Attached are instructions and scripts for carrying out a parameter space scan with ShelfMC, the simulation package for the ARIANNA detector.

Because some of the plotted outputs looked like colored stripes and did not offer any insight into how effective volume changed with some variables, I made some changes to the simulation and plotting scripts so that different maximum, minimum, and increment values can be chosen for each variable. Now rather than having fixed, hard-coded values for all variables, the parameter space scan and plotting is more flexible for use with variable inputs.

This document will explain how to dowload, configure, and run a parameter space search for ShelfMC on a computing cluster. 
These scripts explore the ShelfMC parameter space by varying ATTEN_UP, REFLECT_RATE, ICETHICK, FIRNDEPTH, and STATION_DEPTH for certain rages. 
The ranges and increments can be found in setup.sh. 

In order to vary STATION_DEPTH, some changes were made to the ShelfMC code. Follow these steps to allow STATION_DEPTH to be an input parameter.
1.cd to ShelfMC directory
2.Do $sed -i -e 's/ATDepth/STATION_DEPTH/g' *.cc
3.Open declaration.hh. Replace line 87 "const double ATDepth = 0.;" with "double STATION_DEPTH;"
4.In functions.cc go to line 1829. This is the ReadInput() method. Add the lines below to the end of this method. 
   GetNextNumber(inputfile, number); // new line for station Depth
   STATION_DEPTH  = (double) atof(number.c_str()); //new line
5.Do $make clean all

#######Script Descriptions########
setup.sh -> This script sets up the necessary directories and setup files for all the runs
scheduler.sh -> This script submits and monitors all jobs. 


#######DOWNLOAD########
1.Download setup.sh and scheduler.sh
2.Move both files into your ShelfMC directory
3.Do $chmod u+x setup.sh and $chmod u+x scheduler.sh

######CONFIGURE#######
1.Open setup.sh
2.On line 4, modify the job name
3.On line 6, modify group name
4.On line 11, specify your ShelfMC directory
5.On lines 15-33, specify the minimum and maximum values you wish to simulate for each variable, as well as what value to increment by
6.On line 36, modify your run name
7.On line 37, specify the NNU per run
8.On line 38, specify the starting seed
9.On line 40, specify the number of processors per node on your cluster
10.On lines 42-79, edit the input.txt parameters that you want to keep constant for every run
11.On line 80, specify the location of the LP_gain_manual.txt
12.On line 143, change walltime depending on total NNU. Remember this wall time will be 20x shorter than a single processor run.
13.On line 144, change job prefix
14.On line 146, change the group name if needed 
15.Save file
16.Open scheduler.sh
17.On line 4, specify your ShelfMC directory
18.On line 5, modify run name. Make sure it is the same runName as you have in setup.sh
19.Ensure that lines 15-33 match with setup.sh
20.On lines 62 and 66, replace cond0092 with your username for the cluster
21.On line 69, you can pick how many nodes you want to use at any given time. It is set to 6 intially. 
22.Save file 

#######RUN#######
1.Do $qsub setup.sh
2.Wait for setup.sh to finish. This script is creating the setup files for all runs. This may take about an hour.
3.When setup.sh is done, there should be a new directory in your home directory. Move this directory to your ShelfMC directory.
4.Do $screen to start a new screen that the scheduler can run on. This is incase you lose connection to the cluster mid run. 
5.Make sure that the minimum, maximum, and increment values for each variable match those in setup.sh
6.Do $./scheduler.sh to start script. This script automatically submits jobs and lets you see the status of the runs. This will run for several hours.
7.The scheduler makes a text file of all jobs called jobList.txt in the ShelfMC dir. Make sure to delete jobList.txt before starting a whole new run.


######RESULT#######
1.When Completed, there will be a great amount of data in the run files, about 460GB (This amount varies depending on how many values looped over for all variables.  
2.The run directory is organized in tree, results for particular runs can be found by cd'ing deeper into the tree.
3.In each run directory, there will be a resulting root file, all the setup files, and a log file for the run.
 

#!/bin/bash
#PBS -l walltime=04:00:00
#PBS -l nodes=1:ppn=1,mem=4000mb
#PBS -N hannah_SetupJob
#PBS -j oe
#PBS -A PCON0003
#Jude Rajasekera 3/20/17
#Modified by Hannah Hasan on 09/17/2017

#directories
WorkDir=$TMPDIR   
tmpShelfmc=$HOME/ShelfMC/git_shelfmc #set your ShelfMC directory here


AttenMin=600                      # MINIMUM attenuation length for the simulation      *****ALL UNITS ARE IN METERS*****
AttenMax=1000                     # MAXIMUM attenuation length
AttenInc=400                      # INCREMENT for attenuation length

RadiusMin=3                       # MINIMUM radius
RadiusMax=31                      # MAXIMUM radius
RadiusInc=7                       # INCREMENT

IceMin=500                        # etc...
IceMax=2900
IceInc=400

FirnMin=60
FirnMax=120
FirnInc=60

StDepthMin=0
StDepthMax=200
StDepthInc=50

#controlled variables for run
runName='e18_ParamSpaceScan' #name of run
NNU=10000000 #NNU per run
seed=42 #starting seed for every run, each processor will recieve a different seed (42,43,44,45...)
NNU="$(($NNU / 20))" #calculating processors per node, change 20 to however many processors your cluster has per node
ppn=20 #number of processors per node on cluster
########################### input.txt file ####################################################
input1="#inputs for ARIANNA simulation, do not change order unless you change ReadInput()"
input2="$NNU #NNU, setting to 1 for unique neutrino"
input3="$seed      #seed Seed for Rand3"
input4="18.0    #EXPONENT, !should be exclusive with SPECTRUM"
input5="1000    #ATGap, m, distance between stations"
input6="4       #ST_TYPE, !restrict to 4 now!"
input7="4 #N_Ant_perST, not to be confused with ST_TYPE above"
input8="2 #N_Ant_Trigger, this is the minimum number of AT to trigger"
input9="30      #Z for ST_TYPE=2"
input10="$T   #ICETHICK, thickness of ice including firn, 575m at Moore's Bay"
input11="1       #FIRN, KD: ensure DEPTH_DEPENDENT is off if FIRN is 0"
input12="1.30    #NFIRN 1.30"
input13="$FT      #FIRNDEPTH in meters"
input14="1 #NROWS 12 initially, set to 3 for HEXAGONAL"
input15="1 #NCOLS 12 initially, set to 5 for HEXAGONAL"
input16="0       #SCATTER"
input17="1       #SCATTER_WIDTH,how many times wider after scattering"
input18="0       #SPECTRUM, use spectrum, ! was 1 initially!"
input19="0       #DIPOLE,  add a dipole to the station, useful for st_type=0 and 2"
input20="0       #CONST_ATTENLENGTH, use constant attenuation length if ==1"
input21="$L     #ATTEN_UP, this is the conjuction of the plot attenlength_up and attlength_down when setting REFLECT_RATE=0.5(3dB)"
input22="250     #ATTEN_DOWN, this is the average attenlength_down before Minna Bluff measurement(not used anymore except for CONST_ATTENLENGTH)"
input23="4 #NSIGMA, threshold of trigger"
input24="1      #ATTEN_FACTOR, change of the attenuation length"
input25="0.85    #REFLECT_RATE,power reflection rate at the ice bottom"
input26="0       #GZK, 1 means using GZK flux, 0 means E-2 flux"
input27="0       #FANFLUX, use fenfang's flux which only covers from 10^17 eV to 10^20 eV"
input28="0       #WIDESPECTRUM, use 10^16 eV to 10^21.5 eV as the energy spectrum, otherwise use 17-20"
input29="1       #SHADOWING"
input30="1       #DEPTH_DEPENDENT_N;0 means uniform firn, 1 means n_firn is a function of depth"
input31="0 #HEXAGONAL"
input32="1       #SIGNAL_FLUCT 1=add noise fluctuation to signal or 0=do not"
input33="4.0     #GAINV  gain dependency"
input34="1       #TAUREGENERATION if 1=tau regeneration effect, if 0=original"
input35="$AR     #ST4_R radius in meters between center of station and antenna"
input36="350     #TNOISE noise temperature in Kelvin"
input37="80      #FREQ_LOW low frequency of LPDA Response MHz #was 100"
input38="1000    #FREQ_HIGH high frequency of LPDA Response MHz"
input39="/users/PCON0003/cond0092/ShelfMC/git_shelfmc/GainFiles/LP_gain_manual.txt     #GAINFILENAME"
input40="$SD     #STATION_DEPTH"
#######################################################################################################

cd $TMPDIR   
mkdir $runName
cd $runName

initSeed=$seed
counter=0

for ((L=$AttenMin;L<=$AttenMax;L+=$AttenInc)) #Attenuation length
do
    mkdir Atten_Up$L
    cd Atten_Up$L
    for ((AR=$RadiusMin;AR<=$RadiusMax;AR+=$RadiusInc)) #Station radius (measured from center of radius to antenna
    do
	mkdir AntennaRadius$AR
        cd AntennaRadius$AR
	for ((T=$IceMin;T<=$IceMax;T+=$IceInc)) #Ice thickness
        do
            mkdir IceThick$T
            cd IceThick$T
            for ((FT=$FirnMin;FT<=$FirnMax;FT+=$FirnInc)) #Firn thickness
            do
		mkdir FirnThick$FT
                cd FirnThick$FT
		for ((SD=$StDepthMin;SD<=$StDepthMax;SD+=$StDepthInc)) #Station depth
                do
                    mkdir StationDepth$SD
                    cd StationDepth$SD
                    #####Do file operations###########################################
                    counter=$((counter+1))
                    echo "Counter = $counter ; L = $L ; AR = $AR ; T = $T ; FT = $FT ; SD = $SD " #print variables

                    #define changing lines
                    input21="$L     #ATTEN_UP, this is the conjuction of the plot attenlength_up and attlength_down when setting REFLECT_RATE=0.5(3dB)"
		    input35="$AR     #ST4_R radius in meters between center of station and antenna"
                    input10="$T   #ICETHICK, thickness of ice including firn, 575m at Moore's Bay"
                    input13="$FT      #FIRNDEPTH in meters"
                    input40="$SD       #STATION_DEPTH"
		    
		    for (( i=1; i<=$ppn;i++)) #make 20 setup files for 20 processors
                    do

                        mkdir Setup$i #make setup folder
                        cd Setup$i #go into setup folder
                        seed="$(($initSeed + $i -1))" #calculate seed for this iteration
                        input3="$seed      #seed Seed for Rand3"

                        for j in {1..40} #print all input.txt lines
                        do
                            lineName=input$j
                            echo "${!lineName}" >> input.txt
                        done
			
                        cd ..
                    done
		    
		    pwd=`pwd`
                    #create job file
		    echo '#!/bin/bash' >> run_shelfmc_multithread.sh
		    echo '#PBS -l nodes=1:ppn='$ppn >> run_shelfmc_multithread.sh
		    echo '#PBS -l walltime=00:10:00' >> run_shelfmc_multithread.sh #change walltime as necessary
		    echo '#PBS -N hannah_'$runName'_job' >> run_shelfmc_multithread.sh #change job name as necessary
		    echo '#PBS -j oe'  >> run_shelfmc_multithread.sh
		    echo '#PBS -A PCON0003' >> run_shelfmc_multithread.sh #change group if necessary
		    echo 'cd ' $tmpShelfmc >> run_shelfmc_multithread.sh
		    echo 'runName='$runName  >> run_shelfmc_multithread.sh
		    for (( i=1; i<=$ppn;i++))
		    do
			echo './shelfmc_stripped.exe $runName/'Atten_Up$L'/'AntennaRadius$AR'/'IceThick$T'/'FirnThick$FT'/'StationDepth$SD'/Setup'$i' _'$i'$runName &' >> run_shelfmc_multithread.sh
		    done
		   # echo './shelfmc_stripped.exe $runName/'Atten_Up$L'/'AntennaGap$ATGap'/'IceThick$T'/'FirnThick$FT'/'StationDepth$SD'/Setup1 _01$runName &' >> run_shelfmc_multithread.sh
		    echo 'wait' >> run_shelfmc_multithread.sh
		    echo 'cd $runName/'Atten_Up$L'/'AntennaRadius$AR'/'IceThick$T'/'FirnThick$FT'/'StationDepth$SD >> run_shelfmc_multithread.sh
		    echo 'for (( i=1; i<='$ppn';i++)) #20 iterations' >> run_shelfmc_multithread.sh
		    echo 'do' >> run_shelfmc_multithread.sh
		    echo '  cd Setup$i #cd into setup dir' >> run_shelfmc_multithread.sh
		    echo '  mv *.root ..' >> run_shelfmc_multithread.sh
		    echo '  cd ..' >> run_shelfmc_multithread.sh
		    echo 'done' >> run_shelfmc_multithread.sh
		    echo 'hadd Result_'$runName'.root *.root' >> run_shelfmc_multithread.sh
		    echo 'rm *ShelfMCTrees*' >> run_shelfmc_multithread.sh
		    echo 'rm -rf Setup*' >> run_shelfmc_multithread.sh

		    chmod u+x run_shelfmc_multithread.sh # make executable

                    ##################################################################
                    cd ..
                done
                cd ..
            done
            cd ..
        done
        cd ..
    done
    cd ..
done
cd 

mv $WorkDir/$runName $HOME