionfracs_inter
rm zout
rm zout2
echo end
#-----------------------------------------------------------
done < "$dirneu/ion_redshift"
IFS=$old_IFS # (!)
mv $dirneu/mink_history_inter $dirneu/mink_history
mv $dirneu/ionfracs_inter $dirneu/ion_history
shift 2
echo NEW SIMULATION
done
rm intermed