# This script runs Lumi macros for the full Sim

#number of samples used in sim
SAMPLENUM=100
#-- fix params of simulation --------------------------------------------------
#numer of events used for resolution study
SIMEVENTS=100000
#Declare array with elements for knoss stat. study
ARRAY=(100000)
# get number of elements in the array
ELEMENTS=${#ARRAY[@]}

#Declare array with elements for misalignment scale
#ARRAYD=(0 10 20 30 40 50 70 100 150 200 250 300 350 400 450 500) #mum
#ARRAYD=(0 10 50 100 150 200 250 300 350 400 450 500) #mum
#ARRAYD=(0 10 50 100 150 200 250 300 350 400 450 500) #mum
ARRAYD=(150) #mum
#ARRAYD=(0 10 50 100 150 200 250 300 350 400 450 500) #mum
ELEMENTSD=${#ARRAYD[@]}
#ARRAYA=(0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15) # 1e-3 rad
ARRAYA=(0) # 1e-3 rad
#ARRAYA=(0 3 6 9) # 1e-3 rad
# get number of elements in the array
ELEMENTSA=${#ARRAYA[@]}
#---------------------------------------------------------------------------------------

# reads number of Events, name of run and verbose Level
path="test"
#verbose=0
mom=0

#echo Enter storage-folder:
#read folder
#echo "Storage Path: $folder!"

# echo Enter verbosity Level:
# read verbose
# echo "Verbosity Level is: $verbose!"

echo Enter momentum from "1.5, 4.06, 8.9, 11.91, 15 [GeV/c]":
read mom
echo "Beam momentum is: $mom!"

momStr=`echo $mom | sed -e '{ s/\./_/g; }'`


#echo ${path}
# make data directory, if not there. all data file go there, makes them easier to move around



# let's go
for (( j=0;j<$ELEMENTSD;j++)); do
     for (( ia=0;ia<$ELEMENTSA;ia++)); do
	 for (( i=0;i<$ELEMENTS;i++)); do
	 T="$(date)"
	echo ${T} ": Now we'll do test with "${ARRAY[${i}]} "events for misalignment ~ "${ARRAYD[${j}]} "mum and" ${ARRAYA[${ia}]} "*10e-3 rad">> logSTAT
	path="/home/karavdin/datastorage/AlignmentSamplesStudy/momentum_"${momStr}"/"misalign_${ARRAYD[${j}]}mum_${ARRAYA[${ia}]}_10e-3radDOF111111_${ARRAY[${i}]}_events
if [ ! -d $path ]; then 
  mkdir -p $path
fi
 #echo "Output files will be saved in $path"
if [ ! -d jobs/momentum_${momStr} ]; then 
  mkdir -p jobs/momentum_${momStr}
fi
misalignfile=${path}"/lumi.misalign.par"
#pathold="/home/karavdin/datastorage/AlignmentSamplesStudy/mom_"${momStr}"/"misalign_${ARRAYD[${j}]}mum_${ARRAYA[${ia}]}_10e-3radDOF111111_${ARRAY[${i}]}"_events_0"
pathold="/home/karavdin/datastorage/AlignmentSamplesStudy/momentum_"${momStr}"/"misalign_${ARRAYD[${j}]}mum_${ARRAYA[${ia}]}_10e-3radDOF111111_100000_events_0
resfileold="/home/karavdin/datastorage/AlignmentSamplesStudy/momentum_"${momStr}"/SamplesStudy_"${ARRAYD[${j}]}"mum_"${ARRAYA[${ia}]}"mrad_"${SAMPLENUM}"samples.txt"
cat >jobs/momentum_${momStr}/job_${ARRAYD[${j}]}mum_${ARRAYA[${ia}]}e-3rad_${ARRAY[${i}]}events.sh <<EOF
#!/bin/bash
#
 #PBS -N lumiJob.$start
#PBS -j oe
##PBS -o ${path}/0-job_${start}.log
#PBS -o testLOGfile
#PBS -V
#PBS -l nodes=1:ppn=1,walltime=03:00:00
export PATH=\$PBS_O_PATH
cd \$PBS_O_WORKDIR
cd /home/karavdin/pandaRoot12/macro/lmd
source config.sh

head -14 ${pathold}/lumi.misalign_before_0.par >> ${path}/lumi.misalign_after.par

cd  /home/karavdin/pandaRoot12/mySandbox/myKnossos

./analyze -in '${pathold}/lumi.misalign_before_0.par' -out '${resfileold}' -outroot '${path}/Results.root' -new '${path}/lumi.misalign_after.par' &> ${path}/0p2-alignresults.log
 cp  ${pathold}/lumi.misalign_before_0.par ${path}/lumi.misalign_before.par
 cp  ${path}/lumi.misalign_after.par ${path}/lumi.misalign.par
cp ${pathold}/Lumi_out_MC_and_REC_trks_matches_with_IDs0_before_0.root  ${path}/Lumi_out_MC_and_REC_trks_matches_with_IDs0_before.root
cp ${pathold}/ResidualsHist_before.root ${path}/ResidualsHist_before.root 
rm ${path}/FairRunInfo*
rm ${path}/Lumi_MC_0.root
rm ${path}/Lumi_Params_0.root
rm ${path}/Lumi_digi_0.root
rm ${path}/Lumi_reco_0.root
rm ${path}/Lumi_TCand_0.root
rm ${path}/Lumi_Track_0.root
rm ${path}/Lumi_Geane_0.root

cd /home/karavdin/pandaRoot12/macro/lmd
source config.sh
time root -l -b -q runLumi0SimBox.C\(${SIMEVENTS},$mom,"\"${path}\""\) &> ${path}/10-sim_${ARRAYD[${j}]}mum_${ARRAYA[${ia}]}e-3rad.log
time root -l -b -q runLumi1Digi.C\(${SIMEVENTS},0,"\"${path}\""\) &> ${path}/11-digi_${ARRAYD[${j}]}mum_${ARRAYA[${ia}]}e-3rad.log
time root -l -b -q runLumi2Reco.C\(${SIMEVENTS},0,"\"${path}\""\)  &> ${path}/12-rechit_${ARRAYD[${j}]}mum_${ARRAYA[${ia}]}e-3rad.log
time root -l -b -q runLumi3Finder.C\(${SIMEVENTS},0,"\"${path}\"",0,\"CA\",false\) &> ${path}/13-trksearch_${ARRAYD[${j}]}mum_${ARRAYA[${ia}]}e-3rad.log
time root -l -b -q runLumi4Fitter.C\(${SIMEVENTS},0,"\"${path}\""\)  &> ${path}/14-fit_${ARRAYD[${j}]}mum_${ARRAYA[${ia}]}e-3rad.log
time root -l -b -q runLumi5Geane.C\(${SIMEVENTS},$mom,0,"\"${path}\""\) &> ${path}/15-geane_${ARRAYD[${j}]}mum_${ARRAYA[${ia}]}e-3rad.log

cd /home/karavdin/pandaRoot12/build/bin
 ./rec_mc_match -s 0 -n ${SIMEVENTS} -mom ${mom} -path ${path}

./hits_align -s 0 -n ${ARRAY[${i}]} -path ${path} -out "${path}/TrackForAlign.txt" -outhist "${path}/ResidualsHist_after.root" -v 0 &> ${path}/16-hitres_${ARRAYD[${j}]}mum_${ARRAYA[${ia}]}e-3rad.log

mv  ${path}/Lumi_out_MC_and_REC_trks_matches_with_IDs0.root  ${path}/Lumi_out_MC_and_REC_trks_matches_with_IDs0_after.root
rm ${path}/FairRunInfo*
rm ${path}/Lumi_MC_0.root
rm ${path}/Lumi_Params_0.root
rm ${path}/Lumi_digi_0.root
rm ${path}/Lumi_reco_0.root
rm ${path}/Lumi_TCand_0.root
rm ${path}/Lumi_Track_0.root
rm ${path}/Lumi_Geane_0.root
exit 0
EOF
### submit job to batch system
qsub jobs/momentum_${momStr}/job_${ARRAYD[${j}]}mum_${ARRAYA[${ia}]}e-3rad_${ARRAY[${i}]}events.sh 
echo "Output files will be saved in $path"
	 done
     done
done
exit